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Sample records for juncea ab genome

  1. Seed coat microsculpturing is related to genomic components in wild Brassica juncea and Sinapis arvensis.

    Science.gov (United States)

    Wang, Ying-hao; Wei, Wei; Kang, Ding-ming; Ma, Ke-ping

    2013-01-01

    It has been reported that wild Brassica and related species are widely distributed across Xinjiang, China, and there has been an argument for species identification. Seed coat microsculpturing (SCM) is known to be an excellent character for taxonomic and evolutionary studies. By identifying collections from Xinjiang, China, and combining SCM pattern, flow cytometry, and genome-specific DNA markers as well as sexual compatibility with known species, this study aimed to detect potential relationships between SCM and genomic types in wild Brassica and related species. Three wild collections were found to be tetraploid with a SCM reticulate pattern similar to B. juncea, and containing A and B genome-specific loci, indicating relatively high sexual compatibility with B. juncea. The others were diploid, carrying S-genome-specific DNA markers, and having relatively high sexual compatibility with Sinapis arvensis. Moreover, their SCM was in a rugose pattern similar to that of S. arvensis. It was suggested that SCM, as a morphological characteristic, can reflect genomic type, and be used to distinguish B-genome species such as B. juncea from the related S. arvensis. The relationship between SCM and genomic type can support taxonomic studies of the wild Brassica species and related species.

  2. Seed coat microsculpturing is related to genomic components in wild Brassica juncea and Sinapis arvensis.

    Directory of Open Access Journals (Sweden)

    Ying-hao Wang

    Full Text Available It has been reported that wild Brassica and related species are widely distributed across Xinjiang, China, and there has been an argument for species identification. Seed coat microsculpturing (SCM is known to be an excellent character for taxonomic and evolutionary studies. By identifying collections from Xinjiang, China, and combining SCM pattern, flow cytometry, and genome-specific DNA markers as well as sexual compatibility with known species, this study aimed to detect potential relationships between SCM and genomic types in wild Brassica and related species. Three wild collections were found to be tetraploid with a SCM reticulate pattern similar to B. juncea, and containing A and B genome-specific loci, indicating relatively high sexual compatibility with B. juncea. The others were diploid, carrying S-genome-specific DNA markers, and having relatively high sexual compatibility with Sinapis arvensis. Moreover, their SCM was in a rugose pattern similar to that of S. arvensis. It was suggested that SCM, as a morphological characteristic, can reflect genomic type, and be used to distinguish B-genome species such as B. juncea from the related S. arvensis. The relationship between SCM and genomic type can support taxonomic studies of the wild Brassica species and related species.

  3. Resynthesized Brassica juncea lines with novel organellar genome ...

    Indian Academy of Sciences (India)

    To obtain shoot cultures, shoot apices were ... and culture, plant regeneration and hardening etc. are as described ... Hence two other media were tested for plant regeneration. .... genomes exert a strong influence on reorganization of nuclear.

  4. Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes

    Directory of Open Access Journals (Sweden)

    Gupta Vibha

    2008-03-01

    Full Text Available Abstract Background Extensive mapping efforts are currently underway for the establishment of comparative genomics between the model plant, Arabidopsis thaliana and various Brassica species. Most of these studies have deployed RFLP markers, the use of which is a laborious and time-consuming process. We therefore tested the efficacy of PCR-based Intron Polymorphism (IP markers to analyze genome-wide synteny between the oilseed crop, Brassica juncea (AABB genome and A. thaliana and analyzed the arrangement of 24 (previously described genomic block segments in the A, B and C Brassica genomes to study the evolutionary events contributing to karyotype variations in the three diploid Brassica genomes. Results IP markers were highly efficient and generated easily discernable polymorphisms on agarose gels. Comparative analysis of the segmental organization of the A and B genomes of B. juncea (present study with the A and B genomes of B. napus and B. nigra respectively (described earlier, revealed a high degree of colinearity suggesting minimal macro-level changes after polyploidization. The ancestral block arrangements that remained unaltered during evolution and the karyotype rearrangements that originated in the Oleracea lineage after its divergence from Rapa lineage were identified. Genomic rearrangements leading to the gain or loss of one chromosome each between the A-B and A-C lineages were deciphered. Complete homoeology in terms of block organization was found between three linkage groups (LG each for the A-B and A-C genomes. Based on the homoeology shared between the A, B and C genomes, a new nomenclature for the B genome LGs was assigned to establish uniformity in the international Brassica LG nomenclature code. Conclusion IP markers were highly effective in generating comparative relationships between Arabidopsis and various Brassica species. Comparative genomics between the three Brassica lineages established the major rearrangements

  5. Complete mitochondrial genome sequences of Brassica rapa (Chinese cabbage and mizuna), and intraspecific differentiation of cytoplasm in B. rapa and Brassica juncea.

    Science.gov (United States)

    Hatono, Saki; Nishimura, Kaori; Murakami, Yoko; Tsujimura, Mai; Yamagishi, Hiroshi

    2017-09-01

    The complete sequence of the mitochondrial genome was determined for two cultivars of Brassica rapa . After determining the sequence of a Chinese cabbage variety, 'Oushou hakusai', the sequence of a mizuna variety, 'Chusei shiroguki sensuji kyomizuna', was mapped against the sequence of Chinese cabbage. The precise sequences where the two varieties demonstrated variation were ascertained by direct sequencing. It was found that the mitochondrial genomes of the two varieties are identical over 219,775 bp, with a single nucleotide polymorphism (SNP) between the genomes. Because B. rapa is the maternal species of an amphidiploid crop species, Brassica juncea , the distribution of the SNP was observed both in B. rapa and B. juncea . While the mizuna type SNP was restricted mainly to cultivars of mizuna (japonica group) in B. rapa , the mizuna type was widely distributed in B. juncea . The finding that the two Brassica species have these SNP types in common suggests that the nucleotide substitution occurred in wild B. rapa before both mitotypes were domesticated. It was further inferred that the interspecific hybridization between B. rapa and B. nigra took place twice and resulted in the two mitotypes of cultivated B. juncea .

  6. Analysis of the a genome genetic diversity among brassica napus, b. rapa and b. juncea accessions using specific simple sequence repeat markers

    International Nuclear Information System (INIS)

    Tian, H.; Yan, J.; Zhang, R.; Guo, Y.; Hu, S.; Channa, S.A.

    2017-01-01

    This investigation was aimed at evaluating the genetic diversity of 127 accessions among Brassica napus, B. rapa, and B. juncea by using 15 pairs of the A genome specific simple sequence repeat primers. These 127 accessions could be clearly separated into three groups by cluster analysis, principal component analysis, and population structure analysis separately, and the results analyzed by the three methods were very similar. Group I comprised of mainly B. napus accessions and the most of B. juncea accessions formed Group II, Group III included nearly all of the B. rapa accessions. The result showed that 36.86% of the variance was due to significant differences among populations of species, indicated that abundance genetic diversity existed among the A genome of B. napus, B. rapa, and B. juncea accessions. B. napus, B. rapa, and B. juncea have the abundant genetic diversity in the A genome, and some elite genes can be used to broaden the genetic base of them, especially for B. napus, in future rapeseed breeding program. (author)

  7. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  8. Seed Coat Microsculpturing Is Related to Genomic Components in Wild Brassica juncea and Sinapis arvensis

    OpenAIRE

    Wang, Ying-hao; Wei, Wei; Kang, Ding-ming; Ma, Ke-ping

    2013-01-01

    It has been reported that wild Brassica and related species are widely distributed across Xinjiang, China, and there has been an argument for species identification. Seed coat microsculpturing (SCM) is known to be an excellent character for taxonomic and evolutionary studies. By identifying collections from Xinjiang, China, and combining SCM pattern, flow cytometry, and genome-specific DNA markers as well as sexual compatibility with known species, this study aimed to detect potential relatio...

  9. Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288.

    Science.gov (United States)

    Heng, Shuangping; Wei, Chao; Jing, Bing; Wan, Zhengjie; Wen, Jing; Yi, Bin; Ma, Chaozhi; Tu, Jinxing; Fu, Tingdong; Shen, Jinxiong

    2014-04-30

    Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often the first and key step in unraveling the molecular and genetic basis of CMS in plants. Comparative analysis of the mitochondrial genome of the hau CMS line and its maintainer line in B. juneca (Brassica juncea) may help show the origin of the CMS-associated gene orf288. Through next-generation sequencing, the B. juncea hau CMS mitochondrial genome was assembled into a single, circular-mapping molecule that is 247,903 bp in size and 45.08% in GC content. In addition to the CMS associated gene orf288, the genome contains 35 protein-encoding genes, 3 rRNAs, 25 tRNA genes and 29 ORFs of unknown function. The mitochondrial genome sizes of the maintainer line and another normal type line "J163-4" are both 219,863 bp and with GC content at 45.23%. The maintainer line has 36 genes with protein products, 3 rRNAs, 22 tRNA genes and 31 unidentified ORFs. Comparative analysis the mitochondrial genomes of the hau CMS line and its maintainer line allowed us to develop specific markers to separate the two lines at the seedling stage. We also confirmed that different mitotypes coexist substoichiometrically in hau CMS lines and its maintainer lines in B. juncea. The number of repeats larger than 100 bp in the hau CMS line (16 repeats) are nearly twice of those found in the maintainer line (9 repeats). Phylogenetic analysis of the CMS-associated gene orf288 and four other homologous sequences in Brassicaceae show that orf288 was clearly different from orf263 in Brassica tournefortii despite of strong similarity. The hau CMS mitochondrial genome was highly rearranged when compared with its iso-nuclear maintainer line mitochondrial genome. This study may be useful for studying the

  10. Introgressing subgenome components from Brassica rapa and B. carinata to B. juncea for broadening its genetic base and exploring intersubgenomic heterosis

    Directory of Open Access Journals (Sweden)

    Zili Wei

    2016-11-01

    Full Text Available Brassica juncea (AjAjBjBj, is an allotetraploid that arose from two diploid species, B. rapa (ArAr and B. nigra (BnBn. It is an old oilseed crop with unique favorable traits, but the genetic improvement on this species is limited. We developed an approach to broaden its genetic base within several generations by intensive selection. The Ar subgenome from the Asian oil crop B. rapa (ArAr and the Bc subgenome from the African oil crop B. carinata (BcBcCcCc were combined in a synthesized allohexaploid (ArArBcBcCcCc, which was crossed with traditional B. juncea to generate pentaploid F1 hybrids (ArAjBcBjCc, with subsequent self-pollination to obtain newly synthesized B. juncea (Ar/jAr/jBc/jBc/j. After intensive cytological screening and phenotypic selection of fertility and agronomic traits, a population of new-type B. juncea was obtained and was found to be genetically stable at the F6 generation. The new-type B. juncea possesses good fertility and rich genetic diversity and is distinctly divergent but not isolated from traditional B. juncea, as revealed by population genetic analysis with molecular markers. More than half of its genome was modified, showing exotic introgression and novel variation. In addition to the improvement in some traits of the new-type B. juncea lines, a considerable potential for heterosis was observed in inter-subgenomic hybrids between new-type B. juncea lines and traditional B. juncea accessions. The new-type B. juncea exhibited a stable chromosome number and a novel genome composition through multiple generations, providing insight into how to significantly broaden the genetic base of crops with subgenome introgression from their related species and the potential of exploring inter-subgenomic heterosis for hybrid breeding.

  11. Optimization of an Efficient Non-Tissue Culture Transformation Method for Brassica Juncea

    International Nuclear Information System (INIS)

    Naeem, I.; Munir, I.; Iqbal, A.; Ullah, F.

    2016-01-01

    The major hurdles in successful in vitro transformation of Brassica juncea through standard tissue culture (STC) method are: culture contamination, somaclonal variations, and lack of expertise. Moreover, the current STC method is time consuming and needs continuous electricity. In the present study, the in planta transformation method through floral dip with or without vacuum infiltration was optimized for successful transformation of B. juncea. The B. juncea CV RAYA Anmol was used for transformation through Agrobacterium tumefaciens strain GV3101 harboring the binary vector plasmid pBinGlyBar4-EADcT. Based on the resistance reaction to the herbicide Basta, 20 and 40 resistant seedlings were obtained from 2000 seed germinated from the plants transformed through floral dip and vacuum infiltration methods, respectively. The PCR analyses further confirmed the presence of transgene in 3 floral dipped plants without vacuum infiltration and 17 floral dipped plants with vacuum infiltration, giving the transformation frequencies of 1.5*10/sup -3/ and 8.5*10/sup -3/, respectively. This method, which avoids tissue culture, will reduce the somaclonal variation accompanying prolonged culture of cells in a dedifferentiated state, will facilitate functional genomics and improvement of Brassica juncea with novel desirable traits while reducing time and expense. (author)

  12. Salt tolerance potential of brassica juncea Linn

    Energy Technology Data Exchange (ETDEWEB)

    Ibrar, M; Jabeen, M; Tabassum, J [University of Peshawar (Pakistan). Dept. of Botany; Hussain, F; Ilahi, I [University of Peshawar (Pakistan). Dept. of Pharmacy

    2003-07-01

    The present study showed that percent germination, radicle and plumule lengths of Brassica juncea were adversely affected by increasing the level of salinity. As compared to 95 per cent germination of the control, there were 92.50. 90.00. 90.00, 85.00, 87.50 and 80.00 per cent germinations respectively at 2.5, 5.0, 7.5. 10.0. 12.5 and 15.0 dSm/sup -1/ NaCI salinity levels. Similarly. all the parameters tested in the pot experiments showed gradual decline with the corresponding increasing levels of NaCl salinity. At lower levels of salinity (2.5 and 5.0 dSm/sup -l/), Brassica juncea had reasonably good growth and productivity. It showed greatly reduced growth and at 7.5 and 10.0 dSm/sup -1/ while at 12.5 and 15.0 10.0 dSm/sup -1/ salinity levels it was severely production affected. It is concluded from the present work that Brassica juncea can be grown fairly on mild saline soils for a food, fodder and seed production. (author)

  13. Salt tolerance potential of brassica juncea Linn

    International Nuclear Information System (INIS)

    Ibrar, M.; Jabeen, M.; Tabassum, J.; Hussain, F.; Ilahi, I.

    2003-01-01

    The present study showed that percent germination, radicle and plumule lengths of Brassica juncea were adversely affected by increasing the level of salinity. As compared to 95 per cent germination of the control, there were 92.50. 90.00. 90.00, 85.00, 87.50 and 80.00 per cent germinations respectively at 2.5, 5.0, 7.5. 10.0. 12.5 and 15.0 dSm/sup -1/ NaCI salinity levels. Similarly. all the parameters tested in the pot experiments showed gradual decline with the corresponding increasing levels of NaCl salinity. At lower levels of salinity (2.5 and 5.0 dSm/sup -l/), Brassica juncea had reasonably good growth and productivity. It showed greatly reduced growth and at 7.5 and 10.0 dSm/sup -1/ while at 12.5 and 15.0 10.0 dSm/sup -1/ salinity levels it was severely production affected. It is concluded from the present work that Brassica juncea can be grown fairly on mild saline soils for a food, fodder and seed production. (author)

  14. Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu.

    Science.gov (United States)

    Xia, Kai; Li, Yudong; Sun, Jing; Liang, Xinle

    2016-01-01

    Acetobacter pasteurianus, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. To understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 Mb complete genome sequence (including 0.28 M plasmid sequence) with a G+C content of 52.4% of A. pasteurianus Ab3, which was isolated from the traditional Chinese rice vinegar (Meiguichu) fermentation process. Automatic annotation of the complete genome revealed 2,786 protein-coding genes and 73 RNA genes. The comparative genome analysis among A. pasteurianus strains revealed that A. pasteurianus Ab3 possesses many unique genes potentially involved in acetic acid resistance mechanisms. In particular, two-component systems or toxin-antitoxin systems may be the signal pathway and modulatory network in A. pasteurianus to cope with acid stress. In addition, the large numbers of unique transport systems may also be related to its acid resistance capacity and cell fitness. Our results provide new clues to understanding the underlying mechanisms of acetic acid resistance in Acetobacter species and guiding industrial strain breeding for vinegar fermentation processes.

  15. Nitrogen fertilization of coffee: organic compost and Crotalaria juncea L.

    Directory of Open Access Journals (Sweden)

    João Batista Silva Araujo

    2013-12-01

    Full Text Available Information concerning the response of coffee to organic fertilizers is scarce. This study evaluates the effect of different doses of compost and Crotalaria juncea L. on growth, production and nitrogen nutrition of coffee trees. The treatments consisted of compost at rates of 25, 50, 75 and 100% of the recommended fertilization, with or without the aerial part of C. juncea. C. juncea was grown with NH4-N (2% 15N and applied to coffee. The use of C. juncea increased growth in height and diameter of the coffee canopy. In the first year, the percentage of N derived from C. juncea reached 8.5% at seven months and 4.1% at fifteen months after fertilization. In the second year, the percentage of N derived from C. juncea reached 17.9% N at the early harvest, five months after fertilization. Increased rates of compost increased pH , P , K , Ca , Mg , sum of bases , effective CEC, base saturation and organic matter and reduced potential acidity. 15N allowed the identification of the N contribution from C. juncea with percentage of leaf N derived from Crotalaria juncea from 9.2 to 17.9%.

  16. Inheritance of rapeseed (Brassica napus)-specific RAPD markers and a transgene in the cross B.juncea x (B.juncea x B.napus)

    DEFF Research Database (Denmark)

    Frello, S.; Hansen, K.R.; Jensen, J.

    1995-01-01

    , with B. juncea as the female parent, was successful both in controlled crosses and spontaneously in the field. The controlled backcrossing of selected hybrids to B. juncea, again with B. juncea as the female parent, also resulted in many seeds. The BC1 plants contained from 0 to 20 of the rapeseed RAPD...

  17. SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-Seq data

    Directory of Open Access Journals (Sweden)

    Songbo eHuang

    2011-07-01

    Full Text Available RNA-Seq, a method using next generation sequencing technologies to sequence the transcriptome, facilitates genome-wide analysis of splice junction sites. In this paper, we introduce SOAPsplice, a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. SOAPsplice uses a novel two-step approach consisting of first identifying as many reasonable splice junction candidates as possible, and then, filtering the false positives with two effective filtering strategies. In both simulated and real datasets, SOAPsplice is able to detect many reliable splice junctions with low false positive rate. The improvement gained by SOAPsplice, when compared to other existing tools, becomes more obvious when the depth of sequencing is low. SOAPsplice is freely available at http://soap.genomics.org.cn/soapsplice.html.

  18. Expression analysis of chitinase upon challenge inoculation to Alternaria wounding and defense inducers in Brassica juncea

    Directory of Open Access Journals (Sweden)

    Sandhya Rawat

    2017-03-01

    Full Text Available Chitinases are the hydrolytic enzymes which belong to the pathogenesis-related (PR protein family and play an important role not only in plant defense but also in various abiotic stresses. However, only a limited number of chitinase genes have been characterised in B. juncea. In this study, we have characterised B. juncea class IV chitinase gene (accession no EF586206 in response to fungal infection, salicylic acid (SA, jasmonic acid (JA treatments and wounding. Gene expression studies revealed that the transcript levels of Bjchitinase (BjChp gene increases significantly both in local and distal tissues after Alternaria infection. Bjchitinase gene was also induced by jasmonic acid and wounding but moderately by salicylic acid. A 2.5 kb class IV chitinase promoter of this gene was isolated from B. juncea by Genome walking (accession no KF055403.1. In-silico analysis of this promoter revealed a number of conserved cis-regulatory elements related to defense, wounding and signalling molecules like SA, and JA. For validation, chitinase promoter was fused to the GUS gene, and the resultant construct was then introduced into Arabidopsis plants. Histochemical analysis of T2 transgenic Arabidopsis plants showed that higher GUS activity in leaves after fungal infection, wounding and JA treatment but weakly by SA. GUS activity was seen in meristematic tissues, young leaves, seeds and siliques. Finally investigation has led to the identification of a pathogen-inducible, developmentally regulated and organ-specific promoter. Present study revealed that Bjchitinase (BjChp promoter is induced during biotic and environmental stress and it can be used in developing finely tuned transgenics.

  19. Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B

    Science.gov (United States)

    2013-01-01

    Background Canine osteosarcoma is clinically nearly identical to the human disease, but is common and highly heritable, making genetic dissection feasible. Results Through genome-wide association analyses in three breeds (greyhounds, Rottweilers, and Irish wolfhounds), we identify 33 inherited risk loci explaining 55% to 85% of phenotype variance in each breed. The greyhound locus exhibiting the strongest association, located 150 kilobases upstream of the genes CDKN2A/B, is also the most rearranged locus in canine osteosarcoma tumors. The top germline candidate variant is found at a >90% frequency in Rottweilers and Irish wolfhounds, and alters an evolutionarily constrained element that we show has strong enhancer activity in human osteosarcoma cells. In all three breeds, osteosarcoma-associated loci and regions of reduced heterozygosity are enriched for genes in pathways connected to bone differentiation and growth. Several pathways, including one of genes regulated by miR124, are also enriched for somatic copy-number changes in tumors. Conclusions Mapping a complex cancer in multiple dog breeds reveals a polygenic spectrum of germline risk factors pointing to specific pathways as drivers of disease. PMID:24330828

  20. Genome sequence of Prevotella intermedia SUNY aB G8-9K-3, a biofilm forming strain with drug-resistance.

    Science.gov (United States)

    Moon, Ji-Hoi; Kim, Minjung; Lee, Jae-Hyung

    Prevotella intermedia has long been known to be as the principal etiologic agent of periodontal diseases and associated with various systemic diseases. Previous studies showed that the intra-species difference exists in capacity of biofilm formation, antibiotic resistance, and serological reaction among P. intermedia strains. Here we report the genome sequence of P. intermedia SUNY aB G8-9K-3 (designated ATCC49046) that displays a relatively high antimicrobial resistant and biofilm-forming capacity. Genome sequencing information provides important clues in understanding the genetic bases of phenotypic differences among P. intermedia strains. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  1. Secondary metabolites from Nepeta juncea | Jamila | African Journal ...

    African Journals Online (AJOL)

    The study of the phytochemical investigation on the chemical constituents of the whole plant of Nepeta juncea belonging to the family Lamiaceae resulted in the isolation and characterization of 11 compounds. Nine of these compounds were identified as ursolic acid, oleanolic acid, β-sitosterol, stigmasterol, stigmasterol ...

  2. Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences.

    Science.gov (United States)

    Kim, Chang-Kug; Seol, Young-Joo; Perumal, Sampath; Lee, Jonghoon; Waminal, Nomar Espinosa; Jayakodi, Murukarthick; Lee, Sang-Choon; Jin, Seungwoo; Choi, Beom-Soon; Yu, Yeisoo; Ko, Ho-Cheol; Choi, Ji-Weon; Ryu, Kyoung-Yul; Sohn, Seong-Han; Parkin, Isobel; Yang, Tae-Jin

    2018-05-09

    The concept of U's triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B. oleracea (C)] and derived allotetraploids [B. juncea (AB genome), B. napus (AC), and B. carinata (BC)]. However, comprehensive understanding of Brassica genome evolution has not been fully achieved. Here, we performed low-coverage (2-6×) whole-genome sequencing of 28 accessions of Brassica as well as of Raphanus sativus [R genome] to explore the evolution of six Brassica species based on chloroplast genome and ribosomal DNA variations. Our phylogenomic analyses led to two main conclusions. (1) Intra-species-level chloroplast genome variations are low in the three allotetraploids (2~7 SNPs), but rich and variable in each diploid species (7~193 SNPs). (2) Three allotetraploids maintain two 45SnrDNA types derived from both ancestral species with maternal dominance. Furthermore, this study sheds light on the maternal origin of the AC chloroplast genome. Overall, this study clarifies the genetic relationships of U's triangle species based on a comprehensive genomics approach and provides important genomic resources for correlative and evolutionary studies.

  3. Heterosis as investigated in terms of polyploidy and genetic diversity using designed Brassica juncea amphiploid and its progenitor diploid species.

    Directory of Open Access Journals (Sweden)

    Payal Bansal

    Full Text Available Fixed heterosis resulting from favorable interactions between the genes on their homoeologous genomes in an allopolyploid is considered analogous to classical heterosis accruing from interactions between homologous chromosomes in heterozygous plants of a diploid species. It has been hypothesized that fixed heterosis may be one of the causes of low classical heterosis in allopolyploids. We used Indian mustard (Brassica juncea, 2n = 36; AABB as a model system to analyze this hypothesis due to ease of its resynthesis from its diploid progenitors, B. rapa (2n = 20; AA and B. nigra (2n = 16; BB. Both forms of heterosis were investigated in terms of ploidy level, gene action and genetic diversity. To facilitate this, eleven B. juncea genotypes were resynthesized by hybridizing ten near inbred lines of B. rapa and nine of B. nigra. Three half diallel combinations involving resynthesized B. juncea (11×11 and the corresponding progenitor genotypes of B. rapa (10×10 and B. nigra (9×9 were evaluated. Genetic diversity was estimated based on DNA polymorphism generated by SSR primers. Heterosis and genetic diversity in parental diploid species appeared not to predict heterosis and genetic diversity at alloploid level. There was also no association between combining ability, genetic diversity and heterosis across ploidy. Though a large proportion (0.47 of combinations showed positive values, the average fixed heterosis was low for seed yield but high for biomass yield. The genetic diversity was a significant contributor to fixed heterosis for biomass yield, due possibly to adaptive advantage it may confer on de novo alloploids during evolution. Good general/specific combiners at diploid level did not necessarily produce good general/specific combiners at amphiploid level. It was also concluded that polyploidy impacts classical heterosis indirectly due to the negative association between fixed heterosis and classical heterosis.

  4. AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies

    Directory of Open Access Journals (Sweden)

    Shankavaram Uma

    2006-04-01

    Full Text Available Abstract Background Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. Description AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60 and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different

  5. AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.

    Science.gov (United States)

    Major, Sylvia M; Nishizuka, Satoshi; Morita, Daisaku; Rowland, Rick; Sunshine, Margot; Shankavaram, Uma; Washburn, Frank; Asin, Daniel; Kouros-Mehr, Hosein; Kane, David; Weinstein, John N

    2006-04-06

    Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein lysate arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop precise information on the genes that encode their antigens. Translation among the various protein and gene identifier types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody, protein, and gene information, we initially developed a relational database in Filemaker for our own use. When it became apparent that the information would be useful to many other researchers faced with the need to choose or characterize antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed in Java. AbMiner is a user-friendly, web-based relational database of information on > 600 commercially available antibodies that we validated by Western blot for protein microarray studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety of other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our quality-control data against a pool of 60 diverse cancer cell types (the NCI-60) and also protein expression levels for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection of the listed antibodies. Some other available database resources give information on antibody specificity for one or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in a pool of 60 diverse cell types from nine different tissues of origin. AbMiner is a relational database that

  6. [Genome Rearrangements in Azospirillum brasilense Sp7 with the Involvement of the Plasmid pRhico and the Prophage phiAb-Cd].

    Science.gov (United States)

    Katsy, E I; Petrova, L P

    2015-12-01

    Alphaproteobacteria of the species Azospirillum brasilense have a multicomponent genome that undergoes frequent spontaneous rearrangements, yielding changes in the plasmid profiles of strains. Specifically, variants (Cd, Sp7.K2, Sp7.1, Sp7.4, Sp7.8, etc.) of the type strainA. brasilense Sp7 that had lost a 115-MDa plasmid were previously selected. In many of them, the molecular weight of a 90-MDa plasmid (p90 or pRhico), which is a kind of "depot" for glycopolymer biosynthesis genes, increased. In this study, a collection of primers was designed to the plasmid pRhico and to the DNA of prophage phiAb-Cd integrated in it. The use ofthese primers in polymerase chain reactions allowed the detection of the probable excision of phiAb-Cd phage from the DNA of A. brasilense variants Sp7.4 and Sp7.8 and other alterations of the pRhico structure in A. brasilense strains Cd, Sp7.K2, and Sp7.8. The developed primers and PCR conditions may be recoin mended for primary analysis of spontaneous plasmid rearrangements in A. brasilense Sp7 and related strains.

  7. Radiation induced pseudoisochromosomes in sunn hemp (Crotalaria juncea L.)

    International Nuclear Information System (INIS)

    Gupta, P.K.; Gupta, Rani

    1978-01-01

    In a population of sunn hemp (C. juncea), irradiated with gamma rays (30 Kr), a single plant was found to exhibit the presence of two ring univalents in 75.5% pollen mother cells. This was interpreted as a result of an interchange between the opposite arms of two homologous chromosomes giving rise to pseudoisochromosomes. In few other cells, four univalents and a single quadrivalent were also observed, thus indicating that two other interchanges involved very small segments, one of them between homologous chromosomes and the other between non-homologous chromosomes. (auth.)

  8. Radiation induced pseudoisochromosomes in sunn hemp (Crotalaria juncea L. )

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, P K; Gupta, R [Meerut Univ. (India). Inst. of Advanced Studies

    1978-01-01

    In a population of sunn hemp (C. juncea), irradiated with gamma rays (30 Kr), a single plant was found to exhibit the presence of two ring univalents in 75.5% pollen mother cells. This was interpreted as a result of an interchange between the opposite arms of two homologous chromosomes giving rise to pseudoisochromosomes. In few other cells, four univalents and a single quadrivalent were also observed, thus indicating that two other interchanges involved very small segments, one of them between homologous chromosomes and the other between non-homologous chromosomes.

  9. Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling

    DEFF Research Database (Denmark)

    Wasmund, Kenneth; Cooper, Myriel; Schreiber, Lars

    2016-01-01

    The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affilia......The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene...... that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. The presence of genes encoding...... dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many...

  10. Nitrogen-15 labeling of Crotalaria juncea green manure

    International Nuclear Information System (INIS)

    Ambrosano, Edmilson Jose; Rossetto, Raffaella; Trivelin, Paulo Cesar Ocheuze; Muraoka, Takashi; Bendassolli, Jose Albertino; Cantarella, Heitor; Ambrosano, Glaucia Maria Bovi; Tamiso, Luciano Grassi; Vieira, Felipe de Campos; Prada Neto, Ithamar

    2003-01-01

    Most studies dealing with the utilization of 15 N labeled plant material do not present details about the labeling technique. This is especially relevant for legume species since biological nitrogen fixation difficult plant enrichment. A technique was developed for labeling leguminous plant tissue with 15 N to obtain labeled material for nitrogen dynamics studies. Sun hemp (Crotalaria juncea L.) was grown on a Paleudalf, under field conditions. An amount of 58.32 g of urea with 70.57± 0.04 atom % 15 N was sprayed three times on plants grown on eight 6-m2-plots. The labelled material presented 2.412 atom % 15 N in a total dry matter equivalent to 9 Mg ha -1 This degree of enrichment enables the use of the green manure in pot or field experiments requiring 15 N-labeled material. (author)

  11. Growth of Crotalaria juncea L. supplied with mineral nitrogen

    Directory of Open Access Journals (Sweden)

    Elenira Henrique Miranda Mendonça

    2005-03-01

    Full Text Available Plants of Crotalaria juncea inoculated with Rhizobium were treated with nutrient solution containing 10 or 20mg of either N/NO3 or N/NH4.plant-1.week-1 . The control plants received nutrient solution without N. An investigation was conducted on the effect of these sources of N on growth and nitrogen fixation of plants with 30, 60 and 90 days after sowing (DAS. Those that received mineral N presented higher growth than -N plants, but the presence of nodules occurred in all the treatments. Plants treated with NH4 presented higher N content until 60 days. The highest concentrations of leghemoglobin and protein in nodules were found at 30 DAS and there was no difference in leghemoglobin content between treatments for any age and in protein from 60 DAS. Nitrogenase activity did not vary from 60 to 90 days, with the exception of plants that received 20mg N/NO3, where it was higher at 60 daysPlantas de Crotalaria juncea inoculadas com Rhizobium foram tratadas com solução nutritiva contendo 10 ou 20mg de N/NO3 ou N/NH4.planta-1 .semana-1. As plantas controle receberam solução nutritiva sem N. Foi verificado o efeito destas fontes de N no crescimento e fixação de nitrogênio em plantas com 30, 60 e 90 dias após a semeadura (DAS. Aquelas que receberam N mineral apresentaram maior crescimento que plantas -N, mas a presença de nódulos ocorreu em todos os tratamentos. Plantas tratadas com NH4 apresentaram maior conteúdo de N até os 60 dias. As maiores concentrações de leghemoglobina e proteínas em nódulos foram verificadas aos 30 DAS e não houve diferença no conteúdo de leghemoglobina entre os tratamentos, em nenhuma das idades e em proteínas a partir de 60 DAS. A atividade da nitrogenase não variou dos 60 aos 90 dias, com exceção de plantas que receberam 20mg N/NO3, nas quais esta foi maior aos 60 dias.

  12. Occurrence of metaxenia and false hybrids in Brassica juncea L. cv. Kikarashina × B. napus

    Science.gov (United States)

    Tsuda, Mai; Konagaya, Ken-ichi; Okuzaki, Ayako; Kaneko, Yukio; Tabei, Yutaka

    2011-01-01

    Imported genetically modified (GM) canola (Brassica napus) is approved by Japanese law. Some GM canola varieties have been found around importation sites, and there is public concern that these may have any harmful effects on related species such as reduction of wild relatives. Because B. juncea is distributed throughout Japan and is known to be high crossability with B. napus, it is assumed to be a recipient of B. napus. However, there are few reports for introgression of cross-combination in B. juncea × B. napus. To assess crossability, we artificially pollinated B. juncea with B. napus. After harvesting a large number of progeny seeds, we observed false hybrids and metaxenia of seed coats. Seed coat color was classified into four categories and false hybrids were confirmed by morphological characteristics and random amplified polymorphic DNA (RAPD) markers. Furthermore, the occurrence of false hybrids was affected by varietal differences in B. napus, whereas that of metaxenia was related to hybridity. Therefore, we suggest that metaxenia can be used as a marker for hybrid identification in B. juncea L. cv. Kikarashina × B. napus. Our results suggest that hybrid productivity in B. juncea × B. napus should not be evaluated by only seed productivity, crossability ought to be assessed the detection of true hybrids. PMID:23136472

  13. Subcellular distribution and chemical forms of thorium in Brassica juncea var. foliosa.

    Science.gov (United States)

    Zhou, Sai; Kai, Hailu; Zha, Zhongyong; Fang, Zhendong; Wang, Dingna; Du, Liang; Zhang, Dong; Feng, Xiaojie; Jin, Yongdong; Xia, Chuanqin

    2016-06-01

    Brassica juncea var. foliosa (B. juncea var. foliosa) is a promising species for thorium (Th) phytoextraction due to its large biomass, fast growth rate and high tolerance toward Th. To further understand the mechanisms of Th tolerance, the present study investigated the subcellular distribution and chemical forms of Th found in B. juncea var. foliosa Our results indicated that in both roots and leaves, Th contents in different parts of the cells follow the order of cell wall > membranes and soluble fraction > organelles. In particular, Transmission Electron Microscope (TEM) analysis showed that Th was abundantly located in cell walls of the roots. Additionally, when plants were exposed to different concentrations of Th, we have found that Th existed in B. juncea var. foliosa with different chemical forms. Much of the Th extracted by 2% acetic acid (HAc), 1 M NaCl and HCl in roots with the percentage distribution varied from 47.2% to 62.5%, while in leaves, most of the Th was in the form of residue and the subdominant amount of Th was extracted by HCl, followed by 2% HAc. This suggested that Th compartmentation in cytosol and integration with phosphate or proteins in cell wall might be responsible for the tolerance of B. juncea var. foliosa to the stress of Th. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Pulmonary and hepatic lesions caused by the dehydropyrrolizidine alkaloid-producing plants Crotalaria juncea and Crotalaria retusa in donkeys

    Science.gov (United States)

    The effects and susceptibility of donkeys to Crotalaria juncea and Crotalaria retusa poisoning were determined at high and low doses. Seeds of C. juncea conaining 0.074% of dehyrdropyrrolizidine alkaloids (DHPAs) were administered to three donkeys at 0.3, 0.6 and 1 g/kg body weight daily for 365 day...

  15. Breeding strategy for the improvement of mustard (Brassica Juncea Coss.)

    International Nuclear Information System (INIS)

    Nayar, G.G.

    1980-01-01

    Mutants having desirable agronomic characters were obtained in the high yielding, recommended mustard (B. juncea) varieties Rai 5, RL 9 and Varuna (T 59). Following hybridizations between induced mutants or mutants with other promising varieties, recombinants having superior agronomic traits have been developed. The parent varieties are characterised by open pod arrangement and blackish brown seeds. The mutants and the recombinants have desirable agronomic characters like compact plant type, appressed pods with less shattering nature, yellow seeds, higher oil content and lighter coloured oil. Among the 12 new strains developed at this centre, five have been tested at various locations in the country. At many places, TM-(Trombay Mustard-) cultures outyielded or were at par with the local check varieties. TM-2-11 (Appressed pod mutant) and TM-4 (Yellow bold seeded Mutant) have also been included in the Initial Evaluation Trial of the All India Co-ordinated Research Project in Oilseeds (AICORPO) improvement. Reports so far received from various locations in the country indicate that TM-strains, being relatively early cultures, are suited more for states of Rajasthan, Gujarat, U.P. and Bihar. (author)

  16. Subcellular distribution and chemical forms of thorium in Brassica juncea var. foliosa

    International Nuclear Information System (INIS)

    Zhou, Sai; Kai, Hailu; Zha, Zhongyong; Fang, Zhendong; Wang, Dingna; Du, Liang; Zhang, Dong; Feng, Xiaojie; Jin, Yongdong; Xia, Chuanqin

    2016-01-01

    Brassica juncea var. foliosa (B. juncea var. foliosa) is a promising species for thorium (Th) phytoextraction due to its large biomass, fast growth rate and high tolerance toward Th. To further understand the mechanisms of Th tolerance, the present study investigated the subcellular distribution and chemical forms of Th found in B. juncea var. foliosa Our results indicated that in both roots and leaves, Th contents in different parts of the cells follow the order of cell wall > membranes and soluble fraction > organelles. In particular, Transmission Electron Microscope (TEM) analysis showed that Th was abundantly located in cell walls of the roots. Additionally, when plants were exposed to different concentrations of Th, we have found that Th existed in B. juncea var. foliosa with different chemical forms. Much of the Th extracted by 2% acetic acid (HAc), 1 M NaCl and HCl in roots with the percentage distribution varied from 47.2% to 62.5%, while in leaves, most of the Th was in the form of residue and the subdominant amount of Th was extracted by HCl, followed by 2% HAc. This suggested that Th compartmentation in cytosol and integration with phosphate or proteins in cell wall might be responsible for the tolerance of B. juncea var. foliosa to the stress of Th. - Highlights: • Brassica juncea var. foliosa can adapt to the stress of Th(<200 μM) under hydroponic condition. • Th was selectively distributed on cell wall, membranes and soluble fraction. • Th mainly existed in low-toxicity forms which were benefit for Th tolerance.

  17. Origins and diversity of rush Skeletonweed (Chondrilla juncea) from three continents

    Science.gov (United States)

    J. Gaskin; C. L. Kinter; M. Schwarzlander; G. P. Markin; S. Novak; J. F. Smith

    2013-01-01

    Rush skeletonweed (Chondrilla juncea L.) is an invasive apomictic perennial plant in Australia, South- and North America, accidentally introduced from Eurasia, which shows differential resistance/tolerance to some herbicides and classical biological control agents. Rush skeletonweed biotypes have been locally described using morphology, phenology, isozyme patterns, and...

  18. PCIB an antiauxin enhances microspore embryogenisis in microspore culture of Brassica juncea

    NARCIS (Netherlands)

    Agarwal, P.K.; Agarwal, P.; Custers, J.B.M.; Liu, C.M.; Bhojwani, S.S.

    2006-01-01

    An efficient protocol to improve microspore embryogenesis is established in an important oleiferous crop, Brassica juncea (Indian mustard). Colchicine was used for enhancing microspore embryogenesis and also to obtain doubled haploid embryos. Colchicine at high concentrations (>10 mg l¿1), for 24

  19. Remediation of cadmium by Indian mustard (Brassica juncea L. from cadmium contaminated soil: a phytoextraction study

    Directory of Open Access Journals (Sweden)

    Rajeev Kumar Bhadkariya

    2014-05-01

    Full Text Available Cadmium is a toxic metal for living organisms and an environmental contaminant. Soils in many parts of the world are slightly too moderately contaminated by Cd due to long term use and disposal of Cd-contaminated wastes. Cost effective technologies are needed to remove cadmium from the contaminated sites. Soil phytoextraction is engineering based, low cost and socially accepted developing technology that uses plants to clean up contaminants in soils. This technology can be adopted as a remediation of cadmium from Cd-contaminated soils with the help of Brassica juncea plant. The objective of this work was to evaluate the cadmium (Cd accumulate and the tolerance of Brassica juncea. The Cd accumulates in all parts of plants (roots, stems and leaves. It was found that accumulating efficiency increased with the increase in the concentration of applied cadmium metal solution. Maximum accumulation of cadmium was found in roots than stem and leaves. Phytoextraction coefficient and translocation factor were highest to show the validity of the Brassica juncea species for hyperaccumulation of the Cd metal. These results suggested that Brassica juncea has a high ability to tolerate and accumulate Cd, so it might be a promising plant to be used for phytoextraction of Cd contaminated soil. DOI: http://dx.doi.org/10.3126/ije.v3i2.10533 International Journal of the Environment Vol.3(2 2014: 229-237

  20. Phosphate-assisted phytoremediation of arsenic by Brassica napus and Brassica juncea: Morphological and physiological response.

    Science.gov (United States)

    Niazi, Nabeel Khan; Bibi, Irshad; Fatimah, Ayesha; Shahid, Muhammad; Javed, Muhammad Tariq; Wang, Hailong; Ok, Yong Sik; Bashir, Safdar; Murtaza, Behzad; Saqib, Zulfiqar Ahmad; Shakoor, Muhammad Bilal

    2017-07-03

    In this study, we examined the potential role of phosphate (P; 0, 50, 100 mg kg -1 ) on growth, gas exchange attributes, and photosynthetic pigments of Brassica napus and Brassica juncea under arsenic (As) stress (0, 25, 50, 75 mg kg -1 ) in a pot experiment. Results revealed that phosphate supplementation (P100) to As-stressed plants significantly increased shoot As concentration, dry biomass yield, and As uptake, in addition to the improved morphological and gas exchange attributes and photosynthetic pigments over P0. However, phosphate-assisted increase in As uptake was substantially (up to two times) greater for B. napus, notably due to higher shoot As concentration and dry biomass yield, compared to B. juncea at the P100 level. While phosphate addition in soil (P100) led to enhanced shoot As concentration in B. juncea, it reduced shoot dry biomass, primarily after 50 and 75 mg kg -1 As treatments. The translocation factor and bioconcentration factor values of B. napus were higher than B. juncea for all As levels in the presence of phosphate. This study demonstrates that phosphate supplementation has a potential to improve As phytoextraction efficiency, predominantly for B. napus, by minimizing As-induced damage to plant growth, as well as by improving the physiological and photosynthetic attributes.

  1. Overexpression of NPR1 in Brassica juncea Confers Broad Spectrum Resistance to Fungal Pathogens

    Directory of Open Access Journals (Sweden)

    Sajad Ali

    2017-10-01

    Full Text Available Brassica juncea (Indian mustard is a commercially important oil seed crop, which is highly affected by many biotic stresses. Among them, Alternaria leaf blight and powdery mildew are the most devastating diseases leading to huge yield losses in B. juncea around the world. In this regard, genetic engineering is a promising tool that may possibly allow us to enhance the B. juncea disease resistance against these pathogens. NPR1 (non-expressor of pathogen-related gene 1 is a bonafide receptor of salicylic acid (SA which modulates multiple immune responses in plants especially activation of induced and systemic acquired resistance (SAR. Here, we report the isolation and characterization of new NPR1 homolog (BjNPR1 from B. juncea. The phylogenetic tree constructed based on the deduced sequence of BjNPR1 with homologs from other species revealed that BjNPR1 grouped together with other known NPR1 proteins of Cruciferae family, and was nearest to B. napus. Furthermore, expression analysis showed that BjNPR1 was upregulated after SA treatment and fungal infection but not by jasmonic acid or abscisic acid. To understand the defensive role of this gene, we generated B. juncea transgenic lines overexpressing BjNPR1, and further confirmed by PCR and Southern blotting. The transgenic lines showed no phenotypic abnormalities, and constitutive expression of BjNPR1 activates defense signaling pathways by priming the expression of antifungal PR genes. Moreover, BjNPR1 transgenic lines showed enhanced resistance to Alternaria brassicae and Erysiphe cruciferarum as there was delay in symptoms and reduced disease severity than non-transgenic plants. In addition, the rate of disease spreading to uninfected or distal parts was also delayed in transgenic plants thus suggesting the activation of SAR. Altogether, the present study suggests that BjNPR1 is involved in broad spectrum of disease resistance against fungal pathogens.

  2. Preliminary Phytochemical and Biological activities on Russelia juncea Zucc

    Directory of Open Access Journals (Sweden)

    Maryam Bibi

    2017-12-01

    Full Text Available To probe the ethnomedicinal claims of Russelia juncea Zucc. (Plantaginaceae as prescribed traditionally in the folklore history of medicines. Methods: The dichloromethane and methanol extracts of aerial parts and roots were examined for antimicrobial, antioxidant, antiglycation, insecticidal, leishmanicidal, cytotoxic and phytotoxic activities. Different phytochemical tests were also performed to confirm the presence of various groups of secondary metabolites such as alkaloids, glycosides, saponins, tannins, flavonoids and terpenoids. Results: Phytochemical screening of this plant confirmed the presence of alkaloids, saponins, tannins, flavonoids and terpenoids. Antibacterial activity was only shown by RJRD with 80% inhibition at the concentration of 150µg/ml against Shigella flexneri. Among the tested samples, RJAM and RJRM displayed significant radical scavenging activity up to 93% and 89% with IC50 values of 184.75 ± 4.05µM and 263.01 ± 9.36µM. The significant antiglycation potential was exhibited by RJAD, RJAM and RJRM with 55.35%, 62.25% and 59.22% inhibition and IC50 values of 0.84 ± 0.08mg/ml, 1.37 ± 0.15mg/ml and 1.52 ± 0.10mg/ml respectively. Moderate leishmanicidal activity was exposed by RJAD and RJRM with IC50 values of 73.04 ± 1.05µg/ml and 77.66 ± 0.23µg/ml while RJAM was found to be more potent and exposed significant leishmanicidal activity having IC50 of 48 ± 0.39µg/ml. However, prominent cytotoxic activity was displayed by RJRM with 66.08% inhibition and IC50 of 31.20 ± 3µg/ml. Non-significant antifungal, insecticidal and phytotoxic activities were demonstrated by all the tested samples. Conclusion: All the above contributions give serious attentiveness to scientists to isolate and purify the biologically active phytoconstituents by using advanced scientific methodologies that serve as lead compounds in the synthesis of new therapeutic agents of desired interest in the world of drug discovery.

  3. Propagule pressure, genetic structure, and geographic origins of Chondrilla juncea (Asteraceae): An apomictic invader on three continents

    Science.gov (United States)

    Assessing the propagule pressure and geographic origins of invasive populations using molecular markers provides insights into the invasion process. Rush skeletonweed (Chondrilla juncea) is an apomictic perennial plant that is invasive in Australia, Argentina, Canada and the USA. Invasive biotypes...

  4. Crotalaria (Crotalaria juncea L.) Heavy Metal Uptake in Eastern Hungary

    Science.gov (United States)

    László Phd, M., ,, Dr.

    2009-04-01

    Summary: Soil condition, plant production and ecological protection are most important parts of the sustainable agricultural activity on all over the world nowadays. Soils, their fertility, their content of different macro-, mezo-, micro-, trace elements have almost always dictated the spread of agricultural farmlands, including the plant production-, yield harvest levels and yield element contents possible. The success of agriculturists in the 20th and 21th century, particularly in the Europe has relied on inproved soil fertility managements, appropriate crop production and environmental protection. We can test and improve the situations by using different plant species (Crotalaria juncea L.) x macro nutrients (nitrogen) x chelating agents (Desferal as deferoxamine-mesilate: C25H48N6O8-CH4O3S) methods. Crotalaria has a very potential and important role in soil fertility as a green manure crop in the design of plant rotation to field plant production, in the animal foraging as a fodder-crop with a high protein content (30%) and in the pytoremediation possibilities. Field experiment was carried out on a calcareous chernozem meadow soil (Kunság-region of Hungary, Kunmadaras) in partly of crotalaria experiment series (5 years) in 2001. The agrochemical parameters of the ploughed layer of the region soils were as follows: humus 2.5-3.0%, pH (H2O) 7.7, pH (KCl) 7.0, LE (Lakanen & Erviö 1971 [3])-P2O5 183-218 mg kg-1, LE-K2O 82-115 mg kg-1, LE-Ca 1.3%, LE-Mg 56-60 mg kg-1, LE-Mn 45 mg kg-1 according to soil analysis. Nitrogen (N) x Desferal ("D"-Novartis Pharma AG Basie [7], Switzerland, Suiza 500 mg) x Genotype ("G"-India-University of Agricultural Sciences, Bangalore) x Time (T) experiment involved The N levels were 0, 100, 200 and 300 kg ha-1 year-1, and Desferal 0 and 20 kg ha-1 year-1. The plot size had an area of 4x2=8 m2. Experimental datas were estimated by MANOVA of SPSS. The main results can be summarised as follows: a., At harvest, total air dry phytomass

  5. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  6. Potential for rhizofiltration of uranium using hairy root cultures of Brassica juncea and Chenopodium amaranticolor

    International Nuclear Information System (INIS)

    Eapen, Susan; Suseelan, K.N.; Tivarekar, Suchita; Kotwal, S.A.; Mitra, R.

    2003-01-01

    Hairy root cultures of Brassica juncea and Chenopodium amaranticolor were developed by genetic transformation using Agrobacterium rhizogenes. The stable, transformed root systems demonstrated a high growth rate of 1.5-3. g/g dry weight/day in Murashige and Skoog medium. In the present study, hairy root system was used for removal of uranium from the solution of concentration up to 5000 μM. The results indicated that the hairy roots could remove uranium from the aqueous solution within a short period of incubation. B. juncea could take up 20-23% of uranium from the solution containing up to 5000 μM, when calculated on g/g dry weight basis. C. amaranticolor showed a slow and steady trend in taking up uranium, with 13 uptake from the solution of 5000 μM concentration. Root growth was not affected up to 500 μM of uranium nitrate over a period of 10 days

  7. The chemical toxicity of cesium in Indian mustard (Brassica juncea L.) seedlings

    International Nuclear Information System (INIS)

    Lai, Jin-long; Tao, Zong-ya; Fu, Qian; Han, Na; Wu, Guo; Zhang, Hong; Lu, Hong; Luo, Xue-gang

    2016-01-01

    To distinguish between the radiological and chemical effects of radiocesium, we study the chemical toxicity of cesium in the seedlings of Indian mustard (Brassica juncea L.). In this study, the experiment was designed in two factors and five levels random block design to investigate the interaction effects of Cs and K. Results showed that excessive Cs was one of the main factors influence the growth of Brassica juncea seedlings. And the toxicity of Cs in Brassica juncea is likely to be caused by Cs interacts with K-binding sites in essential K-dependent protein, either competes with K for essential biochemical functions, causing intracellular metabolic disturbance. To test the hypothesis that the toxicity of Cs might cause intracellular metabolic disturbance, next-generation sequencing (NGS)-based Illumina paired-end Solexa sequencing platform was employed to analysis the changes in gene expression, and understand the key genes in B. juncea seedlings responding to the toxicity of Cs. Based on the assembled de novo transcriptome, 2032 DEGs that play significant roles in the response to the toxicity of Cs were identified. Further analysis showed that excessive Cs is disturbance the auxin signal transduction pathway, and inhibited the indoleacetic acid-induced protein (AUX/IAA) genes expression eventually lead the seedlings growth and development be inhibited. The results suggest that disturbances to tryptophan metabolism might be linked to changes in growth. - Highlights: • Analyze the chemical toxicity of cesium in seedlings of Indian mustard. • Distinguish between the radiological and chemical effects of radiocesium. • 2032 DEGs that play significant roles in the response to Cs toxicity were identified. • Excessive Cs is disturbance the auxin signal transduction pathway.

  8. Role of Streptomyces pactum in phytoremediation of trace elements by Brassica juncea in mine polluted soils.

    Science.gov (United States)

    Ali, Amjad; Guo, Di; Mahar, Amanullah; Wang, Zhen; Muhammad, Dost; Li, Ronghua; Wang, Ping; Shen, Feng; Xue, Quanhong; Zhang, Zengqiang

    2017-10-01

    The industrial expansion, smelting, mining and agricultural practices have increased the release of toxic trace elements (TEs) in the environment and threaten living organisms. The microbe-assisted phytoremediation is environmentally safe and provide an effective approach to remediate TEs contaminated soils. A pot experiment was conducted to test the potential of an Actinomycete, subspecies Streptomyces pactum (Act12) along with medical stone compost (MSC) by growing Brassica juncea in smelter and mines polluted soils of Feng County (FC) and Tongguan (TG, China), respectively. Results showed that Zn (7, 28%), Pb (54, 21%), Cd (16, 17%) and Cu (8, 10%) uptake in shoot and root of Brassica juncea was pronounced in FC soil. Meanwhile, the Zn (40, 14%) and Pb (82, 15%) uptake in the shoot and root were also increased in TG soil. Shoot Cd uptake remained below detection, while Cu decreased by 52% in TG soil. The Cd and Cu root uptake were increased by 17% and 33%, respectively. Results showed that TEs uptake in shoot increased with increasing Act12 dose. Shoot/root dry biomass, chlorophyll and carotenoid content in Brassica juncea were significantly influenced by the application of Act12 in FC and TG soil. The antioxidant enzymatic activities (POD, PAL, PPO and CAT) in Brassica juncea implicated enhancement in the plant defense mechanism against the TEs induced stress in contaminated soils. The extraction potential of Brasssica was further evaluated by TF (translocation factor) and MEA (metal extraction amount). Based on our findings, further investigation of Act12 assisted phytoremediation of TEs in the smelter and mines polluted soil and hyperaccumulator species are suggested for future studies. Copyright © 2017. Published by Elsevier Inc.

  9. Uptake and localisation of lead in the root system of Brassica juncea

    International Nuclear Information System (INIS)

    Meyers, Donald E.R.; Auchterlonie, Graeme J.; Webb, Richard I.; Wood, Barry

    2008-01-01

    The uptake and distribution of Pb sequestered by hydroponically grown (14 days growth) Brassica juncea (3 days exposure; Pb activities 3.2, 32 and 217 μM) was investigated. Lead uptake was restricted largely to root tissue. Examination using scanning transmission electron microscopy-energy dispersive spectroscopy revealed substantial and predominantly intracellular uptake at the root tip. Endocytosis of Pb at the plasma membrane was not observed. A membrane transport protein may therefore be involved. In contrast, endocytosis of Pb into a subset of vacuoles was observed, resulting in the formation of dense Pb aggregates. Sparse and predominantly extracellular uptake occurred at some distance from the root tip. X-ray photoelectron spectroscopy confirmed that the Pb concentration was greater in root tips. Heavy metal rhizofiltration using B. juncea might therefore be improved by breeding plants with profusely branching roots. Uptake enhancement using genetic engineering techniques would benefit from investigation of plasma membrane transport mechanisms. - The sites of Pb sequestration within the root system of hydroponically grown Brassica juncea were identified

  10. Brassinosteroids Denigrate the Seasonal Stress through Antioxidant Defense System in Seedlings of Brassica juncea L.

    Directory of Open Access Journals (Sweden)

    Sandeep Kumar

    2014-05-01

    Full Text Available The present work has been undertaken to study the effect of exogenously application of 24-epiBL and 28-homoBL on soluble protein, proline contents and antioxidant defense system of Brassica juncea L. RLM 619 under the influence of seasonal stress. It was observed that 24-epiBL and 28-homoBL treatment enhance the soluble protein, dry weight and shoot length of B. juncea seedlings under seasonal stress. If seeds treated with the different concentrations (10-6, 10-8 and 10-10 M of 24-epiBL and 28-homoBL revealed batter growth, protein and proline contents as compare to untreated seedlings. Similarly the activities of antioxidant enzymes SOD, CAT, APOX, DHAR, PPO and Auxinases were enhanced by the application of different concentration of both brassinosteroids, whereas MDA content was decrease with both brassinosteroids treatments. Then we have concluded that both brassinolides have the seasonal stress ameliorative properties in B. juncea seedlings grown under the influence of seasonal stress. This study culminates to the role of brassinolides as an anti-stress property for protection of plant from various types of stresses.

  11. Feeding behaviour of generalist pests on Brassica juncea: implication for manipulation of glucosinolate biosynthesis pathway for enhanced resistance.

    Science.gov (United States)

    Kumar, Pawan; Augustine, Rehna; Singh, Amarjeet Kumar; Bisht, Naveen C

    2017-10-01

    Differential accumulation of plant defence metabolites has been suggested to have important ecological consequence in the context of plant-insect interactions. Feeding of generalist pests on Brassica juncea showed a distinct pattern with selective exclusion of leaf margins which are high in glucosinolates. Molecular basis of this differential accumulation of glucosinolates could be explained based on differential expression profile of BjuMYB28 homologues, the major biosynthetic regulators of aliphatic glucosinolates, as evident from quantitative real-time PCR and promoter:GUS fusion studies in allotetraploid B. juncea. Constitutive overexpression of selected BjuMYB28 homologues enhanced accumulation of aliphatic glucosinolates in B. juncea. Performance of two generalist pests, Helicoverpa armigera and Spodoptera litura larvae, on transgenic B. juncea plants were poor compared to wild-type plants in a no-choice experiment. Correlation coefficient analysis suggested that weight gain of H. armigera larvae was negatively correlated with gluconapin (GNA) and glucobrassicanapin (GBN), whereas that of S. litura larvae was negatively correlated with GNA, GBN and sinigrin (SIN). Our study explains the significance and possible molecular basis of differential distribution of glucosinolates in B. juncea leaves and shows the potential of overexpressing BjuMYB28 for enhanced resistance of Brassica crops against the tested generalist pests. © 2017 John Wiley & Sons Ltd.

  12. Chrysoperla externa (Neuroptera: Chrysopidae and Utetheisa ornatrix (Lepidoptera: Arctiidae on organically grown Crotalaria juncea (Fabaceae Chrysoperla externa (Neuroptera: Chrysopidae e Utetheisa ornatrix (Lepidoptera: Arctiidae sobre Crotalaria juncea (Fabaceae cultivada organicamente

    Directory of Open Access Journals (Sweden)

    M.A. Costa

    2012-09-01

    Full Text Available Chrysoperla externa (Neuroptera: Chrysopidae larvae can avoid foraging on plants of Crotalaria juncea (Fabaceae after the issuance of floral buds, when the prey of Utetheisa ornatrix (Lepidoptera: Arctiidae incorporate toxic pyrrolizidine alkaloids from this plant. This reduces the predation and favors increasing the number of adults and eggs of this defoliator on crops of this plant. The aim of the present paper was to evaluate some biological and ecological aspects of C. externa and U. ornatrix on the organic crop of C. juncea in the EMBRAPA Maize and Sorghum in Sete Lagoas, Minas Gerais State, Brazil. Chrysoperla externa and U. ornatrix were more abundant in the vegetative and flowering stages of C. juncea, respectively, with caterpillars of this defoliator feeding on leaves and seeds of this plant. The duration of the stages/instars, survival, lifetime fecundity, and oviposition showed that the branches of C. juncea are a suitable food for U. ornatrix. The abundance of adults and larvae of C. externa was lower in the flowering and pods stages of C. juncea, respectively, when the postures of U. ornatrix are present, probably due to the toxicity of the eggs of this prey to this predator. During these stages, C. externa may be reared with alternative hosts, and when the crops of C. juncea are scarce, an artificial diet should be used for rearing this defoliator in the laboratory for biological research and the development of biological control tactics.Larvas de Chrysoperla externa (Neuroptera: Chrysopidae podem evitar o forrageamento sobre plantas de Crotalaria juncea (Fabaceae após a emissão de botões florais, quando presas de Utetheisa ornatrix (Lepidoptera: Arctiidae incorporam alcalóides pirrolizidínicos tóxicos dessa planta. Isso reduz a predação e favorece o aumento do número de adultos e ovos desse desfolhador sobre cultivos dessa planta. O objetivo deste trabalho foi avaliar alguns aspectos biológicos e ecológicos de C

  13. Pemanfaatan Limbah Kotoran Sapi Dan Jerami Kacang Tanah Sebagai Bokashi Cair Bagi Pertumbuhan Tanaman Sawi (Brassica Juncea L.)

    OpenAIRE

    Artiana Artiana; Lilis Hartati; Abrani Sulaiman; Jamzuri Hadie

    2016-01-01

    Has conducted a study entitled " Cow Manure Waste Utilization and Straw Peanut For Liquid Bokashi For Plant Growth mustard (Brassica juncea L.)". This study aimed to analyze the nutrient content in the liquid Bokashi is derived from cow dung and straw peanuts, and study the effect of dosing Bokashi different liquid to the growth of the mustard plant (Brassica juncea L.). Methods using a completely randomized design with one factor at a dose of 125 ml, 250 ml, 375 ml and 500 ml, and as control...

  14. PEMANFAATAN LIMBAH KOTORAN SAPI DAN JERAMI KACANG TANAH SEBAGAI BOKASHI CAIR BAGI PERTUMBUHAN TANAMAN SAWI (Brassica juncea L.)

    OpenAIRE

    Artiana Artiana; Lilis Hartati; Abrani Sulaiman; Jamzuri Hadie

    2016-01-01

    Has conducted a study entitled " Cow Manure Waste Utilization and Straw Peanut For Liquid Bokashi For Plant Growth mustard (Brassica juncea L.)". This study aimed to analyze the nutrient content in the liquid Bokashi is derived from cow dung and straw peanuts, and study the effect of dosing Bokashi different liquid to the growth of the mustard plant (Brassica juncea L.). Methods using a completely randomized design with one factor at a dose of 125 ml, 250 ml, 375 ml and 500 ml, and as control...

  15. Development of transgenic Brassica juncea lines for reduced seed sinapine content by perturbing phenylpropanoid pathway genes.

    Directory of Open Access Journals (Sweden)

    Sachin Kajla

    Full Text Available Sinapine is a major anti-nutritive compound that accumulates in the seeds of Brassica species. When ingested, sinapine imparts gritty flavuor in meat and milk of animals and fishy odor to eggs of brown egg layers, thereby compromising the potential use of the valuable protein rich seed meal. Sinapine content in Brassica juncea germplasm ranges from 6.7 to 15.1 mg/g of dry seed weight (DSW which is significantly higher than the prescribed permissible level of 3.0 mg/g of DSW. Due to limited natural genetic variability, conventional plant breeding approach for reducing the sinapine content has largely been unsuccessful. Hence, transgenic approach for gene silencing was adopted by targeting two genes-SGT and SCT, encoding enzymes UDP- glucose: sinapate glucosyltransferase and sinapoylglucose: choline sinapoyltransferase, respectively, involved in the final two steps of sinapine biosynthetic pathway. These two genes were isolated from B. juncea and eight silencing constructs were developed using three different RNA silencing approaches viz. antisense RNA, RNAi and artificial microRNA. Transgenics in B. juncea were developed following Agrobacterium-mediated transformation. From a total of 1232 independent T0 transgenic events obtained using eight silencing constructs, 25 homozygous lines showing single gene inheritance were identified in the T2 generation. Reduction of seed sinapine content in these lines ranged from 15.8% to 67.2%; the line with maximum reduction had sinapine content of 3.79 mg/g of DSW. The study also revealed that RNAi method was more efficient than the other two methods used in this study.

  16. Micro-PIXE studies of elemental distribution in Cd-accumulating Brassica juncea L

    International Nuclear Information System (INIS)

    Schneider, Thorsten; Haag-Kerwer, Angela; Maetz, Mischa; Niecke, Manfred; Povh, Bogdan; Rausch, Thomas; Schuessler, Arthur

    1999-01-01

    Brassica juncea L. is a high biomass producing crop plant, being able to accumulate Cd and other heavy metals in their roots and shoots. It is a good candidate for efficient phytoextraction of heavy metals - such as Cd - from polluted soils. PIXE and STIM analyses were applied to investigate Cd-uptake in roots and the resulting effects on the elemental distribution of Cd stressed plants. The axial distribution of trace elements as a function of distance from the root tip as well as the radial distribution within cross-sections were analysed. The results are compared with the elemental distribution in control plants

  17. Micro-PIXE studies of elemental distribution in Cd-accumulating Brassica juncea L.

    Science.gov (United States)

    Schneider, Thorsten; Haag-Kerwer, Angela; Maetz, Mischa; Niecke, Manfred; Povh, Bogdan; Rausch, Thomas; Schüßler, Arthur

    1999-10-01

    Brassica juncea L. is a high biomass producing crop plant, being able to accumulate Cd and other heavy metals in their roots and shoots. It is a good candidate for efficient phytoextraction of heavy metals - such as Cd - from polluted soils. PIXE and STIM analyses were applied to investigate Cd-uptake in roots and the resulting effects on the elemental distribution of Cd stressed plants. The axial distribution of trace elements as a function of distance from the root tip as well as the radial distribution within cross-sections were analysed. The results are compared with the elemental distribution in control plants.

  18. Micro-PIXE studies of elemental distribution in Cd-accumulating Brassica juncea L

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Thorsten E-mail: thorsten.schneider@mpi-hd.mpg.de; Haag-Kerwer, Angela; Maetz, Mischa; Niecke, Manfred; Povh, Bogdan; Rausch, Thomas; Schuessler, Arthur

    1999-09-02

    Brassica juncea L. is a high biomass producing crop plant, being able to accumulate Cd and other heavy metals in their roots and shoots. It is a good candidate for efficient phytoextraction of heavy metals - such as Cd - from polluted soils. PIXE and STIM analyses were applied to investigate Cd-uptake in roots and the resulting effects on the elemental distribution of Cd stressed plants. The axial distribution of trace elements as a function of distance from the root tip as well as the radial distribution within cross-sections were analysed. The results are compared with the elemental distribution in control plants.

  19. Agrobacterium mediated transformation of brassica juncea (l.) czern with chitinase gene conferring resistance against fungal infections

    International Nuclear Information System (INIS)

    Ahmad, B.; Ambreen, S.; Khan, I.

    2015-01-01

    Brassica juncea (Czern and Coss., L.) is an important oilseed crop. Since it is attacked by several bacterial and fungal diseases, therefore, we developed an easy and simple protocol for the regeneration and transformation of B. juncea variety RAYA ANMOL to give rise to transgenic plants conferring resistance against various fungal diseases. The transformation was carried out using Agrobacterium with Chitinase gene. This gene was isolated from Streptomyces griseus HUT6037. We used two types of explants for transformation i.e. hypocotyls and cotyledons. Only hypocotyls explants showed good results regarding callus initiation. Different hormonal concentrations were applied i.e. BAP 2, 4 and 6 mgL-1 and NAA 0.1, 0.2 and 0.3 mgL-1. However, high transformation efficiency was observed by supplementing the medium with combination of 2 mgL-1 BAP and 0.2 mgL-1 for initiation of callus. Similarly 10 mgL-1 kanamycin and 200 mgL-1 cefotaxime also proved successful for the selection of transformed callus. In order to confirm the presence of transgenic callus Polymerase chain reaction was performed using specific primers for Chitinase gene. (author)

  20. Production of transgenic brassica juncea with the synthetic chitinase gene (nic) conferring resistance to alternaria brassicicola

    International Nuclear Information System (INIS)

    Munir, I.; Hussan, W.; Kazi, M.; Mian, A.

    2016-01-01

    Brassica juncea is an important oil seed crop throughout the world. The demand and cultivation of oil seed crops has gained importance due to rapid increase in world population and industrialization. Fungal diseases pose a great threat to Brassica productivity worldwide. Absence of resistance genes against fungal infection within crossable germplasms of this crop necessitates deployment of genetic engineering approaches to produce transgenic plants with resistance against fungal infections. In the current study, hypocotyls and cotyledons of Brassica juncea, used as explants, were transformed with Agrobacterium tumefacien strain EHA101 harboring binary vector pEKB/NIC containing synthetic chitinase gene (NIC), an antifungal gene under the control of cauliflower mosaic virus promoter (CaMV35S). Bar genes and nptII gene were used as selectable markers. Presence of chitinase gene in trangenic lines was confirmed by PCR and southern blotting analysis. Effect of the extracted proteins from non-transgenic and transgenic lines was observed on the growth of Alternaria brassicicola, a common disease causing pathogen in brassica crop. In comparison to non-transgenic control lines, the leaf tissue extracts of the transgenic lines showed considerable resistance and antifungal activity against A. brassicicola. The antifungal activity in transgenic lines was observed as corresponding to the transgene copy number. (author)

  1. Changes in the glucosinolate-myrosinase defense system in Brassica juncea cotyledons during seedling development.

    Science.gov (United States)

    Wallace, S K; Eigenbrode, Sanford D

    2002-02-01

    Optimal defense theory (ODT) predicts that plant defenses will be allocated to plant organs and tissues in proportion to their relative fitness values and susceptibilities to attack. This study was designed to test ODT predictions on the myrosinase-glucosinolate defense system in Brassica juncea by examining the relationships between the fitness value of B. juncea cotyledons and the levels and effectiveness of cotyledon defenses. Specifically, we estimated fitness value of cotyledons during plant development by measuring plant growth and seed production after cotyledon damage or removal at successive seedling ages. Cotyledon removal within five days of emergence had a significant impact on growth and seed production, but cotyledon removal at later stages did not. Consistent with ODT, glucosinolate and myrosinase levels in cotyledons also declined with seedling age, as did relative defenses against a generalist herbivore, Spodoptera eridania, as estimated by bioassay. Declines in glucosinolates were as predicted by a passive, allometric dilution model based on cotyledon expansion. Declines in myrosinase activity were significantly more gradual than predicted by allometric dilution, suggesting active retention of myrosinase activity as young cotyledons expand.

  2. Genetic Variability in Glucosinolates in Seed of Brassica juncea: Interest in Mustard Condiment

    Directory of Open Access Journals (Sweden)

    Othmane Merah

    2015-01-01

    Full Text Available Brassica juncea is mostly used for oil production which implies selection of genotypes with low glucosinolates level and high oil content. In contrast, condiment production needs varieties with high level in some glucosinolates including sinigrin. The genetic variability was studied mostly by molecular tools. The objectives were almost the decrease of glucosinolates level in order to use the oilcake for animal feed. The aim of this work is to study the genetic variability for different glucosinolates and their relationships with agronomical traits within a large collection of Brassica juncea genotypes for condiment uses. A collection of 190 genotypes from different origins was studied in Dijon (France. Oil content and total glucosinolates, and sinigrin and gluconapin levels were measured. Flowering and maturation durations, seed yield, and yield components were also measured. Large variability was observed between genotypes for the measured traits within the studied collection. Total glucosinolates varied twofold between extreme genotypes. Values of sinigrin content varied from 0 to more than 134 µmol·g−1. Correlations between glucosinolates traits and both phenological and agronomical characters are presented and discussed for their potential for industrial condiment uses.

  3. PEMANFAATAN LIMBAH KOTORAN SAPI DAN JERAMI KACANG TANAH SEBAGAI BOKASHI CAIR BAGI PERTUMBUHAN TANAMAN SAWI (Brassica juncea L.

    Directory of Open Access Journals (Sweden)

    Artiana Artiana

    2016-12-01

    Full Text Available Has conducted a study entitled " Cow Manure Waste Utilization and Straw Peanut For Liquid Bokashi For Plant Growth mustard (Brassica juncea L.". This study aimed to analyze the nutrient content in the liquid Bokashi is derived from cow dung and straw peanuts, and study the effect of dosing Bokashi different liquid to the growth of the mustard plant (Brassica juncea L.. Methods using a completely randomized design with one factor at a dose of 125 ml, 250 ml, 375 ml and 500 ml, and as control using Bokashi solid. This research was conducted with four replications. Bokashi liquid nutrient content of C of 0,1045%, 0,0461% of N, P and K amounted to 0.0172% at 0.2500%. The content of nutrient dense Bokashi C of 6,0874%, 2,0169% of N, P and K amounted to 0,0218% at 5,7802%. Bokashi dosing different liquid to the growth of mustard (Brassica juncea L. significant effect on the growth of mustard, but still lower than the solid Bokashi. Dose liquid Bokashi most optimal for growing mustard (Brassica juncea L. is at 375 ml.

  4. Factors affecting emission of AITC and subsequent disease control efficacy of Brassica juncea seed meal soil amendment

    Science.gov (United States)

    Soil physical conditions demonstrably affected allyl isothiocyanate (AITC) emitted from Brassica juncea cv Pacific Gold seed meal (SM) amended soil. The AITC concentration detected increased with an increase in temperature from 10 oC to 30 oC. AITC concentration also increased with an increase in so...

  5. De novo transcriptome profiling of cold-stressed siliques during pod filling stages of Indian mustard (Brassica juncea L.

    Directory of Open Access Journals (Sweden)

    Somya eSinha

    2015-10-01

    Full Text Available Low temperature is a major abiotic stress that impedes plant growth and development. Brassica juncea is an economically important oil seed crop and is sensitive to freezing stress during pod filling subsequently leading to abortion of seeds. To understand the cold stress mediated global perturbations in gene expression, whole transcriptome of B. juncea siliques that were exposed to sub-optimal temperature was sequenced. Manually self-pollinated siliques at different stages of development were subjected to either short (6 h or long (12 h durations of chilling stress followed by construction of RNA-seq libraries and deep sequencing using Illumina’s NGS platform. De-novo assembly of B. juncea transcriptome resulted in 133641 transcripts, whose combined length was 117 Mb and N50 value was 1428 bp. We identified 13342 differentially regulated transcripts by pair-wise comparison of 18 transcriptome libraries. Hierarchical clustering of these differentially expressed transcripts along with Spearman correlation analysis identified two major clusters representing early (5-15 DAP and late stages (20-30 DAP of silique development. Detailed analysis led to the discovery of two gene expression clusters whose transcripts were inducible at both durations of the cold stress irrespective of the developmental stages. We further explored the expression patterns of gene families encoding for transcription factors (TFs, transcription regulators (TRs and kinases, and found that cold stress induced protein kinases specifically during early silique development. We validated the digital gene expression profiles of selected transcripts by qPCR and found a high degree of concordance between the two analyses. To our knowledge this is the first report of transcriptome sequencing of cold-stressed B. juncea siliques. The data generated in this study would be a valuable resource for not only understanding the cold stress signaling pathway but also for introducing cold

  6. Nitrogen-15 labeling of Crotalaria juncea green manure Marcação do adubo verde Crotalaria juncea com 15N

    Directory of Open Access Journals (Sweden)

    Edmilson José Ambrosano

    2003-02-01

    Full Text Available Most studies dealing with the utilization of 15N labeled plant material do not present details about the labeling technique. This is especially relevant for legume species since biological nitrogen fixation difficults plant enrichment. A technique was developed for labeling leguminous plant tissue with 15N to obtain labeled material for nitrogen dynamics studies. Sun hemp (Crotalaria juncea L. was grown on a Paleudalf, under field conditions. An amount of 58.32 g of urea with 70.57 ± 0.04 atom % 15N was sprayed three times on plants grown on eight 6-m²-plots. The labelled material presented 2.412 atom % 15N in a total dry matter equivalent to 9 Mg ha-1 This degree of enrichment enables the use of the green manure in pot or field experiments requiring 15N-labeled material.A grande maioria dos estudos com a utilização de material vegetal marcado com o isótopo 15N não apresentam detalhes tão importantes sobre como foram obtidos esses materiais. Em se tratando de marcação de leguminosas as dificuldades em se obter material marcado com 15N são ainda maiores pelo fato de serem plantas fixadoras de nitrogênio. Isso posto foi estabelecida uma técnica de marcação de leguminosas com nitrogênio (15N, com o objetivo de obter material vegetal marcado isotopicamente para estudos de dinâmica do nitrogênio. Cultivou-se a leguminosa crotalária júncea (Crotalaria juncea L., em Argissolo Vermelho Amarelo distrófico, em campo. Ao se aplicarem via foliar 58,32 gramas de uréia em oito canteiros experimentais, (uréia com 70,57 ± 0,04% de átomos de 15N parceladas em três vezes, obteve-se material vegetal marcado seco que continha 2,412 % em átomos de 15N em uma massa seca equivalente a 9 Mg ha-1. Essa marcação permite o uso dessa massa vegetal em estudos de dinâmica de nitrogênio.

  7. Ab initio pseudopotential theory

    International Nuclear Information System (INIS)

    Yin, M.T.; Cohen, M.L.

    1982-01-01

    The ab initio norm-conserving pseudopotential is generated from a reference atomic configuration in which the pseudoatomic eigenvalues and wave functions outside the core region agree with the corresponding ab initio all-electron results within the density-functional formalism. This paper explains why such pseudopotentials accurately reproduce the all-electron results in both atoms and in multiatomic systems. In particular, a theorem is derived to demonstrate the energy- and perturbation-independent properties of ab initio pseudopotentials

  8. Biofumigation with Brassica juncea, Raphanus sativus and Eruca sativa for the management of field populations of the potato cyst nematode Globodera pallida.

    Science.gov (United States)

    Ngala, Bruno M; Haydock, Patrick P J; Woods, Simon; Back, Matthew A

    2015-05-01

    The viability of potato cyst nematode (PCN) populations (Globodera pallida) was evaluated in three field experiments using Brassica juncea, Raphanus sativus and Eruca sativa amendments. These species were summer cultivated and autumn incorporated in experiment 1; in experiment 2, overwintered brassicaceous cover crops were spring incorporated. Experiment 3 involved determination of effects of metconazole application on biomass/glucosinolate production by B. juncea and R. sativus and on PCN pre- and post-incorporation. Glucosinolate contents were determined before incorporation. Following cover crop incorporation, field plots were planted with susceptible potatoes to evaluate the biofumigation effects on PCN reproduction. In experiment 1, PCN population post-potato harvest was reduced (P = 0.03) in B. juncea-treated plots, while R. sativus prevented further multiplication, but in experiment 2 there were no significant effects on PCN reproduction. In experiment 3, B. juncea or R. sativus either untreated or treated with metconazole reduced PCN populations. Glucosinolate concentrations varied significantly between different plant regions and cultivation seasons. Metconazole application increased the sinigrin concentration in B. juncea tissues. Glucosinolate concentrations correlated positively with PCN mortality for summer-cultivated brassicaceous plants. The results demonstrated that B. juncea and R. sativus green manures can play an important role in PCN management, particularly if included in an integrated pest management scheme. © 2014 Society of Chemical Industry.

  9. Effects of inoculation of plant growth-promoting rhizobacteria on metal uptake by Brassica juncea

    International Nuclear Information System (INIS)

    Wu, S.C.; Cheung, K.C.; Luo, Y.M.; Wong, M.H.

    2006-01-01

    A greenhouse study was carried out with Brassica juncea to critically evaluate effects of bacterial inoculation on the uptake of heavy metals from Pb-Zn mine tailings by plants. Application of plant growth-promoting rhizobacteria, including nitrogen-fixing bacteria and phosphate and potassium solubilizers, might play an important role in the further development of phytoremediation techniques. The presence of these beneficial bacteria stimulated plant growth and protected the plant from metal toxicity. Inoculation with rhizobacteria had little influence on the metal concentrations in plant tissues, but produced a much larger above-ground biomass and altered metal bioavailability in the soil. As a consequence, higher efficiency of phytoextraction was obtained compared with control treatments. - Rhizobacteria promoted growth above normal biomass, but did not influence plant metal concentrations

  10. Effects of inoculation of plant growth-promoting rhizobacteria on metal uptake by Brassica juncea

    Energy Technology Data Exchange (ETDEWEB)

    Wu, S.C. [Department of Biology and Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China); Joint Open Laboratory on Soil and Environment between HKBU and ISSCAS (China); Cheung, K.C. [Department of Biology and Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China); Joint Open Laboratory on Soil and Environment between HKBU and ISSCAS (China); Luo, Y.M. [Institute of Soil Science, Chinese Academy of Sciences, Nanjing (China); Joint Open Laboratory on Soil and Environment between HKBU and ISSCAS (China); Wong, M.H. [Department of Biology and Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China) and Joint Open Laboratory on Soil and Environment between HKBU and ISSCAS (China)]. E-mail: mhwong@hkbu.edu.hk

    2006-03-15

    A greenhouse study was carried out with Brassica juncea to critically evaluate effects of bacterial inoculation on the uptake of heavy metals from Pb-Zn mine tailings by plants. Application of plant growth-promoting rhizobacteria, including nitrogen-fixing bacteria and phosphate and potassium solubilizers, might play an important role in the further development of phytoremediation techniques. The presence of these beneficial bacteria stimulated plant growth and protected the plant from metal toxicity. Inoculation with rhizobacteria had little influence on the metal concentrations in plant tissues, but produced a much larger above-ground biomass and altered metal bioavailability in the soil. As a consequence, higher efficiency of phytoextraction was obtained compared with control treatments. - Rhizobacteria promoted growth above normal biomass, but did not influence plant metal concentrations.

  11. Efek Paparan Musik dan Noise pada Karakteristik Morfologi dan Produktivitas Tanaman Sawi Hijau (Brassica Juncea

    Directory of Open Access Journals (Sweden)

    Joko Prasetyo

    2014-04-01

    Full Text Available The objective of present study was to investigate the effect of various sounds on the green mustard’s (Brassica Juncea morphology characteristic and productivity. The plant has been subjected to three various sound, namely classical music (rhythmic violin music, machine and traffic noise, and mixed sound (classical music and traffic noise with 70-75 dB sound pressure level, from germination to harvest for three hours (7-10 am. each day. Six parameters, i.e. germination, plant height, leaf width, leaf lenght, total plant lenght, and fresh weight, related with growth and productivity of plant were been monitored on regular basis.The results showed classical music improves germination up to 15% for 36 hours, plant height 13,5%, leaf width 14,8%, leaf length 14,2%, and wet weight 57,1%. In general, exposure to classical music gives the best results on the morphological characteristics and productivity of green mustard.

  12. evaluation of best planting time of mustard (brassica juncea) strains in southern punjab

    International Nuclear Information System (INIS)

    Aslam, M.; Hussain, G.; Hussain, M.

    2008-01-01

    The study was conducted to find out the proper planting time of newly evolved mustard (Brassica juncea) strains at Regional Agriculture Research Institute, Bahawalpur during the year 2000-2002. The study included 4 planting dates from 1st October to November 15th and three strains i.e. BRS-2 and BRS-10 and KH- 74 along with check RL-18. The 1st fortnight of October proved to be the best sowing time. KH-74 and BRS-2 gave significantly higher yield in wide range of sown period i.e. 1st October to 15th November. The highest grain yield of 2435 and 2341 Kgs, ha were obtained when crop was planted on 1st October and 15th October respectively. (author)

  13. The K Domain Mediates Homologous and Heterologous Interactions Between FLC and SVP Proteins of Brassica juncea

    Directory of Open Access Journals (Sweden)

    Ma Guanpeng

    2015-07-01

    Full Text Available The transcription factors FLOWERING LOCUS C (FLC and SHORT VEGETATIVE PHASE (SVP can interact to form homologous and heterologous protein complexes that regulate flowering time in Brassica juncea Coss. (Mustard.Previous studies showed that protein interactions were mediated by the K domain, which contains the subdomains K1, K2 and K3. However, it remains unknown how the subdomains mediate the interactions between FLC and SVP. In the present study, we constructed several mutants of subdomains K1–K3 and investigated the mechanisms involved in the heterologous interaction of BjFLC/BjSVP and in the homologous interaction of BjFLC/BjFLC or BjSVP/BjSVP. Yeast two-hybrid and β-Galactosidase activity assays showed that the 19 amino acids of the K1 subdomain in BjSVP and the 17 amino acids of the K1 subdomain in BjFLC were functional subdomains that interact with each other to mediate hetero-dimerization. The heterologous interaction was enhanced by the K2 subdomain of BjSVP protein, but weakened by its interhelical domain L2. The heterologous interaction was also enhanced by the K2 subdomain of BjFLC protein, but weakened by its K3 subdomain. The homologous interaction of BjSVP was mediated by the full K-domain. However, the homologous interaction of BjFLC was regulated only by its K1 and weakened by its K2 and K3 subdomains. The results provided new insights into the interactions between FLC and SVP, which will be valuable for further studies on the molecular regulation mechanisms of the regulation of flowering time in B. juncea and other Brassicaceae.

  14. Sulfur utilization by rice and Crotalaria juncea from sulfate - 34S applied to the soil

    Directory of Open Access Journals (Sweden)

    Trivelin Paulo Cesar Ocheuze

    2002-01-01

    Full Text Available In tropical soils with intensive agriculture an increasing sulfur deficiency has been verified in several crops. The low available S in these soils is caused by the continuous use of concentrated NPK fertilizers. The objective of this work was to evaluate the utilization by rice (Oriza sativa L. and crotalaria juncea (Crotalaria juncea L. of sulfur applied to the soil, under greenhouse conditions. Pots with 3 kg of an Argisol (Paleudalf were used to test the isotopic technique with the stable isotope 34S, adding a solution of sodium sulfate labeled with 34S (14.30 ± 0.05 atom % of 34S to the soil (70 mg SO4-S per kg-1 of soil 18 days after sowing both species. The shoots of the crotalaria and rice were harvested, respectively on the 72nd and 122nd days after S fertilization. The concentration and the amount of sulfur in the crotalaria were higher than in rice, due to the higher legume requirement for this nutrient. The sulfur requirement and the short time interval between fertilization and harvest of the crotalaria resulted in a small amount of native SO4-S mineralized in the soil and a small quantity of 34SO4 immobilized by soil microorganisms. Thus, the percentage of sulfur in the crotalaria derived from the fertilizer (Sdff was higher than in the rice (%Sdff crotalaria = 91.3 ± 3.5%; %Sdff rice = 66.3 ± 0.8%. The expressive values of %Sdff indicate a low rate of mineralization of SO4-S probably as a consequence of the low available sulfur content in the soil.

  15. Does salt stress constrain spatial distribution of dune building grasses Ammophila arenaria and Elytrichia juncea on the beach?

    Science.gov (United States)

    van Puijenbroek, Marinka E B; Teichmann, Corry; Meijdam, Noortje; Oliveras, Imma; Berendse, Frank; Limpens, Juul

    2017-09-01

    Rising sea levels threaten coastal safety by increasing the risk of flooding. Coastal dunes provide a natural form of coastal protection. Understanding drivers that constrain early development of dunes is necessary to assess whether dune development may keep pace with sea-level rise. In this study, we explored to what extent salt stress experienced by dune building plant species constrains their spatial distribution at the Dutch sandy coast. We conducted a field transplantation experiment and a glasshouse experiment with two dune building grasses Ammophila arenaria and Elytrigia juncea . In the field, we measured salinity and monitored growth of transplanted grasses in four vegetation zones: (I) nonvegetated beach, (II) E. juncea occurring, (III) both species co-occurring, and (IV) A. arenaria dominant. In the glasshouse, we subjected the two species to six soil salinity treatments, with and without salt spray. We monitored biomass, photosynthesis, leaf sodium, and nutrient concentrations over a growing season. The vegetation zones were weakly associated with summer soil salinity; zone I and II were significantly more saline than zones III and IV. Ammophila arenaria performed equally (zone II) or better (zones III, IV) than E. juncea , suggesting soil salinity did not limit species performance. Both species showed severe winter mortality. In the glasshouse, A. arenaria biomass decreased linearly with soil salinity, presumably as a result of osmotic stress. Elytrigia juncea showed a nonlinear response to soil salinity with an optimum at 0.75% soil salinity. Our findings suggest that soil salinity stress either takes place in winter, or that development of vegetated dunes is less sensitive to soil salinity than hitherto expected.

  16. Comparison of the karyotypes ofPsathyrostachys juncea andP. huashanica (Poaceae) studied by banding techniques

    DEFF Research Database (Denmark)

    Linde-Laursen, Ib; Bothmer, R. von

    1986-01-01

    . The patterns of both taxa are polymorphic, supporting that both taxa are outbreeders. The karyotypic characters suggest that P. juncea is more closely related to P. fragilis than either is to P. huashanica. N-banding stains weakly. Silver nitrate staining demonstrates that nucleolus organizers of both species...... have different nucleolus forming capacities. The presence of micronucleoli suggests that both species have an extra unidentified chromosome with nucleolus forming capacity....

  17. Castasterone confers copper stress tolerance by regulating antioxidant enzyme responses, antioxidants, and amino acid balance in B. juncea seedlings.

    Science.gov (United States)

    Yadav, Poonam; Kaur, Ravdeep; Kanwar, Mukesh Kumar; Sharma, Anket; Verma, Vinod; Sirhindi, Geetika; Bhardwaj, Renu

    2018-01-01

    The aim of the present study was to explore the effect of exogenous application of castasterone (CS) on physiologic and biochemical responses in Brassica juncea seedlings under copper (Cu) stress. Seeds were pre-soaked in different concentrations of CS and grown for 7 days under various levels of Cu. The exposure of B. juncea to higher levels of Cu led to decrease of morphologic parameters, with partial recovery of length and fresh weight in the CS pre-treated seedlings. Metal content was high in both roots and shoots under Cu exposure while the CS pre-treatment reduced the metal uptake. Accumulation of hydrogen peroxide (H 2 O 2 ) and superoxide anion radical (O 2 - ) were chosen as stress biomarker and higher levels of H 2 O 2 (88.89%) and O 2 - (62.11%) showed the oxidative stress in metal treated B. juncea seedlings, however, CS pre-treatment reduced ROS accumulation in Cu-exposed seedlings. The Cu exposures lead to enhance the plant's enzymatic and non-enzymatic antioxidant system. It was observed that enzymatic activities of ascorbate peroxidase (APOX), dehydroascorbate reductase (DHAR), and glutathione reductase (GR), glutathione perxoidase (GPOX) and gultrathione-s-transferase increased while activity of monodehydroascorbate reductase (MDHAR) decreased under Cu stress. The pre-treatment with CS positively affected the activities of enzymes. RT-PCR analysis showed that mRNA transcript levels were correlated with total enzymatic activity of DHAR, GR, GST and GSH. Increase in the gene expression of DHAR (1.85 folds), GR (3.24 folds), GST-1 (2.00 folds) and GSH-S (3.18 folds) was noticed with CS pre-treatment. Overall, the present study shows that Cu exposure induced severe oxidative stress in B. juncea plants and exogenous application of CS improved antioxidative defense system by modulating the ascorbate-glutathione cycle and amino acid metabolism. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Transcriptome analysis of Brassica juncea var. tumida Tsen responses to Plasmodiophora brassicae primed by the biocontrol strain Zhihengliuella aestuarii.

    Science.gov (United States)

    Luo, Yuanli; Dong, Daiwen; Su, Yu; Wang, Xuyi; Peng, Yumei; Peng, Jiang; Zhou, Changyong

    2018-05-01

    Mustard clubroot, caused by Plasmodiophora brassicae, is a serious disease that affects Brassica juncea var. tumida Tsen, a mustard plant that is the raw material for a traditional fermented food manufactured in Chongqing, China. In our laboratory, we screened the antagonistic bacteria Zhihengliuella aestuarii against P. brassicae. To better understand the biocontrol mechanism, three transcriptome analyses of B. juncea var. tumida Tsen were conducted using Illumina HiSeq 4000, one from B. juncea only inoculated with P. brassicae (P), one inoculated with P. brassica and the biocontrol agent Z. aestuarii at the same time (P + B), and the other was the control (H), in which P. brassicae was replaced by sterile water. A total of 19.94 Gb was generated by Illumina HiSeq sequencing. The sequence data were de novo assembled, and 107,617 unigenes were obtained. In total, 5629 differentially expressed genes between biocontrol-treated (P + B) and infected (P) samples were assigned to 126 KEGG pathways. Using multiple testing corrections, 20 pathways were significantly enriched with Qvalue ≤ 0.05. The resistance-related genes, involved in the production of pathogenesis-related proteins, pathogen-associated molecular pattern-triggered immunity, and effector-triggered immunity signaling pathways, calcium influx, salicylic acid pathway, reactive oxygen intermediates, and mitogen-activated protein kinase cascades, and cell wall modification, were obtained. The various defense responses induced by the biocontrol strain combatted the P. brassicae infection. The genes and pathways involved in plant resistance were induced by a biocontrol strain. The transcriptome data explained the molecular mechanism of the potential biocontrol strain against P. brassicae. The data will also serve as an important public information platform to study B. juncea var. tumida Tsen and will be useful for breeding mustard plants resistant to P. brassicae.

  19. Salicylic acid-mediated establishment of the compatibility between Alternaria brassicicola and Brassica juncea is mitigated by abscisic acid in Sinapis alba.

    Science.gov (United States)

    Mazumder, Mrinmoy; Das, Srirupa; Saha, Upala; Chatterjee, Madhuvanti; Bannerjee, Kaushik; Basu, Debabrata

    2013-09-01

    This work addresses the changes in the phytohormonal signature in the recognition of the necrotrophic fungal pathogen Alternaria brassicicola by susceptible Brassica juncea and resistant Sinapis alba. Although B. juncea, S. alba and Arabidopsis all belong to the same family, Brassicaceae, the phytohormonal response of susceptible B. juncea towards this pathogen is unique because the latter two species express non-host resistance. The differential expression of the PR1 gene and the increased level of salicylic acid (SA) indicated that an SA-mediated biotrophic mode of defence response was triggered in B. juncea upon challenge with the pathogen. Compared to B. juncea, resistant S. alba initiated enhanced abscisic acid (ABA) and jasmonic acid (JA) responses following challenge with this pathogen, as revealed by monitoring the expression of ABA-related genes along with the concentration of ABA and JA. Furthermore, these results were verified by the exogenous application of ABA on B. juncea leaves prior to challenge with A. brassicicola, which resulted in a delayed disease progression, followed by the inhibition of the pathogen-mediated increase in SA response and enhanced JA levels. Therefore, it seems that A. brassicicola is steering the defence response towards a biotrophic mode by mounting an SA response in susceptible B. juncea, whereas the enhanced ABA response of S. alba not only counteracts the SA response but also restores the necrotrophic mode of resistance by enhancing JA biosynthesis. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  20. Effects of derived meals from juncea (Brassica juncea, yellow and black seeded canola (Brassica napus and multicarbohydrase enzymes supplementation on apparent metabolizable energy in broiler chickens

    Directory of Open Access Journals (Sweden)

    Balachandar Jayaraman

    2016-09-01

    Full Text Available Two experiments were conducted to determine the nitrogen-corrected apparent metabolizable energy (AMEn of differently processed meals from Juncea (Brassica juncea, yellow and black seeded canola (Brassica napus, with or without supplementation of multi-carbohydrase enzymes (Enz in diets for broiler chickens. The first experiment was a 3 × 2 × 2 factorial arrangement with the main factors being seed type (yellow [Yellow] or black [B1] canola seeds and Juncea seeds, processed at two temperatures (high temperature desolventized-toasted [HTDT] at 95°C or low temperature desolventized-toasted [LTDT] at 57°C, with or without Enz. In Exp. 1, a total of 384 one-day-old male broiler chicks were randomly assigned to 64 battery cages, with 6 birds/cage. The second experiment was a 2 × 2 × 2 factorial arrangement with the main factors being seed type (Yellow or black [B2], seed source (Scott, Saskatchewan or Truro, Nova Scotia and Enz (with or without supplementation. A total of 264 one-day-old male broiler chicks were randomly assigned to 44 battery cages, with 6 birds per cage. In Exp. 1 and 2, all birds were fed a common starter diet from 1 to 14 days of age. From d 15 to 21, the birds were fed one of the test treatments, a basal grower diet or the basal grower diet replaced with 30% test ingredient with celite (0.8% added as an inert marker. Excreta was collected on d 20 and 21. In Exp. 1, there were no interactions (P > 0.05 among seed type, processing temperature and Enz. Processing temperature and dietary Enz did not affect (P > 0.05 AMEn of different canola meals. The AMEn of prepress solvent extracted canola and juncea meals (PSEM from Yellow (11.2 MJ/kg was higher (P  0.05 among seed color, location and Enz. Supplementation of dietary Enz did not affect (P > 0.05 AMEn of different cold press canola meals. The AMEn of cold press canola meals (CPM from Yellow (14.7 MJ/kg was higher (P < 0.05 compared with B2 (12.2

  1. PEMANFAATAN PESTISIDA NABATI PADA PENGENDALIAN HAMA PLUTELLA XYLOSTELLA TANAMAN SAWI (Brassica juncea L. MENUJU PERTANIAN RAMAH LINGKUNGAN

    Directory of Open Access Journals (Sweden)

    suhartini suhartini

    2017-05-01

    ABSTRACT The use of chemical pesticides has many negative impacts on the environment, it is necessary for the use of biological pesticide towards sustainable agriculture or environmentally friendly agriculture. In the village were encountered many types of leaves that can be used as a biological pesticide, and therefore this study aims to determine the effectiveness of pesticide plant extracts of the leaves of some plants covering the leaves of tobacco, elephantopus, yellow wood and green betel on mortality of Plutella xylostella pests in plants mustard greens (Brassica juncea L, heavy wet mustard and mustard leaf damage    This study uses a completely randomized design with the treatment of various crops as a pesticide vegetable. The treatments used 6 kinds (degree ie negative control (P0, the leaves of tobacco (P1, the leaves of elephantopus (P2, the leaves of yellow wood (P3, the leaves of greens betel (P4 and chemical pesticides as a positive control (P5 with each grade of 10 %. Parameters measured were mortality pests, heavy wet mustard greens and mustard greens leaf damage rate. The analysis was performed by one-way ANOVA.    The results showed that the extract from the leaves of tobacco (Nicotiana tabacum, the leaves of elephantopus, the leaves of yellow wood (Arcangelisia flava L. and the leaves of green betel (Piper betle Linn. With a 10 percent concentration of the extract on a variety of  leaves are not yet significant effect on mortality pests Plutella xylostella, heavy wet of mustard greens (brassica juncea l. and severity of leaf mustard greens (brassica juncea l.. The leaf extract the most influence on mortality Plutella xylostella sequential is an extract of the leaves tobacco, the leaves of greens betel, the leaves of yellow wood and the leaves of elephantopus. While the effect on weight of wet mustard greens (Brassica juncea l. in order are as follows: the leaves of yellow wood, the leaves of green betel, the leaves of elephantopus, and the

  2. Variabilidade espacial de atributos de solo e de Crotalaria juncea L. em área severamente erodida

    Directory of Open Access Journals (Sweden)

    A. A. C. Salviano

    1998-03-01

    Full Text Available O trabalho foi desenvolvido numa área de produção comercial de cana-de-açúcar, situada no município de Piracicaba (SP, numa associação de Podzólico Vermelho-Amarelo + solo litólico, no período de novembro de 1994 a março de 1995. Essa área vem sendo explorada com cana-de-açúcar há, aproximadamente, 30 anos e apresentava diversos sulcos de erosão. O objetivo deste trabalho foi caracterizar a variabilidade espacial de atributos de crotalária juncea (Crotalaria juncea L. e de solo em uma área sob condições de erosão severa. A área foi arada e gradeada com incorporação de 4 t ha-1 de calcário, antes da semeadura a lanço de 30 kg ha-1 de semente de crotalária juncea. Uma parcela de 50 x 70 m foi amostrada de acordo com uma malha de 5 por 5 m, totalizando 140 pontos. Foram avaliados atributos químicos do solo superficial (0,00-0,20 m e subsuperficial (0,20-0,40 m, sua granulometria e a espessura de solo remanescente (ES - definida como a camada do solo acima do horizonte C, além da produtividade de matéria seca (MS e altura da crotalária juncea (ALTPL. Os valores de atributos maiores ou menores que quatro desvios-padrões da média foram descartados. A colheita da parte aérea da crotalária foi realizada no início de sua floração, em miniparcelas de 2 x 2,5 m, e calculada a matéria seca. A dependência espacial dos atributos estudados foi avaliada por semivariogramas escalonados. Esses apresentaram dependência espacial, com exceção do P (0,00-0,20 m e K nas duas camadas. Os atributos puderam ser agrupados em três categorias homogêneas quanto ao alcance do semivariograma: atributos químicos do solo (12 a 32 m < componentes de planta (25 a 32 m < frações granulométricas (32 a 42 m. Os atributos que melhor explicaram a produtividade da crotalária juncea foram H + Al, valor T e saturação por bases.

  3. An ab initio molecular

    Indian Academy of Sciences (India)

    mechanisms of two molecular crystals: An ab initio molecular dynamics ... for Computation in Molecular and Materials Science and Department of Chemistry, School of ..... NSAF Foundation of National Natural Science Foun- ... Matter 14 2717.

  4. HHV-6A/B Integration and the Pathogenesis Associated with the Reactivation of Chromosomally Integrated HHV-6A/B.

    Science.gov (United States)

    Collin, Vanessa; Flamand, Louis

    2017-06-26

    Unlike other human herpesviruses, human herpesvirus 6A and 6B (HHV-6A/B) infection can lead to integration of the viral genome in human chromosomes. When integration occurs in germinal cells, the integrated HHV-6A/B genome can be transmitted to 50% of descendants. Such individuals, carrying one copy of the HHV-6A/B genome in every cell, are referred to as having inherited chromosomally-integrated HHV-6A/B (iciHHV-6) and represent approximately 1% of the world's population. Interestingly, HHV-6A/B integrate their genomes in a specific region of the chromosomes known as telomeres. Telomeres are located at chromosomes' ends and play essential roles in chromosomal stability and the long-term proliferative potential of cells. Considering that the integrated HHV-6A/B genome is mostly intact without any gross rearrangements or deletions, integration is likely used for viral maintenance into host cells. Knowing the roles played by telomeres in cellular homeostasis, viral integration in such structure is not likely to be without consequences. At present, the mechanisms and factors involved in HHV-6A/B integration remain poorly defined. In this review, we detail the potential biological and medical impacts of HHV-6A/B integration as well as the possible chromosomal integration and viral excision processes.

  5. Selenite resistant rhizobacteria stimulate SeO(3) (2-) phytoextraction by Brassica juncea in bioaugmented water-filtering artificial beds.

    Science.gov (United States)

    Lampis, Silvia; Ferrari, Anita; Cunha-Queda, A Cristina F; Alvarenga, Paula; Di Gregorio, Simona; Vallini, Giovanni

    2009-09-01

    Selenium is a trace metalloid of global environmental concern. The boundary among its essentiality, deficiency, and toxicity is narrow and mainly depends on the chemical forms and concentrations in which this element occurs. Different plant species-including Brassica juncea-have been shown to play a significant role in Se removal from soil as well as water bodies. Furthermore, the interactions between such plants, showing natural capabilities of metal uptake and their rhizospheric microbial communities, might be exploited to increase both Se scavenging and vegetable biomass production in order to improve the whole phytoextraction efficiency. The aim of the present study was to evaluate the capability of selenite removal of B. juncea grown in hydroponic conditions on artificially spiked effluents. To optimize phytoextraction efficiency, interactions between B. juncea and rhizobacteria were designedly elicited. Firstly, B. juncea was grown on water-filtering agriperlite beds in the presence of three different selenite concentrations, namely, 0.2, 1.0, and 2.0 mM. Plant growth was measured after 3 and 6 weeks of incubation in order to establish the selenite concentration at which the best plant biomass production could be obtained. Afterwards, water-filtering agriperlite beds were inoculated either with a selenium-acclimated microbial community deriving from the rhizosphere of B. juncea grown, erstwhile, in a selenite-amended soil or with axenic cultures of two bacterial strains, vicelike Bacillus mycoides SeITE01 and Stenotrophomonas maltophilia SeITE02, previously isolated and described for their high resistance to selenite. These latter were seeded separately or as a dual consortium. Selenite was amended at a final concentration of 1.0 mM. Total Se content in plant tissues (both shoots and roots), plant biomass production, and persistence of bioaugmented microbial inocula during the experimental time were monitored. Moreover, parameters such as bioconcentration

  6. Assessment of genetic diversity in Brassica juncea Brassicaceae genotypes using phenotypic differences and SSR markers

    Directory of Open Access Journals (Sweden)

    Vinu V.

    2013-12-01

    Full Text Available Las especies de mostaza del género Brassica representan uno de los cultivos de semillas oleaginosas más importantes en India, sin embargo, su diversidad genética es poco conocida. Para la utilización de genotipos en programas de cultivos resulta esencial un mayor conocimiento sobre este tema. Debido a ello, se evaluó la diversidad genética entre 44 genotipos de mostaza de la India Brassica juncea incluyendo variedades y líneas puras de diferentes zonas agro-climáticas de la India y algunos genotipos exóticos Australia, Polonia y China. Para ello, se utilizaron marcadores SSR específicos del genoma A y B y datos fenotípicos del rendimiento de 12 cosechas y sus características. De los 143 primers evaluados, 134 reportaron polimorfismo y un total de 355 alelos fueron amplificados. Se generaron dendrogramas a partir de los coeficientes de similitud de Jaccard y de disimilitud Manhattan, basados en un algoritmo de vinculación promedio UPGMA. Se utilizaron datos de marcadores genéticos y datos fenotípicos. Los genotipos se agruparon en cuatro grupos basados en las distancias genéticas. Ambos patrones de agrupamiento, tanto los basados en los coeficientes de similitud de Jaccard como los basados en los de disimilitud Manhattan, separaron independientemente los genotipos por su genealogía y origen, de una manera efectiva. El PCoA reveló que la agrupación de genotipos basada en datos de marcadores SSR, es más convincente que los datos fenotípicos, sin embargo, se observó que la correlación entre las matrices de distancia fenotípica y genética resultó muy baja r=0.11. Por lo tanto, para estudios de diversidad basados en marcadores moleculares es necesario realizar más pruebas. Los marcadores SSR constituyen herramientas más eficientes para discriminar entre genotipos de B. juncea, que las características cuantitativas.

  7. Biorefinery process for protein extraction from oriental mustard (Brassica juncea (L.) Czern.) using ethanol stillage.

    Science.gov (United States)

    Ratanapariyanuch, Kornsulee; Tyler, Robert T; Shim, Youn Young; Reaney, Martin Jt

    2012-01-12

    Large volumes of treated process water are required for protein extraction. Evaporation of this water contributes greatly to the energy consumed in enriching protein products. Thin stillage remaining from ethanol production is available in large volumes and may be suitable for extracting protein rich materials. In this work protein was extracted from ground defatted oriental mustard (Brassica juncea (L.) Czern.) meal using thin stillage. Protein extraction efficiency was studied at pHs between 7.6 and 10.4 and salt concentrations between 3.4 × 10-2 and 1.2 M. The optimum extraction efficiency was pH 10.0 and 1.0 M NaCl. Napin and cruciferin were the most prevalent proteins in the isolate. The isolate exhibited high in vitro digestibility (74.9 ± 0.80%) and lysine content (5.2 ± 0.2 g/100 g of protein). No differences in the efficiency of extraction, SDS-PAGE profile, digestibility, lysine availability, or amino acid composition were observed between protein extracted with thin stillage and that extracted with NaCl solution. The use of thin stillage, in lieu of water, for protein extraction would decrease the energy requirements and waste disposal costs of the protein isolation and biofuel production processes.

  8. Physiological and Biochemical Changes in Brassica juncea Plants under Cd-Induced Stress

    Directory of Open Access Journals (Sweden)

    Dhriti Kapoor

    2014-01-01

    Full Text Available Plants of Brassica juncea L. var. RLC-1 were exposed for 30 days to different concentrations (0, 0.2, 0.4, and 0.6 mM of cadmium (Cd to analyze the Cd uptake, H2O2 content, hormonal profiling, level of photosynthetic pigments (chlorophyll, carotenoid, and flavonoid, gaseous exchange parameters (photosynthetic rate, vapour pressure deficit, intercellular CO2 concentration, and intrinsic mesophyll rate, antioxidative enzymes (superoxide dismutase, polyphenol oxidase, glutathione-S transferase, and glutathione peroxidase, antioxidant assays (DPPH, ABTS, and total phenolic content, and polyphenols. Results of the present study revealed the increased H2O2 content and Cd uptake with increasing metal doses. UPLC analysis of plants showed the presence of various polyphenols. Gaseous exchange measurements were done by infrared gas analyzer (IRGA, which was negatively affected by metal treatment. In addition, LC/MS study showed the variation in the expression of plant hormones. Level of photosynthetic pigments and activities of antioxidative enzymes were altered significantly in response to metal treatment. In conclusion, the antioxidative defence system of plants got activated due to heavy metal stress, which protects the plants by scavenging free radicals.

  9. A continuous culture system of direct somatic embryogenesis in microspore-derived embryos of Brassica juncea.

    Science.gov (United States)

    Prabhudesai, V; Bhaskaran, S

    1993-03-01

    An efficient culture system has been developed for repeated cycles of somatic embryogenesis in microspore-derived embryos of Brassica juncea without a callus phase. Haploid embryos produced through anther culture showed a high propensity for direct production of somatic embryos in response to 2 mgL(-1) BA and 0.1 mgL(-1) NAA. The embryogenic cultures which comprised the elongated embryonal axis of microspore-derived embryos when explanted and grown on the medium of same composition produced a large number of secondary embryos. These somatic embryos in turn underwent axis elongation and produced more somatic embryos when explanted and cultured. This cycle of repetitive somatic embryogenesis continued with undiminished vigour passage after passage and was monitored for more than a year. Somatic embryos from any passage when isolated at cotyledonary stage and grown on auxin-free medium for 5 days and then on a medium containing NAA (0.1 mgL(-1)), developed into complete plants with a profuse root system and were easily established in the soil. The cytology of the root tips of these plants confirmed their haploid nature. The total absence of callus phase makes the system ideal for continuous cloning of androgenic lines, Agrobacterium-mediated transformation and mutation induction studies.

  10. Metal accumulation, growth, antioxidants and oil yield of Brassica juncea L. exposed to different metals.

    Science.gov (United States)

    Sinha, Sarita; Sinam, Geetgovind; Mishra, Rohit Kumar; Mallick, Shekhar

    2010-09-01

    In agricultural fields, heavy metal contamination is responsible for limiting the crop productivity and quality. This study reports that the plants of Brassica juncea L. cv. Pusa bold grown on contaminated substrates [Cu, Cr(VI), As(III), As(V)] under simulated field conditions have shown translocation of metals to the upper part and its sequestration in the leaves without significantly affecting on oil yield, except for Cr and higher concentration of As(V), compared to control. Decrease in the oil content in As(V) treated plants was observed in a dose dependent manner; however, maximum decrease was recorded in Cr treated plants. Among all the metal treatments, Cr was the most toxic as evident from the decrease in oil content, growth parameters and antioxidants. The accumulation of metals was below the detection limit in the seeds grown on 10 and 30 mg kg(-1) As(III) and Cr(VI); 10 mg kg(-1) As(V)) and thus can be recommended only for oil cultivation. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  11. Pattern of callose deposition during the course of meiotic diplospory in Chondrilla juncea (Asteraceae, Cichorioideae).

    Science.gov (United States)

    Musiał, Krystyna; Kościńska-Pająk, Maria

    2017-07-01

    Total absence of callose in the ovules of diplosporous species has been previously suggested. This paper is the first description of callose events in the ovules of Chondrilla juncea, which exhibits meiotic diplospory of the Taraxacum type. We found the presence of callose in the megasporocyte wall and stated that the pattern of callose deposition is dynamically changing during megasporogenesis. At the premeiotic stage, no callose was observed in the ovules. Callose appeared at the micropylar pole of the cell entering prophase of the first meioticdivision restitution but did not surround the megasporocyte. After the formation of a restitution nucleus, a conspicuous callose micropylar cap and dispersed deposits of callose were detected in the megasporocyte wall. During the formation of a diplodyad, the micropylar callose cap decreased and the walls of a newly formed megaspores showed scattered distribution of callose. Within the older diplodyad, callose was mainly accumulated in the wall between megaspores, as well as in the wall of the micropylar cell; however, a dotted fluorescence of callose was also visible in the wall of the chalazal megaspore. Gradual degradation of callose in the wall of the chalazal cell and intense callose accumulation in the wall of the micropylar cell were related to the selection of the functional megaspore. Thus, our findings may suggest that callose fulfills a similar role both during megasporogenesis in sexual angiosperms and in the course of meiotic diplospory in apomicts and seems to form a regulatory interface between reproductive and somatic cells.

  12. Mercury-induced oxidative stress in Indian mustard (Brassica juncea L.).

    Science.gov (United States)

    Shiyab, Safwan; Chen, Jian; Han, Fengxiang X; Monts, David L; Matta, Fank B; Gu, Mengmeng; Su, Yi; Masad, Motasim A

    2009-10-01

    Mercury, a potent neurotoxin, is released to the environment in significant amounts by both natural processes and anthropogenic activities. No natural hyperaccumulator plant has been reported for mercury phytoremediation. Few studies have been conducted on the physiological responses of Indian mustard, a higher biomass plant with faster growth rates, to mercury pollution. This study investigated the phytotoxicity of mercury to Indian mustard (Brassica juncea L.) and mercury-induced oxidative stress in order to examine the potential application of Indian mustard to mercury phytoremediation. Two common cultivars (Florida Broadleaf and Longstanding) of Indian mustard were grown hydroponically in a mercury-spiked solution. Plant uptake, antioxidative enzymes, peroxides, and lipid peroxidation under mercury stress were investigated. Antioxidant enzymes (catalase, CAT; peroxidase, POD; and superoxide dismutase, SOD) were the most sensitive indices of mercury-induced oxidative response of Indian mustard plants. Indian mustard effectively generated an enzymatic antioxidant defense system (especially CAT) to scavenge H(2)O(2), resulting in lower H(2)O(2) in shoots with higher mercury concentrations. These two cultivars of Indian mustard demonstrated an efficient metabolic defense and adaptation system to mercury-induced oxidative stress. A majority of Hg was accumulated in the roots and low translocations of Hg from roots to shoots were found in two cultivars of Indian mustard. Thus Indian mustard might be a potential candidate plant for phytofiltration/phytostabilization of mercury contaminated waters and wastewater.

  13. The intensity of tyrosine nitration is associated with selenite and selenate toxicity in Brassica juncea L.

    Science.gov (United States)

    Molnár, Árpád; Feigl, Gábor; Trifán, Vanda; Ördög, Attila; Szőllősi, Réka; Erdei, László; Kolbert, Zsuzsanna

    2018-01-01

    Selenium phytotoxicity involves processes like reactive nitrogen species overproduction and nitrosative protein modifications. This study evaluates the toxicity of two selenium forms (selenite and selenate at 0µM, 20µM, 50µM and 100µM concentrations) and its correlation with protein tyrosine nitration in the organs of hydroponically grown Indian mustard (Brassica juncea L.). Selenate treatment resulted in large selenium accumulation in both Brassica organs, while selenite showed slight root-to-shoot translocation resulting in a much lower selenium accumulation in the shoot. Shoot and root growth inhibition and cell viability loss revealed that Brassica tolerates selenate better than selenite. Results also show that relative high amounts of selenium are able to accumulate in Brassica leaves without obvious visible symptoms such as chlorosis or necrosis. The more severe phytotoxicity of selenite was accompanied by more intense protein tyrosine nitration as well as alterations in nitration pattern suggesting a correlation between the degree of Se forms-induced toxicities and nitroproteome size, composition in Brassica organs. These results imply the possibility of considering protein tyrosine nitration as novel biomarker of selenium phytotoxicity, which could help the evaluation of asymptomatic selenium stress of plants. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Nitrogen availability regulates proline and ethylene production and alleviates salinity stress in mustard (Brassica juncea).

    Science.gov (United States)

    Iqbal, Noushina; Umar, Shahid; Khan, Nafees A

    2015-04-15

    Proline content and ethylene production have been shown to be involved in salt tolerance mechanisms in plants. To assess the role of nitrogen (N) in the protection of photosynthesis under salt stress, the effect of N (0, 5, 10, 20 mM) on proline and ethylene was studied in mustard (Brassica juncea). Sufficient N (10 mM) optimized proline production under non-saline conditions through an increase in proline-metabolizing enzymes, leading to osmotic balance and protection of photosynthesis through optimal ethylene production. Excess N (20 mM), in the absence of salt stress, inhibited photosynthesis and caused higher ethylene evolution but lower proline production compared to sufficient N. In contrast, under salt stress with an increased demand for N, excess N optimized ethylene production, which regulates the proline content resulting in recovered photosynthesis. The effect of excess N on photosynthesis under salt stress was further substantiated by the application of the ethylene biosynthesis inhibitor, 1-aminoethoxy vinylglycine (AVG), which inhibited proline production and photosynthesis. Without salt stress, AVG promoted photosynthesis in plants receiving excess N by inhibiting stress ethylene production. The results suggest that a regulatory interaction exists between ethylene, proline and N for salt tolerance. Nitrogen differentially regulates proline production and ethylene formation to alleviate the adverse effect of salinity on photosynthesis in mustard. Copyright © 2015 Elsevier GmbH. All rights reserved.

  15. The influence of different hydroponic conditions on thorium uptake by Brassica juncea var. foliosa.

    Science.gov (United States)

    Wang, Dingna; Zhou, Sai; Liu, Li; Du, Liang; Wang, Jianmei; Huang, Zhenling; Ma, Lijian; Ding, Songdong; Zhang, Dong; Wang, Ruibing; Jin, Yongdong; Xia, Chuanqin

    2015-05-01

    The effects of different hydroponic conditions (such as concentration of thorium (Th), pH, carbonate, phosphate, organic acids, and cations) on thorium uptake by Brassica juncea var. foliosa were evaluated. The results showed that acidic cultivation solutions enhanced thorium accumulation in the plants. Phosphate and carbonate inhibited thorium accumulation in plants, possibly due to the formation of Th(HPO4)(2+), Th(HPO4)2, or Th(OH)3CO3 (-) with Th(4+), which was disadvantageous for thorium uptake in the plants. Organic aids (citric acid, oxalic acid, lactic acid) inhibited thorium accumulation in roots and increased thorium content in the shoots, which suggested that the thorium-organic complexes did not remain in the roots and were beneficial for thorium transfer from the roots to the shoots. Among three cations (such as calcium ion (Ca(2+)), ferrous ion (Fe(2+)), and zinc ion (Zn(2+))) in hydroponic media, Zn(2+) had no significant influence on thorium accumulation in the roots, Fe(2+) inhibited thorium accumulation in the roots, and Ca(2+) was found to facilitate thorium accumulation in the roots to a certain extent. This research will help to further understand the mechanism of thorium uptake in plants.

  16. Soil organisms associated to the weed suppressant Crotalaria juncea (fabaceae and its importance as a refuge for natural enemies Organismos de solo associados à supressora de plantas daninhas Crotalaria juncea (fabaceae e sua importância como refúgio para inimigos naturais

    Directory of Open Access Journals (Sweden)

    W.S Tavares

    2011-09-01

    Full Text Available Soil organisms play an important role in organic crops of Crotalaria juncea (Fabaceae and are associated with the natural conservation of the environment. The present study was aimed to investigate the population of soil organisms in the organic culture of C. juncea, as well as its importance as a refuge for natural enemies. Dalbulus maidis (Hemiptera: Cicadellidae, Diabrotica sp. (Coleoptera: Chrysomelidae, Doru luteipes (Dermaptera: Forficulidae, Gryllus assimilis (Orthoptera: Gryllidae, Lagria villosa (Coleoptera: Lagriidae, Melanotus sp. (Coleoptera: Elateridae, Meloidogyne incognita (Tylenchida: Heteroderidae, Nephila clavipes (Araneae: Nephilidae, Orius insidiosus (Hemiptera: Anthocoridae, Pheidole sp. (Hymenoptera: Myrmicidae, Phyllophaga sp. (Coleoptera: Scarabeidae, Procornitermes sp. (Isoptera: Termitidae, Solenopsis sp. (Hymenoptera: Formicidae, and Utetheisa ornatrix (Lepidoptera: Arctiidae were identified in C. juncea. The organisms that were found during a 3-month period in 144 trenches in C. juncea were pest species (84.47% and natural enemies (15.53% as well. Natural enemies had an average of 11.89 individuals per 1.08 m³ of soil cultivated with C. juncea. The abundance of organisms in the pod stage (5.49% of C. juncea was lower than that in the vegetative (83.50% and flowering (11.01% stages. Crotalaria juncea plants can be used as part of a crop system for Integrated Pest Management.Organismos de solo desempenham um importante papel em cultivos orgânicos de Crotalaria juncea (Fabaceae e estão associados com a conservação natural do ambiente. O presente estudo teve como objetivo investigar a população de organismos de solo no cultivo orgânico de C. juncea, bem como sua importância como um refúgio para inimigos naturais. Dalbulus maidis (Hemiptera: Cicadellidae, Diabrotica sp. (Coleoptera: Chrysomelidae, Doru luteipes (Dermaptera: Forficulidae, Gryllus assimilis (Orthoptera: Gryllidae, Lagria villosa (Coleoptera

  17. SUSTAINABILITY EFFECTS OF Crotalaria juncea L. AND Crotalaria spectabilis ROTH ON SOIL FERTILITY AND SOIL CONSERVATION

    Science.gov (United States)

    László, Márton, ,, Dr.

    2010-05-01

    Sustainable agriculture is defined as the successful management of resources for agriculture to satisfy changing human needs while maintaining or enhancing the quality of the environment and conserving natural resources. A sustained increase of agricultural production becomes a great possibility for international community. In this process a green manure crops application for example crotalaria get a new chance for improvement process on soil fertility and soil conservation. Field experiment was carried out on a calcareous chernozem soil (Experiment station Nagyhörcsök of RISSAC-HAS) in partly of experiment series (3 years) at Hungary in 1998. The soil with about 20% clay, 3% humus, 5% CaCO3 in its ploughed layer. To ensure a sufficient macro and micronutrient supply in the whole experiment, 100 kg N, 100 kg P2O5 and 100 kg K2O were given hectare. The Crotalaria juncea L. and Crotalaria spectabilis ROTH were applied with 2 replications. Each plot has an area of 45 m2 with 230-230 individual plants. In vegetation grown period were measured green and dry matter yield. The soil and plant samples were analysed for the macro and microelements contents. The main results achieved in 1998 are summarized as follows: 1. The green matter yield at before flowering reached 63.8 t ha-1 in case of Crotalaria juncea L. 2. Total dry matter yield at harvest (without roots) fluctuated between 9.6 and 17.0 t ha-1, depending on the crotalaria species. 3. The average of element concentration (including stems, leaves of Crotalaria juncea L. and Crotalaria spectabilis ROTH) before flowering reached to 3.2 % N, 2.3 % Ca, 1.3 % K, 0.39 % Mg, 0.22 % P and 0.24 % S. The content of Al and Fe total 14 - 25, while that of Sr, Mn, Na, B and Ba 2 - 6 ppm in dry matter. The Zn, Cu, Mo, Cr, Se, Ni, As, Pb, Cd and Co concentration did not reach here the value of 1 ppm. 4. The average of biological activated element uptake (including stems, leaves of Crotalaria juncea L. and Crotalaria spectabilis

  18. Morphological and genetic characterization of a new cytoplasmic male sterility system (oxa CMS) in stem mustard (Brassica juncea).

    Science.gov (United States)

    Heng, Shuangping; Liu, Sansan; Xia, Chunxiu; Tang, HongYu; Xie, Fei; Fu, Tingdong; Wan, Zhengjie

    2018-01-01

    KEY MESSAGE: oxa CMS is a new cytoplasmic male sterility type in Brassica juncea. oxa CMS is a cytoplasmic male sterility (CMS) line that has been widely used in the production and cultivation of stem mustard in the southwestern China. In this study, different CMS-type specific mitochondrial markers were used to confirm that oxa CMS is distinct from the pol CMS, ogu CMS, nap CMS, hau CMS, tour CMS, Moricandia arvensis CMS, orf220-type CMS, etc., that have been previously reported in Brassica crops. Pollen grains of the oxa CMS line are sterile with a self-fertility rate of almost 0% and the sterility strain rate and sterility degree of oxa CMS is 100% due to a specific flower structure and flowering habit. Scanning electron microscopy revealed that most pollen grains in mature anthers of the oxa CMS line are empty, flat and deflated. Semi-thin section further showed that the abortive stage of anther development in oxa CMS is initiated at the late uninucleate stage. Abnormally vacuolated microspores caused male sterility in the oxa CMS line. This cytological study combined with marker-assisted selection showed that oxa CMS is a novel CMS type in stem mustard (Brassica juncea). Interestingly, the abortive stage of oxa CMS is later than those in other CMS types reported in Brassica crops, and there is no negative effect on the oxa CMS line growth period. This study demonstrated that this novel oxa CMS has a unique flower structure with sterile pollen grains at the late uninucleate stage. Our results may help to uncover the mechanism of oxa CMS in Brassica juncea.

  19. Effects of phosphate and thiosulphate on arsenic accumulation in Brassica juncea plants grown in soil and in hydroponic culture

    Science.gov (United States)

    Pezzarossa, Beatrice; Petruzzelli, Gianniantonio; Grifoni, Martina; Rosellini, Irene; Malagoli, Mario; Schiavon, Michela

    2013-04-01

    Arsenic is recognised as a toxic metalloid and a strong pollutant in soils of many countries. Thus, the reclamation of contaminated areas is fundamental in order to protect both human health and agricultural production. This study is focused on the assisted phytoextraction, a technology for reclaiming polluted soils that takes advantage of the capability of some plants to extract inorganic elements from soils with the aid of additive agents. The nutrients phosphorus, as phosphate, and sulphur, as thiosulphate, can compete with the form more oxidised of arsenic, both in soil and plant. This study examined the capability of thiosulphate (Th) and phosphate (Ph) to promote the release of As from soil surfaces in order to improve the phytoavailability and thus the absorption of As by Brassica juncea plants. In the first experiment B. juncea plants were grown on a soil that had been sampled from an industrial area strongly contaminated by As (790 mg As kg-1 soil). The second experiment was carried out in hydroponics where As has been added at a concentration (100 microM) similar to the As available concentration measured in soil. In both trials ammonium thiosulphate (at the concentration of 0.27 M in soil, and 400 microM in hydroponics) and potassium hydrogen phosphate (at the concentration of 0.05 M in soil, and 112 microM in hydroponics) were added. The biomass of B. juncea was determined and the accumulation of P, S and As in root and in the above-ground tissues have been analyzed. Our results showed that thiosulphate and phosphate acted either as nutrients and detoxifying agents, due to the stimulation of plant defensive systems, and influenced either the biomass production and the As accumulation in plant tissues. In the plants grown in soil, As accumulated at higher levels in the above-ground part than in the roots and the addition of Th induced a higher biomass production and a higher total As accumulation (concentration x biomass) in the above-ground tissues

  20. Effects of phosphate and thiosulphate on arsenic accumulation in the species Brassica juncea.

    Science.gov (United States)

    Grifoni, Martina; Schiavon, Michela; Pezzarossa, Beatrice; Petruzzelli, Gianniantonio; Malagoli, Mario

    2015-02-01

    Arsenic (As) is recognized as a toxic pollutant in soils of many countries. Since phosphorus (P) and sulphur (S) can influence arsenic mobility and bioavailability, as well as the plant tolerance to As, phytoremediation techniques employed to clean-up As-contaminated areas should consider the interaction between As and these two nutrients. In this study, the bioavailability and accumulation of arsenate in the species Brassica juncea were compared between soil system and hydroponics in relation to P and S concentration of the growth substrate. In one case, plants were grown in pots filled with soil containing 878 mg As kg(-1). The addition of P to soil resulted in increased As desorption and significantly higher As accumulation in plants, with no effect on growth. The absence of toxic effects on plants was likely due to high S in soil, which could efficiently mitigate metal toxicity. In the hydroponic experiment, plants were grown with different combinations of As (0 or 100 μM) and P (56 or 112 μM). S at 400 μM was also added to the nutrient solution of control (-As) and As-treated plants, either individually or in combination with P. The addition of P reduced As uptake by plants, while high S resulted in higher As accumulation and lower P content. These results suggest that S can influence the interaction between P and As for the uptake by plants. The combined increase of P and S in the nutrient solution did not lead to higher accumulation of As, but enhanced As translocation from the root to the shoot. This aspect is of relevance for the phytoremediation of As-contaminated sites.

  1. Development of an efficient regeneration protocol for three genotypes of brassica juncea

    International Nuclear Information System (INIS)

    Bano, R.; Khan, M.H.; Rashid, H.

    2010-01-01

    Two phytohormones, auxins (Naphthalene acetic acid and Indole acetic acid) and cytokinins (Benzyl aminopurine and Kinetin) with concentrations were used to develop an efficient regeneration protocol for 3 genotypes of Brassica juncea (UCD-635, RL-18 and NIFA RAYE). The explants were cultured on MS-medium supplemented with BAP 1.0 mgL/sup -1//NAA 0.1 mgL-1, BAP 2.0 mg L/sup -1//NAA 0.2 mg L/sup -1/, BAP 3.0 mgL/sup -1/ NAA 0.3 mg L-1 and Kinetin 1.0 mg L/sup -1/ IAA 0.1 mg L/sup -1/, Kinetin 2.0 mg L/sup -1//IAA 0.2 mg L/sup -1/, Kinetin 3.0mg L-1/IAA 0.3 mg L/sup -1/. Maximum callus production (65.55) was observed on MS medium containing with BAP 2.0 mgL-1/NAA 0.2 mg L/sup -1/. Maximum shooting (22.31) was observed BAP 3.0 mg L/sup -1//NAA 0.3 mg L/sup -1/ and KIN 3.0 mg L-1/IAA 0.3 mg L/sup -1/. Regeneration efficiency was found maximum (7.13) with BAP 3.0 mg L/sup -1//NAA 0.3 mg L/sup -1/. The three genotypes were found significantly different at p greater or equal to 0.05 in shoots production and regeneration efficiency. (author)

  2. The effects of seed size on hybrids formed between oilseed rape (Brassica napus and wild brown mustard (B. juncea.

    Directory of Open Access Journals (Sweden)

    Yong-Bo Liu

    Full Text Available Seed size has significant implications in ecology, because of its effects on plant fitness. The hybrid seeds that result from crosses between crops and their wild relatives are often small, and the consequences of this have been poorly investigated. Here we report on plant performance of hybrid and its parental transgenic oilseed rape (Brassica napus and wild B. juncea, all grown from seeds sorted into three seed-size categories.Three seed-size categories were sorted by seed diameter for transgenic B. napus, wild B. juncea and their transgenic and non-transgenic hybrids. The seeds were sown in a field at various plant densities. Globally, small-seeded plants had delayed flowering, lower biomass, fewer flowers and seeds, and a lower thousand-seed weight. The seed-size effect varied among plant types but was not affected by plant density. There was no negative effect of seed size in hybrids, but it was correlated with reduced growth for both parents.Our results imply that the risk of further gene flow would probably not be mitigated by the small size of transgenic hybrid seeds. No fitness cost was detected to be associated with the Bt-transgene in this study.

  3. Transgenic Brassica juncea plants expressing MsrA1, a synthetic cationic antimicrobial peptide, exhibit resistance to fungal phytopathogens.

    Science.gov (United States)

    Rustagi, Anjana; Kumar, Deepak; Shekhar, Shashi; Yusuf, Mohd Aslam; Misra, Santosh; Sarin, Neera Bhalla

    2014-06-01

    Cationic antimicrobial peptides (CAPs) have shown potential against broad spectrum of phytopathogens. Synthetic versions with desirable properties have been modeled on these natural peptides. MsrA1 is a synthetic chimera of cecropin A and melittin CAPs with antimicrobial properties. We generated transgenic Brassica juncea plants expressing the msrA1 gene aimed at conferring fungal resistance. Five independent transgenic lines were evaluated for resistance to Alternaria brassicae and Sclerotinia sclerotiorum, two of the most devastating pathogens of B. juncea crops. In vitro assays showed inhibition by MsrA1 of Alternaria hyphae growth by 44-62 %. As assessed by the number and size of lesions and time taken for complete leaf necrosis, the Alternaria infection was delayed and restricted in the transgenic plants with the protection varying from 69 to 85 % in different transgenic lines. In case of S. sclerotiorum infection, the lesions were more severe and spread profusely in untransformed control compared with transgenic plants. The sclerotia formed in the stem of untransformed control plants were significantly more in number and larger in size than those present in the transgenic plants where disease protection of 56-71.5 % was obtained. We discuss the potential of engineering broad spectrum biotic stress tolerance by transgenic expression of CAPs in crop plants.

  4. Path and ridge regression analysis of seed yield and seed yield components of Russian wildrye (Psathyrostachys juncea Nevski) under field conditions

    DEFF Research Database (Denmark)

    Wang, Quanzhen; Zhang, Tiejun; Cui, Jian

    2011-01-01

    The correlations among seed yield components, and their direct and indirect effects on the seed yield (Z) of Russina wildrye (Psathyrostachys juncea Nevski) were investigated. The seed yield components: fertile tillers m-2 (Y1), spikelets per fertile tillers (Y2), florets per spikelet- (Y3), seed...

  5. Atmospheric H2S and SO2 as sulfur sources for Brassica juncea and Brassica rapa: Regulation of sulfur uptake and assimilation

    NARCIS (Netherlands)

    Aghajanzadeh, T.; Hawkesford, M.J.; De Kok, L.J.

    2016-01-01

    Brassica juncea and Brassica rapa were able to utilize foliarly absorbed H2S and SO2 as sulfur source for growth and resulted in a decreased sink capacity of the shoot for sulfur supplied by the root and subsequently in a partial decrease in sulfate uptake capacity of the roots. Sulfate-deprived

  6. Atmospheric H2S and SO2 as sulfur source for Brassica juncea and Brassica rapa: Impact on the glucosinolate composition

    NARCIS (Netherlands)

    Aghajanzadeh, T.; Kopriva, S; Hawkesford, M.J.; Koprivova, A.; De Kok, L.J.

    2015-01-01

    The impact of sulfate deprivation and atmospheric H2S and SO2 nutrition on the content and composition of glucosinolates was studied in Brassica juncea and Brasscia rapa. Both species contained a number of aliphatic and indolic glucosinolates. The total glucosinolate content was more than 5.5-fold

  7. Identification and comprehensive evaluation of reference genes for RT-qPCR analysis of host gene-expression in Brassica juncea-aphid interaction using microarray data.

    Science.gov (United States)

    Ram, Chet; Koramutla, Murali Krishna; Bhattacharya, Ramcharan

    2017-07-01

    Brassica juncea is a chief oil yielding crop in many parts of the world including India. With advancement of molecular techniques, RT-qPCR based study of gene-expression has become an integral part of experimentations in crop breeding. In RT-qPCR, use of appropriate reference gene(s) is pivotal. The virtue of the reference genes, being constant in expression throughout the experimental treatments, needs to be validated case by case. Appropriate reference gene(s) for normalization of gene-expression data in B. juncea during the biotic stress of aphid infestation is not known. In the present investigation, 11 reference genes identified from microarray database of Arabidopsis-aphid interaction at a cut off FDR ≤0.1, along with two known reference genes of B. juncea, were analyzed for their expression stability upon aphid infestation. These included 6 frequently used and 5 newly identified reference genes. Ranking orders of the reference genes in terms of expression stability were calculated using advanced statistical approaches such as geNorm, NormFinder, delta Ct and BestKeeper. The analysis suggested CAC, TUA and DUF179 as the most suitable reference genes. Further, normalization of the gene-expression data of STP4 and PR1 by the most and the least stable reference gene, respectively has demonstrated importance and applicability of the recommended reference genes in aphid infested samples of B. juncea. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  8. BjuB.CYP79F1 Regulates Synthesis of Propyl Fraction of Aliphatic Glucosinolates in Oilseed Mustard Brassica juncea: Functional Validation through Genetic and Transgenic Approaches.

    Directory of Open Access Journals (Sweden)

    Manisha Sharma

    Full Text Available Among the different types of methionine-derived aliphatic glucosinolates (GS, sinigrin (2-propenyl, the final product in 3C GS biosynthetic pathway is considered very important as it has many pharmacological and therapeutic properties. In Brassica species, the candidate gene regulating synthesis of 3C GS remains ambiguous. Earlier reports of GSL-PRO, an ortholog of Arabidopsis thaliana gene At1g18500 as a probable candidate gene responsible for 3C GS biosynthesis in B. napus and B. oleracea could not be validated in B. juncea through genetic analysis. In this communication, we report the isolation and characterization of the gene CYP79F1, an ortholog of A. thaliana gene At1g16410 that is involved in the first step of core GS biosynthesis. The gene CYP79F1 in B. juncea showed presence-absence polymorphism between lines Varuna that synthesizes sinigrin and Heera virtually free from sinigrin. Using this presence-absence polymorphism, CYP79F1 was mapped to the previously mapped 3C GS QTL region (J16Gsl4 in the LG B4 of B. juncea. In Heera, the gene was observed to be truncated due to an insertion of a ~4.7 kb TE like element leading to the loss of function of the gene. Functional validation of the gene was carried out through both genetic and transgenic approaches. An F2 population segregating only for the gene CYP79F1 and the sinigrin phenotype showed perfect co-segregation. Finally, genetic transformation of a B. juncea line (QTL-NIL J16Gsl4 having high seed GS but lacking sinigrin with the wild type CYP79F1 showed the synthesis of sinigrin validating the role of CYP79F1 in regulating the synthesis of 3C GS in B. juncea.

  9. Comparative uptake of plutonium from soils by Brassica juncea and Helianthus annuus

    International Nuclear Information System (INIS)

    Lee, J.H.; Hossner, L.R.; Attrep, M.; Kung, K.S.

    2002-01-01

    Extractability of Pu from soils was most affected by pH and amounts of clay, salts, and carbonates. - Plutonium uptake by Brassica juncea (Indian mustard) and Helianthus annuus (sunflower) from soils with varying chemical composition and contaminated with Pu complexes (Pu-nitrate [ 239 Pu(NO 3 ) 4 ], Pu-citrate [ 239 Pu(C 6 H 5 O 7 ) + ], and Pu-diethylenetriaminepentaacetic acid (Pu-DTPA [ 239 Pu-C 14 H 23 O 10 N 3 ]) was investigated. Sequential extraction of soils incubated with applied Pu was used to determine the distribution of Pu in the various soil fractions. The initial Pu activity levels in soils were 44.40-231.25 Bq g -1 as Pu-nitrate , Pu-citrate, or Pu-DTPA. A difference in Pu uptake between treatments of Pu-nitrate and Pu-citrate without chelating agent was observed only with Indian mustard in acidic Crowley soil. The uptake of Pu by plants was increased with increasing DTPA rates, however, the Pu concentration of plants was not proportionally increased with increasing application rate of Pu to soil. Plutonium uptake from Pu-DTPA was significantly higher from the acid Crowley soil than from the calcareous Weswood soil. The uptake of Pu from the soils was higher in Indian mustard than in sunflower. Sequential extraction of Pu showed that the ion-exchangeable Pu fraction in soils was dramatically increased with DTPA treatment and decreased with time of incubation. Extractability of Pu in all fractions was not different when Pu-nitrate and Pu-citrate were applied to the same soil. More Pu was associated with the residual Pu fraction without DTPA application. Consistent trends with time of incubation for other fractions were not apparent. The ion-exchangeable fraction, assumed as plant-available Pu, was significantly higher in acid soil compared with calcareous soil with or without DTPA treatment. When the calcareous soil was treated with DTPA, the ion-exchangeable Pu was comparatively less influenced. This fraction in the soil was more affected with time

  10. Effects of Nitrogen and Desferal Treatments on CROTALARIA's (Crotalaria juncea Roth) Biomass Production

    Science.gov (United States)

    László Phd, M., ,, Dr.

    2009-04-01

    Presently sustainable agriculture is vital to achieving food security poverty alleviation and environmental protection because land degradation and desertification has occurred in all the world over cutting across a broad spectrum of contrasts in climate, ecosystem types, land uses and socio/economic settings. For this reason improving integrated soil fertility management is appreciationed and has become a major issue of concern on the development plant nutrition and plant production agendas. On plant nutrition level mineral macronutrients so nitrogen and chelating agents of different microelements so Desferal- deferoxamin-methansulfonic are essential for plant growth and development. Crotalari juncea L. is a well-known nutrient indicator fodder and green manure crop with a high yield potential. Field experiment was carried out on a chernozem meadow soil (Kunság- region of Hungary, Kunmadaras) in partly of experiment series (6 years) in 2001. The ploughed layer of region soils contained with about 2.6-3.4% humus and 40-42% clay, had a humus stability index of 0.9-2.5 by Márton (1997), pH (H2O) of 6.5-7.7, pH (KCl) of 5.3-6.8, y1 of 6.7-13.3. The topsoil was poorly supplied with all five macronutrients (N-NO3 1 mg 100 g-1, AL-soluble P2O5 14 mg 100 g-1, AL-K2O 36 mg 100 g-1, Ca 330 mg 100 g-1, Mg 43 mg 100 g-1) and with all four micronutrients (0.5m HNO3 soluble Cu 1 mg kg-1, Zn 1 mg kg-1, Mn 9 mg kg-1, Fe 80 mg kg-1) according to soil analysis. The groundwater depth was 2-3 m. Nitrogen x Desferal (Novartis Pharma AG Basie, Switzerland, Suiza 500mg) x Genotype (Brazíl-EMBRAPA/CNPH, Brazilia-DF, India-University of Agricultural Sciences, Bangalore) x Time experiment involved 4Nx2Dx2Gx3T=48 treatments in 3 replications giving a total of 144 plots. The N levels were 0, 100, 200 and 300 kg ha-1 year-1, and desferal levels 0 and 20 kg ha-1 year-1 with a 100 kg ha-1 year-1 P2O5 and 120 kg ha-1 year-1 K2O basic fertilisation. The plot size had an area of 4x2=8 m2 with

  11. Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in Brassica juncea L.

    Directory of Open Access Journals (Sweden)

    Parul Goel

    Full Text Available In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C and Nitrogen (N are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in B. juncea seedlings. For this, B. juncea seedlings were treated with four combinations of C and N source viz., N source alone (-Suc+N, C source alone (+Suc-N, with N and C source (+Suc+N or without N and C source (-Suc-N. Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (BjNRT1.1, BjNRT1.8 in root tissue and genes involved in nitrate reduction (BjNR1 and BjNR2 in shoot tissue. Moreover, expression of several genes, like BjAMT1.2, BjAMT2 and BjPK in root and two genes BjAMT2 and BjGS1.1 in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in B. juncea by interaction of both carbon and nitrogen.

  12. Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in Brassica juncea L.

    Science.gov (United States)

    Goel, Parul; Bhuria, Monika; Kaushal, Mamta

    2016-01-01

    In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C) and Nitrogen (N) are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source) on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in B. juncea seedlings. For this, B. juncea seedlings were treated with four combinations of C and N source viz., N source alone (-Suc+N), C source alone (+Suc-N), with N and C source (+Suc+N) or without N and C source (-Suc-N). Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (BjNRT1.1, BjNRT1.8) in root tissue and genes involved in nitrate reduction (BjNR1 and BjNR2) in shoot tissue. Moreover, expression of several genes, like BjAMT1.2, BjAMT2 and BjPK in root and two genes BjAMT2 and BjGS1.1 in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in B. juncea by interaction of both carbon and nitrogen. PMID:27637072

  13. Fontes e níveis de salinidade na germinação de sementes de Crotalaria juncea L. Sources and levels of salinity on germination of Crotalaria juncea L. seeds

    Directory of Open Access Journals (Sweden)

    Anísio da Silva Nunes

    2009-06-01

    Full Text Available Objetivou-se avaliar o efeito dos sais cloreto de cálcio (CaCl2, cloreto de sódio (NaCl e cloreto de potássio (KCl na germinação de Crotalaria juncea L. As sementes foram acondicionadas em caixas tipo gerbox, forradas com duas folhas de papel-filtro e umedecidas com as soluções-teste. Em cada tratamento foram utilizadas 200 sementes, dispostas em quatro repetições de 50 sementes. A indução do estresse salino foi realizada com soluções de NaCl, CaCl2 e KCl com potenciais osmóticos de 0; -0,4; -0,8; -1,2;-1,6 e -2,0 MPa. Foram realizadas avaliações de porcentagem de germinação, fitotoxicidade, tamanho de plântulas, matéria seca e IVG. O delineamento experimental utilizado foi o inteiramente casualizado, em esquema fatorial (3x5+1, composto pelas três fontes salinas em cinco doses e uma solução- teste. O aumento da concentração de KCl provocou toxicidade, prejudicando o IVG, a porcentagem de germinação e o crescimento de plântulas de C. juncea, enquanto as concentrações de NaCl e o CaCl2 não interferiram significativamente na germinação das sementes e no vigor de plântulas.This study was carried out in order to evaluate the effect of calcium chloride (CaCl2, sodium chloride (NaCl, and potassium chloride (KCl salts on germination of Crotalaria juncea L. seeds. The seeds were placed in gerbox boxes lined with two filter paper sheets and wet with test-solution. In each treatment, 200 seeds were used, distributed in four replicates of 50 seeds. The induction of the salt stress was done with solutions of NaCl, CaCl2 and KCl with osmotic potential of 0, -0.4, -0.8, -1.2, -1.6, and -2.0 MPa. Germination percentage, phytotoxicity, seedling size, mass of dry matter, and IVG were assessed. The experimental design was completely randomized, in a (3x5+1 factorial structure, composed of three salt sources in five levels and a test-solution. The increasing concentration of KCl caused toxicity, hindering the IVG, the germination

  14. Resultados experimentais com a cultura da Crotalaria juncea L. L., como planta produtora de celulose para papel Results from field trials with Crotalaria juncea L. as fiber plant for paper pulp

    Directory of Open Access Journals (Sweden)

    Júlio César Medina

    1961-01-01

    Full Text Available São apresentados e discutidos os resultados de vários experimentos de campo realizados na Estação Experimental de Tatuí, do Instituto Agronômico, com a Crotalaria juncea L. como planta produtora de celulose para papel. Êsses resultados permitem fazer recomendações úteis sôbre o melhoramento técnico da cultura e da produção, no concernente às questões de variedades, espaçamento, densidade de semeação, época de semeação e época de colheita dos caules.This paper reports the results obtained in sunn hemp (Crotalaria juncea L. field trials carried out at the Tatui Experiment Station, São Paulo State. The trials were designed to study the effect of varieties, spacing x rate of seeding, time of sowing and time of harvesting on sunn hemp fiber production as a raw material for paper pulp. From the results achieved in these trials, the following recommendations can be made for growing sunn hemp as a fiber plant for paper pulp in the State of São Paulo. VARIETY: to use the common variety that is normally sowed for green manuring. TIME OF SOWING: to sow the seeds during october. RATE OF SEED SOWING AND SPACING: to sow the seeds at the rate of 100 lbs/ acre in rows spaced 8 inches apart. TIME OF HARVESTING: to harvest the stalks for mechanical fiber extraction when the seed pods are in the mature stage.

  15. Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica

    Science.gov (United States)

    2011-01-01

    Background Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these cannot easily explain, however, how the diverse mitotypes evolved within each genus or species. We analyzed the evolutionary relationships of Brassica mitotypes by sequencing. Results We sequenced the mitotypes of cam (Brassica rapa), ole (B. oleracea), jun (B. juncea), and car (B. carinata) and analyzed them together with two previously sequenced mitotypes of B. napus (pol and nap). The sizes of whole single circular genomes of cam, jun, ole, and car are 219,747 bp, 219,766 bp, 360,271 bp, and 232,241 bp, respectively. The mitochondrial genome of ole is largest as a resulting of the duplication of a 141.8 kb segment. The jun mitotype is the result of an inherited cam mitotype, and pol is also derived from the cam mitotype with evolutionary modifications. Genes with known functions are conserved in all mitotypes, but clear variation in open reading frames (ORFs) with unknown functions among the six mitotypes was observed. Sequence relationship analysis showed that there has been genome compaction and inheritance in the course of Brassica mitotype evolution. Conclusions We have sequenced four Brassica mitotypes, compared six Brassica mitotypes and suggested a mechanism for mitochondrial genome formation in Brassica, including evolutionary events such as inheritance, duplication, rearrangement, genome compaction, and mutation. PMID:21988783

  16. AB Manpower Plan 2007

    CERN Document Server

    Myers, Stephen

    2007-01-01

    The present exercise is not as such a "manpower plan" but a purely budgetary comparison of known plus requested resources with the known commitments over the period 2007-2012. From a purely budgetary point of view, AB will have the capacity to maintain all those recently hired staff who fulfill the criteria for long term employment at CERN. Following this budgetary exercise, AB proposes to perform a CERN-wide staff work plan so as to compare the manpower available to the quantity of work to be done in the totality of the work-packages. If there is a significant mismatch between these two quantities then we propose the following measures which would create personnel economies and allow us to redress the mismatch by increased recruitment: a new job severance scheme; CERN restructuring; use of the new CERN-ITER agreement; more flexibility in transfers from Materials to Personnel budgets. Failing this a re-examination of possible closure of lower priority facilities may be needed.

  17. Isolation and characterization of useful mutants induced by gamma irradiation in 'Kranti' indian mustard (Brassica juncea)

    International Nuclear Information System (INIS)

    Rai, B.; Kumar, H.

    1998-01-01

    Genetic variability was induced, in the 'Kranti' Indian mustard [Brassica/juncea (L.) Czemj. & Cosson]. utilizing 30,40 and 50 kr doses of gamma-ray Irradiation. 'In M 3 generation, compared with the econtrol, substantial decrease was observed in the mean value of various quantitative characters in the mutagen-treated populations. More variation was induced at 30 kr compared with that at 40 or 50 kr dose. Four mutants were identified ar 30 kr dose, which besides being early in maturity, gave better yield also-compared with the control. The better seed yield of the transmutated plants was due either to increase in seed weight or to increase in number of siliquae/plant

  18. Topsoil drying combined with increased sulfur supply leads to enhanced aliphatic glucosinolates in Brassica juncea leaves and roots.

    Science.gov (United States)

    Tong, Yu; Gabriel-Neumann, Elke; Ngwene, Benard; Krumbein, Angelika; George, Eckhard; Platz, Stefanie; Rohn, Sascha; Schreiner, Monika

    2014-01-01

    The decrease of water availability is leading to an urgent demand to reduce the plants' water supply. This study evaluates the effect of topsoil drying, combined with varying sulfur (S) supply on glucosinolates in Brassica juncea in order to reveal whether a partial root drying may already lead to a drought-induced glucosinolate increase promoted by an enhanced S supply. Without decreasing biomass, topsoil drying initiated an increase in aliphatic glucosinolates in leaves and in topsoil dried roots supported by increased S supply. Simultaneously, abscisic acid was determined, particularly in dehydrated roots, associated with an increased abscisic acid concentration in leaves under topsoil drying. This indicates that the dehydrated roots were the direct interface for the plants' stress response and that the drought-induced accumulation of aliphatic glucosinolates is related to abscisic acid formation. Indole and aromatic glucosinolates decreased, suggesting that these glucosinolates are less involved in the plants' response to drought. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Impact of Indian Mustard (Brassica juncea and Flax (Linum usitatissimum Seed Meal Applications on Soil Carbon, Nitrogen, and Microbial Dynamics

    Directory of Open Access Journals (Sweden)

    Autumn S. Wang

    2012-01-01

    Full Text Available There is a critical need to investigate how land application of dedicated biofuel oilseed meals affects soil ecosystems. In this study, mustard (Brassica juncea and flax (Linum usitatissimum seed meals and sorghum-sudangrass (Sorghum bicolor were added to soil at levels of 0, 1, 2.5, and 5% (w/w. Both the type of amendment and application rate affected soil organic C, total C & N, and C & N mineralization. Mustard meal amendment initially inhibited C mineralization as compared to flax, but >50% of mustard and flax organic C was mineralized within 51 d. Nitrogen mineralization was similar for flax and mustard, except for the 2.5% rate for which a lower proportion of mustard N was converted to nitrate. The mustard meal greatly impacted microbial community composition, appearing to select for specific fungal populations. The potential varying impacts of different oilseed meals on soil ecosystems should be considered when developing recommendations for land application.

  20. 24-Epibrassinolide Restores the Synthesis of Proteins and Amino Acids in Brassica juncea L. Leaves Under Imidacloprid Stress

    Directory of Open Access Journals (Sweden)

    Sharma Anket

    2017-12-01

    Full Text Available Pesticides are applied to protect crops from a variety of insect pests but their application cause toxicity to plants that results, among others, in reduction of protein as well as amino acid contents. The present study is aimed at observing the effect of seed pre-soaking with 24-epibrassinolide (EBL on the protein and amino acid content in the leaves of Brassica juncea L. grown in soil that is amended with pesticide im-idacloprid (IMI. Soil amendment with IMI resulted in a decrease in the contents in leaves of total proteins and 21 amino acids studied. Seed soaking with 100 nM of EBL resulted in the recovery of total protein as well as amino acid contents in leaves, when compared with plants grown in only IMI amended soils.

  1. Evaluation of candidate reference genes for gene expression normalization in Brassica juncea using real time quantitative RT-PCR.

    Directory of Open Access Journals (Sweden)

    Ruby Chandna

    Full Text Available The real time quantitative reverse transcription PCR (qRT-PCR is becoming increasingly important to gain insight into function of genes. Given the increased sensitivity, ease and reproducibility of qRT-PCR, the requirement of suitable reference genes for normalization has become important and stringent. It is now known that the expression of internal control genes in living organism vary considerably during developmental stages and under different experimental conditions. For economically important Brassica crops, only a couple of reference genes are reported till date. In this study, expression stability of 12 candidate reference genes including ACT2, ELFA, GAPDH, TUA, UBQ9 (traditional housekeeping genes, ACP, CAC, SNF, TIPS-41, TMD, TSB and ZNF (new candidate reference genes, in a diverse set of 49 tissue samples representing different developmental stages, stress and hormone treated conditions and cultivars of Brassica juncea has been validated. For the normalization of vegetative stages the ELFA, ACT2, CAC and TIPS-41 combination would be appropriate whereas TIPS-41 along with CAC would be suitable for normalization of reproductive stages. A combination of GAPDH, TUA, TIPS-41 and CAC were identified as the most suitable reference genes for total developmental stages. In various stress and hormone treated samples, UBQ9 and TIPS-41 had the most stable expression. Across five cultivars of B. juncea, the expression of CAC and TIPS-41 did not vary significantly and were identified as the most stably expressed reference genes. This study provides comprehensive information that the new reference genes selected herein performed better than the traditional housekeeping genes. The selection of most suitable reference genes depends on the experimental conditions, and is tissue and cultivar-specific. Further, to attain accuracy in the results more than one reference genes are necessary for normalization.

  2. Outburst in Mira AB?

    Science.gov (United States)

    Karovska, Margarita

    2003-09-01

    The nearby system Mira AB composed of an aging AGB star (Mira A) and a WD companion (Mira B) offers a unique laboratory for studying wind accretion processes, a poorly understood phenomenon in many sources. Recent Chandra ACIS-S Obs.(70ks on 12/6/03; PI.M.Karovska) resolved for the first time the components (~0.6") in X-rays, and detected a new bright soft source (A. This is the first detection of X-rays from an AGB star. This source was not detected by ROSAT in 1993 or recently by XMM 8/03 (AAS/03,J.Kastner), and could be a transient phenomenon. Model fitting shows that the soft X-ray emission is likely several emission lines, rather then a continuum; with ACIS spectral resolution we cannot resolve or identify these lines. We propose a 40ks LETG+HRC-S obs. to identify the lines and determine the emission mechanism.

  3. Uptake of heavy metals and As by Brassica juncea grown in a contaminated soil in Aznalcollar (Spain): The effect of soil amendments

    International Nuclear Information System (INIS)

    Clemente, Rafael; Walker, David J.; Bernal, M. Pilar

    2005-01-01

    Two crops of Brassica juncea (L.) Czern. were grown in a field experiment, at the site affected by the toxic spillage of acidic, metal-rich waste in Aznalcollar (Seville, Spain), to study its metal accumulation and the feasibility of its use for metal phytoextraction. The effects of organic soil amendments (cow manure and mature compost) and lime on biomass production and plant survival were also assessed; plots without organic amendment and without lime were used as controls. Plots, with or without organic amendment, having pH -1 , respectively). The total uptake of heavy metals in the plants was relatively low, emphasising the problems faced when attempting to employ phytoextraction for clean-up of pluri-contaminated sites. - Although organic amendments improved soil conditions and plant growth, the phytoextraction capacity of Brassica juncea (cv. Z1) is too low for efficient soil remediation

  4. Isolation of phytase-producing bacteria from Himalayan soils and their effect on growth and phosphorus uptake of Indian mustard (Brassica juncea).

    Science.gov (United States)

    Kumar, Vinod; Singh, Prashant; Jorquera, Milko A; Sangwan, Punesh; Kumar, Piyush; Verma, A K; Agrawal, Sanjeev

    2013-08-01

    Phytase-producing bacteria (PPB) is being investigated as plant growth promoting rhizobacteria (PGPR) to improve the phosphorus (P) nutrition and growth of plants grown in soil with high phytate content. Phytate is dominant organic P forms in many soils and must be hydrolyzed to be available for plants. Indian mustard (Brassica juncea) is a plant with economic importance in agriculture and phytoremediation, therefore biotechnological tools to improve growth and environmental stress tolerance are needed. In this study, we isolated and characterized PPB from Himalayan soils and evaluated their effect on growth and P uptake by B. juncea under greenhouse conditions. Sixty five PPB were isolated and based on phytate hydrolysis, three efficient PPB were chosen and identified as Acromobacter sp. PB-01, Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13. Selected PPB showed ability to grow at wide range of pH, temperature and salt concentrations as well as to harbour diverse PGPR activities, such as: solubilization of insoluble Ca-phosphate (193-642 μg ml(-1)), production of phytohormone indole acetic acid (5-39 μg ml(-1)) and siderophore. Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13 showed 50 and 70 % inhibition of phytopathogen Rhizoctonia solani, respectively. Greenhouse potting assay also showed that the bacterization of B. juncea seeds with Tetrathiobacter sp. PB-03 and Bacillus sp. PB-13 significantly increased the biomass and P content in 30 days old seedlings. This study reveals the potential of PPB as PGPR to improve the growth of B. juncea.

  5. Uptake of heavy metals and As by Brassica juncea grown in a contaminated soil in Aznalcollar (Spain): The effect of soil amendments

    Energy Technology Data Exchange (ETDEWEB)

    Clemente, Rafael [Department of Soil and Water Conservation and Organic Waste Management. Centro de Edafologia y Biologia Aplicada del Segura, CSIC. Apartado 164, 30100 Espinardo, Murcia (Spain); Walker, David J. [Department of Soil and Water Conservation and Organic Waste Management. Centro de Edafologia y Biologia Aplicada del Segura, CSIC. Apartado 164, 30100 Espinardo, Murcia (Spain); Bernal, M. Pilar [Department of Soil and Water Conservation and Organic Waste Management. Centro de Edafologia y Biologia Aplicada del Segura, CSIC. Apartado 164, 30100 Espinardo, Murcia (Spain)]. E-mail: pbernal@cebas.csic.es

    2005-11-15

    Two crops of Brassica juncea (L.) Czern. were grown in a field experiment, at the site affected by the toxic spillage of acidic, metal-rich waste in Aznalcollar (Seville, Spain), to study its metal accumulation and the feasibility of its use for metal phytoextraction. The effects of organic soil amendments (cow manure and mature compost) and lime on biomass production and plant survival were also assessed; plots without organic amendment and without lime were used as controls. Plots, with or without organic amendment, having pH<5 were limed for the second crop. Soil acidification conditioned plant growth and metal accumulation. The addition of lime and the organic amendments achieved higher plant biomass production, although effects concerning metal bioavailability and accumulation were masked somewhat by pH variability with time and between and within plots. Tissue metal concentrations of B. juncea were elevated for Zn, Cu and Pb, especially in leaves of plants from plots with low pH values (maxima of 2029, 71 and 55 {mu}g g{sup -1}, respectively). The total uptake of heavy metals in the plants was relatively low, emphasising the problems faced when attempting to employ phytoextraction for clean-up of pluri-contaminated sites. - Although organic amendments improved soil conditions and plant growth, the phytoextraction capacity of Brassica juncea (cv. Z1) is too low for efficient soil remediation.

  6. Assessment of the root system of Brassica juncea (L.) czern. and Bidens pilosa L. exposed to lead polluted soils using rhizobox systems.

    Science.gov (United States)

    Graziani, Natalia Soledad; Salazar, María Julieta; Pignata, María Luisa; Rodriguez, Judith Hebelen

    2016-01-01

    The purpose of this study was to compare the behavior of the root system of one of the most frequently cited species in phytoremediation Indian mustard [Brassica juncea (L.) Czern.] and a representative perennial herb (Bidens pilosa L.) native of Argentina, for different concentrations of lead in soils through chemical and visualization techniques of the rhizosphere. Lead polluted soils from the vicinity of a lead recycling plant in the locality of Bouwer, were used in juxtaposed rhizobox systems planted with seedlings of B. juncea and B. pilosa with homogeneous and heterogeneous soil treatments. Root development, pH changes in the rhizosphere, dry weight biomass, lead content of root and aerial parts and potential extraction of lead by rhizosphere exudates were determined. In both species lead was mainly accumulated in roots. However, although B. juncea accumulated more lead than B. pilosa at elevated concentrations in soils, the latter achieved greater root and aerial development. No changes in the pH of the rhizosphere associated to lead were observed, despite different extractive potentials of lead in the exudates of the species analyzed. Our results indicated that Indian mustard did not behave as a hyperaccumulator in the conditions of the present study.

  7. Cell Culture Systems To Study Human Herpesvirus 6A/B Chromosomal Integration.

    Science.gov (United States)

    Gravel, Annie; Dubuc, Isabelle; Wallaschek, Nina; Gilbert-Girard, Shella; Collin, Vanessa; Hall-Sedlak, Ruth; Jerome, Keith R; Mori, Yasuko; Carbonneau, Julie; Boivin, Guy; Kaufer, Benedikt B; Flamand, Louis

    2017-07-15

    Human herpesviruses 6A/B (HHV-6A/B) can integrate their viral genomes in the telomeres of human chromosomes. The viral and cellular factors contributing to HHV-6A/B integration remain largely unknown, mostly due to the lack of efficient and reproducible cell culture models to study HHV-6A/B integration. In this study, we characterized the HHV-6A/B integration efficiencies in several human cell lines using two different approaches. First, after a short-term infection (5 h), cells were processed for single-cell cloning and analyzed for chromosomally integrated HHV-6A/B (ciHHV-6A/B). Second, cells were infected with HHV-6A/B and allowed to grow in bulk for 4 weeks or longer and then analyzed for the presence of ciHHV-6. Using quantitative PCR (qPCR), droplet digital PCR, and fluorescent in situ hybridization, we could demonstrate that HHV-6A/B integrated in most human cell lines tested, including telomerase-positive (HeLa, MCF-7, HCT-116, and HEK293T) and telomerase-negative cell lines (U2OS and GM847). Our results also indicate that inhibition of DNA replication, using phosphonoacetic acid, did not affect HHV-6A/B integration. Certain clones harboring ciHHV-6A/B spontaneously express viral genes and proteins. Treatment of cells with phorbol ester or histone deacetylase inhibitors triggered the expression of many viral genes, including U39 , U90 , and U100 , without the production of infectious virus, suggesting that the tested stimuli were not sufficient to trigger full reactivation. In summary, both integration models yielded comparable results and should enable the identification of viral and cellular factors contributing to HHV-6A/B integration and the screening of drugs influencing viral gene expression, as well as the release of infectious HHV-6A/B from the integrated state. IMPORTANCE The analysis and understanding of HHV-6A/B genome integration into host DNA is currently limited due to the lack of reproducible and efficient viral integration systems. In the

  8. Genome size variation in the genus Avena.

    Science.gov (United States)

    Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A

    2016-03-01

    Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

  9. Bioinformatic analysis of phage AB3, a phiKMV-like virus infecting Acinetobacter baumannii.

    Science.gov (United States)

    Zhang, J; Liu, X; Li, X-J

    2015-01-16

    The phages of Acinetobacter baumannii has drawn increasing attention because of the multi-drug resistance of A. baumanni. The aim of this study was to sequence Acinetobacter baumannii phage AB3 and conduct bioinformatic analysis to lay a foundation for genome remodeling and phage therapy. We isolated and sequenced A. baumannii phage AB3 and attempted to annotate and analyze its genome. The results showed that the genome is a double-stranded DNA with a total length of 31,185 base pairs (bp) and 97 open reading frames greater than 100 bp. The genome includes 28 predicted genes, of which 24 are homologous to phage AB1. The entire coding sequence is located on the negative strand, representing 90.8% of the total length. The G+C mol% was 39.18%, without areas of high G+C content over 200 bp in length. No GC island, tRNA gene, or repeated sequence was identified. Gene lengths were 120-3099 bp, with an average of 1011 bp. Six genes were found to be greater than 2000 bp in length. Genomic alignment and phylogenetic analysis of the RNA polymerase gene showed that similar to phage AB1, phage AB3 is a phiKMV-like virus in the T7 phage family.

  10. Transport of Cd and Zn to seeds of Indian mustard (Brassica juncea) during specific stages of plant growth and development.

    Science.gov (United States)

    Sankaran, Renuka P; Ebbs, Stephen D

    2008-01-01

    The accumulation of excess Cd in the seeds of cereal and other crops compromises their commercial value and presents a potential risk to human health. Indian mustard [Brassica juncea (L.) Czern.] is a moderate accumulator of heavy metals such as Cd and Zn, and the seeds are consumed throughout the world, particularly in the Indian subcontinent. The study here examined the transport of Cd into Indian mustard plants and to seeds as a function of external Cd and the stage of the life cycle (vegetative growth, flowering and seed set) to identify critical developmental windows where transport from roots to seeds was the greatest. Plants were also treated simultaneously with Zn to determine if Zn fertilization mitigated the transport of Cd to seeds. Plants treated with Cd during the seed set accumulated the highest concentrations of Cd, exceeding 8 mg kg(-1) dry weight in some instances. Cadmium accumulated during vegetative growth was not highly redistributed to seeds. No effects of Zn were observed with regard to Cd redistribution to seeds. This may be because of the relatively small Zn : Cd ratios tested. However, the results suggest that if Zn fertilization is to be used to reduce the Cd accumulation in seeds of this species, that plants should be treated during the seed set stage. As the seeds of Indian mustard consistently accumulated Cd to concentrations that exceed acceptable limits for food crops, additional study of Cd redistribution in this species is warranted.

  11. Heavy Metal Contents and Physical Parameters of Aegiceras corniculatum, Brassica juncea, and Litchi chinensis Honeys from Bangladesh

    Directory of Open Access Journals (Sweden)

    Nandita Sarker

    2015-01-01

    Full Text Available The present study was undertaken to determine the heavy metal levels and the physicochemical parameters (pH, electrical conductivity (EC, and ash, moisture, and total sugar content of honeys from Bangladesh. Three different floral honeys were investigated, namely, khalsi (Aegiceras corniculatum, mustard (Brassica juncea, and litchi (Litchi chinensis honeys. The heavy metals in the honeys were determined by using a High Temperature Dry Oxidation method followed by Atomic Absorption Spectroscopy. The mean pH, EC, and ash, moisture, and total sugar contents of the investigated honeys were 3.6, 0.51 mS/cm, 0.18%, 18.83%, and 68.30%, respectively. Iron was the most abundant among all the investigated heavy metals, ranging from 13.51 to 15.44 mg/kg. The mean concentrations of Mn and Zn in the investigated honeys were 0.28 mg/kg and 2.99 mg/kg, respectively. Cd was below the detection limit, and lead was found in some honey samples, but their contents were below the recommended Maximum Acceptable Level. Cr was also found in all of the samples, but its concentration was within the limit. The physicochemical analysis of the honey samples yielded levels within the limits set by the international honey legislation, indicating that the honey samples were of good quality and had acceptable values for maturity, purity, and freshness.

  12. PENGARUH MEDIA TANAM DAN NUTRISI TERHADAP PERTUMBUHAN DAN HASIL TANAMAN PAKCHOI (Brassica juncea L. DENGAN SISTEM HIDROPONIK

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    Balia Perwitasari

    2012-03-01

    Full Text Available Pakchoi (Brassica juncea L.. is one kind of a vegetable crop that has high economic value and high nutrition. The technology of hydroponic is one of alternative cultivation using other media than soil substrates and nutrients. The purpose of this research is to determine the effect of media composition and nutrition on growth and yield of  pakchoi crops and find out which treatment is best for plant growth and yield of pakchoi. Researchcarried outinthe gardenexperiment ina plastichouse, Faculty ofAgriculture, University ofTrunojoyoMadura, at an altitude of±5 mabove sea level, temperature29ºC, and± 75% RH. The research was conductedin December2011 toFebruary2012.The analysis was usednonfaktorialRAL. Treatmentwithcomposemediatypes(raw rice husk, rice huskcharcoal, sand andnutrients(no nutrients, premiumnutrition, nutritiongoodplant. There are ninetreatment, threereplicationsandthreesamples ofthe plant, furthertestswere analyzed byDMRT5%. Results showedthe treatmentcompositionandnutrientmediaprovidesignificantly differentresultsatdifferent ages ofobservationson eachvariableobservation. The besttreatmentcompositioncontained in thehusk charcoalandnutrientmediagoodplant(M2N2. Evidenced by theaverage ofthe highestresultson the length ofthe plant(29.38cm, number of leaves(22.22 strands, leaf area(3226.79 cm2, wetweight(242.19 g and dry weight(13, 27g totalplantpakchoiat age4 MST.

  13. Pathogens present on vegetative organs and seeds of white mustard (Sinapis alba L. and chinese mustad (Brassica juncea L.

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    Barbara Majchrzak

    2013-12-01

    Full Text Available The research was conducted in the years 1999-2001. The aim of the research was to determine the health condition of overground parts and seeds of white niuslard (Sinapis alba L. cv. Metex and chinese mustard (Brassica juncea L. cv. Małopolska. In all the years of the research alternaria blight was found on the leaves of white mustard which injury index ranged from 5,6% in 2001 to 17,6% in 200O. The most dangerous disease of chinese mustard also was alternaria blight and its symptoms were found on leaves and siliques. The strongest infection of leaves was in 2000 (50% and the weakest in 2001 (6,7%. In all the years of the research siliques were rather weak infected (50-8,89%. Besides powdery mildew was found on chinese mustard which injury index ranged from 0,3% in 1999 to 32,3% in 2000. Intensity of diseases was affected generally by the weather conditions. From the seeds of white mustard and chinese mustard were isolated respectively 263 and 137 colonies. Alternaria alternata was the most numerous species which makes respectively 60,9% and 42,3% isolates. Among the fungi pathogenic for white and chinese mustard were also isolated: A. brassicae, Botrytis cinerea and Rhizoctonia solami.

  14. Propagule pressure, genetic structure, and geographic origins of Chondrilla juncea (Asteraceae): an apomictic invader on three continents.

    Science.gov (United States)

    Gaskin, John F; Schwarzländer, Mark; Kinter, C Lynn; Smith, James F; Novak, Stephen J

    2013-09-01

    Assessing propagule pressure and geographic origins of invasive species provides insight into the invasion process. Rush skeletonweed (Chondrilla juncea; Asteraceae) is an apomictic, perennial plant that is invasive in Australia, South America (Argentina), and North America (Canada and the United States). This study comprehensively compares propagule pressure and geographic structure of genotypes to improve our understanding of a clonal invasion and enhance management strategies. • We analyzed 1056 native range plants from Eurasia and 1156 plants from three invaded continents using amplified fragment length polymorphism (AFLP) techniques. We used measures of diversity (Simpson's D) and evenness (E), analysis of molecular variance, and Mantel tests to compare invasions, and genotype similarity to determine origins of invasive genotypes. • We found 682 unique genotypes in the native range, but only 13 in the invaded regions. Each invaded region contained distinct AFLP genotypes, suggesting independent introduction events, probably with different geographic origins. Relatively low propagule pressure was associated with each introduction around the globe, but levels of among-population variation differed. We found exact AFLP genotype matches between the native and invaded ranges for five of the 13 invasive genotypes. • Invasion dynamics can vary across invaded ranges within a species. Intensive sampling for molecular analyses can provide insight for understanding intraspecific invasion dynamics, which can hold significance for the management of plant species, especially by finding origins and distributions of invasive genotypes for classical biological control efforts.

  15. Phytoextraction based on Indian mustard (Brassica juncea arawali planted on spiked soil by aliquot amount of Lead and Nickel

    Directory of Open Access Journals (Sweden)

    Leela Kaur

    2015-12-01

    Full Text Available Phytoextraction is one of the mechanisms of phytoremediation for removal of heavy metals from contaminated soils. The objective of the present study was to investigate the effect of metal chelants, ethelyne diamine tetraacetic acid (EDTA and salicylic acid (SA, on the accumulation of lead and nickel by Indian mustard (Brassica juncea arawali plants in contaminated soil. Plants were treated with Pb and Ni, each at concentrations of 800 mg/l. EDTA and SA were amended at 0.1 M and 1.0 mM respectively. Plants were harvested and oven-dried. Pb and Ni content were estimated using ICP-OES (Varian Vista-MPX CCD Simultaneous ICP-OES. The samples thus prepared were investigated for metals distribution and morphology in different tissues (root, stem and leaf using energy dispersive X-ray analysis (EDAX spectrometer attached to the scanning electron microscope (SEM. Metal distribution study in different tissues (root, stem, leaf was done by SEM/EDS. The results showed that EDTA increased Pb and Ni uptake as compared to SA.

  16. Influence of indian mustard (Brassica juncea) on rhizosphere soil solution chemistry in long-term contaminated soils: a rhizobox study.

    Science.gov (United States)

    Kim, Kwon-Rae; Owens, Gary; Kwon, Soon-lk

    2010-01-01

    This study investigated the influence of Indian mustard (Brassica juncea) root exudation on soil solution properties (pH, dissolved organic carbon (DOC), metal solubility) in the rhizosphere using a rhizobox. Measurement was conducted following the cultivation of Indian mustard in the rhizobox filled four different types of heavy metal contaminated soils (two alkaline soils and two acidic soils). The growth of Indian mustard resulted in a significant increase (by 0.6 pH units) in rhizosphere soil solution pH of acidic soils and only a slight increase (soil solution varied considerably amongst different soils, resulting in significant changes to soil solution metals in the rhizosphere. For example, the soil solution Cd, Cu, Pb, and Zn concentrations increased in the rhizosphere of alkaline soils compared to bulk soil following plant cultivation. In contrast, the soluble concentrations of Cd, Pb, and Zn in acidic soils decreased in rhizosphere soil when compared to bulk soils. Besides the influence of pH and DOC on metal solubility, the increase of heavy metal concentration having high stability constant such as Cu and Pb resulted in a release of Cd and Zn from solid phase to liquid phase.

  17. PHYSIOLOGICAL REACTION OF THE SPECIES BRASSICA JUNCEA (L. CZERN. ON SALINIZED SOILS AMELIORATED WITH ZEOLITIC TUFF, PEAT AND PERLITE

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    Maria Cătălina PASTIA

    2017-12-01

    Full Text Available The physiological reaction of saline stress which Brassica juncea (L. Czern. plants undergo shows a greater growth and fresh substance gain process on previously cultivated soils that were fined with 20% zeolitic tuff and 5.09 g of neutral peat than the ones that had a substrate which hasn’t been cultivated on before that was fined with 5% zeolitic tuff and 1.39 g of perlite. The dry substance values obtained present a positive correlation with the values of fresh substance. Analysis of stomatal conductance enhances the hydric stress of plants which respond to saline stress with osmotic adjustment, accumulating high quantities of water comparing to the witness plant, which induces lower values of stomatal conductance and implicitly values are decreasing for photosynthesis, determining a low productivity. Higher values of stomatal conductance are reached at plants grown on previously cultivated soils fined with 20% zeolitic tuff and peat, and also at the ones grown on uncultivated soils fined with peat (29.45, respectively 30.05 mmol/m2/s.

  18. Effect of sunn hemp (Crotalaria juncea L.) cutting date and planting density on weed suppression in Georgia, USA.

    Science.gov (United States)

    Morris, J Bradley; Chase, Carlene; Treadwell, Danielle; Koenig, Rosie; Cho, Alyssa; Morales-Payan, Jose Pable; Murphy, Tim; Antonious, George F

    2015-01-01

    A field study was conducted in 2008 and 2009 at the USDA, ARS, Plant Genetic Resources Conservation Unit in Griffin, GA, to investigate weed suppression by sunn hemp (Crotalaria juncea L). The objectives were to (1) evaluate the effects of apical meristem removal (AMR) at three dates [5, 6, and 7 wks after planting (WAP) on May 14, 2008 and May 21, 2009] and (2) assess the impact of seeding rates (11, 28, and 45 kg ha(-1)) on weed biomass reduction. Weed species were identified at 4, 8, and 12 wks after sunn hemp planting. Sunn hemp cutting date had no significant effect on weed suppression in 2008 but significant differences for grass weeds at 4, 8, and 12 WAP and for yellow nutsedge at 8 and 12 WAP did occur when compared to the control in 2009. In comparison to the sunn hemp-free control plot in 2009, all three seeding rates had reduced grass weed dry weights at 4, 8, and 12 WAP. The total mass of yellow nutsedge when grown with sunn hemp was reduced compared to the total mass of yellow nutsedge grown in the weedy check for all seeding rates at 8 and 12 WAP. Lower grass weed biomass was observed by 12 WAP for cutting dates and seeding rates during 2008 and 2009. Sunn hemp cutting date and seeding rate reduced branch numbers in both years. The reduction in sunn hemp seeding rates revealed a decrease in weed populations.

  19. Clinical significance of combined detection of multiple serum antibodies (AsAb, EmAb, AcAb, AoAb, ToxAb) in infertile women

    International Nuclear Information System (INIS)

    Chen Jing; Jiang Li; Lu Ya

    2005-01-01

    Objective: To determine the clinical significance of combined detection of multiple serum antibodies in infertile women. Methods; Serum multiple antibodies were examined in 120 infertile women, including 88 failed to get pregnancy and 32 with repeated spontaneous abortion. The antibodies tested were: (1) anti-sperm antibody (AsAb) (2) endometrial antibody (EmAb) (3) anti-cardiophospholipid antibody (AcAb) (4) Anti-ovarian antibody (AoAb) and Toxoplasmosis antibody (ToxAb). Results: In 48 of the infertile women, none of the five antibodies were positive (40% of 120). The rest were: one antibody positive--38/120 or 31.6%; two antibodies positive--31/120 or 25.83%, three and four antibodies positive--4/120 or 3.33%. None of the women were positive with all five antibodies. Conclusion: Immune factor was the chief cause of infertility in women. (authors)

  20. Ab initio vel ex eventu

    Science.gov (United States)

    Thiessen, P. A.; Treder, H.-J.

    Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

  1. Deterioração de sementes de Crotalaria juncea e suas conseqüências em laboratório e campo Deterioration of Crotalaria juncea seeds and its consequences under laboratory and field conditions

    Directory of Open Access Journals (Sweden)

    Jocely Andreuccetti Maeda

    1986-01-01

    Full Text Available Sementes de Crotalaria juncea L. com conteúdos de umidade de 6,3 e 11,1%, foram armazenadas por 84 meses em condições ambientes e às temperaturas controladas de 20 e 30°C, e testadas periodicamente no laboratório quanto a germinação e vigor (índice de velocidade de germinação e no campo quanto a emergência, altura da planta, produção de massa seca (massa vegetal na maturação e de sementes. Até aos 30 meses, não se observaram diferenças significativas de germinação entre as sementes nas diversas condições, apresentando todas porcentagens acima de 90. Dos 30 meses em diante, as sementes armazenadas nas condições de maior umidade e temperatura exibiram maior velocidade de deterioração, notadamente as mantidas com 11,1% de umidade a 30°C, que mostraram germinação e vigor praticamente nulos a partir dos 66 meses. As sementes com 6,3% de umidade mantiveram germinação acima de 90% até aos 84 meses, independente da temperatura. Do quarto ano de plantio em diante, as sementes armazenadas com 11,1% de umidade a 30°C se destacaram negativamente das demais quanto a "stand", produção de massa seca e de sementes. Das condições estudadas, as mais adequadas para a preservação da longevidade das sementes foram a secagem a 6,3% de umidade e manutenção a 20 ou 30°C, tendo as sementes assim armazenadas apresentado, ao final dos sete anos, satisfatórios níveis de germinação e vigor e bom comportamento no campo.Crotalaria juncea L. seeds with 6.3% and 11.1% moisture contents were stored for 84 months under room temperature and controlled conditions (at 20°C and 30°C. The seeds were tested periodically, in the laboratory for germination and vigor (germination speed index and in the field, for emergence, plant height, green matter production (at time of maturation and grain yield. No significant differences among the seeds were observed up to 30 months of storage, under the several conditions, all presenting above 90

  2. First generation annotations for the fathead minnow (Pimephales promelas) genome

    Science.gov (United States)

    Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minno...

  3. The adnAB Locus, Encoding a Putative Helicase-Nuclease Activity, Is Essential in Streptomyces

    Science.gov (United States)

    Zhang, Lingli; Nguyen, Hoang Chuong; Chipot, Ludovic; Piotrowski, Emilie; Bertrand, Claire

    2014-01-01

    Homologous recombination is a crucial mechanism that repairs a wide range of DNA lesions, including the most deleterious ones, double-strand breaks (DSBs). This multistep process is initiated by the resection of the broken DNA ends by a multisubunit helicase-nuclease complex exemplified by Escherichia coli RecBCD, Bacillus subtilis AddAB, and newly discovered Mycobacterium tuberculosis AdnAB. Here we show that in Streptomyces, neither recBCD nor addAB homologues could be detected. The only putative helicase-nuclease-encoding genes identified were homologous to M. tuberculosis adnAB genes. These genes are conserved as a single copy in all sequenced genomes of Streptomyces. The disruption of adnAB in Streptomyces ambofaciens and Streptomyces coelicolor could not be achieved unless an ectopic copy was provided, indicating that adnAB is essential for growth. Both adnA and adnB genes were shown to be inducible in response to DNA damage (mitomycin C) and to be independently transcribed. Introduction of S. ambofaciens adnAB genes in an E. coli recB mutant restored viability and resistance to UV light, suggesting that Streptomyces AdnAB could be a functional homologue of RecBCD and be involved in DNA damage resistance. PMID:24837284

  4. Time course of physiological, biochemical, and gene expression changes under short-term salt stress in Brassica juncea L.

    Directory of Open Access Journals (Sweden)

    Manish Pandey

    2017-06-01

    Full Text Available Salinity-imposed limitations on plant growth are manifested through osmotic and ionic imbalances. However, because salinity-induced responses vary considerably among crop plants, monitoring of such responses at an early stage has relevance. In this study, physiological (seed germination, seed vigor index, root length, shoot length, fresh weight, dry weight and biochemical attributes (osmoprotectants, K+/Na+ ratio were analyzed for a time-course assessment of salt responses in Indian mustard (Brassica juncea L. with an emphasis on early monitoring. The results showed strong correlations for total soluble sugars at germination phase (24 h, proline content in the seedling establishment phase (48 h and various physiological parameters including seed vigor index (R2 = 0.901, shoot length (R2 = 0.982, and fresh weight (R2 = 0.980 at 72 h (adaptation under stress. In addition, transcriptional changes were observed under NaCl treatment for key genes belonging to the family of selective ion transporters (NHX, HKT and abscisic acid synthesis (AAO-3. The status of mitochondrial respiration was also examined as a probe for salinity tolerance at an early stage. The results suggested that although all the analyzed parameters showed correlations (negative or positive with salt stress magnitude, their critical response times differed, with most of the studied biochemical, physiological, or molecular markers providing valuable information only after radicle emergence, whereas mitochondrial respiration via alternative oxidase was useful for the early detection of salt responses.

  5. Application of bokashi and sunn hemp (Crotalaria juncea L. to improve inorganic fertilizer efficiency on maize (Zea mays L.

    Directory of Open Access Journals (Sweden)

    A.I. Yuliana

    2015-10-01

    Full Text Available A field experiment was conducted lo learn about the effect of Bokashi and Sunn hemp (Crotalaria juncea L. on maize production and inorganic fertilizer use efficiency on maize. The experiment was conducted in Jatikerto, Malang; at the altitude of 303 m above sea level, in Alfisol soil type, the average daily temperature ranges 21-33oC, from June to October 2013. The experiment was conducted as factorial, designed in a randomized block design (RBD. The first factor was dose of inorganic fertilizer (100% ; 75% and 50% of recommendation dose. The second factor was the organic fertilizer (Without organic fertilizer20 t Bokashi/ ha, 20 t Sunn hemp/ha, 10 t Bokashi/ha + 10 t Sunn hemp/ha. The results showed that application of 20 t Bokashi/ha, 20 t Sunn hemp/ha, and combination of 10 t Bokashi/ha + 10 t Sunn hemp/ha, along with the application of inorganic fertilizer by dose of 100% increased the yields of maize for about 41.8%; 47.6% and 54.7% (10.73 t/ha; 11.17 t/ha, and 11.71 t/ha, respectively. The yield and nutrient use efficiency in the treatment dose of 100% inorganic fertilizer did not have any significant difference from the application of 20 t Bokashi /ha, 20 t Sunn hemp/ha, and 10 t Bokashi/ha + 10 t Sunn hemp/ha along with doses of inorganic fertilization 75% and 50%. Therefore, the organic fertilizer of 20 t Bokashi/ ha, 20 t Sunn hemp/ha, and combination of 10 t Bokashi/ha + 10 t Sunn hemp/ha could reduce the need of inorganic fertilizer for about 50%.

  6. Alleviation of cadmium toxicity in Brassica juncea L. (Czern. & Coss. by calcium application involves various physiological and biochemical strategies.

    Directory of Open Access Journals (Sweden)

    Parvaiz Ahmad

    Full Text Available Calcium (Ca plays important role in plant development and response to various environmental stresses. However, its involvement in mitigation of heavy metal stress in plants remains elusive. In this study, we examined the effect of Ca (50 mM in controlling cadmium (Cd uptake in mustard (Brassica juncea L. plants exposed to toxic levels of Cd (200 mg L(-1 and 300 mg L(-1. The Cd treatment showed substantial decrease in plant height, root length, dry weight, pigments and protein content. Application of Ca improved the growth and biomass yield of the Cd-stressed mustard seedlings. More importantly, the oil content of mustard seeds of Cd-stressed plants was also enhanced with Ca treatment. Proline was significantly increased in mustard plants under Cd stress, and exogenously sprayed Ca was found to have a positive impact on proline content in Cd-stressed plants. Different concentrations of Cd increased lipid peroxidation but the application of Ca minimized it to appreciable level in Cd-treated plants. Excessive Cd treatment enhanced the activities of antioxidant enzymes superoxide dismutase, ascorbate peroxidase and glutathione reductase, which were further enhanced by the addition of Ca. Additionally, Cd stress caused reduced uptake of essential elements and increased Cd accumulation in roots and shoots. However, application of Ca enhanced the concentration of essential elements and decreased Cd accumulation in Cd-stressed plants. Our results indicated that application of Ca enables mustard plant to withstand the deleterious effect of Cd, resulting in improved growth and seed quality of mustard plants.

  7. Synergistic action of tropospheric ozone and carbon dioxide on yield and nutritional quality of Indian mustard (Brassica juncea (L.) Czern.).

    Science.gov (United States)

    Singh, Satyavan; Bhatia, Arti; Tomer, Ritu; Kumar, Vinod; Singh, B; Singh, S D

    2013-08-01

    Field experiments were conducted in open top chamber during rabi seasons of 2009-10 and 2010-11 at the research farm of the Indian Agricultural Research Institute, New Delhi to study the effect of tropospheric ozone (O3) and carbon dioxide (CO2) interaction on yield and nutritional quality of Indian mustard (Brassica juncea (L.) Czern.). Mustard plants were grown from emergence to maturity under different treatments: charcoal-filtered air (CF, 80-85 % less O3 than ambient O3 and ambient CO2), nonfiltered air (NF, 5-10 % less O3 than ambient O3 and ambient CO2 ), nonfiltered air with elevated carbon dioxide (NF + CO2, NF air and 550 ± 50 ppm CO2), elevated ozone (EO, NF air and 25-35 ppb elevated O3), elevated ozone along with elevated carbon dioxide (EO + CO2, NF air, 25-35 ppb O3 and 550 ± 50 ppm CO2), and ambient chamber less control (AC, ambient O3 and CO2). Elevated O3 exposure led to reduced photosynthesis and leaf area index resulting in decreased seed yield of mustard. Elevated ozone significantly decreased the oil and micronutrient content in mustard. Thirteen to 17 ppm hour O3 exposure (accumulated over threshold of 40 ppm, AOT 40) reduced the oil content by 18-20 %. Elevated CO2 (500 ± 50 ppm) along with EO was able to counter the decline in oil content in the seed, and it increased by 11 to 13 % over EO alone. Elevated CO2, however, decreased protein, calcium, zinc, iron, magnesium, and sulfur content in seed as compared to the nonfiltered control, whereas removal of O3 from air in the charcoal-filtered treatment resulted in a significant increase in the same.

  8. Extraction of Proteins with ABS

    NARCIS (Netherlands)

    Desai, R.K.; Streefland, M.; Wijffels, R.H.; Eppink, M.H.M.

    2016-01-01

    Over the past years, there has been an increasing trend in research on the extraction and purification of proteins using aqueous biphasic systems (ABS) formed by polymers, e.g., polyethylene glycol (PEG). In general, when dealing with protein purification processes, it is essential to maintain their

  9. Ab initio potential for solids

    DEFF Research Database (Denmark)

    Chetty, N.; Stokbro, Kurt; Jacobsen, Karsten Wedel

    1992-01-01

    . At the most approximate level, the theory is equivalent to the usual effective-medium theory. At all levels of approximation, every term in the total-energy expression is calculated ab initio, that is, without any fitting to experiment or to other calculations. Every step in the approximation procedure can...

  10. Ab-initio ZORA calculations

    NARCIS (Netherlands)

    Faas, S.; Snijders, Jaap; van Lenthe, J.H.; HernandezLaguna, A; Maruani, J; McWeeny, R; Wilson, S

    2000-01-01

    In this paper we present the first application of the ZORA (Zeroth Order Regular Approximation of the Dirac Fock equation) formalism in Ab Initio electronic structure calculations. The ZORA method, which has been tested previously in the context of Density Functional Theory, has been implemented in

  11. Modeling of truck's braking dynamics with ABS

    Directory of Open Access Journals (Sweden)

    Maxym DYACHUK

    2014-09-01

    Full Text Available In the article some questions of ABS simulation on the basis of plane vehicle's dynamics and automatic modeling are considered. The author's algorithm of ABS modulators control is presented.

  12. Kajian Hubungan Populasi Tanaman dengan Neraca Unsur Hara Nitrogen dan Fosfor pada Sistem Vertikultur Sawi Hijau (Brassica juncea L dan Kangkung (Ipomea reptana

    Directory of Open Access Journals (Sweden)

    I MADE PURNA WIDANA

    2016-05-01

    Full Text Available Analysis of Relationship Between Crop Density and The Balancing of Both Soil Nitrogenand Phosporus in Verticulture System of Mustard Green (Brassica juncea L and Kale(Ipomea reptana. The relationship between crops density and the balancing of both soilnitrogen and phosphorus in verticulture system remained to be important issue. A glasshouseexperiment had carried out from October 2014 to March 2015 in order to determine (1 theoptimum population density of both mustard greens (Brassica juncea L and kale (Ipomeareptana, (2 soil total-N or available-P balance, and (3 the relatiohships between plantspopulations and soil nutrients balance. A split plot experiment under complete block designwas applied to examine the effect of the main plot (crops type i.e. mustard green and kale andsub plot (crops population i.e 10, 15, 20,25, and 30 crops per planting container 0,12 m2 insize. The results showed that no optimal crops population density had achieved. Themaximum crops population was 30 for both mustard greens and kale. The soil total-N balancewas negative while these was positive for soil available-P balance of P and N negative. Alogarithmic relationships was calculated between soil total-N balance with mustard green,while linier patterns were significant for soil-N balance with kale and available-P balancewith both mustard greens and kale.

  13. Pre-sowing Seed Treatment with 24-Epibrassinolide Ameliorates Pesticide Stress in Brassica juncea L. through the Modulation of Stress Markers

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    Parvaiz Ahmad

    2016-11-01

    Full Text Available The present experiment was designed to assess the effects of seed soaking with 24-epibrassinolide (EBR on the physiology of Brassica juncea L. seedlings grown under imidacloprid (IMI toxicity. Application of EBR increased the length of seedlings, dry weight, and pigment contents, polyphenols, total phenols and organic acids under IMI toxicity. The expression of genes coding key enzymes of pigment, phenols, polyphenols and organic acid biosynthetic pathways was also studied including CHLASE (chlorophyllase, PSY (phytoene synthase, CHS (chalcone synthase and PAL (phenylalanine ammonialyase, CS (citrate synthase, SUCLG1 (succinyl Co-A ligase,, SDH (succinate dehydrogenase, FH (fumarate hydratase, MS (malate synthase. Multiple linear regression analysis revealed that IMI application regressed negatively on seedling length, dry weight and total chlorophyll content. However, EBR seed treatment regressed positively on all of the parameters studied. Moreover, interaction between IMI and EBR showed positive regression for growth parameters, content of pigments, total polyphenol, total phenol and malate, and expression of PSY and PAL. Negative interactions were noticed for the contents of fumarate, succinate and citrate, and expression of CHS and all genes studied related to organic acid metabolism. In conclusion, EBR enhanced the growth and contents of all studied metabolites by regulating the gene expression of B. juncea seedlings under IMI stress.

  14. Insecticidal, food utilisation and biochemical effect of essential oils extracted from seeds of Brassica juncea (Czern. against Spodoptera litura (Lepidoptera: Noctuidae (Fabricius

    Directory of Open Access Journals (Sweden)

    Shallina Gupta

    2017-09-01

    Full Text Available The glucosinolate rich hot and cold hexane extracts of Brassica juncea had a negative effect on the development of Spodoptera litura larvae when they were fed on different concentrations of the extracts. Both larval growth index and pupal growth index declined with treatment. However the hot extract with 3-butenyl isothiocyanate as the predominant compound had a more deleterious effect as at 3125ppm the larvae were unable to complete their development. The nutritional indices too were more adversely affected with hot extract as compared to cold extract. The RGR, RCR, ECI and ECD declined significantly with increase in concentration of the hot hexane extract. The activity of antioxidant enzymes, SOD and catalase decreased while that of phosphatases, GSTs, phenol oxidases increased during the initial treatment duration but decreased on prolonged treatment of the larvae with LC50 concentration of hot extract. A similar trend was observed for glutathione and lipid peroxides but a decrease in ascorbate content was observed as compared to control. The findings reveal a toxic effect of 3-butenylisothiocyanate rich hot hexane extract of B. juncea on S. litura larvae.

  15. Discrimination between Native and Tn6010-Associated oqxAB in Klebsiella spp., Raoultella spp., and other Enterobacteriaceae by Using a Two-Step Strategy

    DEFF Research Database (Denmark)

    Guillard, Thomas; Lebreil, Anne-Laure; Hansen, Lars Hestbjerg

    2015-01-01

    ABSTRACT We developed a two-step PCR-based strategy to detect genes encoding OqxAB, allowing a specific assignment of Tn6010-associated oqxAB in Enterobacteriaceae. Chromosomal location in this setup was confirmed by hybridization with I-CeuI-restricted genomes. This approach led us to find...

  16. AB Levitator and Electricity Storage

    OpenAIRE

    Bolonkin, Alexander

    2007-01-01

    The author researched this new idea - support of flight by any aerial vehicles at significant altitude solely by the magnetic field of the planet. It is shown that current technology allows humans to create a light propulsion (AB engine) which does not depend on air, water or ground terrain. Simultaniosly, this revolutionary thruster is a device for the storage of electricity which is extracted and is replenished (during braking) from/into the storage with 100 percent efficiency. The relative...

  17. Attack modes and defence reactions in pathosystems involving Sclerotinia sclerotiorum, Brassica carinata, B. juncea and B. napus.

    Science.gov (United States)

    Uloth, Margaret B; Clode, Peta L; You, Ming Pei; Barbetti, Martin J

    2016-01-01

    Sclerotinia stem rot (SSR, Sclerotinia sclerotiorum) is a damaging disease of oilseed brassicas world-wide. Host resistance is urgently needed to achieve control, yet the factors that contribute to stem resistance are not well understood. This study investigated the mechanisms of resistance to SSR. Stems of 5-week-old Brassica carinata, B. juncea and B. napus of known resistance were infected via filter paper discs impregnated with S. sclerotiorum mycelium under controlled conditions. Transverse sections of the stem and portions of the stem surface were examined using optical and scanning electron microscopy. The association of anatomical features with the severity of disease (measured by mean lesion length) was determined. Several distinct resistance mechanisms were recorded for the first time in these Brassica-pathogen interactions, including hypersensitive reactions and lignification within the stem cortex, endodermis and in tissues surrounding the lesions. Genotypes showing a strong lignification response 72 h post-infection (hpi) tended to have smaller lesions. Extensive vascular invasion by S. sclerotiorum was observed only in susceptible genotypes, especially in the vascular fibres and xylem. Mean lesion length was negatively correlated with the number of cell layers in the cortex, suggesting progress of S. sclerotiorum is impeded by more cell layers. Hyphae in the centre of lesions became highly vacuolate 72 hpi, reflecting an ageing process in S. sclerotiorum hyphal networks that was independent of host resistance. The infection process of S. sclerotiorum was analogous in B. carinata and B. napus. Infection cushions of the highly virulent isolate of S. sclerotiorum MBRS-1 were grouped together in dense parallel bundles, while hyphae in the infection cushions of a less aggressive isolate WW-3 were more diffuse, and this was unaffected by host genotype. A variety of mechanisms contribute to host resistance against S. sclerotiorum across the three

  18. Transgenic tobacco overexpressing Brassica juncea HMG-CoA synthase 1 shows increased plant growth, pod size and seed yield.

    Directory of Open Access Journals (Sweden)

    Pan Liao

    Full Text Available Seeds are very important not only in the life cycle of the plant but they represent food sources for man and animals. We report herein a mutant of 3-hydroxy-3-methylglutaryl-coenzyme A synthase (HMGS, the second enzyme in the mevalonate (MVA pathway that can improve seed yield when overexpressed in a phylogenetically distant species. In Brassica juncea, the characterisation of four isogenes encoding HMGS has been previously reported. Enzyme kinetics on recombinant wild-type (wt and mutant BjHMGS1 had revealed that S359A displayed a 10-fold higher enzyme activity. The overexpression of wt and mutant (S359A BjHMGS1 in Arabidopsis had up-regulated several genes in sterol biosynthesis, increasing sterol content. To quickly assess the effects of BjHMGS1 overexpression in a phylogenetically more distant species beyond the Brassicaceae, wt and mutant (S359A BjHMGS1 were expressed in tobacco (Nicotiana tabacum L. cv. Xanthi of the family Solanaceae. New observations on tobacco OEs not previously reported for Arabidopsis OEs included: (i phenotypic changes in enhanced plant growth, pod size and seed yield (more significant in OE-S359A than OE-wtBjHMGS1 in comparison to vector-transformed tobacco, (ii higher NtSQS expression and sterol content in OE-S359A than OE-wtBjHMGS1 corresponding to greater increase in growth and seed yield, and (iii induction of NtIPPI2 and NtGGPPS2 and downregulation of NtIPPI1, NtGGPPS1, NtGGPPS3 and NtGGPPS4. Resembling Arabidopsis HMGS-OEs, tobacco HMGS-OEs displayed an enhanced expression of NtHMGR1, NtSMT1-2, NtSMT2-1, NtSMT2-2 and NtCYP85A1. Overall, increased growth, pod size and seed yield in tobacco HMGS-OEs were attributed to the up-regulation of native NtHMGR1, NtIPPI2, NtSQS, NtSMT1-2, NtSMT2-1, NtSMT2-2 and NtCYP85A1. Hence, S359A has potential in agriculture not only in improving phytosterol content but also seed yield, which may be desirable in food crops. This work further demonstrates HMGS function in plant

  19. Adubação orgânica da batata com esterco e, ou, Crotalaria juncea: II - disponibilidade de N, P e K no solo ao longo do ciclo de cultivo Organic fertilization of potato with manure and, or, Crotalaria juncea: II - soil N, P, and K availability throughout the growing season

    OpenAIRE

    Tácio Oliveira da Silva; Rômulo Simões Cezar Menezes

    2007-01-01

    Os solos do Agreste paraibano têm baixa fertilidade e a prática usual de adubação é a incorporação de esterco na época do plantio. Entretanto, dependendo da qualidade do esterco, essa prática pode causar a imobilização de nutrientes do solo durante os primeiros meses de cultivo. É possível que o cultivo e incorporação de Crotalaria juncea, combinado com o esterco, possa promover mineralização mais sincronizada com a demanda de nutrientes pelas plantas. No presente estudo, realizado em 2003, f...

  20. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  1. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  2. AP calculus AB/BC

    CERN Document Server

    Schwartz, Stu

    2013-01-01

    All Access for the AP® Calculus AB & BC Exams Book + Web + Mobile Everything you need to prepare for the Advanced Placement® exam, in a study system built around you! There are many different ways to prepare for an Advanced Placement® exam. What's best for you depends on how much time you have to study and how comfortable you are with the subject matter. To score your highest, you need a system that can be customized to fit you: your schedule, your learning style, and your current level of knowledge. This book, and the free online tools that come with it, will help you personalize your AP® Cal

  3. 14CO2 fixation and allocation of 14C into major biochemical fractions in different parts of Indian mustard (Brassica juncea)

    International Nuclear Information System (INIS)

    Subrahmanyam, D.; Rathore, V.S.

    1993-01-01

    14CO2 fixation and transport of 14C-photosynthates amongst different parts of Indian mustard (Brassica juncea) and the incorporation of 14C into major chemical fractions in different plant parts was studied at ripening stage. Stem and pod together contributed 70 % of the total 14C fixed by the plant. In all plant parts neutral saccharide fraction contained maximum radioactivity immediately after exposing plants to 14CO2. After 24 h, the radioactivity in this fraction declined considerably due to translocation or conversion into other fractions. Concomitantly radioactivity in lipids and pigments, residue and starch fractions increased after 24 h. The 14C allocation patterns in stem and leaves were similar. However, in pods very high radioactivity was recovered from amino and organic acid fractions indicating the presence of active phosphoenolpyruvate carboxylase in pod walls

  4. Mitochondrial nad2 gene is co-transcripted with CMS-associated orfB gene in cytoplasmic male-sterile stem mustard (Brassica juncea).

    Science.gov (United States)

    Yang, Jing-Hua; Zhang, Ming-Fang; Yu, Jing-Quan

    2009-02-01

    The transcriptional patterns of mitochondrial respiratory related genes were investigated in cytoplasmic male-sterile and fertile maintainer lines of stem mustard, Brassica juncea. There were numerous differences in nad2 (subunit 2 of NADH dehydrogenase) between stem mustard CMS and its maintainer line. One novel open reading frame, hereafter named orfB gene, was located at the downstream of mitochondrial nad2 gene in the CMS. The novel orfB gene had high similarity with YMF19 family protein, orfB in Raphanus sativus, Helianthus annuus, Nicotiana tabacum and Beta vulgaris, orfB-CMS in Daucus carota, atp8 gene in Arabidopsis thaliana, 5' flanking of orf224 in B. napus (nap CMS) and 5' flanking of orf220 gene in CMS Brassica juncea. Three copies probed by specific fragment (amplified by primers of nad2F and nad2R from CMS) were found in the CMS line following Southern blotting digested with HindIII, but only a single copy in its maintainer line. Meanwhile, two transcripts were shown in the CMS line following Northern blotting while only one transcript was detected in the maintainer line, which were probed by specific fragment (amplified by primers of nad2F and nad2R from CMS). Meanwhile, the expression of nad2 gene was reduced in CMS bud compared to that in its maintainer line. We thus suggested that nad2 gene may be co-transcripted with CMS-associated orfB gene in the CMS. In addition, the specific fragment that was amplified by primers of nad2F and nad2R just spanned partial sequences of nad2 gene and orfB gene. Such alterations in the nad2 gene would impact the activity of NADH dehydrogenase, and subsequently signaling, inducing the expression of nuclear genes involved in male sterility in this type of cytoplasmic male sterility.

  5. Ploidy and genome composition of Musa germplasm at the ...

    African Journals Online (AJOL)

    GRACE

    2006-07-03

    Jul 3, 2006 ... Musa spp (bananas and plantains) constitute a hybrid-polyploid complex and are classified according to different genome compositions such as AA, BB, AB, AAA, AAB, ABB, AAAA, ABBB, AAAB and. AABB. Knowledge of ploidy and exact genome compositions of the parental material is essential for.

  6. Homology of ab1 and ab3 monoclonal antibodies that neutralize Semliki Forest virus

    NARCIS (Netherlands)

    Fernandez, IM; Bos, NA; Harmsen, M; Verheul, AFM; Snippe, H; Kraaijeveld, CA

    2001-01-01

    A noninternal image monoclonal antiidiotypic antibody (ab2 mAb), designated 1,13A321, that had proved its efficacy as vaccine against infection with Semliki Forest virus (SFV) in BALB/c mice, was used as immunogen to generate a panel of SFV-neutralizing monoclonal anti-anti-idiotypic antibodies (ab3

  7. Solvent (acetone-butanol: ab) production

    Science.gov (United States)

    This article describes production of butanol [acetone-butanol-ethanol, (also called AB or ABE or solvent)] by fermentation using both traditional and current technologies. AB production from agricultural commodities, such as corn and molasses, was an important historical fermentation. Unfortunately,...

  8. Cytoplasmic and Genomic Effects on Meiotic Pairing in Brassica Hybrids and Allotetraploids from Pair Crosses of Three Cultivated Diploids

    Science.gov (United States)

    Cui, Cheng; Ge, Xianhong; Gautam, Mayank; Kang, Lei; Li, Zaiyun

    2012-01-01

    Interspecific hybridization and allopolyploidization contribute to the origin of many important crops. Synthetic Brassica is a widely used model for the study of genetic recombination and “fixed heterosis” in allopolyploids. To investigate the effects of the cytoplasm and genome combinations on meiotic recombination, we produced digenomic diploid and triploid hybrids and trigenomic triploid hybrids from the reciprocal crosses of three Brassica diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC). The chromosomes in the resultant hybrids were doubled to obtain three allotetraploids (B. juncea, AA.BB; B. napus, AA.CC; B. carinata, BB.CC). Intra- and intergenomic chromosome pairings in these hybrids were quantified using genomic in situ hybridization and BAC-FISH. The level of intra- and intergenomic pairings varied significantly, depending on the genome combinations and the cytoplasmic background and/or their interaction. The extent of intragenomic pairing was less than that of intergenomic pairing within each genome. The extent of pairing variations within the B genome was less than that within the A and C genomes, each of which had a similar extent of pairing. Synthetic allotetraploids exhibited nondiploidized meiotic behavior, and their chromosomal instabilities were correlated with the relationship of the genomes and cytoplasmic background. Our results highlight the specific roles of the cytoplasm and genome to the chromosomal behaviors of hybrids and allopolyploids. PMID:22505621

  9. Isolation and Characterization of a Virulent Bacteriophage AB1 of Acinetobacter baumannii

    Directory of Open Access Journals (Sweden)

    Jia Shiru

    2010-04-01

    Full Text Available Abstract Background Acinetobacter baumannii is an emerging nosocomial pathogen worldwide with increasing prevalence of multi-drug and pan-drug resistance. A. baumannii exists widely in natural environment, especially in health care settings, and has been shown difficult to be eradicated. Bacteriophages are often considered alternative agent for controlling bacterial infection and contamination. In this study, we described the isolation and characterization of one virulent bacteriophage AB1 capable of specifically infecting A. baumannii. Results A virulent bacteriophage AB1, specific for infecting a clinical strain A. baumannii KD311, was first isolated from marine sediment sample. Restriction analysis indicated that phage AB1 was a dsDNA virus with an approximate genome size of 45.2 kb to 46.9 kb. Transmission electron microscopy showed that phage AB1 had an icosahedral head with a non-contractile tail and collar or whisker structures, and might be tentatively classified as a member of the Siphoviridae family. Proteomic pattern of phage AB1, generated by SDS-PAGE using purified phage particles, revealed five major bands and six minor bands with molecular weight ranging from 14 to 80 kilo-dalton. Also determined was the adsorption rate of phage AB1 to the host bacterium, which was significantly enhanced by addition of 10 mM CaCl2. In a single step growth test, phage AB1 was shown having a latent period of 18 minutes and a burst size of 409. Moreover, pH and thermal stability of phage AB1 were also investigated. At the optimal pH 6.0, 73.2% of phages survived after 60 min incubation at 50°C. When phage AB1 was used to infect four additional clinical isolates of A. baumannii, one clinical isolate of Stenotrophomonas maltophilia, and Pseudomonas aeruginosa lab strains PAK and PAO1, none of the tested strains was found susceptible, indicating a relatively narrow host range for phage AB1. Conclusion Phage AB1 was capable of eliciting efficient lysis

  10. Collective rotation from ab initio theory

    International Nuclear Information System (INIS)

    Caprio, M.A.; Maris, P.; Vary, J.P.; Smith, R.

    2015-01-01

    Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments and electromagnetic transitions. In this review, NCCI calculations of 7–9 Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction. (author)

  11. AP calculus AB & BC crash course

    CERN Document Server

    Rosebush, J

    2012-01-01

    AP Calculus AB & BC Crash Course - Gets You a Higher Advanced Placement Score in Less Time Crash Course is perfect for the time-crunched student, the last-minute studier, or anyone who wants a refresher on the subject. AP Calculus AB & BC Crash Course gives you: Targeted, Focused Review - Study Only What You Need to Know Crash Course is based on an in-depth analysis of the AP Calculus AB & BC course description outline and actual AP test questions. It covers only the information tested on the exams, so you can make the most of your valuable study time. Written by experienced math teachers, our

  12. Pulmonary and hepatic lesions caused by the dehydropyrrolizidine alkaloid-producing plants Crotalaria juncea and Crotalaria retusa in donkeys.

    Science.gov (United States)

    Pessoa, C R M; Pessoa, A F A; Maia, L A; Medeiros, R M T; Colegate, S M; Barros, S S; Soares, M P; Borges, A S; Riet-Correa, F

    2013-09-01

    The effects and susceptibility of donkeys to Crotalaria juncea and Crotalaria retusa poisoning were determined at high and low doses. Seeds of C. juncea containing 0.074% of dehydropyrrolizidine alkaloids (DHPAs) (isohemijunceines 0.05%, trichodesmine 0.016%, and junceine 0.008%) were administered to three donkeys at 0.3, 0.6 and 1 g/kg body weight (g/kg) daily for 365 days. No clinical signs were observed and, on liver and lung biopsies, the only lesion was a mild liver megalocytosis in the donkeys ingesting 0.6 and 1 g/kg/day. Two other donkeys that received daily doses of 3 and 5 g seed/kg showed initial respiratory signs 70 and 40 days after the start of the administration, respectively. The donkeys were euthanized following severe respiratory signs and the main lung lesions were proliferation of Clara cells and interstitial fibrosis. Three donkeys ingested seeds of C. retusa containing 5.99% of monocrotaline at daily doses of 0.025, 0.05 and 0.1 g/kg for 365 days. No clinical signs were observed and, on liver and lung biopsies, the only lesion was moderate liver megalocytosis in each of the three donkeys. One donkey that received a single dose of 5 g/kg of C. retusa seeds and another that received 1 g/kg daily for 7 days both showed severe clinical signs and died with diffuse centrilobular liver necrosis. No lung lesions were observed. Another donkey that received a single dose of 2.5 g/kg of C. retusa seeds showed no clinical signs. The hepatic and pneumotoxic effects observed are consistent with an etiology involving DHPAs. Furthermore, the occurrence of lung or liver lesions correlates with the type of DHPAs contained in the seeds. Similarly as has been reported for horses, the data herein suggest that in donkeys some DHPAs are metabolized in the liver causing liver disease, whereas others are metabolized in the lung by Clara cells causing lung disease. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  14. Spectral monitoring of AB Aur

    Science.gov (United States)

    Rodríguez Díaz, L. F.; Oostra, B.

    2017-07-01

    The Astronomical Observatory of the Universidad de los Andes in Bogotá, Colombia, did a spectral monitoring during 2014 and 2015 to AB Aurigae, the brightest Herbig Ae/be star in the northern hemisphere. The aim of this project is applying spectral techniques, in order to identify specific features that could help us not only to understand how this star is forming, but also to establish a pattern to explain general star formation processes. We have recorded 19 legible spectra with a resolving power of R = 11,0000, using a 40 cm Meade telescope with an eShel spectrograph, coupled by a 50-micron optical fiber. We looked for the prominent absorption lines, the Sodium doublet at 5890Å and 5896Å, respectively and Magnesium II at 4481Å; to measure radial velocities of the star, but, we did not find a constant value. Instead, it ranges from 15 km/s to 32 km/s. This variability could be explained by means of an oscillation or pulsation of the external layers of the star. Other variabilities are observed in some emission lines: Hα, Hβ, He I at 5876Å and Fe II at 5018Å. It seems this phenomenon could be typical in stars that are forming and have a circumstellar disk around themselves. This variability is associated with the nonhomogeneous surface of the star and the interaction that it has with its disk. Results of this interaction could be seen also in the stellar wind ejected by the star. More data are required in order to look for a possible period in the changes of radial velocity of the star, the same for the variability of He I and Fe II, and phenomena present in Hα. We plan to take new data in January of 2017.

  15. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  16. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  17. Impact of mixed low-molecular-weight organic acids on uranium accumulation and distribution in a variant of mustard (Brassica juncea var. tumida)

    International Nuclear Information System (INIS)

    Fangfang Qi; Dingna Wang; Lijian Ma; Yongdong Jin; Liang Du; Dong Zhang; Chuanqin Xia; Sichuan University, Chengdu

    2014-01-01

    The impact of a mixture of low-molecular-weight organic acids (LMWOAs) composed of CA/MA/OA/LA with a molar ratio of 2.5:2.31:1.15:0.044 on uranium (U) accumulation and distribution in mustard (Brassica juncea var. tumida) was studied in this paper in order to understand the mechanism of rhizosphere-exudation assisted phytoremediation by hydroponic and pot culture experiments. The impact of the mixture of LWMOAs (Mix) on U accumulation showed that in hydroponic conditions Mix could enhance U translocation from root-to-shoot in mustard, but inhibit U uptake in root. In pot experiments, Mix enhanced both root and shoot U accumulation in mustard. The time-dependent kinetics of U uptake in mustard on Mix treatment showed that U content in plant shoots and roots increased with time increasing, and the steady state conditions were obtained at the 8th and 5th day with the U content of 1,528 and 2,300 mg/kg, respectively. Transmission electron microscope and energy dispersive X-ray spectrometry analysis for mustard roots showed that U was mainly observed on cell membrane of mustard roots on Mix treatment. This study would provide new insights for the mixture of LWMOAs-assisted phytoremediation of U-contaminated soil. (author)

  18. Phytoextraction and accumulation of mercury in three plant species: Indian mustard (Brassica juncea), beard grass (Polypogon monospeliensis), and Chinese brake fern (Pteris vittata).

    Science.gov (United States)

    Su, Yi; Han, Fengxiang X; Chen, Jian; Sridhar, B B Maruthi; Monts, David L

    2008-01-01

    The objective of this research was to screen and search for suitable plant species to phytoextract mercury-contaminated soil. Our effort focused on using some of the known metal-accumulating wild-type plants since no natural plant species with mercury-hyperaccumulat ing properties has yet been identified. Three plant species were evaluated for their uptake efficiency for mercury: Indian mustard (Brassica juncea), beard grass (Polypogon monospeliensis), and Chinese brake fern (Pteris vittata). Four sets of experiments were conducted to evaluate the phytoremediation potential of these three plant species: a pot study with potting mix where mercury was provided daily as HgCl2 solution; experiments with freshly mercury-spiked soil; and a study with aged soils contaminated with different mercury sources (HgCl2, Hg(NO3)2, and HgS). Homemade sunlit chambers were also used to study foliar uptake of Hg from ambient air. Among the three plant species, Chinese brake fern showed the least stress symptoms resulting from mercury exposure and had the highest mercury accumulation. Our results indicate that Chinese brake fern may be a potential candidate for mercury phytoextraction. We found that mercury contamination is biologically available for plant uptake and accumulation, even if the original and predominating mercury form is HgS, and also after multiple phytoremediation cycles.

  19. Bacteria–zinc co-localization implicates enhanced synthesis of cysteine-rich peptides in zinc detoxification when Brassica juncea is inoculated with Rhizobium leguminosarum

    Science.gov (United States)

    Adediran, Gbotemi A; Ngwenya, Bryne T; Mosselmans, J Frederick W; Heal, Kate V

    2016-01-01

    Some plant growth promoting bacteria (PGPB) are enigmatic in enhancing plant growth in the face of increased metal accumulation in plants. Since most PGPB colonize the plant root epidermis, we hypothesized that PGPB confer tolerance to metals through changes in speciation at the root epidermis. We employed a novel combination of fluorophore-based confocal laser scanning microscopic imaging and synchrotron based microscopic X-ray fluorescence mapping with X-ray absorption spectroscopy to characterize bacterial localization, zinc (Zn) distribution and speciation in the roots of Brassica juncea grown in Zn contaminated media (400 mg kg−1 Zn) with the endophytic Pseudomonas brassicacearum and rhizospheric Rhizobium leguminosarum. PGPB enhanced epidermal Zn sequestration relative to PGBP-free controls while the extent of endophytic accumulation depended on the colonization mode of each PGBP. Increased root accumulation of Zn and increased tolerance to Zn was associated predominantly with R. leguminosarum and was likely due to the coordination of Zn with cysteine-rich peptides in the root endodermis, suggesting enhanced synthesis of phytochelatins or glutathione. Our mechanistic model of enhanced Zn accumulation and detoxification in plants inoculated with R. leguminosarum has particular relevance to PGPB enhanced phytoremediation of soils contaminated through mining and oxidation of sulphur-bearing Zn minerals or engineered nanomaterials such as ZnS. PMID:26263508

  20. Cloning and characterization of a mitochondrial glyoxalase II from Brassica juncea that is upregulated by NaCl, Zn, and ABA

    International Nuclear Information System (INIS)

    Saxena, Mukesh; Bisht, Rekha; Roy, Suchandra Deb; Sopory, S.K.; Bhalla-Sarin, Neera

    2005-01-01

    A cDNA (1061 bp) Bj glyII was cloned from a mannitol induced library of Brassica juncea. It encoded a protein of 335 amino acids with a molecular weight of 36.52 kDa. The deduced amino acid sequence of the clone showed 92% and 56% identity with Pennisetum and rice glyoxalase II, respectively, and 30% identity was observed with the human glyoxalase II. Search for the identical residues revealed the presence of highly conserved THHHXDH domain which is involved in zinc binding. p-NN and pSORT analysis of this sequence revealed a N-terminal mitochondrial target peptide. The cDNA was cloned in pMAL and a fusion protein with MBP (78 kDa) was expressed in Escherichia coli. The recombinant protein was purified approximately sixfold by affinity purification on amylose column and showed its pH optima at 7.0. The K m was determined to be 120 μM using S-D-lactoylglutathione as substrate. The expression of Bj glyII under various abiotic stress conditions showed that it is upregulated by salinity, heavy metal stress, and ABA

  1. PirAB protein from Xenorhabdus nematophila HB310 exhibits a binary toxin with insecticidal activity and cytotoxicity in Galleria mellonella.

    Science.gov (United States)

    Yang, Qing; Zhang, Jie; Li, Tianhui; Liu, Shen; Song, Ping; Nangong, Ziyan; Wang, Qinying

    2017-09-01

    PirAB (Photorhabdus insect-related proteins, PirAB) toxin was initially found in the Photorhabdus luminescens TT01 strain and has been shown to be a binary toxin with high insecticidal activity. Based on GenBank data, this gene was also found in the Xenorhabdus nematophila genome sequence. The predicted amino acid sequence of pirA and pirB in the genome of X. nematophila showed 51% and 50% identity with those gene sequences from P. luminescens. The purpose of this experiment is to identify the relevant information for this toxin gene in X. nematophila. The pirA, pirB and pirAB genes of X. nematophila HB310 were cloned and expressed in Escherichia coli BL21 (DE3) using the pET-28a vector. A PirAB-fusion protein (PirAB-F) was constructed by linking the pirA and pirB genes with the flexible linker (Gly) 4 DNA encoding sequence and then efficiently expressed in E. coli. The hemocoel and oral insecticidal activities of the recombinant proteins were analyzed against the larvae of Galleria mellonella. The results show that PirA/B alone, PirA/B mixture, co-expressed PirAB protein, and PirAB-F all had no oral insecticidal activity against the second-instar larvae of G. mellonella. Only PirA/B mixture and co-expressed PirAB protein had hemocoel insecticidal activity against G. mellonella fifth-instar larvae, with an LD 50 of 2.718μg/larva or 1.566μg/larva, respectively. Therefore, we confirmed that PirAB protein of X. nematophila HB310 is a binary insecticidal toxin. The successful expression and purification of PirAB laid a foundation for further studies on the function, insecticidal mechanism and expression regulation of the binary toxin. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Clinical significance of determination of serum leptin and AsAb, EmAb levels in infertile women

    International Nuclear Information System (INIS)

    Luo Jian; Zhou Minglian; Sun Gang; He Haoming

    2010-01-01

    Objective: To study the clinical significance of determination of serum leptin, AsAb, and EmAb levels in infertile women. Methods: Serum leptin (with RIA) and AsAb, EmAb (with ELISA) levels were detected in 32 infertile women and 35 controls. Results: Serum leptin levels in infertile women were significantly lower than those in controls (P<0.01). Serum AsAb and EmAb were both positive in 25 of the 32 infertile women (78.1%) and EmAb (one of two Abs) was positive in the rest 7 women (21.9%). These positive rates were also significantly higher than the respective ones in the controls (both P<0.01). Conclusion: Lower serum leptin level with highly positive AsAb and EmAb might be the chief cause of infertility in women. (authors)

  3. ParABS Systems of the Four Replicons of Burkholderia cenocepacia: New Chromosome Centromeres Confer Partition Specificity†

    Science.gov (United States)

    Dubarry, Nelly; Pasta, Franck; Lane, David

    2006-01-01

    Most bacterial chromosomes carry an analogue of the parABS systems that govern plasmid partition, but their role in chromosome partition is ambiguous. parABS systems might be particularly important for orderly segregation of multipartite genomes, where their role may thus be easier to evaluate. We have characterized parABS systems in Burkholderia cenocepacia, whose genome comprises three chromosomes and one low-copy-number plasmid. A single parAB locus and a set of ParB-binding (parS) centromere sites are located near the origin of each replicon. ParA and ParB of the longest chromosome are phylogenetically similar to analogues in other multichromosome and monochromosome bacteria but are distinct from those of smaller chromosomes. The latter form subgroups that correspond to the taxa of their hosts, indicating evolution from plasmids. The parS sites on the smaller chromosomes and the plasmid are similar to the “universal” parS of the main chromosome but with a sequence specific to their replicon. In an Escherichia coli plasmid stabilization test, each parAB exhibits partition activity only with the parS of its own replicon. Hence, parABS function is based on the independent partition of individual chromosomes rather than on a single communal system or network of interacting systems. Stabilization by the smaller chromosome and plasmid systems was enhanced by mutation of parS sites and a promoter internal to their parAB operons, suggesting autoregulatory mechanisms. The small chromosome ParBs were found to silence transcription, a property relevant to autoregulation. PMID:16452432

  4. Ab initio model of porous periclase

    International Nuclear Information System (INIS)

    Drummond, Neil D.; Swift, Damian C.; Ackland, Graeme J.

    2004-01-01

    A two-phase equilibrium equation of state (EOS) for periclase (MgO) was constructed using ab initio quantum mechanics, including a rigorous calculation of quasiharmonic phonon modes. Much of the shock wave data reported for periclase is on porous material. We compared the theoretical EOS with porous data using a simple 'snowplough' treatment and also a model using finite equilibration rates suitable for continuum mechanics simulations. (This model has been applied previously to various heterogeneous explosives as well as other porous materials.) The results were consistent and matched the data well at pressures above the regime affected by strength - and ramp-wave formation - during compaction. Ab initio predictions of the response of porous material have been cited recently as a novel and advanced capability; we feel that this is a fairly routine extension to established ab initio techniques

  5. Adubação orgânica da batata com esterco e, ou, Crotalaria juncea: II - disponibilidade de N, P e K no solo ao longo do ciclo de cultivo

    OpenAIRE

    Silva, Tácio Oliveira da; Menezes, Rômulo Simões Cezar

    2007-01-01

    Os solos do Agreste paraibano têm baixa fertilidade e a prática usual de adubação é a incorporação de esterco na época do plantio. Entretanto, dependendo da qualidade do esterco, essa prática pode causar a imobilização de nutrientes do solo durante os primeiros meses de cultivo. É possível que o cultivo e incorporação de Crotalaria juncea, combinado com o esterco, possa promover mineralização mais sincronizada com a demanda de nutrientes pelas plantas. No presente estudo, realizado em 2003, f...

  6. Ab initio valence calculations in chemistry

    CERN Document Server

    Cook, D B

    1974-01-01

    Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge

  7. Diode laser surgery. Ab interno and ab externo versus conventional surgery in rabbits.

    Science.gov (United States)

    Karp, C L; Higginbotham, E J; Edward, D P; Musch, D C

    1993-10-01

    Fibroblastic proliferation of subconjunctival tissues remains a primary mechanism of failure in filtration surgery. Minimizing the surgical manipulation of episcleral tissues may reduce scarring. Laser sclerostomy surgery involves minimal tissue dissection, and is gaining attention as a method of potentially improving filter duration in high-risk cases. Twenty-five New Zealand rabbits underwent filtration surgery in one eye, and the fellow eye remained as the unoperated control. Ten rabbits underwent ab externo diode laser sclerostomy surgery, ten underwent ab interno diode sclerostomy surgery, and five had posterior sclerostomy procedures. Filtration failure was defined as a less-than-4-mmHg intraocular pressure (IOP) difference between the operative and control eyes. The mean time to failure for the ab externo, ab interno, and conventional posterior sclerostomy techniques measured 17.4 +/- 11.5, 13.1 +/- 6.7, and 6.0 +/- 3.1 days, respectively. In a comparison of the laser-treated groups with the conventional procedure, the time to failure was significantly longer (P = 0.02) for the ab externo filter. The mean ab interno sclerostomy duration was longer than the posterior lip procedure, but this difference was not statistically significant (P = 0.15). The overall level of IOP reduction was similar in the three groups. These data suggest that diode laser sclerostomy is a feasible technique in rabbits, and the ab externo approach resulted in longer filter duration than the conventional posterior lip procedure in this model.

  8. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  9. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  10. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  11. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  12. Thiourea, a ROS scavenger, regulates source-to-sink relationship to enhance crop yield and oil content in Brassica juncea (L..

    Directory of Open Access Journals (Sweden)

    Manish Pandey

    Full Text Available In the present agricultural scenario, the major thrust is to increase crop productivity so as to ensure sustainability. In an earlier study, foliar application of thiourea (TU; a non physiological thiol based ROS scavenger has been demonstrated to enhance the stress tolerance and yield of different crops under field condition. Towards this endeavor, present work deals with the effect of TU on photosynthetic efficiency and source-to-sink relationship of Indian mustard (Brassica juncea for understanding its mode of action. The application of TU increased the efficiency of both PSI and PSII photosystems and vegetative growth of plant. The comparative analysis of sucrose to starch ratio and expression level of sugar transporters confirmed the higher source and sink strength in response to TU treatment. The biochemical evidence in support of this was derived from higher activities of sucrose phosphate synthase and fructose-1,6-bis-phosphatase at source; and sucrose synthase and different classes of invertases at both source and sink. This indicated an overall increase in photoassimilate level at sink. An additional contribution through pod photosynthesis was confirmed through the analysis of phosphoenol pyruvate carboxylase enzyme activity and level of organic acids. The increased photoassimilate level was also co-ordinated with acetyl coA carboxylase mediated oil biosynthesis. All these changes were ultimately reflected in the form of 10 and 20% increase in total yield and oil content, respectively under TU treatment as compared to control. Additionally, no change was observed in oil composition of seeds derived from TU treated plants. The study thus signifies the co-ordinated regulation of key steps of photosynthesis and source-to-sink relationship through the external application of TU resulting in increased crop yield and oil content.

  13. An evaluation of the effects of exogenous ethephon, an ethylene releasing compound, on photosynthesis of mustard (Brassica juncea cultivars that differ in photosynthetic capacity

    Directory of Open Access Journals (Sweden)

    Khan NA

    2004-12-01

    Full Text Available Abstract Background The stimulatory effect of CO2 on ethylene evolution in plants is known, but the extent to which ethylene controls photosynthesis is not clear. Studies on the effects of ethylene on CO2 metabolism have shown conflicting results. Increase or inhibition of photosynthesis by ethylene has been reported. To understand the physiological processes responsible for ethylene-mediated changes in photosynthesis, stomatal and mesophyll effects on photosynthesis and ethylene biosynthesis in response to ethephon treatment in mustard (Brassica juncea cultivars differing in photosynthetic capacity were studied. Results The effects of ethephon on photosynthetic rate (PN, stomatal conductance (gS, carbonic anhydrase (CA activity, 1-aminocyclopropane carboxylic acid synthase (ACS activity and ethylene evolution were similar in both the cultivars. Increasing ethephon concentration up to 1.5 mM increased PN, gS and CA maximally, whereas 3.0 mM ethephon proved inhibitory. ACS activity and ethylene evolution increased with increasing concentrations of ethephon. The corresponding changes in gs and CA activity suggest that the changes in photosynthesis in response to ethephon were triggered by altered stomatal and mesophyll processes. Stomatal conductance changed in parallel with changes in mesophyll photosynthetic properties. In both the cultivars ACS activity and ethylene increased up to 3.0 mM ethephon, but 1.5 mM ethephon caused maximum effects on photosynthetic parameters. Conclusion These results suggest that ethephon affects foliar gas exchange responses. The changes in photosynthesis in response to ethephon were due to stomatal and mesophyll effects. The changes in gS were a response maintaining stable intercellular CO2 concentration (Ci under the given treatment in both the cultivars. Also, the high photosynthetic capacity cultivar, Varuna responded less to ethephon than the low photosynthetic capacity cultivar, RH30. The photosynthetic

  14. Effect of earthworms on growth, photosynthetic efficiency and metal uptake in Brassica juncea L. plants grown in cadmium-polluted soils.

    Science.gov (United States)

    Kaur, Parminder; Bali, Shagun; Sharma, Anket; Vig, Adarsh Pal; Bhardwaj, Renu

    2017-05-01

    The present study has been carried out to examine the role of earthworms in phytoremediation of Cd and its effect on growth, pigment content, expression of genes coding key enzymes of pigments, photosynthetic efficiency and osmoprotectants in Brassica juncea L. plants grown under cadmium (Cd) metal stress. The effect of different Cd concentrations (0.50, 0.75, 1.0, 1.25 mM) was studied in 30 and 60-day-old plants grown in soils containing earthworms. It was observed that earthworm inoculation showed stimulatory effect on phytoremediation capacity and Cd uptake has increased by 49% (in 30-day-old plants) and 35% (in 60-day-old plants) in shoots and 13.3% (in 30-day-old plants) and 10% (in 60-day-old plants) in roots in 30 and 60-day-old plants in Cd (1.25 mM) treatments. Plant growth parameters such as root and shoot length, relative water content and tolerance index were found to increase in the presence of earthworms. Recovery in photosynthetic pigments (chlorophyll and carotenoid) and gas exchange parameters, i.e. net photosynthetic rate (P n ), stomatal conductance (G s ), intercellular CO 2 concentration (C i ) and transpiration rate (E t ), was observed after earthworm's supplementation. Modulation in expression of key enzymes for pigment synthesis, i.e. chlorophyllase, phytoene synthase, chalcone synthase and phenylalanine ammonia lyase, was also observed. The results of our study revealed that earthworms help to mitigate the toxic effects produced by Cd on plant growth and photosynthetic efficiency along with enhanced phytoremediation capacity when co-inoculated with Cd in soil.

  15. Training in AB Department 2004/2005

    CERN Document Server

    Schinzel, Josi; CERN. Geneva. AB Department

    2006-01-01

    This note provides an overview of the training attended by members of the AB Department during the years 2004 and 2005, giving a break-down of the different courses and costs as well as training directions. It describes the organisation of training in the department, and evolution in training directions and planning.

  16. Ab Initio molecular dynamics with excited electrons

    NARCIS (Netherlands)

    Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

    1994-01-01

    A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

  17. An ab initio and TD DFT

    Indian Academy of Sciences (India)

    The photophysical behaviour of N-(2-hydroxy benzylidene) aniline or most commonly known as salicylideneaniline (SA) has been investigated using the ab initio and DFT levels of theory. The quantum chemical calculations show that the optimized non planar enol (1) form of the SA molecule is the most stable conformer ...

  18. Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

    Energy Technology Data Exchange (ETDEWEB)

    McMurdie, Paul J.; Behrens, Sebastien F.; Muller, Jochen A.; Goke, Jonathan; Ritalahti, Kirsti M.; Wagner, Ryan; Goltsman, Eugene; Lapidus, Alla; Holmes, Susan; Loffler, Frank E.; Spormann, Alfred M.

    2009-06-30

    Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms. A comparative analysis that included two previously sequenced Dehalococcoides genomes revealed a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs contain the majority of GEIs and strain-specific genes identified in the four Dehalococcoides genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that putatively encode terminal reductases in organohalide respiration. Only three core rdhA orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core rdhAB, contrasted with the high rdhAB numbers per genome (up to 36 in strain VS), as well as their colocalization with GEIs and other signatures for horizontal transfer, suggests that niche adaptation via organohalide respiration is a fundamental ecological strategy in Dehalococccoides. This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism.

  19. A novel Pseudomonas aeruginosa bacteriophage, Ab31, a chimera formed from temperate phage PAJU2 and P. putida lytic phage AF: characteristics and mechanism of bacterial resistance.

    Directory of Open Access Journals (Sweden)

    Libera Latino

    Full Text Available A novel temperate bacteriophage of Pseudomonas aeruginosa, phage vB_PaeP_Tr60_Ab31 (alias Ab31 is described. Its genome is composed of structural genes related to those of lytic P. putida phage AF, and regulatory genes similar to those of temperate phage PAJU2. The virion structure resembles that of phage AF and other lytic Podoviridae (S. enterica Epsilon 15 and E. coli phiv10 with similar tail spikes. Ab31 was able to infect P. aeruginosa strain PA14 and two genetically related strains called Tr60 and Tr162, out of 35 diverse strains from cystic fibrosis patients. Analysis of resistant host variants revealed different phenotypes, including induction of pigment and alginate overproduction. Whole genome sequencing of resistant variants highlighted the existence of a large deletion of 234 kbp in two strains, encompassing a cluster of genes required for the production of CupA fimbriae. Stable lysogens formed by Ab31 in strain Tr60, permitted the identification of the insertion site. During colonization of the lung in cystic fibrosis patients, P. aeruginosa adapts by modifying its genome. We suggest that bacteriophages such as Ab31 may play an important role in this adaptation by selecting for bacterial characteristics that favor persistence of bacteria in the lung.

  20. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  1. Genetics Home Reference: GM2-gangliosidosis, AB variant

    Science.gov (United States)

    ... Resources Genetic Testing (1 link) Genetic Testing Registry: Tay-Sachs disease, variant AB General Information from MedlinePlus (5 links) ... AB variant Activator Deficiency/GM2 Gangliosidosis Activator-deficient Tay-Sachs disease GM2 Activator Deficiency Disease GM2 gangliosidosis, type AB ...

  2. Towards hydrogen metallization: an Ab initio approach

    International Nuclear Information System (INIS)

    Bernard, St.

    1998-01-01

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H 2 ) 2 which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author)

  3. Ab interno trabeculectomy: patient selection and perspectives

    Science.gov (United States)

    Vinod, Kateki; Gedde, Steven J

    2016-01-01

    Ab interno trabeculectomy is one among several recently introduced minimally invasive glaucoma surgeries that avoid a conjunctival incision and full-thickness sclerostomy involved in traditional glaucoma surgery. Ablation of the trabecular meshwork and inner wall of Schlemm’s canal is performed in an arcuate fashion via a clear corneal incision, alone or in combination with phacoemulsification cataract surgery. Intraocular pressure reduction following ab interno trabeculectomy is limited by resistance in distal outflow pathways and generally stabilizes in the mid-to-high teens. Relief of medication burden has been demonstrated by some studies. A very low rate of complications, most commonly transient hyphema and intraocular pressure elevations in the immediate postoperative period, have been reported. However, available data are derived from small retrospective and prospective case series. Randomized, controlled trials are needed to better elucidate the potential merits of ab interno trabeculectomy in the combined setting versus phacoemulsification cataract surgery alone and to compare it with other minimally invasive glaucoma surgeries. PMID:27574396

  4. Genetic Diversity Studies Based on Morphological Variability, Pathogenicity and Molecular Phylogeny of the Sclerotinia sclerotiorum Population From Indian Mustard (Brassica juncea

    Directory of Open Access Journals (Sweden)

    Pankaj Sharma

    2018-06-01

    Full Text Available White mold or stem rot disease are ubiquitously distributed throughout the world and the causal organism of this disease Sclerotinia sclerotiorum (Lib. de Bary, is known to infect over 400 plant species. Sclerotinia stem rot is one of the most devastating fungal diseases and poses a serious threat to the worldwide cultivation of oilseed Brassica including India. S. sclerotiorum pathogen usually infects the stem but in severe cases leaves and pods also affected at different developmental stages that deteriorate not only the oil quality but also causing the seed and oil yield losses up to 90% depending on the severity of the disease infestation. This study investigated the morphological and molecular characterization of pathogenic S. sclerotiorum (Lib de Bary geographical isolates from oilseed Brassica including Brassica juncea (Indian mustard. The aim of this study was to compare isolates of S. sclerotiorum originated from different agro-climatic conditions and to analyse similarity or differences between them as well as to examine the virulence of this pathogen specifically in Brassica for the first time. The collection of S. sclerotiorum isolates from symptomatic Brassica plants was done and analyzed for morphological features, and molecular characterization. The virulence evaluation test of 65 isolates on four Brassica cultivars has shown 5 of them were highly virulent, 46 were virulent and 14 were moderately virulent. Phylogenetic analysis encompassing all the morphological features, SSR polymorphism, and ITS sequencing has shown the existence of high genetic diversity among the isolates that categorized all the isolates in three evolutionary lineages in the derived dendrogram. Further, genetic variability analysis based on sequences variation in ITS region of all the isolates has shown the existence of either insertions or deletions of the nucleotides in the ITS region has led to the interspecies variability and observed the variation were

  5. Brassica juncea nitric oxide synthase like activity is stimulated by PKC activators and calcium suggesting modulation by PKC-like kinase.

    Science.gov (United States)

    Talwar, Pooja Saigal; Gupta, Ravi; Maurya, Arun Kumar; Deswal, Renu

    2012-11-01

    Nitric oxide (NO) is an important signaling molecule having varied physiological and regulatory roles in biological systems. The fact that nitric oxide synthase (NOS) is responsible for NO generation in animals, prompted major search for a similar enzyme in plants. Arginine dependent NOS like activity (BjNOSla) was detected in Brassica juncea seedlings using oxyhemoglobin and citrulline assays. BjNOSla showed 25% activation by NADPH (0.4 mM) and 40% by calcium (0.4 mM) but the activity was flavin mononucleotide (FMN), flavin dinucleotide (FAD) and calmodulin (CaM) independent. Pharmacological approach using mammalian NOS inhibitors, NBT (300 μM) and l-NAME (5 mM), showed significant inhibition (100% and 67% respectively) supporting that the BjNOSla operates via the oxidative pathway. Most of the BjNOSla activity (80%) was confined to shoot while root showed only 20% activity. Localization studies by NADPH-diaphorase and DAF-2DA staining showed the presence of BjNOSla in guard cells. Kinetic analysis showed positive cooperativity with calcium as reflected by a decreased K(m) (∼13%) and almost two fold increase in V(max). PMA (438 nM), a kinase activator, activated BjNOSla ∼1.9 fold while its inactive analog 4αPDD was ineffective. Calcium and PMA activated the enzyme to ∼3 folds. Interestingly, 1,2-DG6 (2.5 μM) and PS (1 μM) with calcium activated the enzyme activity to ∼7 fold. A significant inhibition of BjNOSla by PKC inhibitors-staurosporine (∼90%) and calphostin-C (∼40%), further supports involvement of PKC-like kinase. The activity was also enhanced by abiotic stress conditions (7-46%). All these findings suggest that BjNOSla generates NO via oxidative pathway and is probably regulated by phosphorylation. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  6. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  7. Ab initio study of isomerism in molecular ions Li2AB+ with 10 valence electrons

    International Nuclear Information System (INIS)

    Charkin, O.P.; Mak-Ki, M.L.; Shlojer, P.R.

    1997-01-01

    Ab initio calculations of surfaces of Li 2 AB + molecular ion potential energy with biatomic anions AB - with 10 valence electrons have been made in the framework of approximations MP2/6-31G 1 /HF/6-31G*+ZPE(HF/6-31G*) and MP4SDTQ/631G*//MP2/6-31G*+ZPE(MP2/6-31G*). Influence of electron correlation on the accuracy of calculations of their structural and vibrational characteristics is studied. The following most favourable structures have been found: linear for Li 2 BO + , Li 2 CN + , and bent one for Li 2 BS + , with cations coordinated at different anion atoms; onium one for AlOLi 2 + , AlSLi 2 + , SiNLi 2 + and SiPLi 2 + with both cations at electronegative atom of anion

  8. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  9. Undoing Gender Through Legislation and Schooling: the Case of AB 537 and AB 394 IN California, USA

    Science.gov (United States)

    Knotts, Greg

    2009-11-01

    This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools have an unconscious acceptance of heteronormativity and gendered norms, which undermines both the spirit and language of these laws. This paper examines how California schools can both change standard practices and realise the transformative social change that laws like AB 537 and AB 394 can instigate. I assert that the systemic implementation of these laws, through the adoption, enforcement and evaluation of existing AB 537 Task Force Recommendations, is necessary for their success. My second assertion is that AB 537 and AB 394 have the potential to change and reconstitute gender-based and heteronormative standards at school sites.

  10. Simulation and Robust Contol of Antilock Braking System ABS

    Directory of Open Access Journals (Sweden)

    David Jordan DELICHRISTOV

    2009-06-01

    Full Text Available This paper deals with simulation and robust control of Antilock Braking System ABS. The briefly are described the main parts of ABS hydraulic system and control algorithm of ABS. Hydraulic system described here is BOSCH ABS 5.x series. The goal of ABS system is vehicle stability and vehicle steering response when braking. If during the braking occurred slip at one or more wheels from any reason, ABS evaluates this by “brake slip” controller. At this moment ABS is trying to use maximal limits of adhesion between tire and road. It means that is necessary control the differences between braking torque and friction torque , which reacts to the wheel via friction reaction tire-road surface. This is realized through the solenoid valves, which are controls (triggered by on the base of PID controller described further in chapter 4. Presented concept is more or less standard for most of the existing ABS systems. The issue should be applied concept of robust ABS control algorithm, which is specific for every type of ABS.

  11. Contribution of EmrAB efflux pumps to colistin resistance in Acinetobacter baumannii.

    Science.gov (United States)

    Lin, Ming-Feng; Lin, Yun-You; Lan, Chung-Yu

    2017-02-01

    Efflux pumps play an important role in antimicrobial resistance for Acinetobacter baumannii. However, the function of the Emr pump system and the relationship between Emr and drug resistance has not been characterized in A. baumannii. In this study, four possible groups of emr-like genes were found by searching a genome database. Among them, A1S_1772 (emrB) and A1S_1773 (emrA) were demonstrated to be co-transcribed as a single operon. Moreover, during osmotic stress, A1S_1772 showed the largest change in gene expression compared to the other emrB-like genes, and deletion of A1S_1772 (AB ΔemrB) significantly slowed cell growth in 20% sucrose. Using a phenotypic microarray analysis, the AB ΔemrB mutant was more susceptible to colistin and nafcillin, paromomycin, spiramycin, and D,L-serine hydroxmate than the wild type. The spot assay, time kill assay and minimal inhibition concentration determination also indicated that the wild type could tolerate colistin better than the AB ΔemrB mutant. Finally, the increased expression levels of all emrB-like genes, including A1S_0775, A1S_0909, A1S_1772, and A1S_1799, in colistin resistance-induced A. baumannii further supported the possible involvement of the emrB genes in A. baumannii colistin resistance. Together, the Emr pump systems in A. baumannii contribute to adaptation to osmotic stress and resistance to colistin.

  12. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  13. Effect of unlabelled monoclonal antibody (MoAb) on biodistribution of /sup 111/Indium labelled (MoAb)

    Energy Technology Data Exchange (ETDEWEB)

    Lamki, L M; Murray, J L; Rosenblum, M G; Patt, Y Z; Babaian, Richard; Unger, M W

    1988-08-01

    We have evaluated immunoscintigraphy in cancer patients using four /sup 111/In-labelled murine monoclonal antibodies (MoAb): 96.5 (anti-P97 of melanoma), ZME-018 (anti-high molecular weight antibody of melanoma), ZCE-025 (anti-CEA for colon cancer) and PAY-276 (anti-prostatic acid phosphatase for prostatic cancer). The effect of increasing the doses of unlabelled MoAb (co-infused with 1 mg labelled MoAb) on the relative body distribution of each labelled MoAb was assessed. Localization in the liver decreased significantly in all cases, with increasing MoAb dose, except for ZME-018. Localization in other organs increased significantly as the liver activity decreased. The spleen activity, however, fell in the case of MoAb ZME-018. Blood-pool activity increased with MoAb dose in all four MoAbs. These findings correlated with the rise in the detection rate of metastases, the plasma half-life, and other pharmacokinetic parameters. However, the dose level at which this correlation occurred varied with each antibody. These data demonstrate the co-infusion of unlabelled MoAb with /sup 111/In-labelled MoAb could alter the organ distribution, pharmacokinetics and tumour uptake in a favourable manner, though the degree to which this occurs depends on the antibody in question.

  14. Biosorption of Acid Blue 290 (AB 290) and Acid Blue 324 (AB 324) dyes on Spirogyra rhizopus

    International Nuclear Information System (INIS)

    Ozer, Ayla; Akkaya, Goenuel; Turabik, Meral

    2006-01-01

    In this study, the biosorption of Acid Blue 290 and Acid Blue 324 on Spirogyra rhizopus, a green algae growing on fresh water, was studied with respect to initial pH, temperature, initial dye concentration and biosorbent concentration. The optimum initial pH and temperature values for AB 290 and AB 324 biosorption were found to be 2.0, 30 deg. C and 3.0, 25 deg. C, respectively. It was observed that the adsorbed AB 290 and AB 324 amounts increased with increasing the initial dye concentration up to 1500 and 750 mg/L, respectively. The Langmuir, Freundlich, Redlich-Peterson and Koble-Corrigan isotherm models were applied to the experimental equilibrium data and the isotherm constants were determined by using Polymath 4.1 software. The monolayer coverage capacities of S. rhizopus for AB 290 and AB 324 dyes were found as 1356.6 mg/g and 367.0 mg/g, respectively. The intraparticle diffusion model and the pseudo-second order kinetic model were applied to the experimental data in order to describe the removal mechanism of these acidic dyes by S. rhizopus. The pseudo-second order kinetic model described very well the biosorption kinetics of AB 290 and AB 324 dyes. Thermodynamic studies showed that the biosorption of AB 290 and AB 324 on S. rhizopus was exothermic in nature

  15. Popular Herbig AE star AB Aur

    International Nuclear Information System (INIS)

    Shevchenko, V.S.

    1987-01-01

    The variability of AB Aur emission line H α , H β , H γ profiles, equivalent widths (EW λ ) and relative intensity have been observed on the photoelectric scanner. During the 20 d observation period EW λ H α ranged from 23.20 to 35.35 A. Mean EW λ H α is 27.25 A, daily average deviation is 3.60 ± 0.07 A. The minimum time of variability is 1 h . The chromospheric lines near-infrared triplet Ca II and KCaII and emission lines H β -H13, P12-P20, 0I 8446.5 A and the variability of other lines have been studied on the photographic and image-tube spectra. The intensity of these lines and EW λ changed 2-4 times during an interval from 1 h to several years. The AB Aur variability nature of emission lines made it possible to assume that the ''deep chromosphere'' is not a centre-symmetrical or axisymmetrical formation but is a conglomerate of different density and speed gas condensations

  16. Ab initio lattice dynamics of metal surfaces

    International Nuclear Information System (INIS)

    Heid, R.; Bohnen, K.-P.

    2003-01-01

    Dynamical properties of atoms on surfaces depend sensitively on their bonding environment and thus provide valuable insight into the local geometry and chemical binding at the boundary of a solid. Density-functional theory provides a unified approach to the calculation of structural and dynamical properties from first principles. Its high accuracy and predictive power for lattice dynamical properties of semiconductor surfaces has been demonstrated in a previous article by Fritsch and Schroeder (Phys. Rep. 309 (1999) 209). In this report, we review the state-of-the-art of these ab initio approaches to surface dynamical properties of metal surfaces. We give a brief introduction to the conceptual framework with focus on recent advances in computational procedures for the ab initio linear-response approach, which have been a prerequisite for an efficient treatment of surface dynamics of noble and transition metals. The discussed applications to clean and adsorbate-covered surfaces demonstrate the high accuracy and reliability of this approach in predicting detailed microscopic properties of the phonon dynamics for a wide range of metallic surfaces

  17. Focused Wind Mass Accretion in Mira AB

    Science.gov (United States)

    Karovska, Margarita; de Val-Borro, M.; Hack, W.; Raymond, J.; Sasselov, D.; Lee, N. P.

    2011-05-01

    At a distance of about only 100pc, Mira AB is the nearest symbiotic system containing an Asymptotic Giant Branch (AGB) star (Mira A), and a compact accreting companion (Mira B) at about 0.5" from Mira A. Symbiotic systems are interacting binaries with a key evolutionary importance as potential progenitors of a fraction of asymmetric Planetary Nebulae, and SN type Ia, cosmological distance indicators. The region of interaction has been studied using high-angular resolution, multiwavelength observations ranging from radio to X-ray wavelengths. Our results, including high-angular resolution Chandra imaging, show a "bridge" between Mira A and Mira B, indicating gravitational focusing of the Mira A wind, whereby components exchange matter directly in addition to the wind accretion. We carried out a study using 2-D hydrodynamical models of focused wind mass accretion to determine the region of wind acceleration and the characteristics of the accretion in Mira AB. We highlight some of our results and discuss the impact on our understanding of accretion processes in symbiotic systems and other detached and semidetached interacting systems.

  18. Quantum phases of AB2 fermionic chains

    International Nuclear Information System (INIS)

    Murcia-Correa, L S; Franco, R; Silva-Valencia, J

    2016-01-01

    A fermionic chain is a one-dimensional system with fermions that interact locally and can jump between sites in the lattice, in particular an AB n chain type, where A and B are sites that exhibit a difference in energy level of Δ and site B is repeated n-times, such that the unit cell has n +1 sites. A limit case of this model, called the ionic Hubbard model (n = 1), has been widely studied due to its interesting physics and applications. In this paper, we study the ground state of an AB 2 chain, which describes the material R 4 [Pt 2 (P 2 O 5 H 2 ) 4 X] · nH 2 O. Specifically, we consider a filling with two electrons per unit cell, and using the density matrix renormalization group method we found that the system exhibits the band insulator and Mott correlated insulator phases, as well as an intermediate phase between them. For couplings of Δ = 2,10 and 20, we estimate the critical points that separate these phases through the structure factor and the energy gap in the sector of charge and spin, finding that the position of the critical point rises as a function of Δ. (paper)

  19. Workshop on automated beam steering and shaping (ABS). Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Lindroos, M [ed.

    1999-09-10

    A workshop on Automated Beam Steering and Shaping (ABS) was held at CERN in December 1998. This was the first workshop dedicated to this subject. The workshop had two major goals: to review the present status of ABS algorithms and systems around the world and to create a worldwide ABS community. These proceedings contain summary reports from all sessions, contributions from several presentations held at the workshop, and a complete set of abstracts for all presentations. (orig.)

  20. Workshop on automated beam steering and shaping (ABS). Proceedings

    International Nuclear Information System (INIS)

    Lindroos, M.

    1999-01-01

    A workshop on Automated Beam Steering and Shaping (ABS) was held at CERN in December 1998. This was the first workshop dedicated to this subject. The workshop had two major goals: to review the present status of ABS algorithms and systems around the world and to create a worldwide ABS community. These proceedings contain summary reports from all sessions, contributions from several presentations held at the workshop, and a complete set of abstracts for all presentations. (orig.)

  1. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  2. Cross-family translational genomics of abiotic stress-responsive genes between Arabidopsis and Medicago truncatula.

    Directory of Open Access Journals (Sweden)

    Daejin Hyung

    Full Text Available Cross-species translation of genomic information may play a pivotal role in applying biological knowledge gained from relatively simple model system to other less studied, but related, genomes. The information of abiotic stress (ABS-responsive genes in Arabidopsis was identified and translated into the legume model system, Medicago truncatula. Various data resources, such as TAIR/AtGI DB, expression profiles and literatures, were used to build a genome-wide list of ABS genes. tBlastX/BlastP similarity search tools and manual inspection of alignments were used to identify orthologous genes between the two genomes. A total of 1,377 genes were finally collected and classified into 18 functional criteria of gene ontology (GO. The data analysis according to the expression cues showed that there was substantial level of interaction among three major types (i.e., drought, salinity and cold stress of abiotic stresses. In an attempt to translate the ABS genes between these two species, genomic locations for each gene were mapped using an in-house-developed comparative analysis platform. The comparative analysis revealed that fragmental colinearity, represented by only 37 synteny blocks, existed between Arabidopsis and M. truncatula. Based on the combination of E-value and alignment remarks, estimated translation rate was 60.2% for this cross-family translation. As a prelude of the functional comparative genomic approaches, in-silico gene network/interactome analyses were conducted to predict key components in the ABS responses, and one of the sub-networks was integrated with corresponding comparative map. The results demonstrated that core members of the sub-network were well aligned with previously reported ABS regulatory networks. Taken together, the results indicate that network-based integrative approaches of comparative and functional genomics are important to interpret and translate genomic information for complex traits such as abiotic stresses.

  3. Identification of Clusters that Condition Resistance to Anthracnose in the Common Bean Differential Cultivars AB136 and MDRK.

    Science.gov (United States)

    Campa, Ana; Trabanco, Noemí; Ferreira, Juan José

    2017-12-01

    The correct identification of the anthracnose resistance systems present in the common bean cultivars AB136 and MDRK is important because both are included in the set of 12 differential cultivars proposed for use in classifying the races of the anthracnose causal agent, Colletrotrichum lindemuthianum. In this work, the responses against seven C. lindemuthianum races were analyzed in a recombinant inbred line population derived from the cross AB136 × MDRK. A genetic linkage map of 100 molecular markers distributed across the 11 bean chromosomes was developed in this population to locate the gene or genes conferring resistance against each race, based on linkage analyses and χ 2 tests of independence. The identified anthracnose resistance genes were organized in clusters. Two clusters were found in AB136: one located on linkage group Pv07, which corresponds to the anthracnose resistance cluster Co-5, and the other located at the end of linkage group Pv11, which corresponds to the Co-2 cluster. The presence of resistance genes at the Co-5 cluster in AB136 was validated through an allelism test conducted in the F 2 population TU × AB136. The presence of resistance genes at the Co-2 cluster in AB136 was validated through genetic dissection using the F 2:3 population ABM3 × MDRK, in which it was directly mapped to a genomic position between 46.01 and 47.77 Mb of chromosome Pv11. In MDRK, two independent clusters were identified: one located on linkage group Pv01, corresponding to the Co-1 cluster, and the second located on LG Pv04, corresponding to the Co-3 cluster. This report enhances the understanding of the race-specific Phaseolus vulgaris-C. lindemuthianum interactions and will be useful in breeding programs.

  4. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  5. The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30

    DEFF Research Database (Denmark)

    Kruse, Thomas; Biedenkopf, Nadine; Hertz, Emil Peter Thrane

    2018-01-01

    Transcription of the Ebola virus genome depends on the viral transcription factor VP30 in its unphosphorylated form, but the underlying molecular mechanism of VP30 dephosphorylation is unknown. Here we show that the Ebola virus nucleoprotein (NP) recruits the host PP2A-B56 protein phosphatase......A-B56 and show that it suppresses Ebola virus transcription and infection. This work dissects the molecular mechanism of VP30 dephosphorylation by PP2A-B56, and it pinpoints this phosphatase as a potential target for therapeutic intervention....

  6. [A STUDY OF THE ISOLATED BACTERIOPHAGE ΦAB-SP7 ADSORPTION ON THE CELL SURFACE OF THE AZOSPIRILLUM BRASILENSE SP7].

    Science.gov (United States)

    Guliy, O I; Karavaeva, O A; Velikov, V A; Sokolov, O I; Pavily, S A; Larionova, O S; Burov, A M; Ignatov, O V

    2016-01-01

    The bacteriophage ΦAb-Sp7 was isolated from the cells of the Azospirillum brasilense Sp7. The morphology, size of the gram-negative colonies, and range of lytic activity against other strains and species of the genus Azospirillum was tested. The isolated phage DNA was examined using electrophoretic and restriction analysis, and the size of the genome were established. The electron microscopy. resuIts show that the phage (capsid) has a strand-like form. The electron microscopy study of the bacteriophage ΦAb-Sp7 adsorption on the A. brasilense Sp7 bacterial surface was performed.

  7. Ab initio electronic stopping power in materials

    International Nuclear Information System (INIS)

    Shukri, Abdullah-Atef

    2015-01-01

    The average energy loss of an ion per unit path length when it is moving through the matter is named the stopping power. The knowledge of the stopping power is essential for a variety of contemporary applications which depend on the transport of ions in matter, especially ion beam analysis techniques and ion implantation. Most noticeably, the use of proton or heavier ion beams in radiotherapy requires the knowledge of the stopping power. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. The linear response dielectric formalism has been widely used in the past to study the electronic stopping power. In particular, the famous pioneering calculations due to Lindhard evaluate the electronic stopping power of a free electron gas. In this thesis, we develop a fully ab initio scheme based on linear response time-dependent density functional theory to predict the impact parameter averaged quantity named the random electronic stopping power (RESP) of materials without any empirical fitting. The purpose is to be capable of predicting the outcome of experiments without any knowledge of target material besides its crystallographic structure. Our developments have been done within the open source ab initio code named ABINIT, where two approximations are now available: the Random-Phase Approximation (RPA) and the Adiabatic Local Density Approximation (ALDA). Furthermore, a new method named 'extrapolation scheme' have been introduced to overcome the stringent convergence issues we have encountered. These convergence issues have prevented the previous studies in literature from offering a direct comparison to experiment. First of all, we demonstrate the importance of describing the realistic ab initio electronic structure by comparing with the historical Lindhard stopping power evaluation. Whereas the Lindhard stopping power provides a first order description that captures the general features of the

  8. Singularities of Type-Q ABS Equations

    Directory of Open Access Journals (Sweden)

    James Atkinson

    2011-07-01

    Full Text Available The type-Q equations lie on the top level of the hierarchy introduced by Adler, Bobenko and Suris (ABS in their classification of discrete counterparts of KdV-type integrable partial differential equations. We ask what singularities are possible in the solutions of these equations, and examine the relationship between the singularities and the principal integrability feature of multidimensional consistency. These questions are considered in the global setting and therefore extend previous considerations of singularities which have been local. What emerges are some simple geometric criteria that determine the allowed singularities, and the interesting discovery that generically the presence of singularities leads to a breakdown in the global consistency of such systems despite their local consistency property. This failure to be globally consistent is quantified by introducing a natural notion of monodromy for isolated singularities.

  9. ABS, MBS and CDO compared : An empirical analysis

    NARCIS (Netherlands)

    Vink, D.; Thibeault, A.

    2008-01-01

    The capital market in which the asset-backed securities are issued and traded is composed of three main categories: ABS, MBS and CDOs. We were able to examine a total number of 3,951 loans (worth €730.25 billion) of which 1,129 (worth €208.94 billion) have been classified as ABS. MBS issues

  10. ABS, MBS and CDO pricing comparisons : An empirical analysis

    NARCIS (Netherlands)

    Vink, D.; Thibeault, A.

    2008-01-01

    The capital market in which asset-backed securities are issued and traded is composed of three main categories: ABS, MBS and CDOs. The authors examined a total of 3,466 loans (worth €548.51 billion) of which 1,102 (worth €163.90 billion) have been classified as ABS. MBS issues represent 1,782 issues

  11. Polyvalent horse F(Ab`) 2 snake antivenom: Development of ...

    African Journals Online (AJOL)

    F(ab´)2 fragments were further purified by Q-Fast Flow chromatography, concentrated by molecular ultrafiltration and sterilized by filtration through 0.22 m membranes. The resulting F(ab´)2 preparations were rich in intact L and in pieces of H IgG(T) chains, as demonstrated by electrophoresis and Western blot and exhibited ...

  12. 12 CFR Appendixes A-B to Part 41 - [Reserved

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 1 2010-01-01 2010-01-01 false [Reserved] A Appendixes A-B to Part 41 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY FAIR CREDIT REPORTING Appendixes A-B to Part 41 [Reserved] ...

  13. Report on enrichment work at AB Atomenergi, 1965-1978

    International Nuclear Information System (INIS)

    Maartensson, M.

    1978-11-01

    A review of the Rand D performed at AB Atomenergi (now Studsvik Energiteknik AB) in the field of enrichment during the period 1965-1978. The report also describes the international development, and discusses the possibilities for continued Swedish efforts in this area. (L.E.)

  14. A Case of Laptop Computer-Induced Erythema Ab Igne

    Directory of Open Access Journals (Sweden)

    Nurettin Özgür Doğan

    2014-12-01

    Full Text Available Erythema ab igne, also known as toasted skin syndrome, is a skin reaction characterized by reticulate erythema, brown pigmentation, and telangiectasia. In some cases, epidermal atrophy and scaling are also identified. The condition is usually caused by prolonged exposure to a source of heat or infrared radiation. Here, we report a case of erythema ab igne associated with laptop computer use.

  15. CRY 1AB trangenic cowpea obtained by nodal electroporation ...

    African Journals Online (AJOL)

    Electroporation-mediated genetic transformation was used to introduce Cry 1 Ab insecticidal gene into cowpea. Nodal buds were electroporated in planta with a plasmid carrying the Cry 1Ab and antibiotic resistance npt II genes driven by a 35S CaMV promoter. T1 seeds derived from electroporated branches were selected ...

  16. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  17. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  18. Undoing Gender through Legislation and Schooling: The Case of AB 537 and AB 394 in California, USA

    Science.gov (United States)

    Knotts, Greg

    2009-01-01

    This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools…

  19. Adubação orgânica da batata com esterco e, ou, Crotalaria juncea: I - produtividade vegetal e estoque de nutrientes no solo em longo prazo Organic fertilization of potato with manure and, or, Crotalaria juncea: I - long term plant productivity and soil nutrient stocks

    Directory of Open Access Journals (Sweden)

    Tácio Oliveira da Silva

    2007-02-01

    Full Text Available No Agreste paraibano, a batata (Solanum tuberosum L. é importante cultura comercial, embora seja limitada pela variabilidade e escassez de chuvas e pela baixa fertilidade do solo. O esterco é a principal fonte de nutrientes utilizada para fertilização do solo, porém geralmente não é disponível em quantidade suficiente nas propriedades rurais para suprir a demanda das culturas agrícolas. Como alternativa tem sido recomendada a adubação verde com Crotalaria juncea L. Realizou-se um experimento, de 1996 a 2002, em um Neossolo Regolítico, com o objetivo de quantificar a produtividade da batata e o estoque de nutrientes no solo, após incorporações anuais de esterco e, ou, crotalária. Os tratamentos consistiram de: incorporação da crotalária (C, adição de 15 t ha-1 de esterco caprino (E, incorporação de crotalária + 7,5 t ha-1 de esterco (CE e testemunha (T. No final do experimento, o tratamento E promoveu aumentos de 73, 45, 221 e 43 % nos teores de N total, P total, P e K extraíveis (Mehlich-1 do solo, respectivamente, em relação à testemunha. Os tratamentos C e CE aumentaram o N total do solo em 76 e 63 %, mas não aumentaram o teor dos outros nutrientes. Os acúmulos médios de massa seca, N, P e K na parte aérea da crotalária nos tratamentos, ao longo dos cinco anos, foram de 3.550, 69, 6 e 55 kg ha-1, respectivamente. As produtividades médias de tubérculos, ao longo dos cinco anos de colheita, foram de 15.204, 12.053, 11.085 e 7.926 kg ha-1 nos tratamentos CE, C, E e T, respectivamente. Apesar de a adição de 15 t ha-1 de esterco ter proporcionado os maiores aumentos nos nutrientes do solo, as maiores produtividades de tubérculos ao longo do período do estudo foram obtidas quando se combinou o plantio e a incorporação de crotalária com a adição de 7,5 t ha-1 de esterco.Potato (Solanum tuberosum L. is an important cash crop in the semi-arid region of Paraíba, Brazil. However, potato productivity is limited

  20. SdAb heterodimer formation using leucine zippers

    Science.gov (United States)

    Goldman, Ellen R.; Anderson, George P.; Brozozog-Lee, P. Audrey; Zabetakis, Dan

    2013-05-01

    Single domain antibodies (sdAb) are variable domains cloned from camel, llama, or shark heavy chain only antibodies, and are among the smallest known naturally derived antigen binding fragments. SdAb derived from immunized llamas are able to bind antigens with high affinity, and most are capable of refolding after heat or chemical denaturation to bind antigen again. We hypothesized that the ability to produce heterodimeric sdAb would enable reagents with the robust characteristics of component sdAb, but with dramatically improved overall affinity through increased avidity. Previously we had constructed multimeric sdAb by genetically linking sdAb that bind non-overlapping epitopes on the toxin, ricin. In this work we explored a more flexible approach; the construction of multivalent binding reagents using multimerization domains. We expressed anti-ricin sdAb that recognize different epitopes on the toxin as fusions with differently charged leucine zippers. When the initially produced homodimers are mixed the leucine zipper domains will pair to produce heterodimers. We used fluorescence resonance energy transfer to confirm heterodimer formation. Surface plasmon resonance, circular dichroism, enzyme linked immunosorbent assays, and fluid array assays were used to characterize the multimer constructs, and evaluate their utility in toxin detection.

  1. Ab interno trabeculectomy in the adult patient.

    Science.gov (United States)

    SooHoo, Jeffrey R; Seibold, Leonard K; Kahook, Malik Y

    2015-01-01

    Glaucoma is a potentially blinding disease that affects millions of people worldwide. The mainstay of treatment is lowering of intraocular pressure (IOP) through the use of medications, laser and/or incisional surgery. The trabecular meshwork (TM) is thought to be the site of significant resistance to aqueous outflow in open angle glaucoma. Theoretically, an incision through TM or TM removal should decrease this resistance and lead to a significant reduction in IOP. This approach, commonly referred to as goniotomy or trabeculotomy, has been validated in the pediatric population and has been associated with long-term IOP control. In adults, however, removal of TM tissue has been historically associated with more limited and short-lived success. More recent evidence, reveals that even adult patients may benefit significantly from removal of diseased TM tissue and can lead to a significant reduction in IOP that is long-lasting and safe. In this review, we discuss current evidence and techniques for ab interno trabeculectomy using various devices in the adult patient.

  2. Phonocatalysis. An ab initio simulation experiment

    Directory of Open Access Journals (Sweden)

    Kwangnam Kim

    2016-06-01

    Full Text Available Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  3. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  5. Growth and "1"3"7Cs uptake and accumulation among 56 Japanese cultivars of Brassica rapa, Brassica juncea and Brassica napus grown in a contaminated field in Fukushima: Effect of inoculation with a Bacillus pumilus strain

    International Nuclear Information System (INIS)

    Djedidi, Salem; Kojima, Katsuhiro; Ohkama-Ohtsu, Naoko; Bellingrath-Kimura, Sonoko Dorothea; Yokoyama, Tadashi

    2016-01-01

    Fifty six local Japanese cultivars of Brassica rapa (40 cultivars), Brassica juncea (10 cultivars) and Brassica napus (6 cultivars) were assessed for variability in growth and "1"3"7Cs uptake and accumulation in association with a Bacillus pumilus strain. Field trial was conducted at a contaminated farmland in Nihonmatsu city, in Fukushima prefecture. Inoculation resulted in different responses of the cultivars in terms of growth and radiocesium uptake and accumulation. B. pumilus induced a significant increase in shoot dry weight in 12 cultivars that reached up to 40% in one B. rapa and three B. juncea cultivars. Differences in radiocesium uptake were observed between the cultivars of each Brassica species. Generally, inoculation resulted in a significant increase in "1"3"7Cs uptake in 22 cultivars, while in seven cultivars it was significantly decreased. Regardless of plant cultivar and bacterial inoculation, the transfer of "1"3"7Cs to the plant shoots (TF) varied by a factor of up to 5 and it ranged from to 0.011 to 0.054. Five inoculated cultivars, showed enhanced shoot dry weights and decreased "1"3"7Cs accumulations, among which two B. rapa cultivars named Bitamina and Nozawana had a significantly decreased "1"3"7Cs accumulation in their shoots. Such cultivars could be utilized to minimize the entry of radiocesium into the food chain; however, verifying the consistency of their radiocesium accumulation in other soils is strongly required. Moreover, the variations in growth and radiocesium accumulation, as influenced by Bacillus inoculation, could help selecting well grown inoculated Brassica cultivars with low radiocesium accumulation in their shoots. - Highlights: • Out of 56 Brassica cultivars, inoculation significantly increased shoot dry weight in 12 cultivars. • Inoculation triggered a significant increase and decrease in "1"3"7Cs uptake, respectively in 22 and 7 cultivars. • Five cultivars had an enhanced shoot dry weight and decreased "1"3"7Cs

  6. Ab initio derivation of model energy density functionals

    International Nuclear Information System (INIS)

    Dobaczewski, Jacek

    2016-01-01

    I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results. (letter)

  7. [Kidney allotransplantation from the AB0-incompatible donors].

    Science.gov (United States)

    Goriaĭnov, V A; Kaabak, M M; Babenko, N N; Shishlo, L A; Morozova, M M; Ragimov, A A; Dazhkova, N G; Salimov, E L

    2013-01-01

    The experience of 28 kidney allotransplantations from the AB0-incompatible donors was analyzed. The comparative group consisted of 38 patients, who received the AB0-compatible organ. The results were assessed using the following parameters: renal function, morphology of the biopsy samples of the transplanted kidney and actuary survival of the recipients with functioning transplants in both groups. The comparative analysis showed no significant difference between the two groups, giving the right to consider the kidney allotransplantation from the AB0-incompatible donors safe and effective.

  8. Revealing strategies of quorum sensing in Azospirillum brasilense strains Ab-V5 and Ab-V6.

    Science.gov (United States)

    Fukami, Josiane; Abrantes, Julia Laura Fernandes; Del Cerro, Pablo; Nogueira, Marco Antonio; Ollero, Francisco Javier; Megías, Manuel; Hungria, Mariangela

    2018-01-01

    Azospirillum brasilense is an important plant-growth promoting bacterium (PGPB) that requires several critical steps for root colonization, including biofilm and exopolysaccharide (EPS) synthesis and cell motility. In several bacteria these mechanisms are mediated by quorum sensing (QS) systems that regulate the expression of specific genes mediated by the autoinducers N-acyl-homoserine lactones (AHLs). We investigated QS mechanisms in strains Ab-V5 and Ab-V6 of A. brasilense, which are broadly used in commercial inoculants in Brazil. Neither of these strains carries a luxI gene, but there are several luxR solos that might perceive AHL molecules. By adding external AHLs we verified that biofilm and EPS production and cell motility (swimming and swarming) were regulated via QS in Ab-V5, but not in Ab-V6. Differences were observed not only between strains, but also in the specificity of LuxR-type receptors to AHL molecules. However, Ab-V6 was outstanding in indole acetic acid (IAA) synthesis and this molecule might mimic AHL signals. We also applied the quorum quenching (QQ) strategy, obtaining transconjugants of Ab-V5 and Ab-V6 carrying a plasmid with acyl-homoserine lactonase. When maize (Zea mays L.) was inoculated with the wild-type and transconjugant strains, plant growth was decreased with the transconjugant of Ab-V5-confirming the importance of an AHL-mediated QS system-but did not affect plant growth promotion by Ab-V6.

  9. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  10. Cloning, purification and preliminary crystallographic studies of the 2AB protein from hepatitis A virus

    International Nuclear Information System (INIS)

    Garriga, Damià; Vives-Adrián, Laia; Buxaderas, Mònica; Ferreira-da-Silva, Frederico; Almeida, Bruno; Macedo-Ribeiro, Sandra; Pereira, Pedro José Barbosa; Verdaguer, Núria

    2011-01-01

    The 2AB protein derived from the nonstructural P2 region of hepatitis A virus has been cloned, purified and crystallized. The preliminary characterization of native and selenomethionine-derivative crystals is reported. The Picornaviridae family contains a large number of human pathogens such as rhinovirus, poliovirus and hepatitis A virus (HAV). Hepatitis A is an infectious disease that causes liver inflammation. It is highly endemic in developing countries with poor sanitation, where infections often occur in children. As in other picornaviruses, the genome of HAV contains one open reading frame encoding a single polyprotein that is subsequently processed by viral proteinases to originate mature viral proteins during and after the translation process. In the polyprotein, the N-terminal P1 region generates the four capsid proteins, while the C-terminal P2 and P3 regions contain the enzymes, precursors and accessory proteins essential for polyprotein processing and virus replication. Here, the first crystals of protein 2AB of HAV are reported. The crystals belonged to space group P4 1 or P4 3 , with unit-cell parameters a = b = 90.42, c = 73.43 Å, and contained two molecules in the asymmetric unit. Native and selenomethionine-derivative crystals diffracted to 2.7 and 3.2 Å resolution, respectively

  11. Cutaneous horn and thermal keratosis in erythema AB igne

    Directory of Open Access Journals (Sweden)

    Sood Apra

    2002-01-01

    Full Text Available A 46 - year - old Kashmiri lady developed erythema ab igne on both legs. She subsequently developed multiple keratoses and a cutaneous horn in the involved skin. An uncommon association of these three clinical conditions is being presented.

  12. Energy conservation campaign at Sandvik AB in Sandviken

    Energy Technology Data Exchange (ETDEWEB)

    Larsson, Rune

    1979-07-01

    Sandvik AB's performed an analysis showing oil consumption for steam production was increasing considerably. Energy conservation measures were implemented to decrease the oil consumption and to make lasting changes.

  13. Realization of prediction of materials properties by ab initio ...

    Indian Academy of Sciences (India)

    Unknown

    alization of the results of ab initio molecular dynamics simulation on atom insertion process to C60 and to carbon nanotube ... micro-clusters to estimate absolute highest occupied mo- .... To analyse the observed properties theoretically,.

  14. Ab Initio Predictions of Structures and Densities of Energetic Solids

    National Research Council Canada - National Science Library

    Rice, Betsy M; Sorescu, Dan C

    2004-01-01

    We have applied a powerful simulation methodology known as ab initio crystal prediction to assess the ability of a generalized model of CHNO intermolecular interactions to predict accurately crystal...

  15. Ab Initio Atomistic Thermodynamics for Surfaces: A Primer

    National Research Council Canada - National Science Library

    Rogal, Jutta; Reuter, Karsten

    2006-01-01

    .... These techniques are referred to as first-principles (or in latin: ab initio) to indicate that they do not rely on empirical or fitted parameters, which then makes them applicable for a wide range of realistic conditions...

  16. AB toxins: a paradigm switch from deadly to desirable.

    Science.gov (United States)

    Odumosu, Oludare; Nicholas, Dequina; Yano, Hiroshi; Langridge, William

    2010-07-01

    To ensure their survival, a number of bacterial and plant species have evolved a common strategy to capture energy from other biological systems. Being imperfect pathogens, organisms synthesizing multi-subunit AB toxins are responsible for the mortality of millions of people and animals annually. Vaccination against these organisms and their toxins has proved rather ineffective in providing long-term protection from disease. In response to the debilitating effects of AB toxins on epithelial cells of the digestive mucosa, mechanisms underlying toxin immunomodulation of immune responses have become the focus of increasing experimentation. The results of these studies reveal that AB toxins may have a beneficial application as adjuvants for the enhancement of immune protection against infection and autoimmunity. Here, we examine similarities and differences in the structure and function of bacterial and plant AB toxins that underlie their toxicity and their exceptional properties as immunomodulators for stimulating immune responses against infectious disease and for immune suppression of organ-specific autoimmunity.

  17. Diffusion of hydrogen interstitials in Zr based AB2 and mischmetal based AB5 alloys

    International Nuclear Information System (INIS)

    Mani, N; Ravi, N; Ramaprabhu, S

    2005-01-01

    The Zr based AB 2 alloys ZrMnFe 0.5 Ni 0.5 , ZrMnFe 0.5 Co 0.5 and mischmetal (Mm) based AB 5 alloy MmNi 3.5 Al 0.5 Fe 0.5 Co 0.5 have been prepared and characterized by means of powder x-ray diffractograms. The hydrogen absorption kinetics of these alloys have been studied in the temperature and pressure ranges 450-650 0 C and 10-100 mbar respectively with a maximum H to host alloy formula unit ratio of 0.01, using a pressure reduction technique. The diffusion coefficient of the hydrogen interstitials has been determined from hydrogen absorption kinetics experiments. The dependence of the diffusion coefficient on the alloy content has been discussed. For Mm based MmNi 3.5 Al 0.5 Fe 0.5 Co 0.5 alloy, the diffusion coefficient is about an order of magnitude higher than that of the Zr based alloys

  18. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  19. A cysteine protease (cathepsin Z) from disk abalone, Haliotis discus discus: Genomic characterization and transcriptional profiling during bacterial infections.

    Science.gov (United States)

    Godahewa, G I; Perera, N C N; Lee, Sukkyoung; Kim, Myoung-Jin; Lee, Jehee

    2017-09-05

    Cathepsin Z (CTSZ) is lysosomal cysteine protease of the papain superfamily. It participates in the host immune defense via phagocytosis, signal transduction, cell-cell communication, proliferation, and migration of immune cells such as monocytes, macrophages, and dendritic cells. Hence, CTSZ is also acknowledged as an acute-phase protein in host immunity. In this study, we sought to identify the CTSZ homolog from disk abalone (AbCTSZ) and characterize it at the molecular, genomic, and transcriptional levels. AbCTSZ encodes a protein with 318 amino acids and a molecular mass of 36kDa. The structure of AbCTSZ reveals amino acid sequences that are characteristic of the signal sequence, pro-peptide, peptidase-C1 papain family cysteine protease domain, mini-loop, HIP motif, N-linked glycosylation sites, active sites, and conserved Cys residues. A pairwise comparison revealed that AbCTSZ shared the highest amino acid homology with its molluscan counterpart from Crassostrea gigas. A multiple alignment analysis revealed the conservation of functionally crucial elements of AbCTSZ, and a phylogenetic study further confirmed a proximal evolutionary relationship with its invertebrate counterparts. Further, an analysis of AbCTSZ genomic structure revealed seven exons separated by six introns, which differs from that of its vertebrate counterparts. Quantitative real time PCR (qPCR) detected the transcripts of AbCTSZ in early developmental stages and in eight different tissues. Higher levels of AbCTSZ transcripts were found in trochophore, gill, and hemocytes, highlighting its importance in the early development and immunity of disk abalone. In addition, we found that viable bacteria (Vibrio parahaemolyticus and Listeria monocytogenes) and bacterial lipopolysaccharides significantly modulated AbCTSZ transcription. Collectively, these lines of evidences suggest that AbCTSZ plays an indispensable role in the innate immunity of disk abalone. Copyright © 2017. Published by Elsevier

  20. Report on the Personnel Dosimetry at AB Atomenergi during 1965

    International Nuclear Information System (INIS)

    Edvardsson, K.A.

    1966-10-01

    This report presents the results of the personnel dosimetry at AB Atomenergi during 1965. No doses exceeding the recommendations of ICRP were reported. For AB Atomenergi the average external total body dose during the year was 60 mrem which corresponds to 89.4 manrem. 31200 gamma films and 5850 neutron films were evaluated. 2067 urine analyses and 692 measurements of body activity were made

  1. Rescue of failed filtering blebs with ab interno trephination.

    Science.gov (United States)

    Shihadeh, Wisam A; Ritch, Robert; Liebmann, Jeffrey M

    2006-06-01

    We evaluated the effectiveness of ab interno automated trephination as a technique for rescuing failed mature filtering blebs. A retrospective chart review of 40 failed blebs of 38 patients who had a posttrephination follow-up period of at least 3 months was done. With success defined as intraocular pressure (IOP) control with other modalities of management. Complications were few. We believe that ab interno trephination is an excellent option for rescuing selected failed filtering blebs.

  2. The 2-alkyl-2H-indazole regioisomers of synthetic cannabinoids AB-CHMINACA, AB-FUBINACA, AB-PINACA, and 5F-AB-PINACA are possible manufacturing impurities with cannabimimetic activities

    OpenAIRE

    Longworth, Mitchell; Banister, Samuel D.; Mack, James B. C.; Glass, Michelle; Connor, Mark; Kassiou, Michael

    2016-01-01

    Indazole-derived synthetic cannabinoids (SCs) featuring an alkyl substituent at the 1-position and l-valinamide at the 3-carboxamide position (e.g., AB-CHMINACA) have been identified by forensic chemists around the world, and are associated with serious adverse health effects. Regioisomerism is possible for indazole SCs, with the 2-alkyl-2H-indazole regioisomer of AB-CHMINACA recently identified in SC products in Japan. It is unknown whether this regiosiomer represents a manufacturing impurit...

  3. Report on the Personnel Dosimetry at AB Atomenergi during 1965

    Energy Technology Data Exchange (ETDEWEB)

    Edvardsson, K A

    1966-10-15

    This report presents the results of the personnel dosimetry at AB Atomenergi during 1965. No doses exceeding the recommendations of ICRP were reported. For AB Atomenergi the average external total body dose during the year was 60 mrem which corresponds to 89.4 manrem. 31200 gamma films and 5850 neutron films were evaluated. 2067 urine analyses and 692 measurements of body activity were made.

  4. Adubação orgânica da batata com esterco e, ou, Crotalaria juncea: II - disponibilidade de N, P e K no solo ao longo do ciclo de cultivo Organic fertilization of potato with manure and, or, Crotalaria juncea: II - soil N, P, and K availability throughout the growing season

    Directory of Open Access Journals (Sweden)

    Tácio Oliveira da Silva

    2007-02-01

    Full Text Available Os solos do Agreste paraibano têm baixa fertilidade e a prática usual de adubação é a incorporação de esterco na época do plantio. Entretanto, dependendo da qualidade do esterco, essa prática pode causar a imobilização de nutrientes do solo durante os primeiros meses de cultivo. É possível que o cultivo e incorporação de Crotalaria juncea, combinado com o esterco, possa promover mineralização mais sincronizada com a demanda de nutrientes pelas plantas. No presente estudo, realizado em 2003, foram conduzidos experimentos de campo e em casa de vegetação para testar essa hipótese. As parcelas de campo foram previamente cultivadas com batata no período de 1996 a 2002 e submetidas anualmente aos seguintes tratamentos: plantio e incorporação da crotalária na época da floração (C; adição de 15 t ha-1 de esterco (E; plantio e incorporação de crotalária + 7,5 t ha-1 de esterco (CE; e testemunha, sem esterco ou crotalária (T. Em 2003, foram aplicados os mesmos tratamentos de adubação orgânica e foi avaliada a dinâmica da decomposição e liberação de nutrientes pelo material vegetal e esterco contidos em sacolas de náilon incorporadas ao solo das parcelas de campo. Também se avaliou a dinâmica da disponibilidade de N, P e K no solo das parcelas de campo, por meio de coletas periódicas de solo. No ensaio em casa de vegetação, foram realizados cultivos sucessivos de capim-buffel (Cenchrus ciliaris L. por um período de 300 dias, utilizando-se amostras do solo das parcelas de campo. As perdas de massa e nutrientes do material incorporado ao solo foram maiores nos primeiros 30 dias da incubação, em todos os tratamentos. No final do ensaio, as proporções de matéria seca e nutrientes remanescentes foram maiores nos tratamentos E e CE que nos tratamentos C e T. No solo das parcelas de campo, o tratamento E aumentou os teores de P e K extraíveis (Mehlich-1 do solo ao longo do período do estudo, porém provocou a

  5. Cyclin dependent kinase inhibitor 2A/B gene deletions are markers of poor prognosis in Indian children with acute lymphoblastic leukemia.

    Science.gov (United States)

    Agarwal, Manisha; Bakhshi, Sameer; Dwivedi, Sadanand N; Kabra, Madhulika; Shukla, Rashmi; Seth, Rachna

    2018-06-01

    Cyclin dependent kinase inhibitor 2A/B (CDKN2A/B) genes are implicated in many malignancies including acute lymphoblastic leukemia (ALL). These tumor suppressor genes, with a key regulatory role in cell cycle are located on chromosome 9p21.3. Previous studies involving CDKN2A/B gene deletions have shown mixed associations with survival outcome in childhood ALL. Hundred and four newly diagnosed children with ALL (1-14 years) were enrolled in this study. Genomic DNA from pretreatment bone marrow/peripheral blood samples of these children was investigated for copy number alterations in CDKN2A/B genes using multiplex ligation dependent probe amplification assay. Immunophenotype subtyping and cytogenetic and molecular analysis of ALL was performed at start of induction chemotherapy in all children. Children were monitored for response to prednisolone (Day 8), complete morphological remission, and minimal residual disease at the end of induction. The minimum postinduction follow-up period was 6 months. CDKN2A/B deletions were seen in 19.8% (18/91) of B lineage acute lymphoblastic leukemia (B-ALL) and 38.5% (5/13) of T lineage acute lymphoblastic leukemia (T-ALL). Monoallelic CDKN2A/B deletions were found in 61.1% of total deletions in B-ALL while all the children with T-ALL harbored biallelic deletions. The prevalence of CDKN2A/B gene deletions was found to be significantly higher in older children (P = 0.002), in those with higher leukocyte count (P = 0.037), and in National Cancer Institute high risk group patients (P = 0.001) in the B-ALL subgroup. Hazard ratio was significantly high for children with CDKN2A/B deletions in total cohort (P = 0.004). Children with CDKN2A/B deletion had significantly lesser event free survival (P = 0.03). CDKN2A/B deletions were significantly more prevalent in T-ALL subgroup and were found to have higher hazard ratio and lesser event free survival in total cohort in our study. © 2018 Wiley Periodicals, Inc.

  6. AB/sub 5/-catalyzed hydrogen evolution cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Hall, D E; Sawada, T; Shepard, V R; Tsujikawa, Y

    1984-01-01

    The AB/sub 5/ metal compounds are highly efficient hydrogen evolution electrocatalysts in alkaline electrolyte. Three types of AB/sub 5/-catalyzed cathode structures were made, using the hydride-forming AB/sub 5/ compounds in particulate form. Plastic-bonded cathodes containing >90 w/o AB/sub 5/ (finished-weight basis) were the most efficient, giving hydrogen evolution overpotentials (/eta/ /SUB H2/ ) of about 0.05 V at 200 mA cm/sup -2/. However, they tended to swell and shed material during electrolysis. Pressed, sintered cathodes containing 40-70 w/o catalyst in a nickel binder gave /eta/ /SUB H2/ about0.08 V; catalyst retention was excellent. Porous, sintered cathode coatings were made with 30-70 w/o AB/sub 5/ catalyst loadings. Their overpotentials were similar to those of the pressed, sintered cathodes. However, at catalyst loadings below about 40 w/o, high overpotentials characteristic of the nickel binder were observed. The structural and electrochemical properties of the three AB/sub 5/-catalyzed cathodes are discussed.

  7. Karyotype characterization of Crotalaria juncea (L. by chromosome banding and physical mapping of 18S-5.8S-26S and 5S rRNA gene sites

    Directory of Open Access Journals (Sweden)

    Mateus Mondin

    2007-01-01

    Full Text Available The chromosomes of Crotalaria juncea, a legume of agronomic interest with a 2n = 16 karyotype composed of metacentric chromosomes, were analyzed using several cytogenetic techniques. C-banding revealed heterochromatic regions around the centromeres in all chromosomes and adjacent to the secondary constriction on the chromosome 1 short arm. Fluorescent staining with the GC-specific chromomycin A3 (CMA highlighted these heterochromatic regions and a tiny site on the chromosome 1 long arm while the AT-specific stain 4'-6-diamidino-2-phenylindole (DAPI induced a reversed pattern. Staining with CMA combined with AT-specific distamycin A (DA counterstaining quenched the pericentromeric regions of all chromosomes, but enhanced fluorescence was observed at the heterochromatic regions around the secondary constriction and on the long arms of chromosomes 1 and 4. Fluorescence in situ hybridization (FISH revealed 18S-5.8S-26S rRNA gene sites (45S rDNA on chromosomes 1 and 4, and one 5S rDNA locus on chromosome 1. All the rDNA sites were co-located with the positive-CMA/DA bands, suggesting they were very rich in GC. Silver staining revealed signals at the main 45S rDNA locus on chromosome 1 and, in some cells, chromosome 4 was labeled. Two small nucleoli were detected in a few interphase cells, suggesting that the minor site on chromosome 4 could be active at some stages of the cell cycle.

  8. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  9. Ab-initio calculation of electronic structure and optical properties of AB-stacked bilayer α-graphyne

    Science.gov (United States)

    Behzad, Somayeh

    2016-09-01

    Monolayer α-graphyne is a new two-dimensional carbon allotrope with many special features. In this work the electronic properties of AA- and AB-stacked bilayers of this material and then the optical properties are studied, using first principle plane wave method. The electronic spectrum has two Dirac cones for AA stacked bilayer α-graphyne. For AB-stacked bilayer, the interlayer interaction changes the linear bands into parabolic bands. The optical spectra of the most stable AB-stacked bilayer closely resemble to that of the monolayer, except for small shifts of peak positions and increasing of their intensity. For AB-stacked bilayer, a pronounced peak has been found at low energies under the perpendicular polarization. This peak can be clearly ascribed to the transitions at the Dirac point as a result of the small degeneracy lift in the band structure.

  10. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  11. Study on Exothermic Oxidation of Acrylonitrile-butadiene-styrene (ABS Resin Powder with Application to ABS Processing Safety

    Directory of Open Access Journals (Sweden)

    Jenq-Renn Chen

    2010-08-01

    Full Text Available Oxidative degradation of commercial grade ABS (Acrylonitrile-butadiene-styrene resin powders was studied by thermal analysis. The instabilities of ABS containing different polybutadiene (PB contents with respect to temperature were studied by Differential Scanning Calorimeter (DSC. Thermograms of isothermal test and dynamic scanning were performed. Three exothermic peaks were observed and related to auto-oxidation, degradation and oxidative decomposition, respectively. Onset temperature of the auto-oxidation was determined to be around 193 °C. However, threshold temperature of oxidation was found to be as low as 140 °C by DSC isothermal testing. Another scan of the powder after degeneration in air showed an onset temperature of 127 °C. Reactive hazards of ABS powders were verified to be the exothermic oxidation of unsaturated PB domains, not the SAN (poly(styrene-acrylonitrile matrix. Heat of oxidation was first determined to be 2,800 ± 40 J per gram of ABS or 4,720 ± 20 J per gram of PB. Thermal hazards of processing ABS powder are assessed by adiabatic temperature rise at process conditions. IR spectroscopy associated with heat of oxidation verified the oxidative mechanism, and these evidences excluded the heat source from the degradation of SAN. A specially prepared powder of ABS without adding anti-oxidant was analyzed by DSC for comparing the exothermic behaviors. Exothermic onset temperatures were determined to be 120 °C and 80 °C by dynamic scanning and isothermal test, respectively. The assessment successfully explained fires and explosions in an ABS powder dryer and an ABS extruder.

  12. Genome-wide identification of significant aberrations in cancer genome.

    Science.gov (United States)

    Yuan, Xiguo; Yu, Guoqiang; Hou, Xuchu; Shih, Ie-Ming; Clarke, Robert; Zhang, Junying; Hoffman, Eric P; Wang, Roger R; Zhang, Zhen; Wang, Yue

    2012-07-27

    Somatic Copy Number Alterations (CNAs) in human genomes are present in almost all human cancers. Systematic efforts to characterize such structural variants must effectively distinguish significant consensus events from random background aberrations. Here we introduce Significant Aberration in Cancer (SAIC), a new method for characterizing and assessing the statistical significance of recurrent CNA units. Three main features of SAIC include: (1) exploiting the intrinsic correlation among consecutive probes to assign a score to each CNA unit instead of single probes; (2) performing permutations on CNA units that preserve correlations inherent in the copy number data; and (3) iteratively detecting Significant Copy Number Aberrations (SCAs) and estimating an unbiased null distribution by applying an SCA-exclusive permutation scheme. We test and compare the performance of SAIC against four peer methods (GISTIC, STAC, KC-SMART, CMDS) on a large number of simulation datasets. Experimental results show that SAIC outperforms peer methods in terms of larger area under the Receiver Operating Characteristics curve and increased detection power. We then apply SAIC to analyze structural genomic aberrations acquired in four real cancer genome-wide copy number data sets (ovarian cancer, metastatic prostate cancer, lung adenocarcinoma, glioblastoma). When compared with previously reported results, SAIC successfully identifies most SCAs known to be of biological significance and associated with oncogenes (e.g., KRAS, CCNE1, and MYC) or tumor suppressor genes (e.g., CDKN2A/B). Furthermore, SAIC identifies a number of novel SCAs in these copy number data that encompass tumor related genes and may warrant further studies. Supported by a well-grounded theoretical framework, SAIC has been developed and used to identify SCAs in various cancer copy number data sets, providing useful information to study the landscape of cancer genomes. Open-source and platform-independent SAIC software is

  13. Genome-wide identification of significant aberrations in cancer genome

    Directory of Open Access Journals (Sweden)

    Yuan Xiguo

    2012-07-01

    Full Text Available Abstract Background Somatic Copy Number Alterations (CNAs in human genomes are present in almost all human cancers. Systematic efforts to characterize such structural variants must effectively distinguish significant consensus events from random background aberrations. Here we introduce Significant Aberration in Cancer (SAIC, a new method for characterizing and assessing the statistical significance of recurrent CNA units. Three main features of SAIC include: (1 exploiting the intrinsic correlation among consecutive probes to assign a score to each CNA unit instead of single probes; (2 performing permutations on CNA units that preserve correlations inherent in the copy number data; and (3 iteratively detecting Significant Copy Number Aberrations (SCAs and estimating an unbiased null distribution by applying an SCA-exclusive permutation scheme. Results We test and compare the performance of SAIC against four peer methods (GISTIC, STAC, KC-SMART, CMDS on a large number of simulation datasets. Experimental results show that SAIC outperforms peer methods in terms of larger area under the Receiver Operating Characteristics curve and increased detection power. We then apply SAIC to analyze structural genomic aberrations acquired in four real cancer genome-wide copy number data sets (ovarian cancer, metastatic prostate cancer, lung adenocarcinoma, glioblastoma. When compared with previously reported results, SAIC successfully identifies most SCAs known to be of biological significance and associated with oncogenes (e.g., KRAS, CCNE1, and MYC or tumor suppressor genes (e.g., CDKN2A/B. Furthermore, SAIC identifies a number of novel SCAs in these copy number data that encompass tumor related genes and may warrant further studies. Conclusions Supported by a well-grounded theoretical framework, SAIC has been developed and used to identify SCAs in various cancer copy number data sets, providing useful information to study the landscape of cancer genomes

  14. Ab initio study of the isomerism of (LiAB)2 salt dimers with 24 valence electrons (AB- = NO-, PO-, NS-, PS-)

    International Nuclear Information System (INIS)

    Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.

    2000-01-01

    The nonempiric calculations of the potential energies surfaces in the vicinity of the key structures of the loose dimer molecules of the (LiNO) 2 , (LiPO) 2 , (LiNS) 2 and (LiPS) 2 lithium salts with 24 valence electrons are accomplished within the frames of the MP2/6-31G * //HF/6-31g * + ZPE(HF/6-31G * and MP4SDTQ/6-31G * //MP2/6-31G * + ZPE(MP2/6-31G * ) approximation. The equilibrium geometrical parameters, relative energies and isomer decay energies, frequencies and IR-intensities of normal vibrations are determined. The geometrical deformations and shifts of vibrational frequencies of the cis- and trans-dianions under the effect of cations by different ways of their coordination as well as tendencies of the molecular properties behaviour in various series of dimers (LiAB) 2 are analyzed. The results obtained are compared with the data of previous calculations of the LiAB salts monomeric molecules, the Li 2 AB + ions with 12 valence electrons and the (LiAB) 2 dimers with 20 valence electrons [ru

  15. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  16. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  17. Genomic selection for the improvement of antibody response to Newcastle disease and avian influenza virus in chickens.

    Directory of Open Access Journals (Sweden)

    Tianfei Liu

    Full Text Available Newcastle disease (ND and avian influenza (AI are the most feared diseases in the poultry industry worldwide. They can cause flock mortality up to 100%, resulting in a catastrophic economic loss. This is the first study to investigate the feasibility of genomic selection for antibody response to Newcastle disease virus (Ab-NDV and antibody response to Avian Influenza virus (Ab-AIV in chickens. The data were collected from a crossbred population. Breeding values for Ab-NDV and Ab-AIV were estimated using a pedigree-based best linear unbiased prediction model (BLUP and a genomic best linear unbiased prediction model (GBLUP. Single-trait and multiple-trait analyses were implemented. According to the analysis using the pedigree-based model, the heritability for Ab-NDV estimated from the single-trait and multiple-trait models was 0.478 and 0.487, respectively. The heritability for Ab-AIV estimated from the two models was 0.301 and 0.291, respectively. The estimated genetic correlation between the two traits was 0.438. A four-fold cross-validation was used to assess the accuracy of the estimated breeding values (EBV in the two validation scenarios. In the family sample scenario each half-sib family is randomly allocated to one of four subsets and in the random sample scenario the individuals are randomly divided into four subsets. In the family sample scenario, compared with the pedigree-based model, the accuracy of the genomic prediction increased from 0.086 to 0.237 for Ab-NDV and from 0.080 to 0.347 for Ab-AIV. In the random sample scenario, the accuracy was improved from 0.389 to 0.427 for Ab-NDV and from 0.281 to 0.367 for Ab-AIV. The multiple-trait GBLUP model led to a slightly higher accuracy of genomic prediction for both traits. These results indicate that genomic selection for antibody response to ND and AI in chickens is promising.

  18. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  19. TITRATION METHOD OF AB0 ANTIBODIES WITH THE USE OF MODERN GEL TECHNOLOGY IN AB0-INCOMPATIBLE TRANSPLANTATION

    Directory of Open Access Journals (Sweden)

    A. K. Porunova

    2014-01-01

    Full Text Available It is shown that developed method of titrating AB0 antibodies allows defi ning the titer of the investigational antibodies more precisely on 1–3 dilution of serum compared to the prototype method (titration method of antibodiesin saline medium on the plane. It is more obvious as it excludes hardly interpretable results due to the possibility of conducting visual assessment of agglutination reaction in the gel card thick column and requires less time foranalysis. The results can be saved for comparison with the results of further research. That is not possible under prototype titration method. Aim: our aim is to create a laboratory technique that can accurately, reliably and clearly produce titration of AB0 system antibodies, including in patients with low initial concentration of agglutinins in the blood; a technique more economical in terms of spending serum and that takes less time.Materials and methods: those modes were empirically chosen which allow titration of AB0 system agglutinins using gel technology based micro typing; to titer group antibodies 1640 serum assays of recipients in AB0-incompatibletransplantation were analyzed.The result of the use of specially developed method in organ transplantation from incompatible blood donors consists in enhancing accuracy, sensitivity of natural, complete and incomplete AB0 system immune antibodies titration, in its clarity, using of blood micro-doses for earlier detection of sensitizing of the patient, which is especially important in Pediatrics. Conclusion: the developed procedure of AB0-antibodies’ titration using modern gel technology makes possible a more precise monitoring of the titer of antibodies that is necessary to predict the graft rejection risk, to select the Protocol of preoperative preparation and postoperative management of patients, to assess the effectiveness of therapy in patients for whom it is diffi cult to fi nd a compatible blood type donor, and for whom today AB

  20. Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

    Science.gov (United States)

    Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro

    2016-12-15

    MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.

  1. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  2. A technique developed for labeling the green manures (sunnhemp and velvet bean) with {sup 15} N for nitrogen dynamic studies; Tecnica para marcacao dos adubos verdes crotalaria juncea e mucuna-preta com {sup 15} N para estudos de dinamica do nitrogenio

    Energy Technology Data Exchange (ETDEWEB)

    Ambrosano, Edmilson Jose [Instituto Agronomico de Campinas, SP (Brazil). Secao de Leguminosas; Trivelin, Paulo Cesar Ocheuze; Muruoka, Takashi [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil)

    1997-07-01

    A technique was developed for labeling the leguminous plant tissue with nitrogen ({sup 15} N) to obtain labelled material for nitrogen dynamic studies. Sunnhemp (crotalaria juncea L.) and velvet beans (Mucuna aterrima, sinonimia Stizolobium aterrimum Piper and Tracy) were grown in pots containing 10 kg of a Red Yellow Podzolic soil, under greenhouse conditions. The rate of 1.2 of nitrogen (ammonium sulphate with 11.37 atom % {sup 15} N) per pot was applied three times. The labelled dried plant material showed 3.177 and 4.337 of atom % {sup 15} N, respectively for velvet beans and sunnhemp. (author)

  3. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  4. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  5. Report on the Personnel Dosimetry at AB Atomenergi during 1964

    International Nuclear Information System (INIS)

    Edvardsson, K.A.; Hagsgaard, S.

    1966-01-01

    This report presents the results of the personnel dosimetry at AB Atomenergi during 1964. No doses exceeding the recommendations of ICRP were reported. The sum of the reported external total body doses during the year was for AB Atomenergi 51.5 manrem which, distributed over the whole company personnel, corresponds to an average dose of about 35 mrem per year and person or less than 1 % of the maximum permissible dose. 31,400 gamma films and 5,800 neutron films were evaluated. The films were changed every month. Urine analyses numbered 2,731 and whole body measurements 485. A comparison is made between dose distributions at AB Atomenergi and at institutions in other countries. The fraction of all personnel carrying dosimeters and exposed to more than a nominal dose seems generally to have been less than 10-20 %

  6. ABS 3D printed solutions for cryogenic applications

    Science.gov (United States)

    Bartolomé, E.; Bozzo, B.; Sevilla, P.; Martínez-Pasarell, O.; Puig, T.; Granados, X.

    2017-03-01

    3D printing has become a common, inexpensive and rapid prototyping technique, enabling the ad hoc fabrication of complex shapes. In this paper, we demonstrate that 3D printed objects in ABS can be used at cryogenic temperatures, offering flexible solutions in different fields. Firstly, a thermo-mechanical characterization of ABS 3D printed specimens at 77 K is reported, which allowed us to delimit the type of cryogenic uses where 3D printed pieces may be implemented. Secondly, we present three different examples where ABS 3D printed objects working at low temperatures have provided specific solutions: (i) SQUID inserts for angular magnetometry (low temperature material characterization field); (ii) a cage support for a metamaterial ;magnetic concentrator; (superconductivity application), and (iii) dedicated tools for cryopreservation in assisted reproductive techniques (medicine field).

  7. Report on the Personnel Dosimetry at AB Atomenergi during 1964

    Energy Technology Data Exchange (ETDEWEB)

    Edvardsson, K A; Hagsgaard, S

    1966-01-15

    This report presents the results of the personnel dosimetry at AB Atomenergi during 1964. No doses exceeding the recommendations of ICRP were reported. The sum of the reported external total body doses during the year was for AB Atomenergi 51.5 manrem which, distributed over the whole company personnel, corresponds to an average dose of about 35 mrem per year and person or less than 1 % of the maximum permissible dose. 31,400 gamma films and 5,800 neutron films were evaluated. The films were changed every month. Urine analyses numbered 2,731 and whole body measurements 485. A comparison is made between dose distributions at AB Atomenergi and at institutions in other countries. The fraction of all personnel carrying dosimeters and exposed to more than a nominal dose seems generally to have been less than 10-20 %.

  8. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  9. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  10. Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.

    Science.gov (United States)

    Feschotte, Cédric; Keswani, Umeshkumar; Ranganathan, Nirmal; Guibotsy, Marcel L; Levine, David

    2009-07-23

    Eukaryotic genomes contain large amount of repetitive DNA, most of which is derived from transposable elements (TEs). Progress has been made to develop computational tools for ab initio identification of repeat families, but there is an urgent need to develop tools to automate the annotation of TEs in genome sequences. Here we introduce REPCLASS, a tool that automates the classification of TE sequences. Using control repeat libraries, we show that the program can classify accurately virtually any known TE types. Combining REPCLASS to ab initio repeat finding in the genomes of Caenorhabditis elegans and Drosophila melanogaster allowed us to recover the contrasting TE landscape characteristic of these species. Unexpectedly, REPCLASS also uncovered several novel TE families in both genomes, augmenting the TE repertoire of these model species. When applied to the genomes of distant Caenorhabditis and Drosophila species, the approach revealed a remarkable conservation of TE composition profile within each genus, despite substantial interspecific covariations in genome size and in the number of TEs and TE families. Lastly, we applied REPCLASS to analyze 10 fungal genomes from a wide taxonomic range, most of which have not been analyzed for TE content previously. The results showed that TE diversity varies widely across the fungi "kingdom" and appears to positively correlate with genome size, in particular for DNA transposons. Together, these data validate REPCLASS as a powerful tool to explore the repetitive DNA landscapes of eukaryotes and to shed light onto the evolutionary forces shaping TE diversity and genome architecture.

  11. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  12. Student Measurements of STFA 10AB (Theta Tauri)

    Science.gov (United States)

    Gillette, Sean; Estrada, Chris; Estrada, Reed; Aguilera, Sophia; Chavez, Valerie; Givens, Jalynn; Lindorfer, Sarah; Michels, Kaylie; Mobley, Makenzie; Reder, Gabriel; Renteria, Kayla; Shattles, Jenna; Wilkin, Aiden; Woodbury, Maisy; Rhoades, Breauna; Rhoades, Mark

    2017-04-01

    Eighth grade students at Vanguard Preparatory School measured the double star STFA 10AB using a 22-inch Newtonian Alt/Az telescope and a Celestron Micro Guide eyepiece. Bellatrix was used as the calibration star. The calculated means of multiple observations of STFA 10AB resulted in a separation of 45.18,” a scale constant of 7.88 arcseconds per division, and position angle of 257.9°. These measurements were compared to the most recent values in the Washington Double Star Catalog.

  13. Report on the Personnel Dosimetry at AB Atomenergi during 1962

    International Nuclear Information System (INIS)

    Edvardsson, K.A.; Hagsgaard, S.

    1963-12-01

    This report presents the results of the personnel dosimetry at AB Atomenergi during 1962. No doses exceeding the recommendations of ICRP have been reported. The sum of the reported external total body doses (≥ 100 mrem/quarter) is for the whole of AB Atomenergi during this year 74. 2 manrem corresponding to about 50 mrem/year and person or 1 % of the maximum permissible dose. 32500 gamma films and 6200 neutron films have been evaluated. The total number of urine analyses is 2700 and of whole body measurements 10

  14. Report on the Personnel Dosimetry at AB Atomenergi during 1962

    Energy Technology Data Exchange (ETDEWEB)

    Edvardsson, K A; Hagsgaard, S

    1964-07-15

    This report presents the results of the personnel dosimetry at AB Atomenergi during 1963. No doses exceeding the recommendations of ICRP have been reported. The sum of the reported external total body doses during the year is for AB Atomenergi 64.2 manrem which, distributed over the whole company personnel, corresponds to about 40 mrem per year and person or about 1 % of the maximum permissible dose. 37800 gamma films and 6700 neutron films have been evaluated. The total number of urine analyses is 3603 and of whole body measurements 211.

  15. Report on the Personnel Dosimetry at AB Atomenergi during 1962

    Energy Technology Data Exchange (ETDEWEB)

    Edvardsson, K A; Hagsgaard, S

    1963-12-15

    This report presents the results of the personnel dosimetry at AB Atomenergi during 1962. No doses exceeding the recommendations of ICRP have been reported. The sum of the reported external total body doses ({>=} 100 mrem/quarter) is for the whole of AB Atomenergi during this year 74. 2 manrem corresponding to about 50 mrem/year and person or 1 % of the maximum permissible dose. 32500 gamma films and 6200 neutron films have been evaluated. The total number of urine analyses is 2700 and of whole body measurements 10.

  16. Use of ab initio quantum chemical methods in battery technology

    Energy Technology Data Exchange (ETDEWEB)

    Deiss, E [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.

  17. Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae.

    Science.gov (United States)

    Nam, Bo-Hye; Kwak, Woori; Kim, Young-Ok; Kim, Dong-Gyun; Kong, Hee Jeong; Kim, Woo-Jin; Kang, Jeong-Ha; Park, Jung Youn; An, Cheul Min; Moon, Ji-Young; Park, Choul Ji; Yu, Jae Woong; Yoon, Joon; Seo, Minseok; Kim, Kwondo; Kim, Duk Kyung; Lee, SaetByeol; Sung, Samsun; Lee, Chul; Shin, Younhee; Jung, Myunghee; Kang, Byeong-Chul; Shin, Ga-Hee; Ka, Sojeong; Caetano-Anolles, Kelsey; Cho, Seoae; Kim, Heebal

    2017-05-01

    Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [ 1 ]. Abalone is an economically important fishery and aquaculture animal that is considered a highly prized seafood delicacy. The total global supply of abalone has increased 5-fold since the 1970s and farm production increased explosively from 50 mt to 103 464 mt in the past 40 years. Additionally, researchers have recently focused on abalone given their reported tumor suppression effect. However, despite the valuable features of this marine animal, no genomic information is available for the Haliotidae family and related research is still limited. To construct the H . discus hannai genome, a total of 580-G base pairs using Illumina and Pacbio platforms were generated with 322-fold coverage based on the 1.8-Gb estimated genome size of H . discus hannai using flow cytometry. The final genome assembly consisted of 1.86 Gb with 35 450 scaffolds (>2 kb). GC content level was 40.51%, and the N50 length of assembled scaffolds was 211 kb. We identified 29 449 genes using Evidence Modeler based on the gene information from ab initio prediction, protein homology with known genes, and transcriptome evidence of RNA-seq. Here we present the first Haliotidae genome, H . discus hannai , with sequencing data, assembly, and gene annotation information. This will be helpful for resolving the lack of genomic information in the Haliotidae family as well as providing more opportunities for understanding gastropod evolution. © The Authors 2017. Published by Oxford University Press.

  18. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  19. Ab initio study of isomerism of Li2AB2 molecules and Li2AB2+ ions with 16 valent electrons

    International Nuclear Information System (INIS)

    Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.

    2000-01-01

    In the framework of MP2(6-31*//HF/6-31G + ZPE(HF/6-31G*) and MP4SDTQ/6-31G*//MP2/6-31G* + ZPE(MP2/6-31G*) approximations ab initio calculations of surfaces of potential energy of molecules of lithium salts of Li 2 AB 2 (Li 2 BeO 2 , L 2 MgO 2 , Li 2 BeS 2 , Li 2 MgS 2 , Li 2 CN 2 , Li 2 SiN 2 , Li 2 CP 2 ) type and ions of Li 2 AB 2 + (Li 2 BO 2 + , Li 2 AlO 2 + , Li 2 BS 2 + , Li 2 AlS 2 + , Li 2 N 3 + , Li 2 PN 2 + , Li 2 P 3 + ) type with 16 valent electrons are done. For oxide and nitride systems global minimum corresponds to symmetric linear structure D ∞h and for their sulfide and phosphorus analogues curved plane or unplane (C 2 ) structure with bond angle φ(LBA)=90-110 Deg are preferable. Equilibrium geometric parameters, relative energies and energies of isomer decomposition, frequencies and IR-intensities of normal vibrations are determined [ru

  20. The food-borne pathogen Campylobacter jejuni depends on the AddAB DNA repair system to defend against bile in the intestinal environment.

    Science.gov (United States)

    Gourley, Christopher R; Negretti, Nicholas M; Konkel, Michael E

    2017-10-31

    Accurate repair of DNA damage is crucial to ensure genome stability and cell survival of all organisms. Bile functions as a defensive barrier against intestinal colonization by pathogenic microbes. Campylobacter jejuni, a leading bacterial cause of foodborne illness, possess strategies to mitigate the toxic components of bile. We recently found that growth of C. jejuni in medium with deoxycholate, a component of bile, caused DNA damage consistent with the exposure to reactive oxygen species. We hypothesized that C. jejuni must repair DNA damage caused by reactive oxygen species to restore chromosomal integrity. Our efforts focused on determining the importance of the putative AddAB DNA repair proteins. A C. jejuni addAB mutant demonstrated enhanced sensitivity to deoxycholate and was impaired in DNA double strand break repair. Complementation of the addAB mutant restored resistance to deoxycholate, as well as function of the DNA double strand break repair system. The importance of these findings translated to the natural host, where the AddAB system was found to be required for efficient C. jejuni colonization of the chicken intestine. This research provides new insight into the molecular mechanism utilized by C. jejuni, and possibly other intestinal pathogens, to survive in the presence of bile.

  1. Electronic brakes. From ABS to brake-by-wire. 2. ed.; Elektronische Bremssysteme. Vom ABS zum Brake-by-Wire

    Energy Technology Data Exchange (ETDEWEB)

    Reichel, H.R.

    2003-07-01

    The book reports trends in vehicle brakes from 1968 to 1998. This was the age of the electronic revolution. The book presents conventional brakes, antiblocking systems (ABS), antislip systems (ASS), brake assistants (BAS), dynamic control systems, and brake-by-wire systems. [German] Das Buch berichtet ueber Entwicklungen an Fahrzeugbremsanlagen in der Zeitspanne von 1968 bis etwa 1998. Diese Zeit war gepraegt vom Vordringen der Elektronik in die Bremsen, was fuer Hersteller und Kunden eine Revolution bedeutete. Behandelt sind: (a) Konventionelle Bremsanlagen, (b) Antiblockiersysteme (ABS), (c) Anti-Schlupf-regelungen (ASR), (d) Bremsassistenten (BAS), (e) Fahrdynamikregelungen (FDR, ESP), (f) Brake-by-Wire (orig.)

  2. AB INITIO calculations of magneto-optical effects

    Czech Academy of Sciences Publication Activity Database

    Kuneš, Jan; Oppeneer, P. M.

    2002-01-01

    Roč. 2, - (2002), s. 141-146 ISSN 1346-7948 R&D Projects: GA AV ČR IAA1010214 Institutional research plan: CEZ:AV0Z1010914 Keywords : electronic structure * ab initio calculation * polar magneto-optical Kerr effect * transitiom metal * uranium intermetallics * CrO 2 Subject RIV: BM - Solid Matter Physics ; Magnetism

  3. Monte Carlo simulation of AB-copolymers with saturating bonds

    DEFF Research Database (Denmark)

    Chertovich, A.C.; Ivanov, V.A.; Khokhlov, A.R.

    2003-01-01

    Structural transitions in a single AB-copolymer chain where saturating bonds can be formed between A- and B-units are studied by means of Monte Carlo computer simulations using the bond fluctuation model. Three transitions are found, coil-globule, coil-hairpin and globule-hairpin, depending...

  4. Early stage precipitation in aluminum alloys : An ab initio study

    NARCIS (Netherlands)

    Zhang, X.

    2017-01-01

    Multiscale computational materials science has reached a stage where many complicated phenomena or properties that are of great importance to manufacturing can be predicted or explained. The word “ab initio study” becomes commonplace as the development of density functional theory has enabled the

  5. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting

  6. STATE OF WORKS ON CREATION ABS FOR PASSENGER CARS

    Directory of Open Access Journals (Sweden)

    E. Getsovich

    2009-01-01

    Full Text Available Numerical modeling of vehicle braking process with ABS are presented. The applicability estimation of control process improvement in dual adaptive control systems is executed. Laboratory experiment results of determining pressure actuator characteristics are published. Piston diameter optimization is provided.

  7. Multiple time step integrators in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-01-01

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

  8. Cyanogen Azide. Ionization Potentials and Ab Initio SCF MO Calculation

    DEFF Research Database (Denmark)

    Bak, Börge; Jansen, Peter; Stafast, Herbert

    1975-01-01

    The Ne(I) and He(I) photoelectron(PE) spectra of cyanogen azide, NCN3, have been recorded at high resolution. Their interpretation is achieved by comparison with the PE spectrum of HN3 and an ab initio LCGO SCF MO calculation. Deviations from Koopmans' theorem of quite different magnitudes...

  9. Ab initio study of alanine polypeptide chain twisting

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.

    2006-01-01

    chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...

  10. Ab initio simulation of dislocation cores in metals

    International Nuclear Information System (INIS)

    Ventelon, L.

    2008-01-01

    In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)

  11. Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics

    NARCIS (Netherlands)

    Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de

    1997-01-01

    The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.

  12. Ab initio electronic properties of dual phosphorus monolayers in silicon

    DEFF Research Database (Denmark)

    Drumm, Daniel W.; Per, Manolo C.; Budi, Akin

    2014-01-01

    In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon...

  13. Quantifying transition voltage spectroscopy of molecular junctions: Ab initio calculations

    DEFF Research Database (Denmark)

    Chen, Jingzhe; Markussen, Troels; Thygesen, Kristian Sommer

    2010-01-01

    Transition voltage spectroscopy (TVS) has recently been introduced as a spectroscopic tool for molecular junctions where it offers the possibility to probe molecular level energies at relatively low bias voltages. In this work we perform extensive ab initio calculations of the nonlinear current...

  14. Ab initio study of phase equilibria in TiCx

    DEFF Research Database (Denmark)

    Korzhavyi, P.A.; Pourovskii, L.V.; Hugosson, H.W.

    2002-01-01

    The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti2C, Ti...

  15. Ab initio and kinetic modeling studies of formic acid oxidation

    DEFF Research Database (Denmark)

    Marshall, Paul; Glarborg, Peter

    2015-01-01

    A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism...

  16. Ab initio calculations and modelling of atomic cluster structure

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Lyalin, Andrey G.; Solov'yov, Andrey V.

    2004-01-01

    The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical...

  17. AB Toxins: A Paradigm Switch from Deadly to Desirable

    Directory of Open Access Journals (Sweden)

    Oludare Odumosu

    2010-06-01

    Full Text Available To ensure their survival, a number of bacterial and plant species have evolved a common strategy to capture energy from other biological systems. Being imperfect pathogens, organisms synthesizing multi-subunit AB toxins are responsible for the mortality of millions of people and animals annually. Vaccination against these organisms and their toxins has proved rather ineffective in providing long-term protection from disease. In response to the debilitating effects of AB toxins on epithelial cells of the digestive mucosa, mechanisms underlying toxin immunomodulation of immune responses have become the focus of increasing experimentation. The results of these studies reveal that AB toxins may have a beneficial application as adjuvants for the enhancement of immune protection against infection and autoimmunity. Here, we examine similarities and differences in the structure and function of bacterial and plant AB toxins that underlie their toxicity and their exceptional properties as immunomodulators for stimulating immune responses against infectious disease and for immune suppression of organ-specific autoimmunity.

  18. Move of Purchasing Offices TS – AB* – AT*

    CERN Multimedia

    FI Department

    2008-01-01

    The TS – AB* - AT* Purchasing Offices and the Purchasing Pool have moved to Building 5 – 2nd and *3rd floors. The phone and fax numbers are unchanged. We apologize for any inconvenience caused by the move. Thank you for your understanding. Finance Department – Purchasing Service.

  19. EST Table: AB046365 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available 1073 aa FBpp0259641|DyakGE14631-PA 10/08/27 47 %/329 aa W03F8.5#CE34386#WBGene00002247#locus:lam- 1#laminin#...AB046365 10/09/29 97 %/1069 aa dbj|BAB21565.1| laminin [Bombyx mori] 10/08/27 40 %/

  20. Information Manual: Procedures, Planning Concepts, Subsystems. ABS Publication No. 3.

    Science.gov (United States)

    California Univ., Berkeley.

    This report, the third in a series which presents the results of a systems analysis of the problem of providing science and engineering buildings at the university level, is a technical manual for using the Academic Building Systems (ABS) approach in programing, designing, and constructing such facilities. The document presents (1) planning…

  1. Bicanonical ab Initio Molecular Dynamics for Open Systems.

    Science.gov (United States)

    Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

    2017-08-08

    Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

  2. Ab initio calculations of mechanical properties: Methods and applications

    Czech Academy of Sciences Publication Activity Database

    Pokluda, J.; Černý, Miroslav; Šob, Mojmír; Umeno, Y.

    2015-01-01

    Roč. 73, AUG (2015), s. 127-158 ISSN 0079-6425 R&D Projects: GA ČR(CZ) GAP108/12/0311 Institutional support: RVO:68081723 Keywords : Ab initio methods * Elastic moduli * Intrinsic hardness * Stability analysis * Theoretical strength * Intrinsic brittleness/ductility Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 31.083, year: 2015

  3. Further Food for Thought on the "ABS Guide"

    Science.gov (United States)

    Hussain, Simon

    2012-01-01

    This paper replies to points raised by the editors of the "ABS Guide", Huw Morris, Charles Harvey, Aidan Kelly and Michael Rowlinson (2011) "Accounting Education: an international journal", 20(6), pp. 561-573) in response to a paper published in a previous issue of "Accounting Education" (Hussain, S. (2011)…

  4. The Properties of Some Simple Covalent Hydrides: An Ab Initio ...

    African Journals Online (AJOL)

    Some properties of the monomeric binary hydrides of the elements of the first two rows of the periodic table have been determined using ab initio molecular orbital theory. The properties in question are the energetic, structural, electronic, topological and vibrational characteristics. In general, a gradual convergence towards ...

  5. Food for Thought on the "ABS Academic Journal Quality Guide"

    Science.gov (United States)

    Hussain, Simon

    2011-01-01

    This paper discusses issues relating to the use of the Association of Business Schools' (ABS) "Academic Journal Quality Guide" within UK business schools. It also looks at several specific issues raised by the Chair of the British Accounting Association/British Accounting and Finance Association regarding the ratings for top…

  6. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  7. Ab initio transport across bismuth selenide surface barriers

    KAUST Repository

    Narayan, Awadhesh; Rungger, Ivan; Droghetti, Andrea; Sanvito, Stefano

    2014-01-01

    © 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results

  8. Identification of the Staphylococcus aureus vfrAB operon, a novel virulence factor regulatory locus.

    Science.gov (United States)

    Bose, Jeffrey L; Daly, Seth M; Hall, Pamela R; Bayles, Kenneth W

    2014-05-01

    During a screen of the Nebraska Transposon Mutant Library, we identified 71 mutations in the Staphylococcus aureus genome that altered hemolysis on blood agar medium. Although many of these mutations disrupted genes known to affect the production of alpha-hemolysin, two of them were associated with an apparent operon, designated vfrAB, that had not been characterized previously. Interestingly, a ΔvfrB mutant exhibited only minor effects on the transcription of the hla gene, encoding alpha-hemolysin, when grown in broth, as well as on RNAIII, a posttranscriptional regulatory RNA important for alpha-hemolysin translation, suggesting that VfrB may function at the posttranscriptional level. Indeed, a ΔvfrB mutant had increased aur and sspAB protease expression under these conditions. However, disruption of the known secreted proteases in the ΔvfrB mutant did not restore hemolytic activity in the ΔvfrB mutant on blood agar. Further analysis revealed that, in contrast to the minor effects of VfrB on hla transcription when strains were cultured in liquid media, the level of hla transcription was decreased 50-fold in the absence of VfrB on solid media. These results demonstrate that while VfrB represses protease expression when strains are grown in broth, hla regulation is highly responsive to factors associated with growth on solid media. Intriguingly, the ΔvfrB mutant displayed increased pathogenesis in a model of S. aureus dermonecrosis, further highlighting the complexity of VfrB-dependent virulence regulation. The results of this study describe a phenotype associated with a class of highly conserved yet uncharacterized proteins found in Gram-positive bacteria, and they shed new light on the regulation of virulence factors necessary for S. aureus pathogenesis.

  9. ParABS system in chromosome partitioning in the bacterium Myxococcus xanthus.

    Directory of Open Access Journals (Sweden)

    Antonio A Iniesta

    Full Text Available Chromosome segregation is an essential cellular function in eukaryotic and prokaryotic cells. The ParABS system is a fundamental player for a mitosis-like process in chromosome partitioning in many bacterial species. This work shows that the social bacterium Myxococcus xanthus also uses the ParABS system for chromosome segregation. Its large prokaryotic genome of 9.1 Mb contains 22 parS sequences near the origin of replication, and it is shown here that M. xanthus ParB binds preferentially to a consensus parS sequence in vitro. ParB and ParA are essential for cell viability in M. xanthus as in Caulobacter crescentus, but unlike in many other bacteria. Absence of ParB results in anucleate cells, chromosome segregation defects and loss of viability. Analysis of ParA subcellular localization shows that it clusters at the poles in all cells, and in some, in the DNA-free cell division plane between two chromosomal DNA masses. This ParA localization pattern depends on ParB but not on FtsZ. ParB inhibits the nonspecific interaction of ParA with DNA, and ParA colocalizes with chromosomal DNA only when ParB is depleted. The subcellular localization of ParB suggests a single ParB-parS complex localized at the edge of the nucleoid, next to a polar ParA cluster, with a second ParB-parS complex migrating after the replication of parS takes place to the opposite nucleoid edge, next to the other polar ParA cluster.

  10. Kinesin-2 KIF3AB exhibits novel ATPase characteristics.

    Science.gov (United States)

    Albracht, Clayton D; Rank, Katherine C; Obrzut, Steven; Rayment, Ivan; Gilbert, Susan P

    2014-10-03

    KIF3AB is an N-terminal processive kinesin-2 family member best known for its role in intraflagellar transport. There has been significant interest in KIF3AB in defining the key principles that underlie the processivity of KIF3AB in comparison with homodimeric processive kinesins. To define the ATPase mechanism and coordination of KIF3A and KIF3B stepping, a presteady-state kinetic analysis was pursued. For these studies, a truncated murine KIF3AB was generated. The results presented show that microtubule association was fast at 5.7 μm(-1) s(-1), followed by rate-limiting ADP release at 12.8 s(-1). ATP binding at 7.5 μm(-1) s(-1) was followed by an ATP-promoted isomerization at 84 s(-1) to form the intermediate poised for ATP hydrolysis, which then occurred at 33 s(-1). ATP hydrolysis was required for dissociation of the microtubule·KIF3AB complex, which was observed at 22 s(-1). The dissociation step showed an apparent affinity for ATP that was very weak (K½,ATP at 133 μm). Moreover, the linear fit of the initial ATP concentration dependence of the dissociation kinetics revealed an apparent second-order rate constant at 0.09 μm(-1) s(-1), which is inconsistent with fast ATP binding at 7.5 μm(-1) s(-1) and a Kd ,ATP at 6.1 μm. These results suggest that ATP binding per se cannot account for the apparent weak K½,ATP at 133 μm. The steady-state ATPase Km ,ATP, as well as the dissociation kinetics, reveal an unusual property of KIF3AB that is not yet well understood and also suggests that the mechanochemistry of KIF3AB is tuned somewhat differently from homodimeric processive kinesins. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.

    Science.gov (United States)

    Cabal, Adriana; Jun, Se-Ran; Jenjaroenpun, Piroon; Wanchai, Visanu; Nookaew, Intawat; Wongsurawat, Thidathip; Burgess, Mary J; Kothari, Atul; Wassenaar, Trudy M; Ussery, David W

    2018-02-14

    Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same

  12. Perspective: Ab initio force field methods derived from quantum mechanics

    Science.gov (United States)

    Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

    2018-03-01

    It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

  13. Effect of monoclonal antibodies (MoAb) to class I and class II HLA antigens on lectin- and MoAb OKT3-induced lymphocyte proliferation.

    Science.gov (United States)

    Akiyama, Y; Zicht, R; Ferrone, S; Bonnard, G D; Herberman, R B

    1985-04-01

    We have examined the effect of several monoclonal antibodies (MoAb) to monomorphic determinants of class II HLA antigens, and MoAb to monomorphic determinants of class I HLA antigens and to beta-2-microglobulin (beta 2-mu) on lectin- and MoAb OKT3-induced proliferation of human peripheral blood mononuclear cells (PBMNC) and cultured T cells (CTC). Some, but not all, anti-class II HLA MoAb inhibited the proliferative response of PBMNC to MoAb OKT3 and pokeweed mitogen (PWM). The degree of inhibitory effect varied considerably. This effect was not limited to anti-class II HLA MoAb since anti-class I HLA MoAb and anti-beta 2-mu MoAb also inhibited MoAb OKT3- or PWM-induced proliferative responses. In contrast, the response of PBMNC to phytohemagglutinin (PHA) and concanavalin A (Con A) was not blocked by any anti-class II HLA MoAb. However, some anti-class II HLA MoAb also inhibited the proliferative response of CTC plus allogeneic peripheral blood adherent accessory cells (AC) to PHA or Con A as well as to MoAb OKT3 or PWM. This may be attributable to the substantially greater class II HLA antigen expression by CTC than by fresh lymphocytes. Pretreatment of either CTC or AC with anti-class II HLA MoAb inhibited OKT3-induced proliferation. In contrast, pretreatment of CTC, but not AC, with anti-class I HLA MoAb inhibited the proliferative response of CTC to OKT3. Pretreatment of CTC with anti-class I HLA MoAb inhibited PHA-, Con A and PWM-induced proliferation, to a greater degree than the anti-class II HLA MoAb. It appears as if lymphocyte activation by different mitogens exhibits variable requirements for the presence of cells expressing major histocompatibility determinants. Binding of Ab to membrane markers may interfere with lymphocyte-AC cooperation, perhaps by inhibiting binding of mitogens to their receptors or by interfering with lymphocyte and AC function. We also have examined the role of class II HLA antigens on CTC by depleting class II HLA-positive cells

  14. Cell division and endoreduplication play important roles in stem swelling of tuber mustard (Brassica juncea Coss. var. tumida Tsen et Lee).

    Science.gov (United States)

    Shi, H; Wang, L L; Sun, L T; Dong, L L; Liu, B; Chen, L P

    2012-11-01

    We investigated spatio-temporal variations in cell division and the occurrence of endoreduplication in cells of tuber mustard stems during development. Cells in the stem had 8C nuclei (C represents DNA content of a two haploid genome), since it is an allotetraploid species derived from diploid Brassica rapa (AA) and B. nigra (BB), thus indicating the occurrence of endoreduplication. Additionally, we observed a dynamic change of cell ploidy in different regions of the swollen stems, with a decrease in 4C proportion in P4-1 and a sharp increase in 8C cells that became the dominant cell type (86.33% at most) in the inner pith cells. Furthermore, cDNAs of 14 cell cycle genes and four cell expansion genes were cloned and their spatial transcripts analysed in order to understand their roles in stem development. The expression of most cell cycle genes peaked in regions of the outer pith (P2 or P3), some genes regulating S/G2 and G2/M (BjCDKB1;2, BjCYCB1;1 and BjCYCB1;2) significantly decrease in P5 and P6, while G1/S regulators (BjE2Fa, BjE2Fb and BjE2Fc) showed a relative high expression level in the inner pith (P5) where cells were undergoing endoreduplication. Coincidentally, BjXTH1and BjXTH2 were exclusively expressed in the endoreduplicated cells. Our results suggest that cells of outer pith regions (P2 and P3) mainly divide for cell proliferation, while cells of the inner pith expand through endoreduplication. Endoreduplication could trigger expression of BjXTH1 and BjXTH2 and thus function in cell expansion of the pith tissue. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  15. The melt rheological behavior of AB, ABA, BAB, and (AB)n block copolymers with monodisperse aramide segments

    NARCIS (Netherlands)

    Araichimani, A.; Dullaert, Konraad; Gaymans, R.J.

    2009-01-01

    The melt rheological behavior of segmented block copolymers with high melting diamide (A) hard segments (HS) and polyether (B) soft segments was studied. The block copolymers can be classified as B (monoblock), AB (diblock), ABA (triblock, diamide end segment), BAB (triblock, diamide mid-segment)

  16. Protective mAbs and Cross-Reactive mAbs Raised by Immunization with Engineered Marburg Virus GPs.

    Directory of Open Access Journals (Sweden)

    Marnie L Fusco

    2015-06-01

    Full Text Available The filoviruses, which include the marburg- and ebolaviruses, have caused multiple outbreaks among humans this decade. Antibodies against the filovirus surface glycoprotein (GP have been shown to provide life-saving therapy in nonhuman primates, but such antibodies are generally virus-specific. Many monoclonal antibodies (mAbs have been described against Ebola virus. In contrast, relatively few have been described against Marburg virus. Here we present ten mAbs elicited by immunization of mice using recombinant mucin-deleted GPs from different Marburg virus (MARV strains. Surprisingly, two of the mAbs raised against MARV GP also cross-react with the mucin-deleted GP cores of all tested ebolaviruses (Ebola, Sudan, Bundibugyo, Reston, but these epitopes are masked differently by the mucin-like domains themselves. The most efficacious mAbs in this panel were found to recognize a novel "wing" feature on the GP2 subunit that is unique to Marburg and does not exist in Ebola. Two of these anti-wing antibodies confer 90 and 100% protection, respectively, one hour post-exposure in mice challenged with MARV.

  17. Preparation, biodistribution, and dosimetry of 188Re-Labeled MoAb ior cea1 and its f(ab')2 fragments by avidin-biotin strategy

    International Nuclear Information System (INIS)

    Ferro-Flores, Guillermina; Pimentel-Gonzalez, Gilmara; Gonzalez-Zavala, Maria Antonia; Murphy, Consuelo Arteaga de; Melendez-Alafort, Laura; Tendilla, Jose I.; Croft, Barbara Y.

    1999-01-01

    The biotinylated monoclonal antibody (MoAb) ior cea1 and its F(ab') 2 fragments were labeled with Re-188 by combination of avidin-biotin strategy. 188 Re-MoAb, 188 Re-MoAb-biotin, 188 Re-F(ab') 2 , and 188 Re-F(ab') 2 -biotin preparations were produced for these studies with specific activities of 1.30±0.18 GBq/mg and from instant freeze-dried kit formulations using ethane-1-hydroxy-1,1-diphosphonic acid (EHDP) as a weak competing ligand. There were no significant differences (p>0.05) between the biodistribution in mice of biotinylated and unbiotinylated 188 Re-labeled immunoconjugates. When avidin was injected as a chase after injection of 188 Re-MoAb-biotin or 188 Re-F(ab') 2 -biotin, the blood radioactivity level decreased approximately 75% (cumulated activity) and the effective dose decreased almost 25% with respect to that of the radioimmunoconjugates in which the chase effect was not used. Our results suggest that 188 Re-labeled biotinylated MoAb ior cea1 and its F(ab') 2 fragments prepared by this method are stable complexes in vivo

  18. Genome analysis methods: Arabidopsis lyrata [PGDBj Registered plant list, Marker list, QTL list, Plant DB link and Genome analysis methods[Archive

    Lifescience Database Archive (English)

    Full Text Available (http://genome.imim.es/software/geneid/) applying dicot and A. thaliana specific matrices 32,670 (v1.0) JGI; http://www.phytozome.net/alyrata v1.0 v1.0 10.1038/ng.807 21478890 ... ...8.3x Arachne 1,309 ... Fgenesh package of ab initio and homology-based gene predictors, EuGene12, and GeneID13

  19. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  20. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  1. Development of Anti-lock Braking System (ABS) for Vehicles Braking

    OpenAIRE

    Minh Vu Trieu; Oamen Godwin; Vassiljeva Kristina; Teder Leo

    2016-01-01

    This paper develops a real laboratory of anti-lock braking system (ABS) for vehicle and conducts real experiments to verify the ability of this ABS to prevent the vehicle wheel from being locked while braking. Two controllers of PID and fuzzy logic are tested for analysis and comparison. This ABS laboratory is designed for bachelor and master students to simulate and analyze performances of ABS with different control techniques on various roads and load conditions. Thi...

  2. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  3. Between Two Fern Genomes

    Science.gov (United States)

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  4. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  5. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  6. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  7. Speed-up of ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo simulations by using an auxiliary potential energy surface

    International Nuclear Information System (INIS)

    Nakayama, Akira; Taketsugu, Tetsuya; Shiga, Motoyuki

    2009-01-01

    Efficiency of the ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo methods is enhanced by employing an auxiliary potential energy surface that is used to update the system configuration via molecular dynamics scheme. As a simple illustration of this method, a dual-level approach is introduced where potential energy gradients are evaluated by computationally less expensive ab initio electronic structure methods. (author)

  8. Standardiserat arbete i produktionssystemet hos Inission Munkfors AB

    OpenAIRE

    Jonas, Arnesson

    2014-01-01

    Sammanfattning Denna rapport behandlar införandet av standardiserat arbete i produktionssystemet hos företaget Inission Munkfors AB. Arbetet har utförts i kursen Examensarbete för högskoleingenjörsexamen i maskinteknik (MSGC17), som ges vid Fakulteten för hälsa, natur & teknikvetenskap på Karlstads universitet.Företaget Inission Munkfors AB har som mål att från år 2012 till år 2017 kunna fördubbla omsättningen och halvera ledtiden, med samma personalstyrka som år 2012 (75st anställda). De...

  9. Computational methods for ab initio detection of microRNAs

    Directory of Open Access Journals (Sweden)

    Malik eYousef

    2012-10-01

    Full Text Available MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by processing via the Microprocessor complex, yielding a hairpin structure. Which is then exported into the cytosol where it is processed by Dicer and then incorporated into the RNA induced silencing complex. All of these biogenesis steps add to the overall specificity of miRNA production and effect. Unfortunately, their modes of action are just beginning to be elucidated and therefore computational prediction algorithms cannot model the process but are usually forced to employ machine learning approaches. This work focuses on ab initio prediction methods throughout; and therefore homology-based miRNA detection methods are not discussed. Current ab initio prediction algorithms, their ties to data mining, and their prediction accuracy are detailed.

  10. Augmented wave ab initio EFG calculations: some methodological warnings

    International Nuclear Information System (INIS)

    Errico, Leonardo A.; Renteria, Mario; Petrilli, Helena M.

    2007-01-01

    We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO 2 . The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects

  11. Augmented wave ab initio EFG calculations: some methodological warnings

    Energy Technology Data Exchange (ETDEWEB)

    Errico, Leonardo A. [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Renteria, Mario [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Petrilli, Helena M. [Instituto de Fisica-DFMT, Universidade de Sao Paulo, C.P. 66318, 05315-970 Sao Paulo, SP (Brazil)]. E-mail: hmpetril@macbeth.if.usp.br

    2007-02-01

    We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO{sub 2}. The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects.

  12. Preparation and characterization of ABS/anhydrous cobalt chloride composites

    Science.gov (United States)

    Shao, Chengli; Shang, Peng; Mao, Yapeng; Li, Qiuying; Wu, Chifei

    2018-01-01

    Anhydrous cobalt chloride (CoCl2) particles filled acrylonitrile-butadiene-styrene (ABS) composites were successfully prepared and investigated. A strong interfacial interaction between CoCl2 particles and ABS matrix was generated by heat pressing at 190 °C for 15 min. SEM results demonstrated that the particles were dispersed uniformly in the matrix. Fourier transform infrared, x-ray photoelectron spectroscopy and electron spin resonance were used for the investigation of the coordination reaction. The interfacial interaction resulted from a solid-state coordination reaction between nitrile groups (-CN) and cobalt ions (Co2+), leading to an increase in mechanical properties and glass transition temperature. Moreover, heat deflection temperatures were measured and proved to achieve an improvement of 30.6 °C when the CoCl2 content was 7 wt%.

  13. Ultra-Low Voltage Class AB Switched Current Memory Cell

    DEFF Research Database (Denmark)

    Igor, Mucha

    1996-01-01

    This paper presents the theoretical basis for the design of class AB switched current memory cells employing floating-gate MOS transistors, suitable for ultra-low-voltage applications. To support the theoretical assumptions circuits based on these cells were designed using a CMOS process with thr......This paper presents the theoretical basis for the design of class AB switched current memory cells employing floating-gate MOS transistors, suitable for ultra-low-voltage applications. To support the theoretical assumptions circuits based on these cells were designed using a CMOS process...... with threshold voltages of 0.9V. Both hand calculations and PSPICE simulations showed that the cells designed allowed a maximum signal range better than +/-13 micoamp, with a supply voltage down to 1V and a quiescent bias current of 1 microamp, resulting in a very high current efficiency and effective power...

  14. Soliton solutions for ABS lattice equations: I. Cauchy matrix approach

    Science.gov (United States)

    Nijhoff, Frank; Atkinson, James; Hietarinta, Jarmo

    2009-10-01

    In recent years there have been new insights into the integrability of quadrilateral lattice equations, i.e. partial difference equations which are the natural discrete analogues of integrable partial differential equations in 1+1 dimensions. In the scalar (i.e. single-field) case, there now exist classification results by Adler, Bobenko and Suris (ABS) leading to some new examples in addition to the lattice equations 'of KdV type' that were known since the late 1970s and early 1980s. In this paper, we review the construction of soliton solutions for the KdV-type lattice equations and use those results to construct N-soliton solutions for all lattice equations in the ABS list except for the elliptic case of Q4, which is left to a separate treatment.

  15. Ab Initio Calculations Of Light-Ion Reactions

    International Nuclear Information System (INIS)

    Navratil, P.; Quaglioni, S.; Roth, R.; Horiuchi, W.

    2012-01-01

    The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.

  16. Complete genome sequence and phylogenetic analyses of an aquabirnavirus isolated from a diseased marbled eel culture in Taiwan.

    Science.gov (United States)

    Wen, Chiu-Ming

    2017-08-01

    An aquabirnavirus was isolated from diseased marbled eels (Anguilla marmorata; MEIPNV1310) with gill haemorrhages and associated mortality. Its genome segment sequences were obtained through next-generation sequencing and compared with published aquabirnavirus sequences. The results indicated that the genome sequence of MEIPNV1310 contains segment A (3099 nucleotides) and segment B (2789 nucleotides). Phylogenetic analysis showed that MEIPNV1310 is closely related to the infectious pancreatic necrosis Ab strain within genogroup II. This genome sequence is beneficial for studying the geographic distribution and evolution of aquabirnaviruses.

  17. Social Media Marketing : CASE: OY SUOMEN LYYRA AB

    OpenAIRE

    Eriksson, Irene

    2012-01-01

    This bachelor thesis was commissioned by Oy Suomen Lyyra Ab, the largest student online media and student card producer for higher education students in Finland. The the-sis objective was to understanding the current social media situation and activity among the students of higher education in Finland, the social media networks that the case company currently uses as well as understanding how to use these networks for successful marketing activities. The quantitative research was conducted in...

  18. Report on the Personnel Dosimetry at AB Atomenergi during 1969

    Energy Technology Data Exchange (ETDEWEB)

    Carlsson, J; Wahlberg, T

    1971-05-15

    This report presents the results of personnel dosimetry at AB Atomenergi during 1969. 24,200 gamma films and 3,300 neutron films were evaluated. 770 urine analyses and 1,150 measurements of body activity were made. The external total body gamma dose for all employees (quarterly doses < 100 mrem are not reported) corresponds to 136 manrem. The highest external total body gamma dose during 1969 to one person was 4,800 mrem

  19. Report on the Personnel Dosimetry at AB Atomenergi during 1968

    Energy Technology Data Exchange (ETDEWEB)

    Carlsson, J; Wahlberg, T

    1969-08-15

    This report presents the results of personnel dosimetry at AB Atomenergi during 1968. 25600 gamma films and 3900 neutron films were evaluated. 1737 urine analyses and 1066 measurements of body activity were made. The external total body gamma dose for all employees (quarterly doses {<=} 100 mrem are not reported) corresponds to 136 manrem. The highest external total body gamma dose during 1968 to one person was 4,500 mrem.

  20. GAUSSIAN 76: an ab initio molecular orbital program

    International Nuclear Information System (INIS)

    Binkley, J.S.; Whiteside, R.; Hariharan, P.C.; Seeger, R.; Hehre, W.J.; Lathan, W.A.; Newton, M.D.; Ditchfield, R.; Pople, J.A.

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans

  1. Report on the Personnel Dosimetry at AB Atomenergi during 1967

    International Nuclear Information System (INIS)

    Carlsson, J.; Wahlberg, T.

    1968-12-01

    This report presents the results of personnel dosimetry at AB Atomenergi during 1967. The external total body gamma dose for all employees (quarterly doses ≤ 100 mrem are not reported) corresponds to 140 manrem. The highest external total body gamma dose during 1967 to one person was 5700 mrem. 24700 gamma films and 3900 neutron films were evaluated. 1988 urine analyses and 989 measurements of body activity were made

  2. Report on the Personnel Dosimetry at AB Atomenergi during 1967

    Energy Technology Data Exchange (ETDEWEB)

    Carlsson, J; Wahlberg, T

    1968-12-15

    This report presents the results of personnel dosimetry at AB Atomenergi during 1967. The external total body gamma dose for all employees (quarterly doses {<=} 100 mrem are not reported) corresponds to 140 manrem. The highest external total body gamma dose during 1967 to one person was 5700 mrem. 24700 gamma films and 3900 neutron films were evaluated. 1988 urine analyses and 989 measurements of body activity were made.

  3. Personality at Work: A Study of Type A-B

    Directory of Open Access Journals (Sweden)

    Amber Raza

    2007-10-01

    Full Text Available The objective of this study was to measure the impact of stressors on personality types in Call Centers. Based on literature survey five potential workplace stressors were identified, namely (1 Task Demands, (2 Role Demands, (3 Interpersonal Demands, (4 Organizational Structure and (5 Organizational Leadership. Based on the literature survey, a relationship model was developed that was inclusive of the above stressors, and three personality types, which were Type A, Type AB and Type B.The sample size for the study was 100. The subjects were supervisors and agents drawn non-randomly from various Call Centers of Karachi. All the subjects completed a questionnaire comprised of 27 questions based on occupational stress index (Srivasta and Singh 1981 and AB Personality Continuum (National Institute of Safety and Health 1975. The three personality types A, B & AB all go through stress, however it is the Type A, which thrives on stress. The sources of stress measured in the study were Task Demand, Role Demand, Interpersonal Demands, Organizational Structure and Organizational Leadership.The stressor that most contributed to the Personality type A’s stress in the study was Interpersonal Demand (0.38, which is justified by the literature review as Personality type A are not team players and prefer to work alone.Whereas Personality type B was stressed because of Role Demand (0.38 which is also proved by the literature review as personality type B are laid back and do not take there roles seriously. Hence it can be concluded that it type A tends to cope well with stress as compared to type AB and type B. The performance of the respondents can be made better if the supervisors are aware of the personality types and thereby motivate them according.

  4. Ab initio study of hot electrons in GaAs

    OpenAIRE

    Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B.; Louie, Steven G.

    2015-01-01

    Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation...

  5. The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

    Science.gov (United States)

    Aversano, Riccardo; Contaldi, Felice; Ercolano, Maria Raffaella; Grosso, Valentina; Iorizzo, Massimo; Tatino, Filippo; Xumerle, Luciano; Dal Molin, Alessandra; Avanzato, Carla; Ferrarini, Alberto; Delledonne, Massimo; Sanseverino, Walter; Cigliano, Riccardo Aiese; Capella-Gutierrez, Salvador; Gabaldón, Toni; Frusciante, Luigi; Bradeen, James M.; Carputo, Domenico

    2015-01-01

    Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes. PMID:25873387

  6. Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)

    2014-09-28

    We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).

  7. Monte Carlo simulation of AB-copolymers with saturating bonds

    CERN Document Server

    Chertovich, A V; Khokhlov, A R; Bohr, J

    2003-01-01

    Structural transitions in a single AB-copolymer chain where saturating bonds can be formed between A-and B-units are studied by means of Monte Carlo computer simulations using the bond fluctuation model. Three transitions are found, coil-globule, coil-hairpin and globule-hairpin, depending on the nature of a particular AB-sequence: statistical random sequence, diblock sequence and 'random-complementary' sequence (one-half of such an AB-sequence is random with Bernoulli statistics while the other half is complementary to the first one). The properties of random-complementary sequences are closer to those of diblock sequences than to the properties of random sequences. The model (although quite rough) is expected to represent some basic features of real RNA molecules, i.e. the formation of secondary structure of RNA due to hydrogen bonding of corresponding bases and stacking interactions of the base pairs in helixes. We introduce the notation of RNA-like copolymers and discuss in what sense the sequences studie...

  8. Ab initio nuclear structure - the large sparse matrix eigenvalue problem

    Energy Technology Data Exchange (ETDEWEB)

    Vary, James P; Maris, Pieter [Department of Physics, Iowa State University, Ames, IA, 50011 (United States); Ng, Esmond; Yang, Chao [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Sosonkina, Masha, E-mail: jvary@iastate.ed [Scalable Computing Laboratory, Ames Laboratory, Iowa State University, Ames, IA, 50011 (United States)

    2009-07-01

    The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab initio no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds 10{sup 10} and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.

  9. Ab initio nuclear structure - the large sparse matrix eigenvalue problem

    International Nuclear Information System (INIS)

    Vary, James P; Maris, Pieter; Ng, Esmond; Yang, Chao; Sosonkina, Masha

    2009-01-01

    The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab initio no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds 10 10 and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.

  10. Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes

    International Nuclear Information System (INIS)

    Draayer, Jerry P.

    2014-01-01

    We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).

  11. Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

    Science.gov (United States)

    Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

    In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

  12. Pressure tracking control of vehicle ABS using piezo valve modulator

    Science.gov (United States)

    Jeon, Juncheol; Choi, Seung-Bok

    2011-03-01

    This paper presents a wheel slip control for the ABS(anti-lock brake system) of a passenger vehicle using a controllable piezo valve modulator. The ABS is designed to optimize for braking effectiveness and good steerability. As a first step, the principal design parameters of the piezo valve and pressure modulator are appropriately determined by considering the braking pressure variation during the ABS operation. The proposed piezo valve consists of a flapper, pneumatic circuit and a piezostack actuator. In order to get wide control range of the pressure, the pressure modulator is desired. The modulator consists of a dual-type cylinder filled with different substances (fluid and gas) and a piston rod moving vertical axis to transmit the force. Subsequently, a quarter car wheel slip model is formulated and integrated with the governing equation of the piezo valve modulator. A sliding mode controller to achieve the desired slip rate is then designed and implemented. Braking control performances such as brake pressure and slip rate are evaluated via computer simulations.

  13. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Makhov, Dmitry V.; Shalashilin, Dmitrii V. [Department of Chemistry, University of Leeds, Leeds LS2 9JT (United Kingdom); Glover, William J.; Martinez, Todd J. [Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  14. Studies on the runaway reaction of ABS polymerization process

    International Nuclear Information System (INIS)

    Hu, K.-H.; Kao, C.-S.; Duh, Y.-S.

    2008-01-01

    Taiwan has the largest acrylonitrile-butadiene-styrene (ABS) copolymer production in the world. Preventing on unexpected exothermic reactions and related emergency relief hazard is essential in the safety control of ABS emulsion polymerization. A VSP2 (Vent Sizing Package 2) apparatus is capable of studying both normal and abnormal conditions (e.g., cooling failure, mischarge, etc.) of industrial process. In this study, the scenarios were verified from the following abnormal conditions: loss of cooling, double charge of initiator, overcharge of monomer, without charge of solvent, and external fire. An external fire with constant heating will promote higher self-heat rate and this is recommended as the worst case scenario of emulsion polymerization on butadiene. Cooling failure coupled with bulk system of reactant was determined to be the credible worst case in ABS emulsion polymerization. Finally, the emergency vent sizing based on thermokinetics from VSP associated with DIERS methodology were used for evaluating the vent sizing and compared to that of the industrial plants

  15. Computational genomics of hyperthermophiles

    NARCIS (Netherlands)

    Werken, van de H.J.G.

    2008-01-01

    With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

  16. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  17. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  18. Structural insights and ab initio sequencing within the DING proteins family

    International Nuclear Information System (INIS)

    Elias, Mikael; Liebschner, Dorothee; Gotthard, Guillaume; Chabriere, Eric

    2011-01-01

    DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated

  19. SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

    Science.gov (United States)

    Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

    2017-10-01

    As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

  20. Structural insights and ab initio sequencing within the DING proteins family

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Mikael, E-mail: mikael.elias@weizmann.ac.il [Weizmann Institute of Science, Rehovot (Israel); Liebschner, Dorothee [CRM2, Nancy Université (France); Gotthard, Guillaume; Chabriere, Eric [AFMB, Université Aix-Marseille II (France)

    2011-01-01

    DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.

  1. nGASP - the nematode genome annotation assessment project

    Energy Technology Data Exchange (ETDEWEB)

    Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

    2008-12-19

    While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C

  2. Towards hydrogen metallization: an Ab initio approach; Vers la metallisation de l`hydrogene: approche AB initio

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, St

    1999-12-31

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.

  3. Towards hydrogen metallization: an Ab initio approach; Vers la metallisation de l`hydrogene: approche AB initio

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, St

    1998-12-31

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.

  4. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  5. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  6. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  7. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  8. The complete mitochondrial genome of Ambastaia sidthimunki (Cypriniformes: Cobitidae).

    Science.gov (United States)

    Yu, Peng; Wei, Min; Yang, Qichao; Yang, Yingming; Wan, Quan

    2016-09-01

    Ambastaia sidthimunki is a beautiful small-sized fish and it was categorized as Endangered B2ab (iii,v) in the IUCN Red List. In this study, we reported the complete mitochondrial genome of the A. sidthimunki. The mitochondrial genome sequence was a circular molecule with 16,574 bp in length, and it contained 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, an L-strand replication origin (OL) and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 26.94% for C, 15.55% for G, 31.84% for A and 25.67% for T, with an AT content of 57.51%. This research contributes new molecular data for the conservation of this Endangered species.

  9. Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria.

    Science.gov (United States)

    Ghai, Rohit; Mehrshad, Maliheh; Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco

    2017-01-01

    Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a 'trojan horse' strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.

  10. Ab initio study of isomerism in molecular Li2AB+ ions with 12 and 14 valence electrons

    International Nuclear Information System (INIS)

    Charkin, O.P.; Klimenko, N.M.; Mak-Ki, M.L.; Shlojer, P.R.

    1997-01-01

    Ab initio calculations of potential energy surfaces (PES) of molecular ions Li 2 AB + with 12 and 14 valence electrons have been made in the framework of approximations MP2/6-31G*//HF/6-31G*+ZPE(HF/6-31G*) and MP4SDTQ/6-31*//MP2/6-31G*+ZPE(MP2/6-31G*). The following most favourable structures have been found: a double-terminal linear for LiNO + (a triplet); a plane bicyclic one for Li 2 OF + , Li 2 SCl + , Li 2 NO + (a singlet) and Li 2 PS + (a singlet), where both cations are coordinated to A-B bond; rectangular (T-shaped) for Li 2 OCl + and SFLi + , as well as for LiNS + and POLi 2 + ions in singlet and triplet states; in the form of a half-opened butterfly for Li 2 PS + (a triplet) and Li 2 SCl +

  11. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  12. Draft Genome Sequence of Lactobacillus sp. Strain TCF032-E4, Isolated from Fermented Radish.

    Science.gov (United States)

    Mao, Yuejian; Chen, Meng; Horvath, Philippe

    2015-07-30

    Here, we report the draft genome sequence of Lactobacillus sp. strain TCF032-E4 (= CCTCC AB2015090 = DSM 100358), isolated from a Chinese fermented radish. The total length of the 57 contigs is about 2.9 Mb, with a G+C content of 43.5 mol% and 2,797 predicted coding sequences (CDSs). Copyright © 2015 Mao et al.

  13. Genome Sequence of Enterococcus faecium Strain ICIS 96 Demonstrating Intermicrobial Antagonism Associated with Bacteriocin Production.

    Science.gov (United States)

    Pashkova, Tatiana M; Vasilchenko, Alexey S; Khlopko, Yuriy A; Kochkina, Elena E; Kartashova, Olga L; Sycheva, Maria V

    2018-03-08

    We report here the complete genome sequence of Enterococcus faecium strain ICIS 96, which was isolated from the feces of a horse. Bacteriological characterization of strain ICIS 96 revealed the absence of pathogenicity factors, while its spectrum of antagonistic activity was found to be broad, having activities associated with both Gram-positive and Gram-negative bacteria. Analysis of the E. faecium ICIS 96 genome revealed five genes associated with antimicrobial activity (enterocin [ent] A, ent B, lactobin A/cerein 7b, and ent L50 A/B). No genes that correlate with human pathogenicity were identified. Copyright © 2018 Pashkova et al.

  14. Genome sequence of the photoarsenotrophic bacterium Ectothiorhodospira sp. strain BSL-9, isolated from a hypersaline alkaline arsenic-rich extreme environment

    Science.gov (United States)

    Hernandez-Maldonado, Jaime; Stoneburner, Brendon; Boren, Alison; Miller, Laurence; Rosen, Michael R.; Oremland, Ronald S.; Saltikov, Chad W

    2016-01-01

    The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.

  15. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PROCEDURES AND REQUIREMENTS FOR PLANT-INCORPORATED PROTECTANTS...

  16. Genome-derived vaccines.

    Science.gov (United States)

    De Groot, Anne S; Rappuoli, Rino

    2004-02-01

    Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

  17. The Banana Genome Hub

    Science.gov (United States)

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  18. Genomic instability following irradiation

    International Nuclear Information System (INIS)

    Hacker-Klom, U.B.; Goehde, W.

    2001-01-01

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  19. Traditional medicine and genomics

    Directory of Open Access Journals (Sweden)

    Kalpana Joshi

    2010-01-01

    Full Text Available ′Omics′ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  20. Traditional medicine and genomics.

    Science.gov (United States)

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    'Omics' developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  1. Bacillus subtilis genome diversity.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  2. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  3. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  4. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  5. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  6. Cooperative effects in spherical spasers: Ab initio analytical model

    Science.gov (United States)

    Bordo, V. G.

    2017-06-01

    A fully analytical semiclassical theory of cooperative optical processes which occur in an ensemble of molecules embedded in a spherical core-shell nanoparticle is developed from first principles. Both the plasmonic Dicke effect and spaser generation are investigated for the designs in which a shell/core contains an arbitrarily large number of active molecules in the vicinity of a metallic core/shell. An essential aspect of the theory is an ab initio account of the feedback from the core/shell boundaries which significantly modifies the molecular dynamics. The theory provides rigorous, albeit simple and physically transparent, criteria for both plasmonic superradiance and surface plasmon generation.

  7. Tailoring magnetoresistance at the atomic level: An ab initio study

    KAUST Repository

    Tao, Kun

    2012-01-05

    The possibility of manipulating the tunneling magnetoresistance (TMR) of antiferromagnetic nanostructures is predicted in the framework of ab initio calculations. By the example of a junction composed of an antiferromagnetic dimer and a spin-polarized scanning tunneling microscopy tip we show that the TMR can be tuned and even reversed in sign by lateral and vertical movements of the tip. Moreover, our finite-bias calculations demonstrate that the magnitude and the sign of the TMR can also be tuned by an external voltage. © 2012 American Physical Society.

  8. Tailoring magnetoresistance at the atomic level: An ab initio study

    KAUST Repository

    Tao, Kun; Stepanyuk, V. S.; Rungger, I.; Sanvito, S.

    2012-01-01

    The possibility of manipulating the tunneling magnetoresistance (TMR) of antiferromagnetic nanostructures is predicted in the framework of ab initio calculations. By the example of a junction composed of an antiferromagnetic dimer and a spin-polarized scanning tunneling microscopy tip we show that the TMR can be tuned and even reversed in sign by lateral and vertical movements of the tip. Moreover, our finite-bias calculations demonstrate that the magnitude and the sign of the TMR can also be tuned by an external voltage. © 2012 American Physical Society.

  9. Computer integrated construction at AB building in reprocessing plant

    International Nuclear Information System (INIS)

    Takami, Masahiro; Azuchi, Takehiro; Sekiguchi, Kenji

    1999-01-01

    JNFL (Japan Nuclear Fuel Limited) is now processing with construction of the spent nuclear fuel reprocessing plant at Rokkasho Village in Aomori Prefecture, which is coming near to the busiest period of construction. Now we are trying to complete the civil work of AB Building and KA Building in a very short construction term by applying CIC (Computer Integrated Construction) concept, in spite of its hard construction conditions, such as the massive and complicated building structure, interferences with M and E (Mechanical and Electrical) work, severe winter weather, remote site location, etc. The key technologies of CIC are three-dimensional CAD, information network, and prefabrication and mechanization of site work. (author)

  10. Ab initio calculations on hydrogen storage in porous carbons

    International Nuclear Information System (INIS)

    Maresca, O.; Marinelli, F.; Pellenq, R.J.M.; Duclaux, L.; Azais, Ph.; Conard, J.

    2005-01-01

    We have investigated through ab initio computations the possible ways to achieve efficient hydrogen storage on carbons. Firstly, we have considered how the curvature of a carbon surface could affect the chemisorption of atomic H 0 Secondly, we show that electron donor elements such as Li and K, used as dopants for the carbon substrate, strongly enhance the physi-sorption energy of H 2 , allowing in principle its storage in this type of material at room temperature under mild conditions of pressure. (authors)

  11. Routine calculation of ab initio melting curves: application to aluminum

    OpenAIRE

    Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean

    2014-01-01

    We present a simple, fast, and reliable method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of [Lin et al., J. Chem. Phys. 119, 11792 (2003)] and its improved version given by [Desjarlais, Phys. Rev. E, 88, 062145 (2013)]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find t...

  12. TiAl doping by vanadium: ab initio study

    International Nuclear Information System (INIS)

    Smirnova, E.A.; Isaev, Eh.I.; Vekilov, Yu.Kh.

    2004-01-01

    Tetragonality degree in TiAl and vanadium doping effect on it were studied using the methods of calculation based on approximation of coherent potential and ab initio pseudopotentials. It is shown that vanadium substitution for Ti sublattice atoms entails increase in tetragonality degree but with substitution of the atoms in aluminium sublattice the tetragonality of the TiAl:V alloy decreases and at the content of vanadium about 8 at. % the lattice becomes actually cubical. In its turn, it may result in increase in TiAl ductility, the alloy being brittle at low temperatures [ru

  13. Ab initio calculation of tensile strength in iron

    Czech Academy of Sciences Publication Activity Database

    Friák, Martin; Šob, Mojmír; Vitek, V.

    2003-01-01

    Roč. 83, 31-34 (2003), s. 3529-3537 ISSN 1478-6435. [Multiscale Materials Modelling: Working Theory for Industry /1./. London, 17.06.2002-20.06.2002] R&D Projects: GA AV ČR IAA1041302; GA ČR GA202/03/1351; GA MŠk OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * electronic structure * theoretical tensile strength Subject RIV: BM - Solid Matter Physics ; Magnetism

  14. Ab initio molecular dynamics in a finite homogeneous electric field.

    Science.gov (United States)

    Umari, P; Pasquarello, Alfredo

    2002-10-07

    We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

  15. Magnetoband structures of AB-stacked zigzag nanographite ribbons

    Energy Technology Data Exchange (ETDEWEB)

    Chang, C.P.; Chiu, C.W.; Shyu, F.L.; Chen, R.B.; Lin, M.F

    2002-12-30

    Magnetoband structures of AB-stacked zigzag nanographite ribbons are studied by the tight-binding model. The magnetic field changes band width, energy space, and energy dispersions (the produce of Landau subbands and Landau levels). It causes many zero energy points. Such points and corresponding localized states are studied in detail. There are certain important differences between localized states and edge states. Oscillation period of Landau subbands are determined by these points. The interribbon interactions also affect magnetoband structures, such as energy dispersions, band width, oscillation period of Landau subbands, and flux dependence of Hofstadter butterflies.

  16. Genomics and fish adaptation

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  17. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  18. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  19. Genomic definition of species

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  20. Structural genomics in endocrinology

    NARCIS (Netherlands)

    Smit, J. W.; Romijn, J. A.

    2001-01-01

    Traditionally, endocrine research evolved from the phenotypical characterisation of endocrine disorders to the identification of underlying molecular pathophysiology. This approach has been, and still is, extremely successful. The introduction of genomics and proteomics has resulted in a reversal of

  1. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  2. Annotating individual human genomes.

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J

    2011-10-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. ANNOTATING INDIVIDUAL HUMAN GENOMES*

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.

    2014-01-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162

  4. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  5. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  6. The human genome project

    International Nuclear Information System (INIS)

    Worton, R.

    1996-01-01

    The Human Genome Project is a massive international research project, costing 3 to 5 billion dollars and expected to take 15 years, which will identify the all the genes in the human genome - i.e. the complete sequence of bases in human DNA. The prize will be the ability to identify genes causing or predisposing to disease, and in some cases the development of gene therapy, but this new knowledge will raise important ethical issues

  7. Decoding the human genome

    CERN Multimedia

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E

    2002-01-01

    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  8. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  9. Human Germline Genome Editing

    OpenAIRE

    Ormond, Kelly E.; Mortlock, Douglas P.; Scholes, Derek T.; Bombard, Yvonne; Brody, Lawrence C.; Faucett, W. Andrew; Garrison, Nanibaa’ A.; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E.

    2017-01-01

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Gen...

  10. RadGenomics project

    Energy Technology Data Exchange (ETDEWEB)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

    2002-06-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  11. Comparative Genome Viewer

    International Nuclear Information System (INIS)

    Molineris, I.; Sales, G.

    2009-01-01

    The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

  12. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  13. RadGenomics project

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

    2002-01-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  14. Ultrafast comparison of personal genomes

    OpenAIRE

    Mauldin, Denise; Hood, Leroy; Robinson, Max; Glusman, Gustavo

    2017-01-01

    We present an ultra-fast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into 'genome fingerprints' that can be readily compared across sequencing technologies and reference versions. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. This enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative s...

  15. Equations of state of heavy metals: ab initio approaches; Equations d'etat des metaux lourds: approches ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, S.; Jollet, F.; Jomard, G.; Siberchicot, B.; Torrent, M.; Zerah, G.; Amadon, B.; Bouchet, J.; Richard, N.; Robert, G. [CEA Bruyeres-le-Chatel, 91 (France)

    2005-07-01

    The determination of equations of states of heavy metals through ab initio calculation, i.e. without any adjustable parameter, allows to access to pressure and temperature thermodynamic conditions sometimes inaccessible to experiment. To perform such calculations, density functional theory (DFT) is a good starting point: when electronic densities are homogeneous enough, the local density approximation (LDA) remarkably accounts for thermodynamic properties of heavy metals, such as tantalum, or the light actinides, as well for static properties - equilibrium volume, elastic constants - as for dynamical quantities like phonon spectra. For heavier elements, like neptunium or plutonium, relativistic effects and strong electronic interactions must be taken into account, which requires more sophisticated theoretical approaches. (authors)

  16. Improved radioimaging and tumor localization with monoclonal F(ab')2

    International Nuclear Information System (INIS)

    Wahl, R.L.; Parker, C.W.; Philpott, G.W.

    1983-01-01

    Monoclonal anti-tumor antibodies have great promise for radioimmunodetection and localization of tumors. Fab and F(ab')2 fragments, which lack the Fc fragment of antibody (Ab), are cleared more rapidly from the circulation and may have less nonspecific tissue binding than intact Ab. In radioimaging studies using a murine monoclonal antibody to carcinoembryonic antigen in a human colon carcinoma xenografted into hamsters, F(ab')2 fragments were shown superior to Fab fragments and intact antibody for scintiscanning. In double-label experiments with anti-CEA antibody and control monoclonal IgG, F(ab')2 fragments were found to give better and more rapid specific tumor localization than intact antibody or Fab fragments. F(ab')2 fragments offer significant promise for tumor imaging and possibly therapy

  17. Pengaruh bahan pengisi serat kaca terhadap sifat fisik dan kristalinitas polipaduan PC/ABS

    Directory of Open Access Journals (Sweden)

    Dwi Wahini Nurhajati

    2017-06-01

    Full Text Available This research aimed to determine the effects of the addition of glass fibers on the physical and crystallinity properties of PC/ABS polyblends. The ratio of PC/ABS used in this research was 75/25, while the addition of glass fibers ranged from 0; 5; 10; to 15 phr (based on the weight of PC/ABS. Polyblends of PC/ABS/glass fibers were prepared in a twin screw extruder. The test results showed that density and tensile strength of PC/ABS polyblends increased with an increase in the glass fiber content. The presence of glass fibers decreased MFI and impact strength of these PC/ABS polyblends. The functional groups were determined by the fourier transform infrared (FTIR spectrophotometer while crystallinity was examined using X-ray diffractometer (XRD.

  18. Microhook ab interno trabeculotomy, a novel minimally invasive glaucoma surgery

    Directory of Open Access Journals (Sweden)

    Tanito M

    2017-12-01

    Full Text Available Masaki Tanito Division of Ophthalmology, Matsue Red Cross Hospital, Matsue, Japan Abstract: Trabeculotomy (LOT is performed to reduce the intraocular pressure in patients with glaucoma, both in children and adults. It relieves the resistance to aqueous flow by cleaving the trabecular meshwork and the inner walls of Schlemm’s canal. Microhook ab interno LOT (µLOT, a novel minimally invasive glaucoma surgery, incises trabecular meshwork using small hooks that are inserted through corneal side ports. An initial case series reported that both µLOT alone and combination of µLOT and cataract surgery normalize the intraocular pressure during the early postoperative period in Japanese patients with glaucoma. Microhook can incise the inner wall of Schlemm’s canal without damaging its outer wall easier than the regular straight knife that is used during goniotomy. Advantages of µLOT include: a wider extent of LOT (two-thirds of the circumference, a simpler surgical technique, being less invasiveness to the ocular surface, a shorter surgical time than traditional ab externo LOT, and no requirement for expensive devices. In this paper, the surgical technique of µLOT and tips of the technique are introduced. Keywords: trabecular meshwork, Schlemm’s canal, intraocular pressure, surgical procedure, glaucoma

  19. Ab initio theory and calculations of X-ray spectra

    International Nuclear Information System (INIS)

    Rehr, J.J.; Kas, J.J.; Prange, M.P.; Sorini, A.P.; Takimoto, Y.; Vila, F.

    2009-01-01

    There has been dramatic progress in recent years both in the calculation and interpretation of various x-ray spectroscopies. However, current theoretical calculations often use a number of simplified models to account for many-body effects, in lieu of first principles calculations. In an effort to overcome these limitations we describe in this article a number of recent advances in theory and in theoretical codes which offer the prospect of parameter free calculations that include the dominant many-body effects. These advances are based on ab initio calculations of the dielectric and vibrational response of a system. Calculations of the dielectric function over a broad spectrum yield system dependent self-energies and mean-free paths, as well as intrinsic losses due to multielectron excitations. Calculations of the dynamical matrix yield vibrational damping in terms of multiple-scattering Debye-Waller factors. Our ab initio methods for determining these many-body effects have led to new, improved, and broadly applicable x-ray and electron spectroscopy codes. (authors)

  20. Step growth of an AB2 monomer, with cycle formation

    DEFF Research Database (Denmark)

    Cameron, Colin; Fawcett, Allan H.; Hetherington, Cecil R.

    1998-01-01

    A computer-based lattice model of the step growth reaction of an AB2 monomer, the next elaborate system after an AB monomer, has been devised that allows the simultaneous and explicit occurrence of inter- and intramolecular reactions of A and B groups of the flexible and moving molecules according...... with fractal characteristics. Growth stops when each molecule contains a cycle. For the model explored, in which six lattice sites are used for each monomer, the limiting value of the number average degree of polymerization, 〈x〉n,∞, is 14.6(±0.3) (after infinite time). The occurrence within the system of rings...... of m residues (m=1,2,3,...) is found to depend upon m and the extent of reaction of the A groups, pa, according to Rm=C0pm am-2.71, the constant C0 reflecting the structure of the lattice and the monomer, and being shown to determine the final degree of polymerization. The exponent of the integers m...

  1. (4)He Thermophysical Properties: New Ab Initio Calculations.

    Science.gov (United States)

    Hurly, John J; Mehl, James B

    2007-01-01

    Since 2000, atomic physicists have reduced the uncertainty of the helium-helium "ab initio" potential; for example, from approximately 0.6 % to 0.1 % at 4 bohr, and from 0.8 % to 0.1 % at 5.6 bohr. These results led us to: (1) construct a new inter-atomic potential ϕ 07, (2) recalculate values of the second virial coefficient, the viscosity, and the thermal conductivity of (4)He from 1 K to 10,000 K, and (3), analyze the uncertainties of the thermophysical properties that propagate from the uncertainty of ϕ 07 and from the Born-Oppenheimer approximation of the electron-nucleon quantum mechanical system. We correct minor errors in a previous publication [J. J. Hurly and M. R. Moldover, J. Res. Nat. Inst. Standards Technol. 105, 667 (2000)] and compare our results with selected data published after 2000. The ab initio results tabulated here can serve as standards for the measurement of thermophysical properties.

  2. 4He Thermophysical Properties: New Ab Initio Calculations

    Science.gov (United States)

    Hurly, John J.; Mehl, James B.

    2007-01-01

    Since 2000, atomic physicists have reduced the uncertainty of the helium-helium “ab initio” potential; for example, from approximately 0.6 % to 0.1 % at 4 bohr, and from 0.8 % to 0.1 % at 5.6 bohr. These results led us to: (1) construct a new inter-atomic potential ϕ07, (2) recalculate values of the second virial coefficient, the viscosity, and the thermal conductivity of 4He from 1 K to 10,000 K, and (3), analyze the uncertainties of the thermophysical properties that propagate from the uncertainty of ϕ07 and from the Born-Oppenheimer approximation of the electron-nucleon quantum mechanical system. We correct minor errors in a previous publication [J. J. Hurly and M. R. Moldover, J. Res. Nat. Inst. Standards Technol. 105, 667 (2000)] and compare our results with selected data published after 2000. The ab initio results tabulated here can serve as standards for the measurement of thermophysical properties. PMID:27110456

  3. Ab initio thermodynamic model for magnesium carbonates and hydrates.

    Science.gov (United States)

    Chaka, Anne M; Felmy, Andrew R

    2014-09-04

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

  4. Development and Application of Loop-Mediated Isothermal Amplification Assays for Rapid Visual Detection of cry2Ab and cry3A Genes in Genetically-Modified Crops

    Directory of Open Access Journals (Sweden)

    Feiwu Li

    2014-08-01

    Full Text Available The cry2Ab and cry3A genes are two of the most important insect-resistant exogenous genes and had been widely used in genetically-modified crops. To develop more effective alternatives for the quick identification of genetically-modified organisms (GMOs containing these genes, a rapid and visual loop-mediated isothermal amplification (LAMP method to detect the cry2Ab and cry3A genes is described in this study. The LAMP assay can be finished within 60 min at an isothermal condition of 63 °C. The derived LAMP products can be obtained by a real-time turbidimeter via monitoring the white turbidity or directly observed by the naked eye through adding SYBR Green I dye. The specificity of the LAMP assay was determined by analyzing thirteen insect-resistant genetically-modified (GM crop events with different Bt genes. Furthermore, the sensitivity of the LAMP assay was evaluated by diluting the template genomic DNA. Results showed that the limit of detection of the established LAMP assays was approximately five copies of haploid genomic DNA, about five-fold greater than that of conventional PCR assays. All of the results indicated that this established rapid and visual LAMP assay was quick, accurate and cost effective, with high specificity and sensitivity. In addition, this method does not need specific expensive instruments or facilities, which can provide a simpler and quicker approach to detecting the cry2Ab and cry3A genes in GM crops, especially for on-site, large-scale test purposes in the field.

  5. Development and application of loop-mediated isothermal amplification assays for rapid visual detection of cry2Ab and cry3A genes in genetically-modified crops.

    Science.gov (United States)

    Li, Feiwu; Yan, Wei; Long, Likun; Qi, Xing; Li, Congcong; Zhang, Shihong

    2014-08-27

    The cry2Ab and cry3A genes are two of the most important insect-resistant exogenous genes and had been widely used in genetically-modified crops. To develop more effective alternatives for the quick identification of genetically-modified organisms (GMOs) containing these genes, a rapid and visual loop-mediated isothermal amplification (LAMP) method to detect the cry2Ab and cry3A genes is described in this study. The LAMP assay can be finished within 60 min at an isothermal condition of 63 °C. The derived LAMP products can be obtained by a real-time turbidimeter via monitoring the white turbidity or directly observed by the naked eye through adding SYBR Green I dye. The specificity of the LAMP assay was determined by analyzing thirteen insect-resistant genetically-modified (GM) crop events with different Bt genes. Furthermore, the sensitivity of the LAMP assay was evaluated by diluting the template genomic DNA. Results showed that the limit of detection of the established LAMP assays was approximately five copies of haploid genomic DNA, about five-fold greater than that of conventional PCR assays. All of the results indicated that this established rapid and visual LAMP assay was quick, accurate and cost effective, with high specificity and sensitivity. In addition, this method does not need specific expensive instruments or facilities, which can provide a simpler and quicker approach to detecting the cry2Ab and cry3A genes in GM crops, especially for on-site, large-scale test purposes in the field.

  6. Genomics using the Assembly of the Mink Genome

    DEFF Research Database (Denmark)

    Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

    2018-01-01

    The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

  7. The B-subdomain of the Xenopus laevis XFIN KRAB-AB domain is responsible for its weaker transcriptional repressor activity compared to human ZNF10/Kox1.

    Science.gov (United States)

    Born, Nadine; Thiesen, Hans-Jürgen; Lorenz, Peter

    2014-01-01

    The Krüppel-associated box (KRAB) domain interacts with the nuclear hub protein TRIM28 to initiate or mediate chromatin-dependent processes like transcriptional repression, imprinting or suppression of endogenous retroviruses. The prototype KRAB domain initially identified in ZNF10/KOX1 encompasses two subdomains A and B that are found in hundreds of zinc finger transcription factors studied in human and murine genomes. Here we demonstrate for the first time transcriptional repressor activity of an amphibian KRAB domain. After sequence correction, the updated KRAB-AB domain of zinc finger protein XFIN from the frog Xenopus laevis was found to confer transcriptional repression in reporter assays in Xenopus laevis A6 kidney cells as well as in human HeLa, but not in the minnow Pimephales promelas fish cell line EPC. Binding of the XFIN KRAB-AB domain to human TRIM28 was demonstrated in a classical co-immunoprecipitation approach and visualized in a single-cell compartmentalization assay. XFIN-AB displayed reduced potency in repression as well as lower strength of interaction with TRIM28 compared to ZNF10 KRAB-AB. KRAB-B subdomain swapping between the two KRAB domains indicated that it was mainly the KRAB-B subdomain of XFIN that was responsible for its lower capacity in repression and binding to human TRIM28. In EPC fish cells, ZNF10 and XFIN KRAB repressor activity could be partially restored to low levels by adding exogenous human TRIM28. In contrast to XFIN, we did not find any transcriptional repression activity for the KRAB-like domain of human PRDM9 in HeLa cells. PRDM9 is thought to harbor an evolutionary older domain related to KRAB whose homologs even occur in invertebrates. Our results support the notion that functional bona fide KRAB domains which confer transcriptional repression and interact with TRIM28 most likely co-evolved together with TRIM28 at the beginning of tetrapode evolution.

  8. Genome size analyses of Pucciniales reveal the largest fungal genomes.

    Science.gov (United States)

    Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

    2014-01-01

    Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  9. The combined benefits of motorcycle antilock braking systems (ABS) in preventing crashes and reducing crash severity.

    Science.gov (United States)

    Rizzi, Matteo; Kullgren, Anders; Tingvall, Claes

    2016-01-01

    Several studies have reported the benefits of motorcycle antilock braking systems (ABS) in reducing injury crashes, due to improved stability and braking performance. Both aspects may prevent crashes but may also reduce the crash severity when a collision occurs. However, it is still unknown to what extent the reductions in injury crashes with ABS may be due to a combination of these mechanisms. Swedish hospital and police reports (2003-2012) were used. The risk for permanent medical impairment (RPMI) was calculated, showing the risk of at least 1 or 10% permanent medical impairment. In total, 165 crashes involving ABS-equipped motorcycles were compared with 500 crashes with similar motorcycles without ABS. The analysis was performed in 3 steps. First, the reduction in emergency care visits with ABS was calculated using an induced exposure approach. Secondly, the injury mitigating effects of ABS were investigated. The mean RPMI 1+ and RPMI 10+ were analyzed for different crash types. The distributions of impairing injuries (PMI 1+) and severely impairing injuries (PMI 10+) were also analyzed. In the third step, the total reduction of PMI 1+ and PMI 10+ injured motorcyclists was calculated by combining the reductions found in the previous steps. An additional analysis of combined braking systems (CBS) together with ABS was also performed. The results showed that emergency care visits were reduced by 47% with ABS. In the second step, it was found that the mean RPMI 1+ and RPMI 10+ with ABS were 15 and 37% lower, respectively. Finally, the third step showed that the total reductions in terms of crash avoidance and mitigation of PMI 1+ and PMI 10+ injured motorcyclists with ABS were 67 and 55%, respectively. However, PMI 1+ and PMI 10+ leg injuries were not reduced by ABS to the same extent. Indications were found suggesting that the benefits of ABS together with CBS may be greater than ABS alone. This article indicated that motorcycle ABS reduced impairing injuries

  10. Identification of Bacillus thuringiensis Cry1AbMod binding-proteins from Spodoptera frugiperda.

    Science.gov (United States)

    Martínez de Castro, Diana L; García-Gómez, Blanca I; Gómez, Isabel; Bravo, Alejandra; Soberón, Mario

    2017-12-01

    Bacillus thuringiensis Cry toxins are currently used for pest control in transgenic crops but evolution of resistance by the insect pests threatens the use of this technology. The Cry1AbMod toxin was engineered to lack the alpha helix-1 of the parental Cry1Ab toxin and was shown to counter resistance to Cry1Ab and Cry1Ac toxins in different insect species including the fall armyworm Spodoptera frugiperda. In addition, Cry1AbMod showed enhanced toxicity to Cry1Ab-susceptible S. frugiperda populations. To gain insights into the mechanisms of this Cry1AbMod-enhanced toxicity, we isolated the Cry1AbMod toxin binding proteins from S. frugiperda brush border membrane vesicles (BBMV), which were identified by pull-down assay and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The LC-MS/MS results indicated that Cry1AbMod toxin could bind to four classes of aminopeptidase (N1, N3, N4 y N5) and actin, with the highest amino acid sequence coverage acquired for APN 1 and APN4. In addition to these proteins, we found other proteins not previously described as Cry toxin binding proteins. This is the first report that suggests the interaction between Cry1AbMod and APN in S. frugiperda. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Comparative Study of Electroless Copper Film on Different Self-Assembled Monolayers Modified ABS Substrate

    Directory of Open Access Journals (Sweden)

    Jiushuai Xu

    2014-04-01

    Full Text Available Copper films were grown on (3-Mercaptopropyltrimethoxysilane (MPTMS, (3-Aminopropyltriethoxysilane (APTES and 6-(3-(triethoxysilylpropylamino-1,3,5- triazine-2,4-dithiol monosodium (TES self-assembled monolayers (SAMs modified acrylonitrile-butadiene-styrene (ABS substrate via electroless copper plating. The copper films were examined using scanning electron microscopy (SEM and X-ray diffraction (XRD. Their individual deposition rate and contact angle were also investigated to compare the properties of SAMs and electroless copper films. The results indicated that the formation of copper nuclei on the TES-SAMs modified ABS substrate was faster than those on the MPTMS-SAMs and APTES-SAMs modified ABS substrate. SEM images revealed that the copper film on TES-SAM modified ABS substrate was smooth and uniform, and the density of copper nuclei was much higher. Compared with that of TES-SAMs modified resin, the coverage of copper nuclei on MPTMS and APTES modified ABS substrate was very limited and the copper particle size was too big. The adhesion property test demonstrated that all the SAMs enhanced the interfacial interaction between copper plating and ABS substrate. XRD analysis showed that the copper film deposited on SAM-modified ABS substrate had a structure with Cu(111 preferred orientation, and the copper film deposited on TES-SAMs modified ABS substrate is better than that deposited on MPTMS-SAMs or APTES-SAMs modified ABS resins in electromigrtion resistance.

  12. Development of Anti-lock Braking System (ABS) for Vehicles Braking

    Science.gov (United States)

    Minh, Vu Trieu; Oamen, Godwin; Vassiljeva, Kristina; Teder, Leo

    2016-11-01

    This paper develops a real laboratory of anti-lock braking system (ABS) for vehicle and conducts real experiments to verify the ability of this ABS to prevent the vehicle wheel from being locked while braking. Two controllers of PID and fuzzy logic are tested for analysis and comparison. This ABS laboratory is designed for bachelor and master students to simulate and analyze performances of ABS with different control techniques on various roads and load conditions. This paper provides educational theories and practices on the design of control for system dynamics.

  13. Initial Chemical Events in CL-20 Under Extreme Conditions: An Ab Initio Molecular Dynamics Study

    National Research Council Canada - National Science Library

    Isaev, Olexandr; Kholod, Yana; Gorb, Leonid; Qasim, Mohammad; Fredrickson, Herb; Leszczynski, Jerzy

    2006-01-01

    .... In the present study molecular structure, electrostatic potential, vibrational spectrum and dynamics of thermal decomposition of CL-20 have been investigated by static and dynamic methods of ab...

  14. Effects of 4WD and ABS of safe driving on slippery roads; Tei {mu} ji ni okeru 4WD to ABS no koka to unten sosa hoho

    Energy Technology Data Exchange (ETDEWEB)

    Kojima, Y [National Research Inst. of Police Science, Tokyo (Japan); Takigami, K; Asano, K [Japan Safe Driving Center, Tokyo (Japan); Nagai, M [Tokyo University of Agriculture and Technology, Tokyo (Japan)

    1997-10-01

    Effects of 4WD and ABS on safe driving were examined by brake, obstacle avoidance, acceleration, cornering and lane-changing tests on slippery road. The braking operations, used in these tests, are full, intermitted and modulated brakings. As the results of discussion, the major findings are (1) ABS is effective to shorten the stopping distance and to increase the ability of obstacle avoidance in many cases, (2) `Modulated Braking (without wheel locks)` has the same function as ABS, and (3) 4WD is effective to increase the stability while accelerating, cornering and lane-changing. 5 refs., 6 figs.

  15. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  16. Experimental Induction of Genome Chaos.

    Science.gov (United States)

    Ye, Christine J; Liu, Guo; Heng, Henry H

    2018-01-01

    Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.

  17. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  18. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  19. Cyclodialysis ab interno as a surgical approach to intractable glaucoma.

    Science.gov (United States)

    Jordan, Jens F; Dietlein, Thomas S; Dinslage, Sven; Lüke, Christoph; Konen, Walter; Krieglstein, Günter K

    2007-08-01

    In glaucoma filtration surgery, the problem of subconjunctival scarring has still not been satisfactorily solved. Suprachoroidal drainage of aqueous humour offers a promising, alternative option for intractable glaucoma. We here present a clinical study on the surgical approach of gonioscopic cyclodialysis ab interno. Twenty-eight eyes of 20 patients with intractable glaucoma were included in this prospective, consecutive, case-control study. The eyes had had a mean of 4.4 +/- 2.4 previous antiglaucomatous interventions. Baseline intraocular pressure (IOP) was 34.3 +/- 10.5 mmHg despite maximum therapy. Under gonioscopic control, cyclodialysis ab interno was performed over two clock times to gain access to the suprachoroidal space. No additional trabecular meshwork surgery was performed. Success was defined as a lowering of IOP to below 21 mmHg without the need for further medication or intervention. Mean postoperative IOP was 14.6 +/- 12.4 mmHg. Mean follow-up (FU) for all eyes was 121.8 days. After a mean of 60 days, 21 eyes (75%) needed further surgical intervention. Qualified success was seen in four eyes (14.3%), with a mean FU of 383.6 days. Three eyes (10.7%) showed absolute success after a mean FU period of 202.7 days. In our series, we obtained the best results for phakic eyes, followed by pseudophakic and aphakic eyes. The results of this study do not provide convincing evidence of the functional efficacy of cyclodialysis ab interno. Nevertheless, the technique is easy to perform and offers safe and atraumatic access to the resorptive capability of the choroid. Conjunctival manipulation is avoided. Contrary to reports in the current literature, in our series, the best results were obtained for phakic eyes, though the small number of eyes included does not allow reliable statistics. Further studies will need to focus on the use of different space-retaining substances or a widening of the cyclodialysis cleft to improve surgical outcome.

  20. Genome position specific priors for genomic prediction

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø

    2012-01-01

    casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects...... for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed Results...

  1. Evolutionary dynamics of 3D genome architecture following polyploidization in cotton.

    Science.gov (United States)

    Wang, Maojun; Wang, Pengcheng; Lin, Min; Ye, Zhengxiu; Li, Guoliang; Tu, Lili; Shen, Chao; Li, Jianying; Yang, Qingyong; Zhang, Xianlong

    2018-02-01

    The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes. We also show that the formation of TAD boundaries during polyploidization preferentially occurs in open chromatin, coinciding with the deposition of active chromatin modification. Furthermore, analysis of inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. This study advances our understanding of chromatin organization in plants and sheds new light on the relationship between 3D genome evolution and transcriptional regulation.

  2. [Phylogenetic analysis of genomes of Vibrio cholerae strains isolated on the territory of Rostov region].

    Science.gov (United States)

    Kuleshov, K V; Markelov, M L; Dedkov, V G; Vodop'ianov, A S; Kermanov, A V; Pisanov, R V; Kruglikov, V D; Mazrukho, A B; Maleev, V V; Shipulin, G A

    2013-01-01

    Determination of origin of 2 Vibrio cholerae strains isolated on the territory of Rostov region by using full genome sequencing data. Toxigenic strain 2011 EL- 301 V. cholerae 01 El Tor Inaba No. 301 (ctxAB+, tcpA+) and nontoxigenic strain V. cholerae O1 Ogawa P- 18785 (ctxAB-, tcpA+) were studied. Sequencing was carried out on the MiSeq platform. Phylogenetic analysis of the genomes obtained was carried out based on comparison of conservative part of the studied and 54 previously sequenced genomes. 2011EL-301 strain genome was presented by 164 contigs with an average coverage of 100, N50 parameter was 132 kb, for strain P- 18785 - 159 contigs with a coverage of69, N50 - 83 kb. The contigs obtained for strain 2011 EL-301 were deposited in DDBJ/EMBL/GenBank databases with access code AJFN02000000, for strain P-18785 - ANHS00000000. 716 protein-coding orthologous genes were detected. Based on phylogenetic analysis strain P- 18785 belongs to PG-1 subgroup (a group of predecessor strains of the 7th pandemic). Strain 2011EL-301 belongs to groups of strains of the 7th pandemic and is included into the cluster with later isolates that are associated with cases of cholera in South Africa and cases of import of cholera to the USA from Pakistan. The data obtained allows to establish phylogenetic connections with V cholerae strains isolated earlier.

  3. Genomics of Volvocine Algae

    Science.gov (United States)

    Umen, James G.; Olson, Bradley J.S.C.

    2015-01-01

    Volvocine algae are a group of chlorophytes that together comprise a unique model for evolutionary and developmental biology. The species Chlamydomonas reinhardtii and Volvox carteri represent extremes in morphological diversity within the Volvocine clade. Chlamydomonas is unicellular and reflects the ancestral state of the group, while Volvox is multicellular and has evolved numerous innovations including germ-soma differentiation, sexual dimorphism, and complex morphogenetic patterning. The Chlamydomonas genome sequence has shed light on several areas of eukaryotic cell biology, metabolism and evolution, while the Volvox genome sequence has enabled a comparison with Chlamydomonas that reveals some of the underlying changes that enabled its transition to multicellularity, but also underscores the subtlety of this transition. Many of the tools and resources are in place to further develop Volvocine algae as a model for evolutionary genomics. PMID:25883411

  4. Genomics of Preterm Birth

    Science.gov (United States)

    Swaggart, Kayleigh A.; Pavlicev, Mihaela; Muglia, Louis J.

    2015-01-01

    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms. PMID:25646385

  5. Genomics of Salmonella Species

    Science.gov (United States)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  6. Effect of gamma irradiation on nutritional components and Cry1Ab protein in the transgenic rice with a synthetic cry1Ab gene from Bacillus thuringiensis

    International Nuclear Information System (INIS)

    Wu Dianxing; Ye Qingfu; Wang Zhonghua; Xia Yingwu

    2004-01-01

    The effects of gamma irradiation on the transgenic rice containing a synthetic cry1Ab gene from Bacillus thuringiensis were investigated. There was almost no difference in the content of the major nutritional components, i.e. crude protein, crude lipid, eight essential amino acids and total ash between the irradiated grains and the non-irradiated transgenic rice. However, the amounts of Cry1Ab protein and apparent amylose in the irradiated transgenic rice were reduced significantly by the doses higher than 200 Gy. In vivo observation showed that Cry1Ab protein contents also decreased in the fresh leaf tissues of survival seedlings after irradiation with 200 Gy or higher doses and showed inhibition of seedling growth. The results indicate that gamma irradiation might improve the quality of transgenic rice due to removal of the toxic Cry1Ab protein

  7. Erythema Ab igne after footbath with Chinese herbal remedies

    Directory of Open Access Journals (Sweden)

    Jeng-Feng Chen

    2011-01-01

    Full Text Available Erythema ab igne (EAI is a reticulated, telangiectatic, and hyperpigmented skin eruption resulting from chronic exposure to long-term moderate heat. The incidence has decreased substantially today because of the advent of modern central heating systems. Recently, we encountered a patient who developed EAI after 2 weeks of footbaths with Chinese herbal remedies, which she used to treat her acute ankle sprain. Alternative Chinese medicine, such as herbal footbath, is a prevalent medical practice to treat acute pains as well as many chronic musculoskeletal ailments among Chinese and Asian populations. It has also become increasingly popular in Western countries in the past decade. Herein, we would like to report an uncommon case of iatrogenic EAI caused by footbath and raise the attention of clinicians to such rare, potentially malignant-transforming, dermatosis.

  8. Simple calculation of ab initio melting curves: Application to aluminum.

    Science.gov (United States)

    Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean

    2015-03-01

    We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003)] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013)]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost.

  9. Ab initio study of II-(VI){sub 2} dichalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, P; Vidal, J; Lincot, D, E-mail: polsson@kth.se [Institut de R and D sur l' energie photovoltaique (IRDEP), UMR 7174-EDF-CNRS-ENSCP, 6 quai Watier, 78401 Chatou Cedex (France)

    2011-10-12

    The structural stabilities of the (Zn,Cd)(S,Se,Te){sub 2} dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe{sub 2} pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications. (paper)

  10. A hydronitrogen solid: high pressure ab initio evolutionary structure searches

    International Nuclear Information System (INIS)

    Hu Anguang; Zhang Fan

    2011-01-01

    High pressure ab initio evolutionary structure searches resulted in a hydronitrogen solid with a composition of (NH) 4 . The structure searches also provided two molecular isomers, ammonium azide (AA) and trans-tetrazene (TTZ) which were previously discovered experimentally and can be taken as molecular precursors for high pressure synthesis of the hydronitrogen solid. The computed pressure versus enthalpy diagram showed that the transformation pressure to the hydronitrogen solid is 36 GPa from AA and 75 GPa from TTZ. Its metastability was analyzed by the phonon dispersion spectrum and room-temperature vibrational density of state together with the transformation energy barrier back to molecular phases at 298 K. The predicted energy barrier of 0.21 eV/atom means that the proposed hydronitrogen solid should be very stable at ambient conditions. (fast track communication)

  11. High-throughput ab-initio dilute solute diffusion database.

    Science.gov (United States)

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-07-19

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.

  12. The ab-initio density matrix renormalization group in practice.

    Science.gov (United States)

    Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic

    2015-01-21

    The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

  13. Superfluid 3He A-B surface tension

    International Nuclear Information System (INIS)

    Bartkowiak, M.; Haley, R.P.; Fisher, S.N.; Guenault, A.M.; Pickett, G.R.; Skyba, P.

    2003-01-01

    We have made two different measurements of interfacial energies below 300 μK, at zero pressure and in magnetic fields up to 400 mT. A variable magnetic field profile allows us to stabilize and precisely manipulate the position of the A-B interface. First, we can derive the difference in wall wetting energies from the behaviour of the phase boundary as it enters and exits a stack of glass capillary tubes. Secondly, we can measure the surface tension from the level of over- or under-magnetization needed to force the interface through an aperture. These are the first surface energy measurements in high magnetic fields in the zero-temperature limit. Our results are in surprising agreement with earlier measurements at high pressure close to T c

  14. The ab-initio density matrix renormalization group in practice

    Energy Technology Data Exchange (ETDEWEB)

    Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Nakatani, Naoki [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Catalysis Research Center, Hokkaido University, Kita 21 Nishi 10, Sapporo, Hokkaido 001-0021 (Japan)

    2015-01-21

    The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

  15. Quantitative verification of ab initio self-consistent laser theory.

    Science.gov (United States)

    Ge, Li; Tandy, Robert J; Stone, A D; Türeci, Hakan E

    2008-10-13

    We generalize and test the recent "ab initio" self-consistent (AISC) time-independent semiclassical laser theory. This self-consistent formalism generates all the stationary lasing properties in the multimode regime (frequencies, thresholds, internal and external fields, output power and emission pattern) from simple inputs: the dielectric function of the passive cavity, the atomic transition frequency, and the transverse relaxation time of the lasing transition.We find that the theory gives excellent quantitative agreement with full time-dependent simulations of the Maxwell-Bloch equations after it has been generalized to drop the slowly-varying envelope approximation. The theory is infinite order in the non-linear hole-burning interaction; the widely used third order approximation is shown to fail badly.

  16. Ab initio elastic properties and tensile strength of crystalline hydroxyapatite.

    Science.gov (United States)

    Ching, W Y; Rulis, Paul; Misra, A

    2009-10-01

    We report elastic constant calculation and a "theoretical" tensile experiment on stoichiometric hydroxyapatite (HAP) crystal using an ab initio technique. These results compare favorably with a variety of measured data. Theoretical tensile experiments are performed on the orthorhombic cell of HAP for both uniaxial and biaxial loading. The results show considerable anisotropy in the stress-strain behavior. It is shown that the failure behavior of the perfect HAP crystal is brittle for tension along the z-axis with a maximum stress of 9.6 GPa at 10% strain. Biaxial failure envelopes from six "theoretical" loading tests show a highly anisotropic pattern. Structural analysis of the crystal under various stages of tensile strain reveals that the deformation behavior manifests itself mainly in the rotation of the PO(4) tetrahedron with concomitant movements of both the columnar and axial Ca ions. These results are discussed in the context of mechanical properties of bioceramic composites relevant to mineralized tissues.

  17. Ab initio methods for electron-molecule collisions

    International Nuclear Information System (INIS)

    Collins, L.A.; Schneider, B.I.

    1987-01-01

    This review concentrates on the recent advances in treating the electronic aspect of the electron-molecule interaction and leaves to other articles the description of the rotational and vibrational motions. Those methods which give the most complete treatment of the direct, exchange, and correlation effects are focused on. Such full treatments are generally necessary at energies below a few Rydbergs (≅ 60 eV). This choice unfortunately necessitates omission of those active and vital areas devoted to the development of model potentials and approximate scattering formulations. The ab initio and model approaches complement each other and are both extremely important to the full explication of the electron-scattering process. Due to the rapid developments of recent years, the approaches that provide the fullest treatment are concentrated on. 81 refs

  18. Ab initio Eliashberg Theory: Making Genuine Predictions of Superconducting Features

    Science.gov (United States)

    Sanna, Antonio; Flores-Livas, José A.; Davydov, Arkadiy; Profeta, Gianni; Dewhurst, Kay; Sharma, Sangeeta; Gross, E. K. U.

    2018-04-01

    We present an application of Eliashberg theory of superconductivity to study a set of novel superconducting systems with a wide range of structural and chemical properties. The set includes three intercalated group-IV honeycomb layered structures, SH3 at 200 GPa (the superconductor with the highest measured critical temperature), the similar system SeH3 at 150 GPa, and a lithium doped mono-layer of black phosphorus. The theoretical approach we adopt is a recently developed, fully ab initio Eliashberg approach that takes into account the Coulomb interaction in a full energy-resolved fashion avoiding any free parameters like μ*. This method provides reasonable estimations of superconducting properties, including TC and the excitation spectra of superconductors.

  19. Ab Initio Symmetry-Adapted No-Core Shell Model

    International Nuclear Information System (INIS)

    Draayer, J P; Dytrych, T; Launey, K D

    2011-01-01

    A multi-shell extension of the Elliott SU(3) model, the SU(3) symmetry-adapted version of the no-core shell model (SA-NCSM), is described. The significance of this SA-NCSM emerges from the physical relevance of its SU(3)-coupled basis, which – while it naturally manages center-of-mass spuriosity – provides a microscopic description of nuclei in terms of mixed shape configurations. Since typically configurations of maximum spatial deformation dominate, only a small part of the model space suffices to reproduce the low-energy nuclear dynamics and hence, offers an effective symmetry-guided framework for winnowing of model space. This is based on our recent findings of low-spin and high-deformation dominance in realistic NCSM results and, in turn, holds promise to significantly enhance the reach of ab initio shell models.

  20. Ab Initio Analysis of Auger-Assisted Electron Transfer.

    Science.gov (United States)

    Hyeon-Deuk, Kim; Kim, Joonghan; Prezhdo, Oleg V

    2015-01-15

    Quantum confinement in nanoscale materials allows Auger-type electron-hole energy exchange. We show by direct time-domain atomistic simulation and analytic theory that Auger processes give rise to a new mechanism of charge transfer (CT) on the nanoscale. Auger-assisted CT eliminates the renown Marcus inverted regime, rationalizing recent experiments on CT from quantum dots to molecular adsorbates. The ab initio simulation reveals a complex interplay of the electron-hole and charge-phonon channels of energy exchange, demonstrating a variety of CT scenarios. The developed Marcus rate theory for Auger-assisted CT describes, without adjustable parameters, the experimental plateau of the CT rate in the region of large donor-acceptor energy gap. The analytic theory and atomistic insights apply broadly to charge and energy transfer in nanoscale systems.

  1. Ebolavirus comparative genomics

    Science.gov (United States)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S.; Pedersen, Thomas D.; Wassenaar, Trudy M.; Ussery, David W.

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. This information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). PMID:26175035

  2. Brief Guide to Genomics: DNA, Genes and Genomes

    Science.gov (United States)

    ... clinic. Most new drugs based on genome-based research are estimated to be at least 10 to 15 years away, though recent genome-driven efforts in lipid-lowering therapy have considerably shortened that interval. According ...

  3. American brachytherapy society (ABS) guidelines for brachytherapy of esophageal cancer

    International Nuclear Information System (INIS)

    Nag, Subir; Gaspar, Laurie; Herskovic, Arnold; Mantravadi, Prasad; Speiser, Burton

    1996-01-01

    Introduction: There is wide variation in the indications, techniques, treatment regimens and dosimetry being used to treat cancer of the esophagus and no guidelines exist for optimal therapy. Methods: The Clinical Research Committee of the ABS met to formulate consensus guidelines for brachytherapy in esophageal cancer. Results: Good candidates for brachytherapy include patients with unifocal disease, with thoracic tumor 10 cm primary regional lymph adenopathy or tumor located in the gastro-esophageal junction or cervical esophagus. Contraindications include tracheo-esophageal fistula or stenosis that cannot be by-passed. The esophageal or nasogastric tube inserted should have a diameter of 6-10 mm whenever possible. If 5FU-based chemotherapy and 50 Gy external beam (EBRT) are used, it is suggested that the low dose rate brachytherapy (LDR) dose be 20 Gy at 0.4-1 Gy/hr, prescribed at 1 cm from the source. If high dose rate (HDR) is used, the dose recommended is 10 Gy in 2 weekly fractions of 5 Gy each, given after EBRT. Chemotherapy is not usually given concurrently with brachytherapy, and when it is, the brachytherapy dose is reduced. The length of esophagus treated by brachytherapy includes the post-EBRT involved area and a 1-2 cm margin proximally and distally. Supportive care, given during EBRT includes an antifungal agent (e.g., diflucan) and carafate. Gradual dilatation of the esophagus is required post-treatment for esophageal strictures. Conclusion: Guidelines were developed for brachytherapy in esophageal cancer. As more clinical data becomes available, these guidelines will be updated by the ABS

  4. H3+: Ab initio calculation of the vibration spectrum

    International Nuclear Information System (INIS)

    Carney, G.D.; Porter, R.N.

    1976-01-01

    The vibration spectrum of H 3 + is calculated from the representation of a previously reported [J. Chem Phys. 60, 4251 (1974)] ab initio potential-energy surface in a fifth degree Simons--Parr--Finlan (SPF) expansion. Morse- and harmonic-oscillator basis functions are used to describe the motions of the three oscillators and the Harris--Engerholm--Gwinn quadrature technique is used to obtain matrix elements of the Hamiltonian in the basis of vibrational configurations. Our variational method is thus analogous to configuration--interaction calculations for electronic states. The ground state is found to have a zero-point energy of 4345 cm -1 and a vibrationally averaged geometry of R 1 =R 2 =0.91396 A, theta=60.0012degree, where theta is the angle between the two equivalent bonds. The transition frequencies for the E and A 1 fundamentals are nu-bar/sub E/=2516 cm -1 and nu-bar/sub A/=3185 cm -1 and those for the corresponding first overtones of the bending mode are 2nu-bar/sub E/=5004 +- 4 cm -1 and 2nu-bar/sub A/=4799 cm -1 . The first overtone of the breathing mode is 6264 cm -1 . The first-excited A 1 vibration state is metastable with a dipole--radiation lifetime of 3 sec. Transition frequencies, Einstein coefficients, and lifetimes are reported for a total of 21 transitions. Analysis of results for Dunham number and normal-coordinate expansions in comparison with those for SPF expansion show the latter to be superior for ab initio vibrational calculations. A scheme for possible direct measurement of the fundamental A 1 and E vibrational bands is suggested

  5. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D

    2015-01-01

    to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from Illumina....... Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  6. Cry1A(b)16 toxin from Bacillus thuringiensis: Theoretical refinement of three-dimensional structure and prediction of peptides as molecular markers for detection of genetically modified organisms.

    Science.gov (United States)

    Plácido, Alexandra; Coelho, Andreia; Abreu Nascimento, Lucas; Gomes Vasconcelos, Andreanne; Fátima Barroso, Maria; Ramos-Jesus, Joilson; Costa, Vladimir; das Chagas Alves Lima, Francisco; Delerue-Matos, Cristina; Martins Ramos, Ricardo; Marani, Mariela M; Roberto de Souza de Almeida Leite, José

    2017-07-01

    Transgenic maize produced by the insertion of the Cry transgene into its genome became the second most cultivated crop worldwide. Cry gene from Bacillus thuringiensis kurstaki expresses protein derivatives of crystalline endotoxins which confer insect resistance onto the maize crop. Mandatory labeling of processed food containing or made by genetically modified organisms is in force in many countries, so, it is very urgent to develop fast and practical methods for GMO identification, for example, biosensors. In the absence of an available empirical structure of Cry1A(b)16 protein, a theoretical model was effectively generated, in this work, by homology modeling and molecular dynamics simulations based on two available homologous protein structures. Molecular dynamics simulations were carried out to refine the selected model, and an analysis of its global structure was performed. The refined models of Cry1A(b)16 showed a standard fold and structural characteristics similar to those seen in Bacillus thuringiensis Cry1A(a) insecticidal toxin and Bacillus thuringiensis serovar kurstaki Cry1A(c) toxin. After in silico analysis of Cry1A(b)16, two immunoreactive candidate peptides were selected and specific polyclonal antibodies were produced resulting in antibody-peptide interaction. Biosensing devices are expected to be developed for detection of the Cry1A(b) protein as a marker of transgenic maize in food. Proteins 2017; 85:1248-1257. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  7. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  8. Expression of Cry1Ab and Cry2Ab by a polycistronic transgene with a self-cleavage peptide in rice.

    Directory of Open Access Journals (Sweden)

    Qichao Zhao

    Full Text Available Insect resistance to Bacillus thuringiensis (Bt crystal protein is a major threat to the long-term use of transgenic Bt crops. Gene stacking is a readily deployable strategy to delay the development of insect resistance while it may also broaden insecticidal spectrum. Here, we report the creation of transgenic rice expressing discrete Cry1Ab and Cry2Ab simultaneously from a single expression cassette using 2A self-cleaving peptides, which are autonomous elements from virus guiding the polycistronic viral gene expression in eukaryotes. The synthetic coding sequences of Cry1Ab and Cry2Ab, linked by the coding sequence of a 2A peptide from either foot and mouth disease virus or porcine teschovirus-1, regardless of order, were all expressed as discrete Cry1Ab and Cry2Ab at high levels in the transgenic rice. Insect bioassays demonstrated that the transgenic plants were highly resistant to lepidopteran pests. This study suggested that 2A peptide can be utilized to express multiple Bt genes at high levels in transgenic crops.

  9. phiGENOME: an integrative navigation throughout bacteriophage genomes.

    Science.gov (United States)

    Stano, Matej; Klucar, Lubos

    2011-11-01

    phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

    Science.gov (United States)

    Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

  11. First insight into the genome of an uncultivated crenarchaeote from soil

    DEFF Research Database (Denmark)

    Quaiser, Achim; Ochsenreiter, Torsten; Klenk, Hans-Peter

    2002-01-01

    RNA genes and of several protein encoding genes (e.g. DNA polymerase, FixAB, glycosyl transferase) confirmed the specific affiliation of the genomic fragment with the non-thermophilic clade of the crenarchaeota. Content and structure of the genomic fragment indicated that the archaea from soil differ......Molecular phylogenetic surveys based on the characterization of 16S rRNA genes have revealed that soil is an environment particularly rich in microbial diversity. A clade of crenarchaeota (archaea) has frequently been detected among many other novel lineages of uncultivated bacteria. In this study...... we have initiated a genomic approach for the characterization of uncultivated microorganisms from soil. We have developed a procedure based on a two-phase electrophoresis technique that allows the fast and reliable purification of concentrated and clonable, high molecular weight DNA. From this DNA we...

  12. Leonid Apananski müüs AB Grupi maa oma firmale / Silva Männik

    Index Scriptorium Estoniae

    Männik, Silva, 1974-

    1999-01-01

    Ilmunud ka: Den za Dnjom Nov/26 lk. 8. Apananski müüs AB Kindlustuse Grupile kuulunud Maakri tänava kinnistu. Skeem: AB Grupist on välja viidud ligikaudu 70 milj. krooni. Ilmunud ka: Den za Dnjom 23. nov. lk. 3

  13. Ab interno trabeculectomy: ultrastructural evidence and early tissue response in a human eye.

    Science.gov (United States)

    Ferrari, Ettore; Ortolani, Fulvia; Petrelli, Lucia; Contin, Magali; Pognuz, Derri Roman; Marchini, Maurizio; Bandello, Francesco

    2007-10-01

    To report the results of ultrastructural analysis of the postoperative effects of ab interno trabeculectomy in a human eye. Department of Ophthalmology, Palmanova Hospital, Palmanova, Udine, Italy. A 60-year-old woman with cataract and glaucoma had enucleation for a choroidal melanoma 10 days after ab interno trabeculectomy combined with phacoemulsification. A second ab interno trabeculectomy was performed after enucleation to evaluate the outcomes of the previous trabeculectomy. Light and transmission electron microscopy analyses were performed on samples excised from areas (1) not subjected to a procedure (control samples), (2) that had ab interno trabeculectomy before enucleation, and (3) that had ab interno trabeculectomy immediately after enucleation. Control samples showed normal trabecular features. Semithin sections of all ab interno trabeculectomy samples showed full-thickness removal of trabeculum segments, with Schlemm's canal lumen opening into the anterior chamber and apparent preservation of the adjacent structures. On ultrathin sections of samples that had ab interno trabeculectomy before enucleation, the endothelium lining the outer wall of Schlemm's canal and other angle components showed intact ultrastructural features. In trabecular beams that were not removed, the extracellular matrix appeared to have maintained its fine texture and was free of activated fibroblasts or leucocyte infiltrates. Observations confirm that ab interno trabeculectomy causes direct communication between Schlemm's canal lumen and the anterior chamber in vivo and immediately after enucleation during the early postoperative period. The absence of an evident inflammatory reaction in the examined case should be considered with caution because of possible tumor-induced immune suppression.

  14. Inhibition of cholera toxin and other AB toxins by polyphenolic compounds

    Science.gov (United States)

    All AB-type protein toxins have intracellular targets despite an initial extracellular location. These toxins use different methods to reach the cytosol and have different effects on the target cell. Broad-spectrum inhibitors against AB toxins are therefore hard to develop because the toxins use dif...

  15. Ab initio and Gordon--Kim intermolecular potentials for two nitrogen molecules

    International Nuclear Information System (INIS)

    Ree, F.H.; Winter, N.W.

    1980-01-01

    Both ab initio MO--LCAO--SCF and the electron-gas (or Gordon--Kim) methods have been used to compute the intermolecular potential (Phi) of N 2 molecules for seven different N 2 --N 2 orientations. The ab initio calculations were carried out using a [4s3p] contracted Gaussian basis set with and without 3d polarization functions. The larger basis set provides adequate results for Phi>0.002 hartree or intermolecular separations less than 6.5--7 bohr. We use a convenient analytic expression to represent the ab initio data in terms of the intermolecular distance and three angles defining the orientations of the two N 2 molecules. The Gordon--Kim method with Rae's self-exchange correction yields Phi, which agrees reasonably well over a large repulsive range. However, a detailed comparison of the electron kinetic energy contributions shows a large difference between the ab initio and the Gordon--Kim calculations. Using the ab initio data we derive an atom--atom potential of the two N 2 molecules. Although this expression does not accurately fit the data at some orientations, its spherical average agrees with the corresponding average of the ab initio Phi remarkably well. The spherically averaged ab initio Phi is also compared with the corresponding quantities derived from experimental considerations. The approach of the ab initio Phi to the classical quadrupole--quadrupole interaction at large intermolecular separation is also discussed

  16. Modeling Disordered Materials with a High Throughput ab-initio Approach

    Science.gov (United States)

    2015-11-13

    Modeling Disordered Materials with a High Throughput ab - initio Approach Kesong Yang,1 Corey Oses,2 and Stefano Curtarolo3, 4 1Department of...J. Furthmüller, Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set, Phys. Rev. B 54, 11169–11186 (1996

  17. Explicit and Implicit Subject Bias in the "ABS Journal Quality Guide"

    Science.gov (United States)

    Hoepner, Andreas G. F.; Unerman, Jeffrey

    2012-01-01

    This paper addresses issues raised in two recent papers published in this journal about the UK "Association of Business Schools' Journal Quality Guide (ABS Guide)". While much of the debate about journal rankings in general, and the "ABS Guide" in particular, has focused on the construction, power and (mis)use of these…

  18. Embedded atom approach for gold–silicon system from ab initio

    Indian Academy of Sciences (India)

    In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the 'force matching' method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various ...

  19. Ultra-low-power, class-AB, CMOS four-quadrant current multiplier

    NARCIS (Netherlands)

    Sawigun, C.; Serdijn, W.A.

    2009-01-01

    A class-AB four-quadrant current multiplier constituted by a class-AB current amplifier and a current splitter which can handle input signals in excess of ten times the bias current is presented. The proposed circuit operation is based on the exponential characteristic of BJTs or subthreshold

  20. Phosphoric acid doped AB-PBI membranes and its applications in high temperature PEMFC

    DEFF Research Database (Denmark)

    He, Ronghuan; Qingfeng, Li; Bjerrum, Niels

    2005-01-01

    Poly(2,5-benzimidazole) (ab-PBI) was prepared from 3,4-diaminobenzoic acid via a polymerisation reaction. The obtained polymer exhibits excellent thermal stability in a temperature range ….. The membrane of ab-PBI when doped with phosphoric acid at room temperaturepresents high proton conductivity...