Many applications in computational science and engineering require the computation of eigenvalues and vectors of dense symmetric or Hermitian matrices. For example, in DFT （density functional theory） calculations on...Many applications in computational science and engineering require the computation of eigenvalues and vectors of dense symmetric or Hermitian matrices. For example, in DFT （density functional theory） calculations on modern supercomputers 10% to 30% of the eigenvalues and eigenvectors of huge dense matrices have to be calculated. Therefore, performance and parallel scaling of the used eigensolvers is of upmost interest. In this article different routines of the linear algebra packages ScaLAPACK and Elemental for parallel solution of the symmetric eigenvalue problem are compared concerning their performance on the BlueGene/P supercomputer. Parameters for performance optimization are adjusted for the different data distribution methods used in the two libraries. It is found that for all test cases the new library Elemental which uses a two-dimensional element by element distribution of the matrices to the processors shows better performance than the old ScaLAPACK library which uses a block-cyclic distribution.展开更多
In order to marker dominant nuclear gene Ms2 with a blue grain, a 4E disomic addition line ＇xiaoyanlanli＇（2n=44, AABBDD＋4EII） as the male parent to pollinate with male-sterile plants of durum wheat, controlled by...In order to marker dominant nuclear gene Ms2 with a blue grain, a 4E disomic addition line ＇xiaoyanlanli＇（2n=44, AABBDD＋4EII） as the male parent to pollinate with male-sterile plants of durum wheat, controlled by a dominant nuclear gene Ms2, and a durum wheat line 89-2343 with Ms2 and blue seed marker on the same addition chromosome was developed. The genotype 89-2343 was crossed and backcrossed with a common wheat genotype 7739-3 to produce male fertile plants with blue seeds （MFP-BS）. To combine the blue seed marker, dwarf male-sterile plants carrying RhtlO and Ms2 were fertilized by pollen from selected MFP-BS. At last, the combination of blue seed marker, Ms2 and RhtlO was successfully produced. The segregation ratio of male sterility, seed color as well as chromosome configurations of the combinations suggested that the blue seed marker, Ms2 and RhtlO were located on the same chromosome. Cytological analysis indicated that the male sterile wheat line with a blue seed marker was 43 in chromosome number, with an additional chromosome. The transmission rate for blue seed male-sterile plants was 22.1% in common. In addition, the potential value for blue marker sterile lines in wheat breeding and hybrid production is discussed.展开更多
otrA resembles elongation factor G （EF-G） and is considered to be an oxytetracycline （OTC）-resistance determinant in Streptomyces rimosus. In order to determine whether otrA also conferred resistance to OTC and ot...otrA resembles elongation factor G （EF-G） and is considered to be an oxytetracycline （OTC）-resistance determinant in Streptomyces rimosus. In order to determine whether otrA also conferred resistance to OTC and other aminoglycosides to Streptomyces coelicolor, the otrA gene from S. rimosus M527 was cloned under the control of the strong ermE promoter. The resulting plasmid, pIB139-otrA, was introduced into S. coeficolor M145 by intergenedc conjugation, yielding the recombinant strain S. coelicolor M145-OA. As expected S. coelicolor M145-OA exhibited higher resistance levels specifically to OTC and aminoglycosides gentamycin, hygromycin, streptomycin, and spectinomycin. However, unexpectedly, S. coelicolor M14-~OA on solid medium showed an accelerated aerial mycelia formation, a precocious sporulation, and an enhanced actinorhodin （Act） production. Upon growth in 5-L fermentor, the amount of intra- and extracellular Act production was 6-fold and 2-fold higher, respectively, than that of the original strain. Consistently, reverse transcription polymerase chain reaction （RT-PCR） analysis revealed that the transcrip- tional level of pathway-specific regulatory gene acUl-orf4 was significantly enhanced in S. coelicolor M145-OA compared with in S. coelicolor M145.展开更多
Streptothricins (STs) are used commercially to treat bacterial and fungal diseases in agriculture. Mining of the sequenced microbial genomes uncovered two cryptic ST clusters from Streptomyces sp. C and Streptomyces s...Streptothricins (STs) are used commercially to treat bacterial and fungal diseases in agriculture. Mining of the sequenced microbial genomes uncovered two cryptic ST clusters from Streptomyces sp. C and Streptomyces sp. TP-A0356. The ST cluster from S. sp. TP-A0356 was verified by successful heterologous expression in Streptomyces coelicolor M145. Two new ST analogs were produced together with streptothricin F and streptothricin D in the heterologous host. The ST cluster was further confirmed by inactivation of gene stnO, which was proposed encoding an aminomutase supplying -lysines for the poly-β-Lys chain formation. A putative biosynthetic pathway for STs is proposed based on bioinformatics analyses of the ST genes and experimental evidence.展开更多
文摘Many applications in computational science and engineering require the computation of eigenvalues and vectors of dense symmetric or Hermitian matrices. For example, in DFT （density functional theory） calculations on modern supercomputers 10% to 30% of the eigenvalues and eigenvectors of huge dense matrices have to be calculated. Therefore, performance and parallel scaling of the used eigensolvers is of upmost interest. In this article different routines of the linear algebra packages ScaLAPACK and Elemental for parallel solution of the symmetric eigenvalue problem are compared concerning their performance on the BlueGene/P supercomputer. Parameters for performance optimization are adjusted for the different data distribution methods used in the two libraries. It is found that for all test cases the new library Elemental which uses a two-dimensional element by element distribution of the matrices to the processors shows better performance than the old ScaLAPACK library which uses a block-cyclic distribution.
文摘In order to marker dominant nuclear gene Ms2 with a blue grain, a 4E disomic addition line ＇xiaoyanlanli＇（2n=44, AABBDD＋4EII） as the male parent to pollinate with male-sterile plants of durum wheat, controlled by a dominant nuclear gene Ms2, and a durum wheat line 89-2343 with Ms2 and blue seed marker on the same addition chromosome was developed. The genotype 89-2343 was crossed and backcrossed with a common wheat genotype 7739-3 to produce male fertile plants with blue seeds （MFP-BS）. To combine the blue seed marker, dwarf male-sterile plants carrying RhtlO and Ms2 were fertilized by pollen from selected MFP-BS. At last, the combination of blue seed marker, Ms2 and RhtlO was successfully produced. The segregation ratio of male sterility, seed color as well as chromosome configurations of the combinations suggested that the blue seed marker, Ms2 and RhtlO were located on the same chromosome. Cytological analysis indicated that the male sterile wheat line with a blue seed marker was 43 in chromosome number, with an additional chromosome. The transmission rate for blue seed male-sterile plants was 22.1% in common. In addition, the potential value for blue marker sterile lines in wheat breeding and hybrid production is discussed.
基金Project supported by the National Natural Science Foundation of China(No.31772213)the Excellent Youth Fund of Zhejiang Province,China(No.LR17C140002)
文摘otrA resembles elongation factor G （EF-G） and is considered to be an oxytetracycline （OTC）-resistance determinant in Streptomyces rimosus. In order to determine whether otrA also conferred resistance to OTC and other aminoglycosides to Streptomyces coelicolor, the otrA gene from S. rimosus M527 was cloned under the control of the strong ermE promoter. The resulting plasmid, pIB139-otrA, was introduced into S. coeficolor M145 by intergenedc conjugation, yielding the recombinant strain S. coelicolor M145-OA. As expected S. coelicolor M145-OA exhibited higher resistance levels specifically to OTC and aminoglycosides gentamycin, hygromycin, streptomycin, and spectinomycin. However, unexpectedly, S. coelicolor M14-~OA on solid medium showed an accelerated aerial mycelia formation, a precocious sporulation, and an enhanced actinorhodin （Act） production. Upon growth in 5-L fermentor, the amount of intra- and extracellular Act production was 6-fold and 2-fold higher, respectively, than that of the original strain. Consistently, reverse transcription polymerase chain reaction （RT-PCR） analysis revealed that the transcrip- tional level of pathway-specific regulatory gene acUl-orf4 was significantly enhanced in S. coelicolor M145-OA compared with in S. coelicolor M145.
基金supported in part by the National Natural Science Foundation of China (31170037)Ministry of Science and Technology of China (2013CB734003)the China Postdoctoral Science Foundation (2013M530755)
文摘Streptothricins (STs) are used commercially to treat bacterial and fungal diseases in agriculture. Mining of the sequenced microbial genomes uncovered two cryptic ST clusters from Streptomyces sp. C and Streptomyces sp. TP-A0356. The ST cluster from S. sp. TP-A0356 was verified by successful heterologous expression in Streptomyces coelicolor M145. Two new ST analogs were produced together with streptothricin F and streptothricin D in the heterologous host. The ST cluster was further confirmed by inactivation of gene stnO, which was proposed encoding an aminomutase supplying -lysines for the poly-β-Lys chain formation. A putative biosynthetic pathway for STs is proposed based on bioinformatics analyses of the ST genes and experimental evidence.
