Interview with René Yáñez, artist, co-founder of the Galería de la Raza, San Francisco, CA, USA, August 13, 2001 Entretien avec René Yáñez, artiste, co-fondateur de la Galería de la Raza, San Francisco, CA, Etats-Unis

Directory of Open Access Journals (Sweden)

Gérard Selbach

2009-10-01

Full Text Available René Yáñez is an all-round visual artist and visionary, now in his sixties. He came out of the Chicano movement of the 70’s and was instrumental in founding the Galería de la Raza in the Mission district of San Francisco. He remained some fifteen years as its director, curating exhibitions, directing and promoting emerging artists of all kinds. He then worked as director of cultural programming at the Mexican Museum until its closure. René Yáñez co-produced Mexican performance artist Astrid H...

Identification and description of three families with familial Alzheimer disease that segregate variants in the SORL1 gene.

Science.gov (United States)

Thonberg, Håkan; Chiang, Huei-Hsin; Lilius, Lena; Forsell, Charlotte; Lindström, Anna-Karin; Johansson, Charlotte; Björkström, Jenny; Thordardottir, Steinunn; Sleegers, Kristel; Van Broeckhoven, Christine; Rönnbäck, Annica; Graff, Caroline

2017-06-09

Alzheimer disease (AD) is a progressive neurodegenerative disorder and the most common form of dementia. The majority of AD cases are sporadic, while up to 5% are families with an early onset AD (EOAD). Mutations in one of the three genes: amyloid beta precursor protein (APP), presenilin 1 (PSEN1) or presenilin 2 (PSEN2) can be disease causing. However, most EOAD families do not carry mutations in any of these three genes, and candidate genes, such as the sortilin-related receptor 1 (SORL1), have been suggested to be potentially causative. To identify AD causative variants, we performed whole-exome sequencing on five individuals from a family with EOAD and a missense variant, p.Arg1303Cys (c.3907C > T) was identified in SORL1 which segregated with disease and was further characterized with immunohistochemistry on two post mortem autopsy cases from the same family. In a targeted re-sequencing effort on independent index patients from 35 EOAD-families, a second SORL1 variant, c.3050-2A > G, was found which segregated with the disease in 3 affected and was absent in one unaffected family member. The c.3050-2A > G variant is located two nucleotides upstream of exon 22 and was shown to cause exon 22 skipping, resulting in a deletion of amino acids Gly1017- Glu1074 of SORL1. Furthermore, a third SORL1 variant, c.5195G > C, recently identified in a Swedish case control cohort included in the European Early-Onset Dementia (EU EOD) consortium study, was detected in two affected siblings in a third family with familial EOAD. The finding of three SORL1-variants that segregate with disease in three separate families with EOAD supports the involvement of SORL1 in AD pathology. The cause of these rare monogenic forms of EOAD has proven difficult to find and the use of exome and genome sequencing may be a successful route to target them.

Lactobacillus salivarius REN counteracted unfavorable 4-nitroquinoline-1-oxide-induced changes in colonic microflora of rats.

Science.gov (United States)

Zhang, Ming; Qiao, Xuewei; Zhao, Liang; Jiang, Lu; Ren, Fazheng

2011-12-01

Probiotics and carcinogens both have a significant effect on the microfloral composition of the human intestine. The objective of this study was to investigate the impact of an important carcinogen, 4-Nitroquinoline-1-Oxide on colonic microflora and the efficacy of the probiotic Lactobacillus salivarius REN as an agent of counteracting these effects. Using denaturing gradient gel electrophoresis (DGGE) combined with redundancy analysis, we demonstrated that both 4-Nitroquinoline-1-Oxide and L. salivarius REN significantly altered the bacterial communities of rat colons. A total of 27 bacterial strains were identified as being affected by treatment with 4-Nitroquinoline-1-Oxide or L. salivarius REN using a t-value biplot combined with band sequencing. 4-Nitroquinoline-1-Oxide treatment increased the abundance of two potential pathogens (one Helicobacter strain and one Desulfovibrio strain), as well as reducing the abundance of two potentially beneficial strains (one Ruminococcaceae strain and one Rumen bacteria). The Helicobacter strain was initally detected in carcinogen-treated rat intestinal microflora, but L. salivarius REN treatment effectively suppressed the growth of the Helicobacter strain. These results suggested that L. salivarius REN may be a potential probiotic, efficiently acting against the initial infection with, and the growth of pathogenic bacteria.

Countering the Segregation of Transition-Metal Ions in LiMn1/3 Co1/3 Ni1/3 O2 Cathode for Ultralong Life and High-Energy Li-Ion Batteries.

Science.gov (United States)

Luo, Dong; Fang, Shaohua; Tamiya, Yu; Yang, Li; Hirano, Shin-Ichi

2016-08-01

High-voltage layered lithium transition-metal oxides are very promising cathodes for high-energy Li-ion batteries. However, these materials often suffer from a fast degradation of cycling stability due to structural evolutions. It seriously impedes the large-scale application of layered lithium transition-metal oxides. In this work, an ultralong life LiMn1/3 Co1/3 Ni1/3 O2 microspherical cathode is prepared by constructing an Mn-rich surface. Its capacity retention ratio at 700 mA g(-1) is as large as 92.9% after 600 cycles. The energy dispersive X-ray maps of electrodes after numerous cycles demonstrate that the ultralong life of the as-prepared cathode is attributed to the mitigation of TM-ions segregation. Additionally, it is discovered that layered lithium transition-metal oxide cathodes with an Mn-rich surface can mitigate the segregation of TM ions and the corrosion of active materials. This study provides a new strategy to counter the segregation of TM ions in layered lithium transition-metal oxides and will help to the design and development of high-energy cathodes with ultralong life. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gametocidal genes of Aegilops: segregation distorters in wheat-Aegilops wide hybridization.

Science.gov (United States)

Niranjana, M

2017-08-01

Aegilops is a genus belonging to the family Poaceace, which have played an indispensible role in the evolution of bread wheat and continues to do so by transferring genes by wide hybridization. Being the secondary gene pool of wheat, gene transfer from Aegilops poses difficulties and segregation distortion is common. Gametocidal genes are the most well characterized class of segregation distorters reported in interspecific crosses of wheat with Aegilops. These "selfish" genetic elements ensure their preferential transmission to progeny at the cost of gametes lacking them without providing any phenotypic benefits to the plant, thereby causing a proportional reduction in fertility. Gametocidal genes (Gc) have been reported in different species of Aegilops belonging to the sections Aegilops (Ae. geniculata and Ae. triuncialis), Cylindropyrum (Ae. caudata and Ae. cylindrica), and Sitopsis (Ae. longissima, Ae. sharonensis, and Ae. speltoides). Gametocidal activity is mostly confined to 2, 3, and 4 homeologous groups of C, S, S 1 , S sh , and M g genomes. Removal of such genes is necessary for successful alien gene introgression and can be achieved by mutagenesis or allosyndetic pairing. However, there are some instances where Gc genes are constructively utilized for development of deletion stocks in wheat, improving genetic variability and chromosome engineering.

CO-induced Pd segregation and the effect of subsurface Pd on CO adsorption on CuPd surfaces

International Nuclear Information System (INIS)

Padama, A A B; Villaos, R A B; Albia, J R; Diño, W A; Nakanishi, H; Kasai, H

2017-01-01

We report results of our study on the adsorption of CO on CuPd surfaces with bulk stoichiometric and nonstoichiometric layers using density functional theory (DFT). We found that the presence of Pd atoms in the subsurface layer promotes the adsorption of CO. We also observed CO-induced Pd segregation on the CuPd surface and we attribute this to the strong CO–Pd interaction. Lastly, we showed that the adsorption of CO promotes Pd–Pd interaction as compared to the pristine surface which promotes strong Cu–Pd interaction. These results indicate that CO adsorption on CuPd surfaces can be tuned by taking advantage of the CO-induced segregation and by considering the role of subsurface Pd atoms. (paper)

Inheritance and segregation of exogenous genes in transgenic cotton

Indian Academy of Sciences (India)

Three transgenic cotton varieties (lines) were chosen for the study of inheritance and segregation of foreign Bt (Bacillus thuringiensis toxin) and tfdA genes in cotton. The transformed cotton varieties CCRI 30 and NewCott 33B expressing the Bt cryIA gene, and cotton line TFD expressing the tfdA gene were crossed with ...

JIU-REN YIN

Indian Academy of Sciences (India)

Home; Journals; Bulletin of Materials Science. JIU-REN YIN. Articles written in Bulletin of Materials Science. Volume 40 Issue 6 October 2017 pp 1255-1261. Molecular dynamics study on the relaxation properties of bilayered graphene with defects · WEI ZHANG JIU-REN YIN PING ZHANG YAN-HUAI DING YONG J IANG.

Influenza NA and PB1 Gene Segments Interact during the Formation of Viral Progeny: Localization of the Binding Region within the PB1 Gene

Directory of Open Access Journals (Sweden)

Brad Gilbertson

2016-08-01

Full Text Available The influenza A virus genome comprises eight negative-sense viral RNAs (vRNAs that form individual ribonucleoprotein (RNP complexes. In order to incorporate a complete set of each of these vRNAs, the virus uses a selective packaging mechanism that facilitates co-packaging of specific gene segments but whose molecular basis is still not fully understood. Recently, we used a competitive transfection model where plasmids encoding the A/Puerto Rico/8/34 (PR8 and A/Udorn/307/72 (Udorn PB1 gene segments were competed to show that the Udorn PB1 gene segment is preferentially co-packaged into progeny virions with the Udorn NA gene segment. Here we created chimeric PB1 genes combining both Udorn and PR8 PB1 sequences to further define the location within the Udorn PB1 gene that drives co-segregation of these genes and show that nucleotides 1776–2070 of the PB1 gene are crucial for preferential selection. In vitro assays examining specific interactions between Udorn NA vRNA and purified vRNAs transcribed from chimeric PB1 genes also supported the importance of this region in the PB1-NA interaction. Hence, this work identifies an association between viral genes that are co-selected during packaging. It also reveals a region potentially important in the RNP-RNP interactions within the supramolecular complex that is predicted to form prior to budding to allow one of each segment to be packaged in the viral progeny. Our study lays the foundation to understand the co-selection of specific genes, which may be critical to the emergence of new viruses with pandemic potential.

Identification of a RAPD marker linked to the Co-6 anthracnose resistant gene in common bean cultivar AB 136

Directory of Open Access Journals (Sweden)

Alzate-Marin Ana Lilia

2000-01-01

Full Text Available The pathogenic variability of the fungus Colletotrichum lindemuthianum represents an obstacle for the creation of resistant common bean (Phaseolus vulgaris L. varieties. Gene pyramiding is an alternative strategy for the development of varieties with durable resistance. RAPD markers have been proposed as a means to facilitate pyramiding of resistance genes without the need for multiple inoculations of the pathogens. The main aims of this work were to define the inheritance pattern of resistance present in common bean cultivar AB 136 in segregating populations derived from crosses with cultivar Rudá (susceptible to most C. lindemuthianum races and to identify RAPD markers linked to anthracnose resistance. The two progenitors, populations F1 and F2, F2:3 families and backcross-derived plants were inoculated with race 89 of C. lindemuthianum under environmentally controlled greenhouse conditions. The results indicate that a single dominant gene, Co-6, controls common bean resistance to this race, giving a segregation ratio between resistant and susceptible plants of 3:1 in the F2, 1:0 in the backcrosses to AB 136 and 1:1 in the backcross to Rudá. The segregation ratio of F2:3 families derived from F2 resistant plants was 1:2 (homozygous to heterozygous resistant. Molecular marker analyses in the F2 population identified a DNA band of approximately 940 base pairs (OPAZ20(940, linked in coupling phase at 7.1 cM of the Co-6 gene. This marker is being used in our backcross breeding program to develop Rudá-derived common bean cultivars resistant to anthracnose and adapted to central Brazil.

Lutter øren

DEFF Research Database (Denmark)

Bekker-Nielsen, Tønnes

2003-01-01

Ifølge den romerske forfatter Pomponius Mela levede der engang ved Vadehavet et folk, panotierne, med øren så store at de kunne slå dem omkring sig som værn mod kulden.......Ifølge den romerske forfatter Pomponius Mela levede der engang ved Vadehavet et folk, panotierne, med øren så store at de kunne slå dem omkring sig som værn mod kulden....

The selfish Segregation Distorter gene complex of Drosophila melanogaster.

Science.gov (United States)

Larracuente, Amanda M; Presgraves, Daven C

2012-09-01

Segregation Distorter (SD) is an autosomal meiotic drive gene complex found worldwide in natural populations of Drosophila melanogaster. During spermatogenesis, SD induces dysfunction of SD(+) spermatids so that SD/SD(+) males sire almost exclusively SD-bearing progeny rather than the expected 1:1 Mendelian ratio. SD is thus evolutionarily "selfish," enhancing its own transmission at the expense of its bearers. Here we review the molecular and evolutionary genetics of SD. Genetic analyses show that the SD is a multilocus gene complex involving two key loci--the driver, Segregation distorter (Sd), and the target of drive, Responder (Rsp)--and at least three upward modifiers of distortion. Molecular analyses show that Sd encodes a truncated duplication of the gene RanGAP, whereas Rsp is a large pericentromeric block of satellite DNA. The Sd-RanGAP protein is enzymatically wild type but mislocalized within cells and, for reasons that remain unclear, appears to disrupt the histone-to-protamine transition in drive-sensitive spermatids bearing many Rsp satellite repeats but not drive-insensitive spermatids bearing few or no Rsp satellite repeats. Evolutionary analyses show that the Sd-RanGAP duplication arose recently within the D. melanogaster lineage, exploiting the preexisting and considerably older Rsp satellite locus. Once established, the SD haplotype collected enhancers of distortion and suppressors of recombination. Further dissection of the molecular genetic and cellular basis of SD-mediated distortion seems likely to provide insights into several important areas currently understudied, including the genetic control of spermatogenesis, the maintenance and evolution of satellite DNAs, the possible roles of small interfering RNAs in the germline, and the molecular population genetics of the interaction of genetic linkage and natural selection.

UV-induced mitotic co-segregation of genetic markers in Candida albicans: Evidence for linkage

International Nuclear Information System (INIS)

Crandall, M.

1983-01-01

Parasexual genetic studies of the medically important yeast Candida albicans were performed using the method of UV-induced mitotic segregation. UV-irradiation of the Hoffmann-La Roche type culture of C. albicans yielded a limited spectrum of mutants at a relatively high fequency. This observation suggested natural heterozygosity. Canavanine-sensitive (CanS) segregants were induced at a frequency of 7.6 . 10 -3 . Double mutants that were both CanS and methionine (Met - ) auxotrophs were induced at a frequency of 7.4 . 10 -3 . The single Met - segregant class was missing indicating linkage. UV-induced CanS or Met - CanS segregants occurred occasionally in twin-sectored colonies. Analyses of the sectors as well as the observed and missing classes of segregants indicated that genes met and can are linked in the cis configuration. The proposed gene order is: centromere - met - can. Thus, it is concluded that the Hoffmann-La Roche strain of C. albicans is naturally heterozygous at two linked loci. These findings are consistent with diploidy. (orig.)

Monuments on Gemiler Ada and Karacaören Ada

OpenAIRE

Masuda, Tomoyuki

1995-01-01

Contents : 1. Church I on Gemiler Ada, 2. Church II on Gemiler Ada, 3. Church III on Gemiler Ada, 4. Church IV on Gemiler Ada, 5. Basilica on Karacaören Ada, 6. Painted Tomb on Karacaören Ada, 7. The Baptistery and the Chronology of Construction of the Karacaören Ada Basilica Complex, 8. Ölüdeniz Beach Basilica, 9. Iskender Basilica on Ölüdeniz Lagoon, 10. Mustafa Basilica near Beştaş Cove.

Effects of Lactobacillus salivarius Ren on cancer prevention and intestinal microbiota in 1, 2-dimethylhydrazine-induced rat model.

Science.gov (United States)

Zhang, Ming; Fan, Xing; Fang, Bing; Zhu, Chengzhen; Zhu, Jun; Ren, Fazheng

2015-06-01

Probiotics have been suggested as a prophylactic measure in colon cancer. The aim of this study was to investigate the impact of Lactobacillus salivarius Ren (Ren) in modulating colonic microbiota structure and colon cancer incidence in a rat model after injection with 1,2-dimethyl hydrazine (DMH). The results indicated that oral administration of Ren could effectively suppress DMH-induced colonic carcinogenesis. A significant decrease in cancer incidence (87.5% to 25%) was detected in rats fed with a dose of 5 × 10(10) CFU/kg bodyweight per day. Using denaturing gradient gel electrophoresis and Real-time PCR combined with multivariate statistical methods, we demonstrated that injection with DMH significantly altered the rat gut microbiota, while Ren counteracted these DMH-induced adverse effects and promoted reversion of the gut microbiota close to the healthy state. Tvalue biplots followed by band sequencing identified 21 bacterial strains as critical variables affected by DMH and Ren. Injection of DMH significantly increased the amount of Ruminococcus species (sp.) and Clostridiales bacteria, as well as decreasing the Prevotella sp. Administration of Ren reduced the amount of Ruminococcus sp., Clostridiales bacteria, and Bacteroides dorei, and increased the amount of Prevotella. Real-time PCR results were consistent with the results derived by t-value biplots. These findings suggested that Ren is a potential agent for colon cancer prevention. In conclusion, the results in the present study suggest a potential therapeutic approach based on the modulation of intestinal microflora by probiotics may be beneficial in the prevention of colorectal carcinogenesis.

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

Science.gov (United States)

N'Diaye, Amidou; Haile, Jemanesh K; Fowler, D Brian; Ammar, Karim; Pozniak, Curtis J

2017-01-01

Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms

Directory of Open Access Journals (Sweden)

Amidou N’Diaye

2017-08-01

Full Text Available Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called ‘large p, small n’ problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers. While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat and Norstar × Cappelle Desprez (bread wheat. The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF, we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez. Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase

René Wellek a Pražská škola

Czech Academy of Sciences Publication Activity Database

Sládek, Ondřej

2016-01-01

Roč. 1, č. 1 (2016), s. 19-30 ISSN 2453-8507 Institutional support: RVO:68378068 Keywords : literary theory ; structuralism ; poetics ; Wellek, René ; Prague School * structuralism * poetics * Wellek, René * Prague School * Prague linguistic circle * Mukařovský, Jan Subject RIV: AJ - Letters, Mass-media, Audiovision

nomalous Interface and Surface Strontium Segregation in (La_1-ySr_y)₂CoO₄ /La_1-xSr_xCoO_3- Heterostructured Thin Films

Energy Technology Data Exchange (ETDEWEB)

Feng, Zhenxing [Massachusetts Institute of Technology (MIT); Yacoby, Yuzhak [Massachusetts Institute of Technology (MIT); Gadre, Milind [Massachusetts Institute of Technology (MIT); Lee, Yueh-Lin [Massachusetts Institute of Technology (MIT); Hong, W. [Harvard University; Zhou, Hua [Argonne National Laboratory (ANL); Biegalski, Michael D [ORNL; Christen, Hans M [ORNL; Adler, Stuart [University of Washington; Morgan, Dane [University of Wisconsin, Madison; Shao-Horn, Yang [Massachusetts Institute of Technology (MIT)

2014-01-01

Heterostructured materials have shown unusual physiochemical properties at the interfaces such as two dimensional electron gas systems, high-temperature superconductivity, and enhanced catalysis. Here we report the first atomic-scale evidence of the microscopic structure of a perovskite/Ruddlesden-Popper heterostructure (having La1-xSrxCoO3- /(La1-ySry)2CoO4 ), and anomalous strontium segregation at the interface and in the Ruddlesden-Popper structure using direct X-ray methods combined with ab initio calculations. The remarkably enhanced activity of such heterostructured surfaces relative to bulk perovskite and Ruddlesden-Popper oxides previously shown for oxygen electrocatalysis at elevated temperatures can be attributed to reduced thermodynamic penalty of oxygen vacancies in the oxide structure associated with Sr segregation observed in the heterostructure. Our findings provide insights for the design of highly active catalysts for energy conversion and storage applications.

CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs.

Science.gov (United States)

van Wolfswinkel, Josien C; Claycomb, Julie M; Batista, Pedro J; Mello, Craig C; Berezikov, Eugene; Ketting, René F

2009-10-02

We have studied the function of a conserved germline-specific nucleotidyltransferase protein, CDE-1, in RNAi and chromosome segregation in C. elegans. CDE-1 localizes specifically to mitotic chromosomes in embryos. This localization requires the RdRP EGO-1, which physically interacts with CDE-1, and the Argonaute protein CSR-1. We found that CDE-1 is required for the uridylation of CSR-1 bound siRNAs, and that in the absence of CDE-1 these siRNAs accumulate to inappropriate levels, accompanied by defects in both meiotic and mitotic chromosome segregation. Elevated siRNA levels are associated with erroneous gene silencing, most likely through the inappropriate loading of CSR-1 siRNAs into other Argonaute proteins. We propose a model in which CDE-1 restricts specific EGO-1-generated siRNAs to the CSR-1 mediated, chromosome associated RNAi pathway, thus separating it from other endogenous RNAi pathways. The conserved nature of CDE-1 suggests that similar sorting mechanisms may operate in other animals, including mammals.

Effect of atmospheric CO{sub 2} on surface segregation and phase formation in La{sub 0.6}Sr{sub 0.4}Co{sub 0.2}Fe{sub 0.8}O{sub 3−δ} thin films

Energy Technology Data Exchange (ETDEWEB)

Yu, Yang [Division of Materials Science and Engineering, Boston University, Brookline, MA 02446 (United States); Luo, Heng [Department of Mechanical Engineering, Boston University, Boston, MA 02215 (United States); Cetin, Deniz [Division of Materials Science and Engineering, Boston University, Brookline, MA 02446 (United States); Lin, Xi [Division of Materials Science and Engineering, Boston University, Brookline, MA 02446 (United States); Department of Mechanical Engineering, Boston University, Boston, MA 02215 (United States); Ludwig, Karl [Division of Materials Science and Engineering, Boston University, Brookline, MA 02446 (United States); Department of Physics, Boston University, Boston, MA 02215 (United States); Pal, Uday; Gopalan, Srikanth [Division of Materials Science and Engineering, Boston University, Brookline, MA 02446 (United States); Department of Mechanical Engineering, Boston University, Boston, MA 02215 (United States); Basu, Soumendra, E-mail: basu@bu.edu [Division of Materials Science and Engineering, Boston University, Brookline, MA 02446 (United States); Department of Mechanical Engineering, Boston University, Boston, MA 02215 (United States)

2014-12-30

Highlights: • LSCF exhibits Sr surface segregation on high-temperature annealing. • The presence of atmospheric CO{sub 2} enhances the kinetics of Sr surface segregation. • At high-CO{sub 2} partial pressures, there is a significant coverage of the surface by Sr-rich phases. • The increase in kinetics is attributed to increased thermodynamic driving force for SrCO{sub 3} formation. - Abstract: The effects of atmospheric CO{sub 2} on surface segregation and phase formation in La{sub 0.6}Sr{sub 0.4}Co{sub 0.2}Fe{sub 0.8}O{sub 3−δ} (LSCF-6428) were investigated. (0 0 1)-oriented LSCF-6428 thin films were deposited on lattice matched (1 1 0)-oriented NdGaO{sub 3} (NGO) substrates by pulsed laser deposition (PLD). Using the synchrotron technique of total reflection X-ray fluorescence (TXRF), it was found that the kinetics of Sr surface segregation was enhanced when annealing at 800 °C in a high-CO{sub 2} partial pressure, as compared to a similar anneal in a CO{sub 2}-free atmosphere, with the oxygen partial pressure being constant in both cases. Hard X-ray photoelectron spectroscopy (HAXPES) measurements showed that the contribution of the surface carbonate to surface oxide phases increased significantly for the sample annealed in the high-CO{sub 2} atmosphere. Atomic force microscopy (AFM) studies showed enhanced surface phase formation during the high-CO{sub 2} partial pressure anneal. Density functional theory (DFT) calculations provide a thermodynamic basis for the enhanced kinetics of surface segregation in the presence of atmospheric CO{sub 2}.

41 CFR 60-1.8 - Segregated facilities.

Science.gov (United States)

2010-07-01

... 41 Public Contracts and Property Management 1 2010-07-01 2010-07-01 true Segregated facilities. 60...; Compliance Reports § 60-1.8 Segregated facilities. To comply with its obligations under the Order, a contractor must ensure that facilities provided for employees are provided in such a manner that segregation...

THE SEGREGATION PATTERN OF INSECT RESISTANCE GENES IN THE PROGENIES AND CROSSES OF TRANSGENIC ROJOLELE RICE

Directory of Open Access Journals (Sweden)

Satoto Satoto

2016-10-01

Full Text Available Successful application of genetic transformation technique, especially in developing rice variety resistant to brown plant hopper and stem borer, will depend on transgene being expressed and the gene inherited in a stable and predictable manner. This study aimed to analyse transgene segregation pattern of the progenies and the crosses of transgenic rice cv. Rojolele harboring cry1Ab and gna genes. The third generation (T2 of fivetransgenic Rojolele events containing gna and/or cry1Ab were evaluated for two generations to identify the homozygous lines and to study their inheritance. The homozygous lines were selected based on the result of PCR technique. The segregation patterns of gna and cry1Ab were studied in eight F2 populations derived from Rojolele x transgenic Rojolele homozygous for cry1Ab and or gna and their reciprocal crosses. Data  resulted from PCR of F2 population were analysed using a Chi Square test. The study obtained six homozygous lines for gna, namely A22- 1-32, A22-1-37, C72-1-9, F11-1-48, K21-1-39, K21-1-48, and two homozygous lines for cry1Ab, namely K21-1-39 and K21- 1-48. Both cry1Ab and gna transgenes had been inherited through selfing and crossing with their wild type as indicated from the F1 containing gna and cry1Ab as many as 48.4% and 47.4%, respectively. In six of the eight crosses, gna was inherited in a 3:1 ratio consistent with Mendelian inheritance of a single dominant locus, while in the remaining two crosses, gna was segregated in a 1:1 ratio. The presence of cry1Ab in F2 populations also showed a 3:1 segregation ratio in all crosses. In the F2 population derived from F1 plant containing cry1Ab and gna, both transgenes segregated in a 9:3:3:1 dihybrid segregation ratio. This study will add to the diversity of genetic sources for insect resistance and allow further use of these transgenic lines for pyramiding resistance to brown plant hopper and stem borer or  separately in rice breeding programs whenever

Renæssancen i svøb

DEFF Research Database (Denmark)

  Hvornår holder middelalderen op og afløses af renæssancen? Og kan det virkelig passe at renæssancen i Danmark først slår igennem 150 år efter den italienske? Disse spørgsmål mødtes en række forskere og specialister om og diskuterede i det danske renæssanceår 2006. Resultatet blev 13 nye bidrag ...

Functional role of oppA encoding an oligopeptide-binding protein from Lactobacillus salivarius Ren in bile tolerance.

Science.gov (United States)

Wang, Guohong; Li, Dan; Ma, Xiayin; An, Haoran; Zhai, Zhengyuan; Ren, Fazheng; Hao, Yanling

2015-08-01

Lactobacillus salivarius is a member of the indigenous microbiota of the human gastrointestinal tract (GIT), and some L. salivarius strains are considered as probiotics. Bile tolerance is a crucial property for probiotic bacteria to survive the transit through the GIT and exert their beneficial effects. In this work, the functional role of oppA encoding an oligopeptide transporter substrate-binding protein from L. salivarius Ren in bile salt tolerance was investigated. In silico analysis revealed that the oppA gene encodes a 61.7-kDa cell surface-anchored hydrophilic protein with a canonical lipoprotein signal peptide. Homologous overexpression of OppA was shown to confer 20-fold higher tolerance to 0.5 % oxgall in L. salivarius Ren. Furthermore, the recombinant strain exhibited 1.8-fold and 3.6-fold higher survival when exposed to the sublethal concentration of sodium taurocholate and sodium taurodeoxycholate, respectively, while no significant change was observed when exposed to sodium glycocholate and sodium glycodeoxycholate (GDCA). Our results indicate that OppA confers specific resistance to taurine-conjugated bile salts in L. salivarius Ren. In addition, the OppA overexpression strain also showed significant increased resistance to heat and salt stresses, suggesting the protective role of OppA against multiple stresses in L. salivarius Ren.

Angiogenic Gene Signature Derived from Subtype Specific Cell Models Segregate Proneural and Mesenchymal Glioblastoma

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Aman Sharma

2017-07-01

Full Text Available Intertumoral molecular heterogeneity in glioblastoma identifies four major subtypes based on expression of molecular markers. Among them, the two clinically interrelated subtypes, proneural and mesenchymal, are the most aggressive with proneural liable for conversion to mesenchymal upon therapy. Using two patient-derived novel primary cell culture models (MTA10 and KW10, we developed a minimal but unique four-gene signature comprising genes vascular endothelial growth factor A (VEGF-A, vascular endothelial growth factor B (VEGF-B and angiopoietin 1 (ANG1, angiopoietin 2 (ANG2 that effectively segregated the proneural (MTA10 and mesenchymal (KW10 glioblastoma subtypes. The cell culture preclassified as mesenchymal showed elevated expression of genes VEGF-A, VEGF-B and ANG1, ANG2 as compared to the other cell culture model that mimicked the proneural subtype. The differentially expressed genes in these two cell culture models were confirmed by us using TCGA and Verhaak databases and we refer to it as a minimal multigene signature (MMS. We validated this MMS on human glioblastoma tissue sections with the use of immunohistochemistry on preclassified (YKL-40 high or mesenchymal glioblastoma and OLIG2 high or proneural glioblastoma tumor samples (n = 30. MMS segregated mesenchymal and proneural subtypes with 83% efficiency using a simple histopathology scoring approach (p = 0.008 for ANG2 and p = 0.01 for ANG1. Furthermore, MMS expression negatively correlated with patient survival. Importantly, MMS staining demonstrated spatiotemporal heterogeneity within each subclass, adding further complexity to subtype identification in glioblastoma. In conclusion, we report a novel and simple sequencing-independent histopathology-based biomarker signature comprising genes VEGF-A, VEGF-B and ANG1, ANG2 for subtyping of proneural and mesenchymal glioblastoma.

Characterization of novel and uncharacterized p53 SNPs in the Chinese population--intron 2 SNP co-segregates with the common codon 72 polymorphism.

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Beng Hooi Phang

Full Text Available Multiple single nucleotide polymorphisms (SNPs have been identified in the tumor suppressor gene p53, though the relevance of many of them is unclear. Some of them are also differentially distributed in various ethnic populations, suggesting selective functionality. We have therefore sequenced all exons and flanking regions of p53 from the Singaporean Chinese population and report here the characterization of some novel and uncharacterized SNPs - four in intron 1 (nucleotide positions 8759/10361/10506/11130, three in intron 3 (11968/11969/11974 and two in the 3'UTR (19168/19514. Allelic frequencies were determined for all these and some known SNPs, and were compared in a limited scale to leukemia and lung cancer patient samples. Intron 2 (11827 and 7 (14181/14201 SNPs were found to have a high minor allele frequency of between 26-47%, in contrast to the lower frequencies found in the US population, but similar in trend to the codon 72 polymorphism (SNP12139 that shows a distribution pattern correlative with latitude. Several of the SNPs were linked, such as those in introns 1, 3 and 7. Most interestingly, we noticed the co-segregation of the intron 2 and the codon 72 SNPs, the latter which has been shown to be expressed in an allele-specific manner, suggesting possible regulatory cross-talk. Association analysis indicated that the T/G alleles in both the co-segregating intron 7 SNPs and a 4tagSNP haplotype was strongly associated increased susceptibility to lung cancer in non-smoker females [OR: 1.97 (1.32, 3.394]. These data together demonstrate high SNP diversity in p53 gene between different populations, highlighting ethnicity-based differences, and their association with cancer risk.

FBN1 gene mutation defines the profibrillin to fibrillin processing site and segregates with tall stature in a family

Energy Technology Data Exchange (ETDEWEB)

Grossfield, J.; Cao, S.; Milewicz, D. [Univ. of Texas Medical School, Houston, TX (United States)] [and others

1994-09-01

Dermal fibroblasts from a 13-year-old boy with skeletal features of the Marfan syndrome were used to study fibrillin synthesis and processing. Synthesis and secretion of profibrillin was normal but only half of the secreted profibrillin was converted to fibrillin, an extracellular proteolytic processing that removes a 20 kDa fragment from the protein. All the secreted profibrillin was processed to fibrillin in control cells. Only the processed form of fibrillin was deposited into the extracellular matrix in both the proband`s and the control cells. Electron microscopic examination of rotary shadowed microfibrils made by the proband`s fibroblasts were indistinguishable from control cells. Screening exons in the 3{prime} end of the FBN1 gene revealed a heterozygous C to T transition at nucleotide 5482 of the FBN1 cDNA changing R 1828 to W. This mutation disrupts a known consensus sequence recognized by a cellular protease and is located in the carboxy terminus at a site predicted to remove a 19 kD fragment. The proband and his 22-year-old brother, also heterozygous for the mutation, have had normal echocardiograms and ophthalmologic exams. The mutation segregated in the proband`s three generation family with autosomal dominant inheritance of height (> 90th percentile) and no known cardiovascular or ocular problems, including the 67-year-old grandmother (exams pending). The mutation was not found in 90 chromosomes from unrelated individuals. In summary, (1) the mutation identifies the cleavage site for the conversion of profibrillin to fibrillin; (2) the characterized mutation segregates in the family with tall stature without known cardiovascular or ocular problems; (3) this mutation potentially defines the phenotype associated with a {open_quotes}null{close_quotes} allele for the FBN1 gene.

René Goupil: patron saint of anesthetists.

Science.gov (United States)

Quintal, J

1995-06-01

René Goupil, the patron saint of anesthetists, is addressed mainly as a 17th century French surgeon who practiced his art in North America. He is also presented as a Jesuit martyr and saint. The article freely borrows from past writings of Jesuits on René Goupil.

Segregation assisted microtwinning during creep of a polycrystalline L12-hardened Co-base superalloy

International Nuclear Information System (INIS)

Freund, Lisa P.; Messé, Olivier M.D.M.; Barnard, Jonathan S.; Göken, Mathias; Neumeier, Steffen; Rae, Catherine M.F.

2017-01-01

A polycrystalline L1 2 -hardened Co-base superalloy was creep deformed at 750 °C. The investigation of the deformed microstructure in the transmission electron microscope revealed microtwinning to be the prevailing deformation mechanism. The detected twins spanned the entire grain and cut through both, γ and γ′. Detailed high-resolution transmission electron microscopy investigations indicated that twin growth takes place by the slip of single a/6 〈112〉 partial dislocations along the twin boundary. Further analysis of the twin boundaries in the γ′ phase revealed segregation of elements known to decrease the stacking fault energy and a local depletion of γ′ forming elements. We propose that this segregation behavior enables subsequent a/6〈112〉 dislocations to easily slip along the twin boundary and further thicken the twins in the process.

[Inheritance of bc1 gene in intersubspecific hybrids of rice (Oryza sativa L.)].

Science.gov (United States)

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.

Association of the polymorphism 12109g>A from the REN gene as a risk factor for preterm birth

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Irám P Rodríguez-Sánchez

2016-11-01

Full Text Available Introduction: Preterm birth is the most important cause of neonatal mortality and morbidity. It is a multifactorial disease with different etiologies, including genetic factors. Genetic variability is represented by single nucleotide polymorphisms (SNPs in genes of proteins involved in the contractile activity. We determine the association between SNP 12109G> A in REN associated with preterm birth and premature rupture of membrane. Materials and methods: A study of cases (N=112, 22–36 weeks of gestation; mean: 31, 95% confidence interval 30.7–32.2 and controls (N=66; 38–40 weeks of gestation from the last menstrual period; mean: 39.8, 95% confidence interval 38.9–39.4 was performed. Genomic DNA was isolated in all patients from peripheral blood. The SNP 12109G> A (Mbo I in REN was typified by PCR-restriction fragment length polymorphism. Results: A significant difference in the case group for the SNP 12109G>A was observed. The A allele was increased in women with preterm birth (81% cases vs. 15% control, p A has odds ratio 6.62 (95% confidence interval 3.14–14.15, which means a high risk of preterm birth/premature rupture of membrane in presence of allele A, both in homozygotes and in heterozygotes. Conclusion: Allelic frequency of A of SNP 12109G>A was higher in women with preterm birth than in women with normal vaginal delivery and could be considered a risk factor.

Gene editing by co-transformation of TALEN and chimeric RNA/DNA oligonucleotides on the rice OsEPSPS gene and the inheritance of mutations.

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Mugui Wang

Full Text Available Although several site-specific nucleases (SSNs, such as zinc-finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and the clustered regularly interspaced short palindromic repeat (CRISPR/Cas, have emerged as powerful tools for targeted gene editing in many organisms, to date, gene targeting (GT in plants remains a formidable challenge. In the present study, we attempted to substitute a single base in situ on the rice OsEPSPS gene by co-transformation of TALEN with chimeric RNA/DNA oligonucleotides (COs, including different strand composition such as RNA/DNA (C1 or DNA/RNA (C2 but contained the same target base to be substituted. In contrast to zero GT event obtained by the co-transformation of TALEN with homologous recombination plasmid (HRP, we obtained one mutant showing target base substitution although accompanied by undesired deletion of 12 bases downstream the target site from the co-transformation of TALEN and C1. In addition to this typical event, we also obtained 16 mutants with different length of base deletions around the target site among 105 calli lines derived from transformation of TALEN alone (4/19 as well as co-transformation of TELAN with either HRP (5/30 or C1 (2/25 or C2 (5/31. Further analysis demonstrated that the homozygous gene-edited mutants without foreign gene insertion could be obtained in one generation. The induced mutations in transgenic generation were also capable to pass to the next generation stably. However, the genotypes of mutants did not segregate normally in T1 population, probably due to lethal mutations. Phenotypic assessments in T1 generation showed that the heterozygous plants with either one or three bases deletion on target sequence, called d1 and d3, were more sensitive to glyphosate and the heterozygous d1 plants had significantly lower seed-setting rate than wild-type.

Origin, evolution, and population genetics of the selfish Segregation Distorter gene duplication in European and African populations of Drosophila melanogaster.

Science.gov (United States)

Brand, Cara L; Larracuente, Amanda M; Presgraves, Daven C

2015-05-01

Meiotic drive elements are a special class of evolutionarily "selfish genes" that subvert Mendelian segregation to gain preferential transmission at the expense of homologous loci. Many drive elements appear to be maintained in populations as stable polymorphisms, their equilibrium frequencies determined by the balance between drive (increasing frequency) and selection (decreasing frequency). Here we show that a classic, seemingly balanced, drive system is instead characterized by frequent evolutionary turnover giving rise to dynamic, rather than stable, equilibrium frequencies. The autosomal Segregation Distorter (SD) system of the fruit fly Drosophila melanogaster is a selfish coadapted meiotic drive gene complex in which the major driver corresponds to a partial duplication of the gene Ran-GTPase activating protein (RanGAP). SD chromosomes segregate at similar, low frequencies of 1-5% in natural populations worldwide, consistent with a balanced polymorphism. Surprisingly, our population genetic analyses reveal evidence for parallel, independent selective sweeps of different SD chromosomes in populations on different continents. These findings suggest that, rather than persisting at a single stable equilibrium, SD chromosomes turn over frequently within populations. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Gene number determination and genetic polymorphism of the gamma delta T cell co-receptor WC1 genes

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Chen Chuang

2012-10-01

Full Text Available Abstract Background WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1+ γδ T cells. We have previously identified partial or complete genomic sequences for thirteen different WC1 genes through annotation of the bovine genome Btau_3.1 build. We also identified two WC1 cDNA sequences from other cattle that did not correspond to sequences in the Btau_3.1 build. Their absence in the Btau_3.1 build may have reflected gaps in the genome assembly or polymorphisms among animals. Since the response of γδ T cells to bacterial challenge is determined by WC1 gene expression, it was critical to understand whether individual cattle or breeds differ in the number of WC1 genes or display polymorphisms. Results Real-time quantitative PCR using DNA from the animal whose genome was sequenced (“Dominette” and sixteen other animals representing ten breeds of cattle, showed that the number of genes coding for WC1 co-receptors is thirteen. The complete coding sequences of those thirteen WC1 genes is presented, including the correction of an error in the WC1-2 gene due to mis-assembly in the Btau_3.1 build. All other cDNA sequences were found to agree with the previous annotation of complete or partial WC1 genes. PCR amplification and sequencing of the most variable N-terminal SRCR domain (domain 1 which has the SRCR “a” pattern of each of the thirteen WC1 genes showed that the sequences are highly conserved among individuals and breeds. Of 160 sequences of domain 1 from three breeds of cattle, no additional sequences beyond the thirteen described WC1 genes were found. Analysis of the complete WC1 cDNA sequences indicated that the thirteen WC1 genes code for three distinct WC1 molecular forms. Conclusion The bovine WC1 multi-gene family is composed of thirteen genes coding for three structural forms whose

On an integrable deformed affinsphären equation. A reciprocal gasdynamic connection

International Nuclear Information System (INIS)

Rogers, C.; Huang, Yehui

2012-01-01

The integrable affinsphären equation originally arose in a geometric context but has an interesting gasdynamic connection. Here, an integrable deformed version of the affinsphären equation is derived in a novel manner via the action of reciprocal transformations on a related anisentropic gasdynamics system. A linear representation for the deformed affinsphären equation is constructed by means of the reciprocal transformations. The latter are then employed to derive a class of exact solutions in parametric form. -- Highlights: ► A deformed affinsphären equation is derived via a reciprocal transformation. ► A linear representation for the deformed affinsphären equation is constructed. ► A class of exact solutions of the deformed affinsphären equation is presented.

Søren Buus. Thirty years of psychoacoustic inspiration

DEFF Research Database (Denmark)

Poulsen, Torben

2005-01-01

Søren Buus did his MSc at the Acoustics Laboratory, Technical University of Denmark (DTU), in 1975 on the topic headphone calibration. He showed the importance of reliable reference values for psychoacoustic research and Søren was a great inspiration for my work (Scand. Audiol. 20, 205–207 (1991...

Major Gene for Field Stem Rust Resistance Co-Locates with Resistance Gene Sr12 in 'Thatcher' Wheat.

Science.gov (United States)

Hiebert, Colin W; Kolmer, James A; McCartney, Curt A; Briggs, Jordan; Fetch, Tom; Bariana, Harbans; Choulet, Frederic; Rouse, Matthew N; Spielmeyer, Wolfgang

2016-01-01

Stem rust, caused by Puccinia graminis (Pgt), is a damaging disease of wheat that can be controlled by utilizing effective stem rust resistance genes. 'Thatcher' wheat carries complex resistance to stem rust that is enhanced in the presence of the resistance gene Lr34. The purpose of this study was to examine APR in 'Thatcher' and look for genetic interactions with Lr34. A RIL population was tested for stem rust resistance in field nurseries in Canada, USA, and Kenya. BSA was used to find SNP markers associated with reduced stem rust severity. A major QTL was identified on chromosome 3BL near the centromere in all environments. Seedling testing showed that Sr12 mapped to the same region as the QTL for APR. The SNP markers were physically mapped and the region carrying the resistance was searched for sequences with homology to members of the NB-LRR resistance gene family. SNP marker from one NB-LRR-like sequence, NB-LRR3 co-segregated with Sr12. Two additional populations, including one that lacked Lr34, were tested in field nurseries. NB-LRR3 mapped near the maximum LOD for reduction in stem rust severity in both populations. Lines from a population that segregated for Sr12 and Lr34 were tested for seedling Pgt biomass and infection type, as well as APR to field stem rust which showed an interaction between the genes. We concluded that Sr12, or a gene closely linked to Sr12, was responsible for 'Thatcher'-derived APR in several environments and this resistance was enhanced in the presence of Lr34.

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes.

Science.gov (United States)

Jensen, Philip J; Fazio, Gennaro; Altman, Naomi; Praul, Craig; McNellis, Timothy W

2014-04-04

Apple tree breeding is slow and difficult due to long generation times, self-incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose steady-state transcript abundance was associated with inheritance of specific traits segregating in an apple (Malus × domestica) rootstock F1 breeding population, including resistance to powdery mildew (Podosphaera leucotricha) disease and woolly apple aphid (Eriosoma lanigerum). Transcription profiling was performed for 48 individual F1 apple trees from a cross of two highly heterozygous parents, using RNA isolated from healthy, actively-growing shoot tips and a custom apple DNA oligonucleotide microarray representing 26,000 unique transcripts. Genome-wide expression profiles were not clear indicators of powdery mildew or woolly apple aphid resistance phenotype. However, standard differential gene expression analysis between phenotypic groups of trees revealed relatively small sets of genes with trait-associated expression levels. For example, thirty genes were identified that were differentially expressed between trees resistant and susceptible to powdery mildew. Interestingly, the genes encoding twenty-four of these transcripts were physically clustered on chromosome 12. Similarly, seven genes were identified that were differentially expressed between trees resistant and susceptible to woolly apple aphid, and the genes encoding five of these transcripts were also clustered, this time on chromosome 17. In each case, the gene clusters were in the vicinity of previously identified major quantitative trait loci for the corresponding trait. Similar results were obtained for a series of molecular traits. Several of the differentially expressed genes were used to develop DNA polymorphism markers linked to powdery mildew disease and woolly apple aphid resistance. Gene expression profiling

Functional characterization of the origin of replication of pRN1 from Sulfolobus islandicus REN1H1.

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Chijioke J Joshua

Full Text Available Plasmid pRN1 from Sulfolobus islandicus REN1H1 is believed to replicate by a rolling circle mechanism but its origin and mechanism of replication are not well understood. We sought to create minimal expression vectors based on pRN1 that would be useful for heterologous gene expression in S. acidocaldarius, and in the process improve our understanding of the mechanism of replication. We constructed and transformed shuttle vectors that harbored different contiguous stretches of DNA from pRN1 into S. acidocaldarius E4-39, a uracil auxotroph. A 232-bp region 3' of orf904 was found to be critical for pRN1 replication and is therefore proposed to be the putative origin of replication. This 232-bp region contains a 100-bp stem-loop structure believed to be the double-strand origin of replication. The loop of the 100-bp structure contains a GTG tri-nucleotide motif, a feature that was previously reported to be important for the primase activity of Orf904. This putative origin and the associated orf56 and orf904 were identified as the minimal replicon of pRN1 because transformants of plasmids lacking any of these three features were not recovered. Plasmids lacking orf904 and orf56 but harboring the putative origin were transformable when orf904 and orf56 were provided in-trans; a 75-bp region 5' of the orf904 start codon was found to be essential for this complementation. Detailed knowledge of the pRN1 origin of replication will broaden the application of the plasmid as a genetic tool for Sulfolobus species.

Left-right symmetry breaking in mice by left-right dynein may occur via a biased chromatid segregation mechanism, without directly involving the Nodal gene

Energy Technology Data Exchange (ETDEWEB)

Sauer, Stephan; Klar, Amar J. S., E-mail: sauers@mail.nih.gov, E-mail: klara@mail.nih.gov [Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD (United States)

2012-11-16

Ever since cloning the classic iv (inversedviscerum) mutation identified the “left-right dynein” (lrd) gene in mice, most research on body laterality determination has focused on its function in motile cilia at the node embryonic organizer. This model is attractive, as it links chirality of cilia architecture to asymmetry development. However, lrd is also expressed in blastocysts and embryonic stem cells, where it was shown to bias the segregation of recombined sister chromatids away from each other in mitosis. These data suggested that lrd is part of a cellular mechanism that recognizes and selectively segregates sister chromatids based on their replication history: old “Watson” versus old “Crick” strands. We previously proposed that the mouse left-right axis is established via an asymmetric cell division prior to/or during gastrulation. In this model, left-right dynein selectively segregates epigenetically differentiated sister chromatids harboring a hypothetical “left-right axis development 1” (“lra1”) gene during the left-right axis establishing cell division. Here, asymmetry development would be ultimately governed by the chirality of the cytoskeleton and the DNA molecule. Our model predicts that randomization of chromatid segregation in lrd mutants should produce embryos with 25% situs solitus, 25% situs inversus, and 50% embryonic death due to heterotaxia and isomerism. Here we confirmed this prediction by using two distinct lrd mutant alleles. Other than lrd, thus far Nodal gene is the most upstream function implicated in visceral organs laterality determination. We next tested whether the Nodal gene constitutes the lra1 gene hypothesized in the model by testing mutant’s effect on 50% embryonic lethality observed in lrd mutants. Since Nodal mutation did not suppress lethality, we conclude that Nodal is not equivalent to the lra1 gene. In summary, we describe the origin of 50% lethality in lrd mutant mice not yet explained by any other

Left-right symmetry breaking in mice by left-right dynein may occur via a biased chromatid segregation mechanism, without directly involving the Nodal gene

International Nuclear Information System (INIS)

Sauer, Stephan; Klar, Amar J. S.

2012-01-01

Ever since cloning the classic iv (inversedviscerum) mutation identified the “left-right dynein” (lrd) gene in mice, most research on body laterality determination has focused on its function in motile cilia at the node embryonic organizer. This model is attractive, as it links chirality of cilia architecture to asymmetry development. However, lrd is also expressed in blastocysts and embryonic stem cells, where it was shown to bias the segregation of recombined sister chromatids away from each other in mitosis. These data suggested that lrd is part of a cellular mechanism that recognizes and selectively segregates sister chromatids based on their replication history: old “Watson” versus old “Crick” strands. We previously proposed that the mouse left-right axis is established via an asymmetric cell division prior to/or during gastrulation. In this model, left-right dynein selectively segregates epigenetically differentiated sister chromatids harboring a hypothetical “left-right axis development 1” (“lra1”) gene during the left-right axis establishing cell division. Here, asymmetry development would be ultimately governed by the chirality of the cytoskeleton and the DNA molecule. Our model predicts that randomization of chromatid segregation in lrd mutants should produce embryos with 25% situs solitus, 25% situs inversus, and 50% embryonic death due to heterotaxia and isomerism. Here we confirmed this prediction by using two distinct lrd mutant alleles. Other than lrd, thus far Nodal gene is the most upstream function implicated in visceral organs laterality determination. We next tested whether the Nodal gene constitutes the lra1 gene hypothesized in the model by testing mutant’s effect on 50% embryonic lethality observed in lrd mutants. Since Nodal mutation did not suppress lethality, we conclude that Nodal is not equivalent to the lra1 gene. In summary, we describe the origin of 50% lethality in lrd mutant mice not yet explained by any other

Left-right symmetry breaking in mice by left-right dynein may occur via a biased chromatid segregation mechanism, without directly involving the Nodal gene

Directory of Open Access Journals (Sweden)

Stephan eSauer

2012-11-01

Full Text Available Ever since cloning the classic iv mutation identified the ‘left-right dynein’ (lrd gene in mice, most research on body laterality determination has focused on its function in motile cilia at the node embryonic organizer. This model is attractive, as it links chirality of cilia architecture to asymmetry development. However, lrd is also expressed in blastocysts and embryonic stem cells, where it was shown to bias the segregation of recombined sister chromatids away from each other in mitosis. These data suggested that lrd is part of a cellular mechanism that recognizes and selectively segregates sister chromatids based on their replication history: old ‘Watson’ vs. old ‘Crick’ strands. We previously proposed that the mouse left-right axis is established via an asymmetric cell division prior to/or during gastrulation. In this model, left-right dynein selectively segregates epigenetically differentiated sister chromatids harboring a hypothetical ‘left-right axis development 1’ (‘lra1’ gene during the left-right axis establishing cell division. Here, asymmetry development would be ultimately governed by the chirality of the cytoskeleton and the DNA molecule. Our model predicts that randomization of chromatid segregation in lrd mutants should produce embryos with 25% situs solitus, 25% situs inversus, and 50% embryonic death due to heterotaxia and isomerism. Here we confirmed this prediction by using two distinct lrd mutant alleles. Other than lrd, thus far Nodal gene is the most upstream function implicated in visceral organs laterality determination. We next tested whether the Nodal gene constitutes the lra1 gene hypothesized in the model by testing mutant’s effect on 50% embryonic lethality observed in lrd mutants. Since Nodal mutation did not suppress lethality, we conclude that Nodal is not equivalent to the lra1 gene. In summary, we describe the origin of 50% lethality in lrd mutant mice not yet explained by any other

Major Gene for Field Stem Rust Resistance Co-Locates with Resistance Gene Sr12 in ‘Thatcher’ Wheat

Science.gov (United States)

Hiebert, Colin W.; Kolmer, James A.; McCartney, Curt A.; Briggs, Jordan; Fetch, Tom; Bariana, Harbans; Choulet, Frederic; Rouse, Matthew N.; Spielmeyer, Wolfgang

2016-01-01

Stem rust, caused by Puccinia graminis (Pgt), is a damaging disease of wheat that can be controlled by utilizing effective stem rust resistance genes. ‘Thatcher’ wheat carries complex resistance to stem rust that is enhanced in the presence of the resistance gene Lr34. The purpose of this study was to examine APR in ‘Thatcher’ and look for genetic interactions with Lr34. A RIL population was tested for stem rust resistance in field nurseries in Canada, USA, and Kenya. BSA was used to find SNP markers associated with reduced stem rust severity. A major QTL was identified on chromosome 3BL near the centromere in all environments. Seedling testing showed that Sr12 mapped to the same region as the QTL for APR. The SNP markers were physically mapped and the region carrying the resistance was searched for sequences with homology to members of the NB-LRR resistance gene family. SNP marker from one NB-LRR-like sequence, NB-LRR3 co-segregated with Sr12. Two additional populations, including one that lacked Lr34, were tested in field nurseries. NB-LRR3 mapped near the maximum LOD for reduction in stem rust severity in both populations. Lines from a population that segregated for Sr12 and Lr34 were tested for seedling Pgt biomass and infection type, as well as APR to field stem rust which showed an interaction between the genes. We concluded that Sr12, or a gene closely linked to Sr12, was responsible for ‘Thatcher’-derived APR in several environments and this resistance was enhanced in the presence of Lr34. PMID:27309724

The Role of a Novel TRMT1 Gene Mutation and Rare GRM1 Gene Defect in Intellectual Disability in Two Azeri Families.

Science.gov (United States)

Davarniya, Behzad; Hu, Hao; Kahrizi, Kimia; Musante, Luciana; Fattahi, Zohreh; Hosseini, Masoumeh; Maqsoud, Fariba; Farajollahi, Reza; Wienker, Thomas F; Ropers, H Hilger; Najmabadi, Hossein

2015-01-01

Cognitive impairment or intellectual disability (ID) is a widespread neurodevelopmental disorder characterized by low IQ (below 70). ID is genetically heterogeneous and is estimated to affect 1-3% of the world's population. In affected children from consanguineous families, autosomal recessive inheritance is common, and identifying the underlying genetic cause is an important issue in clinical genetics. In the framework of a larger project, aimed at identifying candidate genes for autosomal recessive intellectual disorder (ARID), we recently carried out single nucleotide polymorphism-based genome-wide linkage analysis in several families from Ardabil province in Iran. The identification of homozygosity-by-descent loci in these families, in combination with whole exome sequencing, led us to identify possible causative homozygous changes in two families. In the first family, a missense variant was found in GRM1 gene, while in the second family, a frameshift alteration was identified in TRMT1, both of which were found to co-segregate with the disease. GRM1, a known causal gene for autosomal recessive spinocerebellar ataxia (SCAR13, MIM#614831), encodes the metabotropic glutamate receptor1 (mGluR1). This gene plays an important role in synaptic plasticity and cerebellar development. Conversely, the TRMT1 gene encodes a tRNA methyltransferase that dimethylates a single guanine residue at position 26 of most tRNAs using S-adenosyl methionine as the methyl group donor. We recently presented TRMT1 as a candidate gene for ARID in a consanguineous Iranian family (Najmabadi et al., 2011). We believe that this second Iranian family with a biallelic loss-of-function mutation in TRMT1 gene supports the idea that this gene likely has function in development of the disorder.

Evidence of a major gene from Bayesian segregation analyses of liability to osteochondral diseases in pigs.

Science.gov (United States)

Kadarmideen, Haja N; Janss, Luc L G

2005-11-01

Bayesian segregation analyses were used to investigate the mode of inheritance of osteochondral lesions (osteochondrosis, OC) in pigs. Data consisted of 1163 animals with OC and their pedigrees included 2891 animals. Mixed-inheritance threshold models (MITM) and several variants of MITM, in conjunction with Markov chain Monte Carlo methods, were developed for the analysis of these (categorical) data. Results showed major genes with significant and substantially higher variances (range 1.384-37.81), compared to the polygenic variance (sigmau2). Consequently, heritabilities for a mixed inheritance (range 0.65-0.90) were much higher than the heritabilities from the polygenes. Disease allele frequencies range was 0.38-0.88. Additional analyses estimating the transmission probabilities of the major gene showed clear evidence for Mendelian segregation of a major gene affecting osteochondrosis. The variants, MITM with informative prior on sigmau2, showed significant improvement in marginal distributions and accuracy of parameters. MITM with a "reduced polygenic model" for parameterization of polygenic effects avoided convergence problems and poor mixing encountered in an "individual polygenic model." In all cases, "shrinkage estimators" for fixed effects avoided unidentifiability for these parameters. The mixed-inheritance linear model (MILM) was also applied to all OC lesions and compared with the MITM. This is the first study to report evidence of major genes for osteochondral lesions in pigs; these results may also form a basis for underpinning the genetic inheritance of this disease in other animals as well as in humans.

Candidacy of a chitin-inducible gibberellin-responsive gene for a major locus affecting plant height in rice that is closely linked to Green Revolution gene sd1.

Science.gov (United States)

Kovi, Mallikarjuna Rao; Zhang, Yushan; Yu, Sibin; Yang, Gaiyu; Yan, Wenhao; Xing, Yongzhong

2011-09-01

Appropriate plant height is crucial for lodging resistance to improve the rice crop yield. The application of semi-dwarf 1 led to the green revolution in the 1960s, by predominantly increasing the rice yield. However, the frequent use of single sd1 gene sources may cause genetic vulnerability to pests and diseases. Identifying useful novel semi-dwarf genes is important for the genetic manipulation of plant architecture in practical rice breeding. In this study, introgression lines derived from two parents contrasting in plant height, Zhenshan 97 and Pokkali were employed to locate a gene with a large effect on plant height by the bulk segregant analysis method. A major gene, ph1, was mapped to a region closely linked to sd1 on chromosome 1; the additive effects of ph1 were more than 50 cm on the plant height and 2 days on the heading date in a BC(4)F(2) population and its progeny. ph1 was then fine mapped to BAC AP003227. Gene annotation indicated that LOC_OS01g65990 encoding a chitin-inducible gibberellin-responsive protein (CIGR), which belongs to the GRAS family, might be the right candidate gene of ph1. Co-segregation analysis of the candidate gene-derived marker finally confirmed its identity as the candidate gene. A higher expression level of the CIGR was detected in all the tested tissues in tall plants compared to those of short plants, especially in the young leaf sheath containing elongating tissues, which indicated its importance role in regulating plant height. ph1 showed a tremendous genetic effect on plant height, which is distinct from sd1 and could be a new resource for breeding semi-dwarf varieties.

Two rare deletions upstream of the NRXN1 gene (2p16.3) affecting the non-coding mRNA AK127244 segregate with diverse psychopathological phenotypes in a family

DEFF Research Database (Denmark)

Duong, L. T. T.; Hoeffding, L. K.; Petersen, K. B.

2015-01-01

127244 in addition to the pathogenic 15q11.2 deletion in distinct family members. The two deletions upstream of the NRXN1 gene were found to segregate with psychiatric disorders in the family and further similar deletions have been observed in patients diagnosed with autism spectrum disorder. Thus, we...... susceptibility. In this study, we describe a family affected by a wide range of psychiatric disorders including early onset schizophrenia, schizophreniform disorder, and affective disorders. Microarray analysis identified two rare deletions immediately upstream of the NRXN1 gene affecting the non-coding mRNA AK...... suggest that non-coding regions upstream of the NRXN1 gene affecting AK127244 might (as NRXN1) contain susceptibility regions for a wide spectrum of neuropsychiatric disorders. (C) 2015 Elsevier Masson SAS. All rights reserved....

A novel ATP1A2 gene mutation in an Irish familial hemiplegic migraine kindred.

LENUS (Irish Health Repository)

Fernandez, Desiree M

2012-02-03

OBJECTIVE: We studied a large Irish Caucasian pedigree with familial hemiplegic migraine (FHM) with the aim of finding the causative gene mutation. BACKGROUND: FHM is a rare autosomal-dominant subtype of migraine with aura, which is linked to 4 loci on chromosomes 19p13, 1q23, 2q24, and 1q31. The mutations responsible for hemiplegic migraine have been described in the CACNA1A gene (chromosome 19p13), ATP1A2 gene (chromosome 1q23), and SCN1A gene (chromosome 2q24). METHODS: We performed linkage analyses in this family for chromosome 1q23 and performed mutation analysis of the ATP1A2 gene. RESULTS: Linkage to the FHM2 locus on chromosome 1 was demonstrated. Mutation screening of the ATP1A2 gene revealed a G to C substitution in exon 22 resulting in a novel protein variant, D999H, which co-segregates with FHM within this pedigree and is absent in 50 unaffected individuals. This residue is also highly conserved across species. CONCLUSIONS: We propose that D999H is a novel FHM ATP1A2 mutation.

Chiasmata promote monopolar attachment of sister chromatids and their co-segregation toward the proper pole during meiosis I.

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Yukinobu Hirose

2011-03-01

Full Text Available The chiasma is a structure that forms between a pair of homologous chromosomes by crossover recombination and physically links the homologous chromosomes during meiosis. Chiasmata are essential for the attachment of the homologous chromosomes to opposite spindle poles (bipolar attachment and their subsequent segregation to the opposite poles during meiosis I. However, the overall function of chiasmata during meiosis is not fully understood. Here, we show that chiasmata also play a crucial role in the attachment of sister chromatids to the same spindle pole and in their co-segregation during meiosis I in fission yeast. Analysis of cells lacking chiasmata and the cohesin protector Sgo1 showed that loss of chiasmata causes frequent bipolar attachment of sister chromatids during anaphase. Furthermore, high time-resolution analysis of centromere dynamics in various types of chiasmate and achiasmate cells, including those lacking the DNA replication checkpoint factor Mrc1 or the meiotic centromere protein Moa1, showed the following three outcomes: (i during the pre-anaphase stage, the bipolar attachment of sister chromatids occurs irrespective of chiasma formation; (ii the chiasma contributes to the elimination of the pre-anaphase bipolar attachment; and (iii when the bipolar attachment remains during anaphase, the chiasmata generate a bias toward the proper pole during poleward chromosome pulling that results in appropriate chromosome segregation. Based on these results, we propose that chiasmata play a pivotal role in the selection of proper attachments and provide a backup mechanism that promotes correct chromosome segregation when improper attachments remain during anaphase I.

[An exceptional human relationship (Michael P. Kierkegaard, Søren Kierkegaard)].

Science.gov (United States)

Jacobs, R

1978-01-01

There were a father and a son, Michael and Sören Kierkegaard, both highly talented, imaginitive, witty, humorous, especially interested in shrewd dialectrical dialogues respectively debates, both profound melancholy ponderers. But according to very own individuality their congeniality wasn't absolute. The father, being under a questionable rigorous opinion of sin, suffered from undeserved divine grace since early childhood. And Michael Kierkegaard made Sören anxious with the religious experience of original sin. This anxiety moved (touched or affected) the sensitive son mighty. Nevertheless he should not despair hopelessly like his unlucky father. On the contrary: Sørens incomparable melancholy, mental agony and anxiety (fear or anguish) forced the faith, existing independently of them, in a radical refining. That is why Sören Kierkegaard succeeded in sublimation of all psychological and philosophic (al) attitudes (or opinions) in the sphere of religiousness. And the result? A novel philosophy of life: Christian existentialism.

Molecular characterization of barley 3H semi-dwarf genes.

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Haobing Li

Full Text Available The barley chromosome 3H accommodates many semi-dwarfing genes. To characterize these genes, the two-rowed semi-dwarf Chinese barley landrace 'TX9425' was crossed with the Australian barley variety 'Franklin' to generate a doubled haploid (DH population, and major QTLs controlling plant height have been identified in our previous study. The major QTL derived from 'TX9425' was targeted to investigate the allelism of the semi-dwarf gene uzu in barley. Twelve sets of near-isogenic lines and a large NILF2 fine mapping population segregating only for the dwarfing gene from 'TX9425' were developed. The semi-dwarfing gene in 'TX9425' was located within a 2.8 cM region close to the centromere on chromosome 3H by fine mapping. Molecular cloning and sequence analyses showed that the 'TX9425'-derived allele contained a single nucleotide substitution from A to G at position 2612 of the HvBRI1 gene. This was apparently the same mutation as that reported in six-rowed uzu barley. Markers co-segregating with the QTL were developed from the sequence of the HvBRI1 gene and were validated in the 'TX9425'/'Franklin' DH population. The other major dwarfing QTL derived from the Franklin variety was distally located on chromosome 3HL and co-segregated with the sdw1 diagnostic marker hv20ox2. A third dwarfing gene, expressed only in winter-sown trials, was identified and located on chromosome 3HS. The effects and interactions of these dwarfing genes under different growing conditions are discussed. These results improve our understanding of the genetic mechanisms controlling semi-dwarf stature in barley and provide diagnostic markers for the selection of semi-dwarfness in barley breeding programs.

Suppression of Genomic Instabilities Caused by Chromosome Mis-segregation: A Perspective From Studying BubR1 and Sgo1

Science.gov (United States)

Dai, Wei

2013-01-01

Aneuploidy is a major manifestation of chromosomal instability, which is defined as a numerical abnormality of chromosomes in diploid cells. It is highly prevalent in a variety of human malignancies. Increased chromosomal instability is the major driving force for tumor development and progression. To suppress genomic stability during cell division, eukaryotic cells have evolved important molecular mechanisms, commonly referred to as checkpoints. The spindle checkpoint ensures that cells with defective mitotic spindles or a defective interaction between the spindles and kinetochores do not initiate chromosomal segregation during mitosis. Extensive studies have identified and characterized more than a dozen genes that play important roles in the regulation of the spindle checkpoint in mammalian cells. During the past decade, we have carried out extensive investigation of the role of BubR1 (Bub1-related kinase) and Sgo1 (shugoshin 1), two important gene products that safeguard accurate chromosome segregation during mitosis. This mini-review summarizes our studies, as well as those by other researchers in the field, on the functions of these two checkpoint proteins and their molecular regulation during mitosis. Further elucidation of the molecular mechanisms of the spindle checkpoint regulation has the potential to identify important mitotic targets for rational anticancer drug design. PMID:20040454

Suppression of Genomic Instabilities Caused by Chromosome Mis-segregation: A Perspective From Studying BubR1 and Sgo1

Directory of Open Access Journals (Sweden)

Wei Dai

2009-12-01

Full Text Available Aneuploidy is a major manifestation of chromosomal instability, which is defined as a numerical abnormality of chromosomes in diploid cells. It is highly prevalent in a variety of human malignancies. Increased chromosomal instability is the major driving force for tumor development and progression. To suppress genomic stability during cell division, eukaryotic cells have evolved important molecular mechanisms, commonly referred to as checkpoints. The spindle checkpoint ensures that cells with defective mitotic spindles or a defective interaction between the spindles and kinetochores do not initiate chromosomal segregation during mitosis. Extensive studies have identified and characterized more than a dozen genes that play important roles in the regulation of the spindle checkpoint in mammalian cells. During the past decade, we have carried out extensive investigation of the role of BubR1 (Bub1-related kinase and Sgo1 (shugoshin 1, two important gene products that safeguard accurate chromosome segregation during mitosis. This mini-review summarizes our studies, as well as those by other researchers in the field, on the functions of these two checkpoint proteins and their molecular regulation during mitosis. Further elucidation of the molecular mechanisms of the spindle checkpoint regulation has the potential to identify important mitotic targets for rational anticancer drug design.

A CO-FISH assay to assess sister chromatid segregation patterns in mitosis of mouse embryonic stem cells.

Science.gov (United States)

Sauer, Stephan; Burkett, Sandra S; Lewandoski, Mark; Klar, Amar J S

2013-05-01

Sister chromatids contain identical DNA sequence but are chiral with respect to both their helical handedness and their replication history. Emerging evidence from various model organisms suggests that certain stem cells segregate sister chromatids nonrandomly to either maintain genome integrity or to bias cellular differentiation in asymmetric cell divisions. Conventional methods for tracing of old vs. newly synthesized DNA strands generally lack resolution for individual chromosomes and employ halogenated thymidine analogs with profound cytotoxic effects on rapidly dividing cells. Here, we present a modified chromosome orientation fluorescence in situ hybridization (CO-FISH) assay, where identification of individual chromosomes and their replication history is achieved in subsequent hybridization steps with chromosome-specific DNA probes and PNA telomere probes. Importantly, we tackle the issue of BrdU cytotoxicity and show that our method is compatible with normal mouse ES cell biology, unlike a recently published related protocol. Results from our CO-FISH assay show that mitotic segregation of mouse chromosome 7 is random in ES cells, which contrasts previously published results from our laboratory and settles a controversy. Our straightforward protocol represents a useful resource for future studies on chromatid segregation patterns of in vitro-cultured cells from distinct model organisms.

The Role of a Novel TRMT1 Gene Mutation and Rare GRM1 Gene Defect in Intellectual Disability in Two Azeri Families.

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Behzad Davarniya

Full Text Available Cognitive impairment or intellectual disability (ID is a widespread neurodevelopmental disorder characterized by low IQ (below 70. ID is genetically heterogeneous and is estimated to affect 1-3% of the world's population. In affected children from consanguineous families, autosomal recessive inheritance is common, and identifying the underlying genetic cause is an important issue in clinical genetics. In the framework of a larger project, aimed at identifying candidate genes for autosomal recessive intellectual disorder (ARID, we recently carried out single nucleotide polymorphism-based genome-wide linkage analysis in several families from Ardabil province in Iran. The identification of homozygosity-by-descent loci in these families, in combination with whole exome sequencing, led us to identify possible causative homozygous changes in two families. In the first family, a missense variant was found in GRM1 gene, while in the second family, a frameshift alteration was identified in TRMT1, both of which were found to co-segregate with the disease. GRM1, a known causal gene for autosomal recessive spinocerebellar ataxia (SCAR13, MIM#614831, encodes the metabotropic glutamate receptor1 (mGluR1. This gene plays an important role in synaptic plasticity and cerebellar development. Conversely, the TRMT1 gene encodes a tRNA methyltransferase that dimethylates a single guanine residue at position 26 of most tRNAs using S-adenosyl methionine as the methyl group donor. We recently presented TRMT1 as a candidate gene for ARID in a consanguineous Iranian family (Najmabadi et al., 2011. We believe that this second Iranian family with a biallelic loss-of-function mutation in TRMT1 gene supports the idea that this gene likely has function in development of the disorder.

The Role of a Novel TRMT1 Gene Mutation and Rare GRM1 Gene Defect in Intellectual Disability in Two Azeri Families

Science.gov (United States)

Kahrizi, Kimia; Musante, Luciana; Fattahi, Zohreh; Hosseini, Masoumeh; Maqsoud, Fariba; Farajollahi, Reza; Wienker, Thomas F.; Ropers, H. Hilger; Najmabadi, Hossein

2015-01-01

Cognitive impairment or intellectual disability (ID) is a widespread neurodevelopmental disorder characterized by low IQ (below 70). ID is genetically heterogeneous and is estimated to affect 1–3% of the world’s population. In affected children from consanguineous families, autosomal recessive inheritance is common, and identifying the underlying genetic cause is an important issue in clinical genetics. In the framework of a larger project, aimed at identifying candidate genes for autosomal recessive intellectual disorder (ARID), we recently carried out single nucleotide polymorphism-based genome-wide linkage analysis in several families from Ardabil province in Iran. The identification of homozygosity-by-descent loci in these families, in combination with whole exome sequencing, led us to identify possible causative homozygous changes in two families. In the first family, a missense variant was found in GRM1 gene, while in the second family, a frameshift alteration was identified in TRMT1, both of which were found to co-segregate with the disease. GRM1, a known causal gene for autosomal recessive spinocerebellar ataxia (SCAR13, MIM#614831), encodes the metabotropic glutamate receptor1 (mGluR1). This gene plays an important role in synaptic plasticity and cerebellar development. Conversely, the TRMT1 gene encodes a tRNA methyltransferase that dimethylates a single guanine residue at position 26 of most tRNAs using S-adenosyl methionine as the methyl group donor. We recently presented TRMT1 as a candidate gene for ARID in a consanguineous Iranian family (Najmabadi et al., 2011). We believe that this second Iranian family with a biallelic loss-of-function mutation in TRMT1 gene supports the idea that this gene likely has function in development of the disorder. PMID:26308914

Cardiac remodeling during and after renin-angiotensin system stimulation in Cyp1a1-Ren2 transgenic rats

DEFF Research Database (Denmark)

Heijnen, Bart Fj; Pelkmans, Leonie Pj; Danser, Ah Jan

2013-01-01

This study investigated renin-angiotensin system (RAS)-induced cardiac remodeling and its reversibility in the presence and absence of high blood pressure (BP) in Cyp1a1-Ren2 transgenic inducible hypertensive rats (IHR). In IHR (pro)renin levels and BP can be dose-dependently titrated by oral...... administration of indole-3-carbinol (I3C). Young (four-weeks old) and adult (30-weeks old) IHR were fed I3C for four weeks (leading to systolic BP >200 mmHg). RAS-stimulation was stopped and animals were followed-up for a consecutive period. Cardiac function and geometry was determined echocardiographically...

Chromosome segregation in plant meiosis

Directory of Open Access Journals (Sweden)

Linda eZamariola

2014-06-01

Full Text Available Faithful chromosome segregation in meiosis is essential for ploidy stability over sexual life cycles. In plants, defective chromosome segregation caused by gene mutations or other factors leads to the formation of unbalanced or unreduced gametes creating aneuploid or polyploid progeny, respectively. Accurate segregation requires the coordinated execution of conserved processes occurring throughout the two meiotic cell divisions. Synapsis and recombination ensure the establishment of chiasmata that hold homologous chromosomes together allowing their correct segregation in the first meiotic division, which is also tightly regulated by cell-cycle dependent release of cohesin and monopolar attachment of sister kinetochores to microtubules. In meiosis II, bi-orientation of sister kinetochores and proper spindle orientation correctly segregate chromosomes in four haploid cells. Checkpoint mechanisms acting at kinetochores control the accuracy of kinetochore-microtubule attachment, thus ensuring the completion of segregation. Here we review the current knowledge on the processes taking place during chromosome segregation in plant meiosis, focusing on the characterization of the molecular factors involved.

Dialyzer reuse following manual reprocessing with a new sterilant, RenNew-D.

Science.gov (United States)

Gagnon, R; Adkar, V; Kaye, M

1987-04-01

Dialysis patients are at risk for toxicity from formaldehyde used in the reprocessing of dialyzers for reuse; therefore, replacing formaldehyde as a dialyzer sterilant would be advantageous. The potential for RenNew-D as a sterilizing agent was investigated in seven stable in-center hemodialysis patients over 20 consecutive dialyses with cuprammonium cellulose hollow-fiber dialyzers. Treatment with RenNew-D showed no toxicity to patients or dialyzers except for two blood leaks occurring in one patient. The mean number of dialyzer uses was 4.9. In all the dialyzers that passed functional testing small solute clearances were maintained with reuse. The ability of RenNew-D to improve the biocompatibility of reused dialyzers was documented with mean neutrophil counts falling to only 78% of initial values during first reuse of dialyzers processed with RenNew-D compared with a decrease in neutrophil count to 2% of initial values during first use of the same dialyzers. Our results suggest that RenNew-D may be a useful alternative to formaldehyde for the purpose of dialyzer reuse. A reuse procedure that includes processing with RenNew-D is associated with improved biocompatibility, possibly because of maintenance of the blood-derived membrane coating established during prior dialysis.

Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms.

Science.gov (United States)

Tannenbaum, Emmanuel; Sherley, James L; Shakhnovich, Eugene I

2005-04-01

This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes of chromosome segregation: (1) random segregation, where the daughter chromosomes of a given parent chromosome segregate randomly into the stem cell and its differentiating sister cell and (2) "immortal DNA strand" co-segregation, for which the stem cell retains the daughter chromosomes with the oldest parent strands. Immortal strand co-segregation is a mechanism, originally proposed by [Cairns Nature (London) 255, 197 (1975)], by which stem cells preserve the integrity of their genomes. For random segregation, we develop an ordered strand pair formulation of the dynamics, analogous to the ordered strand pair formalism developed for quasispecies dynamics involving semiconservative replication with imperfect lesion repair (in this context, lesion repair is taken to mean repair of postreplication base-pair mismatches). Interestingly, a similar formulation is possible with immortal strand co-segregation, despite the fact that this segregation mechanism is age dependent. From our model we are able to mathematically show that, when lesion repair is imperfect, then immortal strand co-segregation leads to better preservation of the stem cell lineage than random chromosome segregation. Furthermore, our model allows us to estimate the optimal lesion repair efficiency for preserving an adult stem cell population for a given period of time. For human stem cells, we obtain that mispaired bases still present after replication and cell division should be left untouched, to avoid potentially fixing a mutation in both DNA strands.

Glassy behavior in the layered perovskites La2−xSrxCoO4(1.1≤x≤1.3)

International Nuclear Information System (INIS)

Mukherjee, S.; Mukherjee, Rajarshi; Banerjee, S.; Ranganathan, R.; Kumar, Uday

2012-01-01

The glassy behavior of the phase segregated state in the layered cobaltite La 2−x Sr x CoO 4 has been studied. The role of the inter-cluster interactions as well as the disordered spins at the paramagnetic–ferromagnetic interface, behind the observed glassy behavior have been investigated. The disordered spins at the interface appear to be strongly pinned, and they contribute little to the observed glassy behavior. On the other hand, the inter-cluster interactions play the key role. Both the Co 4+ and Co 3+ ions are in the intermediate spin state. - Highlights: ► Phase segregated state of cobaltite La 2−x Sr x CoO 4 for (1.1≤x≤1.3) to find the origin of the observed glassy behavior. ► Result of the frequency dependent ac susceptibility measurement excludes the possibility of any spin glass phase, hints strong inter-cluster interactions. ► Relaxation experiments confirm the system to be a collection of clusters with two preferred sizes. ► The glassy behavior originates from strong inter-cluster interactions.

Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast.

Directory of Open Access Journals (Sweden)

Gianni Liti

2009-09-01

Full Text Available In yeast, as in humans, telomere length varies among individuals and is controlled by multiple loci. In a quest to define the extent of variation in telomere length, we screened 112 wild-type Saccharomyces sensu stricto isolates. We found extensive telomere length variation in S. paradoxus isolates. This phenotype correlated with their geographic origin: European strains were observed to have extremely short telomeres (400 bp. Insertions of a URA3 gene near telomeres allowed accurate analysis of individual telomere lengths and telomere position effect (TPE. Crossing the American and European strains resulted in F1 spores with a continuum of telomere lengths consistent with what would be predicted if many quantitative trait loci (QTLs were involved in length maintenance. Variation in TPE is similarly quantitative but only weakly correlated with telomere length. Genotyping F1 segregants indicated several QTLs associated with telomere length and silencing variation. These QTLs include likely candidate genes but also map to regions where there are no known genes involved in telomeric properties. We detected transgressive segregation for both phenotypes. We validated by reciprocal hemizygosity that YKU80 and TLC1 are telomere-length QTLs in the two S. paradoxus subpopulations. Furthermore, we propose that sequence divergence within the Ku heterodimer generates negative epistasis within one of the allelic combinations (American-YKU70 and European-YKU80 resulting in very short telomeres.

Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast.

Science.gov (United States)

Liti, Gianni; Haricharan, Svasti; Cubillos, Francisco A; Tierney, Anna L; Sharp, Sarah; Bertuch, Alison A; Parts, Leopold; Bailes, Elizabeth; Louis, Edward J

2009-09-01

In yeast, as in humans, telomere length varies among individuals and is controlled by multiple loci. In a quest to define the extent of variation in telomere length, we screened 112 wild-type Saccharomyces sensu stricto isolates. We found extensive telomere length variation in S. paradoxus isolates. This phenotype correlated with their geographic origin: European strains were observed to have extremely short telomeres (400 bp). Insertions of a URA3 gene near telomeres allowed accurate analysis of individual telomere lengths and telomere position effect (TPE). Crossing the American and European strains resulted in F1 spores with a continuum of telomere lengths consistent with what would be predicted if many quantitative trait loci (QTLs) were involved in length maintenance. Variation in TPE is similarly quantitative but only weakly correlated with telomere length. Genotyping F1 segregants indicated several QTLs associated with telomere length and silencing variation. These QTLs include likely candidate genes but also map to regions where there are no known genes involved in telomeric properties. We detected transgressive segregation for both phenotypes. We validated by reciprocal hemizygosity that YKU80 and TLC1 are telomere-length QTLs in the two S. paradoxus subpopulations. Furthermore, we propose that sequence divergence within the Ku heterodimer generates negative epistasis within one of the allelic combinations (American-YKU70 and European-YKU80) resulting in very short telomeres.

Making the semiconductor-metal transition in a growth-dominant phase-change alloy InSb for double density blu-ray super-RENS-ROM disc

Energy Technology Data Exchange (ETDEWEB)

Hyot, Berangere [CEA, LETI, MINATEC, F- 38054 Grenoble (France)

2012-10-15

Phenomenologically, a semiconductor-metal transition is characterized by a sudden change in electrical properties but also in optical behaviours, as a consequence of a change in electron behaviour. The ability to induce a reversible semiconductor-metal transition in a material by varying conditions such as applied temperature or electrical field, results in attractive changes in properties that have fuelled the curiosity of scientists. In this paper, we discuss the interest of such materials exhibiting the reversible semiconductor-metal transition in the development of the next generation of optical Bly-ray discs (BD), the so-called super-resolution near field structure (super-RENS) discs and we show that InSb semiconductor material exhibits huge variations of its optical properties during the optically (thermally)-induced solid-to-liquid change corresponding to a semiconductor-metal transition. First success in the video playback on HDTV (High Definition TeleVision) display from 50 GB (BD capacity x 2) InSb-based super-RENS-ROM discs including a high definition video content with 1920 x 1080 pixels was realized in September 2009 by the super-RENS consortium joining three partners: AIST (National Institute of Advanced Industrial Science and Technology), Mitsubishi Electric Co. and LETI. Snapshot of high definition video content from InSb-based super-RENS-ROM disc corresponding to 50 GB per layer (BD capacity x 2) displayed on HDTV. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Hormad1 mutation disrupts synaptonemal complex formation, recombination, and chromosome segregation in mammalian meiosis.

Directory of Open Access Journals (Sweden)

Yong-Hyun Shin

2010-11-01

Full Text Available Meiosis is unique to germ cells and essential for reproduction. During the first meiotic division, homologous chromosomes pair, recombine, and form chiasmata. The homologues connect via axial elements and numerous transverse filaments to form the synaptonemal complex. The synaptonemal complex is a critical component for chromosome pairing, segregation, and recombination. We previously identified a novel germ cell-specific HORMA domain encoding gene, Hormad1, a member of the synaptonemal complex and a mammalian counterpart to the yeast meiotic HORMA domain protein Hop1. Hormad1 is essential for mammalian gametogenesis as knockout male and female mice are infertile. Hormad1 deficient (Hormad1(-/ (- testes exhibit meiotic arrest in the early pachytene stage, and synaptonemal complexes cannot be visualized by electron microscopy. Hormad1 deficiency does not affect localization of other synaptonemal complex proteins, SYCP2 and SYCP3, but disrupts homologous chromosome pairing. Double stranded break formation and early recombination events are disrupted in Hormad1(-/ (- testes and ovaries as shown by the drastic decrease in the γH2AX, DMC1, RAD51, and RPA foci. HORMAD1 co-localizes with γH2AX to the sex body during pachytene. BRCA1, ATR, and γH2AX co-localize to the sex body and participate in meiotic sex chromosome inactivation and transcriptional silencing. Hormad1 deficiency abolishes γH2AX, ATR, and BRCA1 localization to the sex chromosomes and causes transcriptional de-repression on the X chromosome. Unlike testes, Hormad1(-/ (- ovaries have seemingly normal ovarian folliculogenesis after puberty. However, embryos generated from Hormad1(-/ (- oocytes are hyper- and hypodiploid at the 2 cell and 8 cell stage, and they arrest at the blastocyst stage. HORMAD1 is therefore a critical component of the synaptonemal complex that affects synapsis, recombination, and meiotic sex chromosome inactivation and transcriptional silencing.

Analysis of transgenic wheat (Triticum aestivum L.) harboring a maize (Zea mays L.) gene for plastid EF-Tu: segregation pattern, expression and effects of the transgene.

Science.gov (United States)

Fu, Jianming; Ristic, Zoran

2010-06-01

We previously reported that transgenic wheat (Triticum aestivum L.) carrying a maize (Zea mays L.) gene (Zmeftu1) for chloroplast protein synthesis elongation factor, EF-Tu, displays reduced thermal aggregation of leaf proteins, reduced injury to photosynthetic membranes (thylakoids), and enhanced rate of CO(2) fixation following exposure to heat stress (18 h at 45 degrees C) [Fu et al. in Plant Mol Biol 68:277-288, 2008]. In the current study, we investigated the segregation pattern and expression of the transgene Zmeftu1 and determined the grain yield of transgenic plants after exposure to a brief heat stress (18 h at 45 degrees C). We also assessed thermal aggregation of soluble leaf proteins in transgenic plants, testing the hypothesis that increased levels of EF-Tu will lead to a non-specific protection of leaf proteins against thermal aggregation. The transgenic wheat displayed a single-gene pattern of segregation of Zmeftu1. Zmeftu1 was expressed, and the transgenic plants synthesized and accumulated three anti-EF-Tu cross-reacting polypeptides of similar molecular mass but different pI, suggesting the possibility of posttranslational modification of this protein. The transgenic plants also showed better grain yield after exposure to heat stress compared with their non-transgenic counterparts. Soluble leaf proteins of various molecular masses displayed lower thermal aggregation in transgenic than in non-transgenic wheat. The results suggest that overexpression of chloroplast EF-Tu can be beneficial to wheat tolerance to heat stress. Moreover, the results also support the hypothesis that EF-Tu contributes to heat tolerance by acting as a molecular chaperone and protecting heat-labile proteins from thermal aggregation in a non-specific manner.

Søren Kjørup

DEFF Research Database (Denmark)

2009-01-01

Film om filosofi- og æstetikprofessoren Søren Kjørup om kunst og kommunikation, billeder og museer, semiotik og videnskabsteori, med optagelser fra hans mange virkefelter på Roskilde Universitet, i København, Norge og Paris. Fysisk medie: DVD-film med booklet ISAN: 978-87-992867-0-6...

Lack of co-ordinate expression of the alpha1(I) and alpha1(III) procollagen genes in fibroblast clonal cultures.

Science.gov (United States)

Yamaguchi, Y; Crane, S; Zhou, L; Ochoa, S M; Falanga, V

2000-12-01

Several extracellular matrix genes, most notably alpha1(I) and alpha1(III) procollagen, are reported to be co-ordinately expressed in cultures of dermal fibroblasts. However, it remains unclear whether the expression of these genes is truly co-ordinate or whether it may be the result of averaging the phenotypic expression of different fibroblast subpopulations present within each culture. Objectives To determine by Northern analysis the correlation between alpha1(I) and alpha1(III) procollagen mRNA levels in clonal populations of human dermal fibroblasts. As previously described, clonal cultures were derived from parent strains of human dermal fibroblasts by a microscopically controlled dilution technique and by stimulation of single cells with low oxygen tension in the early phases of clonal growth. In agreement with previous reports, we found that baseline steady-state levels of alpha1(I) procollagen mRNA were co-ordinately regulated with the alpha1(III) procollagen mRNA in 26 parent strains (r = 0. 9003; P ordinate regulation observed in non-clonal cultures, suggesting that these two genes operate under different sets of regulatory controls. This clonal heterogeneity may provide additional flexibility to the process of tissue repair and fibroblast clonal expansion.

A novel homozygous variant in the SMOC1 gene underlying Waardenburg anophthalmia syndrome.

Science.gov (United States)

Ullah, Asmat; Umair, Muhammad; Ahmad, Farooq; Muhammad, Dost; Basit, Sulman; Ahmad, Wasim

2017-01-01

Waardenburg anophthalmia syndrome (WAS), also known as ophthalmo-acromelic syndrome or anophthalmia-syndactyly, is a rare congenital disorder that segregates in an autosomal recessive pattern. Clinical features of the syndrome include malformation of the eyes and the skeleton. Mostly, WAS is caused by mutations in the SMOC-1 gene. The present report describes a large consanguineous family of Pakistani origin segregating Waardenburg anophthalmia syndrome in an autosomal recessive pattern. Genotyping followed by Sanger sequencing was performed to search for a candidate gene. SNP genotyping using AffymetrixGeneChip Human Mapping 250K Nsp array established a single homozygous region among affected members on chromosome 14q23.1-q24.3 harboring the SMOC1 gene. Sequencing of the gene revealed a novel homozygous missense mutation (c.812G>A; p.Cys271Tyr) in the family. This is the first report of Waardenburg anophthalmia syndrome caused by a SMOC1 variant in a Pakistani population. The mutation identified in the present investigation extends the body of evidence implicating the gene SMOC-1 in causing WAS.

Collective motion of cells mediates segregation and pattern formation in co-cultures.

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Elod Méhes

Full Text Available Pattern formation by segregation of cell types is an important process during embryonic development. We show that an experimentally yet unexplored mechanism based on collective motility of segregating cells enhances the effects of known pattern formation mechanisms such as differential adhesion, mechanochemical interactions or cell migration directed by morphogens. To study in vitro cell segregation we use time-lapse videomicroscopy and quantitative analysis of the main features of the motion of individual cells or groups. Our observations have been extensive, typically involving the investigation of the development of patterns containing up to 200,000 cells. By either comparing keratocyte types with different collective motility characteristics or increasing cells' directional persistence by the inhibition of Rac1 GTP-ase we demonstrate that enhanced collective cell motility results in faster cell segregation leading to the formation of more extensive patterns. The growth of the characteristic scale of patterns generally follows an algebraic scaling law with exponent values up to 0.74 in the presence of collective motion, compared to significantly smaller exponents in case of diffusive motion.

Novel heterozygous nonsense mutation of the OPTN gene segregating in a Danish family with ALS

DEFF Research Database (Denmark)

Tümer, Zeynep; Bertelsen, Birgitte; Gredal, Ole

2012-01-01

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder. About 10% of ALS cases are familial (FALS) and the genetic defect is known only in approximately 20%-30% of these cases. The most common genetic cause of ALS is SOD1 (superoxide dismutase 1) mutation. Very recently......, mutations of the optineurin gene (OPTN), which is involved in open-angle glaucoma, were identified in 3 Japanese patients/families with ALS, and subsequently in a few FALS patients of European descent. We found a heterozygous nonsense mutation (c.493C>T, p.Gln165X, exon 6) in the OPTN gene in a Danish...... patient with ALS, and the mutation segregated from his affected father. The p.Gln165X mutation could not be detected in 1070 healthy Danish controls, in 1000 Danish individuals with metabolic phenotypes or in 64 sporadic ALS (SALS) cases. The p.Gln165X mutation described in this study is the first...

Genetic Segregation Analysis of a Rapeseed Dwarf Mutant

International Nuclear Information System (INIS)

Xiang, G.; Yu, S.; Zhang, T.; Zhao, J.; Lei, S.; Du, C.

2016-01-01

Dwarf resources in Brassica napus are very important for developing high-yield cultivars through dwarf-type and lodging-resistant breeding. However, few dwarf varieties have been available for this species. Here, we reported a new rapeseed dwarf mutant GRC1157, which exhibits obvious phenotypic variations on dwarf. Six generations (P /sub 1/, P/sub 1/, F/sub 1/, F/sub 1/, B/sub 1/, and B/sub 1/) were produced from a cross between dwarf mutant GRC1157 and an elite tall-type line XR16 to analyze genetic inheritances of plant height (PH), numbers of the 1st valid branch (VBN), main inflorescence length (MIL), pod numbers per main inflorescence (MPN), pod length (PL) and seed numbers per pod (PSN) using the mixed major gene plus polygene inheritance model. The genetic analysis shows different traits were controlled by different inheritance models: PH and PL by two pairs of additive-dominant-epistatic major genes plus additive-dominant-epistatic polygenes, MPN and PSN by two-pair additive-dominant-epistatic major genes plus additive-dominant polygenes, MIL by two-pair additive-dominant-epistatic major genes and VBN by one-pair additive-dominant major genes plus additive-dominant-epistatic polygenes. Furthermore, positive correlations between PH and some other traits were observed, suggesting that some traits may be co-regulated by several linkage or same loci/genes. In addition, high heritability (40.35-93.7 percent) were found for five traits (except VBN) in different segregating generations, indicating these traits were mainly affected by hereditary factors and suitable for early artificial selection. In sum, the dwarf mutant GRC1157 can serve as a valuable resource for rapeseed dwarf breeding and the genetic analysis in this study provided a foundation for further mapping and cloning dwarf genes in mutant GRC1157. (author)

Evolutionary dynamics of adult stem cells: Comparison of random and immortal strand segregation mechanisms

OpenAIRE

Tannenbaum, Emmanuel; Sherley, James L.; Shakhnovich, Eugene I.

2004-01-01

This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes of chromosome segregation: (1) Random segregation, where the daughter chromosomes of a given parent chromosome segregate randomly into the stem cell and its differentiating sister cell. (2) ``Immortal DNA strand'' co-segregation, for which the stem cell reta...

Søren Kierkegaard

DEFF Research Database (Denmark)

Klausen, Søren Harnow

This book is a succinct guide to Søren Kierkegaard’s contribution to educational thought. Kierkegaard is not usually known as an educational thinker, but the book shows how his key notions and ideas are nevertheless highly relevant to educational theory and practice. It places them within...... the context of Kierkegaard’s philosophy and the philosophy of his time, while also exploring their significance to issues of contemporary concern, like the question of how far education should aim at fostering useful skills or support more ambitious goals. The central topics are Kierkegaard’s diagnosis...

Synthesis of ReN3 Thin Films by Magnetron Sputtering

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G. Soto

2014-01-01

Full Text Available In this work ReNx films were prepared by reactive magnetron sputtering at room temperature and deposited on a silicon wafer. It was found that the diffractograms of the nitrogen-rich rhenium film are consistent with those produced by high-pressure high-temperature methods, under the assumption that the film is oriented on the substrate. Using density functional calculations it was found that the composition of this compound could be ReN3, instead of ReN2, as stated on previous works. The ReN3 compound fits in the Ama2 (40 orthorhombic space group, and due to the existence of N3 anions between Re layers it should be categorized as an azide. The material is exceptionally brittle and inherently unstable under indentation testing.

Identification of two new mutations in the GPR98 and the PDE6B genes segregating in a Tunisian family.

Science.gov (United States)

Hmani-Aifa, Mounira; Benzina, Zeineb; Zulfiqar, Fareeha; Dhouib, Houria; Shahzadi, Amber; Ghorbel, Abdelmonem; Rebaï, Ahmed; Söderkvist, Peter; Riazuddin, Sheikh; Kimberling, William J; Ayadi, Hammadi

2009-04-01

Autosomal recessive retinitis pigmentosa (ARRP) is a genetically heterogeneous disorder. ARRP could be associated with extraocular manifestations that define specific syndromes such as Usher syndrome (USH) characterized by retinal degeneration and congenital hearing loss (HL). The USH type II (USH2) associates RP and mild-to-moderate HL with preserved vestibular function. At least three genes USH2A, the very large G-protein-coupled receptor, GPR98, and DFNB31 are responsible for USH2 syndrome. Here, we report on the segregation of non-syndromic ARRP and USH2 syndrome in a consanguineous Tunisian family, which was previously used to define USH2B locus. With regard to the co-occurrence of these two different pathologies, clinical and genetic reanalysis of the extended family showed (i) phenotypic heterogeneity within USH2 patients and (ii) excluded linkage to USH2B locus. Indeed, linkage analysis disclosed the cosegregation of the USH2 phenotype with the USH2C locus markers, D5S428 and D5S618, whereas the ARRP perfectly segregates with PDE6B flanking markers D4S3360 and D4S2930. Molecular analysis revealed two new missense mutations, p.Y6044C and p.W807R, occurring in GPR98 and PDE6B genes, respectively. In conclusion, our results show that the USH2B locus at chromosome 3p23-24.2 does not exist, and we therefore withdraw this locus designation. The combination of molecular findings for GPR98 and PDE6B genes enable us to explain the phenotypic heterogeneity and particularly the severe ocular affection first observed in one USH2 patient. This report presents an illustration of how consanguinity could increase familial clustering of multiple hereditary diseases within the same family.

Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae.

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Jared W Wenger

2010-05-01

Full Text Available Fermentation of xylose is a fundamental requirement for the efficient production of ethanol from lignocellulosic biomass sources. Although they aggressively ferment hexoses, it has long been thought that native Saccharomyces cerevisiae strains cannot grow fermentatively or non-fermentatively on xylose. Population surveys have uncovered a few naturally occurring strains that are weakly xylose-positive, and some S. cerevisiae have been genetically engineered to ferment xylose, but no strain, either natural or engineered, has yet been reported to ferment xylose as efficiently as glucose. Here, we used a medium-throughput screen to identify Saccharomyces strains that can increase in optical density when xylose is presented as the sole carbon source. We identified 38 strains that have this xylose utilization phenotype, including strains of S. cerevisiae, other sensu stricto members, and hybrids between them. All the S. cerevisiae xylose-utilizing strains we identified are wine yeasts, and for those that could produce meiotic progeny, the xylose phenotype segregates as a single gene trait. We mapped this gene by Bulk Segregant Analysis (BSA using tiling microarrays and high-throughput sequencing. The gene is a putative xylitol dehydrogenase, which we name XDH1, and is located in the subtelomeric region of the right end of chromosome XV in a region not present in the S288c reference genome. We further characterized the xylose phenotype by performing gene expression microarrays and by genetically dissecting the endogenous Saccharomyces xylose pathway. We have demonstrated that natural S. cerevisiae yeasts are capable of utilizing xylose as the sole carbon source, characterized the genetic basis for this trait as well as the endogenous xylose utilization pathway, and demonstrated the feasibility of BSA using high-throughput sequencing.

Fine mapping and identification of a candidate gene for the barley Un8 true loose smut resistance gene.

Science.gov (United States)

Zang, Wen; Eckstein, Peter E; Colin, Mark; Voth, Doug; Himmelbach, Axel; Beier, Sebastian; Stein, Nils; Scoles, Graham J; Beattie, Aaron D

2015-07-01

The candidate gene for the barley Un8 true loose smut resistance gene encodes a deduced protein containing two tandem protein kinase domains. In North America, durable resistance against all known isolates of barley true loose smut, caused by the basidiomycete pathogen Ustilago nuda (Jens.) Rostr. (U. nuda), is under the control of the Un8 resistance gene. Previous genetic studies mapped Un8 to the long arm of chromosome 5 (1HL). Here, a population of 4625 lines segregating for Un8 was used to delimit the Un8 gene to a 0.108 cM interval on chromosome arm 1HL, and assign it to fingerprinted contig 546 of the barley physical map. The minimal tilling path was identified for the Un8 locus using two flanking markers and consisted of two overlapping bacterial artificial chromosomes. One gene located close to a marker co-segregating with Un8 showed high sequence identity to a disease resistance gene containing two kinase domains. Sequence of the candidate gene from the parents of the segregating population, and in an additional 19 barley lines representing a broader spectrum of diversity, showed there was no intron in alleles present in either resistant or susceptible lines, and fifteen amino acid variations unique to the deduced protein sequence in resistant lines differentiated it from the deduced protein sequences in susceptible lines. Some of these variations were present within putative functional domains which may cause a loss of function in the deduced protein sequences within susceptible lines.

A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes.

Science.gov (United States)

Sahoo, Dipak K; Abeysekara, Nilwala S; Cianzio, Silvia R; Robertson, Alison E; Bhattacharyya, Madan K

2017-01-01

Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs) (F7 families) were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR)-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance.

A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes.

Directory of Open Access Journals (Sweden)

Dipak K Sahoo

Full Text Available Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs (F7 families were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance.

Interaction between ALDH2*1*1 and DRD2/ANKK1 TaqI A1A1 genes may be associated with antisocial personality disorder not co-morbid with alcoholism.

Science.gov (United States)

Lu, Ru-Band; Lee, Jia-Fu; Huang, San-Yuan; Lee, Sheng-Yu; Chang, Yun-Hsuan; Kuo, Po-Hsiu; Chen, Shiou-Lan; Chen, Shih-Heng; Chu, Chun-Hsien; Lin, Wei-Wen; Wu, Pei-Lin; Ko, Huei-Chen

2012-09-01

Previous studies on acetaldehyde dehydrogenase 2 (ALDH2) focused on drinking behavior or alcoholism because the ALDH2*2 allele protects against the risk of developing alcoholism. The mechanism provides that the ALDH2 gene's protective effect is also involved in dopamine metabolism. The interaction of the ALDH2 gene with neurotransmitters, such as dopamine, is suggested to be related to alcoholism. Because alcoholism is often co-morbid with antisocial personality disorder (ASPD), previous association studies on antisocial alcoholism cannot differentiate whether those genes relate to ASPD with alcoholism or ASPD only. This study examined the influence of the interaction effect of the ALDH2*1*1, *1*2 or *2*2 polymorphisms with the dopamine 2 receptor (DRD2) Taq I polymorphism on ASPD. Our 541 Han Chinese male participants were classified into three groups: antisocial alcoholism (ASPD co-morbid with alcohol dependence, antisocial ALC; n = 133), ASPD without alcoholism (ASPD not co-morbid with alcohol dependence, antisocial non-ALC; n = 164) and community controls (healthy volunteers from the community; n = 244). Compared with healthy controls, individuals with the DRD2 A1/A1 and the ALDH2*1/*1 genotypes were at a 5.39 times greater risk for antisocial non-ALC than were those with other genotypes. Our results suggest that the DRD2/ANKK1 and ALDH2 genes interacted in the antisocial non-ALC group; a connection neglected in previous studies caused by not separating antisocial ALC from ASPD. Our study made this distinction and showed that these two genes may be associated ASPD without co-morbid alcoholism. © 2010 The Authors, Addiction Biology © 2010 Society for the Study of Addiction.

Large clusters of co-expressed genes in the Drosophila genome.

Science.gov (United States)

Boutanaev, Alexander M; Kalmykova, Alla I; Shevelyov, Yuri Y; Nurminsky, Dmitry I

2002-12-12

Clustering of co-expressed, non-homologous genes on chromosomes implies their co-regulation. In lower eukaryotes, co-expressed genes are often found in pairs. Clustering of genes that share aspects of transcriptional regulation has also been reported in higher eukaryotes. To advance our understanding of the mode of coordinated gene regulation in multicellular organisms, we performed a genome-wide analysis of the chromosomal distribution of co-expressed genes in Drosophila. We identified a total of 1,661 testes-specific genes, one-third of which are clustered on chromosomes. The number of clusters of three or more genes is much higher than expected by chance. We observed a similar trend for genes upregulated in the embryo and in the adult head, although the expression pattern of individual genes cannot be predicted on the basis of chromosomal position alone. Our data suggest that the prevalent mechanism of transcriptional co-regulation in higher eukaryotes operates with extensive chromatin domains that comprise multiple genes.

Dose dependence of radiation-induced segregation in Ni-1 at% Si

International Nuclear Information System (INIS)

Rehn, L.E.; Okamoto, P.R.; Wiedersich, H.

1979-01-01

Measurements have been made of alloy composition as a function of depth from the external surface in Ni-1 at% Si specimens after irradiation with 3-MeV 58 Ni + ions to several different doses at nominal temperatures of 525 and 600 0 C. Very rapid segregation of Si toward the external surface ocurred during irradiation. Surface concentrations of Si in excess of the 10 at% solubility limit were found at both irradiation temperatures after a dose of only approximately 0.05 dpa. The rate of segregation decreased markedly in the dose range from approximately 1-10 dpa. Qualitative agreement was found between the experimental observations and calculations made using a modified Johnson-Lam segregation mode (1976). The present investigation suggests that radiation-induced segregation may significantly alter the mechanical behavior of irradiated alloys long before the onset of void swelling. (Auth.)

(3-Aminopropyl)-4-methylpiperazine End-capped Poly(1,4-butanediol diacrylate-co-4-amino-1-butanol)-based Multilayer Films for Gene Delivery

Science.gov (United States)

Li, Cuicui; Tzeng, Stephany Y; Tellier, Liane E.; Green, Jordan J

2013-01-01

Biodegradable polyelectrolyte surfaces for gene delivery were created through electrospinning of biodegradable polycations combined with iterative solution-based multilayer coating. Poly(β-amino ester) (PBAE) poly(1,4-butanediol diacrylate-co-4-amino-1-butanol) end-capped with 1-(3-aminopropyl)-4-methylpiperazine was utilized due to its ability to electrostatically interact with anionic molecules like DNA, its biodegradability, and its low cytotoxicity. A new DNA release system was developed for sustained release of DNA over 24 hours, accompanied by high exogenous gene expression in primary human glioblastoma (GB) cells. Electrospinning a different PBAE, poly(1,4-butanediol diacrylate-co-4,4′-trimethylenedipiperidine), and its combination with polyelectrolyte 1-(3-aminopropyl)-4-methylpiperazine end-capped poly(1,4-butanediol diacrylate-co-4-amino-1-butanol)-based multilayers are promising for DNA release and intracellular delivery from a surface. PMID:23755861

(3-aminopropyl)-4-methylpiperazine end-capped poly(1,4-butanediol diacrylate-co-4-amino-1-butanol)-based multilayer films for gene delivery.

Science.gov (United States)

Li, Cuicui; Tzeng, Stephany Y; Tellier, Liane E; Green, Jordan J

2013-07-10

Biodegradable polyelectrolyte surfaces for gene delivery were created through electrospinning of biodegradable polycations combined with iterative solution-based multilayer coating. Poly(β-amino ester) (PBAE) poly(1,4-butanediol diacrylate-co-4-amino-1-butanol) end-capped with 1-(3-aminopropyl)-4-methylpiperazine was utilized because of its ability to electrostatically interact with anionic molecules like DNA, its biodegradability, and its low cytotoxicity. A new DNA release system was developed for sustained release of DNA over 24 h, accompanied by high exogenous gene expression in primary human glioblastoma (GB) cells. Electrospinning a different PBAE, poly(1,4-butanediol diacrylate-co-4,4'-trimethylenedipiperidine), and its combination with polyelectrolyte 1-(3-aminopropyl)-4-methylpiperazine end-capped poly(1,4-butanediol diacrylate-co-4-amino-1-butanol)-based multilayers are promising for DNA release and intracellular delivery from a surface.

Changes in Air CO2 Concentration Differentially Alter Transcript Levels of NtAQP1 and NtPIP2;1 Aquaporin Genes in Tobacco Leaves

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Francesca Secchi

2016-04-01

Full Text Available The aquaporin specific control on water versus carbon pathways in leaves is pivotal in controlling gas exchange and leaf hydraulics. We investigated whether Nicotiana tabacum aquaporin 1 (NtAQP1 and Nicotiana tabacum plasma membrane intrinsic protein 2;1 (NtPIP2;1 gene expression varies in tobacco leaves subjected to treatments with different CO2 concentrations (ranging from 0 to 800 ppm, inducing changes in photosynthesis, stomatal regulation and water evaporation from the leaf. Changes in air CO2 concentration ([CO2] affected net photosynthesis (Pn and leaf substomatal [CO2] (Ci. Pn was slightly negative at 0 ppm air CO2; it was one-third that of ambient controls at 200 ppm, and not different from controls at 800 ppm. Leaves fed with 800 ppm [CO2] showed one-third reduced stomatal conductance (gs and transpiration (E, and their gs was in turn slightly lower than in 200 ppm– and in 0 ppm–treated leaves. The 800 ppm air [CO2] strongly impaired both NtAQP1 and NtPIP2;1 gene expression, whereas 0 ppm air [CO2], a concentration below any in vivo possible conditions and specifically chosen to maximize the gene expression alteration, increased only the NtAQP1 transcript level. We propose that NtAQP1 expression, an aquaporin devoted to CO2 transport, positively responds to CO2 scarcity in the air in the whole range 0–800 ppm. On the contrary, expression of NtPIP2;1, an aquaporin not devoted to CO2 transport, is related to water balance in the leaf, and changes in parallel with gs. These observations fit in a model where upregulation of leaf aquaporins is activated at low Ci, while downregulation occurs when high Ci saturates photosynthesis and causes stomatal closure.

Meiotic gene conversion mutants in Saccharomyces cerevisiae. I. Isolation and characterization of PMS1-1 and PMS1-2

International Nuclear Information System (INIS)

Williamson, M.S.; Game, J.C.; Fogel, S.

1985-01-01

The PMS1 mutants, isolated on the basis of sharply elevated meiotic prototroph frequencies for two closely linked HIS4 alleles, display pleiotropic phenotypes in meiotic and mitotic cells. Two isolates carrying recessive mutations in PMS1 were characterized. They identify a function required to maintain low postmeiotic segregation (PMS) frequencies at many heterozygous sites. In addition, they are mitotic mutators. In mutant diploids, spore viability is reduced, and among survivors, gene conversion and postmeiotic segregation frequencies are increased, but reciprocal exchange frequencies are not affected. The conversion event pattern is also dramatically changed in multiply marked regions in PMS1 homozygotes. The PMS1 locus maps near MET4 on chromosome XIV. The PMS1 gene may identify an excision-resynthesis long patch mismatch correction function or a function that facilitates correction tract elongation. The PMS1 gene product may also play an important role in spontaneous mitotic mutation avoidance and correction of mismatches in heteroduplex DNA formed during spontaneous and UV-induced mitotic recombination. Based on meiotic recombination models emphasizing mismatch correction in heteroduplex DNA intermediates, this interpretation is favored, but alternative interpretations involving longer recombination intermediates in the mutants are also considered

Co-ordinate regulation of lactate metabolism genes in yeast: the role of the lactate permease gene JEN1.

Science.gov (United States)

Lodi, T; Fontanesi, F; Guiard, B

2002-01-01

In the yeast Saccharomyces cerevisiae, the first step in lactate metabolism is its transport across the plasma membrane, a proton symport process mediated by the product of the gene JEN1. Under aerobic conditions, the expression of JEN1 is regulated by the carbon source: the gene is repressed by glucose and induced by non-fermentable substrates. JEN1 expression is also controlled by oxygen availability, but is unaffected by the absence of haem biosynthesis. JEN1 is negatively regulated by the repressors Mig1p and Mig2p, and requires Cat8p for full derepression. In this report we demonstrate that, in addition to these regulators, the Hap2/3/4/5 complex interacts specifically with a CAAT-box element in the JEN1 promoter, and acts to derepress JEN1 expression. We also provide evidence for transcriptional stimulation of JEN1 by the protein kinase Snf1p. Data are presented which provide a better understanding of the molecular mechanisms implicated in the co-regulation of genes involved in the metabolism of lactate.

Nicholas Steno and Renè Descartes

DEFF Research Database (Denmark)

Olden-Jørgensen, Sebastian

2009-01-01

Den danske videnskabsmand Niels Steensen (1638-86) læste allerede som ung student Renè Descartes og blev grebet af hans metode, som han forblev tro i hele sit videnskabelige virke. Cartesianismen kan beskrives som Steensens videnskabelige paradigme (Kuhn), men det var også et paradigme, han testede...

A Reserva Ecológica Nacional (REN: sua importância para o ambiente e ordenamento do território

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Ana Ramos Pereira

2000-12-01

Full Text Available THE NATIONAL ECOLOGICAL RESERVE (REN: ENVIRONMENT AND MANAGEMENT IMPLICATIONS. The National Ecological Reserve (REN defined in Decree-Law 93/90 of March 5th is the «basic and diversified biophysical structure that guarantees environmental protection, through the creation of restricted areas» at rish through erosion (littoral or slope, flooding and aquifer recharge. The REN valuation, whose main aspects are referred to here, was carried out by means of an analysis of Municipal Master Plans (PDM and a survey sent to all local authorities. As it was impossible to analyse the PDM of every district, a dis- trict differentiation was completed based on the biophysical index (Fig. 1 and 2, subsequently crossed by the district human pressure to obtain the district spatial differentiation of the environmental strain (Fig. 3. This allowed a standard district to be selected where the REN was analysed in full detail (Fig. 4 to 9. The survey allowed for the evaluation of the main conflicts in other districts between the REN and the goals of the PDM to be assessed, including the issues concerning the delimitation and the way the REN is seen by the councils and the citizens. The REN includes physical and biophysical systems (slope, fluvial, aquifer and littoral that tend never to coincide with the administrative divisions. It is urgent that a national network be created of REN areas, planned and managed through more integrated means and an inter-municipal collaboration that can only be effective if environmental education is promoted, on both formal and informal terms.

Dr.Zhang Ren's Experience in Acupuncture Treatment of Obstinate Eye Diseases

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

@@ Dr.Zhang Ren (張仁), the board chairman of Shanghai Acupuncture Association, has been engaging in acupuncture treatment for more than 30years, during which he has kept on exploring the acupuncture therapies for obstinate diseases,especially for the obstinate eye diseases, ant summed up rich experience in this aspect. The following is a summary of what the author has learned from Dr. Zhang Ren.

The Consequences of Chromosome Segregation Errors in Mitosis and Meiosis

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Tamara Potapova

2017-02-01

Full Text Available Mistakes during cell division frequently generate changes in chromosome content, producing aneuploid or polyploid progeny cells. Polyploid cells may then undergo abnormal division to generate aneuploid cells. Chromosome segregation errors may also involve fragments of whole chromosomes. A major consequence of segregation defects is change in the relative dosage of products from genes located on the missegregated chromosomes. Abnormal expression of transcriptional regulators can also impact genes on the properly segregated chromosomes. The consequences of these perturbations in gene expression depend on the specific chromosomes affected and on the interplay of the aneuploid phenotype with the environment. Most often, these novel chromosome distributions are detrimental to the health and survival of the organism. However, in a changed environment, alterations in gene copy number may generate a more highly adapted phenotype. Chromosome segregation errors also have important implications in human health. They may promote drug resistance in pathogenic microorganisms. In cancer cells, they are a source for genetic and phenotypic variability that may select for populations with increased malignance and resistance to therapy. Lastly, chromosome segregation errors during gamete formation in meiosis are a primary cause of human birth defects and infertility. This review describes the consequences of mitotic and meiotic errors focusing on novel concepts and human health.

Sr-Al-Si co-segregated regions in eutectic Si phase of Sr-modified Al-10Si alloy.

Science.gov (United States)

Timpel, M; Wanderka, N; Schlesiger, R; Yamamoto, T; Isheim, D; Schmitz, G; Matsumura, S; Banhart, J

2013-09-01

The addition of 200 ppm strontium to an Al-10 wt% Si casting alloy changes the morphology of the eutectic silicon phase from coarse plate-like to fine fibrous networks. In order to clarify this modification mechanism the location of Sr within the eutectic Si phase has been investigated by a combination of high-resolution methods. Whereas three-dimensional atom probe tomography allows us to visualise the distribution of Sr on the atomic scale and to analyse its local enrichment, transmission electron microscopy yields information about the crystallographic nature of segregated regions. Segregations with two kinds of morphologies were found at the intersections of Si twin lamellae: Sr-Al-Si co-segregations of rod-like morphology and Al-rich regions of spherical morphology. Both are responsible for the formation of a high density of multiple twins and promote the anisotropic growth of the eutectic Si phase in specific crystallographic directions during solidification. The experimental findings are related to the previously postulated mechanism of "impurity induced twinning". Copyright © 2012 Elsevier B.V. All rights reserved.

Die politische Quacksalberei des libertären Paternalismus

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Schramme Thomas

2016-07-01

Full Text Available Der libertäre Paternalismus befürwortet Eingriffe in die Entscheidungsfindung von Bürgern, ohne ihnen Optionen völlig nehmen zu wollen. Vielmehr soll die Lenkung des Willens durch Schubser (nudges geschehen. Im folgenden Beitrag möchte ich zeigen, dass der libertäre Paternalismus auf tönernen Füßen steht. Ich bediene mich dabei des polemischen Bilds von Quacksalbern. Dieses Bild passt zu meinem argumentativen Vorgehen, da ich erstens zeigen will, dass der libertäre Paternalismus falsche Diagnosen über vermeintliche Krankheiten der Willensbildung stellt, und zweitens, dass er die falsche Therapie empfiehlt. Im ersten Teil des Artikels kritisiere ich die Diagnose des libertären Paternalismus, wonach Menschen in ihrer Entscheidungsfindung systematisch fehlschlagen. Die Auswirkungen der zugrundeliegenden psychologischen Forschung werden missinterpretiert und damit vielen menschlichen Entscheidungen eine Art Defekt zugeschrieben. Der zweite Teil des Beitrags hinterfragt die Therapie des libertären Paternalismus. Für entsprechende Interventionen in die Wahlarchitektonik muss Wissen erlangt werden über die Richtung, in welche die Menschen jeweils geschubst werden sollten. Die hier genannte epistemische Aufgabe kann mit den theoretischen Mitteln des libertären Paternalismus nicht gelöst werden.

Glassy behavior in the layered perovskites La{sub 2-x}Sr{sub x}CoO{sub 4}(1.1{<=}x{<=}1.3)

Energy Technology Data Exchange (ETDEWEB)

Mukherjee, S., E-mail: sanseb68@yahoo.co.in [Department of Physics, University of Burdwan, Burdwan 713104 (India); Mukherjee, Rajarshi [Department .of Physics, University of Burdwan, Burdwan 713104 (India); Banerjee, S.; Ranganathan, R. [Saha Institute of Nuclear Physics, Kolkata 700 064 (India); Kumar, Uday [Department of Physical Sciences, Indian Institute of Science Education and Research - Kolkata, Mohonpur 741252 (India)

2012-03-15

The glassy behavior of the phase segregated state in the layered cobaltite La{sub 2-x}Sr{sub x}CoO{sub 4} has been studied. The role of the inter-cluster interactions as well as the disordered spins at the paramagnetic-ferromagnetic interface, behind the observed glassy behavior have been investigated. The disordered spins at the interface appear to be strongly pinned, and they contribute little to the observed glassy behavior. On the other hand, the inter-cluster interactions play the key role. Both the Co{sup 4+} and Co{sup 3+} ions are in the intermediate spin state. - Highlights: Black-Right-Pointing-Pointer Phase segregated state of cobaltite La{sub 2-x}Sr{sub x}CoO{sub 4} for (1.1{<=}x{<=}1.3) to find the origin of the observed glassy behavior. Black-Right-Pointing-Pointer Result of the frequency dependent ac susceptibility measurement excludes the possibility of any spin glass phase, hints strong inter-cluster interactions. Black-Right-Pointing-Pointer Relaxation experiments confirm the system to be a collection of clusters with two preferred sizes. Black-Right-Pointing-Pointer The glassy behavior originates from strong inter-cluster interactions.

Status of clean gene (selection marker-free)technology | Afolabi ...

African Journals Online (AJOL)

... (2) site-specific recombination systems and (3) intra-chromosomal recombination. (B) Gene replacement or Targeted gene replacement; and (C) transformation with multiple T-DNAs, which could result in linked and/or unlinked co-integration of transgenes. Unlinked transgenes are then segregated out during meiosis.

A bulk segregant gene expression analysis of a peach population reveals components of the underlying mechanism of the fruit cold response.

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Clara Pons

Full Text Available Peach fruits subjected for long periods of cold storage are primed to develop chilling injury once fruits are shelf ripened at room temperature. Very little is known about the molecular changes occurring in fruits during cold exposure. To get some insight into this process a transcript profiling analyses was performed on fruits from a PopDG population segregating for chilling injury CI responses. A bulked segregant gene expression analysis based on groups of fruits showing extreme CI responses indicated that the transcriptome of peach fruits was modified already during cold storage consistently with eventual CI development. Most peach cold-responsive genes have orthologs in Arabidopsis that participate in cold acclimation and other stresses responses, while some of them showed expression patterns that differs in fruits according to their susceptibility to develop mealiness. Members of ICE1, CBF1/3 and HOS9 regulons seem to have a prominent role in differential cold responses between low and high sensitive fruits. In high sensitive fruits, an alternative cold response program is detected. This program is probably associated with dehydration/osmotic stress and regulated by ABA, auxins and ethylene. In addition, the observation that tolerant siblings showed a series of genes encoding for stress protective activities with higher expression both at harvest and during cold treatment, suggests that preprogrammed mechanisms could shape fruit ability to tolerate postharvest cold-induced stress. A number of genes differentially expressed were validated and extended to individual genotypes by medium-throughput RT-qPCR. Analyses presented here provide a global view of the responses of peach fruits to cold storage and highlights new peach genes that probably play important roles in the tolerance/sensitivity to cold storage. Our results provide a roadmap for further experiments and would help to develop new postharvest protocols and gene directed breeding

A bulk segregant gene expression analysis of a peach population reveals components of the underlying mechanism of the fruit cold response.

Science.gov (United States)

Pons, Clara; Martí, Cristina; Forment, Javier; Crisosto, Carlos H; Dandekar, Abhaya M; Granell, Antonio

2014-01-01

Peach fruits subjected for long periods of cold storage are primed to develop chilling injury once fruits are shelf ripened at room temperature. Very little is known about the molecular changes occurring in fruits during cold exposure. To get some insight into this process a transcript profiling analyses was performed on fruits from a PopDG population segregating for chilling injury CI responses. A bulked segregant gene expression analysis based on groups of fruits showing extreme CI responses indicated that the transcriptome of peach fruits was modified already during cold storage consistently with eventual CI development. Most peach cold-responsive genes have orthologs in Arabidopsis that participate in cold acclimation and other stresses responses, while some of them showed expression patterns that differs in fruits according to their susceptibility to develop mealiness. Members of ICE1, CBF1/3 and HOS9 regulons seem to have a prominent role in differential cold responses between low and high sensitive fruits. In high sensitive fruits, an alternative cold response program is detected. This program is probably associated with dehydration/osmotic stress and regulated by ABA, auxins and ethylene. In addition, the observation that tolerant siblings showed a series of genes encoding for stress protective activities with higher expression both at harvest and during cold treatment, suggests that preprogrammed mechanisms could shape fruit ability to tolerate postharvest cold-induced stress. A number of genes differentially expressed were validated and extended to individual genotypes by medium-throughput RT-qPCR. Analyses presented here provide a global view of the responses of peach fruits to cold storage and highlights new peach genes that probably play important roles in the tolerance/sensitivity to cold storage. Our results provide a roadmap for further experiments and would help to develop new postharvest protocols and gene directed breeding strategies to better

Mapping and Genetic Structure Analysis of the Anthracnose Resistance Locus Co-1HY in the Common Bean (Phaseolus vulgaris L..

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Mingli Chen

Full Text Available Anthracnose is a destructive disease of the common bean (Phaseolus vulgaris L.. The Andean cultivar Hongyundou has been demonstrated to possess strong resistance to anthracnose race 81. To study the genetics of this resistance, the Hongyundou cultivar was crossed with a susceptible genotype Jingdou. Segregation of resistance for race 81 was assessed in the F2 population and F2:3 lines under controlled conditions. Results indicate that Hongyundou carries a single dominant gene for anthracnose resistance. An allele test by crossing Hongyundou with another resistant cultivar revealed that the resistance gene is in the Co-1 locus (therefore named Co-1HY. The physical distance between this locus and the two flanking markers was 46 kb, and this region included four candidate genes, namely, Phvul.001G243500, Phvul.001G243600, Phvul.001G243700 and Phvul.001G243800. These candidate genes encoded serine/threonine-protein kinases. Expression analysis of the four candidate genes in the resistant and susceptible cultivars under control condition and inoculated treatment revealed that all the four candidate genes are expressed at significantly higher levels in the resistant genotype than in susceptible genotype. Phvul.001G243600 and Phvul.001G243700 are expressed nearly 15-fold and 90-fold higher in the resistant genotype than in the susceptible parent before inoculation, respectively. Four candidate genes will provide useful information for further research into the resistance mechanism of anthracnose in common bean. The closely linked flanking markers identified here may be useful for transferring the resistance allele Co-1HY from Hongyundou to elite anthracnose susceptible common bean lines.

Mapping and Genetic Structure Analysis of the Anthracnose Resistance Locus Co-1HY in the Common Bean (Phaseolus vulgaris L.).

Science.gov (United States)

Chen, Mingli; Wu, Jing; Wang, Lanfen; Mantri, Nitin; Zhang, Xiaoyan; Zhu, Zhendong; Wang, Shumin

2017-01-01

Anthracnose is a destructive disease of the common bean (Phaseolus vulgaris L.). The Andean cultivar Hongyundou has been demonstrated to possess strong resistance to anthracnose race 81. To study the genetics of this resistance, the Hongyundou cultivar was crossed with a susceptible genotype Jingdou. Segregation of resistance for race 81 was assessed in the F2 population and F2:3 lines under controlled conditions. Results indicate that Hongyundou carries a single dominant gene for anthracnose resistance. An allele test by crossing Hongyundou with another resistant cultivar revealed that the resistance gene is in the Co-1 locus (therefore named Co-1HY). The physical distance between this locus and the two flanking markers was 46 kb, and this region included four candidate genes, namely, Phvul.001G243500, Phvul.001G243600, Phvul.001G243700 and Phvul.001G243800. These candidate genes encoded serine/threonine-protein kinases. Expression analysis of the four candidate genes in the resistant and susceptible cultivars under control condition and inoculated treatment revealed that all the four candidate genes are expressed at significantly higher levels in the resistant genotype than in susceptible genotype. Phvul.001G243600 and Phvul.001G243700 are expressed nearly 15-fold and 90-fold higher in the resistant genotype than in the susceptible parent before inoculation, respectively. Four candidate genes will provide useful information for further research into the resistance mechanism of anthracnose in common bean. The closely linked flanking markers identified here may be useful for transferring the resistance allele Co-1HY from Hongyundou to elite anthracnose susceptible common bean lines.

Comparison of gene co-networks reveals the molecular mechanisms of the rice (Oryza sativa L.) response to Rhizoctonia solani AG1 IA infection.

Science.gov (United States)

Zhang, Jinfeng; Zhao, Wenjuan; Fu, Rong; Fu, Chenglin; Wang, Lingxia; Liu, Huainian; Li, Shuangcheng; Deng, Qiming; Wang, Shiquan; Zhu, Jun; Liang, Yueyang; Li, Ping; Zheng, Aiping

2018-05-05

Rhizoctonia solani causes rice sheath blight, an important disease affecting the growth of rice (Oryza sativa L.). Attempts to control the disease have met with little success. Based on transcriptional profiling, we previously identified more than 11,947 common differentially expressed genes (TPM > 10) between the rice genotypes TeQing and Lemont. In the current study, we extended these findings by focusing on an analysis of gene co-expression in response to R. solani AG1 IA and identified gene modules within the networks through weighted gene co-expression network analysis (WGCNA). We compared the different genes assigned to each module and the biological interpretations of gene co-expression networks at early and later modules in the two rice genotypes to reveal differential responses to AG1 IA. Our results show that different changes occurred in the two rice genotypes and that the modules in the two groups contain a number of candidate genes possibly involved in pathogenesis, such as the VQ protein. Furthermore, these gene co-expression networks provide comprehensive transcriptional information regarding gene expression in rice in response to AG1 IA. The co-expression networks derived from our data offer ideas for follow-up experimentation that will help advance our understanding of the translational regulation of rice gene expression changes in response to AG1 IA.

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

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Lemay Danielle G

2012-09-01

Full Text Available Abstract Background In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously. Results Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication. Mammalian gene neighborhoods contain highly and variably expressed genes. Co-localized noisy gene pairs exhibit lower evolutionary conservation of their adjacent genome locations, suggesting that their shared transcriptional background may be disadvantageous. Genes that are essential to mammalian survival and reproduction are less likely to occur in neighborhoods, although neighborhoods are enriched with genes that function in mitosis. We also found that gene orientation and protein-protein interactions are partially responsible for maintenance of gene neighborhoods. Conclusions Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The

Coupling of microphase separation and dewetting in weakly segregated diblock co-polymer ultrathin films.

Science.gov (United States)

Yan, Derong; Huang, Haiying; He, Tianbai; Zhang, Fajun

2011-10-04

We have studied the coupling behavior of microphase separation and autophobic dewetting in weakly segregated poly(ε-caprolactone)-block-poly(L-lactide) (PCL-b-PLLA) diblock co-polymer ultrathin films on carbon-coated mica substrates. At temperatures higher than the melting point of the PLLA block, the co-polymer forms a lamellar structure in bulk with a long period of L ∼ 20 nm, as determined using small-angle X-ray scattering. The relaxation procedure of ultrathin films with an initial film thickness of h = 10 nm during annealing has been followed by atomic force microscopy (AFM). In the experimental temperature range (100-140 °C), the co-polymer dewets to an ultrathin film of itself at about 5 nm because of the strong attraction of both blocks with the substrate. Moreover, the dewetting velocity increases with decreasing annealing temperatures. This novel dewetting kinetics can be explained by a competition effect of the composition fluctuation driven by the microphase separation with the dominated dewetting process during the early stage of the annealing process. While dewetting dominates the relaxation procedure and leads to the rupture of the ultrathin films, the composition fluctuation induced by the microphase separation attempts to stabilize them because of the matching of h to the long period (h ∼ 1/2L). The temperature dependence of these two processes leads to this novel relaxation kinetics of co-polymer thin films. © 2011 American Chemical Society

Potenzielle Arzneimittelwechsel-wirkungen und unerwünschte Arzneimittelwirkungen bei stationären dermatologischen Patienten.

Science.gov (United States)

Koch, Lukas; Kränke, Birger; Aberer, Werner

2016-11-01

Informationen zur Häufigkeit von Arzneimittelwechselwirkungen und unerwünschten Arzneimittelwirkungen zu präsentieren und Hilfestellung zu leisten, wie diese wichtigen Probleme in der pharmakologischen Behandlung stationärer dermatologischer Patienten minimiert werden können. Die Medikation von 1 099 stationären dermatologischen Patienten wurde retrospektiv mittels einer Internet-basierten Software für Medikamenteninteraktionen (Diagnosia ® Check) auf Arzneimittelwechselwirkungen und unerwünschte Arzneimittelwirkungen analysiert. Wir beschreiben eine Gesamthäufigkeit relevanter Arzneimittelwechselwirkungen von 51,7 % mit durchschnittlich 3,2 Interaktionen pro betroffenem stationären Patienten. Arzneimittelkombinationen, die gemieden werden sollten, wurden bei 5,7 % der Studienpopulation festgestellt. Der wichtigste Risikofaktor war die Gesamtzahl der verabreichten Medikamente. Die Arzneimittelgruppen, die bei der Mehrzahl der Wechselwirkungen beteiligt waren, waren Analgetika, Herz-Kreislauf-Medikamente und gerinnungshemmende Medikamente sowie Antidepressiva. Das Risiko unerwünschte Arzneimittelwirkungen auszubilden wurde bei 53,1 % der stationären Patienten als "hoch" eingestuft. Die fünf wichtigsten unerwünschten Nebenwirkungen in dieser Patientengruppe waren Blutungen, Obstipation, anticholinerge Effekte, Sedierung und orthostatische Effekte. Potenzielle Arzneimittelwechselwirkungen sowie unerwünschte Arzneimittelwirkungen sind bei stationären dermatologischen Patienten alarmierend häufig. Bei jedem zweiten Patienten besteht die Gefahr, derartige Wechselwirkungen oder unerwünschte Nebenwirkungen zu erleiden und jeder zwanzigste Patient erhält eine Arzneimittelkombination, die nicht verabreicht werden sollte. Erhöhte Wachsamkeit ist erforderlich, um die gefährdeten Patienten zu erkennen. © 2016 Deutsche Dermatologische Gesellschaft (DDG). Published by John Wiley & Sons Ltd.

St. René: the Patron Saint of Anaesthetists and a Patron Saint of Canada.

Science.gov (United States)

Calverley, R K

1980-01-01

René Goupil, the Patron Saint of Anaesthetists, and a Patron Saint of Canada, was born in Angers, France in 1608 and studied surgery. He joined the Jesuits as a donné or volunteer worker in 1640 and served in the then tiny colony of Quebec as one of the first medical workers of Canada. After earning meritorious praise for his skills, he again volunteered to attend the Hurons at Sainte Marie, a mission far beyond the frontiers. René's canoe party was ambushed. He was captured by the Mohawks and endured eight weeks of cruel torture before being killed on September 29, 1642. René was the first of eight North American martyrs whose dedication was recognized by canonization in 1930. St. René was appointed Patron Saint of Anaesthetists in 1951.

Identifying key genes in rheumatoid arthritis by weighted gene co-expression network analysis.

Science.gov (United States)

Ma, Chunhui; Lv, Qi; Teng, Songsong; Yu, Yinxian; Niu, Kerun; Yi, Chengqin

2017-08-01

This study aimed to identify rheumatoid arthritis (RA) related genes based on microarray data using the WGCNA (weighted gene co-expression network analysis) method. Two gene expression profile datasets GSE55235 (10 RA samples and 10 healthy controls) and GSE77298 (16 RA samples and seven healthy controls) were downloaded from Gene Expression Omnibus database. Characteristic genes were identified using metaDE package. WGCNA was used to find disease-related networks based on gene expression correlation coefficients, and module significance was defined as the average gene significance of all genes used to assess the correlation between the module and RA status. Genes in the disease-related gene co-expression network were subject to functional annotation and pathway enrichment analysis using Database for Annotation Visualization and Integrated Discovery. Characteristic genes were also mapped to the Connectivity Map to screen small molecules. A total of 599 characteristic genes were identified. For each dataset, characteristic genes in the green, red and turquoise modules were most closely associated with RA, with gene numbers of 54, 43 and 79, respectively. These genes were enriched in totally enriched in 17 Gene Ontology terms, mainly related to immune response (CD97, FYB, CXCL1, IKBKE, CCR1, etc.), inflammatory response (CD97, CXCL1, C3AR1, CCR1, LYZ, etc.) and homeostasis (C3AR1, CCR1, PLN, CCL19, PPT1, etc.). Two small-molecule drugs sanguinarine and papaverine were predicted to have a therapeutic effect against RA. Genes related to immune response, inflammatory response and homeostasis presumably have critical roles in RA pathogenesis. Sanguinarine and papaverine have a potential therapeutic effect against RA. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing.

Science.gov (United States)

Huo, Heqiang; Henry, Isabelle M; Coppoolse, Eric R; Verhoef-Post, Miriam; Schut, Johan W; de Rooij, Han; Vogelaar, Aat; Joosen, Ronny V L; Woudenberg, Leo; Comai, Luca; Bradford, Kent J

2016-11-01

Lettuce (Lactuca sativa) seeds exhibit thermoinhibition, or failure to complete germination when imbibed at warm temperatures. Chemical mutagenesis was employed to develop lettuce lines that exhibit germination thermotolerance. Two independent thermotolerant lettuce seed mutant lines, TG01 and TG10, were generated through ethyl methanesulfonate mutagenesis. Genetic and physiological analyses indicated that these two mutations were allelic and recessive. To identify the causal gene(s), we applied bulked segregant analysis by whole genome sequencing. For each mutant, bulked DNA samples of segregating thermotolerant (mutant) seeds were sequenced and analyzed for homozygous single-nucleotide polymorphisms. Two independent candidate mutations were identified at different physical positions in the zeaxanthin epoxidase gene (ABSCISIC ACID DEFICIENT 1/ZEAXANTHIN EPOXIDASE, or ABA1/ZEP) in TG01 and TG10. The mutation in TG01 caused an amino acid replacement, whereas the mutation in TG10 resulted in alternative mRNA splicing. Endogenous abscisic acid contents were reduced in both mutants, and expression of the ABA1 gene from wild-type lettuce under its own promoter fully complemented the TG01 mutant. Conventional genetic mapping confirmed that the causal mutations were located near the ZEP/ABA1 gene, but the bulked segregant whole genome sequencing approach more efficiently identified the specific gene responsible for the phenotype. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Template DNA-strand co-segregation and asymmetric cell division in skeletal muscle stem cells.

Science.gov (United States)

Shinin, Vasily; Gayraud-Morel, Barbara; Tajbakhsh, Shahragim

2009-01-01

Stem cells are present in all tissues and organs, and are crucial for normal regulated growth. How the pool size of stem cells and their progeny is regulated to establish the tissue prenatally, then maintain it throughout life, is a key question in biology and medicine. The ability to precisely locate stem and progenitors requires defining lineage progression from stem to differentiated cells, assessing the mode of cell expansion and self-renewal and identifying markers to assess the different cell states within the lineage. We have shown that during lineage progression from a quiescent adult muscle satellite cell to a differentiated myofibre, both symmetric and asymmetric divisions take place. Furthermore, we provide evidence that a sub-population of label retaining satellite cells co-segregate template DNA strands to one daughter cell. These findings provide a means of identifying presumed stem and progenitor cells within the lineage. In addition, asymmetric segregation of template DNA and the cytoplasmic protein Numb provides a landmark to define cell behaviour as self-renewal and differentiation decisions are being executed.

Stripe segregation and magnetic coupling in the nickelate La 5/3Sr1/3NiO4

KAUST Repository

Schwingenschlögl, Udo

2009-03-02

We investigate the consequences of the stripe formation in the nickelate La5/3Sr1/3NiO4 for the details of its crystal structure and electronic states. Our data are based on numerical simulations within density functional theory (DFT) and the generalized gradient approximation (GGA). The on-site Coulomb interaction is included in terms of the LDA+U scheme. Structure optimization of preliminary experimental data indicates a strong interaction between the structural and electronic degrees of freedom. In particular, we find a segregation of the diagonal filled stripes induced by a delicate interplay with the magnetic coupling. Beyond the cooperative effect of stripe segregation and spin order, distinct octahedral distortions are essential for the formation of an insulating state. © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic scale study of grain boundary segregation before carbide nucleation in Ni-Cr-Fe Alloys

Science.gov (United States)

Li, Hui; Xia, Shuang; Liu, Wenqing; Liu, Tingguang; Zhou, Bangxin

2013-08-01

Three dimensional chemical information concerning grain boundary segregation before carbide nucleation was characterized by atom probe tomography in two Ni-Cr-Fe alloys which were aged at 500 °C for 0.5 h after homogenizing treatment. B, C and Si atoms segregation at grain boundary in Alloy 690 was observed. B, C, N and P atoms segregation at grain boundary in 304 austenitic stainless steel was observed. C atoms co-segregation with Cr atoms at the grain boundaries both in Alloy 690 and 304 austenitic stainless steel was found, and its effect on the carbide nucleation was discussed. The amount of each segregated element at grain boundaries in the two Ni-Cr-Fe alloys were analyzed quantitatively. Comparison of the grain boundary segregation features of the two Ni-Cr-Fe alloys were carried out based on the experimental results. The impurity and solute atoms segregate inhomogeneously in the same grain boundary both in 304 SS and Alloy 690. The grain boundary segregation tendencies (Sav) are B (11.8 ± 1.4) > P (5.4 ± 1.4) > N (4.7 ± 0.3) > C (3.7 ± 0.4) in 304 SS, and B (6.9 ± 0.9) > C (6.7 ± 0.4) > Si (1.5 ± 0.2) in Alloy 690. Cr atoms may co-segregate with C atoms at grain boundaries before carbide nucleation at the grain boundaries both in 304 SS and Alloy 690. Ni atoms generally deplete at grain boundary both in 304 SS and Alloy 690. The literature shows that the Ni atoms may co-segregate with P atoms at grain boundaries [28], but the P atoms segregation do not leads to Ni segregation in the current study. In the current study, Fe atoms may segregate or deplete at grain boundary in Alloy 690. But Fe atoms generally deplete at grain boundary in 304 SS. B atoms have the strongest grain boundary segregation tendency both in 304 SS and Alloy 690. The grain boundary segregation tendency and Gibbs free energy of B in 304 SS is higher than in Alloy 690. C atoms are easy to segregate at grain boundaries both in 304 SS and Alloy 690. The grain boundary segregation

Whole-exome sequencing of a pedigree segregating asthma

Directory of Open Access Journals (Sweden)

DeWan Andrew T

2012-10-01

Full Text Available Abstract Background Despite the success of genome-wide association studies for asthma, few, if any, definitively causal variants have been identified and there is still a substantial portion of the heritability of the disease yet to be discovered. Some of this “missing heritability” may be accounted for by family-specific coding variants found to be segregating with asthma. Methods To identify family-specific variants segregating with asthma, we recruited one family from a previous study of asthma as reporting multiple asthmatic and non-asthmatic children. We performed whole-exome sequencing on all four children and both parents and identified coding variants segregating with asthma that were not found in other variant databases. Results Ten novel variants were identified that were found in the two affected offspring and affected mother, but absent in the unaffected father and two unaffected offspring. Of these ten, variants in three genes (PDE4DIP, CBLB, and KALRN were deemed of particular interest based on their functional prediction scores and previously reported function or asthma association. We did not identify any common risk variants segregating with asthma, however, we did observe an increase in the number of novel, nonsynonymous variants in asthma candidate genes in the asthmatic children compared to the non-asthmatic children. Conclusions This is the first report applying exome sequencing to identify asthma susceptibility variants. Despite having sequenced only one family segregating asthma, we have identified several potentially functional variants in interesting asthma candidate genes. This will provide the basis for future work in which more families will be sequenced to identify variants across families that cluster within genes.

A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis.

Science.gov (United States)

Bakker, Erin; Achenbach, Ute; Bakker, Jeroen; van Vliet, Joke; Peleman, Johan; Segers, Bart; van der Heijden, Stefan; van der Linde, Piet; Graveland, Robert; Hutten, Ronald; van Eck, Herman; Coppoolse, Eric; van der Vossen, Edwin; Bakker, Jaap; Goverse, Aska

2004-06-01

The resistance gene H1 confers resistance to the potato cyst nematode Globodera rostochiensis and is located at the distal end of the long arm of chromosome V of potato. For marker enrichment of the H1 locus, a bulked segregant analysis (BSA) was carried out using 704 AFLP primer combinations. A second source of markers tightly linked to H1 is the ultra-high-density (UHD) genetic map of the potato cross SH x RH. This map has been produced with 387 AFLP primer combinations and consists of 10,365 AFLP markers in 1,118 bins (http://www.dpw.wageningen-ur.nl/uhd/). Comparing these two methods revealed that BSA resulted in one marker/cM and the UHD map in four markers/cM in the H1 interval. Subsequently, a high-resolution genetic map of the H1 locus has been developed using a segregating F(1) SH x RH population consisting of 1,209 genotypes. Two PCR-based markers were designed at either side of the H1 gene to screen the 1,209 genotypes for recombination events. In the high-resolution genetic map, two of the four co-segregating AFLP markers could be separated from the H1 gene. Marker EM1 is located at a distance of 0.2 cM, and marker EM14 is located at a distance of 0.8 cM. The other two co-segregating markers CM1 (in coupling) and EM15 (in repulsion) could not be separated from the H1 gene.

Adsorption-Driven Surface Segregation of the Less Reactive Alloy Component

DEFF Research Database (Denmark)

Andersson, Klas Jerker; Calle Vallejo, Federico; Rossmeisl, Jan

2009-01-01

Counterintuitive to expectations and all prior observations of adsorbate-induced surface segregation of the more reactive alloy component (the one forming the stronger bond with the adsorbate), we show that CO adsorption at elevated pressures and temperatures pulls the less reactive Cu to the sur......Counterintuitive to expectations and all prior observations of adsorbate-induced surface segregation of the more reactive alloy component (the one forming the stronger bond with the adsorbate), we show that CO adsorption at elevated pressures and temperatures pulls the less reactive Cu...... to the surface of a CuPt near-surface alloy. The Cu surface segregation is driven by the formation of a stable self-organized CO/CuPt surface alloy structure and is rationalized in terms of the radically stronger Pt−CO bond when Cu is present in the first surface layer of Pt. The results, which are expected...

Evidence of major genes affecting stress response in rainbow trout using Bayesian methods of complex segregation analysis

DEFF Research Database (Denmark)

Vallejo, R L; Rexroad III, C E; Silverstein, J T

2009-01-01

As a first step toward the genetic mapping of QTL affecting stress response variation in rainbow trout, we performed complex segregation analyses (CSA) fitting mixed inheritance models of plasma cortisol by using Bayesian methods in large full-sib families of rainbow trout. To date, no studies have...... been conducted to determine the mode of inheritance of stress response as measured by plasma cortisol response when using a crowding stress paradigm and CSA in rainbow trout. The main objective of this study was to determine the mode of inheritance of plasma cortisol after a crowding stress....... The results from fitting mixed inheritance models with Bayesian CSA suggest that 1 or more major genes with dominant cortisol-decreasing alleles and small additive genetic effects of a large number of independent genes likely underlie the genetic variation of plasma cortisol in the rainbow trout families...

G-NEST: A gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Science.gov (United States)

In previous studies, gene neighborhoods--spatial clusters of co-expressed genes in the genome--have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Sc...

A cohort of balanced reciprocal translocations associated with dyslexia: identification of two putative candidate genes at DYX1

DEFF Research Database (Denmark)

Buonincontri, Roberta; Bache, Iben; Silahtaroglu, Asli

2011-01-01

Dyslexia is one of the most common neurodevelopmental disorders where likely many genes are involved in the pathogenesis. So far six candidate dyslexia genes have been proposed, and two of these were identified by rare chromosomal translocations in affected individuals. By systematic re......-examination of all translocation carriers in Denmark, we have identified 16 different translocations associated with dyslexia. In four families, where the translocation co-segregated with the phenotype, one of the breakpoints concurred (at the cytogenetic level) with either a known dyslexia linkage region--at 15q21...... (DYX1), 2p13 (DYX3) and 1p36 (DYX8)--or an unpublished linkage region at 19q13. As a first exploitation of this unique cohort, we identify three novel candidate dyslexia genes, ZNF280D and TCF12 at 15q21, and PDE7B at 6q23.3, by molecular mapping of the familial translocation with the 15q21 breakpoint....

The avant-garde is not dead / René Block ; intervjueerinud Eero Epner

Index Scriptorium Estoniae

Block, René, 1942-

2010-01-01

Intervjuu saksa galeristi ja kuraatori René Blockiga, kes 1964. a. avas Berliinis galerii, kus eksponeeris J. Beuysi, S. Polke, G. Richteri jt. töid. Töötamisest kuraatorina alates 1970. aastatest, biennaalide tulevikust, avangardist. René Blocki galeriis 1966. a. toimunud Joseph Beuys'i performance'ist "Kuidas seletada kunsti surnud jänesele", millest inspireerituna teater NO99 lõi samanimelise lavastuse

Missense variants in AIMP1 gene are implicated in autosomal recessive intellectual disability without neurodegeneration.

Science.gov (United States)

Iqbal, Zafar; Püttmann, Lucia; Musante, Luciana; Razzaq, Attia; Zahoor, Muhammad Yasir; Hu, Hao; Wienker, Thomas F; Garshasbi, Masoud; Fattahi, Zohreh; Gilissen, Christian; Vissers, Lisenka E L M; de Brouwer, Arjan P M; Veltman, Joris A; Pfundt, Rolph; Najmabadi, Hossein; Ropers, Hans-Hilger; Riazuddin, Sheikh; Kahrizi, Kimia; van Bokhoven, Hans

2016-03-01

AIMP1/p43 is a multifunctional non-catalytic component of the multisynthetase complex. The complex consists of nine catalytic and three non-catalytic proteins, which catalyze the ligation of amino acids to their cognate tRNA isoacceptors for use in protein translation. To date, two allelic variants in the AIMP1 gene have been reported as the underlying cause of autosomal recessive primary neurodegenerative disorder. Here, we present two consanguineous families from Pakistan and Iran, presenting with moderate to severe intellectual disability, global developmental delay, and speech impairment without neurodegeneration. By the combination of homozygosity mapping and next generation sequencing, we identified two homozygous missense variants, p.(Gly299Arg) and p.(Val176Gly), in the gene AIMP1 that co-segregated with the phenotype in the respective families. Molecular modeling of the variants revealed deleterious effects on the protein structure that are predicted to result in reduced AIMP1 function. Our findings indicate that the clinical spectrum for AIMP1 defects is broader than witnessed so far.

Missense variants in AIMP1 gene are implicated in autosomal recessive intellectual disability without neurodegeneration

Science.gov (United States)

Iqbal, Zafar; Püttmann, Lucia; Musante, Luciana; Razzaq, Attia; Zahoor, Muhammad Yasir; Hu, Hao; Wienker, Thomas F; Garshasbi, Masoud; Fattahi, Zohreh; Gilissen, Christian; Vissers, Lisenka ELM; de Brouwer, Arjan PM; Veltman, Joris A; Pfundt, Rolph; Najmabadi, Hossein; Ropers, Hans-Hilger; Riazuddin, Sheikh; Kahrizi, Kimia; van Bokhoven, Hans

2016-01-01

AIMP1/p43 is a multifunctional non-catalytic component of the multisynthetase complex. The complex consists of nine catalytic and three non-catalytic proteins, which catalyze the ligation of amino acids to their cognate tRNA isoacceptors for use in protein translation. To date, two allelic variants in the AIMP1 gene have been reported as the underlying cause of autosomal recessive primary neurodegenerative disorder. Here, we present two consanguineous families from Pakistan and Iran, presenting with moderate to severe intellectual disability, global developmental delay, and speech impairment without neurodegeneration. By the combination of homozygosity mapping and next generation sequencing, we identified two homozygous missense variants, p.(Gly299Arg) and p.(Val176Gly), in the gene AIMP1 that co-segregated with the phenotype in the respective families. Molecular modeling of the variants revealed deleterious effects on the protein structure that are predicted to result in reduced AIMP1 function. Our findings indicate that the clinical spectrum for AIMP1 defects is broader than witnessed so far. PMID:26173967

AMPK activation represses the human gene promoter of the cardiac isoform of acetyl-CoA carboxylase: Role of nuclear respiratory factor-1

Energy Technology Data Exchange (ETDEWEB)

Adam, Tasneem; Opie, Lionel H. [Hatter Cardiovascular Research Institute, Faculty of Health Sciences, University of Cape Town, Observatory 7925 (South Africa); Essop, M. Faadiel, E-mail: mfessop@sun.ac.za [Cardio-Metabolic Research Group (CMRG), Department of Physiological Sciences, Stellenbosch University, Stellenbosch 7600 (South Africa)

2010-07-30

Research highlights: {yields} AMPK inhibits acetyl-CoA carboxylase beta gene promoter activity. {yields} Nuclear respiratory factor-1 inhibits acetyl-CoA carboxylase beta promoter activity. {yields} AMPK regulates acetyl-CoA carboxylase beta at transcriptional level. -- Abstract: The cardiac-enriched isoform of acetyl-CoA carboxylase (ACC{beta}) produces malonyl-CoA, a potent inhibitor of carnitine palmitoyltransferase-1. AMPK inhibits ACC{beta} activity, lowering malonyl-CoA levels and promoting mitochondrial fatty acid {beta}-oxidation. Previously, AMPK increased promoter binding of nuclear respiratory factor-1 (NRF-1), a pivotal transcriptional modulator controlling gene expression of mitochondrial proteins. We therefore hypothesized that NRF-1 inhibits myocardial ACC{beta} promoter activity via AMPK activation. A human ACC{beta} promoter-luciferase construct was transiently transfected into neonatal cardiomyocytes {+-} a NRF-1 expression construct. NRF-1 overexpression decreased ACC{beta} gene promoter activity by 71 {+-} 4.6% (p < 0.001 vs. control). Transfections with 5'-end serial promoter deletions revealed that NRF-1-mediated repression of ACC{beta} was abolished with a pPII{beta}-18/+65-Luc deletion construct. AMPK activation dose-dependently reduced ACC{beta} promoter activity, while NRF-1 addition did not further decrease it. We also investigated NRF-1 inhibition in the presence of upstream stimulatory factor 1 (USF1), a known transactivator of the human ACC{beta} gene promoter. Here NRF-1 blunted USF1-dependent induction of ACC{beta} promoter activity by 58 {+-} 7.5% (p < 0.001 vs. control), reversed with a dominant negative NRF-1 construct. NRF-1 also suppressed endogenous USF1 transcriptional activity by 55 {+-} 6.2% (p < 0.001 vs. control). This study demonstrates that NRF-1 is a novel transcriptional inhibitor of the human ACC{beta} gene promoter in the mammalian heart. Our data extends AMPK regulation of ACC{beta} to the transcriptional level.

Identification and characterization of pin and thrum alleles of two genes that co-segregate with the Primula S locus.

Science.gov (United States)

Li, Jinhong; Webster, Margaret; Furuya, Masaki; Gilmartin, Philip M

2007-07-01

The study of heteromorphy in Primula over the past 140 years has established the reproductive significance of this breeding system. Plants produce either thrum or pin flowers that demonstrate reciprocal herkogamy. Thrums have short styles and produce large pollen from anthers at the mouth of the flower; pins have long styles and produce small pollen from anthers located within the corolla tube. The control of heteromorphy is orchestrated by the S locus with dominant (S) and recessive (s) alleles that comprise a co-adapted linkage group of genes. Thrum plants are heterozygous (Ss) and pin plants are homozygous (ss). Reciprocal crosses between the two forms are required for fertilization; within-morph crosses are impeded by a sporophytic self-incompatibility system. Rare recombination events within the S locus produce self-fertile homostyles. As a first step towards identifying genes located at the S locus, we used fluorescent differential display to screen for differential gene expression in pin and thrum flowers. Rather than only detecting differentially regulated genes, we identified two S locus linked genes by virtue of allelic variation between pin and thrum transcripts. Analysis of pin and thrum plants together with homostyle recombinant reveals that one gene flanks the locus, whereas the other shows complete linkage. One gene is related to Arabidopsis flower-timing genes Col9 and Col10; the other encodes a small predicted membrane protein of unknown function. Notwithstanding the diallelic behaviour of the Primula S locus, analysis of pin and thrum plants reveal three alleles for each gene: two pin and one thrum.

Amelogenesis Imperfecta: 1 Family, 2 Phenotypes, and 2 Mutated Genes.

Science.gov (United States)

Prasad, M K; Laouina, S; El Alloussi, M; Dollfus, H; Bloch-Zupan, A

2016-12-01

Amelogenesis imperfecta (AI) is a clinically and genetically heterogeneous group of diseases characterized by enamel defects. The authors have identified a large consanguineous Moroccan family segregating different clinical subtypes of hypoplastic and hypomineralized AI in different individuals within the family. Using targeted next-generation sequencing, the authors identified a novel heterozygous nonsense mutation in COL17A1 (c.1873C>T, p.R625*) segregating with hypoplastic AI and a novel homozygous 8-bp deletion in C4orf26 (c.39_46del, p.Cys14Glyfs*18) segregating with hypomineralized-hypoplastic AI in this family. This study highlights the phenotypic and genotypic heterogeneity of AI that can exist even within a single consanguineous family. Furthermore, the identification of novel mutations in COL17A1 and C4orf26 and their correlation with distinct AI phenotypes can contribute to a better understanding of the pathophysiology of AI and the contribution of these genes to amelogenesis. © International & American Associations for Dental Research 2016.

Cytological localization of adenosine kinase, nucleoside phosphorylase-1, and esterase-10 genes on mouse chromosome 14

International Nuclear Information System (INIS)

Samuelson, L.C.; Farber, R.A.

1985-01-01

The authors have determined the regional locations on mouse chromosome 14 of the genes for mouse adenosine kinase (ADK), nucleoside phosphorylase- 1 (NP-1), and esterase-10 (ES-10) by analysis of rearranged mouse chromosomes in gamma-irradiated Chinese hamster X mouse hybrid cell lines. Irradiated clones were screened for expression of the murine forms of these enzymes; segregant clones that expressed only one or two of the three markers were karyotyped. The patterns of enzyme expression in these segregants were correlated with the presence of rearranged chromosomes. The Adk gene was localized to bands A2 to B, Np-1 to bands B to C1, and Es-10 to bands D2 to E2

Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

Energy Technology Data Exchange (ETDEWEB)

Vogelsang, Matjaz; Comino, Aleksandra; Zupanec, Neja [Department for Biosynthesis and Biotransformation, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Hudler, Petra [Medical Center for Molecular Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana (Slovenia); Komel, Radovan [Department for Biosynthesis and Biotransformation, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Medical Center for Molecular Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana (Slovenia)

2009-10-28

Loss of DNA mismatch repair (MMR) in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC). Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T) were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene.

Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

Directory of Open Access Journals (Sweden)

Hudler Petra

2009-10-01

Full Text Available Abstract Background Loss of DNA mismatch repair (MMR in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC. Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Methods Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. Results The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Conclusion Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene.

Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

International Nuclear Information System (INIS)

Vogelsang, Matjaz; Comino, Aleksandra; Zupanec, Neja; Hudler, Petra; Komel, Radovan

2009-01-01

Loss of DNA mismatch repair (MMR) in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC). Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T) were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene

Mitochondrial ASncmtRNA-1 and ASncmtRNA-2 as potent targets to inhibit tumor growth and metastasis in the RenCa murine renal adenocarcinoma model.

Science.gov (United States)

Borgna, Vincenzo; Villegas, Jaime; Burzio, Verónica A; Belmar, Sebastián; Araya, Mariela; Jeldes, Emanuel; Lobos-González, Lorena; Silva, Verónica; Villota, Claudio; Oliveira-Cruz, Luciana; Lopez, Constanza; Socias, Teresa; Castillo, Octavio; Burzio, Luis O

2017-07-04

Knockdown of antisense noncoding mitochondrial RNAs (ASncmtRNAs) induces apoptosis in several human and mouse tumor cell lines, but not normal cells, suggesting this approach for a selective therapy against different types of cancer. Here we show that in vitro knockdown of murine ASncmtRNAs induces apoptotic death of mouse renal adenocarcinoma RenCa cells, but not normal murine kidney epithelial cells. In a syngeneic subcutaneous RenCa model, treatment delayed and even reversed tumor growth. Since the subcutaneous model does not reflect the natural microenviroment of renal cancer, we used an orthotopic model of RenCa cells inoculated under the renal capsule. These studies showed inhibition of tumor growth and metastasis. Direct metastasis assessment by tail vein injection of RenCa cells also showed a drastic reduction in lung metastatic nodules. In vivo treatment reduces survivin, N-cadherin and P-cadherin levels, providing a molecular basis for metastasis inhibition. In consequence, the treatment significantly enhanced mouse survival in these models. Our results suggest that the ASncmtRNAs could be potent and selective targets for therapy against human renal cell carcinoma.

Establishment of a molecular genetic map of distal mouse chromosome 1: further definition of a conserved linkage group syntenic with human chromosome 1q.

Science.gov (United States)

Seldin, M F; Morse, H C; LeBoeuf, R C; Steinberg, A D

1988-01-01

A linkage map of distal mouse chromosome 1 was constructed by restriction fragment length polymorphism analysis of DNAs from seven sets of recombinant inbred (RI) strains. The data obtained with seven probes on Southern hybridization combined with data from previous studies suggest the gene order Cfh, Pep-3/Ren-1,2, Ly-5, Lamb-2, At-3, Apoa-2/Ly-17,Spna-1. These results confirm and extend analyses of a large linkage group which includes genes present on a 20-30 cM span of mouse chromosome 1 and those localized to human chromosome 1q21-32. Moreover, the data indicate similar relative positions of human and mouse complement receptor-related genes REN, CD45, LAMB2, AT3, APOA2, and SPTA. These results suggest that mouse gene analyses may help in detailed mapping of human genes within such a syntenic group.

Pst I restriction fragment length polymorphism of human placental alkaline phosphatase gene: Mendelian in segregation and localization of mutation site in the gene

International Nuclear Information System (INIS)

Tsavaler, L.; Penhallow, R.C.; Sussman, H.H.

1988-01-01

The pattern of inheritance of a Pst I restriction fragment length polymorphism (RFLP) of the human placental alkaline phosphatase gene was studied in nine nuclear families by Southern blot hybridization analysis of genomic DNA. The dimorphic RFLP is defined by the presence of allelic fragments 1.0 kilobase and 0.8 kilobase long. The results of this study show that the two alleles of the Pst I RFLP of the placental alkaline phosphatase gene segregate as codominant traits according to Mendelian expectations. For a polymorphism to be useful as a genetic marker the probability that an offspring is informative (PIC) must be at least 0.15. The allelic frequency of the 1.0-kilobase allele is 0.21, which correlates to a probability that an offspring is informative of 0.275 and is indicative of a useful polymorphism. By using probes derived from different regions of the placental alkaline phosphatase cDNA, the mutated Pst I site causing the RFLP was located in the penultimate intron 2497 base pairs downstream from the transcriptional initiation site

Constitutive gene expression profile segregates toxicity in locally advanced breast cancer patients treated with high-dose hyperfractionated radical radiotherapy

International Nuclear Information System (INIS)

Henríquez Hernández, Luis Alberto; Lara, Pedro Carlos; Pinar, Beatriz; Bordón, Elisa; Gallego, Carlos Rodríguez; Bilbao, Cristina; Pérez, Leandro Fernández; Morales, Amílcar Flores

2009-01-01

Breast cancer patients show a wide variation in normal tissue reactions after radiotherapy. The individual sensitivity to x-rays limits the efficiency of the therapy. Prediction of individual sensitivity to radiotherapy could help to select the radiation protocol and to improve treatment results. The aim of this study was to assess the relationship between gene expression profiles of ex vivo un-irradiated and irradiated lymphocytes and the development of toxicity due to high-dose hyperfractionated radiotherapy in patients with locally advanced breast cancer. Raw data from microarray experiments were uploaded to the Gene Expression Omnibus Database http://www.ncbi.nlm.nih.gov/geo/ (GEO accession GSE15341). We obtained a small group of 81 genes significantly regulated by radiotherapy, lumped in 50 relevant pathways. Using ANOVA and t-test statistical tools we found 20 and 26 constitutive genes (0 Gy) that segregate patients with and without acute and late toxicity, respectively. Non-supervised hierarchical clustering was used for the visualization of results. Six and 9 pathways were significantly regulated respectively. Concerning to irradiated lymphocytes (2 Gy), we founded 29 genes that separate patients with acute toxicity and without it. Those genes were gathered in 4 significant pathways. We could not identify a set of genes that segregates patients with and without late toxicity. In conclusion, we have found an association between the constitutive gene expression profile of peripheral blood lymphocytes and the development of acute and late toxicity in consecutive, unselected patients. These observations suggest the possibility of predicting normal tissue response to irradiation in high-dose non-conventional radiation therapy regimens. Prospective studies with higher number of patients are needed to validate these preliminary results

A powerful score-based test statistic for detecting gene-gene co-association.

Science.gov (United States)

Xu, Jing; Yuan, Zhongshang; Ji, Jiadong; Zhang, Xiaoshuai; Li, Hongkai; Wu, Xuesen; Xue, Fuzhong; Liu, Yanxun

2016-01-29

The genetic variants identified by Genome-wide association study (GWAS) can only account for a small proportion of the total heritability for complex disease. The existence of gene-gene joint effects which contains the main effects and their co-association is one of the possible explanations for the "missing heritability" problems. Gene-gene co-association refers to the extent to which the joint effects of two genes differ from the main effects, not only due to the traditional interaction under nearly independent condition but the correlation between genes. Generally, genes tend to work collaboratively within specific pathway or network contributing to the disease and the specific disease-associated locus will often be highly correlated (e.g. single nucleotide polymorphisms (SNPs) in linkage disequilibrium). Therefore, we proposed a novel score-based statistic (SBS) as a gene-based method for detecting gene-gene co-association. Various simulations illustrate that, under different sample sizes, marginal effects of causal SNPs and co-association levels, the proposed SBS has the better performance than other existed methods including single SNP-based and principle component analysis (PCA)-based logistic regression model, the statistics based on canonical correlations (CCU), kernel canonical correlation analysis (KCCU), partial least squares path modeling (PLSPM) and delta-square (δ (2)) statistic. The real data analysis of rheumatoid arthritis (RA) further confirmed its advantages in practice. SBS is a powerful and efficient gene-based method for detecting gene-gene co-association.

Multiscale Embedded Gene Co-expression Network Analysis.

Directory of Open Access Journals (Sweden)

Won-Min Song

2015-11-01

Full Text Available Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3, the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA by: i introducing quality control of co-expression similarities, ii parallelizing embedded network construction, and iii developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs. We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA. MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

Multiscale Embedded Gene Co-expression Network Analysis.

Science.gov (United States)

Song, Won-Min; Zhang, Bin

2015-11-01

Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG) has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3), the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA) by: i) introducing quality control of co-expression similarities, ii) parallelizing embedded network construction, and iii) developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs). We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA). MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

MspI and PvuII polymorphisms in the Na,K-ATPase. beta. subunit gene ATP1B1

Energy Technology Data Exchange (ETDEWEB)

Shull, M.M.; Pugh, D.G.; Lane, L.K.; Lingrel, J.B. (Univ. of Cincinnati College of Medicine, OH (USA))

1990-02-25

ATP1B HH1.2 is a 1.2 kb HindIII fragment from the 3{prime} portion of the human Na,K-ATPase {beta} subunit gene, ATP1B1. MspI identifies a two allele polymorphism (M1: 6.7 kb, M2: 5.3 kb). PvuII also detects a two-allele polymorphism (P1: 5.1 kb, P2: 4.7 kb). ATP1B1 has been assigned to chromosome 1q by somatic cell hybrid analysis. Codominant segregation of the MspI RFLP was observed in one two-generation family (5 individuals). Codominant segregation of the PvuII RFLP was observed in a two-generation (8 individuals) and a three-generation (12 individuals) family.

Genetic Architecture of Male Sterility and Segregation Distortion in Drosophila pseudoobscura Bogota–USA Hybrids

Science.gov (United States)

Phadnis, Nitin

2011-01-01

Understanding the genetic basis of reproductive isolation between recently diverged species is a central problem in evolutionary genetics. Here, I present analyses of the genetic architecture underlying hybrid male sterility and segregation distortion between the Bogota and USA subspecies of Drosophila pseudoobscura. Previously, a single gene, Overdrive (Ovd), was shown to be necessary but not sufficient for both male sterility and segregation distortion in F1 hybrids between these subspecies, requiring several interacting partner loci for full manifestation of hybrid phenomena. I map these partner loci separately on the Bogota X chromosome and USA autosomes using a combination of different mapping strategies. I find that hybrid sterility involves a single hybrid incompatibility of at least seven interacting partner genes that includes three large-effect loci. Segregation distortion involves three loci on the Bogota X chromosome and one locus on the autosomes. The genetic bases of hybrid sterility and segregation distortion are at least partially—but not completely—overlapping. My results lay the foundation for fine-mapping experiments to identify the complete set of genes that interact with Overdrive. While individual genes that cause hybrid sterility or inviability have been identified in a few cases, my analysis provides a comprehensive look at the genetic architecture of all components of a hybrid incompatibility underlying F1 hybrid sterility. Such an analysis would likely be unfeasible for most species pairs due to their divergence time and emphasizes the importance of young species pairs such as the D. pseudoobscura subspecies studied here. PMID:21900263

Genetic architecture of male sterility and segregation distortion in Drosophila pseudoobscura Bogota-USA hybrids.

Science.gov (United States)

Phadnis, Nitin

2011-11-01

Understanding the genetic basis of reproductive isolation between recently diverged species is a central problem in evolutionary genetics. Here, I present analyses of the genetic architecture underlying hybrid male sterility and segregation distortion between the Bogota and USA subspecies of Drosophila pseudoobscura. Previously, a single gene, Overdrive (Ovd), was shown to be necessary but not sufficient for both male sterility and segregation distortion in F(1) hybrids between these subspecies, requiring several interacting partner loci for full manifestation of hybrid phenomena. I map these partner loci separately on the Bogota X chromosome and USA autosomes using a combination of different mapping strategies. I find that hybrid sterility involves a single hybrid incompatibility of at least seven interacting partner genes that includes three large-effect loci. Segregation distortion involves three loci on the Bogota X chromosome and one locus on the autosomes. The genetic bases of hybrid sterility and segregation distortion are at least partially--but not completely--overlapping. My results lay the foundation for fine-mapping experiments to identify the complete set of genes that interact with Overdrive. While individual genes that cause hybrid sterility or inviability have been identified in a few cases, my analysis provides a comprehensive look at the genetic architecture of all components of a hybrid incompatibility underlying F(1) hybrid sterility. Such an analysis would likely be unfeasible for most species pairs due to their divergence time and emphasizes the importance of young species pairs such as the D. pseudoobscura subspecies studied here.

The Relationship Between Transcript Expression Levels of Nuclear Encoded (TFAM, NRF1 and Mitochondrial Encoded (MT-CO1 Genes in Single Human Oocytes During Oocyte Maturation

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Ghaffari Novin M.

2015-06-01

Full Text Available In some cases of infertility in women, human oocytes fail to mature when they reach the metaphase II (MII stage. Mitochondria plays an important role in oocyte maturation. A large number of mitochondrial DNA (mtDNA, copied in oocytes, is essential for providing adenosine triphosphate (ATP during oocyte maturation. The purpose of this study was to identify the relationship between transcript expression levels of the mitochondrial encoded gene (MT-CO1 and two nuclear encoded genes, nuclear respiratory factor 1 (NRF1 and mitochondrial transcription factor A (TFAM in various stages of human oocyte maturation. Nine consenting patients, age 21-35 years old, with male factors were selected for ovarian stimulation and intracytoplasmic sperm injection (ICSI procedures. mRNA levels of mitochondrial- related genes were performed by singlecell TaqMan® quantitative real-time polymerase chain reaction (qRT-PCR. There was no significant relationship between the relative expression levels in germinal vesicle (GV stage oocytes (p = 0.62. On the contrary, a significant relationship was seen between the relative expression levels of TFAM and NRF1 and the MT-CO1 genes at the stages of metaphase I (MI and MII (p = 0.03 and p = 0.002. A relationship exists between the transcript expression levels of TFAM and NRF1, and MT-CO1 genes in various stages of human oocyte maturation.

POSSIBLE RELATED FUNCTIONS OF THE NON-HOMOLOGOUS CO-REGULATED GENE PAIR PDCD10 AND SERPINI1

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Concetta Scimone

2017-04-01

Full Text Available Gene expression in mammalians is a very finely controlled mechanism, and bidirectional promoters can be considered one of the most compelling examples of the accuracy of genic expression coordination. As recently reported, a bidirectional promoter regulates the expression of the PDCD10(whose mutations cause familial Cerebral Cavernous Malformations (CCMs and SERPINI1 gene pair, even though they are non-homologous genes. The aim of this study was to identify any potential common roles of these two coregulated genes. An in-silico approach was used to identify functional correlations, using the BioGraph, IPA® and Cytoscape tools and the KEGG pathway database. The results obtained show that PDCD10 and SERPINI1 may co-regulate some cellular processes, particularly those related to focal adhesion maintenance. All common pathways identified for PDCD10 and SERPINI1 are closely associated with the pathogenic characteristics of CCMs; we thus hypothesize that genes involved in these networks may contribute to the development of CCMs.

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.

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Li, Lin; Briskine, Roman; Schaefer, Robert; Schnable, Patrick S; Myers, Chad L; Flagel, Lex E; Springer, Nathan M; Muehlbauer, Gary J

2016-11-04

Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant subgenome. However, the landscape of co-expression network divergence of duplicate genes in maize is still largely uncharacterized. To address the consequence of gene duplication on co-expression network divergence, we developed a gene co-expression network from RNA-seq data derived from 64 different tissues/stages of the maize reference inbred-B73. WGD, tandem and inserted gene duplications exhibited distinct regulatory divergence. Inserted duplicate genes were more likely to be singletons in the co-expression networks, while WGD duplicate genes were likely to be co-expressed with other genes. Tandem duplicate genes were enriched in the co-expression pattern where co-expressed genes were nearly identical for the duplicates in the network. Older gene duplications exhibit more extensive co-expression variation than younger duplications. Overall, non-syntenic genes primarily from inserted duplications show more co-expression divergence. Also, such enlarged co-expression divergence is significantly related to duplication age. Moreover, subgenome dominance was not observed in the co-expression networks - maize1 and maize2 exhibit similar levels of intra subgenome correlations. Intriguingly, the level of inter subgenome co-expression was similar to the level of intra subgenome correlations, and genes from specific subgenomes were not likely to be the enriched in co-expression network modules and the hub genes were not predominantly from any specific subgenomes in maize. Our work provides a comprehensive analysis of maize co-expression network divergence for three different types of gene duplications and identifies potential relationships between duplication types

Marker-assisted pyramiding of brown planthopper (Nilaparvata lugens Stål) resistance genes Bph1 and Bph2 on rice chromosome 12.

Science.gov (United States)

Sharma, Prem N; Torii, Akihide; Takumi, Shigeo; Mori, Naoki; Nakamura, Chiharu

2004-01-01

Brown planthopper (BPH) (Nilaparvata lugens Stål) is a significant insect pest of rice (Oryza sativa L.). We constructed a gene-pyramided japonica line, in which two BPH resistance genes Bph1 and Bph2 on the long arm of chromosome 12 independently derived from two indica resistance lines were combined through the recombinant selection. The gene-pyramiding was achieved based on the previously constructed high-resolution linkage maps of the two genes. Two co-dominant and four dominant PCR-based markers flanking the loci were used to select for a homozygous recombinant line in a segregating population that was derived from a cross between the parental homozygous single-gene introgression lines. BPH bioassay showed that the resistance level of the pyramided line was equivalent to that of the Bph1-single introgression line, which showed a higher level of resistance than the Bph2-single introgression line. The pyramid line should provide a useful experimental means for studying the fine structure of the chromosomal region covering these two major BPH resistance genes.

Ala397Asp mutation of myosin VIIA gene segregating in a Spanish family with type-Ib Usher syndrome.

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Espinós, C; Millán, J M; Sánchez, F; Beneyto, M; Nájera, C

1998-06-01

In the current study, 12 Spanish families affected by type-I Usher syndrome, that was previously linked to chromosome 11q, were screened for the presence of mutations in the N-terminal coding portion of the motor domain of the myosin VIIA gene by single-strand conformation polymorphism analysis of the first 14 exons. A mutation (Ala397Asp) segregating with the disease was identified, and several polymorphisms were also detected. It is presumed that the other USHIB mutations in these families could be located in the unscreened regions of the gene.

Effect of RenNew-D as a sterilant on the performance of reused dialyzers.

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Gagnon, R F; Adkar, V; Kaye, M

1986-12-01

RenNew-D (Alcide), a novel demand-release sporocidal agent, was employed instead of formaldehyde in the reprocessing for reuse of cuprophan hollow fiber dialyzers (Gambro) and the performance of these dialyzers was evaluated over 40 consecutive dialyses in six patients on maintenance hemodialysis. When RenNew-D was part of automated reprocessing performed with 4.3% bleach as specified by the manufacturer (Lixivitron), dialyzer survival was prolonged (16.7 +/- 7.2 uses) and hemodialysis neutropenia was unchanged with reuse. When RenNew-D was part of manual reprocessing conducted in the absence of bleach, marked improvement in dialyzer biocompatibility was observed but with a decreased survival (4.8 +/- 3.0). The majority of dialyzer failures were due to a fall in fiber bundle volume below a 85% set limit. Small solute clearances were maintained with both types of reprocessing. Dialyses were well tolerated throughout. Our data suggest that RenNew-D is a safe and efficacious product which can serve as a valuable alternative to formaldehyde for the purpose of dialyzer reuse.

ESR1 Is Co-Expressed with Closely Adjacent Uncharacterised Genes Spanning a Breast Cancer Susceptibility Locus at 6q25.1

Science.gov (United States)

Dunbier, Anita K.; Anderson, Helen; Ghazoui, Zara; Lopez-Knowles, Elena; Pancholi, Sunil; Ribas, Ricardo; Drury, Suzanne; Sidhu, Kally; Leary, Alexandra; Martin, Lesley-Ann; Dowsett, Mitch

2011-01-01

Approximately 80% of human breast carcinomas present as oestrogen receptor α-positive (ER+ve) disease, and ER status is a critical factor in treatment decision-making. Recently, single nucleotide polymorphisms (SNPs) in the region immediately upstream of the ER gene (ESR1) on 6q25.1 have been associated with breast cancer risk. Our investigation of factors associated with the level of expression of ESR1 in ER+ve tumours has revealed unexpected associations between genes in this region and ESR1 expression that are important to consider in studies of the genetic causes of breast cancer risk. RNA from tumour biopsies taken from 104 postmenopausal women before and after 2 weeks treatment with an aromatase (oestrogen synthase) inhibitor was analyzed on Illumina 48K microarrays. Multiple-testing corrected Spearman correlation revealed that three previously uncharacterized open reading frames (ORFs) located immediately upstream of ESR1, C6ORF96, C6ORF97, and C6ORF211 were highly correlated with ESR1 (Rs = 0.67, 0.64, and 0.55 respectively, FDRaccount for the correlations. The correlations were maintained in cultured cells. An ERα antagonist did not affect the ORFs' expression or their correlation with ESR1, suggesting their transcriptional co-activation is not directly mediated by ERα. siRNA inhibition of C6ORF211 suppressed proliferation in MCF7 cells, and C6ORF211 positively correlated with a proliferation metagene in tumours. In contrast, C6ORF97 expression correlated negatively with the metagene and predicted for improved disease-free survival in a tamoxifen-treated published dataset, independently of ESR1. Our observations suggest that some of the biological effects previously attributed to ER could be mediated and/or modified by these co-expressed genes. The co-expression and function of these genes may be important influences on the recently identified relationship between SNPs in this region and breast cancer risk. PMID:21552322

Mutation in the gene encoding 1-aminocyclopropane-1-carboxylate synthase 4 (CitACS4) led to andromonoecy in watermelon.

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Ji, Gaojie; Zhang, Jie; Zhang, Haiying; Sun, Honghe; Gong, Guoyi; Shi, Jianting; Tian, Shouwei; Guo, Shaogui; Ren, Yi; Shen, Huolin; Gao, Junping; Xu, Yong

2016-09-01

Although it has been reported previously that ethylene plays a critical role in sex determination in cucurbit species, how the andromonoecy that carries both the male and hermaphroditic flowers is determined in watermelon is still unknown. Here we showed that the watermelon gene 1-aminocyclopropane-1-carboxylate synthase 4 (CitACS4), expressed specifically in carpel primordia, determines the andromonoecy in watermelon. Among four single nucleotide polymorphism (SNPs) and one InDel identified in the coding region of CitACS4, the C364W mutation located in the conserved box 6 was co-segregated with andromonoecy. Enzymatic analyses showed that the C364W mutation caused a reduced activity in CitACS4. We believe that the reduced CitACS4 activity may hamper the programmed cell death in stamen primordia, leading to the formation of hermaphroditic flowers. © 2016 Institute of Botany, Chinese Academy of Sciences.

René Sand (Belgium, President 1946 – 1953

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2008-07-01

Full Text Available The extraordinary significance of the life and work of René Sand lies in his central position as a mediator, promoter and coordinator of social work on an increasingly international level during the interwar-period and it can hardly be overestimated.

Analysis of T-DNA integration and generative segregation in transgenic winter triticale (x Triticosecale Wittmack

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Hensel Goetz

2012-09-01

Full Text Available Abstract Background While the genetic transformation of the major cereal crops has become relatively routine, to date only a few reports were published on transgenic triticale, and robust data on T-DNA integration and segregation have not been available in this species. Results Here, we present a comprehensive analysis of stable transgenic winter triticale cv. Bogo carrying the selectable marker gene HYGROMYCIN PHOSPHOTRANSFERASE (HPT and a synthetic green fluorescent protein gene (gfp. Progeny of four independent transgenic plants were comprehensively investigated with regard to the number of integrated T-DNA copies, the number of plant genomic integration loci, the integrity and functionality of individual T-DNA copies, as well as the segregation of transgenes in T1 and T2 generations, which also enabled us to identify homozygous transgenic lines. The truncation of some integrated T-DNAs at their left end along with the occurrence of independent segregation of multiple T-DNAs unintendedly resulted in a single-copy segregant that is selectable marker-free and homozygous for the gfp gene. The heritable expression of gfp driven by the maize UBI-1 promoter was demonstrated by confocal laser scanning microscopy. Conclusions The used transformation method is a valuable tool for the genetic engineering of triticale. Here we show that comprehensive molecular analyses are required for the correct interpretation of phenotypic data collected from the transgenic plants.

A role for recombination junctions in the segregation of mitochondrial DNA in yeast.

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Lockshon, D; Zweifel, S G; Freeman-Cook, L L; Lorimer, H E; Brewer, B J; Fangman, W L

1995-06-16

In S. cerevisiae, mitochondrial DNA (mtDNA) molecules, in spite of their high copy number, segregate as if there were a small number of heritable units. The rapid segregation of mitochondrial genomes can be analyzed using mtDNA deletion variants. These small, amplified genomes segregate preferentially from mixed zygotes relative to wild-type mtDNA. This segregation advantage is abolished by mutations in a gene, MGT1, that encodes a recombination junction-resolving enzyme. We show here that resolvase deficiency causes a larger proportion of molecules to be linked together by recombination junctions, resulting in the aggregation of mtDNA into a small number of cytological structures. This change in mtDNA structure can account for the increased mitotic loss of mtDNA and the altered pattern of mtDNA segregation from zygotes. We propose that the level of unresolved recombination junctions influences the number of heritable units of mtDNA.

Atomic scale study of grain boundary segregation before carbide nucleation in Ni–Cr–Fe Alloys

Energy Technology Data Exchange (ETDEWEB)

Li, Hui, E-mail: huili@shu.edu.cn [Key Laboratory for Microstructures, Shanghai University, Shanghai 200444 (China); Institute of Materials, Shanghai University, Shanghai 200072 (China); Xia, Shuang [Institute of Materials, Shanghai University, Shanghai 200072 (China); Liu, Wenqing [Key Laboratory for Microstructures, Shanghai University, Shanghai 200444 (China); Liu, Tingguang; Zhou, Bangxin [Institute of Materials, Shanghai University, Shanghai 200072 (China)

2013-08-15

Highlights: • Impurities segregated at grain boundaries were observed by atom probe tomography. • The comparison of segregation features in two Ni–Cr–Fe alloys was studied by APT. • C and Cr atoms co-segregated at grain boundaries before carbide precipitation. -- Abstract: Three dimensional chemical information concerning grain boundary segregation before carbide nucleation was characterized by atom probe tomography in two Ni–Cr–Fe alloys which were aged at 500 °C for 0.5 h after homogenizing treatment. B, C and Si atoms segregation at grain boundary in Alloy 690 was observed. B, C, N and P atoms segregation at grain boundary in 304 austenitic stainless steel was observed. C atoms co-segregation with Cr atoms at the grain boundaries both in Alloy 690 and 304 austenitic stainless steel was found, and its effect on the carbide nucleation was discussed. The amount of each segregated element at grain boundaries in the two Ni–Cr–Fe alloys were analyzed quantitatively. Comparison of the grain boundary segregation features of the two Ni–Cr–Fe alloys were carried out based on the experimental results.

Combined equilibrium and non-equilibrium phosphorus segregation to grain boundaries in a 2.25Cr1Mo steel

International Nuclear Information System (INIS)

Song, S.-H.; Shen, D.-D.; Yuan, Z.-X.; Liu, J.; Xu, T.-D.; Weng, L.-Q.

2003-01-01

Grain boundary segregation of phosphorus in a P-doped 2.25Cr1Mo steel during ageing at 540 deg. C after quenching from 980 deg. C is examined by Auger electron spectroscopy. The segregation is a combined effect of equilibrium segregation and non-equilibrium segregation. The effect of phosphorus non-equilibrium segregation is to enhance the kinetics of its equilibrium segregation

Source Segregation and Collection of Source-Segregated Waste

DEFF Research Database (Denmark)

Christensen, Thomas Højlund; Matsufuji, Y.

2011-01-01

of optimal handling of the waste. But in a few cases, the waste must also be separated at source, for example removing the protective plastic cover from a commercial advertisement received by mail, prior to putting the advertisement into the waste collection bin for recyclable paper. These issues are often...... in wastes segregation addressing: - Purpose of source segregation. - Segregation criteria and guidance. - Segregation potentials and efficiencies. - Systems for collecting segregated fraction....

[Polymorphisms of the multiple drug resistance gene (MDR1) in Mapuche, Mestizo and Maori populations in Chile].

Science.gov (United States)

Wielandt, Ana María; Vollrath, Valeska; Chianale, José

2004-09-01

There are significant differences in drug responses among different ethnic groups. The multidrug transporter P-gp, encoded by the MDR1 gene, plays a key role in determining drug bioavailability, and an association between a polymorphism in exon 26 (C3435T) and lower P-gp expression has been found. The co-segregation of this polymorphism with the polymorphism in exon 12 (C1236T) and in exon 21 (G2677T/A) determines several MDR1 haplotypes in humans. To characterize the polymorphisms of exons 26, 21 and 12 of the MDR1 gene in different Chilean populations. Using a polymerase chain reaction and restriction fragment length polymorphism technique, we studied the allelic frequencies and the distribution of MDR1 haplotypes in 3 Chilean populations: Mestizo (n=104), Mapuche (n=96, living in the National Reservation of the Huapi Island, Ranico Lake) and Maori (n=52, living in Eastern Island). The frequency of the normal MDR1*1 haplotype, without mutations, was lower in Mapuches than in Mestizos or Maoris (p0.0.5), but lower than the frequencies reported in Caucasians or Asians (p<0.05). We found significant differences in the frequencies of genetic polymorphisms of the MDR1 gene in Chilean populations, related to the ethnic origins of our ancestors.

Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes

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Allan Andrew C

2008-07-01

Full Text Available Abstract Background Transcription factors (TFs co-ordinately regulate target genes that are dispersed throughout the genome. This co-ordinate regulation is achieved, in part, through the interaction of transcription factors with conserved cis-regulatory motifs that are in close proximity to the target genes. While much is known about the families of transcription factors that regulate gene expression in plants, there are few well characterised cis-regulatory motifs. In Arabidopsis, over-expression of the MYB transcription factor PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT 1 leads to transgenic plants with elevated anthocyanin levels due to the co-ordinated up-regulation of genes in the anthocyanin biosynthetic pathway. In addition to the anthocyanin biosynthetic genes, there are a number of un-associated genes that also change in expression level. This may be a direct or indirect consequence of the over-expression of PAP1. Results Oligo array analysis of PAP1 over-expression Arabidopsis plants identified genes co-ordinately up-regulated in response to the elevated expression of this transcription factor. Transient assays on the promoter regions of 33 of these up-regulated genes identified eight promoter fragments that were transactivated by PAP1. Bioinformatic analysis on these promoters revealed a common cis-regulatory motif that we showed is required for PAP1 dependent transactivation. Conclusion Co-ordinated gene regulation by individual transcription factors is a complex collection of both direct and indirect effects. Transient transactivation assays provide a rapid method to identify direct target genes from indirect target genes. Bioinformatic analysis of the promoters of these direct target genes is able to locate motifs that are common to this sub-set of promoters, which is impossible to identify with the larger set of direct and indirect target genes. While this type of analysis does not prove a direct interaction between protein and DNA

Meiotic and pedigree segregation analyses in carriers of t(4;8)(p16;p23.1) differing in localization of breakpoint positions at 4p subband 4p16.3 and 4p16.1.

Science.gov (United States)

Midro, Alina T; Zollino, Marcella; Wiland, Ewa; Panasiuk, Barbara; Iwanowski, Piotr S; Murdolo, Marina; Śmigiel, Robert; Sąsiadek, Maria; Pilch, Jacek; Kurpisz, Maciej

2016-02-01

The purpose of this study was to compare meiotic segregation in sperm cells from two carriers with t(4;8)(p16;p23.1) reciprocal chromosome translocations (RCTs), differing in localization of the breakpoint positions at the 4p subband-namely, 4p16.3 (carrier 1) and 4p16.1 (carrier 2)-and to compare data of the pedigree analyses performed by direct method. Three-color fluorescent in situ hybridization (FISH) on sperm cells and FISH mapping for the evaluation of the breakpoint positions, data from pedigrees, and direct segregation analysis of the pedigrees were performed. Similar proportions of normal/balanced and unbalanced sperm cells were found in both carriers. The most common was an alternate type of segregation (about 52 % and about 48 %, respectively). Unbalanced adjacent I and adjacent II karyotypes were found in similar proportions about 15 %. The direct segregation analysis (following Stengel-Rutkowski) of the pedigree of carriers of t(4;8)(p16.1;p23.1) was performed and results were compared with the data of the pedigree segregation analysis obtained earlier through the indirect method. The probability of live-born progeny with unbalanced karyotype for carriers of t(4;8)(p16.1;p23.1) was moderately high at 18.8 %-comparable to the value obtained using the indirect method for the same carriership, which was 12 %. This was, however, markedly lower than the value of 41.2 % obtained through the pedigree segregation indirect analysis estimated for carriers of t(4;8)(p16.3;p23.1), perhaps due to the unique composition of genes present within the 4p16.1-4p 16.3 region. Revealed differences in pedigree segregation analysis did not correspond to the very similar profile of meiotic segregation patterns presented by carrier 1 and carrier 2. Most probably, such discordances may be due to differences in embryo survival rates arising from different genetic backgrounds.

Chromium downregulates the expression of Acetyl CoA Carboxylase 1 gene in lipogenic tissues of domestic goats: a potential strategy for meat quality improvement.

Science.gov (United States)

Najafpanah, Mohammad Javad; Sadeghi, Mostafa; Zali, Abolfazl; Moradi-Shahrebabak, Hossein; Mousapour, Hojatollah

2014-06-15

Acetyl CoA Carboxylase 1 (ACC1) is a biotin-dependent enzyme that catalyzes the carboxylation of Acetyl CoA to form Malonyl CoA, the key intermediate metabolite in fatty acid synthesis. In this study, the mRNA expression of the ACC1 gene was evaluated in four different tissues (liver, visceral fat, subcutaneous fat, and longissimus muscle) of the domestic goat (Capra hircus) kids feeding on four different levels of trivalent chromium (0, 0.5, 1, and 1.5mg/day) as food supplementation. RT-qPCR technique was used for expression analyses and heat shock protein 90 gene (HSP-90) was considered as reference gene for data normalization. Our results revealed that 1.5mg/day chromium significantly reduced the expression of the ACC1 gene in liver, visceral fat, and subcutaneous fat tissues, but not in longissimus muscles (Pmeat quality in domestic animals. Copyright © 2014 Elsevier B.V. All rights reserved.

Modification of barley powdery mildew resistance controlled by the gene M1-a212

International Nuclear Information System (INIS)

Torp, J.; Joergensen, J.H.

1989-01-01

Full text: The barley line Sultan 5 carries resistance gene M1-a12. Seeds were treated with EMS or NaN 3 . Among 10381 M 1 -spike progenies inoculated with M1-a12 a-virulent isolates of Erysiphe graminis, 25 segregated for less resistant infection type. Among 10 mutants analyzed, 9 had mutant allels of M1-a12 and one had a recessive mutant gene in a different locus acting as a ''suppressor'' of M1-a12. (author)

A novel heterozygous mutation in the Indian hedgehog gene (IHH) is associated with brachydactyly type A1 in a Chinese family.

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Liu, Mugen; Wang, Xu; Cai, Zhou; Tang, Zhaohui; Cao, Kangsheng; Liang, Bo; Ren, Xiang; Liu, Jing Yu; Wang, Qing K

2006-01-01

Brachydactyly type A1 (BDA1) is caused by mutations in the Indian hedgehog gene, IHH, on chromosome 2q35-36. In this study, a large five-generation Chinese family with BDA1 was identified and characterized. All affected family members demonstrated significant homogeneous phenotype and some unique clinical features different from those associated with the reported BDA1 mutations in IHH. Linkage analysis showed that the BDA1 gene in the family was linked to marker D2S126 close to IHH with a LOD score of 4.74 at a recombination fraction of 0. DNA sequence analysis revealed a heterozygous C to T transition at nucleotide 461 of IHH, resulting in a novel T154I substitution. The T154I mutation co-segregated with all affected individuals in the family, and was not present in normal family members or 200 normal controls. These results expand the spectrum of clinical phenotype associated with IHH mutations.

Linkage of genes for laminin B1 and B2 subunits on chromosome 1 in mouse.

Science.gov (United States)

Elliott, R W; Barlow, D; Hogan, B L

1985-08-01

We have used cDNA clones for the B1 and B2 subunits of laminin to find restriction fragment length DNA polymorphisms for the genes encoding these polypeptides in the mouse. Three alleles were found for LamB2 and two for LamB1 among the inbred mouse strains. The segregation of these polymorphisms among recombinant inbred strains showed that these genes are tightly linked in the central region of mouse Chromosome 1 between Sas-1 and Ly-m22, 7.4 +/- 3.2 cM distal to the Pep-3 locus. There is no evidence in the mouse for pseudogenes for these proteins.

ESR1 is co-expressed with closely adjacent uncharacterised genes spanning a breast cancer susceptibility locus at 6q25.1.

Directory of Open Access Journals (Sweden)

Anita K Dunbier

2011-04-01

Full Text Available Approximately 80% of human breast carcinomas present as oestrogen receptor α-positive (ER+ve disease, and ER status is a critical factor in treatment decision-making. Recently, single nucleotide polymorphisms (SNPs in the region immediately upstream of the ER gene (ESR1 on 6q25.1 have been associated with breast cancer risk. Our investigation of factors associated with the level of expression of ESR1 in ER+ve tumours has revealed unexpected associations between genes in this region and ESR1 expression that are important to consider in studies of the genetic causes of breast cancer risk. RNA from tumour biopsies taken from 104 postmenopausal women before and after 2 weeks treatment with an aromatase (oestrogen synthase inhibitor was analyzed on Illumina 48K microarrays. Multiple-testing corrected Spearman correlation revealed that three previously uncharacterized open reading frames (ORFs located immediately upstream of ESR1, C6ORF96, C6ORF97, and C6ORF211 were highly correlated with ESR1 (Rs =  0.67, 0.64, and 0.55 respectively, FDR<1 × 10(-7. Publicly available datasets confirmed this relationship in other groups of ER+ve tumours. DNA copy number changes did not account for the correlations. The correlations were maintained in cultured cells. An ERα antagonist did not affect the ORFs' expression or their correlation with ESR1, suggesting their transcriptional co-activation is not directly mediated by ERα. siRNA inhibition of C6ORF211 suppressed proliferation in MCF7 cells, and C6ORF211 positively correlated with a proliferation metagene in tumours. In contrast, C6ORF97 expression correlated negatively with the metagene and predicted for improved disease-free survival in a tamoxifen-treated published dataset, independently of ESR1. Our observations suggest that some of the biological effects previously attributed to ER could be mediated and/or modified by these co-expressed genes. The co-expression and function of these genes may be

Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.

Science.gov (United States)

Li, Jin; Wang, Limei; Guo, Maozu; Zhang, Ruijie; Dai, Qiguo; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Xuan, Ping; Zhang, Mingming

2015-01-01

In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.

First-principles investigation into the effect of Cr on the segregation of multi-H at the Fe Σ3 (1 1 1) grain boundary

Energy Technology Data Exchange (ETDEWEB)

He, Bingling; Xiao, Wei; Hao, Wei [School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Tian, Zhixue, E-mail: tian@cp.prec.eng.osaka-u.ac.jp [Division of Precision Science and Technology and Applied Physics, Graduate School of Engineering, Osaka University, 2-1, Yamada-oka, Suita, Osaka 565-0871 (Japan)

2013-10-15

First-principles calculations were carried out to investigate the effect of Cr on segregation of multiple H atoms in the Σ3 (1 1 1) grain boundary in bcc Fe. In the absence of Cr, four H atoms can be trapped at the interstitial site of the Fe grain boundary (areal density: 28 nm{sup −2}), and no H{sub 2} molecules are formed. The presence of Cr, however, suppresses the segregation tendency of H and only two H atoms can be trapped at this grain boundary. Although the volume expansion associated with the segregation of Cr to the grain boundary promotes H segregation, such a booting effect is unable to remedy the repulsion of H resulted from charge density increase in the grain boundary core. As a consequence, Cr mitigates H aggregation at the Σ3 (1 1 1) grain boundary in bcc Fe.

BcII RFLP for the human vimentin gene

Energy Technology Data Exchange (ETDEWEB)

Marcus, E M; Smith, B A; Telenius, H; Ponder, B A.J.; Mathew, C G.P. [Haddow Laboratories, Surrey (England); Landsvater, R M; Buys, C H.C.M. [State Univ. of Groningen (Netherlands); Ferrari, S [Temple University Medical School, Philadelphia, PA (USA)

1988-09-26

A 1.1 kb cDNA clone (hp4F1) encoding the human vimentin gene was identified in a human library by screening with 4F1, a hamster vimentin cDNA. BcII (TGATCA) recognizes a two allele polymorphism: bands A1 at 8.1 kb, and A2 at 3.6 kb. The allele frequency was determined in 47 unrelated Caucasian individuals. The RFLP was mapped to chromosome 10pter-10q23 using somatic cell hybrids and to 10p13 by in situ hybridization. Co-dominant segregation was observed in 2 informative families.

Interface segregation behavior in thermal aged austenitic precipitation strengthened stainless steel.

Science.gov (United States)

Li, Hui; Song, Hui; Liu, Wenqing; Xia, Shuang; Zhou, Bangxin; Su, Cheng; Ding, Wenyan

2015-12-01

The segregation of various elements at grain boundaries, precipitate/matrix interfaces were analyzed using atom probe tomography in an austenitic precipitation strengthened stainless steel aged at 750 °C for different time. Segregation of P, B and C at all types of interfaces in all the specimens were observed. However, Si segregated at all types of interfaces only in the specimen aged for 16 h. Enrichment of Ti at grain boundaries was evident in the specimen aged for 16 h, while Ti did not segregate at other interfaces. Mo varied considerably among interface types, e.g. from segregated at grain boundaries in the specimens after all the aging time to never segregate at γ'/γ phase interfaces. Cr co-segregated with C at grain boundaries, although carbides still did not nucleate at grain boundaries yet. Despite segregation tendency variations in different interface types, the segregation tendency evolution variation of different elements depending aging time were analyzed among all types of interfaces. Based on the experimental results, the enrichment factors, Gibbs interface excess and segregation free energies of segregated elements were calculated and discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

MCNP-REN: a Monte Carlo tool for neutron detector design

International Nuclear Information System (INIS)

Abhold, M.E.; Baker, M.C.

2002-01-01

The development of neutron detectors makes extensive use of the predictions of detector response through the use of Monte Carlo techniques in conjunction with the point reactor model. Unfortunately, the point reactor model fails to accurately predict detector response in common applications. For this reason, the general Monte Carlo code developed at Los Alamos National Laboratory, Monte Carlo N-Particle (MCNP), was modified to simulate the pulse streams that would be generated by a neutron detector and normally analyzed by a shift register. This modified code, MCNP-Random Exponentially Distributed Neutron Source (MCNP-REN), along with the Time Analysis Program, predicts neutron detector response without using the point reactor model, making it unnecessary for the user to decide whether or not the assumptions of the point model are met for their application. MCNP-REN is capable of simulating standard neutron coincidence counting as well as neutron multiplicity counting. Measurements of mixed oxide fresh fuel were taken with the Underwater Coincidence Counter, and measurements of highly enriched uranium reactor fuel were taken with the active neutron interrogation Research Reactor Fuel Counter and compared to calculation. Simulations completed for other detector design applications are described. The method used in MCNP-REN is demonstrated to be fundamentally sound and shown to eliminate the need to use the point model for detector performance predictions

Radiation-induced segregation on defect clusters in single-phase concentrated solid-solution alloys

International Nuclear Information System (INIS)

Lu, Chenyang; Yang, Taini; Jin, Ke; Gao, Ning; Xiu, Pengyuan; Zhang, Yanwen; Gao, Fei; Bei, Hongbin; Weber, William J.; Sun, Kai; Dong, Yan; Wang, Lumin

2017-01-01

A group of single-phase concentrated solid-solution alloys (SP-CSAs), including NiFe, NiCoFe, NiCoFeCr, as well as a high entropy alloy NiCoFeCrMn, was irradiated with 3 MeV Ni"2"+ ions at 773 K to a fluence of 5 × 10"1"6 ions/cm"2 for the study of radiation response with increasing compositional complexity. Advanced transmission electron microscopy (TEM) with electron energy loss spectroscopy (EELS) was used to characterize the dislocation loop distribution and radiation-induced segregation (RIS) on defect clusters in the SP-CSAs. The results show that a higher fraction of faulted loops exists in the more compositionally complex alloys, which indicate that increasing compositional complexity can extend the incubation period and delay loop growth. The RIS behaviors of each element in the SP-CSAs were observed as follows: Ni and Co tend to enrich, but Cr, Fe and Mn prefer to deplete near the defect clusters. RIS level can be significantly suppressed by increasing compositional complexity due to the sluggish atom diffusion. According to molecular static (MS) simulations, “disk” like segregations may form near the faulted dislocation loops in the SP-CSAs. Segregated elements tend to distribute around the whole faulted loop as a disk rather than only around the edge of the loop.

Monograph of Keçiören Municipality

Directory of Open Access Journals (Sweden)

Savaş Zafer Şahin

2015-12-01

Full Text Available In Turkey, urban administration can be defined from a judicial perspective as the bundle of powers vested in municipalities. It is known that throughout republican history, municipalities, using these powers, have differentiated themselves via their own internal dynamics in parallel to the evolution of public policy and changes in legislation. Yet, it is obvious that there are important gaps in understanding this differentiation taking into consideration the structural conditions of individual municipalities. In particular, in order to thoroughly understand municipalities, it is important to consider periodical pictures of how each municipality has been affected by waves of decentralization and centralization experienced over the last thirty years. In this respect, this monograph, using the same monographic approach developed for the Çankaya Municipality, provides a picture of the existing situation of Ankara’s Keçiören Municipality and presents related problems and potential. This monograph, based on qualitative and quantitative research, presents a holistic evaluation of Keçiören Municipality in terms of its external environment, provision of services, decision-making processes, use of technology and communications.

Interface segregation behavior in thermal aged austenitic precipitation strengthened stainless steel

Energy Technology Data Exchange (ETDEWEB)

Li, Hui [Key Laboratory for Microstructures, Shanghai University, Shanghai 200444 (China); Technical Department, Jiuli Hi-Tech Metals Co., Ltd., Huzhou 313008 (China); Song, Hui [Key Laboratory for Microstructures, Shanghai University, Shanghai 200444 (China); Liu, Wenqing, E-mail: wqliu@staff.shu.edu.cn [Key Laboratory for Microstructures, Shanghai University, Shanghai 200444 (China); Institute of Materials, Shanghai University, Shanghai 200072 (China); Xia, Shuang; Zhou, Bangxin [Institute of Materials, Shanghai University, Shanghai 200072 (China); Su, Cheng; Ding, Wenyan [Technical Department, Jiuli Hi-Tech Metals Co., Ltd., Huzhou 313008 (China)

2015-12-15

The segregation of various elements at grain boundaries, precipitate/matrix interfaces were analyzed using atom probe tomography in an austenitic precipitation strengthened stainless steel aged at 750 °C for different time. Segregation of P, B and C at all types of interfaces in all the specimens were observed. However, Si segregated at all types of interfaces only in the specimen aged for 16 h. Enrichment of Ti at grain boundaries was evident in the specimen aged for 16 h, while Ti did not segregate at other interfaces. Mo varied considerably among interface types, e.g. from segregated at grain boundaries in the specimens after all the aging time to never segregate at γ′/γ phase interfaces. Cr co-segregated with C at grain boundaries, although carbides still did not nucleate at grain boundaries yet. Despite segregation tendency variations in different interface types, the segregation tendency evolution variation of different elements depending aging time were analyzed among all types of interfaces. Based on the experimental results, the enrichment factors, Gibbs interface excess and segregation free energies of segregated elements were calculated and discussed. - Highlights: • Solute atoms segregated at interfaces were analyzed in an austenitic stainless steel. • The comparison of segregation in different interfaces was studied by APT. • The evolution of interface segregation during aging treatment was discussed.

Genetic analysis of fertility restoration genes for WAtype cytoplasmic ...

African Journals Online (AJOL)

Pollen staining test with 1% I2KI solution showed segregation ratio of 15:1 (fertile: sterile), representing two nuclear independent dominant genes controlling the trait carried by fertile parent DN-33-18. Segregation for spikelet fertility in F2 confirmed the results of pollen fertility test. Molecular tagging of fertility restorer genes ...

A missense mutation in the CRBN gene that segregates with intellectual disability and self-mutilating behaviour in a consanguineous Saudi family.

Science.gov (United States)

Sheereen, Atia; Alaamery, Manal; Bawazeer, Shahad; Al Yafee, Yusra; Massadeh, Salam; Eyaid, Wafaa

2017-04-01

Autosomal-recessive non-syndromic intellectual disability (ARNS-ID) is an aetiologically heterogeneous disorder. Although little is known about the function of human cereblon (CRBN), its relationship to mild cognitive deficits suggests that it is involved in the basic processes of human memory and learning. We aim to identify the genetic cause of intellectual disability and self-mutilation in a consanguineous Saudi family with five affected members. Clinical whole-exome sequencing was performed on the proband patient, and Sanger sequencing was done to validate and confirm segregation in other family members. A missense variant (c. 1171T>C) in the CRBN gene was identified in five individuals with severe intellectual disability (ID) in a consanguineous Saudi family. The homozygous variant was co-segregating in the family with the phenotype of severe ID, seizures and self-mutilating behaviour. The missense mutation (p.C391R) reported here results in the replacement of a conserved cysteine residue by an arginine in the CULT (cereblon domain of unknown activity, binding cellular ligands and thalidomide) domain of CRBN, which contains a zinc-binding site. These findings thus contribute to a growing list of ID disorders caused by CRBN mutations, broaden the spectrum of phenotypes attributable to ARNS-ID and provide new insight into genotype-phenotype correlations between CRBN mutations and the aetiology of ARNS-ID. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

ETV ekraanigraafika on Euroopa parimate seas / René Vilbre

Index Scriptorium Estoniae

Vilbre, René, 1970-

2011-01-01

Euroopa avalik-õiguslikle telejaamade konkurentsis valiti ETV ekraanigraafika viie parima hulka. Finaali pääses ETV kahes kategoorias - "Best design package" ja "Best use of audio". Intervjuu vaheklippide autori René Vilbrega. Võttemeeskonda kuulusid veel toimetaja Anu Välba, operaatorid Kristjan-Jaak Nuudi ja Ergo Treier

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes

Directory of Open Access Journals (Sweden)

Paules Richard S

2007-11-01

Full Text Available Abstract Background A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with microarray data and the complexity of the experimental designs make the acquisition of co-expressed genes a challenge. We developed a novel method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes, designated as EPIG. The approach utilizes the underlying structure of gene expression data to extract patterns and identify co-expressed genes that are responsive to experimental conditions. Results Through evaluation of the correlations among profiles, the magnitude of variation in gene expression profiles, and profile signal-to-noise ratio's, EPIG extracts a set of patterns representing co-expressed genes. The method is shown to work well with a simulated data set and microarray data obtained from time-series studies of dauer recovery and L1 starvation in C. elegans and after ultraviolet (UV or ionizing radiation (IR-induced DNA damage in diploid human fibroblasts. With the simulated data set, EPIG extracted the appropriate number of patterns which were more stable and homogeneous than the set of patterns that were determined using the CLICK or CAST clustering algorithms. However, CLICK performed better than EPIG and CAST with respect to the average correlation between clusters/patterns of the simulated data. With real biological data, EPIG extracted more dauer-specific patterns than CLICK. Furthermore, analysis of the IR/UV data revealed 18 unique patterns and 2661 genes out of approximately 17,000 that were identified as significantly expressed and categorized to the patterns by EPIG. The time-dependent patterns displayed similar and dissimilar responses between IR and UV treatments. Gene Ontology analysis applied to each pattern-related subset of co-expressed genes revealed underlying

Plasmid segregation mechanisms

DEFF Research Database (Denmark)

Ebersbach, G.; Gerdes, Kenn

2005-01-01

Bacterial plasmids encode partitioning (par) loci that ensure ordered plasmid segregation prior to cell division. par loci come in two types: those that encode actin-like ATPases and those that encode deviant Walker-type ATPases. ParM, the actin-like ATPase of plasmid R1, forms dynamic filaments...... that segregate plasmids paired at mid-cell to daughter cells. Like microtubules, ParM filaments exhibit dynamic instability (i.e., catastrophic decay) whose regulation is an important component of the DNA segregation process. The Walker box ParA ATPases are related to MinD and form highly dynamic, oscillating...... filaments that are required for the subcellular movement and positioning of plasmids. The role of the observed ATPase oscillation is not yet understood. However, we propose a simple model that couples plasmid segregation to ParA oscillation. The model is consistent with the observed movement...

Uncovering co-expression gene network modules regulating fruit acidity in diverse apples.

Science.gov (United States)

Bai, Yang; Dougherty, Laura; Cheng, Lailiang; Zhong, Gan-Yuan; Xu, Kenong

2015-08-16

Acidity is a major contributor to fruit quality. Several organic acids are present in apple fruit, but malic acid is predominant and determines fruit acidity. The trait is largely controlled by the Malic acid (Ma) locus, underpinning which Ma1 that putatively encodes a vacuolar aluminum-activated malate transporter1 (ALMT1)-like protein is a strong candidate gene. We hypothesize that fruit acidity is governed by a gene network in which Ma1 is key member. The goal of this study is to identify the gene network and the potential mechanisms through which the network operates. Guided by Ma1, we analyzed the transcriptomes of mature fruit of contrasting acidity from six apple accessions of genotype Ma_ (MaMa or Mama) and four of mama using RNA-seq and identified 1301 fruit acidity associated genes, among which 18 were most significant acidity genes (MSAGs). Network inferring using weighted gene co-expression network analysis (WGCNA) revealed five co-expression gene network modules of significant (P acidity. Overall, this study provides important insight into the Ma1-mediated gene network controlling acidity in mature apple fruit of diverse genetic background.

Induction of Th1 type response by DNA vaccinations with N, M, and E genes against SARS-CoV in mice

International Nuclear Information System (INIS)

Jin Huali; Xiao Chong; Chen Ze; Kang Youmin; Ma Yijie; Zhu Kaichun; Xie Qifa; Tu Yixian; Yu Yang; Wang Bin

2005-01-01

Vaccination against the SARS-CoV infection is an attractive means to control the spread of viruses in public. In this study, we employed a DNA vaccine technology with the levamisole, our newly discovered chemical adjuvant, to generate Th1 type of response. To avoid the enhancement antibody issue, genes encoding the nucleocapsid, membrane, and envelope protein of SARS-CoV were cloned and their expressions in mammalian cells were determined. After the intramuscular introduction into animals, we observed that the constructs of the E, M, and N genes could induce high levels of specific antibodies, T cell proliferations, IFN-γ, DTH responses, and in vivo cytotoxic T cells activities specifically against SARS-CoV antigens. The highest immune responses were generated by the construct encoding the nucleocapsid protein. The results suggest that the N, M, and E genes could be used as the targets to prevent SARS-CoV infection in the DNA vaccine development

RFLP for the human retinoic acid receptor gene RAR-. beta

Energy Technology Data Exchange (ETDEWEB)

Datson, N A; Oostra, B A [Erasmus Univ., Rotterdam (Netherlands); van der Saag, P T [Netherlands Institute for Developmental Biology, Utrecht (Netherlands)

1989-11-11

1.4 kb Mae I fragment containing the entire RAR-{beta} ORF was cloned into the Sma I site of pTZ18U, yielding the plasmid pCOD20. Msp I digestion of genomic DNA and hybridization with the pCOD20 probe detects a two allele polymorphism with allelic fragments of 8.1 and 7.7 kb. The human RAR-{beta} gene has been localized to the p24 band of chromosome 3. Co-dominant segregation of the alleles was observed in 4 Caucasian families.

Despite similar reduction of blood pressure and renal ANG II and ET-1 levels aliskiren but not losartan normalizes albuminuria in hypertensive Ren-2 rats

Czech Academy of Sciences Publication Activity Database

Vaňourková, Z.; Kramer, H. J.; Husková, Z.; Červenka, L.; Vaněčková, Ivana

2010-01-01

Roč. 59, č. 3 (2010), s. 339-345 ISSN 0862-8408 Grant - others:GA ČR(CZ) GA305/07/0167; GA ČR(CZ) GC305/07/J004 Institutional research plan: CEZ:AV0Z50110509 Keywords : Ren- rats * albuminuria * RAS blockade Subject RIV: FA - Cardiovascular Diseases incl. Cardiotharic Surgery Impact factor: 1.646, year: 2010

Genetics and mapping of a novel downy mildew resistance gene, Pl(18), introgressed from wild Helianthus argophyllus into cultivated sunflower (Helianthus annuus L.).

Science.gov (United States)

Qi, L L; Foley, M E; Cai, X W; Gulya, T J

2016-04-01

A novel downy mildew resistance gene, Pl(18), was introgressed from wild Helianthus argophyllus into cultivated sunflower and genetically mapped to linkage group 2 of the sunflower genome. The new germplasm, HA-DM1, carrying Pl(18) has been released to the public. Sunflower downy mildew (DM) is considered to be the most destructive foliar disease that has spread to every major sunflower-growing country of the world, except Australia. A new dominant downy mildew resistance gene (Pl 18) transferred from wild Helianthus argophyllus (PI 494573) into cultivated sunflower was mapped to linkage group (LG) 2 of the sunflower genome using bulked segregant analysis with 869 simple sequence repeat (SSR) markers. Phenotyping 142 BC1F2:3 families derived from the cross of HA 89 and H. argophyllus confirmed the single gene inheritance of resistance. Since no other Pl gene has been mapped to LG2, this gene was novel and designated as Pl (18). SSR markers CRT214 and ORS203 flanked Pl(18) at a genetic distance of 1.1 and 0.4 cM, respectively. Forty-six single nucleotide polymorphism (SNP) markers that cover the Pl(18) region were surveyed for saturation mapping of the region. Six co-segregating SNP markers were 1.2 cM distal to Pl(18), and another four co-segregating SNP markers were 0.9 cM proximal to Pl(18). The new BC2F4-derived germplasm, HA-DM1, carrying Pl(18) has been released to the public. This new line is highly resistant to all Plasmopara halstedii races identified in the USA providing breeders with an effective new source of resistance against downy mildew in sunflower. The molecular markers that were developed will be especially useful in marker-assisted selection and pyramiding of Pl resistance genes because of their close proximity to the gene and the availability of high-throughput SNP detection assays.

Evaluation of endogenous control gene(s) for gene expression studies in human blood exposed to 60Co γ-rays ex vivo

International Nuclear Information System (INIS)

Vaiphei, S. Thangminlal; Keppen, Joshua; Nongrum, Saibadaiahun; Sharan, R.N.; Chaubey, R.C.; Kma, L.

2015-01-01

In gene expression studies, it is critical to normalize data using a stably expressed endogenous control gene in order to obtain accurate and reliable results. However, we currently do not have a universally applied endogenous control gene for normalization of data for gene expression studies, particularly those involving 60 Co γ-ray-exposed human blood samples. In this study, a comparative assessment of the gene expression of six widely used housekeeping endogenous control genes, namely 18S, ACTB, B2M, GAPDH, MT-ATP6 and CDKN1A, was undertaken for a range of 60 Co γ-ray doses (0.5, 1.0, 2.0 and 4.0 Gy) at 8.4 Gy min -1 at 0 and 24 h post-irradiation time intervals. Using the NormFinder algorithm, real-time PCR data obtained from six individuals (three males and three females) were analyzed with respect to the threshold cycle (Ct) value and abundance, ΔCt pair-wise comparison, intra- and inter-group variability assessments, etc. GAPDH, either alone or in combination with 18S, was found to be the most suitable endogenous control gene and should be used in gene expression studies, especially those involving qPCR of γ-ray-exposed human blood samples. (author)

Novel mutations in the genes TGM1 and ALOXE3 underlying autosomal recessive congenital ichthyosis

Science.gov (United States)

Ullah, Rahim; Ansar, Muhammad; Durrani, Zaka Ullah; Lee, Kwanghyuk; Santos-Cortez, Regie Lyn P.; Muhammad, Dost; Ali, Mahboob; Zia, Muhammad; Ayub, Muhammad; Khan, Suliman; Smith, Josh D.; Nickerson, Deborah A.; Shendure, Jay; Bamshad, Michael; Leal, Suzanne M.; Ahmad, Wasim

2016-01-01

Background Ichthyoses are clinically characterized by scaling or hyperkeratosis of the skin or both. It can be an isolated condition limited to the skin or appear secondarily with involvement of other cutaneous or systemic abnormalities. Methods The present study investigated clinical and molecular characterization of three consanguineous families (A, B, C) segregating two different forms of autosomal recessive congenital ichthyosis (ARCI). Linkage in three consanguineous families (A, B, C) segregating two different forms of ARCI was searched by typing microsatellite and single nucleotide polymorphism marker analysis. Sequencing of the two genes TGM1 and ALOXE3 was performed by the dideoxy chain termination method. Results Genome-wide linkage analysis established linkage in family A to TGM1 gene on chromosome 14q11 and in families B and C to ALOXE3 gene on chromosome 17p13. Subsequently, sequencing of these genes using samples from affected family members led to the identification of three novel mutations: a missense variant p.Trp455Arg in TGM1 (family A); a nonsense variant p.Arg140* in ALOXE3 (family B); and a complex rearrangement in ALOXE3 (family C). Conclusion The present study further extends the spectrum of mutations in the two genes involved in causing ARCI. Characterizing the clinical spectrum resulting from mutations in the TGM1 and ALOXE3 genes will improve diagnosis and may direct clinical care of the family members. PMID:26578203

驯鹿的皮蝇蛆线粒体CO1基因序列分析%Sequence analysis of mitochondrial cytochrome oxidase 1 (CO1) gene of warble fly larvae from reindeer

Institute of Scientific and Technical Information of China (English)

高慧; 杨晓野; 李云章; 莫内; 阿拉腾保力格; 赵治国; 王瑞

2011-01-01

The specificity of mitochondrial cytochrome oxidaae 1 ( CO1) gene sequence of warble fly larvae of unknown species from reindeer in Inner Mongolia region of China were analyzed by molecular biological techniques. The results showed that the size of CO1 gene fragment from UEA7 to UEA10 was approximately 689 bp. The analysis of phylogenic tree showed that the unknown species from the reindeer in Inner Mongolia had high homology with Hypoderma diana France isolate. The differences analysis between the different fly species showed:the sequences between Hypodermatidae and Oestridae were obviously different, ranged from 19. 3％ to 25. 5％ . The divergences of different fly larvae in deer ranged from 1. 9％ to 25. 5％ . The divergences of Hypoderma. ranged from 6. 7％ to 18. 7％. The divergences of Cephenemyia. ranged from 1. 9％ to 9. 6％ and the variation of the different Hypoderma diana strains was 6. 0％. It suggested that the nucleotide sequences of the mitochondrial CO1 genes could indicate the phylogenetic relationships among different genera, species and strains to some extent.%利用分子生物学技术对内蒙古驯鹿未定种皮蝇蛆线粒体CO1基因种属特异性序列进行了研究.DNA核苷酸测序结果证实:该种皮蝇线粒体CO1种属特异性基因UEA7到UEA10特殊目标编码区域片段长度约为689 bp;种系发生进化树和同源性分析显示其与鹿皮蝇法国株同源性非常接近,因此确定内蒙古地区感染驯鹿的皮蝇蛆为鹿皮蝇(Hypoderma diana).不同蝇种间差异性分析显示:皮蝇科(Hypodermatidae)与狂蝇科(Oestridae)之间序列差异明显,差异性为19.3%～25.5%;寄生于鹿的不同蝇蛆种间差异性为1.9%～25.5%;皮蝇属(Hypoderma)不同种间差异性为6.7%～18.7%;鹿蝇属(Cephenemyia)不同种间差异性为1.9%～9.6%;而同种不同株的鹿皮蝇差异性为6.0%;说明生物线粒体CO1基因核苷酸序列在一定程度上可反映出种属及株间在进化上的差异性.

GeneCAT--novel webtools that combine BLAST and co-expression analyses

DEFF Research Database (Denmark)

Mutwil, Marek; Obro, Jens; Willats, William G T

2008-01-01

The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second...... orthologs in the plant model organisms Arabidopsis thaliana and Hordeum vulgare (Barley). GeneCAT is equipped with expression data for the model plant A. thaliana, and first to introduce co-expression mining tools for the monocot Barley. GeneCAT is available at http://genecat.mpg.de....

The alpha-spectrin gene is on chromosome 1 in mouse and man.

Science.gov (United States)

Huebner, K; Palumbo, A P; Isobe, M; Kozak, C A; Monaco, S; Rovera, G; Croce, C M; Curtis, P J

1985-06-01

By using alpha-spectrin cDNA clones of murine and human origin and somatic cell hybrids segregating either mouse or human chromosomes, the gene for alpha-spectrin has been mapped to chromosome 1 in both species. This assignment of the mouse alpha-spectrin gene to mouse chromosome 1 by DNA hybridization strengthens the previous identification of the alpha-spectrin locus in mouse with the sph locus, which previously was mapped by linkage analysis to mouse chromosome 1, distal to the Pep-3 locus. By in situ hybridization to human metaphase chromosomes, the human alpha-spectrin gene has been localized to 1q22-1q25; interestingly, the locus for a non-Rh-linked form of elliptocytosis has been provisionally mapped to band 1q2 by family linkage studies.

Pekon palvonta René Girardin uskontoteorian valossa / Tuukka Sandström

Index Scriptorium Estoniae

Sandström, Tuukka

2005-01-01

Prantsuse filosoofi René Girardi ideedest primitiivse religiooni kohta. Setumaal veel 20. sajandi alguses levinud viljakusjumal Peko kultusest ja iga-aastasest uue Peko papi valimise rituaalist R. Girardi tõlgenduse valguses

Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses.

Science.gov (United States)

Cubillos, Francisco A; Brice, Claire; Molinet, Jennifer; Tisné, Sebastién; Abarca, Valentina; Tapia, Sebastián M; Oporto, Christian; García, Verónica; Liti, Gianni; Martínez, Claudio

2017-06-07

Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1 , PDC1 , CPS1 , ASI2 , LYP1 , and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics. Copyright © 2017 Cubillos et al.

Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

Directory of Open Access Journals (Sweden)

Francisco A. Cubillos

2017-06-01

Full Text Available Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics.

The Argonaute protein TbAGO1 contributes to large and mini-chromosome segregation and is required for control of RIME retroposons and RHS pseudogene-associated transcripts.

Science.gov (United States)

Durand-Dubief, Mickaël; Absalon, Sabrina; Menzer, Linda; Ngwabyt, Sandra; Ersfeld, Klaus; Bastin, Philippe

2007-12-01

The protist Trypanosoma brucei possesses a single Argonaute gene called TbAGO1 that is necessary for RNAi silencing. We previously showed that in strain 427, TbAGO1 knock-out leads to a slow growth phenotype and to chromosome segregation defects. Here we report that the slow growth phenotype is linked to defects in segregation of both large and mini-chromosome populations, with large chromosomes being the most affected. These phenotypes are completely reversed upon inducible re-expression of TbAGO1 fused to GFP, demonstrating their link with TbAGO1. Trypanosomes that do not express TbAGO1 show a general increase in the abundance of transcripts derived from the short retroposon RIME (Ribosomal Interspersed Mobile Element). Supplementary large RIME transcripts emerge in the absence of RNAi, a phenomenon coupled to the disappearance of short transcripts. These fluctuations are reversed by inducible expression of GFP::TbAGO1. Furthermore, we use a combination of Northern blots, RT-PCR and sequencing to reveal that RNAi controls expression of transcripts derived from RHS (Retrotransposon Hot Spot) pseudogenes (RHS genes with retro-element(s) integrated within their coding sequence). Absence of RNAi also leads to an increase of steady-state transcripts from regular RHS genes (those without retro-element), indicating a role for pseudogene in control of gene expression. However, analysis of retroposon abundance and arrangement in the genome of multiple clonal cell lines of TbAGO1-/- failed to reveal movement of mobile elements despite the increased amounts of retroposon transcripts.

An active role for endogenous beta-1,3-glucanase genes in transgene-mediated co-suppression in tobacco.

Science.gov (United States)

Sanders, Matthew; Maddelein, Wendy; Depicker, Anna; Van Montagu, Marc; Cornelissen, Marc; Jacobs, John

2002-11-01

Post-transcriptional gene silencing (PTGS) is characterized by the accumulation of short interfering RNAs that are proposed to mediate sequence-specific degradation of cognate and secondary target mRNAs. In plants, it is unclear to what extent endogenous genes contribute to this process. Here, we address the role of the endogenous target genes in transgene-mediated PTGS of beta-1,3-glucanases in tobacco. We found that mRNA sequences of the endogenous glucanase glb gene with varying degrees of homology to the Nicotiana plumbaginifolia gn1 transgene are targeted by the silencing machinery, although less efficiently than corresponding transgene regions. Importantly, we show that endogene-specific nucleotides in the glb sequence provide specificity to the silencing process. Consistent with this finding, small sense and antisense 21- to 23-nucleotide RNAs homologous to the endogenous glb gene were detected. Combined, these data demonstrate that a co-suppressed endogenous glucan ase gene is involved in signal amplification and selection of homologous targets, and show that endogenous genes can actively participate in PTGS in plants. The findings are introduced as a further sophistication of the post-transciptional silencing model.

Differential gene expression in notochord and nerve cord fate segregation in the Ciona intestinalis embryo.

Science.gov (United States)

Kobayashi, Kenji; Yamada, Lixy; Satou, Yutaka; Satoh, Nori

2013-09-01

During early embryogenesis, embryonic cells gradually restrict their developmental potential and are eventually destined to give rise to one type of cells. Molecular mechanisms underlying developmental fate restriction are one of the major research subjects within developmental biology. In this article, this subject was addressed by combining blastomere isolation with microarray analysis. During the 6th cleavage of the Ciona intestinalis embryo, from the 32-cell to the 64-cell stage, four mother cells divide into daughter cells with two distinct fates, one giving rise to notochord precursor cells and the other to nerve cord precursors. Approximately 2,200 each of notochord and nerve cord precursor cells were isolated, and their mRNA expression profiles were compared by microarray. This analysis identified 106 and 68 genes, respectively, that are differentially expressed in notochord and nerve cord precursor cells. These included not only genes for transcription factors and signaling molecules but also those with generalized functions observed in many types of cells. In addition, whole-mount in situ hybridization showed dynamic spatial expression profiles of these genes during segregation of the two fates: partitioning of transcripts present in the mother cells into either type of daughter cells, and initiation of preferential gene expression in either type of cells. Copyright © 2013 Wiley Periodicals, Inc.

Castration Has Antihypertensive and Organoprotective Effects in Male but Not in Female Heterozygous Ren-2 Rats

Czech Academy of Sciences Publication Activity Database

Vaněčková, Ivana; Husková, Z.; Vaňourková, Z.; Červenka, L.

2011-01-01

Roč. 34, č. 1 (2011), s. 46-52 ISSN 1420-4096 R&D Projects: GA MŠk(CZ) 1M0510 Institutional research plan: CEZ:AV0Z50110509 Keywords : Ren-2 rats * hypertension * sexual dimorphism * age * sex hormones * renin-angiotensin system Subject RIV: FA - Cardiovascular Diseases incl. Cardiotharic Surgery Impact factor: 1.464, year: 2011

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle.

Science.gov (United States)

Lim, Dajeong; Lee, Seung-Hwan; Kim, Nam-Kuk; Cho, Yong-Min; Chai, Han-Ha; Seong, Hwan-Hoo; Kim, Heebal

2013-01-01

Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean Cattle

Directory of Open Access Journals (Sweden)

Dajeong Lim

2013-01-01

Full Text Available Marbling (intramuscular fat is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the ‘marbling score’ trait and systemically analyzed the network topology in Hanwoo (Korean cattle. As a result, we determined 3 modules (gene groups that showed statistically significant results for marbling score. In particular, one module (denoted as red has a statistically significant result for marbling score (p = 0.008 and intramuscular fat (p = 0.02 and water capacity (p = 0.006. From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

Evaluation of endogenous control gene(s) for gene expression studies in human blood exposed to 60Co γ-rays ex vivo.

Science.gov (United States)

Vaiphei, S Thangminlal; Keppen, Joshua; Nongrum, Saibadaiahun; Chaubey, R C; Kma, L; Sharan, R N

2015-01-01

In gene expression studies, it is critical to normalize data using a stably expressed endogenous control gene in order to obtain accurate and reliable results. However, we currently do not have a universally applied endogenous control gene for normalization of data for gene expression studies, particularly those involving (60)Co γ-ray-exposed human blood samples. In this study, a comparative assessment of the gene expression of six widely used housekeeping endogenous control genes, namely 18S, ACTB, B2M, GAPDH, MT-ATP6 and CDKN1A, was undertaken for a range of (60)Co γ-ray doses (0.5, 1.0, 2.0 and 4.0 Gy) at 8.4 Gy min(-1) at 0 and 24 h post-irradiation time intervals. Using the NormFinder algorithm, real-time PCR data obtained from six individuals (three males and three females) were analyzed with respect to the threshold cycle (Ct) value and abundance, ΔCt pair-wise comparison, intra- and inter-group variability assessments, etc. GAPDH, either alone or in combination with 18S, was found to be the most suitable endogenous control gene and should be used in gene expression studies, especially those involving qPCR of γ-ray-exposed human blood samples. © The Author 2014. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

ICan: an integrated co-alteration network to identify ovarian cancer-related genes.

Science.gov (United States)

Zhou, Yuanshuai; Liu, Yongjing; Li, Kening; Zhang, Rui; Qiu, Fujun; Zhao, Ning; Xu, Yan

2015-01-01

Over the last decade, an increasing number of integrative studies on cancer-related genes have been published. Integrative analyses aim to overcome the limitation of a single data type, and provide a more complete view of carcinogenesis. The vast majority of these studies used sample-matched data of gene expression and copy number to investigate the impact of copy number alteration on gene expression, and to predict and prioritize candidate oncogenes and tumor suppressor genes. However, correlations between genes were neglected in these studies. Our work aimed to evaluate the co-alteration of copy number, methylation and expression, allowing us to identify cancer-related genes and essential functional modules in cancer. We built the Integrated Co-alteration network (ICan) based on multi-omics data, and analyzed the network to uncover cancer-related genes. After comparison with random networks, we identified 155 ovarian cancer-related genes, including well-known (TP53, BRCA1, RB1 and PTEN) and also novel cancer-related genes, such as PDPN and EphA2. We compared the results with a conventional method: CNAmet, and obtained a significantly better area under the curve value (ICan: 0.8179, CNAmet: 0.5183). In this paper, we describe a framework to find cancer-related genes based on an Integrated Co-alteration network. Our results proved that ICan could precisely identify candidate cancer genes and provide increased mechanistic understanding of carcinogenesis. This work suggested a new research direction for biological network analyses involving multi-omics data.

(3-Aminopropyl)-4-methylpiperazine End-capped Poly(1,4-butanediol diacrylate-co-4-amino-1-butanol)-based Multilayer Films for Gene Delivery

OpenAIRE

Li, Cuicui; Tzeng, Stephany Y; Tellier, Liane E.; Green, Jordan J

2013-01-01

Biodegradable polyelectrolyte surfaces for gene delivery were created through electrospinning of biodegradable polycations combined with iterative solution-based multilayer coating. Poly(β-amino ester) (PBAE) poly(1,4-butanediol diacrylate-co-4-amino-1-butanol) end-capped with 1-(3-aminopropyl)-4-methylpiperazine was utilized due to its ability to electrostatically interact with anionic molecules like DNA, its biodegradability, and its low cytotoxicity. A new DNA release system was developed ...

"Darkness Overcomes You": Shaun Tan and Søren Kierkegaard

Science.gov (United States)

Johansen, Martin Blok

2015-01-01

This article analyses Shaun Tan's picturebook "The Red Tree" using some of the central concepts of existentialism developed by the Danish philosopher Søren Kierkegaard. Kierkegaard argued that being a person entails a coming-to-be ["tilblivelse"], and for the person this coming-to-be manifests itself as a task. The task is to…

Characterization of chemically induced liver injuries using gene co-expression modules.

Directory of Open Access Journals (Sweden)

Gregory J Tawa

Full Text Available Liver injuries due to ingestion or exposure to chemicals and industrial toxicants pose a serious health risk that may be hard to assess due to a lack of non-invasive diagnostic tests. Mapping chemical injuries to organ-specific damage and clinical outcomes via biomarkers or biomarker panels will provide the foundation for highly specific and robust diagnostic tests. Here, we have used DrugMatrix, a toxicogenomics database containing organ-specific gene expression data matched to dose-dependent chemical exposures and adverse clinical pathology assessments in Sprague Dawley rats, to identify groups of co-expressed genes (modules specific to injury endpoints in the liver. We identified 78 such gene co-expression modules associated with 25 diverse injury endpoints categorized from clinical pathology, organ weight changes, and histopathology. Using gene expression data associated with an injury condition, we showed that these modules exhibited different patterns of activation characteristic of each injury. We further showed that specific module genes mapped to 1 known biochemical pathways associated with liver injuries and 2 clinically used diagnostic tests for liver fibrosis. As such, the gene modules have characteristics of both generalized and specific toxic response pathways. Using these results, we proposed three gene signature sets characteristic of liver fibrosis, steatosis, and general liver injury based on genes from the co-expression modules. Out of all 92 identified genes, 18 (20% genes have well-documented relationships with liver disease, whereas the rest are novel and have not previously been associated with liver disease. In conclusion, identifying gene co-expression modules associated with chemically induced liver injuries aids in generating testable hypotheses and has the potential to identify putative biomarkers of adverse health effects.

Cell membrane thermo-stability studies through joint segregation analysis in various wheat populations

International Nuclear Information System (INIS)

Ullah, K.; Khan, N.U.; Gul, S.; Khan, S.J.

2014-01-01

Using joint segregation analysis (JSA) technique as statistical approach, mixed inheritance analysis for cell plasma membrane as membrane thermal stability (MTS) was assayed in two parental lines (P1, P2) and their four populations (F1, BC1, BC2, F2) of four wheat crosses, viz., Hashim-08 * LU-26, Farid-06 * Shafaq, Parula * Blue Silver and TD-1 * D-97603 at Faculty of Agriculture, Gomal University, Dera Ismail Khan, Pakistan during crop season 2011-12. Results revealed that MTS was under control of two mixed groups of genes i.e., additive-dominant-epistatic major genes plus additive-dominant-epistasis of polygenes (model E) in Hashim-08 * LU-26 and Farid-06 * Shafaq crosses, respectively. In cross Parula * Blue Silver, it was governed by mixed genes i.e. one major-gene and additive-dominance-epistatic polygenes (model D). However, in cross TD-1 * D-97603, the MTS was under the influence of mixed epistasis of two major genes plus polygenes (model E-1). Polygene variation and polygene heritability were higher than major gene variation and heritability in crosses Hashim-08 * LU-26 and Farid-06 * Shafaq. In crosses Parula * Blue Silver and TD-1 * D-97603, the major gene variation and heritability were higher than polygene variation and heritability, indicating maximum contribution of the major genes. While in cross TD-1 * D-97603, epistatic components were also positive and due to which the polygene heritability was almost zero. Moderate to high environmental variation in the MTS for segregating generations revealed that the said trait was highly persuaded by the environment. However, the genetic behavior of the MTS suggested that early selection for MTS in the crosses Hashim-08 * LU-26 and Farid-06 * Shafaq would be efficient. Whereas, the delayed selection in crosses Parula * Blue Silver and TD-1 * D-97603 until the accumulation of maximum favorable genes will be effective. (author)

Ni And Co Segregations On Selective Surface Facets And Rational Design Of Layered Lithium Transition-metal Oxide Cathodes

Energy Technology Data Exchange (ETDEWEB)

Yan, Pengfei; Zheng, Jianming; Zheng, Jiaxin; Wang, Zhiguo; Teng, Gaofeng; Kuppan, Saravanan; Xiao, Jie; Chen, Guoying; Zhang, Jiguang; Wang, Chong M.; Pan, Feng

2016-05-05

The chemical processes occurring on the surface of cathode materials during battery cycling play a crucial role in determining battery’s performance. However, our understanding on such surface chemistry is far from clear due to the complexity of redox chemistry during battery charge/discharge. In this work, through intensive aberration corrected STEM investigation on eight layered oxide cathode materials, we report two important findings on the pristine oxides. First, Ni and Co show strong plane selectivity when building up their respective surface segregation layers (SSL). Specifically, Ni-SSL is exclusively developed on (200)m facet in Li-Mn-rich oxides (monoclinic C2/m symmetry) and (012)h facet in Mn-Ni equally rich oxides (hexagonal R-3m symmetry), while Co-SSL has a strong preference to (20-2)m plane with minimal Co-SSL also developed on some other planes in LMR cathodes. Structurally, Ni-SSLs tend to form spinel-like lattice while Co-SSLs are in a rock-salt-like structure. Secondly, by increasing Ni concentration in these layered oxides, Ni and Co SSLs can be suppressed and even eliminated. Our findings indicate that Ni and Co SSLs are tunable through controlling particle morphology and oxide composition, which opens up a new way for future rational design and synthesis of cathode materials.

Isak Dinesen Reading Søren Kierkegaard

DEFF Research Database (Denmark)

Bunch, Mads

Not only did Isak Dinesen (Karen Blixen, 1885-1962) read the works of her fellow-countryman, the Danish philosopher Søren Kierkegaard (1813-1855), closely, she also created a surprisingly large number of tales that critically engage Kierkegaard’s works. In this thorough comparative study, Mads Bu...... and develops from the early tale ‘Carnival’ (1926-27) to ‘The Dreamers’ (1934), ‘The Pearls’ (1942), ‘Babette’s Feast’ (1950) and her last tale ‘Ehrengard’ (1963). Bunch’s close readings reveal that Dinesen’s ironical counter-tales concerning Kierkegaard border at times on sheer parody....

Magnetic Hysteresis in Nanocomposite Films Consisting of a Ferromagnetic AuCo Alloy and Ultrafine Co Particles

Directory of Open Access Journals (Sweden)

Federico Chinni

2017-06-01

Full Text Available One fundamental requirement in the search for novel magnetic materials is the possibility of predicting and controlling their magnetic anisotropy and hence the overall hysteretic behavior. We have studied the magnetism of Au:Co films (~30 nm thick with concentration ratios of 2:1, 1:1, and 1:2, grown by magnetron sputtering co-deposition on natively oxidized Si substrates. They consist of a AuCo ferromagnetic alloy in which segregated ultrafine Co particles are dispersed (the fractions of Co in the AuCo alloy and of segregated Co increase with decreasing the Au:Co ratio. We have observed an unexpected hysteretic behavior characterized by in-plane anisotropy and crossed branches in the loops measured along the hard magnetization direction. To elucidate this phenomenon, micromagnetic calculations have been performed for a simplified system composed of two exchange-coupled phases: a AuCo matrix surrounding a Co cluster, which represents an aggregate of particles. The hysteretic features are qualitatively well reproduced provided that the two phases have almost orthogonal anisotropy axes. This requirement can be plausibly fulfilled assuming a dominant magnetoelastic character of the anisotropy in both phases. The achieved conclusions expand the fundamental knowledge on nanocomposite magnetic materials, offering general guidelines for tuning the hysteretic properties of future engineered systems.

Self-organized carbon-rich stripe formation from competitive carbon and aluminium segregation at Fe0.85Al0.15(1 1 0) surfaces

Science.gov (United States)

Dai, Zongbei; Borghetti, Patrizia; Mouchaal, Younes; Chenot, Stéphane; David, Pascal; Jupille, Jacques; Cabailh, Gregory; Lazzari, Rémi

2018-06-01

By combining Scanning Tunnelling Microscopy, Low Energy Electron Diffraction and X-ray Photoelectron Spectroscopy, it was found that the surface of A2 random alloy Fe0.85Al0.15(1 1 0) is significantly influenced by the segregation of aluminium but also of carbon bulk impurities. Below ∼ 900 K, carbon segregates in the form of self-organized protruding stripes separated by ∼ 5 nm that run along the [ 0 0 1 ] B bulk direction and cover up to 34% of the surface. Their C 1s spectroscopic signature that is dominated by graphitic carbon peaks around 900 K. Above this temperature, the surface carbon concentration decays by redissolution in the bulk, whereas an intense aluminium segregation is observed giving rise to a hexagonal superstructure. The present findings is interpreted by a competitive segregation between the two elements.

Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability.

Science.gov (United States)

Riazuddin, S; Hussain, M; Razzaq, A; Iqbal, Z; Shahzad, M; Polla, D L; Song, Y; van Beusekom, E; Khan, A A; Tomas-Roca, L; Rashid, M; Zahoor, M Y; Wissink-Lindhout, W M; Basra, M A R; Ansar, M; Agha, Z; van Heeswijk, K; Rasheed, F; Van de Vorst, M; Veltman, J A; Gilissen, C; Akram, J; Kleefstra, T; Assir, M Z; Grozeva, D; Carss, K; Raymond, F L; O'Connor, T D; Riazuddin, S A; Khan, S N; Ahmed, Z M; de Brouwer, A P M; van Bokhoven, H; Riazuddin, S

2017-11-01

Intellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1-3% of the general population. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause autosomal recessive ID (ARID) has lagged behind, predominantly due to non-availability of sizeable families. Here we present the results of exome sequencing in 121 large consanguineous Pakistani ID families. In 60 families, we identified homozygous or compound heterozygous DNA variants in a single gene, 30 affecting reported ID genes and 30 affecting novel candidate ID genes. Potential pathogenicity of these alleles was supported by co-segregation with the phenotype, low frequency in control populations and the application of stringent bioinformatics analyses. In another eight families segregation of multiple pathogenic variants was observed, affecting 19 genes that were either known or are novel candidates for ID. Transcriptome profiles of normal human brain tissues showed that the novel candidate ID genes formed a network significantly enriched for transcriptional co-expression (P<0.0001) in the frontal cortex during fetal development and in the temporal-parietal and sub-cortex during infancy through adulthood. In addition, proteins encoded by 12 novel ID genes directly interact with previously reported ID proteins in six known pathways essential for cognitive function (P<0.0001). These results suggest that disruptions of temporal parietal and sub-cortical neurogenesis during infancy are critical to the pathophysiology of ID. These findings further expand the existing repertoire of genes involved in ARID, and provide new insights into the molecular mechanisms and the transcriptome map of ID.

MCNP-REN a Monte Carlo tool for neutron detector design

CERN Document Server

Abhold, M E

2002-01-01

The development of neutron detectors makes extensive use of the predictions of detector response through the use of Monte Carlo techniques in conjunction with the point reactor model. Unfortunately, the point reactor model fails to accurately predict detector response in common applications. For this reason, the general Monte Carlo code developed at Los Alamos National Laboratory, Monte Carlo N-Particle (MCNP), was modified to simulate the pulse streams that would be generated by a neutron detector and normally analyzed by a shift register. This modified code, MCNP-Random Exponentially Distributed Neutron Source (MCNP-REN), along with the Time Analysis Program, predicts neutron detector response without using the point reactor model, making it unnecessary for the user to decide whether or not the assumptions of the point model are met for their application. MCNP-REN is capable of simulating standard neutron coincidence counting as well as neutron multiplicity counting. Measurements of mixed oxide fresh fuel w...

Co-expression of an Erwinia chrysanthemi pectate lyase-encoding gene (pelE) and an E. carotovora polygalacturonase-encoding gene (peh1) in Saccharomyces cerevisiae.

Science.gov (United States)

Laing, E; Pretorius, I S

1993-05-01

A pectate lyase (PL)-encoding gene (pelE) from Erwinia chrysanthemi and a polygalacturonase (PG)-encoding gene (peh1) from E. carotovora were each inserted between a novel yeast expression-secretion cassette and a yeast gene terminator, and cloned separately into a yeast-centromeric shuttle vector (YCp50), generating recombinant plasmids pAMS12 and pAMS13. Transcription initiation signals present in the expression-secretion cassette were derived from the yeast alcohol dehydrogenase gene promoter (ADC1P), whereas the transcription termination signals were derived from the yeast tryptophan synthase gene terminator (TRP5T). Secretion of PL and PG was directed by the signal sequence of the yeast mating pheromone alpha-factor (MF alpha 1s). A pectinase cassette comprising ADC1P-MF alpha 1s-pelE-TRP5T and ADC1P-MF alpha 1s-peh1-TRP5T was subcloned into YCp50, generating plasmid pAMS14. Subsequently, the dominant selectable Geneticin G418-resistance (GtR) marker, APH1, inserted between the yeast uridine diphosphoglucose 4-epimerase gene promoter (GAL10P) and yeast orotidine-5'-phosphate carboxylase gene terminator (URA3T), was cloned into pAMS14, resulting in plasmid pAMS15. Plasmids pAMS12, pAMS13 and pAMS14 were transformed into a laboratory strain of Saccharomyces cerevisiae, whereas pAMS15 was stably introduced into two commercial wine yeast strains. DNA-DNA and DNA-RNA hybridization analyses revealed the presence of these plasmids, and the pelE and peh1 transcripts in the yeast transformants, respectively. A polypectate agarose assay indicated the extracellular production of biologically active PL and PG by the S. cerevisiae transformants and confirmed that co-expression of the pelE and peh1 genes synergistically enhanced pectate degradation.

36 CFR 254.6 - Segregative effect.

Science.gov (United States)

2010-07-01

... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Segregative effect. 254.6... ADJUSTMENTS Land Exchanges § 254.6 Segregative effect. (a) If a proposal is made to exchange Federal lands... segregative effect terminates as follows: (1) Automatically, upon issuance of a patent or other document of...

Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean.

Science.gov (United States)

Burt, Andrew J; William, H Manilal; Perry, Gregory; Khanal, Raja; Pauls, K Peter; Kelly, James D; Navabi, Alireza

2015-01-01

Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co-4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co-4 is localized. Three SCAR markers with known linkage to Co-4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies. It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

Waste segregation

International Nuclear Information System (INIS)

Clark, D.E.; Colombo, P.

1982-01-01

A scoping study has been undertaken to determine the state-of-the-art of waste segregation technology as applied to the management of low-level waste (LLW). Present-day waste segregation practices were surveyed through a review of the recent literature and by means of personal interviews with personnel at selected facilities. Among the nuclear establishments surveyed were Department of Energy (DOE) laboratories and plants, nuclear fuel cycle plants, public and private laboratories, institutions, industrial plants, and DOE and commercially operated shallow land burial sites. These survey data were used to analyze the relationship between waste segregation practices and waste treatment/disposal processes, to assess the developmental needs for improved segregation technology, and to evaluate the costs and benefits associated with the implementation of waste segregation controls. This task was planned for completion in FY 1981. It should be noted that LLW management practices are now undergoing rapid change such that the technology and requirements for waste segregation in the near future may differ significantly from those of the present day. 8 figures

Effect of stratification on segregation in carbon dioxide miscible flooding in a water-flooded oil reservoir

International Nuclear Information System (INIS)

Bhatti, A.A.; Mahmood, S.M.; Amjad, B.

2013-01-01

Oil reservoirs are subjected to tertiary recovery by deploying any enhanced oil recovery (EOR) technique for the recovery of left over oil. Amongst many EOR methods one of the widely applied worldwide is CO/sub 2/ flooding through miscible, near miscible or immiscible displacement processes. CO/sub 2/ flooding process responds to a number of reservoir and fluid characteristics. These characteristics have strong effect on overall efficiency of the displacement process. Better understanding of the effect of different characteristics on displacement process is important to plan an efficient displacement process. In this work, the effect of stratification resulting in gravity segregation of the injected fluid is studied in an oil reservoir which is water-flooded during secondary phase of recovery. Sensitivity analysis is performed through successive simulation on Eclipse 300 (compositional) reservoir simulator. Process involves the continuous CO/sub 2/ injection in an oil reservoir with more than 1/3rd of original oil in place left after water flooding. Reservoir model with four different permeability layers is studied. Four patterns by changing the arrangement of the permeabilities of the layers are analysed. The effect of different arrangement or stratification on segregation of CO/sub 2/ and ultimately on the incremental oil recovery, is investigated. It has been observed that out of four arrangements, upward fining pattern relatively overcame the issue of the segregation of CO/sub 2/ and consequently 33% more oil with half injection volume is recovered when compared with the downward fining pattern. (author)

The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation.

Science.gov (United States)

Claycomb, Julie M; Batista, Pedro J; Pang, Ka Ming; Gu, Weifeng; Vasale, Jessica J; van Wolfswinkel, Josien C; Chaves, Daniel A; Shirayama, Masaki; Mitani, Shohei; Ketting, René F; Conte, Darryl; Mello, Craig C

2009-10-02

RNAi-related pathways regulate diverse processes, from developmental timing to transposon silencing. Here, we show that in C. elegans the Argonaute CSR-1, the RNA-dependent RNA polymerase EGO-1, the Dicer-related helicase DRH-3, and the Tudor-domain protein EKL-1 localize to chromosomes and are required for proper chromosome segregation. In the absence of these factors chromosomes fail to align at the metaphase plate and kinetochores do not orient to opposing spindle poles. Surprisingly, the CSR-1-interacting small RNAs (22G-RNAs) are antisense to thousands of germline-expressed protein-coding genes. Nematodes assemble holocentric chromosomes in which continuous kinetochores must span the expressed domains of the genome. We show that CSR-1 interacts with chromatin at target loci but does not downregulate target mRNA or protein levels. Instead, our findings support a model in which CSR-1 complexes target protein-coding domains to promote their proper organization within the holocentric chromosomes of C. elegans.

Common MspI RFLP of the human fibronectin gene (FN1)

Energy Technology Data Exchange (ETDEWEB)

Gardella, R; Colombi, M; Barlati, S

1988-02-25

The probe used, pFH154, contains a sequence of 2.5 kb of the fibronectin cDNA inserted in pAT153/Pvu/8 plasmid vector. The recombinant plasmid and the HindIII/BamHI purified cDNA insert give identical patterns. MspI (C/CGG) (Promega Biotec) detects invariant bands at 8.5, 4.2, 2.5, 2.1, 1.55, 1.4, 1.1 and 0.75 kb in addition to a simple two allele polymorphism with a band at either 0.35 kb (F1) or 2.7 kb (F2). Co-dominant segregation was demonstrated in 6 families.

Søren Kierkegaard og blikkets koder

DEFF Research Database (Denmark)

Linnet, Ragni

this in the work of the landscape painter J.L. Lundbye. Lundbye was keenly interested in Kierkegaard, which can be traced in the formal qualities of some of his paintings. The thesis also shows that Søren Kierkegaard has an independent and systematic pictorial theory that is based on such aspects as close...... kinship to music (and time as time) are screened off. Hegel's thesis of 'an art after art', i.e. the death of the idealistic, beautiful work and its resurrection in a prosaic pictorial expression in which the formal qualities are at the centre, is not incorporated in the Danish reception, so that Hegel...

WT1 Is Necessary for the Proliferation and Migration of Cells of Renin Lineage Following Kidney Podocyte Depletion

Directory of Open Access Journals (Sweden)

Natalya V. Kaverina

2017-10-01

Full Text Available Wilms' tumor suppressor 1 (WT1 plays an important role in cell proliferation and mesenchymal-epithelial balance in normal development and disease. Here, we show that following podocyte depletion in three experimental models, and in patients with focal segmental glomerulosclerosis (FSGS and membranous nephropathy, WT1 increased significantly in cells of renin lineage (CoRL. In an animal model of FSGS in RenWt1fl/fl reporter mice with inducible deletion of WT1 in CoRL, CoRL proliferation and migration to the glomerulus was reduced, and glomerular disease was worse compared with wild-type mice. To become podocytes, CoRL undergo mesenchymal-to-epithelial transformation (MET, typified by reduced staining for mesenchymal markers (MYH11, SM22, αSMA and de novo expression of epithelial markers (E-cadherin and cytokeratin18. Evidence for changes in MET markers was barely detected in RenWt1fl/fl mice. Our results show that following podocyte depletion, WT1 plays essential roles in CoRL proliferation and migration toward an adult podocyte fate.

Anoressia e mimesi secondo René Girard

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Rosa Sidella

2011-01-01

Full Text Available Anorexia and Mimesis in René Girard’s Thought - One of the basic premises of Girard’s thought is the theory of mimetic desire, for which, in all human relationships, the Other as a model is perceived as a rival. Mimesis is also found in narcissism, in love relationships and eating disorders, such as anorexia and bulimia, which cannot and should not be classified only in psychoanalytic terms. In fact, we should in such cases consider cultural and social contexts, which also impose prescriptions about the care and appearance of the body.

Multi-scale modelling of Suzuki segregation in γ′ precipitates in Ni and Co-base superalloys

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Srimannarayana P.

2014-01-01

Full Text Available The high temperature strength of alloys with (γ + γ′ microstructure is primarily due to the resistance of the ordered precipitate to cutting by matrix dislocations. Such shearing requires higher stresses since it involves the creation of a planar fault. Planar fault energy is known to be dependent on composition. This implies that the composition on the fault may be different from that in the bulk for energetic reasons. Such segregation (or desegregation of specific alloying elements to the fault may result in Suzuki strengthening which has not been explored extensively in these systems. In this work, segregation (or desegregation of alloying elements to planar faults was studied computationally in Ni3(Al,Ti and Co3(W,Al type γ′ precipitates. The composition dependence of APB energy and heat of mixing were evaluated from first principle electronic structure calculations. A phase field model incorporating the first principles results, was used to simulate the motion of an extended superdislocation under stress concurrently with composition evolution. Results reveal that in both systems, significant (desegregation occurs on equilibration. On application of stress, solutes were dragged along with the APB in some cases. Additionally, it was also noted the velocity of the superdislocation under an applied stress is strongly dependent on atomic mobility (i.e. diffusivity.

An AFLP marker linked to the Pm-1 gene that confers resistance to Podosphaera xanthii race 1 in Cucumis melo

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Ana Paula Matoso Teixeira

2008-01-01

Full Text Available Brazil produced 330,000 metric tons of melons in 2005, principally in the Northeast region where one of the most important melon pathogens is the powdery mildew fungus Podosphaera xanthii. The disease is controlled mainly by incorporating single dominant resistance genes into commercial hybrids. We report on linkage analysis of the Pm-1 resistance gene, introgressed from the AF125Pm-1 Cantalupensis Charentais-type breeding line into the yellow-fleshed melon (Group Inodorus breeding line AF426-S by backcrossing to produce the resistant line AF426-R, and the amplified fragment length polymorphism (AFLP marker M75/H35_155 reported to be polymorphic between AF426-S and AF426-R. Segregation analysis of M75/H35_155 using a backcross population of 143 plants derived from [AF426-R x AF426-S] x AF426-S and screened for resistance to P. xanthii race 1 produced a recombination frequency of 4.9%, indicating close linkage between M75/H35_155 and Pm-1. Using the same segregating population, the M75/H35_155 marker had previously been reported to be distantly linked to Prv¹, a gene conferring resistance to papaya ringspot virus-type W. Since M75/H35_155 is linked to Prv¹ at a distance of 40.9 cM it is possible that Pm-1 and Prv¹ are also linked.

DAX1 suppresses FXR transactivity as a novel co-repressor

Energy Technology Data Exchange (ETDEWEB)

Li, Jin; Lu, Yan; Liu, Ruya; Xiong, Xuelian; Zhang, Zhijian; Zhang, Xianfeng [Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Metabolism, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025 (China); Ning, Guang, E-mail: guangning@gmail.com.cn [Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Metabolism, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025 (China); The Key Laboratory of Endocrine Tumors and The Division of Endocrine and Metabolic Diseases, E-Institute of Shanghai Universities, Shanghai 200025 (China); Li, Xiaoying, E-mail: lixy@sibs.ac.cn [Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Metabolism, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025 (China); The Key Laboratory of Endocrine Tumors and The Division of Endocrine and Metabolic Diseases, E-Institute of Shanghai Universities, Shanghai 200025 (China)

2011-09-09

Highlights: {yields} DAX1 is co-localized with FXR and interacts with FXR. {yields} DAX1 acts as a negative regulator of FXR. {yields} Three LXXLL motifs in the N-terminus of DAX1 were required. {yields} DAX1 suppresses FXR transactivation by competing with co-activators. -- Abstract: Bile acid receptor FXR (farnesoid X receptor) is a key regulator of hepatic bile acid, glucose and lipid homeostasis through regulation of numerous genes involved in the process of bile acid, triglyceride and glucose metabolism. DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenital critical region on X chromosome, gene 1) is an atypical member of the nuclear receptor family due to lack of classical DNA-binding domains and acts primarily as a co-repressor of many nuclear receptors. Here, we demonstrated that DAX1 is co-localized with FXR in the nucleus and acted as a negative regulator of FXR through a physical interaction with FXR. Our study showed that over-expression of DAX1 down-regulated the expression of FXR target genes, whereas knockdown of DAX1 led to their up-regulation. Furthermore, three LXXLL motifs in the N-terminus of DAX1 were required for the full repression of FXR transactivation. In addition, our study characterized that DAX1 suppresses FXR transactivation via competing with co-activators such as SRC-1 and PGC-1{alpha}. In conclusion, DAX1 acts as a co-repressor to negatively modulate FXR transactivity.

DAX1 suppresses FXR transactivity as a novel co-repressor

International Nuclear Information System (INIS)

Li, Jin; Lu, Yan; Liu, Ruya; Xiong, Xuelian; Zhang, Zhijian; Zhang, Xianfeng; Ning, Guang; Li, Xiaoying

2011-01-01

Highlights: → DAX1 is co-localized with FXR and interacts with FXR. → DAX1 acts as a negative regulator of FXR. → Three LXXLL motifs in the N-terminus of DAX1 were required. → DAX1 suppresses FXR transactivation by competing with co-activators. -- Abstract: Bile acid receptor FXR (farnesoid X receptor) is a key regulator of hepatic bile acid, glucose and lipid homeostasis through regulation of numerous genes involved in the process of bile acid, triglyceride and glucose metabolism. DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenital critical region on X chromosome, gene 1) is an atypical member of the nuclear receptor family due to lack of classical DNA-binding domains and acts primarily as a co-repressor of many nuclear receptors. Here, we demonstrated that DAX1 is co-localized with FXR in the nucleus and acted as a negative regulator of FXR through a physical interaction with FXR. Our study showed that over-expression of DAX1 down-regulated the expression of FXR target genes, whereas knockdown of DAX1 led to their up-regulation. Furthermore, three LXXLL motifs in the N-terminus of DAX1 were required for the full repression of FXR transactivation. In addition, our study characterized that DAX1 suppresses FXR transactivation via competing with co-activators such as SRC-1 and PGC-1α. In conclusion, DAX1 acts as a co-repressor to negatively modulate FXR transactivity.

Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean.

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Andrew J Burt

Full Text Available Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris. Alleles at the Co-4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08 where Co-4 is localized. Three SCAR markers with known linkage to Co-4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies. It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

Different segregation patterns in five carriers due to a pericentric inversion of chromosome 1.

Science.gov (United States)

Luo, Yuqin; Xu, Chenming; Sun, Yixi; Wang, Liya; Chen, Songchang; Jin, Fan

2014-12-01

Pericentric inversion can produce recombinant gametes; however, meiotic segregation studies on the relationship between the frequency of recombinants and the inverted segment size are rare. Triple-color fluorescence in situ hybridization (FISH) was performed to analyze the meiotic behavior in five inv(1) carriers with different breakpoints. Recombination gametes were absent in Patient 1, whereas the percentages of the recombinants in Patients 2, 3, 4, and 5 were of 9.2%, 15.3%, 17.3%, and 40.9%, respectively. A significant difference was present for the frequencies of the recombinant spermatozoa among the five patients (p 0.05). The meiotic segregation of nine inv(1) carriers (including those presented in this paper) is now available. A significant correlation was discovered between the rate of recombination and the proportion of the chromosome implicated in the inversion (R = 0.9435, p < 0.001). The frequency of the recombinant gametes was directly related to the proportion of the chromosome that was inverted. Sperm-FISH allowed an additional comprehension of the patterns of meiotic segregation and provided accurate genetic counseling.

Figure-ground segregation requires two distinct periods of activity in V1: a transcranial magnetic stimulation study.

Science.gov (United States)

Heinen, Klaartje; Jolij, Jacob; Lamme, Victor A F

2005-09-08

Discriminating objects from their surroundings by the visual system is known as figure-ground segregation. This process entails two different subprocesses: boundary detection and subsequent surface segregation or 'filling in'. In this study, we used transcranial magnetic stimulation to test the hypothesis that temporally distinct processes in V1 and related early visual areas such as V2 or V3 are causally related to the process of figure-ground segregation. Our results indicate that correct discrimination between two visual stimuli, which relies on figure-ground segregation, requires two separate periods of information processing in the early visual cortex: one around 130-160 ms and the other around 250-280 ms.

Tetranucleotide repeat polymorphism at the human prostatic acid phosphatase (ACPP) gene

Energy Technology Data Exchange (ETDEWEB)

Polymeropoulos, M H; Xiao, Hong; Rath, D S; Merril, C R [National Inst. of Mental Health Neuroscience Center, Washington, DC (United States)

1991-09-11

The polymorphic (AAAT){sub n} repeat begins at base pair 2342 of the human prostatic acid phosphatase gene on chromosome 3q21-qter. The polymorphism can be typed using the polymerase chain reaction (PCR) as described previously. The predicted length of the amplified sequence was 275 bp. Co-dominant segregation was observed in two informative families. The human prostatic acid phosphatase gene has been assigned to chromosome 3q21-qter.

La crítica de René Girard al humanismo

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Moreno Fernández, Agustín

2016-06-01

Full Text Available In René Girard’s work there are a lot of critics to the humanism and the humanists. First of all, in this article we will deal with a definition of this concept and his historiographic problem. There is a big contrast between the topics and ideals of the humanism and the mimetic theory. We study the explicit Girard’s critics to the humanists and finally we present one perspective that allows to consider himself like a humanist thinker.La obra de René Girard está salpicada de críticas al humanismo y a los humanistas. En este estudio nos preguntamos en primer lugar qué es el humanismo, haciéndonos cargo de la problemática historiográfica. Presentamos el contraste existente entre los tópicos e ideales humanistas y las ideas que se derivan de la teoría mimética. Estudiamos las críticas explícitas de Girard a los humanistas y, por último, adoptamos una perspectiva que permite calificarlo a él mismo como un humanista.

Applied thermodynamics: Grain boundary segregation

Czech Academy of Sciences Publication Activity Database

Lejček, Pavel; Zheng, L.; Hofmann, S.; Šob, Mojmír

2014-01-01

Roč. 16, č. 3 (2014), s. 1462-1484 ISSN 1099-4300 R&D Projects: GA ČR(CZ) GAP108/12/0311; GA ČR GAP108/12/0144; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68378271 ; RVO:68081723 Keywords : interfacial segregation * Gibbs energy of segregation * enthalpy * entropy * volume * grain boundaries * iron Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.502, year: 2014

Mechanismen der intrinsischen Cisplatinhypersensitivität bei der testikulären Keimzelltumor-Linie NTERA-2D1

OpenAIRE

Alber, Christiane

2011-01-01

Mit Einführung von Cisplatin gelang ein Durchbruch in der Therapie testikulärer Keimzelltumore, deren Heilungsrate auf über 80% gesteigert werden konnte. Die Ursache der Hypersensitivität von Hodenkarzinomen gegenüber Cisplatin ist bis heute nicht abschließend geklärt, für die Medizin jedoch von hohem Interesse, da hieraus möglicherweise neue Ansätze für die Therapie anderer Tumorentitäten gewonnen werden könnten. In der vorliegenden Arbeit konnte die hohe Sensitivität der testikulären Keimze...

Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio Genome

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Daryi Wang

2009-08-01

Full Text Available Neighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson’s correlation coefficient R>0.7 is low (0.24% ~ 0.67%; however, it is still significantly higher than that of random pairs. In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance. Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes’ co-expression are also discussed.

LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes.

Science.gov (United States)

Wang, Dapeng; Zhang, Yubin; Fan, Zhonghua; Liu, Guiming; Yu, Jun

2012-01-01

Animal genes of different lineages, such as vertebrates and arthropods, are well-organized and blended into dynamic chromosomal structures that represent a primary regulatory mechanism for body development and cellular differentiation. The majority of genes in a genome are actually clustered, which are evolutionarily stable to different extents and biologically meaningful when evaluated among genomes within and across lineages. Until now, many questions concerning gene organization, such as what is the minimal number of genes in a cluster and what is the driving force leading to gene co-regulation, remain to be addressed. Here, we provide a user-friendly database-LCGbase (a comprehensive database for lineage-based co-regulated genes)-hosting information on evolutionary dynamics of gene clustering and ordering within animal kingdoms in two different lineages: vertebrates and arthropods. The database is constructed on a web-based Linux-Apache-MySQL-PHP framework and effective interactive user-inquiry service. Compared to other gene annotation databases with similar purposes, our database has three comprehensible advantages. First, our database is inclusive, including all high-quality genome assemblies of vertebrates and representative arthropod species. Second, it is human-centric since we map all gene clusters from other genomes in an order of lineage-ranks (such as primates, mammals, warm-blooded, and reptiles) onto human genome and start the database from well-defined gene pairs (a minimal cluster where the two adjacent genes are oriented as co-directional, convergent, and divergent pairs) to large gene clusters. Furthermore, users can search for any adjacent genes and their detailed annotations. Third, the database provides flexible parameter definitions, such as the distance of transcription start sites between two adjacent genes, which is extendable to genes that flanking the cluster across species. We also provide useful tools for sequence alignment, gene

High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust, anthracnose, and angular leaf spot diseases.

Science.gov (United States)

Valentini, Giseli; Gonçalves-Vidigal, Maria Celeste; Hurtado-Gonzales, Oscar P; de Lima Castro, Sandra Aparecida; Cregan, Perry B; Song, Qijian; Pastor-Corrales, Marcial A

2017-08-01

Co-segregation analysis and high-throughput genotyping using SNP, SSR, and KASP markers demonstrated genetic linkage between Ur-14 and Co-3 4 /Phg-3 loci conferring resistance to the rust, anthracnose and angular leaf spot diseases of common bean. Rust, anthracnose, and angular leaf spot are major diseases of common bean in the Americas and Africa. The cultivar Ouro Negro has the Ur-14 gene that confers broad spectrum resistance to rust and the gene cluster Co-3 4 /Phg-3 containing two tightly linked genes conferring resistance to anthracnose and angular leaf spot, respectively. We used co-segregation analysis and high-throughput genotyping of 179 F 2:3 families from the Rudá (susceptible) × Ouro Negro (resistant) cross-phenotyped separately with races of the rust and anthracnose pathogens. The results confirmed that Ur-14 and Co-3 4 /Phg-3 cluster in Ouro Negro conferred resistance to rust and anthracnose, respectively, and that Ur-14 and the Co-3 4 /Phg-3 cluster were closely linked. Genotyping the F 2:3 families, first with 5398 SNPs on the Illumina BeadChip BARCBEAN6K_3 and with 15 SSR, and eight KASP markers, specifically designed for the candidate region containing Ur-14 and Co-3 4 /Phg-3, permitted the creation of a high-resolution genetic linkage map which revealed that Ur-14 was positioned at 2.2 cM from Co-3 4 /Phg-3 on the short arm of chromosome Pv04 of the common bean genome. Five flanking SSR markers were tightly linked at 0.1 and 0.2 cM from Ur-14, and two flanking KASP markers were tightly linked at 0.1 and 0.3 cM from Co-3 4 /Phg-3. Many other SSR, SNP, and KASP markers were also linked to these genes. These markers will be useful for the development of common bean cultivars combining the important Ur-14 and Co-3 4 /Phg-3 genes conferring resistance to three of the most destructive diseases of common bean.

Genetische Veränderungen an primären Prostatakarzinom-Biopsien in Korrelation zum klinischen Verlauf

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Steiner T

2002-01-01

Full Text Available Die der Entstehung des Prostatakarzinoms zugrundeliegenden bzw. mit einem Progreß vergesellschafteten genetischen Veränderungen sind noch weitgehend unbekannt. Ziel der vorliegenden retrospektiven Untersuchung war die Erfassung genetischer Aberrationen an paraffineigebettetem Material primärer Prostatakarzinom-Biopsien und die Korrelation der Daten zum klinischen Verlauf. In 28 karzinomtragenden primären Prostatabiopsien wurden die Tumorareale gekennzeichnet. Nach Dissektion der Tumorzellen wurden die Proben mittels "comparative genomic hybridization" (CGH analysiert. Daten zum klinischen Verlauf der Patienten wurden erfaßt. Die mittlere Nachbeobachtungszeit betrug 36 Monate, alle Patienten wurden hormonablativ behandelt. 11 Patienten (39 % wiesen unter laufender Therapie einen Tumorprogreß auf. In 25 (88 % der 28 untersuchten Tumorareale konnten genetische Aberrationen detektiert werden, im Mittel fanden wir 4,8 Aberrationen je Tumor. Das Verhältnis Verlust / Zugewinn betrug 1,3 / 1. Folgende chromosomale Veränderungen wurden häufig festgestellt: Verluste von 6q in 40 %; von 8p in 32 %; von 16q in 21 %; von 18q in 21 %; Zugewinne von 8q in 32 %; von 17 in 43 %. In Korrelation zum klinischen Verlauf fand sich ein Zugewinn von 8q signifikant häufiger bei Patienten, welche im Beobachtungszeitraum einen Tumorprogreß entwickelten (64 % vs. 12 %; p = 0,0001. In der primären Tumorbiopsie waren bei progredienten Patienten im Mittel 5,3, bei Patienten ohne Tumorprogreß 3,8 Aberrationen je Tumor nachzuweisen. Unsere Ergebnisse zeigen, daß Veränderungen der Chromosomen 6q, 8, 16q, 17 und 18q regelmäßig beim Prostatakarzinom auftreten. Karzinome mit klinisch ungünstigem Verlauf weisen bereits in der primären Biopsie eine hohe genetische Instabilität auf.

Involvement of co-repressor LUH and the adapter proteins SLK1 and SLK2 in the regulation of abiotic stress response genes in Arabidopsis.

Science.gov (United States)

Shrestha, Barsha; Guragain, Bhuwan; Sridhar, Vaniyambadi V

2014-02-24

During abiotic stress many genes that are important for growth and adaptation to stress are expressed at elevated levels. However, the mechanisms that keep the stress responsive genes from expressing under non stress conditions remain elusive. Recent genetic characterization of the co-repressor LEUNIG_HOMOLOG (LUH) and transcriptional adaptor proteins SEUSS-LIKE1 (SLK1) and SLK2 have been proposed to function redundantly in diverse developmental processes; however their function in the abiotic stress response is unknown. Moreover, the molecular functions of LUH, SLK1 and SLK2 remain obscure. Here, we show the molecular function of LUH, SLK1 and SLK2 and the role of this complex in the abiotic stress response. The luh, slk1 and slk2 mutant plants shows enhanced tolerance to salt and osmotic stress conditions. SLK1 and SLK2 interact physically with the LUFS domain in LUH forming SLK1-LUH and SLK2-LUH co-repressor complexes to inhibit the transcription. LUH has repressor activity, whereas SLK1 and SLK2 function as adaptors to recruit LUH, which in turn recruits histone deacetylase to the target sequences to repress transcription. The stress response genes RD20, MYB2 and NAC019 are expressed at elevated levels in the luh, slk1 and slk2 mutant plants. Furthermore, these stress response genes are associated with decreased nucleosome density and increased acetylation levels at H3K9 and H3K14 in the luh, slk1 and slk2 mutant plants. Our results indicate that SLK1, SLK2 and LUH form a co-repressor complex. LUH represses by means of an epigenetic process involving histone modification to facilitate the condensation of chromatin thus preventing transcription at the target genes.

Lyden Sker - et interview med Torben Ulrich og Søren Kjærgaard

DEFF Research Database (Denmark)

Kristensen, Thomas Bjørnsten

2009-01-01

Da musikeren, poeten og tennisspilleren Torben Ulrich i Seattle mødte jazzpianisten og komponisten Søren Kjærgaard udviklede det sig til en dybdegående udforskning af feltet mellem lyd og ord, stilhed og puls, rum og nærvær. Deres fælles bestræbelser kulminerede i foråret 2009 med det eksperiment......Da musikeren, poeten og tennisspilleren Torben Ulrich i Seattle mødte jazzpianisten og komponisten Søren Kjærgaard udviklede det sig til en dybdegående udforskning af feltet mellem lyd og ord, stilhed og puls, rum og nærvær. Deres fælles bestræbelser kulminerede i foråret 2009 med det...

Calculation and evaluation of the activation cross sections for 187Re(n,2n)186m,gRe reactions

International Nuclear Information System (INIS)

Huang Xiaolong; Lu Hanlin; Zhou Chunmei

1998-01-01

The activation cross sections for 187 Re(n,2n) 186m,g Re reactions are calculated using UNF code. The calculations are in good agreement with the re-evaluated measured data. Finally the excitation function for 187 Re(n,2n) 186m,g Re reactions are evaluated and recommended based on present calculations and evaluated decay data

Intracellular insulin-receptor dissociation and segregation in a rat fibroblast cell line transfected with a human insulin receptor gene

International Nuclear Information System (INIS)

Levy, J.R.; Olefsky, J.M.

1988-01-01

The cellular processing of insulin and insulin receptors was studied using a rat fibroblast cell line that had been transfected with a normal human insulin receptor gene, expressing approximately 500 times the normal number of native fibroblasts insulin receptors. These cells bind and internalize insulin normally. Biochemically assays based on the selective precipitation by polyethylene glycol of intact insulin-receptor complexes but not of free intracellular insulin were developed to study the time course of intracellular insulin-receptor dissociation. Fibroblasts were incubated with radiolabeled insulin at 4 0 C, and internalization of insulin-receptor complexes was initiated by warming the cells to 37 0 C. Within 2 min, 90% of the internalized radioactivity was composed of intact insulin-receptor complexes. The dissociation of insulin from internalized insulin-receptor complexes was markedly inhibited by monensin and chloroquine. Furthermore, chloroquine markedly increased the number of cross-linkable intracellular insulin-receptor complexes, as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis autoradiography. These findings suggest that acidification of intracellular vesicles is responsible for insulin-receptor dissociation. Physical segregation of dissociated intracellular insulin from its receptor was monitored. The results are consistent with the view that segregation of insulin and receptor occurs 5-10 min after initiation of dissociation. These studies demonstrate the intracellular itinerary of insulin-receptor complexes, including internalization, dissociation of insulin from the internalized receptor within an acidified compartment, segregation of insulin from the receptor, and subsequent ligand degradation

Identification and Functional Characterization of a Novel Mutation in the Human Calcium-Sensing Receptor That Co-Segregates With Autosomal-Dominant Hypocalcemia

Directory of Open Access Journals (Sweden)

Anne Qvist Rasmussen

2018-04-01

characteristics of the mutation co-segregated with their individual phenotype.

Plk1 is essential for proper chromosome segregation during meiosis I/meiosis II transition in pig oocytes.

Science.gov (United States)

Zhang, Zixiao; Chen, Changchao; Ma, Liying; Yu, Qiuchen; Li, Shuai; Abbasi, Benazir; Yang, Jiayi; Rui, Rong; Ju, Shiqiang

2017-08-29

Polo-like kinase 1 (Plk1), as a characteristic regulator in meiosis, organizes multiple biological events of cell division. Although Plk1 has been implicated in various functions in somatic cell mitotic processes, considerably less is known regarding its function during the transition from metaphase I (MI) to metaphase II (MII) stage in oocyte meiotic progression. In this study, the possible role of Plk1 during the MI-to-MII stage transition in pig oocytes was addressed. Initially, the spatiotemporal expression and subcellular localization pattern of Plk1 were revealed in pig oocytes from MI to MII stage using indirect immunofluorescence and confocal microscopy imaging techniques combined with western blot analyses. Moreover, a highly selective Plk1 inhibitor, GSK461364, was used to determine the potential role of Plk1 during this MI-to-MII transition progression. Upon expression, Plk1 exhibited a specific dynamic intracellular localization, and co-localization of Plk1 with α-tubulin was revealed in the meiotic spindle of pig oocyte during the transition from MI to MII stage. GSK461364 treatment significantly blocked the first polar body (pbI) emission in a dose-dependent manner and resulted in a failure of meiotic maturation, with a larger percentage of the GSK461364-treated oocytes arresting in the anaphase-telophase I (ATI) stage. Further subcellular structure examination results showed that inhibition of Plk1 with GSK461364 had no visible effect on spindle assembly but caused a significantly higher proportion of the treated oocytes to have obvious defects in homologous chromosome segregation at ATI stage. Thus, these results indicate that Plk1 plays an essential role during the meiosis I/meiosis II transition in porcine oocytes, and the regulation is associated with Plk1's effects on homologous chromosome segregation in the ATI stage.

Polymorphisms of renin-angiotensin system and natriuretic peptide receptor A genes in patients of Greek origin with a history of myocardial infarction.

Science.gov (United States)

Karayannis, George; Tsezou, Aspasia; Giannatou, Eirini; Papanikolaou, Vassilios; Giamouzis, Gregory; Triposkiadis, Filippos

2010-11-01

We assessed the association between (CA)n repeat polymorphism of angiotensinogen (AGT), 250 base pair (bp) insertion/deletion (I/D) of angiotensin-converting enzyme (ACE), tetranucleotide repeat polymorphism (TCTG)n of renin (REN), (CT)n repeat polymorphism of the natriuretic peptide receptor A (NPRA) genes, and the presence and extent of coronary artery disease (CAD) in Greek patients with a history of myocardial infarction (MI). A total of 158 post-MI patients referred for coronary angiography were compared with 144 controls. The SS genotype of the AGT gene was related with an increased risk for 3-vessel CAD (odds ratio [OR], 1.94; 95% confidence interval [CI], 1.05-3.61; P = .041), whereas the SL genotype was related with a decreased risk (OR, 0.44; 95% CI, 0.22-0.87; P = .019). Moreover, there was a trend for the SL genotype of the REN gene toward increased risk for CAD. There was a significant association between (CA)n polymorphism of the AGT gene and the extent of CAD in Greek patients with a history of MI.

Radiation-induced segregation in Cu-Au alloys

International Nuclear Information System (INIS)

Hashimoto, T.; Rehn, L.E.; Okamoto, P.R.

1987-01-01

Radiation-induced segregation in a Cu-lat.% Au alloy was investigated using in-situ Rutherford backscattering spectrometry. Irradiation with 1.8-MeV helium produced nonequilibrium gold atom depletion in the near surface region. The amount of segregation was measured as a function of dose, dose rate, and temperature. Segregation was observed in the temperature range between about 300 and 500 0 C. For a calculated dose rate of 3.9 x 10/sup -5/ dpa/s, the radiation-induced segregation rate peaked near 400 0 C. Theoretical analysis based on the Johnson-Lam model predicted that the amount of segregation would be directly proportional to dose at the early stage of irradiation, would deviate from linearity with a continuously decreasing slope of intermediate doses, and finally approach a constant value after high doses. The analysis also predicted that the segregation rate would vary as the - 1/4th power of the dose rate at constant dose in the low temperature region. These predictions were all verified experimentally. A procedure for extracting relative defect production efficiencies from similar measurements is discussed

ArrayVigil: a methodology for statistical comparison of gene signatures using segregated-one-tailed (SOT) Wilcoxon's signed-rank test.

Science.gov (United States)

Khan, Haseeb Ahmad

2005-01-28

Due to versatile diagnostic and prognostic fidelity molecular signatures or fingerprints are anticipated as the most powerful tools for cancer management in the near future. Notwithstanding the experimental advancements in microarray technology, methods for analyzing either whole arrays or gene signatures have not been firmly established. Recently, an algorithm, ArraySolver has been reported by Khan for two-group comparison of microarray gene expression data using two-tailed Wilcoxon signed-rank test. Most of the molecular signatures are composed of two sets of genes (hybrid signatures) wherein up-regulation of one set and down-regulation of the other set collectively define the purpose of a gene signature. Since the direction of a selected gene's expression (positive or negative) with respect to a particular disease condition is known, application of one-tailed statistics could be a more relevant choice. A novel method, ArrayVigil, is described for comparing hybrid signatures using segregated-one-tailed (SOT) Wilcoxon signed-rank test and the results compared with integrated-two-tailed (ITT) procedures (SPSS and ArraySolver). ArrayVigil resulted in lower P values than those obtained from ITT statistics while comparing real data from four signatures.

Entwicklung einer Methode zur monetären Bewertung des Wassers für ein Unternehmen unter Einbeziehung des Wasser-Fußabdrucks

OpenAIRE

Hentschel, Nora

2011-01-01

Wassernutzung und Abbau der Frischwasser-Ressourcen sind heutzutage ein Thema, das als so wichtig wahrgenommen wird wie der Klimawandel. Wasser wird somit zunehmend Auswirkungen auf den ökonomischen Wert von Unternehmen haben. Ziel der vorliegenden Arbeit ist es, den monetären Wert des Wassers mithilfe des Wasser-Fußabdrucks zu bestimmen. Hierfür werden nach einer kurzen Einführung in Kapitel 2 der ökologische Fußabdruck, der CO2-Fußabdruck und der Wasser-Fußabdruck kurz vorgestellt und in...

The strength of co-authorship in gene name disambiguation

Directory of Open Access Journals (Sweden)

Farkas Richárd

2008-01-01

Full Text Available Abstract Background A biomedical entity mention in articles and other free texts is often ambiguous. For example, 13% of the gene names (aliases might refer to more than one gene. The task of Gene Symbol Disambiguation (GSD – a special case of Word Sense Disambiguation (WSD – is to assign a unique gene identifier for all identified gene name aliases in biology-related articles. Supervised and unsupervised machine learning WSD techniques have been applied in the biomedical field with promising results. We examine here the utilisation potential of the fact – one of the special features of biological articles – that the authors of the documents are known through graph-based semi-supervised methods for the GSD task. Results Our key hypothesis is that a biologist refers to each particular gene by a fixed gene alias and this holds for the co-authors as well. To make use of the co-authorship information we decided to build the inverse co-author graph on MedLine abstracts. The nodes of the inverse co-author graph are articles and there is an edge between two nodes if and only if the two articles have a mutual author. We introduce here two methods using distances (based on the graph of abstracts for the GSD task. We found that a disambiguation decision can be made in 85% of cases with an extremely high (99.5% precision rate just by using information obtained from the inverse co-author graph. We incorporated the co-authorship information into two GSD systems in order to attain full coverage and in experiments our procedure achieved precision of 94.3%, 98.85%, 96.05% and 99.63% on the human, mouse, fly and yeast GSD evaluation sets, respectively. Conclusion Based on the promising results obtained so far we suggest that the co-authorship information and the circumstances of the articles' release (like the title of the journal, the year of publication can be a crucial building block of any sophisticated similarity measure among biological articles

Von kleinen Stupsern und großen Schubsern – Politik und Ethik des Libertären Paternalismus auf dem Prüfstand

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Drerup Johannes

2016-07-01

Full Text Available Das von Cass Sunstein und Richard Thaler ausgearbeitete Projekt eines Libertären Paternalismus stellt fraglos einen der zurzeit meistdiskutierten neopaternalistischen Theorieentwürfe dar. Als hybride Mischung zwischen Theorieprogramm, politischer Bewegung und praxis- und anwendungsorientiertem Policy-Manual, das zuweilen Züge eines populären philosophischen Lebensratgebers trägt, hat Libertärer Paternalismus viel Zuspruch, aber auch heftige Kritik auf sich gezogen, die in diesem Aufsatz auf ihre Plausibilität geprüft werden. Zu diesem Zweck geben die Autoren zunächst einen kurzen Überblick über Ausgangspunkte, Leitorientierungen und Problemvorgaben des Theorie- und Politikprogramms des Libertären Paternalismus. In einem zweiten Schritt werden zentrale (metaphorische Konzepte und Unterscheidungen des libertär paternalistischen Rationales vorgestellt und problematisiert. Daran anschließend werden drei der prominentesten Kritikpunkte an Libertärem Paternalismus auf den Prüfstand gestellt. Hierzu gehören der Manipulationseinwand, Kritiken, die sich auf grundlegende Rechtfertigungsprobleme des Libertären Paternalismus beziehen, und Einwände, die auf langfristige negative Folgen des Nudging verweisen („Slippery-Slope-Argumente“.

The conversion in the René Girard’s mimetic theory

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Agustín Moreno Fernández

2014-12-01

Full Text Available One of the specific peculiarities of René Girard’s mimetic theory is the recovery of the concept of conversion. In this article we expose, in a detailed way, the three senses of the conversion according to his thinking: novelistic, religious and epistemological. There is an interaction between the three senses and also different significations for each other.

Co-factors necessary for PPAR mediated transactivation of endogenous target genes

DEFF Research Database (Denmark)

Grøntved, Lars; Nielsen, Ronni; Stunnenberg, Henk

of endogenous target gene in different cell types are elusive. To mutually compare the ability of the PPAR subtypes to activate endogenous target genes in a given cell, PPARa, PPARb/d and PPARg2 were HA tagged and rapidly, equally and synchronously expressed using adenoviral delivery. Within a few hours after...... subtype specific activation of target genes. Accumulating evidence suggests that transcriptional co-factors can function as master regulators for nuclear receptors and impose promoter selectivity. To study co-factor necessity for PPAR mediated transactivation of endogenous target genes, specific co...

Promotion of Pt-Ru/C catalysts driven by heat treated induced surface segregation for methanol oxidation reaction

International Nuclear Information System (INIS)

Wei Yuchen; Liu Chenwei; Chang Weijung; Wang Kuanwen

2011-01-01

Research highlights: → Thermal treatments on the Pt-Ru/C induce different extents of surface segregation. → O 2 treatment results in obvious Ru segregation and formation of RuO 2 . → Catalysts treated in H 2 have the excellent CO de-poisoning ability. → N 2 treatment suppresses the surface Pt depletion and hence promotes the MOR. - Abstract: Carbon supported Pt-Ru/C (1:1) alloy catalysts supplied by E-TEK are widely used for fuel cell research. Heat treatments in various atmospheres are conducted for the promotion of the methanol oxidation reaction (MOR) and the investigation of the structure-activity relationship (SAR) of the catalysts. The alloy structures, surface compositions, surface species, and electro-catalytic activities of the alloy catalysts are characterized by X-ray diffraction (XRD), temperature-programmed reduction (TPR), X-ray photoelectron spectroscopy (XPS), and cyclic voltammetry (CV), respectively. The as-received Pt-Ru/C catalysts have a Ru rich in the inner core and Pt rich on the outer shell structure. Thermal treatments on the catalysts induce Ru surface segregation in different extents and thereby lead to their alteration of the alloying degrees. O 2 treatment results in obvious Ru segregation and formation of RuO 2 . Catalysts treated in H 2 have the highest I f /I b value in the CV scans among all samples, indicating the catalysts have the excellent CO de-poisoning ability as evidenced by anodic CO stripping experiments. N 2 treatment may serve as an adjustment process for the surface composition and structure of the catalysts, which can suppress the surface Pt depletion (∼60% Pt on the surface), make the components stable and hence promote the MOR significantly.

Promotion of Pt-Ru/C catalysts driven by heat treated induced surface segregation for methanol oxidation reaction

Energy Technology Data Exchange (ETDEWEB)

Wei Yuchen; Liu Chenwei; Chang Weijung [Institute of Materials Science and Engineering, National Central University, Taoyuan 32001, Taiwan (China); Wang Kuanwen, E-mail: kuanwen.wang@gmail.com [Institute of Materials Science and Engineering, National Central University, Taoyuan 32001, Taiwan (China)

2011-01-12

Research highlights: > Thermal treatments on the Pt-Ru/C induce different extents of surface segregation. > O{sub 2} treatment results in obvious Ru segregation and formation of RuO{sub 2}. > Catalysts treated in H{sub 2} have the excellent CO de-poisoning ability. > N{sub 2} treatment suppresses the surface Pt depletion and hence promotes the MOR. - Abstract: Carbon supported Pt-Ru/C (1:1) alloy catalysts supplied by E-TEK are widely used for fuel cell research. Heat treatments in various atmospheres are conducted for the promotion of the methanol oxidation reaction (MOR) and the investigation of the structure-activity relationship (SAR) of the catalysts. The alloy structures, surface compositions, surface species, and electro-catalytic activities of the alloy catalysts are characterized by X-ray diffraction (XRD), temperature-programmed reduction (TPR), X-ray photoelectron spectroscopy (XPS), and cyclic voltammetry (CV), respectively. The as-received Pt-Ru/C catalysts have a Ru rich in the inner core and Pt rich on the outer shell structure. Thermal treatments on the catalysts induce Ru surface segregation in different extents and thereby lead to their alteration of the alloying degrees. O{sub 2} treatment results in obvious Ru segregation and formation of RuO{sub 2}. Catalysts treated in H{sub 2} have the highest I{sub f}/I{sub b} value in the CV scans among all samples, indicating the catalysts have the excellent CO de-poisoning ability as evidenced by anodic CO stripping experiments. N{sub 2} treatment may serve as an adjustment process for the surface composition and structure of the catalysts, which can suppress the surface Pt depletion ({approx}60% Pt on the surface), make the components stable and hence promote the MOR significantly.

Molecular implications from ssr markers for stripe rust (puccinia striiformis F.Sp. tritici) resistance gene in bread wheat line N95175

International Nuclear Information System (INIS)

Ali, M.; Ji, W.G.; Hu, Y.G; Zhong, H.; Wang, C.Y.; Baloch, G.M.

2010-01-01

Stripe rust caused by Puccinia striiformis f. sp. tritici is one of the most devastating diseases of wheat in China as well as in Pakistan. In the present studies F2 population was established by crossing N95175 resistant to stripe rust race CYR32 with two susceptible lines Huixianhong and Abbondanza to molecularly tag resistance gene existing in wheat line N95175. The segregation of phenotype was accorded with an expected 3:1 ratio in both combinations studied and fit the model of a single dominant gene controlling stripe rust resistance in N95175. Thirty five SSR primer pairs were screened on the parents and bulks and also on individuals since resistance gene to be located in chromosome 1B. The result indicated that most of resistant plants amplified same band as resistant parent while susceptible plants amplified same as susceptible parents studied and considered that markers co-segregated with resistant loci in N95175. This yellow rust resistance gene was considered to be Yr26 originally thought to be also located in chromosome arm 1BS linked to marker loci Xgwm273 and Xgwm11 with genetic distances ranging from 1.075cM to 2.74cM in both combinations studied. However, the closest loci were observed 2.67cM for Xgwm273 and 1.075cM for Xgwm11 in Huixianhong XN95175 and Abbondanza XN95175 crosses respectively. Hence, it has been concluded that the PCR-based micro satellite markers Xgwm273 and Xgwm11 located in chromosome 1B were shown to be very effective for the detection of Yr26 gene in segregating population and can be applied in future wheat breeding strategies. (author)

Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family.

Science.gov (United States)

Rafiullah, Rafiullah; Aslamkhan, Muhammad; Paramasivam, Nagarajan; Thiel, Christian; Mustafa, Ghulam; Wiemann, Stefan; Schlesner, Matthias; Wade, Rebecca C; Rappold, Gudrun A; Berkel, Simone

2016-02-01

Intellectual disability (ID) is a neurodevelopmental disorder affecting 1%-3% of the population worldwide. It is characterised by high phenotypic and genetic heterogeneity and in most cases the underlying cause of the disorder is unknown. In our study we investigated a large consanguineous family from Baluchistan, Pakistan, comprising seven affected individuals with a severe form of autosomal recessive ID (ARID) and epilepsy, to elucidate a putative genetic cause. Whole exome sequencing (WES) of a trio, including a child with ID and epilepsy and its healthy parents that were part of this large family, revealed a homozygous missense variant p.R53Q in the lectin mannose-binding 2-like (LMAN2L) gene. This homozygous variant was co-segregating in the family with the phenotype of severe ID and infantile epilepsy; unaffected family members were heterozygous variant carriers. The variant was predicted to be pathogenic by five different in silico programmes and further three-dimensional structure modelling of the protein suggests that variant p.R53Q may impair protein-protein interaction. LMAN2L (OMIM: 609552) encodes for the lectin, mannose-binding 2-like protein which is a cargo receptor in the endoplasmic reticulum important for glycoprotein transport. Genome-wide association studies have identified an association of LMAN2L to different neuropsychiatric disorders. This is the first report linking LMAN2L to a phenotype of severe ARID and seizures, indicating that the deleterious homozygous p.R53Q variant very likely causes the disorder. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Effector-mediated discovery of a novel resistance gene against Bremia lactucae in a nonhost lettuce species.

Science.gov (United States)

Giesbers, Anne K J; Pelgrom, Alexandra J E; Visser, Richard G F; Niks, Rients E; Van den Ackerveken, Guido; Jeuken, Marieke J W

2017-11-01

Candidate effectors from lettuce downy mildew (Bremia lactucae) enable high-throughput germplasm screening for the presence of resistance (R) genes. The nonhost species Lactuca saligna comprises a source of B. lactucae R genes that has hardly been exploited in lettuce breeding. Its cross-compatibility with the host species L. sativa enables the study of inheritance of nonhost resistance (NHR). We performed transient expression of candidate RXLR effector genes from B. lactucae in a diverse Lactuca germplasm set. Responses to two candidate effectors (BLR31 and BLN08) were genetically mapped and tested for co-segregation with disease resistance. BLN08 induced a hypersensitive response (HR) in 55% of the L. saligna accessions, but responsiveness did not co-segregate with resistance to Bl:24. BLR31 triggered an HR in 5% of the L. saligna accessions, and revealed a novel R gene providing complete B. lactucae race Bl:24 resistance. Resistant hybrid plants that were BLR31 nonresponsive indicated other unlinked R genes and/or nonhost QTLs. We have identified a candidate avirulence effector of B. lactucae (BLR31) and its cognate R gene in L. saligna. Concurrently, our results suggest that R genes are not required for NHR of L. saligna. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Characterization of differentially expressed genes using high-dimensional co-expression networks

DEFF Research Database (Denmark)

Coelho Goncalves de Abreu, Gabriel; Labouriau, Rodrigo S.

2010-01-01

We present a technique to characterize differentially expressed genes in terms of their position in a high-dimensional co-expression network. The set-up of Gaussian graphical models is used to construct representations of the co-expression network in such a way that redundancy and the propagation...... that allow to make effective inference in problems with high degree of complexity (e.g. several thousands of genes) and small number of observations (e.g. 10-100) as typically occurs in high throughput gene expression studies. Taking advantage of the internal structure of decomposable graphical models, we...... construct a compact representation of the co-expression network that allows to identify the regions with high concentration of differentially expressed genes. It is argued that differentially expressed genes located in highly interconnected regions of the co-expression network are less informative than...

Thermal Coefficient of Linear Expansion Modified by Dendritic Segregation in Nickel-Iron Alloys

Science.gov (United States)

Ogorodnikova, O. M.; Maksimova, E. V.

2018-05-01

The paper presents investigations of thermal properties of Fe-Ni and Fe-Ni-Co casting alloys affected by the heterogeneous distribution of their chemical elements. It is shown that nickel dendritic segregation has a negative effect on properties of studied invars. A mathematical model is proposed to explore the influence of nickel dendritic segregation on the thermal coefficient of linear expansion (TCLE) of the alloy. A computer simulation of TCLE of Fe-Ni-Co superinvars is performed with regard to a heterogeneous distribution of their chemical elements over the whole volume. The ProLigSol computer software application is developed for processing the data array and results of computer simulation.

Review of Formen des Klärens by Christian Erbacher

Directory of Open Access Journals (Sweden)

Tea Jankovic

2016-06-01

Full Text Available Book review of Christian Erbacher's Formen des Klärens, Literarisch-Philosophische Darstellungsmittel in Wittgensteins Schriften, Münster: mentis 2015. *** Christian Erbacher’s Formen des Klärens, Literarisch-Philosophische Darstellungsmittel in Wittgensteins Schriften, which I would translate as Forms of Elucidating, Literary-Philosophical Means of Presentation in Wittgenstein’s Works, comprises and critically analyzes the most important phases of almost a hundred years of both English and German speaking Wittgenstein scholarship on the form of his literary-philosophical presentation. Furthermore, Erbacher demonstrates a thorough first hand knowledge of Wittgenstein’s manuscripts and manner of work, while at the same time offering an interpretation of the Tractatus logico-philosophicus, as well as later works, that is capable of comprehending both Wittgenstein’s serious and intense ethical and aesthetic preoccupations, as well as his significant contributions to logic and philosophy of language. Furthermore, despite its density, Erbacher’s slender book admirably achieves an elegant lucidity. Thus it performatively shows the unity of aesthetic-rhetorical form and philosophical content, as well as the ethical ideal of clarity at the core of Wittgenstein’s concerns.

Surface Segregation in YSZ

DEFF Research Database (Denmark)

Bay, Lasse; Zachau-Christiansen, Birgit; Jacobsen, Torben

1998-01-01

The space charge layer formed due to segregation of yttria and oxygen ion vacancies in YSZ is described by a simple model. Effects of impurities segregation are omitted.......The space charge layer formed due to segregation of yttria and oxygen ion vacancies in YSZ is described by a simple model. Effects of impurities segregation are omitted....

Genetic analysis and fine mapping of LH1 and LH2, a set of complementary genes controlling late heading in rice (Oryza sativa L.).

Science.gov (United States)

Liu, Shuang; Wang, Feng; Gao, Li Jun; Li, Jin Hua; Li, Rong Bai; Gao, Han Liang; Deng, Guo Fu; Yang, Jin Shui; Luo, Xiao Jin

2012-12-01

Heading date in rice (Oryza sativa L.) is a critical agronomic trait with a complex inheritance. To investigate the genetic basis and mechanism of gene interaction in heading date, we conducted genetic analysis on segregation populations derived from crosses among the indica cultivars Bo B, Yuefeng B and Baoxuan 2. A set of dominant complementary genes controlling late heading, designated LH1 and LH2, were detected by molecular marker mapping. Genetic analysis revealed that Baoxuan 2 contains both dominant genes, while Bo B and Yuefeng B each possess either LH1 or LH2. Using larger populations with segregant ratios of 3 : 1, we fine-mapped LH1 to a 63-kb region near the centromere of chromosome 7 flanked by markers RM5436 and RM8034, and LH2 to a 177-kb region on the short arm of chromosome 8 between flanking markers Indel22468-3 and RM25. Some candidate genes were identified through sequencing of Bo B and Yuefeng B in these target regions. Our work provides a solid foundation for further study on gene interaction in heading date and has application in marker-assisted breeding of photosensitive hybrid rice in China.

Multigenerational Brazilian family with malignant hyperthermia and a novel mutation in the RYR1 gene.

Science.gov (United States)

Matos, A R; Sambuughin, N; Rumjanek, F D; Amoedo, N D; Cunha, L B P; Zapata-Sudo, G; Sudo, R T

2009-12-01

Malignant hyperthermia (MH) is a pharmacogenetic disease triggered in susceptible individuals by the administration of volatile halogenated anesthetics and/or succinylcholine, leading to the development of a hypermetabolic crisis, which is caused by abnormal release of Ca2+ from the sarcoplasmic reticulum, through the Ca2+ release channel ryanodine receptor 1 (RyR1). Mutations in the RYR1 gene are associated with MH in the majority of susceptible families. Genetic screening of a 5-generation Brazilian family with a history of MH-related deaths and a previous MH diagnosis by the caffeine halothane contracture test (CHCT) in some individuals was performed using restriction and sequencing analysis. A novel missense mutation, Gly4935Ser, was found in an important functional and conserved locus of this gene, the transmembrane region of RyR1. In this family, 2 MH-susceptible individuals previously diagnosed with CHCT carry this novel mutation and another 24 not previously diagnosed members also carry it. However, this same mutation was not found in another MH-susceptible individual whose CHCT was positive to the test with caffeine but not to the test with halothane. None of the 5 MH normal individuals of the family, previously diagnosed by CHCT, carry this mutation, nor do 100 controls from control Brazilian and USA populations. The Gly4932Ser variant is a candidate mutation for MH, based on its co-segregation with disease phenotype, absence among controls and its location within the protein.

Development and dissection of diagnostic SNP markers for the downy mildew resistance genes Pl Arg and Pl 8 and maker-assisted gene pyramiding in sunflower (Helianthus annuus L.).

Science.gov (United States)

Qi, L L; Talukder, Z I; Hulke, B S; Foley, M E

2017-06-01

Diagnostic DNA markers are an invaluable resource in breeding programs for successful introgression and pyramiding of disease resistance genes. Resistance to downy mildew (DM) disease in sunflower is mediated by Pl genes which are known to be effective against the causal fungus, Plasmopara halstedii. Two DM resistance genes, Pl Arg and Pl 8 , are highly effective against P. halstedii races in the USA, and have been previously mapped to the sunflower linkage groups (LGs) 1 and 13, respectively, using simple sequence repeat (SSR) markers. In this study, we developed high-density single nucleotide polymorphism (SNP) maps encompassing the Pl arg and Pl 8 genes and identified diagnostic SNP markers closely linked to these genes. The specificity of the diagnostic markers was validated in a highly diverse panel of 548 sunflower lines. Dissection of a large marker cluster co-segregated with Pl Arg revealed that the closest SNP markers NSA_007595 and NSA_001835 delimited Pl Arg to an interval of 2.83 Mb on the LG1 physical map. The SNP markers SFW01497 and SFW06597 delimited Pl 8 to an interval of 2.85 Mb on the LG13 physical map. We also developed sunflower lines with homozygous, three gene pyramids carrying Pl Arg , Pl 8 , and the sunflower rust resistance gene R 12 using the linked SNP markers from a segregating F 2 population of RHA 340 (carrying Pl 8 )/RHA 464 (carrying Pl Arg and R 12 ). The high-throughput diagnostic SNP markers developed in this study will facilitate marker-assisted selection breeding, and the pyramided sunflower lines will provide durable resistance to downy mildew and rust diseases.

Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids.

Science.gov (United States)

Lu, X; Zhou, H; Pan, Y-B; Chen, C Y; Zhu, J R; Chen, P H; Li, Y-R; Cai, Q; Chen, R K

2015-12-28

No information is available on segregation analysis of DNA markers involving both pollen and self-progeny. Therefore, we used capillary electrophoresis- and fluorescence-based DNA fingerprinting together with single pollen collection and polymerase chain reaction (PCR) to investigate simple sequence repeat (SSR) marker segregation among 964 single pollens and 288 self-progenies (S1) of sugarcane cultivar LCP 85-384. Twenty SSR DNA fragments (alleles) were amplified by five polymorphic SSR markers. Only one non-parental SSR allele was observed in 2392 PCRs. SSR allele inheritance was in accordance with Mendelian laws of segregation and independent assortment. Highly significant correlation coefficients were found between frequencies of observed and expected genotypes in pollen and S1 populations. Within the S1 population, the most frequent genotype of each SSR marker was the parental genotype of the same marker. The number of genotypes was higher in pollen than S1 population. PIC values of the five SSR markers were greater in pollen than S1 populations. Eleven of 20 SSR alleles (55%) were segregated in accordance with Mendelian segregation ratios expected from pollen and S1 populations of a 2n = 10x polyploid. Six of 20 SSR alleles were segregated in a 3:1 (presence:absence) ratio and were simplex markers. Four and one alleles were segregated in 77:4 and 143:1 ratios and considered duplex and triplex markers, respectively. Segregation ratios of remaining alleles were unexplainable. The results provide information about selection of crossing parents, estimation of seedling population optimal size, and promotion of efficient selection, which may be valuable for sugarcane breeders.

Segregation and stability at Pt3Ni(1 1 1) surfaces and Pt75Ni25 nanoparticles

International Nuclear Information System (INIS)

Fowler, Ben; Lucas, Christopher A.; Omer, Ahmed; Wang, Guofeng; Stamenkovic, Vojislav R.; Markovic, Nenad M.

2008-01-01

Using in situ surface X-ray diffraction we have determined the atomic structure and stability of a Pt 3 Ni(1 1 1) surface in the electrochemical environment. Surface segregation leads to a pure Pt(1 1 1) skin with enrichment of Ni in the sub-surface atomic layer that determines the surface electronic structure. The Pt-skin surface exhibits inward relaxation upon the adsorption of oxygenated species and this explains the surface stability compared to pure Pt(1 1 1). Using Monte Carlo calculations it is shown that nanoparticles with the same surface composition and stochiometry are energetically stable

Two non-target recessive genes confer resistance to the anti-oomycete microtubule inhibitor zoxamide in Phytophthora capsici.

Directory of Open Access Journals (Sweden)

Yang Bi

Full Text Available This study characterized isolates of P. capsici that had developed a novel mechanism of resistance to zoxamide, which altered the minimum inhibition concentration (MIC but not the EC50. Molecular analysis revealed that the β-tubulin gene of the resistant isolates contained no mutations and was expressed at the same level as in zoxamide-sensitive isolates. This suggested that P. capsici had developed a novel non-target-site-based resistance to zoxamide. Analysis of the segregation ratio of zoxamide-resistance in the sexual progeny of the sensitive isolates PCAS1 and PCAS2 indicated that the resistance to zoxamide was controlled by one or more recessive nuclear genes. Furthermore, the segregation of resistance in the F1, F2, and BC1 progeny was in accordance with the theoretical ratios of the χ(2 test (P>0.05, which suggested that the resistance to zoxamide was controlled by two recessive genes, and that resistance to zoxamide occurred when at least one pair of these alleles was homozygous. This implies that the risk of zoxamide-resistance in P. capsici is low to moderate. Nevertheless this potential for resistance should be monitored closely, especially if two compatible mating types co-exist in the same field.

An unedited 1.1 kb mitochondrial orfB gene transcript in the Wild Abortive Cytoplasmic Male Sterility (WA-CMS system of Oryza sativa L. subsp. indica

Directory of Open Access Journals (Sweden)

Maiti Mrinal K

2010-03-01

Full Text Available Abstract Background The application of hybrid rice technology has significantly increased global rice production during the last three decades. Approximately 90% of the commercially cultivated rice hybrids have been derived through three-line breeding involving the use of WA-CMS lines. It is believed that during the 21st century, hybrid rice technology will make significant contributions to ensure global food security. This study examined the poorly understood molecular basis of the WA-CMS system in rice. Results RFLPs were detected for atp6 and orfB genes in sterile and fertile rice lines, with one copy of each in the mt-genome. The RNA profile was identical in both lines for atp6, but an additional longer orfB transcript was identified in sterile lines. 5' RACE analysis of the long orfB transcript revealed it was 370 bp longer than the normal transcript, with no indication it was chimeric when compared to the genomic DNA sequence. cDNA clones of the longer orfB transcript in sterile lines were sequenced and the transcript was determined unedited. Sterile lines were crossed with the restorer and maintainer lines, and fertile and sterile F1 hybrids were respectively generated. Both hybrids contained two types of orfB transcripts. However, the long transcript underwent editing in the fertile F1 hybrids and remained unedited in the sterile lines. Additionally, the editing of the 1.1 kb orfB transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny; and the presence of unedited long orfB transcripts was detected in the sterile plants from the F2 segregating population. Conclusion This study helped to assign plausible operative factors responsible for male-sterility in the WA cytoplasm of rice. A new point of departure to dissect the mechanisms governing the CMS-WA system in rice has been identified, which can be applied to further harness the opportunities afforded by hybrid vigor in rice.

Human estrogen receptor (ESR) gene locus: PssI dimorphism

Energy Technology Data Exchange (ETDEWEB)

Coleman, R T; Taylor, J E; Frossard, P M [California Biotechnology Inc., Mountain View, CA (USA); Shine, J J [Garvan Institute, Darlinghurst (Australia)

1988-07-25

pESR-2, a 2.1 kb partial cDNA containing the entire translated sequence of the human estrogen receptor mRNA isolated from MCF-7 human breast cancer cells, was subcloned in the Eco RI site of pBR322. PssI (PuGGNCCPy) identifies a single two-allele polymorphism with bands at either 1.7 or 1.4 kb, as well as invariant bands at 12.6, 9.3, 4.1, 3.7, 2.4, 2.2, and 1.2 kb. Its frequency was studied in 77 unrelated North American Caucasians. The human estrogen receptor gene has been localized to 6q24 -- q27 by in situ hybridization. Co-dominant segregation is demonstrated in one family (8 individuals).

The multiple roles of Bub1 in chromosome segregation during mitosis and meiosis

Energy Technology Data Exchange (ETDEWEB)

Marchetti, Francesco; Venkatachalam, Sundaresan

2009-06-19

Aneuploidy, any deviation from an exact multiple of the haploid number of chromosomes, is a common occurrence in cancer and represents the most frequent chromosomal disorder in newborns. Eukaryotes have evolved mechanisms to assure the fidelity of chromosome segregation during cell division that include a multiplicity of checks and controls. One of the main cell division control mechanisms is the spindle assembly checkpoint (SAC) that monitors the proper attachment of chromosomes to spindle fibers and prevents anaphase until all kinetochores are properly attached. The mammalian SAC is composed by at least 14 evolutionary-conserved proteins that work in a coordinated fashion to monitor the establishment of amphitelic attachment of all chromosomes before allowing cell division to occur. Among the SAC proteins, the budding uninhibited by benzimidazole protein 1 (Bub1), is a highly conserved protein of prominent importance for the proper functioning of the SAC. Studies have revealed many roles for Bub1 in both mitosis and meiosis, including the localization of other SAC proteins to the kinetochore, SAC signaling, metaphase congression and the protection of the sister chromatid cohesion. Recent data show striking sex specific differences in the response to alterations in Bub1 activity. Proper Bub1 functioning is particularly important during oogenesis in preventing the generation of aneuploid gametes that can have detrimental effects on the health status of the fetus and the newborn. These data suggest that Bub1 is a master regulator of SAC and chromosomal segregation in both mitosis and meiosis. Elucidating its many essential functions in regulating proper chromosome segregation can have important consequences for preventing tumorigenesis and developmental abnormalities.

A PLSPM-Based Test Statistic for Detecting Gene-Gene Co-Association in Genome-Wide Association Study with Case-Control Design

Science.gov (United States)

Zhang, Xiaoshuai; Yang, Xiaowei; Yuan, Zhongshang; Liu, Yanxun; Li, Fangyu; Peng, Bin; Zhu, Dianwen; Zhao, Jinghua; Xue, Fuzhong

2013-01-01

For genome-wide association data analysis, two genes in any pathway, two SNPs in the two linked gene regions respectively or in the two linked exons respectively within one gene are often correlated with each other. We therefore proposed the concept of gene-gene co-association, which refers to the effects not only due to the traditional interaction under nearly independent condition but the correlation between two genes. Furthermore, we constructed a novel statistic for detecting gene-gene co-association based on Partial Least Squares Path Modeling (PLSPM). Through simulation, the relationship between traditional interaction and co-association was highlighted under three different types of co-association. Both simulation and real data analysis demonstrated that the proposed PLSPM-based statistic has better performance than single SNP-based logistic model, PCA-based logistic model, and other gene-based methods. PMID:23620809

Low pH induces co-ordinate regulation of gene expression in oesophageal cells.

Science.gov (United States)

Duggan, Shane P; Gallagher, William M; Fox, Edward J P; Abdel-Latif, Mohammed M; Reynolds, John V; Kelleher, Dermot

2006-02-01

The development of gastro-oesophageal reflux disease (GORD) is known to be a causative risk factor in the evolution of adenocarcinoma of the oesophagus. The major component of this reflux is gastric acid. However, the impact of low pH on gene expression has not been extensively studied in oesophageal cells. This study utilizes a transcriptomic and bioinformatic approach to assess regulation of gene expression in response to low pH. In more detail, oesophageal adenocarcinoma cell lines were exposed to a range of pH environments. Affymetrix microarrays were used for gene-expression analysis and results were validated using cycle limitation and real-time RT-PCR analysis, as well as northern and western blotting. Comparative promoter transcription factor binding site (TFBS) analysis (MatInspector) of hierarchically clustered gene-expression data was employed to identify the elements which may co-ordinately regulate individual gene clusters. Initial experiments demonstrated maximal induction of EGR1 gene expression at pH 6.5. Subsequent array experimentation revealed significant induction of gene expression from such functional categories as DNA damage response (EGR1-4, ATF3) and cell-cycle control (GADD34, GADD45, p57). Changes in expression of EGR1, EGR3, ATF3, MKP-1, FOSB, CTGF and CYR61 were verified in separate experiments and in a variety of oesophageal cell lines. TFBS analysis of promoters identified transcription factors that may co-ordinately regulate gene-expression clusters, Cluster 1: Oct-1, AP4R; Cluster 2: NF-kB, EGRF; Cluster 3: IKRS, AP-1F. Low pH has the ability to induce genes and pathways which can provide an environment suitable for the progression of malignancy. Further functional analysis of the genes and clusters identified in this low pH study is likely to lead to new insights into the pathogenesis and therapeutics of GORD and oesophageal cancer.

Two critical periods in early visual cortex during figure–ground segregation

Science.gov (United States)

Wokke, Martijn E; Sligte, Ilja G; Steven Scholte, H; Lamme, Victor A F

2012-01-01

The ability to distinguish a figure from its background is crucial for visual perception. To date, it remains unresolved where and how in the visual system different stages of figure–ground segregation emerge. Neural correlates of figure border detection have consistently been found in early visual cortex (V1/V2). However, areas V1/V2 have also been frequently associated with later stages of figure–ground segregation (such as border ownership or surface segregation). To causally link activity in early visual cortex to different stages of figure–ground segregation, we briefly disrupted activity in areas V1/V2 at various moments in time using transcranial magnetic stimulation (TMS). Prior to stimulation we presented stimuli that made it possible to differentiate between figure border detection and surface segregation. We concurrently recorded electroencephalographic (EEG) signals to examine how neural correlates of figure–ground segregation were affected by TMS. Results show that disruption of V1/V2 in an early time window (96–119 msec) affected detection of figure stimuli and affected neural correlates of figure border detection, border ownership, and surface segregation. TMS applied in a relatively late time window (236–259 msec) selectively deteriorated performance associated with surface segregation. We conclude that areas V1/V2 are not only essential in an early stage of figure–ground segregation when figure borders are detected, but subsequently causally contribute to more sophisticated stages of figure–ground segregation such as surface segregation. PMID:23170239

Two critical periods in early visual cortex during figure-ground segregation.

Science.gov (United States)

Wokke, Martijn E; Sligte, Ilja G; Steven Scholte, H; Lamme, Victor A F

2012-11-01

The ability to distinguish a figure from its background is crucial for visual perception. To date, it remains unresolved where and how in the visual system different stages of figure-ground segregation emerge. Neural correlates of figure border detection have consistently been found in early visual cortex (V1/V2). However, areas V1/V2 have also been frequently associated with later stages of figure-ground segregation (such as border ownership or surface segregation). To causally link activity in early visual cortex to different stages of figure-ground segregation, we briefly disrupted activity in areas V1/V2 at various moments in time using transcranial magnetic stimulation (TMS). Prior to stimulation we presented stimuli that made it possible to differentiate between figure border detection and surface segregation. We concurrently recorded electroencephalographic (EEG) signals to examine how neural correlates of figure-ground segregation were affected by TMS. Results show that disruption of V1/V2 in an early time window (96-119 msec) affected detection of figure stimuli and affected neural correlates of figure border detection, border ownership, and surface segregation. TMS applied in a relatively late time window (236-259 msec) selectively deteriorated performance associated with surface segregation. We conclude that areas V1/V2 are not only essential in an early stage of figure-ground segregation when figure borders are detected, but subsequently causally contribute to more sophisticated stages of figure-ground segregation such as surface segregation.

Metastasis: objections to the same-gene model

NARCIS (Netherlands)

Bernards, R.A.; Weinberg, R.A.

2002-01-01

Sir— The model of cancer metastasis suggested by René Bernards and Robert A. Weinberg in their Concepts essay (Nature 418, 823; 2002) is, in my view, a tautology. The suggestion that the same genes are exclusively responsible both for cancer-cell metastasis and for the emergence

Reanalysis of multi-temporal aerial images of Storglaciären, Sweden (1959–99 – Part 1: Determination of length, area, and volume changes

Directory of Open Access Journals (Sweden)

W. Haeberli

2010-09-01

Full Text Available Storglaciären, located in the Kebnekaise massif in northern Sweden, has a long history of glaciological research. Early photo documentations date back to the late 19th century. Measurements of front position variations and distributed mass balance have been carried out since 1910 and 1945/46, respectively. In addition to these in-situ measurements, aerial photographs have been taken at decadal intervals since the beginning of the mass balance monitoring program and were used to produce topographic glacier maps. Inaccuracies in the maps were a challenge to early attempts to derive glacier volume changes and resulted in major differences when compared to the direct glaciological mass balances. In this study, we reanalyzed dia-positives of the original aerial photographs of 1959, -69, -80, -90 and -99 based on consistent photogrammetric processing. From the resulting digital elevation models and orthophotos, changes in length, area, and volume of Storglaciären were computed between the survey years, including an assessment of related errors. Between 1959 and 1999, Storglaciären lost an ice volume of 19×106 m3, which corresponds to a cumulative ice thickness loss of 5.69 m and a mean annual loss of 0.14 m. This ice loss resulted largely from a strong volume loss during the period 1959–80 and was partly compensated during the period 1980–99. As a consequence, the glacier shows a strong retreat in the 1960s, a slowing in the 1970s, and pseudo-stationary conditions in the 1980s and 1990s.

FePt and CoPt nanoparticles prepared by micellar method. Effects of A1{yields}L1{sub 0} transition on oxidation resistance and magnetic properties

Energy Technology Data Exchange (ETDEWEB)

Han, Luyang

2011-02-15

In this thesis FePt and CoPt alloy nanoparticles are prepared with reverse micelles. The metallic nanoparticles with diameters of 2-12 nm and interparticle distances of 20-140 nm are obtained on Si substrates. The magnetic properties of FePt and CoPt nanoparticles as well as oxidation behavior of FePt nanoparticles are investigated. X-ray magnetic circular dichroism (XMCD) measurements on 5.8 nm FePt nanoparticles after hydrogen plasma reduction at 300 C reveals that the magnetic moment per Fe atom and magnetic anisotropy energy match chemically disordered FePt in A1 phase. Annealing at 650 C transform portion of FePt particles to chemically ordered L1{sub 0} phase. The presense of nanoparticles in L1{sub 0} phase is identified by high-resolution transmission electronmicroscopy (HRTEM) investigation, where it is also observed that large fraction of the particles contain defects such as twin boundaries and stacking faults. By increasing the annealing temperature or prolonging annealing time, ratio of transformed particles increases. The average magnetic anisotropy energy of the transformed particles is below 30% of the value of bulk FePt in L1{sub 0} phase. Annealing at above 750 C, however, decreases the average magnetic anisotropy in the sample. Similar A1 {yields} L1{sub 0} transition is observed in FePt nanoparticles with different diameters as well as in CoPt nanoparticles. The spin moment of Fe in FePt nanoparticles decreases with smaller particle diameter, while the orbital moment stays almost constant. Magnetic moments at room temperature are significantly reduced compared to those at low temperature, suggesting the Curie temperatures in FePt and CoPt nanoparticles are significantly lower than in the bulk. The annealing also induces Pt segregation towards the surface in FePt nanoparticles, which is identified by the decreased apparent Fe content measured by X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS). The segregation of Pt

Solidification Segregation and Homogenization Behavior of 1Cr-1.25Mo-0.25V Steel Ingot

Energy Technology Data Exchange (ETDEWEB)

Kim, Dong-Bae [Dae-gu Mechatronics and Materials Institute, Daegu (Korea, Republic of); Na, Young-Sang; Seo, Seong-Moon [Korea Institute of Materials Science, Changwon (Korea, Republic of); Lee, Je-Hyun [Changwon National University, Changwon (Korea, Republic of)

2016-09-15

As a first step to optimizing the homogenization heat treatment following high temperature upset forging, the solidification segregation and the homogenization behaviors of solute elements were quantitatively analyzed for 1Cr-1.25Mo-0.25V steel ingot by electron probe micro-analysis (EPMA). The random sampling approach, which was designed to generate continuous compositional profiles of each solute element, was employed to clarify the segregation and homogenization behaviors. In addition, ingot castings of lab-scale and a 16-ton-sized 1Cr-1.25Mo-0.25V steel were simulated using the finite element method in three dimensions to understand the size effect of the ingot on the microsegregation and its reduction during the homogenization heat treatment. It was found that the microsegregation in a large-sized ingot was significantly reduced by the promotion of solid state diffusion due to the extremely low cooling rate. On the other hand, from the homogenization point of view, increasing the ingot size causes a dramatic increase in the dendrite arm spacing, and hence the homogenization of microsegregation in a large-sized ingot appears to be practically difficult.

Co-segregation of Norrie disease and idiopathic pulmonary hypertension in a family with a microdeletion of the NDP region at Xp11.3-p11.4.

Science.gov (United States)

Staropoli, John F; Xin, Winnie; Sims, Katherine B

2010-11-01

Norrie disease is a rare X-linked congenital retinal vasculopathy that may be accompanied by sensorineural deafness, mental retardation, and other neurological deficits. Here we present a family in which Norrie disease co-segregated with either early-onset idiopathic pulmonary hypertension or sudden death preceded by a period of progressive dyspnea. Neither Norrie disease, nor its atypical variants described to date, have been associated with this extended clinical phenotype. Molecular analysis of the Norrie disease gene (NDP) and adjacent loci was performed by multiplex ligation-dependent probe amplification and comparative genomic hybridisation. Affected males in this family showed an inherited hemizygous deletion restricted to NDP and two immediately telomeric genes, monoamine oxidase-B (MAO-B) and monoamine oxidase-A (MAO-A), which encode closely related enzymes that metabolize biogenic amines including serotonin, dopamine, and norepinephrine. Sequencing of the deletion junction showed an unusual pattern in which a region of microhomology flanked intervening genomic sequence. Because abnormalities of biogenic amines, particularly serotonin, have been implicated in the pathophysiology of pulmonary hypertension, we propose that presumed MAO deficiency in these patients may represent a novel risk factor for pulmonary hypertension, particularly forms with very early onset. Fine-mapping of other microdeletions at this locus may provide insights into additional mechanisms for nonrecurrent genomic rearrangements at this and other chromosomal loci.

Identification of a novel CLRN1 gene mutation in Usher syndrome type 3: two case reports.

Science.gov (United States)

Yoshimura, Hidekane; Oshikawa, Chie; Nakayama, Jun; Moteki, Hideaki; Usami, Shin-Ichi

2015-05-01

This study examines the CLRN1 gene mutation analysis in Japanese patients who were diagnosed with Usher syndrome type 3 (USH3) on the basis of clinical findings. Genetic analysis using massively parallel DNA sequencing (MPS) was conducted to search for 9 causative USH genes in 2 USH3 patients. We identified the novel pathogenic mutation in the CLRN1 gene in 2 patients. The missense mutation was confirmed by functional prediction software and segregation analysis. Both patients were diagnosed as having USH3 caused by the CLRN1 gene mutation. This is the first report of USH3 with a CLRN1 gene mutation in Asian populations. Validating the presence of clinical findings is imperative for properly differentiating among USH subtypes. In addition, mutation screening using MPS enables the identification of causative mutations in USH. The clinical diagnosis of this phenotypically variable disease can then be confirmed. © The Author(s) 2015.

Gender Segregation Small Firms

OpenAIRE

Kenneth R Troske; William J Carrington

1992-01-01

This paper studies interfirm gender segregation in a unique sample of small employers. We focus on small firms because previous research on interfirm segregation has studied only large firms and because it is easier to link the demographic characteristics of employers and employees in small firms. This latter feature permits an assessment of the role of employer discrimination in creating gender segregation. Our first finding is that interfirm segregation is prevalent among small employers. I...

Patterns of Residential Segregation.

Directory of Open Access Journals (Sweden)

Rémi Louf

Full Text Available The spatial distribution of income shapes the structure and organisation of cities and its understanding has broad societal implications. Despite an abundant literature, many issues remain unclear. In particular, all definitions of segregation are implicitely tied to a single indicator, usually rely on an ambiguous definition of income classes, without any consensus on how to define neighbourhoods and to deal with the polycentric organization of large cities. In this paper, we address all these questions within a unique conceptual framework. We avoid the challenge of providing a direct definition of segregation and instead start from a definition of what segregation is not. This naturally leads to the measure of representation that is able to identify locations where categories are over- or underrepresented. From there, we provide a new measure of exposure that discriminates between situations where categories co-locate or repel one another. We then use this feature to provide an unambiguous, parameter-free method to find meaningful breaks in the income distribution, thus defining classes. Applied to the 2014 American Community Survey, we find 3 emerging classes-low, middle and higher income-out of the original 16 income categories. The higher-income households are proportionally more present in larger cities, while lower-income households are not, invalidating the idea of an increased social polarisation. Finally, using the density-and not the distance to a center which is meaningless in polycentric cities-we find that the richer class is overrepresented in high density zones, especially for larger cities. This suggests that density is a relevant factor for understanding the income structure of cities and might explain some of the differences observed between US and European cities.

BanII dimorphic site located in the third intron of the human apolipoprotein AI (APOA1) gene

Energy Technology Data Exchange (ETDEWEB)

Coleman, R T; Kresnak, M T; Frossard, P M

1988-02-11

A 0.7kb fragment generated by AvaII digestion of pBL13AI, a 0.965kb full-length human apolipoprotein AI cDNA was cloned into the EcoRI site of pBR322. The apoAI cDNA was isolated from a lambdagt10 human fetal liver cDNA library. BanII (GPuGCPyC) (International Biotechnologies, Inc.) identifies two invariant bands at 1122bp and 417bp, and a single two-allele polymorphism with bands at either 274bp or 452bp. The human apolipoprotein AI-CIII-AIV gene complex has been localized on the long arm of chromosome 11 by Southern blot analysis of human-chinese hamster cell hybrids. Co-dominant segregation has been observed in two families (13 individuals). The BanII restriction map was constructed from DNA sequence data of the human apoAI gene. The 452bp fragment is generated by the loss of a BanII dimorphic site in the third intron of the apoAI gene, between the 178bp and the 274bp fragments.

Evolution of HBV S-gene in the backdrop of HDV co-infection.

Science.gov (United States)

Baig, Samina; Abidi, Syed H; Azam, Zahid; Majid, Shahid; Khan, Saeed; Khanani, Muhammad R; Ali, Syed

2018-04-16

HBV-HDV co-infected people have a higher chance of developing cirrhosis, fulminant hepatitis, and hepatocellular carcinoma (HCC) compared to those infected only with HBV. The present study was conducted to investigate HBV genotypes and phylogeny among HBV mono-infected and HBV-HDV co-infected patients, as well as analyze mutations in the surface gene of HBV in mono-infected and co-infected patients. A total of 100 blood samples (50 co-infected with HBV and HDV, and 50 mono-infected with HBV only) were collected for this study. HBV DNA was extracted from patient sera and partial surface antigen gene was amplified from HBV genome using polymerase chain reaction. HBV S gene was sequenced from 49 mono-infected and 36 co-infected patients and analyzed to identify HBV genotypes and phylogenetic patterns. Subsequently, HBV S amino acid sequences were analyzed for mutational differences between sequences from mono- and co-infected patients. HBV genotype D was predominantly found in both mono-infected as well as co-infected patients. Phylogenetic analysis showed the divergence of HBV sequences, between mono- and co-infected patients, into two distinct clusters. HBV S gene mutation analysis revealed certain mutations in HBV-HDV co-infected subjects to be distinct from those found in mono-infected patients. This might indicate the evolution of HBV S gene under selection pressures generated from HDV coinfection. © 2018 Wiley Periodicals, Inc.

Prokaryotic DNA segregation by an actin-like filament

DEFF Research Database (Denmark)

Møller-Jensen, Jakob; Bugge Jensen, Rasmus; Löwe, Jan

2002-01-01

The mechanisms responsible for prokaryotic DNA segregation are largely unknown. The partitioning locus (par) encoded by the Escherichia coli plasmid R1 actively segregates its replicon to daughter cells. We show here that the ParM ATPase encoded by par forms dynamic actin-like filaments with prop...... point for ParM polymerization. Hence, we provide evidence for a simple prokaryotic analogue of the eukaryotic mitotic spindle apparatus.......The mechanisms responsible for prokaryotic DNA segregation are largely unknown. The partitioning locus (par) encoded by the Escherichia coli plasmid R1 actively segregates its replicon to daughter cells. We show here that the ParM ATPase encoded by par forms dynamic actin-like filaments...

Evolution of HBV S-gene in the backdrop of HDV co-infection.

Science.gov (United States)

Baig, Samina; Abidi, Syed H; Azam, Zahid; Majid, Shahid; Khan, Saeed; Khanani, Muhammad R; Ali, Syed

2018-04-12

HBV-HDV co-infected people have a higher chance of developing cirrhosis, fulminant hepatitis, and hepatocellular carcinoma (HCC) compared to those infected only with HBV. The present study was conducted to investigate HBV genotypes and phylogeny among HBV mono-infected and HBV-HDV co-infected patients, as well as analyze mutations in the surface gene of HBV in mono-infected and co-infected patients. A total of 100 blood samples (50 co-infected with HBV and HDV, and 50 mono-infected with HBV only) were collected for this study. HBV DNA was extracted from patient sera and partial surface antigen gene was amplified from HBV genome using polymerase chain reaction. HBV S gene was sequenced from 49 mono-infected and 36 co-infected patients and analyzed to identify HBV genotypes and phylogenetic patterns. Subsequently, HBV S amino acid sequences were analyzed for mutational differences between sequences from mono- and co-infected patients. HBV genotype D was predominantly found in both mono-infected as well as co-infected patients. Phylogenetic analysis showed the divergence of HBV sequences, between mono- and co-infected patients, into two distinct clusters. HBV S gene mutation analysis revealed certain mutations in HBV-HDV co-infected subjects to be distinct from those found in mono-infected patients. In this study, we found that HBV S gene sequences from mono- and co-infected patients exhibit distinct mutation profiles. This might indicate the evolution of HBV S gene under selection pressures generated from HDV coinfection. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia

Directory of Open Access Journals (Sweden)

Borlawsky Tara B

2010-10-01

Full Text Available Abstract Background Chronic lymphocytic leukemia (CLL is the most common adult leukemia. It is a highly heterogeneous disease, and can be divided roughly into indolent and progressive stages based on classic clinical markers. Immunoglobin heavy chain variable region (IgVH mutational status was found to be associated with patient survival outcome, and biomarkers linked to the IgVH status has been a focus in the CLL prognosis research field. However, biomarkers highly correlated with IgVH mutational status which can accurately predict the survival outcome are yet to be discovered. Results In this paper, we investigate the use of gene co-expression network analysis to identify potential biomarkers for CLL. Specifically we focused on the co-expression network involving ZAP70, a well characterized biomarker for CLL. We selected 23 microarray datasets corresponding to multiple types of cancer from the Gene Expression Omnibus (GEO and used the frequent network mining algorithm CODENSE to identify highly connected gene co-expression networks spanning the entire genome, then evaluated the genes in the co-expression network in which ZAP70 is involved. We then applied a set of feature selection methods to further select genes which are capable of predicting IgVH mutation status from the ZAP70 co-expression network. Conclusions We have identified a set of genes that are potential CLL prognostic biomarkers IL2RB, CD8A, CD247, LAG3 and KLRK1, which can predict CLL patient IgVH mutational status with high accuracies. Their prognostic capabilities were cross-validated by applying these biomarker candidates to classify patients into different outcome groups using a CLL microarray datasets with clinical information.

The Impact of Vocational Schools on the Regional Development Akören Ali Rıza Ercan Vocational School Example

Directory of Open Access Journals (Sweden)

Refika Atalay

2017-07-01

Full Text Available The regional development difference which has globally become a major problem even for developing countries is one of important problems of Turkey's economy. The regional dualism in the country's economy brings with many economic and social problems such as the immigration, the income inequality, the unplanned urbanization etc. The vocational schools established generally in localities less than ten thousand people contribute to remove the development difference of these localities by providing social and economic benefits as well as by training skilled staff to the locality where they are located. In this study we investigated the impact of vocational schools in the removal of the regional development difference and we made use of primary and secondary sources. Firstly, we scanned the literatures concerning this study, then we made survey with the students which study in Akören Ali Riza Ercan Vocational School. By taking the 5% significance level and the 5% margin of error into consideration in this study we used the SPSS for Windows statistics program in the evaluation of data taken as 317 students sample among the main body of 1,240 students. We tried to present solution proposals by studying the expectations and problems of the students as well as the contribution of the Akören Ali Riza Ercan Vocational School to the development of Akören district.

Human amyloid beta protein gene locus: HaeIII RFLP

Energy Technology Data Exchange (ETDEWEB)

Taylor, J E; Gonzalez-DeWhitt, P A; Fuller, F; Cordell, B; Frossard, P M [California Biotechnology Inc., Mountain View (USA); Tinklenberg, J R; Davies, H D; Eng, L F; Yesavage, J A [Stanford Univ. School of Medicine, Palo Alto, CA (USA)

1988-07-25

A 2.2 kb EcoRI-EcoRI fragment from the 5{prime} end of the human amyloid beta protein cDNA was isolated from a human fibroblast cDNA library and subcloned into pGEM3. HaeIII (GGCC) detects 6 invariant bands at 0.5 kb, 1.0 kb, 1.1 kb, 1.3 kb, 1.4 kb and 1.6 kb and a two-allele polymorphism with bands at either 1.9 kb or 2.1 kb. Its frequency was studied in 50 North Americans. Human amyloid beta protein gene mapped to the long arm of chromosome 21 (21q11.2-21q21) by Southern blot analysis of human-rodent somatic cell hybrids. Co-dominant segregation was observed in two families (15 individuals).

Schwerpunktseminar : "Dazugehören? Umgang mit Minderheiten" / Liliāna Vancāne

Index Scriptorium Estoniae

Vancāne, Liliāna

2016-01-01

17. -20. märtsini 2016 Tartus toimunud seminarist "Dazugehören? Umgang mit Minderheiten. Estland und Lettland gestern-heutu-morgen". Seminarist sotsiaalse kuuluvuse ja vähemuste teemal. Suurepäraselt korraldatud ürituse parim osa oli töötuba

René Girard, Le bouc émissaire

OpenAIRE

Pailler, Jean-Marie

2017-01-01

René Girard est mort le 4 novembre 2015. Un retirage d’une de ses œuvres majeures, Le bouc émissaire, publiée en 1982, a eu lieu vers la fin de ce même mois. Ce retirage d’opportunité nécrologique allait, hélas, s’avérer plus opportun encore que prévu. Entre-temps s’était produite la tuerie du Bataclan, le 13 novembre. Cet événement et la chaîne de ceux qui ont suivi se prêtent à plusieurs lectures. L’une des plus suggestives – et des moins rassurantes – est celle qui fait appel aux rivalités...

Image segregation in strabismic amblyopia.

Science.gov (United States)

Levi, Dennis M

2007-06-01

Humans with naturally occurring amblyopia show deficits thought to involve mechanisms downstream of V1. These include excessive crowding, abnormal global image processing, spatial sampling and symmetry detection and undercounting. Several recent studies suggest that humans with naturally occurring amblyopia show deficits in global image segregation. The current experiments were designed to study figure-ground segregation in amblyopic observers with documented deficits in crowding, symmetry detection, spatial sampling and counting, using similar stimuli. Observers had to discriminate the orientation of a figure (an "E"-like pattern made up of 17 horizontal Gabor patches), embedded in a 7x7 array of Gabor patches. When the 32 "background" patches are vertical, the "E" pops-out, due to segregation by orientation and performance is perfect; however, if the background patches are all, or mostly horizontal, the "E" is camouflaged, and performance is random. Using a method of constant stimuli, we varied the number of "background" patches that were vertical and measured the probability of correct discrimination of the global orientation of the E (up/down/left/right). Surprisingly, amblyopes who showed strong crowding and deficits in symmetry detection and counting, perform normally or very nearly so in this segregation task. I therefore conclude that these deficits are not a consequence of abnormal segregation of figure from background.

Spectrum of mutations in the renin-angiotensin system genes in autosomal recessive renal tubular dysgenesis

DEFF Research Database (Denmark)

Gribouval, Olivier; Morinière, Vincent; Pawtowski, Audrey

2012-01-01

, pulmonary hypoplasia, and refractory arterial hypotension. The disease is linked to mutations in the genes encoding several components of the renin-angiotensin system (RAS): AGT (angiotensinogen), REN (renin), ACE (angiotensin-converting enzyme), and AGTR1 (angiotensin II receptor type 1). Here, we review...... the series of 54 distinct mutations identified in 48 unrelated families. Most of them are novel and ACE mutations are the most frequent, observed in two-thirds of families (64.6%). The severity of the clinical course was similar whatever the mutated gene, which underlines the importance of a functional RAS...

René Metras, un hombre de nuestro tiempo. Galeria René Metras y la vanguardia estética en Barcelona

Directory of Open Access Journals (Sweden)

Mª del Carmen Briones Brú

2013-07-01

Full Text Available El propósito de este trabajo es reconocer y poner de relieve la figura, no siempre reconocida en los medios artísticos actuales de un hombre, René Metras. Vinculado desde los años cuarenta a movimientos artísticos catalanes de posguerra, participó con los intelectuales y jóvenes artistas catalanes, con su esfuerzo, ímpetu y dedicación personal, siendo una figura muy significativa en los primeros momentos de las vanguardias del arte español de los años 50 y 60. En octubre de 1962 abre las puertas de la galería que lleva su nombre, en la calle Consejo de Ciento, 331 de Barcelona alentado por la idea de mostrar al público barcelonés un arte distinto e innovador al que se mostraba en la mayoría de las galerías de arte. Pionero en mostrar lo que pasaba fuera de nuestro país, desde su inauguración apostó por las vanguardias europeas y, en sus salas, pudo verse por primera vez a los grandes artistas del siglo XX; promovió, fiel a su ideario, a jóvenes y relevantes artistas catalanes y del resto de la Península, defendiendo con pureza y rigor el arte abstracto e informalista. René Metras no sólo abrió sus puertas a Barcelona, también abrió Barcelona al mundo artístico internacional, siendo su galería un referente mundial de la vanguardia estética de Barcelona.

Complex segregation analysis of craniomandibular osteopathy in Deutsch Drahthaar dogs.

Science.gov (United States)

Vagt, J; Distl, O

2018-01-01

This study investigated familial relationships among Deutsch Drahthaar dogs with craniomandibular osteopathy and examined the most likely mode of inheritance. Sixteen Deutsch Drahthaar dogs with craniomandibular osteopathy were diagnosed using clinical findings, radiography or computed tomography. All 16 dogs with craniomandibular osteopathy had one common ancestor. Complex segregation analyses rejected models explaining the segregation of craniomandibular osteopathy through random environmental variation, monogenic inheritance or an additive sex effect. Polygenic and mixed major gene models sufficiently explained the segregation of craniomandibular osteopathy in the pedigree analysis and offered the most likely hypotheses. The SLC37A2:c.1332C>T variant was not found in a sample of Deutsch Drahthaar dogs with craniomandibular osteopathy, nor in healthy controls. Craniomandibular osteopathy is an inherited condition in Deutsch Drahthaar dogs and the inheritance seems to be more complex than a simple Mendelian model. Copyright © 2017 Elsevier Ltd. All rights reserved.

Radiation induced phosphorus segregation in austenitic and ferritic alloys

International Nuclear Information System (INIS)

Brimhall, J.L.; Baer, D.R.; Jones, R.H.

1984-01-01

The radiation induced surface segregation (RIS) of phosphorus in stainless steel attained a maximum at a dose of 0.8 dpa then decreased continually with dose. This decrease in the surface segregation of phosphorus at high dose levels has been attributed to removal of the phosphorus layer by ion sputtering. Phosphorus is not replenished since essentially all of the phosphorus within the irradiation zone has been segregated to the surface. Sputter removal can explain the previously reported absence of phosphorus segregation in ferritic alloys irradiated at high dosessup(1,2) (>1 dpa) since irradiation of ferritic alloys to low doses has shown measurable RIS. This sputtering phenomenon places an inherent limitation to the heavy ion irradiation technique for the study of surface segregation of impurity elements. The magnitude of the segregation in ferritics is still much less than in stainless steel which can be related to the low damage accumulation in these alloys. (orig.)

Integrated schools, segregated curriculum: effects of within-school segregation on adolescent health behaviors and educational aspirations.

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Walsemann, Katrina M; Bell, Bethany A

2010-09-01

We examined the extent to which within-school segregation, as measured by unevenness in the distribution of Black and White adolescents across levels of the English curriculum (advanced placement-international baccalaureate-honors, general, remedial, or no English), was associated with smoking, drinking, and educational aspirations, which previous studies found are related to school racial/ethnic composition. We analyzed data from wave 1 of the National Longitudinal Study of Adolescent Health, restricting our sample to non-Hispanic Blacks (n=2731) and Whites (n=4158) who from 1994 to 1995 attended high schools that enrolled Black and White students. White female students had higher predicted probabilities of smoking or drinking than did Black female students; the largest differences were in schools with high levels of within-school segregation. Black male students had higher predicted probabilities of high educational aspirations than did White male students in schools with low levels of within-school segregation; this association was attenuated for Black males attending schools with moderate or high levels of within-school segregation. Our results provide evidence that within-school segregation may influence both students' aspirations and their behaviors.

Asymmetric segregation and self-renewal of hematopoietic stem and progenitor cells with endocytic Ap2a2.

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Ting, Stephen B; Deneault, Eric; Hope, Kristin; Cellot, Sonia; Chagraoui, Jalila; Mayotte, Nadine; Dorn, Jonas F; Laverdure, Jean-Philippe; Harvey, Michael; Hawkins, Edwin D; Russell, Sarah M; Maddox, Paul S; Iscove, Norman N; Sauvageau, Guy

2012-03-15

The stem cell-intrinsic model of self-renewal via asymmetric cell division (ACD) posits that fate determinants be partitioned unequally between daughter cells to either activate or suppress the stemness state. ACD is a purported mechanism by which hematopoietic stem cells (HSCs) self-renew, but definitive evidence for this cellular process remains open to conjecture. To address this issue, we chose 73 candidate genes that function within the cell polarity network to identify potential determinants that may concomitantly alter HSC fate while also exhibiting asymmetric segregation at cell division. Initial gene-expression profiles of polarity candidates showed high and differential expression in both HSCs and leukemia stem cells. Altered HSC fate was assessed by our established in vitro to in vivo screen on a subcohort of candidate polarity genes, which revealed 6 novel positive regulators of HSC function: Ap2a2, Gpsm2, Tmod1, Kif3a, Racgap1, and Ccnb1. Interestingly, live-cell videomicroscopy of the endocytic protein AP2A2 shows instances of asymmetric segregation during HSC/progenitor cell cytokinesis. These results contribute further evidence that ACD is functional in HSC self-renewal, suggest a role for Ap2a2 in HSC activity, and provide a unique opportunity to prospectively analyze progeny from HSC asymmetric divisions.

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

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Marion Ouedraogo

Full Text Available BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

Proto-oncogene FBI-1 (Pokemon/ZBTB7A) Represses Transcription of the Tumor Suppressor Rb Gene via Binding Competition with Sp1 and Recruitment of Co-repressors*S⃞

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Jeon, Bu-Nam; Yoo, Jung-Yoon; Choi, Won-Il; Lee, Choong-Eun; Yoon, Ho-Geun; Hur, Man-Wook

2008-01-01

FBI-1 (also called Pokemon/ZBTB7A) is a BTB/POZ-domain Krüppel-like zinc-finger transcription factor. Recently, FBI-1 was characterized as a proto-oncogenic protein, which represses tumor suppressor ARF gene transcription. The expression of FBI-1 is increased in many cancer tissues. We found that FBI-1 potently represses transcription of the Rb gene, a tumor suppressor gene important in cell cycle arrest. FBI-1 binds to four GC-rich promoter elements (FREs) located at bp –308 to –188 of the Rb promoter region. The Rb promoter also contains two Sp1 binding sites: GC-box 1 (bp –65 to –56) and GC-box 2 (bp –18 to –9), the latter of which is also bound by FBI-1. We found that FRE3 (bp –244 to –236) is also a Sp1 binding element. FBI-1 represses transcription of the Rb gene not only by binding to the FREs, but also by competing with Sp1 at the GC-box 2 and the FRE3. By binding to the FREs and/or the GC-box, FBI-1 represses transcription of the Rb gene through its POZ-domain, which recruits a co-repressor-histone deacetylase complex and deacetylates histones H3 and H4 at the Rb gene promoter. FBI-1 inhibits C2C12 myoblast cell differentiation by repressing Rb gene expression. PMID:18801742

TBLR1 regulates the expression of nuclear hormone receptor co-repressors

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Brown Stuart

2006-08-01

Full Text Available Abstract Background Transcription is regulated by a complex interaction of activators and repressors. The effectors of repression are large multimeric complexes which contain both the repressor proteins that bind to transcription factors and a number of co-repressors that actually mediate transcriptional silencing either by inhibiting the basal transcription machinery or by recruiting chromatin-modifying enzymes. Results TBLR1 [GenBank: NM024665] is a co-repressor of nuclear hormone transcription factors. A single highly conserved gene encodes a small family of protein molecules. Different isoforms are produced by differential exon utilization. Although the ORF of the predominant form contains only 1545 bp, the human gene occupies ~200 kb of genomic DNA on chromosome 3q and contains 16 exons. The genomic sequence overlaps with the putative DC42 [GenBank: NM030921] locus. The murine homologue is structurally similar and is also located on Chromosome 3. TBLR1 is closely related (79% homology at the mRNA level to TBL1X and TBL1Y, which are located on Chromosomes X and Y. The expression of TBLR1 overlaps but is distinct from that of TBL1. An alternatively spliced form of TBLR1 has been demonstrated in human material and it too has an unique pattern of expression. TBLR1 and the homologous genes interact with proteins that regulate the nuclear hormone receptor family of transcription factors. In resting cells TBLR1 is primarily cytoplasmic but after perturbation the protein translocates to the nucleus. TBLR1 co-precipitates with SMRT, a co-repressor of nuclear hormone receptors, and co-precipitates in complexes immunoprecipitated by antiserum to HDAC3. Cells engineered to over express either TBLR1 or N- and C-terminal deletion variants, have elevated levels of endogenous N-CoR. Co-transfection of TBLR1 and SMRT results in increased expression of SMRT. This co-repressor undergoes ubiquitin-mediated degradation and we suggest that the stabilization of

Analysis of essential Arabidopsis nuclear genes encoding plastid-targeted proteins.

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Savage, Linda J; Imre, Kathleen M; Hall, David A; Last, Robert L

2013-01-01

The Chloroplast 2010 Project (http://www.plastid.msu.edu/) identified and phenotypically characterized homozygous mutants in over three thousand genes, the majority of which encode plastid-targeted proteins. Despite extensive screening by the community, no homozygous mutant alleles were available for several hundred genes, suggesting that these might be enriched for genes of essential function. Attempts were made to generate homozygotes in ~1200 of these lines and 521 of the homozygous viable lines obtained were deposited in the Arabidopsis Biological Resource Center (http://abrc.osu.edu/). Lines that did not yield a homozygote in soil were tested as potentially homozygous lethal due to defects either in seed or seedling development. Mutants were characterized at four stages of development: developing seed, mature seed, at germination, and developing seedlings. To distinguish seed development or seed pigment-defective mutants from seedling development mutants, development of seeds was assayed in siliques from heterozygous plants. Segregating seeds from heterozygous parents were sown on supplemented media in an attempt to rescue homozygous seedlings that could not germinate or survive in soil. Growth of segregating seeds in air and air enriched to 0.3% carbon dioxide was compared to discover mutants potentially impaired in photorespiration or otherwise responsive to CO2 supplementation. Chlorophyll fluorescence measurements identified CO2-responsive mutants with altered photosynthetic parameters. Examples of genes with a viable mutant allele and one or more putative homozygous-lethal alleles were documented. RT-PCR of homozygotes for potentially weak alleles revealed that essential genes may remain undiscovered because of the lack of a true null mutant allele. This work revealed 33 genes with two or more lethal alleles and 73 genes whose essentiality was not confirmed with an independent lethal mutation, although in some cases second leaky alleles were identified.

Analysis of essential Arabidopsis nuclear genes encoding plastid-targeted proteins.

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Linda J Savage

Full Text Available The Chloroplast 2010 Project (http://www.plastid.msu.edu/ identified and phenotypically characterized homozygous mutants in over three thousand genes, the majority of which encode plastid-targeted proteins. Despite extensive screening by the community, no homozygous mutant alleles were available for several hundred genes, suggesting that these might be enriched for genes of essential function. Attempts were made to generate homozygotes in ~1200 of these lines and 521 of the homozygous viable lines obtained were deposited in the Arabidopsis Biological Resource Center (http://abrc.osu.edu/. Lines that did not yield a homozygote in soil were tested as potentially homozygous lethal due to defects either in seed or seedling development. Mutants were characterized at four stages of development: developing seed, mature seed, at germination, and developing seedlings. To distinguish seed development or seed pigment-defective mutants from seedling development mutants, development of seeds was assayed in siliques from heterozygous plants. Segregating seeds from heterozygous parents were sown on supplemented media in an attempt to rescue homozygous seedlings that could not germinate or survive in soil. Growth of segregating seeds in air and air enriched to 0.3% carbon dioxide was compared to discover mutants potentially impaired in photorespiration or otherwise responsive to CO2 supplementation. Chlorophyll fluorescence measurements identified CO2-responsive mutants with altered photosynthetic parameters. Examples of genes with a viable mutant allele and one or more putative homozygous-lethal alleles were documented. RT-PCR of homozygotes for potentially weak alleles revealed that essential genes may remain undiscovered because of the lack of a true null mutant allele. This work revealed 33 genes with two or more lethal alleles and 73 genes whose essentiality was not confirmed with an independent lethal mutation, although in some cases second leaky alleles

Direct sequencing of FAH gene in Pakistani tyrosinemia type 1 families reveals a novel mutation.

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Ijaz, Sadaqat; Zahoor, Muhammad Yasir; Imran, Muhammad; Afzal, Sibtain; Bhinder, Munir A; Ullah, Ihsan; Cheema, Huma Arshad; Ramzan, Khushnooda; Shehzad, Wasim

2016-03-01

Hereditary tyrosinemia type 1 (HT1) is a rare inborn error of tyrosine catabolism with a worldwide prevalence of one out of 100,000 live births. HT1 is clinically characterized by hepatic and renal dysfunction resulting from the deficiency of fumarylacetoacetate hydrolase (FAH) enzyme, caused by recessive mutations in the FAH gene. We present here the first report on identification of FAH mutations in HT1 patients from Pakistan with a novel one. Three Pakistani families, each having one child affected with HT1, were enrolled over a period of 1.5 years. Two of the affected children had died as they were presented late with acute form. All regions of the FAH gene spanning exons and splicing sites were amplified by polymerase chain reaction (PCR) and mutation analysis was carried out by direct sequencing. Results of sequencing were confirmed by restriction fragment length polymorphism (PCR-RFLP) analysis. Three different FAH mutations, one in each family, were found to co-segregate with the disease phenotype. Two of these FAH mutations have been known (c.192G>T and c.1062+5G>A [IVS12+5G>A]), while c.67T>C (p.Ser23Pro) was a novel mutation. The novel variant was not detected in any of 120 chromosomes from normal ethnically matched individuals. Most of the HT1 patients die before they present to hospitals in Pakistan, as is indicated by enrollment of only three families in 1.5 years. Most of those with late clinical presentation do not survive due to delayed diagnosis followed by untimely treatment. This tragic condition advocates the establishment of expanded newborn screening program for HT1 within Pakistan.

Co je na životě tak zvláštního? Příklad redukcionismu René Descarta (What is so special about life? The example of René Descartes‘ reductionism

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Vladimír Vodička

2017-03-01

Full Text Available History of philosophy offers many examples capable of informing discussions related to questions, topics and problems, which are actual for both philosophy and particular scientific fields. Explanation of the nature of life is such a topic. Although current debates have been paying attention to the impact of scientific findings on our understanding of the phenomenon of life, the very definition of life falls in to the continuum between philosophy and science, the endeavor to capture origin of life and possibilities of creating artificial life bring up both theoretical and practical questions alike. In this paper we approach to the analysis of the standpoint of one of the most important philosophical authorities of modern philosophy, René Descartes. By the analysis of his approach to the nature of life we try to amend his reception and intellectual legacy of not so well appreciated part of his works.

Drosophila arginine methyltransferase 1 (DART1) is an ecdysone receptor co-repressor

International Nuclear Information System (INIS)

Kimura, Shuhei; Sawatsubashi, Shun; Ito, Saya; Kouzmenko, Alexander; Suzuki, Eriko; Zhao, Yue; Yamagata, Kaoru; Tanabe, Masahiko; Ueda, Takashi; Fujiyama, Sari; Murata, Takuya; Matsukawa, Hiroyuki; Takeyama, Ken-ichi; Yaegashi, Nobuo

2008-01-01

Histone arginine methylation is an epigenetic marker that regulates gene expression by defining the chromatin state. Arginine methyltransferases, therefore, serve as transcriptional co-regulators. However, unlike other transcriptional co-regulators, the physiological roles of arginine methyltransferases are poorly understood. Drosophila arginine methyltransferase 1 (DART1), the mammalian PRMT1 homologue, methylates the arginine residue of histone H4 (H4R3me2). Disruption of DART1 in Drosophila by imprecise P-element excision resulted in low viability during metamorphosis in the pupal stages. In the pupal stage, an ecdysone hormone signal is critical for developmental progression. DART1 interacted with the nuclear ecdysone receptor (EcR) in a ligand-dependent manner, and co-repressed EcR in intact flies. These findings suggest that DART1, a histone arginine methyltransferase, is a co-repressor of EcR that is indispensable for normal pupal development in the intact fly

Gene-Transformation-Induced Changes in Chemical Functional Group Features and Molecular Structure Conformation in Alfalfa Plants Co-Expressing Lc-bHLH and C1-MYB Transcriptive Flavanoid Regulatory Genes: Effects of Single-Gene and Two-Gene Insertion.

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Heendeniya, Ravindra G; Yu, Peiqiang

2017-03-20

Alfalfa ( Medicago sativa L.) genotypes transformed with Lc-bHLH and Lc transcription genes were developed with the intention of stimulating proanthocyanidin synthesis in the aerial parts of the plant. To our knowledge, there are no studies on the effect of single-gene and two-gene transformation on chemical functional groups and molecular structure changes in these plants. The objective of this study was to use advanced molecular spectroscopy with multivariate chemometrics to determine chemical functional group intensity and molecular structure changes in alfalfa plants when co-expressing Lc-bHLH and C1-MYB transcriptive flavanoid regulatory genes in comparison with non-transgenic (NT) and AC Grazeland (ACGL) genotypes. The results showed that compared to NT genotype, the presence of double genes ( Lc and C1 ) increased ratios of both the area and peak height of protein structural Amide I/II and the height ratio of α-helix to β-sheet. In carbohydrate-related spectral analysis, the double gene-transformed alfalfa genotypes exhibited lower peak heights at 1370, 1240, 1153, and 1020 cm -1 compared to the NT genotype. Furthermore, the effect of double gene transformation on carbohydrate molecular structure was clearly revealed in the principal component analysis of the spectra. In conclusion, single or double transformation of Lc and C1 genes resulted in changing functional groups and molecular structure related to proteins and carbohydrates compared to the NT alfalfa genotype. The current study provided molecular structural information on the transgenic alfalfa plants and provided an insight into the impact of transgenes on protein and carbohydrate properties and their molecular structure's changes.

Spatial segregation in eastern North Pacific skate assemblages.

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Joseph J Bizzarro

Full Text Available Skates (Rajiformes: Rajoidei are common mesopredators in marine benthic communities. The spatial associations of individual species and the structure of assemblages are of considerable importance for effective monitoring and management of exploited skate populations. This study investigated the spatial associations of eastern North Pacific (ENP skates in continental shelf and upper continental slope waters of two regions: central California and the western Gulf of Alaska. Long-term survey data were analyzed using GIS/spatial analysis techniques and regression models to determine distribution (by depth, temperature, and latitude/longitude and relative abundance of the dominant species in each region. Submersible video data were incorporated for California to facilitate habitat association analysis. We addressed three main questions: 1 Are there regions of differential importance to skates?, 2 Are ENP skate assemblages spatially segregated?, and 3 When skates co-occur, do they differ in size? Skate populations were highly clustered in both regions, on scales of 10s of kilometers; however, high-density regions (i.e., hot spots were segregated among species. Skate densities and frequencies of occurrence were substantially lower in Alaska as compared to California. Although skates are generally found on soft sediment habitats, Raja rhina exhibited the strongest association with mixed substrates, and R. stellulata catches were greatest on rocky reefs. Size segregation was evident in regions where species overlapped substantially in geographic and depth distribution (e.g., R. rhina and Bathyraja kincaidii off California; B. aleutica and B. interrupta in the Gulf of Alaska. Spatial niche differentiation in skates appears to be more pronounced than previously reported.

Spatial segregation in eastern North Pacific skate assemblages.

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Bizzarro, Joseph J; Broms, Kristin M; Logsdon, Miles G; Ebert, David A; Yoklavich, Mary M; Kuhnz, Linda A; Summers, Adam P

2014-01-01

Skates (Rajiformes: Rajoidei) are common mesopredators in marine benthic communities. The spatial associations of individual species and the structure of assemblages are of considerable importance for effective monitoring and management of exploited skate populations. This study investigated the spatial associations of eastern North Pacific (ENP) skates in continental shelf and upper continental slope waters of two regions: central California and the western Gulf of Alaska. Long-term survey data were analyzed using GIS/spatial analysis techniques and regression models to determine distribution (by depth, temperature, and latitude/longitude) and relative abundance of the dominant species in each region. Submersible video data were incorporated for California to facilitate habitat association analysis. We addressed three main questions: 1) Are there regions of differential importance to skates?, 2) Are ENP skate assemblages spatially segregated?, and 3) When skates co-occur, do they differ in size? Skate populations were highly clustered in both regions, on scales of 10s of kilometers; however, high-density regions (i.e., hot spots) were segregated among species. Skate densities and frequencies of occurrence were substantially lower in Alaska as compared to California. Although skates are generally found on soft sediment habitats, Raja rhina exhibited the strongest association with mixed substrates, and R. stellulata catches were greatest on rocky reefs. Size segregation was evident in regions where species overlapped substantially in geographic and depth distribution (e.g., R. rhina and Bathyraja kincaidii off California; B. aleutica and B. interrupta in the Gulf of Alaska). Spatial niche differentiation in skates appears to be more pronounced than previously reported.

Segregation-mobility feedback for bidisperse shallow granular flows: Towards understanding segregation in geophysical flows

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Thornton, A.; Denissen, I.; Weinhart, T.; Van der Vaart, K.

2017-12-01

The flow behaviour of shallow granular chute flows for uniform particles is well-described by the hstop-rheology [1]. Geophysical flows, however, are often composed of highly non-uniform particles that differ in particle (size, shape, composition) or contact (friction, dissipation, cohesion) properties. The flow behaviour of such mixtures can be strongly influenced by particle segregation effects. Here, we study the influence of particle size-segregation on the flow behaviour of bidisperse flows using experiments and the discrete particle method. We use periodic DPM to derive hstop-rheology for the bi-dispersed granular shallow layer equations, and study their dependence on the segregation profile. In the periodic box simulations, size-segregation results in an upward coarsening of the size distribution with the largest grains collecting at the top of the flow. In geophysical flows, the fact the flow velocity is greatest at the top couples with the vertical segregation to preferentially transported large particles to the front. The large grains may be overrun, resegregated towards the surface and recirculated before being shouldered aside into lateral levees. Theoretically it has been suggested this process should lead to a breaking size-segregation (BSS) wave located between a large-particle-rich front and a small-particle-rich tail [2,3]. In the BSS wave large particles that have been overrun rise up again to the free-surface while small particles sink to the bed. We present evidence for the existences of the BSS wave. This is achieved through the study of three-dimensional bidisperse granular flows in a moving-bed channel. Our analysis demonstrates a relation between the concentration of small particles in the flow and the amount of basal slip, in which the structure of the BSS wave plays a key role. This leads to a feedback between the mean bulk flow velocity and the process of size-segregation. Ultimately, these findings shed new light on the recirculation of

El cuerpo violentado en La carne de René, de Virgilio Piñera

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Rogelio Castro Rocha

2014-04-01

  The body is one of the most common motifs in the narration of the Cuban writer Virgilio Piñera (1912-1979. This paper analyses its configuration in the novel La carne de René (1952. As a starting, point two approaches to the protagonist’s body are distinguished. First, there are those who want to "corrupt" its physicality for pleasure – however René wants his body to remain intact – and second, there are those who want to modify its corporeality from physical aggression by using cruel methods that violate and wound the body, with the aim of worshipping the pain. To reinforce my analysis, I rely on some notions of the body that were carried out by Jean-Luc Nancy who sees the body as a limit of senses and Gilles Deleuze who elaborates on the "body without organs".

Correlates of figure-ground segregation in fMRI.

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Skiera, G; Petersen, D; Skalej, M; Fahle, M

2000-01-01

We investigated which correlates of figure-ground-segregation can be detected by means of functional magnetic resonance imaging (fMRI). Five subjects were scanned with a Siemens Vision 1.5 T system. Motion, colour, and luminance-defined checkerboards were presented with alternating control conditions containing one of the two features of the checkerboard. We find a segregation-specific activation in V1 for all subjects and all stimuli and conclude that neural mechanisms exist as early as in the primary visual cortex that are sensitive to figure-ground segregation.

Habitat segregation in fish assemblages

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Ibbotson, A.T.

1990-01-01

The segregation of habitats of fish assemblages found in the chalk streams and rivers within the Wessex, South West and Southern Water Authority boundaries in southern England have been examined. Habitat segregation is the most frequent type of resource partitioning in natural communities. The habitat of individual fish species will be defined in order to determine the following: (1) the requirements of each species in terms of depth, current velocity, substrate, cover etc.; (2) identify the ...

Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, Carbon fixation in A. ferrooxidans

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Esparza Mario

2010-08-01

Full Text Available Abstract Background Acidithiobacillus ferrooxidans is chemolithoautotrophic γ-proteobacterium that thrives at extremely low pH (pH 1-2. Although a substantial amount of information is available regarding CO2 uptake and fixation in a variety of facultative autotrophs, less is known about the processes in obligate autotrophs, especially those living in extremely acidic conditions, prompting the present study. Results Four gene clusters (termed cbb1-4 in the A. ferrooxidans genome are predicted to encode enzymes and structural proteins involved in carbon assimilation via the Calvin-Benson-Bassham (CBB cycle including form I of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO, EC 4.1.1.39 and the CO2-concentrating carboxysomes. RT-PCR experiments demonstrated that each gene cluster is a single transcriptional unit and thus is an operon. Operon cbb1 is divergently transcribed from a gene, cbbR, encoding the LysR-type transcriptional regulator CbbR that has been shown in many organisms to regulate the expression of RubisCO genes. Sigma70-like -10 and -35 promoter boxes and potential CbbR-binding sites (T-N11-A/TNA-N7TNA were predicted in the upstream regions of the four operons. Electrophoretic mobility shift assays (EMSAs confirmed that purified CbbR is able to bind to the upstream regions of the cbb1, cbb2 and cbb3 operons, demonstrating that the predicted CbbR-binding sites are functional in vitro. However, CbbR failed to bind the upstream region of the cbb4 operon that contains cbbP, encoding phosphoribulokinase (EC 2.7.1.19. Thus, other factors not present in the assay may be required for binding or the region lacks a functional CbbR-binding site. The cbb3 operon contains genes predicted to encode anthranilate synthase components I and II, catalyzing the formation of anthranilate and pyruvate from chorismate. This suggests a novel regulatory connection between CO2 fixation and tryptophan biosynthesis. The presence of a form II RubisCO

Applied Thermodynamics: Grain Boundary Segregation

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Pavel Lejček

2014-03-01

Full Text Available Chemical composition of interfaces—free surfaces and grain boundaries—is generally described by the Langmuir–McLean segregation isotherm controlled by Gibbs energy of segregation. Various components of the Gibbs energy of segregation, the standard and the excess ones as well as other thermodynamic state functions—enthalpy, entropy and volume—of interfacial segregation are derived and their physical meaning is elucidated. The importance of the thermodynamic state functions of grain boundary segregation, their dependence on volume solid solubility, mutual solute–solute interaction and pressure effect in ferrous alloys is demonstrated.

Effect of co-culture with enterocinogenic E. faecium on L. monocytogenes key virulence gene expression

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Eleftherios H. Drosinos

2016-08-01

Full Text Available The aim of the present study was to assess the expression of key virulence genes during co-culture of L. monocytogenes with a bacteriocinogenic E. faecium strain in liquid growth medium. For that purpose, BHI broth was inoculated with 7 log CFU·mL–1 L. monocytogenes and 4, 5 or 6 log CFU·mL–1 E. faecium. Sampling took place after 8 and 24 h of incubation, corresponding to the maximum and minimum of enterocin production, respectively. The RNA was extracted, stabilized and expression of prfA, sigB, hly, plcA, plcB, inlA, inlB, inlC and inlJ, was assessed by RT-qPCR. Most of the genes were downregulated during co-culture at 5 °C. Moreover, a statistically significant effect of the inoculum level was evident in most of the cases. On the contrary, no effect on the transcription level of most of the genes was observed during co-culture at 37 °C.

The SCA1 (Spinocerebellar ataxia type 1 and MJD (Machado-Joseph disease CAG repeats in normal individuals: segregation analysis and allele frequencies

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Cláudia Emília Vieira Wiezel

2003-01-01

Full Text Available Spinocerebellar ataxia type 1 (SCA1 and Machado-Joseph disease (MJD/SCA3 are autosomal dominant neurodegenerative diseases caused by expansions of a CAG trinucleotide repeat in the SCA1 and MJD genes. These expanded sequences are unstable upon transmission, leading to an intergeneration increase in the number of repeats (dynamic mutation. The transmission of the CAG repeat was studied in normal mother-father-child trios, referred for paternity testing (SCA1, n = 367; MJD, n = 879. No segregation distortion was detected. The CAG allele frequencies were determined in 330 unrelated individuals (fathers from couples tested for paternity. The allele frequency distributions did not differ from those previously reported for European populations. The estimated values for the statistic parameters indicating diversity at the SCA1 locus did not differ much from those reported previously for other STRs in the Brazilian population, while those for the MJD locus were close to or higher than the maximum values of previous reports. This shows that SCA1 and MJD are highly informative loci for applications in genetic and population studies and for forensic analysis.

Identification of candidate genes and molecular markers for heat-induced brown discoloration of seed coats in cowpea [Vigna unguiculata (L.) Walp].

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Pottorff, Marti; Roberts, Philip A; Close, Timothy J; Lonardi, Stefano; Wanamaker, Steve; Ehlers, Jeffrey D

2014-05-01

Heat-induced browning (Hbs) of seed coats is caused by high temperatures which discolors the seed coats of many legumes, affecting the visual appearance and quality of seeds. The genetic determinants underlying Hbs in cowpea are unknown. We identified three QTL associated with the heat-induced browning of seed coats trait, Hbs-1, Hbs-2 and Hbs-3, using cowpea RIL populations IT93K-503-1 (Hbs positive) x CB46 (hbs negative) and IT84S-2246 (Hbs positive) x TVu14676 (hbs negative). Hbs-1 was identified in both populations, accounting for 28.3% -77.3% of the phenotypic variation. SNP markers 1_0032 and 1_1128 co-segregated with the trait. Within the syntenic regions of Hbs-1 in soybean, Medicago and common bean, several ethylene forming enzymes, ethylene responsive element binding factors and an ACC oxidase 2 were observed. Hbs-1 was identified in a BAC clone in contig 217 of the cowpea physical map, where ethylene forming enzymes were present. Hbs-2 was identified in the IT93K-503-1 x CB46 population and accounted for of 9.5 to 12.3% of the phenotypic variance. Hbs-3 was identified in the IT84S-2246 x TVu14676 population and accounted for 6.2 to 6.8% of the phenotypic variance. SNP marker 1_0640 co-segregated with the heat-induced browning phenotype. Hbs-3 was positioned on BAC clones in contig512 of the cowpea physical map, where several ACC synthase 1 genes were present. The identification of loci determining heat-induced browning of seed coats and co-segregating molecular markers will enable transfer of hbs alleles into cowpea varieties, contributing to higher quality seeds.

Different gene expression of Normal lymphobloastoid cells which exposure to different dose of 60Co γ-ray

International Nuclear Information System (INIS)

Xiao Yao; Yang Jian; Gao Xian; Qin Yanghua; Sun Ding; Hai Ling

2008-01-01

Objective: To study on the gene expression of normal lymphoblastoid cells(AHH-1) which exposure to difference dose of 60 Co γ-ray, analyses the essential different biological effect.. Methods Human AHH-1 normal line was irradiated by 60 Co γ-rays. Used human cDNA microarray to develop the transcriptional levels of the genes by hybridizing the mRNA of cells 8 h after exposured in different dose and the control cells. Cluster analysis, discrimination and bolting were used to filter the effective genes of differential expression. Results The results of data analysis showed 23 genes of differential expression closely related to biological effect of 2.0 Gy radiation, 5 genes express changed only by 0.5 Gy radiation, 5 genes express apparently both in 2.0 Gy and 0.5 Gy radiation. Conclusion: The different dose γ-rays radiation-induced significant changes in gene expression, such as PAPLN, TP53INP1, PTENP1, FOS and TPR seem to be some important components of cellular radioresponse. (authors)

Micro and Macro Segregation in Alloys Solidifying with Equiaxed Morphology

Science.gov (United States)

Stefanescu, Doru M.; Curreri, Peter A.; Leon-Torres, Jose; Sen, Subhayu

1996-01-01

To understand macro segregation formation in Al-Cu alloys, experiments were run under terrestrial gravity (1g) and under low gravity during parabolic flights (10(exp -2) g). Alloys of two different compositions (2% and 5% Cu) were solidified at two different cooling rates. Systematic microscopic and SEM observations produced microstructural and segregation maps for all samples. These maps may be used as benchmark experiments for validation of microstructure evolution and segregation models. As expected, the macro segregation maps are very complex. When segregation was measured along the central axis of the sample, the highest macro segregation for samples solidified at 1g was obtained for the lowest cooling rate. This behavior is attributed to the longer time available for natural convection and shrinkage flow to affect solute redistribution. In samples solidified under low-g, the highest macro-segregation was obtained at the highest cooling rate. In general, low-gravity solidification resulted in less segregation. To explain the experimental findings, an analytical (Flemings-Nereo) and a numerical model were used. For the numerical model, the continuum formulation was employed to describe the macroscopic transports of mass, energy, and momentum, associated with the microscopic transport phenomena, for a two-phase system. The model proposed considers that liquid flow is driven by thermal and solutal buoyancy, and by solidification shrinkage. The Flemings-Nereo model explains well macro segregation in the initial stages of low-gravity segregation. The numerical model can describe the complex macro segregation pattern and the differences between low- and high-gravity solidification.

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Directory of Open Access Journals (Sweden)

Rasley Amy

2006-06-01

Full Text Available Abstract Background There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. Results Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1 comparative analysis of signal versus control and (2 clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns. Conclusion We have developed Array2BIO – a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org.

René Turlay (1932-2002)

CERN Multimedia

2002-01-01

René Turlay, one of the four discoverers of Charge Parity (CP) violation, died on 29 November 2002 after battling with serious illness for over a year. As a brilliant French physicist, he has left his mark on CERN where he took part in several major experiments and chaired the LEP Experiments Committee (LEPC). He spent almost all his career at the CEA in Saclay which he joined in 1957. His first work with the Saturne synchrotron concerned the study of p meson production in nucleon-nucleon collisions at 2.3 GeV. After gaining his doctorate, he went to Princeton in 1962 as a post-doc. He played a major role in the memorable experiment at Brookhaven's AGS accelerator where together with James Christenson, James Cronin and Val Fitch he discovered the CP violation phenomenon in weak interactions. This discovery gave Andrey Sakharov a key to explaining the predominance of matter over antimatter and sowed the seeds of the model of the three quark families. On returning to France at the end of 1964, he ...

Rare A2ML1 variants confer susceptibility to otitis media

Science.gov (United States)

Santos-Cortez, Regie Lyn P.; Chiong, Charlotte M.; Reyes-Quintos, Ma. Rina T.; Tantoco, Ma. Leah C.; Wang, Xin; Acharya, Anushree; Abbe, Izoduwa; Giese, Arnaud P.; Smith, Joshua D.; Allen, E. Kaitlynn; Li, Biao; Cutiongco-de la Paz, Eva Maria; Garcia, Marieflor Cristy; Llanes, Erasmo Gonzalo D.V.; Labra, Patrick John; Gloria-Cruz, Teresa Luisa I.; Chan, Abner L.; Wang, Gao T.; Daly, Kathleen A.; Shendure, Jay; Bamshad, Michael J.; Nickerson, Deborah A.; Patel, Janak A.; Riazuddin, Saima; Sale, Michele M.; Chonmaitree, Tasnee; Ahmed, Zubair M.; Abes, Generoso T.; Leal, Suzanne M.

2015-01-01

A duplication variant within middle-ear-specific gene A2ML1 co-segregates with otitis media in an indigenous Filipino pedigree (LOD score=7.5 at reduced penetrance) and lies within a founder haplotype that is also shared by three otitis-prone European- and Hispanic-American children, but is absent in non-otitis-prone children and >62,000 next-generation sequences. Seven additional A2ML1 variants were identified in six otitis-prone children. Collectively our studies support a role for A2ML1 in the pathophysiology of otitis media. PMID:26121085

Mechanisms of mtDNA segregation and mitochondrial signalling in cells with the pathogenic A3243G mutation

NARCIS (Netherlands)

Jahangir Tafrechi, Roshan Sakineh

2008-01-01

Using newly developed single cell A3243G mutation load assays a novel mechanism of mtDNA segregation was identified in which the multi-copy mtDNA nucleoid takes a central position. Furthermore, likely due to low level changes in gene expression, no genes or gene sets could be identified with gene

A co-expression gene network associated with developmental regulation of apple fruit acidity.

Science.gov (United States)

Bai, Yang; Dougherty, Laura; Cheng, Lailiang; Xu, Kenong

2015-08-01

Apple fruit acidity, which affects the fruit's overall taste and flavor to a large extent, is primarily determined by the concentration of malic acid. Previous studies demonstrated that the major QTL malic acid (Ma) on chromosome 16 is largely responsible for fruit acidity variations in apple. Recent advances suggested that a natural mutation that gives rise to a premature stop codon in one of the two aluminum-activated malate transporter (ALMT)-like genes (called Ma1) is the genetic causal element underlying Ma. However, the natural mutation does not explain the developmental changes of fruit malate levels in a given genotype. Using RNA-seq data from the fruit of 'Golden Delicious' taken at 14 developmental stages from 1 week after full-bloom (WAF01) to harvest (WAF20), we characterized their transcriptomes in groups of high (12.2 ± 1.6 mg/g fw, WAF03-WAF08), mid (7.4 ± 0.5 mg/g fw, WAF01-WAF02 and WAF10-WAF14) and low (5.4 ± 0.4 mg/g fw, WAF16-WAF20) malate concentrations. Detailed analyses showed that a set of 3,066 genes (including Ma1) were expressed not only differentially (P FDR < 0.05) between the high and low malate groups (or between the early and late developmental stages) but also in significant (P < 0.05) correlation with malate concentrations. The 3,066 genes fell in 648 MapMan (sub-) bins or functional classes, and 19 of them were significantly (P FDR < 0.05) co-enriched or co-suppressed in a malate dependent manner. Network inferring using the 363 genes encompassed in the 19 (sub-) bins, identified a major co-expression network of 239 genes. Since the 239 genes were also differentially expressed between the early (WAF03-WAF08) and late (WAF16-WAF20) developmental stages, the major network was considered to be associated with developmental regulation of apple fruit acidity in 'Golden Delicious'.

Acyl-CoA-binding protein/diazepam-binding inhibitor gene and pseudogenes

DEFF Research Database (Denmark)

Mandrup, S; Hummel, R; Ravn, S

1992-01-01

Acyl-CoA-binding protein (ACBP) is a 10 kDa protein isolated from bovine liver by virtue of its ability to bind and induce the synthesis of medium-chain acyl-CoA esters. Surprisingly, it turned out to be identical to a protein named diazepam-binding Inhibitor (DBI) claimed to be an endogenous mod...... have molecularly cloned and characterized the ACBP/DBI gene family in rat. The rat ACBP/DBI gene family comprises one expressed gene and four processed pseudogenes of which one was shown to exist in two allelic forms. The expressed gene is organized into four exons and three introns...

Rapid mass segregation in small stellar clusters

Science.gov (United States)

Spera, Mario; Capuzzo-Dolcetta, Roberto

2017-12-01

In this paper we focus our attention on small-to-intermediate N-body systems that are, initially, distributed uniformly in space and dynamically `cool' (virial ratios Q=2T/|Ω| below ˜0.3). In this work, we study the mass segregation that emerges after the initial violent dynamical evolution. At this scope, we ran a set of high precision N-body simulations of isolated clusters by means of HiGPUs, our direct summation N-body code. After the collapse, the system shows a clear mass segregation. This (quick) mass segregation occurs in two phases: the first shows up in clumps originated by sub-fragmentation before the deep overall collapse; this segregation is partly erased during the deep collapse to re-emerge, abruptly, during the second phase, that follows the first bounce of the system. In this second stage, the proper clock to measure the rate of segregation is the dynamical time after virialization, which (for cold and cool systems) may be significantly different from the crossing time evaluated from initial conditions. This result is obtained for isolated clusters composed of stars of two different masses (in the ratio mh/ml=2), at varying their number ratio, and is confirmed also in presence of a massive central object (simulating a black hole of stellar size). Actually, in stellar systems starting their dynamical evolution from cool conditions, the fast mass segregation adds to the following, slow, secular segregation which is collisionally induced. The violent mass segregation is an effect persistent over the whole range of N (128 ≤ N ≤1,024) investigated, and is an interesting feature on the astronomical-observational side, too. The semi-steady state reached after virialization corresponds to a mass segregated distribution function rather than that of equipartition of kinetic energy per unit mass as it should result from violent relaxation.

Regulation of a transcription factor network by Cdk1 coordinates late cell cycle gene expression.

Science.gov (United States)

Landry, Benjamin D; Mapa, Claudine E; Arsenault, Heather E; Poti, Kristin E; Benanti, Jennifer A

2014-05-02

To maintain genome stability, regulators of chromosome segregation must be expressed in coordination with mitotic events. Expression of these late cell cycle genes is regulated by cyclin-dependent kinase (Cdk1), which phosphorylates a network of conserved transcription factors (TFs). However, the effects of Cdk1 phosphorylation on many key TFs are not known. We find that elimination of Cdk1-mediated phosphorylation of four S-phase TFs decreases expression of many late cell cycle genes, delays mitotic progression, and reduces fitness in budding yeast. Blocking phosphorylation impairs degradation of all four TFs. Consequently, phosphorylation-deficient mutants of the repressors Yox1 and Yhp1 exhibit increased promoter occupancy and decreased expression of their target genes. Interestingly, although phosphorylation of the transcriptional activator Hcm1 on its N-terminus promotes its degradation, phosphorylation on its C-terminus is required for its activity, indicating that Cdk1 both activates and inhibits a single TF. We conclude that Cdk1 promotes gene expression by both activating transcriptional activators and inactivating transcriptional repressors. Furthermore, our data suggest that coordinated regulation of the TF network by Cdk1 is necessary for faithful cell division.

Co-existence and niche segregation of three small bovid species in southern Mozambique

NARCIS (Netherlands)

Prins, HHT; de Boer, WF; van Oeveren, H; Correia, A; Mafuca, J; Olff, H; Boer, Willem F. de

Niche segregation among three small antelopes - red duiker, common duiker and suni - was investigated in a coastal savanna woodland/forest mosaic. It was expected that these similar-sized concentrate selectors would show differentiation in diet choice to decrease competition. Diet composition did

Complete genome sequence of Lactobacillus salivarius Ren, a probiotic strain with anti-tumor activity.

Science.gov (United States)

Sun, Erna; Ren, Fazheng; Liu, Songling; Ge, Shaoyang; Zhang, Ming; Guo, Huiyuan; Jiang, Lu; Zhang, Hao; Zhao, Liang

2015-09-20

Lactobacillus salivarius Ren (LsR) (CGMCC No. 3606) is a probiotic strain that was isolated from the feces of a healthy centenarian living in Bama, Guangxi, China. Previous studies have shown that this strain decreases 4-nitroquinoline 1-oxide (4-NQO)-induced genotoxicity in vitro. It also suppresses 4-NQO-induced oral carcinogenesis and 1,2-dimethylhydrazine (DMH)-induced colorectal carcinogenesis, and therefore may be used as an adjuvant therapeutic agent for cancer. Here, we report the complete genome sequence of LsR that consists of a circular chromosome of 1751,565 bp and two plasmids (pR1, 176,951 bp; pR2, 49,848 bp). Copyright © 2015 Elsevier B.V. All rights reserved.

Exome Sequencing and Linkage Analysis Identified Novel Candidate Genes in Recessive Intellectual Disability Associated with Ataxia.

Science.gov (United States)

Jazayeri, Roshanak; Hu, Hao; Fattahi, Zohreh; Musante, Luciana; Abedini, Seyedeh Sedigheh; Hosseini, Masoumeh; Wienker, Thomas F; Ropers, Hans Hilger; Najmabadi, Hossein; Kahrizi, Kimia

2015-10-01

Intellectual disability (ID) is a neuro-developmental disorder which causes considerable socio-economic problems. Some ID individuals are also affected by ataxia, and the condition includes different mutations affecting several genes. We used whole exome sequencing (WES) in combination with homozygosity mapping (HM) to identify the genetic defects in five consanguineous families among our cohort study, with two affected children with ID and ataxia as major clinical symptoms. We identified three novel candidate genes, RIPPLY1, MRPL10, SNX14, and a new mutation in known gene SURF1. All are autosomal genes, except RIPPLY1, which is located on the X chromosome. Two are housekeeping genes, implicated in transcription and translation regulation and intracellular trafficking, and two encode mitochondrial proteins. The pathogenesis of these variants was evaluated by mutation classification, bioinformatic methods, review of medical and biological relevance, co-segregation studies in the particular family, and a normal population study. Linkage analysis and exome sequencing of a small number of affected family members is a powerful new technique which can be used to decrease the number of candidate genes in heterogenic disorders such as ID, and may even identify the responsible gene(s).

Auditory stream segregation using amplitude modulated bandpass noise

Directory of Open Access Journals (Sweden)

Yingjiu eNie

2015-08-01

Full Text Available The purpose of this study was to investigate the roles of spectral overlap and amplitude modulation (AM rate for stream segregation for noise signals, as well as to test the build-up effect based on these two cues. Segregation ability was evaluated using an objective paradigm with listeners’ attention focused on stream segregation. Stimulus sequences consisted of two interleaved sets of bandpass noise bursts (A and B bursts. The A and B bursts differed in spectrum, AM-rate, or both. The amount of the difference between the two sets of noise bursts was varied. Long and short sequences were studied to investigate the build-up effect for segregation based on spectral and AM-rate differences. Results showed the following: 1. Stream segregation ability increased with greater spectral separation. 2. Larger AM-rate separations were associated with stronger segregation abilities. 3. Spectral separation was found to elicit the build-up effect for the range of spectral differences assessed in the current study. 4. AM-rate separation interacted with spectral separation suggesting an additive effect of spectral separation and AM-rate separation on segregation build-up. The findings suggest that, when normal-hearing listeners direct their attention toward segregation, they are able to segregate auditory streams based on reduced spectral contrast cues that vary by the amount of spectral overlap. Further, regardless of the spectral separation they were able to use AM-rate difference as a secondary/weaker cue. Based on the spectral differences, listeners can segregate auditory streams better as the listening duration is prolonged—i.e. sparse spectral cues elicit build-up segregation; however, AM-rate differences only appear to elicit build-up when in combination with spectral difference cues.

Differential gene expression in Xylella fastidiosa 9a5c during co-cultivation with the endophytic bacterium Methylobacterium mesophilicum SR1.6/6.

Science.gov (United States)

Dourado, Manuella Nóbrega; Santos, Daiene Souza; Nunes, Luiz Roberto; Costa de Oliveira, Regina Lúcia Batista da; de Oliveira, Marcus Vinicius; Araújo, Welington Luiz

2015-12-01

Xylella fastidiosa, the causal agent of citrus variegated chlorosis (CVC), colonizes plant xylem, reducing sap flow, and inducing internerval chlorosis, leaf size reduction, necrosis, and harder and smaller fruits. This bacterium may be transmitted from plant to plant by sharpshooter insects, including Bucephalogonia xanthopis. The citrus endophytic bacterium Methylobacterium mesophilicum SR1.6/6 colonizes citrus xylem and previous studies showed that this strain is also transferred from plant to plant by B. xanthopis (Insecta), suggesting that this endophytic bacterium may interact with X. fastidiosa in planta and inside the insect vector during co-transmission by the same insect vector. To better understand the X. fastidiosa behavior in the presence of M. mesophilicum, we evaluated the X. fastidiosa transcriptional profile during in vitro interaction with M. mesophilicum SR1.6/6. The results showed that during co-cultivation, X. fastidiosa down-regulated genes related to growth and up-regulated genes related to energy production, stress, transport, and motility, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Elucidating gene function and function evolution through comparison of co-expression networks in plants

Directory of Open Access Journals (Sweden)

Marek eMutwil

2014-08-01

Full Text Available The analysis of gene expression data has shown that transcriptionally coordinated (co-expressed genes are often functionally related, enabling scientists to use expression data in gene function prediction. This Focused Review discusses our original paper (Large-scale co-expression approach to dissect secondary cell wall formation across plant species, Frontiers in Plant Science 2:23. In this paper we applied cross-species analysis to co-expression networks of genes involved in cellulose biosynthesis. We show that the co-expression networks from different species are highly similar, indicating that whole biological pathways are conserved across species. This finding has two important implications. First, the analysis can transfer gene function annotation from well-studied plants, such as Arabidopsis, to other, uncharacterized plant species. As the analysis finds genes that have similar sequence and similar expression pattern across different organisms, functionally equivalent genes can be identified. Second, since co-expression analyses are often noisy, a comparative analysis should have higher performance, as parts of co-expression networks that are conserved are more likely to be functionally relevant. In this Focused Review, we outline the comparative analysis done in the original paper and comment on the recent advances and approaches that allow comparative analyses of co-function networks. We hypothesize that, in comparison to simple co-expression analysis, comparative analysis would yield more accurate gene function predictions. Finally, by combining comparative analysis with genomic information of green plants, we propose a possible composition of cellulose biosynthesis machinery during earlier stages of plant evolution.

An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks.

Science.gov (United States)

Botía, Juan A; Vandrovcova, Jana; Forabosco, Paola; Guelfi, Sebastian; D'Sa, Karishma; Hardy, John; Lewis, Cathryn M; Ryten, Mina; Weale, Michael E

2017-04-12

Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of clusters of genes (modules). We propose k-means clustering as an additional processing step to conventional WGCNA, which we have implemented in the R package km2gcn (k-means to gene co-expression network, https://github.com/juanbot/km2gcn ). We assessed our method on networks created from UKBEC data (10 different human brain tissues), on networks created from GTEx data (42 human tissues, including 13 brain tissues), and on simulated networks derived from GTEx data. We observed substantially improved module properties, including: (1) few or zero misplaced genes; (2) increased counts of replicable clusters in alternate tissues (x3.1 on average); (3) improved enrichment of Gene Ontology terms (seen in 48/52 GCNs) (4) improved cell type enrichment signals (seen in 21/23 brain GCNs); and (5) more accurate partitions in simulated data according to a range of similarity indices. The results obtained from our investigations indicate that our k-means method, applied as an adjunct to standard WGCNA, results in better network partitions. These improved partitions enable more fruitful downstream analyses, as gene modules are more biologically meaningful.

Fine mapping of the genic male-sterile ms 1 gene in Capsicum annuum L.

Science.gov (United States)

Jeong, Kyumi; Choi, Doil; Lee, Jundae

2018-01-01

The genomic region cosegregating with the genic male-sterile ms 1 gene of Capsicum annuum L. was delimited to a region of 869.9 kb on chromosome 5 through fine mapping analysis. A strong candidate gene, CA05g06780, a homolog of the Arabidopsis MALE STERILITY 1 gene that controls pollen development, was identified in this region. Genic male sterility caused by the ms 1 gene has been used for the economically efficient production of massive hybrid seeds in paprika (Capsicum annuum L.), a colored bell-type sweet pepper. Previously, a CAPS marker, PmsM1-CAPS, located about 2-3 cM from the ms 1 locus, was reported. In this study, we constructed a fine map near the ms 1 locus using high-resolution melting (HRM) markers in an F 2 population consisting of 1118 individual plants, which segregated into 867 male-fertile and 251 male-sterile plants. A total of 12 HRM markers linked to the ms 1 locus were developed from 53 primer sets targeting intraspecific SNPs derived by comparing genome-wide sequences obtained by next-generation resequencing analysis. Using this approach, we narrowed down the region cosegregating with the ms 1 gene to 869.9 kb of sequence. Gene prediction analysis revealed 11 open reading frames in this region. A strong candidate gene, CA05g06780, was identified; this gene is a homolog of the Arabidopsis MALE STERILITY 1 (MS1) gene, which encodes a PHD-type transcription factor that regulates pollen and tapetum development. Sequence comparison analysis suggested that the CA05g06780 gene is the strongest candidate for the ms 1 gene of paprika. To summarize, we developed a cosegregated marker, 32187928-HRM, for marker-assisted selection and identified a strong candidate for the ms 1 gene.

Segregation of acetylcholine and GABA in the rat superior cervical ganglia: functional correlation.

Directory of Open Access Journals (Sweden)

Diana eElinos

2016-04-01

Full Text Available Sympathetic neurons have the capability to segregate their neurotransmitters (NTs and co-transmitters to separate varicosities of single axons; furthermore, in culture, these neurons can even segregate classical transmitters. In vivo sympathetic neurons employ acetylcholine (ACh and other classical NTs such as gamma aminobutyric acid (GABA. Herein, we explore whether these neurons in vivo segregate these classical NTs in the superior cervical ganglia of the rat. We determined the topographical distribution of GABAergic varicosities, somatic GABAA receptor, as well as the regional distribution of the segregation of ACh and GABA. We evaluated possible regional differences in efficacy of ganglionic synaptic transmission, in the sensitivity of GABAA receptor to GABA and to the competitive antagonist picrotoxin (PTX. We found that sympathetic preganglionic neurons in vivo do segregate ACh and GABA. GABAergic varicosities and GABAA receptor expression showed a rostro-caudal gradient along ganglia; in contrast, segregation exhibited a caudo-rostral gradient. These uneven regional distributions in expression of GABA, GABAA receptors, and level segregation correlate with stronger synaptic transmission found in the caudal region. Accordingly, GABAA receptors of rostral region show larger sensitivity to GABA and PTX. These results suggest the presence of different types of GABAA receptors in each region that result in a different regional levels of endogenous GABA inhibition. Finally, we discuss a possible correlation of these different levels of GABA modulation and the function of the target organs innervated by rostral and caudal ganglionic neurons.

Co-existence and niche segregation of three small bovid species in southern Mozambique

NARCIS (Netherlands)

Prins, H.H.T.; Boer, de W.F.; Oeveren, van H.; Correia, A.; Mafuca, J.; Olff, H.

2006-01-01

Niche segregation among three small antelopes ¿ red duiker, common duiker and suni ¿ was investigated in a coastal savanna woodland/forest mosaic. It was expected that these similar-sized concentrate selectors would show differentiation in diet choice to decrease competition. Diet composition did

Comparison of inbred mouse substrains reveals segregation of maladaptive fear phenotypes

Directory of Open Access Journals (Sweden)

Stephanie J Temme

2014-08-01

Full Text Available Maladaptive fear, such as fear that is persistent or easily generalized to a nonthreatening stimuli, is associated with anxiety-related disorders in humans. In the laboratory, maladaptive fear can be modeled in rodents using Pavlovian fear conditioning. Recently, an inbred mouse strain known as 129S1/SvImJ, or 129S1 have been reported as exhibiting impairments in fear extinction and enhanced fear generalization. With a long-term goal of identifying segregating genetic markers of maladaptive fear, we used Pavlovian fear conditioning to characterize a closely related substrain designated as 129S6/SvEvTac, or 129S6. Here we report that, like 129S1 animals, 129S6 mice exhibit appropriate levels of fear upon conditioning, but are unable to extinguish fear memories once they are consolidated. Importantly, the maladaptive fear phenotype in this inbred stain can be segregated by sub-strain when probed using conditioning protocols designed to assess generalized fear. We find that unlike the 129S1 substrain, mice from the 129S6 sub-strain do not generalize conditioned fear to previously novel contexts and can learn to discriminate between two similar contexts when trained using a discrimination protocol. These results suggest that at least two forms of maladaptive fear (deficits in fear extinction and fear generalization can be can be functionally segregated, further suggesting that the underlying neurobiology is heritable. Given the observation that two closely related sub-strains can exhibit different constellations of maladaptive fear suggests that these findings could be exploited to facilitate the identification of candidate genes for anxiety-related disorders.

Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes.

Science.gov (United States)

Xu, Xuewen; Yu, Ting; Xu, Ruixue; Shi, Yang; Lin, Xiaojian; Xu, Qiang; Qi, Xiaohua; Weng, Yiqun; Chen, Xuehao

2016-03-01

A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.

Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes.

Science.gov (United States)

Wada, Masayoshi; Takahashi, Hiroki; Altaf-Ul-Amin, Md; Nakamura, Kensuke; Hirai, Masami Y; Ohta, Daisaku; Kanaya, Shigehiko

2012-07-15

Operon-like arrangements of genes occur in eukaryotes ranging from yeasts and filamentous fungi to nematodes, plants, and mammals. In plants, several examples of operon-like gene clusters involved in metabolic pathways have recently been characterized, e.g. the cyclic hydroxamic acid pathways in maize, the avenacin biosynthesis gene clusters in oat, the thalianol pathway in Arabidopsis thaliana, and the diterpenoid momilactone cluster in rice. Such operon-like gene clusters are defined by their co-regulation or neighboring positions within immediate vicinity of chromosomal regions. A comprehensive analysis of the expression of neighboring genes therefore accounts a crucial step to reveal the complete set of operon-like gene clusters within a genome. Genome-wide prediction of operon-like gene clusters should contribute to functional annotation efforts and provide novel insight into evolutionary aspects acquiring certain biological functions as well. We predicted co-expressed gene clusters by comparing the Pearson correlation coefficient of neighboring genes and randomly selected gene pairs, based on a statistical method that takes false discovery rate (FDR) into consideration for 1469 microarray gene expression datasets of A. thaliana. We estimated that A. thaliana contains 100 operon-like gene clusters in total. We predicted 34 statistically significant gene clusters consisting of 3 to 22 genes each, based on a stringent FDR threshold of 0.1. Functional relationships among genes in individual clusters were estimated by sequence similarity and functional annotation of genes. Duplicated gene pairs (determined based on BLAST with a cutoff of EOperon-like clusters tend to include genes encoding bio-machinery associated with ribosomes, the ubiquitin/proteasome system, secondary metabolic pathways, lipid and fatty-acid metabolism, and the lipid transfer system. Copyright © 2012 Elsevier B.V. All rights reserved.

Identification and analysis of chemical constituents and rat serum metabolites in Suan-Zao-Ren granule using ultra high performance liquid chromatography quadrupole time-of-flight mass spectrometry combined with multiple data processing approaches.

Science.gov (United States)

Du, Yiyang; He, Bosai; Li, Qing; He, Jiao; Wang, Di; Bi, Kaishun

2017-07-01

Suan-Zao-Ren granule is widely used to treat insomnia in China. However, because of the complexity and diversity of the chemical compositions in traditional Chinese medicine formula, the comprehensive analysis of constituents in vitro and in vivo is rather difficult. In our study, an ultra high performance liquid chromatography with quadrupole time-of-flight mass spectrometry and the PeakView® software, which uses multiple data processing approaches including product ion filter, neutral loss filter, and mass defect filter, method was developed to characterize the ingredients and rat serum metabolites in Suan-Zao-Ren granule. A total of 101 constituents were detected in vitro. Under the same analysis conditions, 68 constituents were characterized in rat serum, including 35 prototype components and 33 metabolites. The metabolic pathways of main components were also illustrated. Among them, the metabolic pathways of timosaponin AI were firstly revealed. The bioactive compounds mainly underwent the phase I metabolic pathways including hydroxylation, oxidation, hydrolysis, and phase II metabolic pathways including sulfate conjugation, glucuronide conjugation, cysteine conjugation, acetycysteine conjugation, and glutathione conjugation. In conclusion, our results showed that this analysis approach was extremely useful for the in-depth pharmacological research of Suan-Zao-Ren granule and provided a chemical basis for its rational. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exclusion of candidate genes from the chromosome 1q juvenile glaucoma region and mapping of the peripheral cannabis receptor gene (CNR2) to chromosome 1

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Sunden, S.L.F.; Nichols, B.E.; Alward, W.L.M. [Univ. of Iowa, Iowa City, IA (United States)] [and others

1994-09-01

Juvenile onset primary open angle glaucoma has been mapped by linkage to 1q21-q31. Several candidate genes were evaluated in the same family used to identify the primary linkage. Atrionatriuretic peptide receptor A (NPR1) and laminin C1 (LAMC1) have been previously mapped to this region and could putatively play a role in the pathogenesis of glaucoma. A third gene, the peripheral cannabis receptor (CNR2) was not initially mapped in humans but was a candidate because of the relief that cannabis affords some patients with primary open angle glaucoma. Microsatellites associated with NPR1 and LAMC1 revealed multiple recombinations in affected members of this pedigree. CNR2 was shown to be on chromosome 1 by PCR amplification of a 150 bp fragment of the 3{prime} untranslated region in monochromosomal somatic cell hybrids (NIGMS panel No. 2). These primers also revealed a two allele single strand conformation polymorphism which showed multiple recombinants with juvenile onset primary open angle glaucoma in large pedigrees, segregating this disorder. The marker was then mapped to 1p34-p36 by linkage, with the most likely location between liver alkaline phosphatase (ALPL) and alpha-L-1 fucosidase (FUCA1).

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine).

Science.gov (United States)

Wong, Darren C J; Sweetman, Crystal; Drew, Damian P; Ford, Christopher M

2013-12-16

Gene expression datasets in model plants such as Arabidopsis have contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine, Vitis vinifera. The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the Affymetrix Vitis vinifera GeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis

Prevalence and phylogenetic analysis of HTLV-1 in a segregated population in Iran.

Science.gov (United States)

Rafatpanah, Houshang; Torkamani, Mahmood; Valizadeh, Narges; Vakili, Rosita; Meshkani, Baratali; Khademi, Hassan; Gerayli, Sina; Mozhgani, Sayed Hamid Reza; Rezaee, Seyed Abdolrahim

2016-07-01

Human T-lymphotropic virus type 1 (HTLV-1) infection is an important health issue that affects a variety of endemic areas. The Khorasan province, mainly its capital Mashhad in northeastern Iran, was reported to be as one of these endemic regions. Torbat-e Heydarieh, a large city Southwest border to Mashhad with a segregated population was investigated for the prevalence and associated risk factors of HTLV-1 infection in 400 randomly selected individuals. Blood samples were tested for the presence of HTLV-1 antibodies via the ELISA method and then were confirmed by an Immunoblot test. For the presence of HTLV-1 in lymphocytes of infected subjects, PCR was performed on LTR and TAX regions. DNA sequencing of LTR fragment was also carried out to determine the phylogenetic of HTLV-1, using the Maximum likelihood method. HTLV-1 sero-reactivity (sero-prevalence) among the study population was 2% (8/400), of which 1.25% had HTLV-1 provirus in lymphocytes (actual prevalence). HTLV-1 infection was significantly associated with the age, marital status, and history of blood transfusion (P cosmopolitan subtype A. HTLV-1 prevalence in Torbat-e Heydarieh (1.25%) is low comparing to those of both Mashhad (2-3%) and Neishabour (3.5-5%) in the province of Khorasan. Thus, traveling mobility and population mixing such as marriage, bureaucratic affairs, occupation, and economic activities could be the usual routs of HTLV-1 new wave of spreading in this segregated city. © 2015 Wiley Periodicals, Inc.

miRNA-mediated functional changes through co-regulating function related genes.

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Jie He

Full Text Available BACKGROUND: MicroRNAs play important roles in various biological processes involving fairly complex mechanism. Analysis of genome-wide miRNA microarray demonstrate that a single miRNA can regulate hundreds of genes, but the regulative extent on most individual genes is surprisingly mild so that it is difficult to understand how a miRNA provokes detectable functional changes with such mild regulation. RESULTS: To explore the internal mechanism of miRNA-mediated regulation, we re-analyzed the data collected from genome-wide miRNA microarray with bioinformatics assay, and found that the transfection of miR-181b and miR-34a in Hela and HCT-116 tumor cells regulated large numbers of genes, among which, the genes related to cell growth and cell death demonstrated high Enrichment scores, suggesting that these miRNAs may be important in cell growth and cell death. MiR-181b induced changes in protein expression of most genes that were seemingly related to enhancing cell growth and decreasing cell death, while miR-34a mediated contrary changes of gene expression. Cell growth assays further confirmed this finding. In further study on miR-20b-mediated osteogenesis in hMSCs, miR-20b was found to enhance osteogenesis by activating BMPs/Runx2 signaling pathway in several stages by co-repressing of PPARγ, Bambi and Crim1. CONCLUSIONS: With its multi-target characteristics, miR-181b, miR-34a and miR-20b provoked detectable functional changes by co-regulating functionally-related gene groups or several genes in the same signaling pathway, and thus mild regulation from individual miRNA targeting genes could have contributed to an additive effect. This might also be one of the modes of miRNA-mediated gene regulation.