Genetic manipulation(either restraint or enhancement)of the biosynthesis pathway ofα-linolenic acid(ALA)in seed oil is an important goal in Brassica napus breeding.B.napus is a tetraploid plant whose genome often har...Genetic manipulation(either restraint or enhancement)of the biosynthesis pathway ofα-linolenic acid(ALA)in seed oil is an important goal in Brassica napus breeding.B.napus is a tetraploid plant whose genome often har-bors four and six homologous copies,respectively,of the two fatty acid desaturases FAD2 and FAD3,which con-trol the last two steps of ALA biosynthesis during seed oil accumulation.In this study,we compared their promoters,coding sequences,and expression levels in three high-ALA inbred lines 2006L,R8Q10,and YH25005,a low-ALA line A28,a low-ALA/high-oleic-acid accession SW,and the wildtype ZS11.The expression levels of most FAD2 and FAD3 homologs in the three high-ALA accessions were higher than those in ZS11 and much higher than those in A28 and SW.The three high-ALA accessions shared similar sequences with the pro-moters and CDSs of BnFAD3.C4 and BnFAD3.A3.In A28 and SW,substitution of three amino acid residues in BnFAD2.A5 and BnFAD2.C5,an absence of BnFAD2.C1 locus,and a 549 bp long deletion on the BnFAD3.A3 promoter were detected.The profile of BnFAD2 mutation in the two low-ALA accessions A28 and SW is different from that reported in previous studies.The mutations in BnFAD3 in the high-ALA accessions are reported for thefirst time.In identifying the sites of these mutations,we provide detailed information to aid the design of mole-cular markers for accelerated breeding schemes.展开更多
This research is focused on the analysis of the sequence stratigraphic units of F3 Block,within a wave-dominated delta of Plio–Pleistocene age.Three wells of F3 block and a 3D seismic data,are utilized in this resear...This research is focused on the analysis of the sequence stratigraphic units of F3 Block,within a wave-dominated delta of Plio–Pleistocene age.Three wells of F3 block and a 3D seismic data,are utilized in this research.The conventional techniques of 3D seismic interpretation were utilized to mark the 11 surfaces on the seismic section.Integration of seismic sequence stratigraphic interpretation,using well logs,and subsequent 3D geostatistical modeling,using seismic data,aided to evaluate the shallow hydrocarbon traps.The resulting models were obtained using System Tract and Facies models,which were generated by using sequential stimulation method and their variograms made by spherical method,moreover,these models are validated via histograms.The CDF curve generated from upscaling of well logs using geometric method,shows a good relation with less percentage of errors(1 to 2 for Facies and 3 to 4 for System Tract models)between upscaled and raw data that complements the resulted models.These approaches help us to delineate the best possible reservoir,lateral extent of system tracts(LST and/or HST)in the respective surface,and distribution of sand and shale in the delta.The clinoform break points alteration observed on seismic sections,also validates the sequence stratigraphic interpretation.The GR log-based Facies model and sequence stratigraphy-based System Tract model of SU-04-2 showed the reservoir characteristics,presence of sand bodies and majorly LST,respectively,mainly adjacent to the main fault of the studied area.Moreover,on the seismic section,SU-04-2 exhibits the presence of gas pockets at the same location that also complements the generated Facies and System Tract models.The generated models can be utilized for any similar kind of study and for the further research in the F3 block reservoir characterization.展开更多
The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure a...The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function. This study investigated the role that CSRP3 plays in chicken skeletal muscle. First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared. Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed. The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles. A total of 650 genes with at least 1.5-fold differences(Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing. Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly(P<0.05) enriched both in differentially expressed genes and all expressed genes. The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation(Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction. Meanwhile, two fast myosin heavy chain genes(MyH1B and MyH1E)were upregulated(Q<0.05) upon CSRP3 silencing. These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E.展开更多
Development of efficient gene prediction algorithms is one of the fundamental efforts in gene prediction study in the area of genomics. In genomic signal processing the basic step of the identification of protein codi...Development of efficient gene prediction algorithms is one of the fundamental efforts in gene prediction study in the area of genomics. In genomic signal processing the basic step of the identification of protein coding regions in DNA sequences is based on the period-3 property exhibited by nucleotides in exons. Several approaches based on signal processing tools and numerical representations have been applied to solve this problem, trying to achieve more accurate predictions. This paper presents a new indicator sequence based on amino acid sequence, called as aminoacid indicator sequence, derived from DNA string that uses the existing signal processing based time-domain and frequency domain methods to predict these regions within the billions long DNA sequence of eukaryotic cells which reduces the computational load by one-third. It is known that each triplet of bases, called as codon, instructs the cell machinery to synthesize an amino acid. The codon sequence therefore uniquely identifies an amino acid sequence which defines a protein. Thus the protein coding region is attributed by the codons in amino acid sequence. This property is used for detection of period-3 regions using amino acid sequence. Physico-chemical properties of amino acids are used for numerical representation. Various accuracy measures such as exonic peaks, discriminating factor, sensitivity, specificity, miss rate, wrong rate and approximate correlation are used to demonstrate the efficacy of the proposed predictor. The proposed method is validated on various organisms using the standard data-set HMR195, Burset and Guigo and KEGG. The simulation result shows that the proposed method is an effective approach for protein coding prediction.展开更多
Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. A...Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide （NT） sequence identities and 95.1-100% amino acid （AA） sequence identities. The P3 coding regions of the 16 SMV isolates share high identities （92.4-98.9% NT and 96.0-100% AA） with the reported Korean isolates, followed by the USA isolates （88.5-97.9% NT and 91.4-98.6% AA）, and share low identities （80.5-85.2% NT and 82.1-84.7% AA） with the reported HZ 1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus （WMV）, with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.展开更多
Forecasting subtle traps by sequence stratigraphy and 3D seismic data is a sensitive topic in hydrocarbon exploration. Research on subtle traps by geophysical data is the most popular and difficult. Based on the suffi...Forecasting subtle traps by sequence stratigraphy and 3D seismic data is a sensitive topic in hydrocarbon exploration. Research on subtle traps by geophysical data is the most popular and difficult. Based on the sufficiently drilling data, log data, core data and 3D seismic data, sediment sequence of Qikou depression, Huanghua basin was partitioned by using sequence stratigraphy theory. Each sediment sequence system mode was built. Sediment faces of subtle traps were pointed out. Dominating factors forming subtle traps were analyzed. Sandstone seismic rock physics and its response were studied in Tertiary System. Sandstone geophysical response and elastic modulus vary laws with pressure, temperature, porosity, depth were built. Experimental result and practice shows that it is possible using seismic information forecasting subtle traps. Integrated using geology, log, drilling data, special seismic processing technique, interpretation technique, high precision horizon calibration technique, 3D seismic visualizing interpretation, seismic coherence analysis, attribute analysis, logging-constrained inversion, time frequency analysis, subtle trapsobject is identified and interpreted. Finally, advantage object of subtle trap in this area was determined. Bottomland sand stratigraphic and lithologic reservoirs in Qinan slope zone have been founded by means of high resolution 3D seismic data field technique, high resolution 3D seismic data processing technique and seismic wave impendence inversion technique.展开更多
Type division and controlling factor analysis of 3rd-order sequence are of practical significance to tec-tonic analysis, sedimentary environment identification, and other geological researches. Based on the comprehens...Type division and controlling factor analysis of 3rd-order sequence are of practical significance to tec-tonic analysis, sedimentary environment identification, and other geological researches. Based on the comprehensive analysis of carbon and oxygen isotope trends, paleobathymetry and spectral-frequency of representative well logs, 3rd-order sequences can be divided into 3 types： （a） global sea level （GSL） sequence mainly controlled by GSL change;（b） tectonic sequence mainly controlled by regional tectonic activity;and （c） composite sequence jointly controlled by GSL change and regional tectonic activity. This study aims to identify the controlling factors of 3rd-order sequences and to illustrate a new method for classification of 3rd-order sequences of the middle Permian strata in the Sichuan Basin, China. The middle Permian strata in the Sichuan Basin consist of 3 basin-contrastive 3rd-order sequences, i.e., PSQ1, PSQ2 and PSQ3. Of these, PSQ1 is a GSL sequence while PSQ2 and PSQ3 are composite sequences. The results suggest that the depositional environment was stable during the deposition of PSQ1, but was activated by tectonic activity during the deposition of the middle Permian Maokou Formation.展开更多
By screening the worker （Apis cerana cerana） heads cDNA library using a fragment of the mrjp3 gene of Apis cerana as probe, 120 positive clones were obtained. The clone containing A. cerana cerana MRJP3 （AccMRJP3）...By screening the worker （Apis cerana cerana） heads cDNA library using a fragment of the mrjp3 gene of Apis cerana as probe, 120 positive clones were obtained. The clone containing A. cerana cerana MRJP3 （AccMRJP3） cDNA was selected. Based on the sequencing of the inserts of the positive clone, a sequence of AccMRJP3 cDNA which is 1 887 bp long including a poly （A） tail was obtained. The AccMRJP3 cDNA encompassed an open-reading frame （ORF） with 1 779 bp encoding 593 amino acids. The un-translated regions （UTR） of the 5′ end and 3′end are 46 bp and 160 bp in length, respectively. Similar to AmMRJP3 and AdMRJP3, the putative AccMRJP3 also has a repetitive region. The comparison of the repetitive region of AccMRJP3, AmMRJP3 and AdMRJP3 shows some differences between them.展开更多
基金The study was financially supported by Projects from Shaanxi Province(2021LLRH-07-03-01 and 2023-ZDLNY-07)Yangling Seed Industry Innovation(YLzy-yc2021-01).The funders had no role in study design,data collection and analysis,decision to publish,or preparation of the manuscript.
文摘Genetic manipulation(either restraint or enhancement)of the biosynthesis pathway ofα-linolenic acid(ALA)in seed oil is an important goal in Brassica napus breeding.B.napus is a tetraploid plant whose genome often har-bors four and six homologous copies,respectively,of the two fatty acid desaturases FAD2 and FAD3,which con-trol the last two steps of ALA biosynthesis during seed oil accumulation.In this study,we compared their promoters,coding sequences,and expression levels in three high-ALA inbred lines 2006L,R8Q10,and YH25005,a low-ALA line A28,a low-ALA/high-oleic-acid accession SW,and the wildtype ZS11.The expression levels of most FAD2 and FAD3 homologs in the three high-ALA accessions were higher than those in ZS11 and much higher than those in A28 and SW.The three high-ALA accessions shared similar sequences with the pro-moters and CDSs of BnFAD3.C4 and BnFAD3.A3.In A28 and SW,substitution of three amino acid residues in BnFAD2.A5 and BnFAD2.C5,an absence of BnFAD2.C1 locus,and a 549 bp long deletion on the BnFAD3.A3 promoter were detected.The profile of BnFAD2 mutation in the two low-ALA accessions A28 and SW is different from that reported in previous studies.The mutations in BnFAD3 in the high-ALA accessions are reported for thefirst time.In identifying the sites of these mutations,we provide detailed information to aid the design of mole-cular markers for accelerated breeding schemes.
文摘This research is focused on the analysis of the sequence stratigraphic units of F3 Block,within a wave-dominated delta of Plio–Pleistocene age.Three wells of F3 block and a 3D seismic data,are utilized in this research.The conventional techniques of 3D seismic interpretation were utilized to mark the 11 surfaces on the seismic section.Integration of seismic sequence stratigraphic interpretation,using well logs,and subsequent 3D geostatistical modeling,using seismic data,aided to evaluate the shallow hydrocarbon traps.The resulting models were obtained using System Tract and Facies models,which were generated by using sequential stimulation method and their variograms made by spherical method,moreover,these models are validated via histograms.The CDF curve generated from upscaling of well logs using geometric method,shows a good relation with less percentage of errors(1 to 2 for Facies and 3 to 4 for System Tract models)between upscaled and raw data that complements the resulted models.These approaches help us to delineate the best possible reservoir,lateral extent of system tracts(LST and/or HST)in the respective surface,and distribution of sand and shale in the delta.The clinoform break points alteration observed on seismic sections,also validates the sequence stratigraphic interpretation.The GR log-based Facies model and sequence stratigraphy-based System Tract model of SU-04-2 showed the reservoir characteristics,presence of sand bodies and majorly LST,respectively,mainly adjacent to the main fault of the studied area.Moreover,on the seismic section,SU-04-2 exhibits the presence of gas pockets at the same location that also complements the generated Facies and System Tract models.The generated models can be utilized for any similar kind of study and for the further research in the F3 block reservoir characterization.
基金supported by the earmarked fund for China Agriculture Research System (CARS-41)the earmarked fund for Jiangsu Agricultural Industry Technology System, China (JATS[2021]396)+6 种基金the Special Fund for Major Breeding Programs in Jiangsu Province (PZCZ201728)the Natural Science Foundation of Jiangsu Province (BK20161322, BK20211121, and BK20210955)the Projects of Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province (JQLAB-ZZ-201703)the Open Project Program of Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, China (JILAR-KF202020)the Yangzhou Science and Technology Support Program for Modem Agriculture (YZ2021029)the Jiangsu Provincal Agricultural Independent Innovation Fund Project (CX(21)2011-1)the Independent Scientific Foundation of Public Welfare Scientific Institutes of Jiangsu Province (BM2018026)。
文摘The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function. This study investigated the role that CSRP3 plays in chicken skeletal muscle. First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared. Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed. The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles. A total of 650 genes with at least 1.5-fold differences(Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing. Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly(P<0.05) enriched both in differentially expressed genes and all expressed genes. The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation(Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction. Meanwhile, two fast myosin heavy chain genes(MyH1B and MyH1E)were upregulated(Q<0.05) upon CSRP3 silencing. These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E.
文摘Development of efficient gene prediction algorithms is one of the fundamental efforts in gene prediction study in the area of genomics. In genomic signal processing the basic step of the identification of protein coding regions in DNA sequences is based on the period-3 property exhibited by nucleotides in exons. Several approaches based on signal processing tools and numerical representations have been applied to solve this problem, trying to achieve more accurate predictions. This paper presents a new indicator sequence based on amino acid sequence, called as aminoacid indicator sequence, derived from DNA string that uses the existing signal processing based time-domain and frequency domain methods to predict these regions within the billions long DNA sequence of eukaryotic cells which reduces the computational load by one-third. It is known that each triplet of bases, called as codon, instructs the cell machinery to synthesize an amino acid. The codon sequence therefore uniquely identifies an amino acid sequence which defines a protein. Thus the protein coding region is attributed by the codons in amino acid sequence. This property is used for detection of period-3 regions using amino acid sequence. Physico-chemical properties of amino acids are used for numerical representation. Various accuracy measures such as exonic peaks, discriminating factor, sensitivity, specificity, miss rate, wrong rate and approximate correlation are used to demonstrate the efficacy of the proposed predictor. The proposed method is validated on various organisms using the standard data-set HMR195, Burset and Guigo and KEGG. The simulation result shows that the proposed method is an effective approach for protein coding prediction.
基金supported by the National Natural Science Foundation of China(30671266,31101164)the National Basic Research Program of China(2006CB101708,2009CB118404)+2 种基金the National 863 Program of China(2006AA100104)the 111 Project from Ministry of Education of China(B08025)the Youth Science and Technology Innovation Foundation of Nanjing Agriculture University,China(KJ2010002)
文摘Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide （NT） sequence identities and 95.1-100% amino acid （AA） sequence identities. The P3 coding regions of the 16 SMV isolates share high identities （92.4-98.9% NT and 96.0-100% AA） with the reported Korean isolates, followed by the USA isolates （88.5-97.9% NT and 91.4-98.6% AA）, and share low identities （80.5-85.2% NT and 82.1-84.7% AA） with the reported HZ 1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus （WMV）, with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.
基金Project(2003034470) supported by the Postdoctoral Science Foundation of China project supported by the Postdoctoral Science Foundation of Central South University
文摘Forecasting subtle traps by sequence stratigraphy and 3D seismic data is a sensitive topic in hydrocarbon exploration. Research on subtle traps by geophysical data is the most popular and difficult. Based on the sufficiently drilling data, log data, core data and 3D seismic data, sediment sequence of Qikou depression, Huanghua basin was partitioned by using sequence stratigraphy theory. Each sediment sequence system mode was built. Sediment faces of subtle traps were pointed out. Dominating factors forming subtle traps were analyzed. Sandstone seismic rock physics and its response were studied in Tertiary System. Sandstone geophysical response and elastic modulus vary laws with pressure, temperature, porosity, depth were built. Experimental result and practice shows that it is possible using seismic information forecasting subtle traps. Integrated using geology, log, drilling data, special seismic processing technique, interpretation technique, high precision horizon calibration technique, 3D seismic visualizing interpretation, seismic coherence analysis, attribute analysis, logging-constrained inversion, time frequency analysis, subtle trapsobject is identified and interpreted. Finally, advantage object of subtle trap in this area was determined. Bottomland sand stratigraphic and lithologic reservoirs in Qinan slope zone have been founded by means of high resolution 3D seismic data field technique, high resolution 3D seismic data processing technique and seismic wave impendence inversion technique.
基金key project carried out in 2008-2011financially supported by the National Major Special Science and Technology Project (Grant No. 2008ZX05004-001)Major Special Issue of the China National Petroleum Corporation (Grant No. 2008E-0702)
文摘Type division and controlling factor analysis of 3rd-order sequence are of practical significance to tec-tonic analysis, sedimentary environment identification, and other geological researches. Based on the comprehensive analysis of carbon and oxygen isotope trends, paleobathymetry and spectral-frequency of representative well logs, 3rd-order sequences can be divided into 3 types： （a） global sea level （GSL） sequence mainly controlled by GSL change;（b） tectonic sequence mainly controlled by regional tectonic activity;and （c） composite sequence jointly controlled by GSL change and regional tectonic activity. This study aims to identify the controlling factors of 3rd-order sequences and to illustrate a new method for classification of 3rd-order sequences of the middle Permian strata in the Sichuan Basin, China. The middle Permian strata in the Sichuan Basin consist of 3 basin-contrastive 3rd-order sequences, i.e., PSQ1, PSQ2 and PSQ3. Of these, PSQ1 is a GSL sequence while PSQ2 and PSQ3 are composite sequences. The results suggest that the depositional environment was stable during the deposition of PSQ1, but was activated by tectonic activity during the deposition of the middle Permian Maokou Formation.
基金the National Natural Science Foundation of China(30200206) Zhejiang Provincial Natural Science Foundation of China(302113).
文摘By screening the worker （Apis cerana cerana） heads cDNA library using a fragment of the mrjp3 gene of Apis cerana as probe, 120 positive clones were obtained. The clone containing A. cerana cerana MRJP3 （AccMRJP3） cDNA was selected. Based on the sequencing of the inserts of the positive clone, a sequence of AccMRJP3 cDNA which is 1 887 bp long including a poly （A） tail was obtained. The AccMRJP3 cDNA encompassed an open-reading frame （ORF） with 1 779 bp encoding 593 amino acids. The un-translated regions （UTR） of the 5′ end and 3′end are 46 bp and 160 bp in length, respectively. Similar to AmMRJP3 and AdMRJP3, the putative AccMRJP3 also has a repetitive region. The comparison of the repetitive region of AccMRJP3, AmMRJP3 and AdMRJP3 shows some differences between them.
