Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using co...Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes.展开更多
N-acetylneuraminic acid(NeuAc)is an important nutrient that plays a key role in brain development in infants NeuAc is mainly produced by extraction from natural resources such as edible birds’s nests,crucian eggs,cav...N-acetylneuraminic acid(NeuAc)is an important nutrient that plays a key role in brain development in infants NeuAc is mainly produced by extraction from natural resources such as edible birds’s nests,crucian eggs,caviar and human breast milk.The extraction process is complicated,resulting in the disadvantages of low NeuAc content and low recovery rate.In this study,a crude enzyme immobilization-based cell-free system(CEICFS)was developed for efficient NeuAc biosynthesis.First,N-terminal coding sequences that improved the expression levels of N-acetylglucosamine-2-epimerase(AGE)and N-acetylneuraminic acid aldolase(NanA)were obtained by high-throughput screening.And these sequences resulted in up to 1.5-fold(1.2-fold)increase in AGE(NanA)enzyme levels.And then,a CEICFS for NeuAc biosynthesis was proposed by directly immobilizing crude enzyme containing AGE and NanA on amino resin.Subsequently,NeuAc production from GlcNAc using CEICFS in one reactor was carried out,resulting 68 g/L of NeuAc and the highest productivity of 6.8 g/L/h.Further,the enzyme activity was still higher than 75%after five repeated uses.The functional properties of CEICFS were studied and compared to those of the free enzyme,immobilization can extend the application of enzyme to some harsh environments,such as low temperature and acidic environment.Therefore,CEICFS with excellent heat resistance,storage stability and reusability exhibit great potential for industrial application.展开更多
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
Modeling non coding background sequences appropriately is important for the detection of regulatory elements from DNA sequences. Based on the chi square statistic test, some explanations about why to choose higher ...Modeling non coding background sequences appropriately is important for the detection of regulatory elements from DNA sequences. Based on the chi square statistic test, some explanations about why to choose higher order Markov chain model and how to automatically select the proper order are given in this paper. The chi square test is first run on synthetic data sets to show that it can efficiently find the proper order of Markov chain. Using chi square test, distinct higher order context dependences inherent in ten sets of sequences of yeast S.cerevisiae from other literature have been found. So the Markov chain with higher order would be more suitable for modeling the non coding background sequences than an independent model.展开更多
In order to exploit the evolution and find novel low-molecular-weight glutenin subunit (LMW-GS) for improvement of common wheat quality, thirteen variants from a somatic hybrid introgression line II-12 between Triti...In order to exploit the evolution and find novel low-molecular-weight glutenin subunit (LMW-GS) for improvement of common wheat quality, thirteen variants from a somatic hybrid introgression line II-12 between Triticum aestivum cv. Jinan 177 (JN177) and Agropyron elongatum were characterized via genomic PCR. Four clones were pseudogenes because they contained an internal stop codon. The remaining nine variants contained intact open reading frames (ORFs). Sequence alignment indicates that the proteins deduced from the nine ORFs have similar primary structure with LMW-GS cloned from its parents previously. However, they have some unique modifications in the structures. For example, EU292737 contains not only an extra Cys residue in the C-terminal domain but also a long repetitive domain. Both EU 159511 and EU292738 start their first Cys residue in the N-terminal repetitive domain, but not in the N-conserved domain traditionally. These structural alterations may have positive contributions to wheat flour quality. The results of phylogeny showed that most LMW-GS variances from 11-12 were homologous to those from parent JN177 and other wheat lines. The reason for quick evolution of LMW-GS in 11-12 was discussed.展开更多
To avoid the complexity and inefficiency for specific applications of the current software architecture, a novel approach using partial evaluation is proposed to improve the running performance of components. The gene...To avoid the complexity and inefficiency for specific applications of the current software architecture, a novel approach using partial evaluation is proposed to improve the running performance of components. The generic program was specialized into domain-specific realization for the known knowledge and environments. The syntax and semantic(adj.) were analyzed based on byte code instruction sequences, and partial evaluation rules depicted how to perform the specialization. The partial evaluation for object-oriented programs was implemented. The experimental results show that partial evaluation is effective to speed up the running efficiency. The more generality and scalability can be obtained by the integration of partial evaluation with the favorable design mechanisms and compiler optimization technology.展开更多
In Direct Sequence Code Division Multiple Access (DS-CDMA) systems,the chip wave-form affects the implementation,system bandwidth,envelope uniformity,eye pattern and Multiple user Access Interference (MAI). In this pa...In Direct Sequence Code Division Multiple Access (DS-CDMA) systems,the chip wave-form affects the implementation,system bandwidth,envelope uniformity,eye pattern and Multiple user Access Interference (MAI). In this paper,based on an elementary density function of a second order polynomial,a class of second order continuity pulses is proposed. From this class of pulses,we can find some members having faster decaying rate,bigger eye opening,more uniform envelope and stronger anti-MAI capability than the Nyquist waveform. The normalized-bandwidth-pulse-shape-factor product,the decaying rate of the tail of the time waveform,the opening of the eye diagram,and the envelope uniformity of the second order continuity pulses are addressed in the paper that provide the basic information for the selection of the chip pulse for CDMA systems.展开更多
In this paper, the complexity and performance of the Auxiliary Vector (AV) based reduced-rank filtering are addressed. The AV filters presented in the previous papers have the general form of the sum of the signature ...In this paper, the complexity and performance of the Auxiliary Vector (AV) based reduced-rank filtering are addressed. The AV filters presented in the previous papers have the general form of the sum of the signature vector of the desired signal and a set of weighted AVs,which can be classified as three categories according to the orthogonality of their AVs and the optimality of the weight coefficients of the AVs. The AV filter with orthogonal AVs and optimal weight coefficients has the best performance, but requires considerable computational complexity and suffers from the numerical unstable operation. In order to reduce its computational load while keeping the superior performance, several low complexity algorithms are proposed to efficiently calculate the AVs and their weight coefficients. The diagonal loading technique is also introduced to solve the numerical unstability problem without complexity increase. The performance of the three types of AV filters is also compared through their application to Direct Sequence Code Division Multiple Access (DS-CDM A) systems for interference suppression.展开更多
With the support from the National Natural Science Foundation of China,Prof.Huang Yanyi(黄岩谊)led a team at Peking University to demonstrate a novel approach,which combined fluorogenic sequencingby-synthesis(SBS)chem...With the support from the National Natural Science Foundation of China,Prof.Huang Yanyi(黄岩谊)led a team at Peking University to demonstrate a novel approach,which combined fluorogenic sequencingby-synthesis(SBS)chemistry with an information theory-based error-correction coding scheme to展开更多
The weight hierarchy of a linear[n;k;q]code C over GF(q) is the sequence(d_1,d_2,…,d_k)where d_r is the smallest support of any r-dimensional subcode of C. "Determining all possible weight hierarchies of general...The weight hierarchy of a linear[n;k;q]code C over GF(q) is the sequence(d_1,d_2,…,d_k)where d_r is the smallest support of any r-dimensional subcode of C. "Determining all possible weight hierarchies of general linear codes" is a basic theoretical issue and has important scientific significance in communication system.However,it is impossible for g-ary linear codes of dimension k when q and k are slightly larger,then a reasonable formulation of the problem is modified as: "Determine almost all weight hierarchies of general g-ary linear codes of dimension k".In this paper,based on the finite projective geometry method,the authors study g-ary linear codes of dimension 5 in class IV,and find new necessary conditions of their weight hierarchies,and classify their weight hierarchies into6 subclasses.The authors also develop and improve the method of the subspace set,thus determine almost all weight hierarchies of 5-dimensional linear codes in class IV.It opens the way to determine the weight hierarchies of the rest two of 5-dimensional codes(classes III and VI),and break through the difficulties.Furthermore,the new necessary conditions show that original necessary conditions of the weight hierarchies of k-dimensional codes were not enough(not most tight nor best),so,it is important to excogitate further new necessary conditions for attacking and solving the fc-dimensional problem.展开更多
文摘Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes.
基金the National Key Research and Development Program of China(2020YFA0908300)National Science Fund for Excellent Young Scholars(32222069)+2 种基金National Natural Science Foundation of China(32172349)Natural Science Foundation of Jiangsu Province(BK20200085)Key Research and Development Program of Jiangsu Province(BE2019628).
文摘N-acetylneuraminic acid(NeuAc)is an important nutrient that plays a key role in brain development in infants NeuAc is mainly produced by extraction from natural resources such as edible birds’s nests,crucian eggs,caviar and human breast milk.The extraction process is complicated,resulting in the disadvantages of low NeuAc content and low recovery rate.In this study,a crude enzyme immobilization-based cell-free system(CEICFS)was developed for efficient NeuAc biosynthesis.First,N-terminal coding sequences that improved the expression levels of N-acetylglucosamine-2-epimerase(AGE)and N-acetylneuraminic acid aldolase(NanA)were obtained by high-throughput screening.And these sequences resulted in up to 1.5-fold(1.2-fold)increase in AGE(NanA)enzyme levels.And then,a CEICFS for NeuAc biosynthesis was proposed by directly immobilizing crude enzyme containing AGE and NanA on amino resin.Subsequently,NeuAc production from GlcNAc using CEICFS in one reactor was carried out,resulting 68 g/L of NeuAc and the highest productivity of 6.8 g/L/h.Further,the enzyme activity was still higher than 75%after five repeated uses.The functional properties of CEICFS were studied and compared to those of the free enzyme,immobilization can extend the application of enzyme to some harsh environments,such as low temperature and acidic environment.Therefore,CEICFS with excellent heat resistance,storage stability and reusability exhibit great potential for industrial application.
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Modeling non coding background sequences appropriately is important for the detection of regulatory elements from DNA sequences. Based on the chi square statistic test, some explanations about why to choose higher order Markov chain model and how to automatically select the proper order are given in this paper. The chi square test is first run on synthetic data sets to show that it can efficiently find the proper order of Markov chain. Using chi square test, distinct higher order context dependences inherent in ten sets of sequences of yeast S.cerevisiae from other literature have been found. So the Markov chain with higher order would be more suitable for modeling the non coding background sequences than an independent model.
基金supported by the National High Technology Research and Development Program(No.2006AA10Z173 and 2006011001020)the Natural Science Foundation of Shandong Province(Y2007D48)
文摘In order to exploit the evolution and find novel low-molecular-weight glutenin subunit (LMW-GS) for improvement of common wheat quality, thirteen variants from a somatic hybrid introgression line II-12 between Triticum aestivum cv. Jinan 177 (JN177) and Agropyron elongatum were characterized via genomic PCR. Four clones were pseudogenes because they contained an internal stop codon. The remaining nine variants contained intact open reading frames (ORFs). Sequence alignment indicates that the proteins deduced from the nine ORFs have similar primary structure with LMW-GS cloned from its parents previously. However, they have some unique modifications in the structures. For example, EU292737 contains not only an extra Cys residue in the C-terminal domain but also a long repetitive domain. Both EU 159511 and EU292738 start their first Cys residue in the N-terminal repetitive domain, but not in the N-conserved domain traditionally. These structural alterations may have positive contributions to wheat flour quality. The results of phylogeny showed that most LMW-GS variances from 11-12 were homologous to those from parent JN177 and other wheat lines. The reason for quick evolution of LMW-GS in 11-12 was discussed.
基金Sponsored by the National High-Tech Research and Development Program of China (Grant No 2001AA113160,2004AA104280,and 2007AA010302)the National Natural Science Foundation of China(Grant No90718004)
文摘To avoid the complexity and inefficiency for specific applications of the current software architecture, a novel approach using partial evaluation is proposed to improve the running performance of components. The generic program was specialized into domain-specific realization for the known knowledge and environments. The syntax and semantic(adj.) were analyzed based on byte code instruction sequences, and partial evaluation rules depicted how to perform the specialization. The partial evaluation for object-oriented programs was implemented. The experimental results show that partial evaluation is effective to speed up the running efficiency. The more generality and scalability can be obtained by the integration of partial evaluation with the favorable design mechanisms and compiler optimization technology.
基金Supported by University Natural Science Research Pro-ject of Jiangsu (No.03KJB510088)National Natural Science Foundation of China (No.60572130).
文摘In Direct Sequence Code Division Multiple Access (DS-CDMA) systems,the chip wave-form affects the implementation,system bandwidth,envelope uniformity,eye pattern and Multiple user Access Interference (MAI). In this paper,based on an elementary density function of a second order polynomial,a class of second order continuity pulses is proposed. From this class of pulses,we can find some members having faster decaying rate,bigger eye opening,more uniform envelope and stronger anti-MAI capability than the Nyquist waveform. The normalized-bandwidth-pulse-shape-factor product,the decaying rate of the tail of the time waveform,the opening of the eye diagram,and the envelope uniformity of the second order continuity pulses are addressed in the paper that provide the basic information for the selection of the chip pulse for CDMA systems.
文摘In this paper, the complexity and performance of the Auxiliary Vector (AV) based reduced-rank filtering are addressed. The AV filters presented in the previous papers have the general form of the sum of the signature vector of the desired signal and a set of weighted AVs,which can be classified as three categories according to the orthogonality of their AVs and the optimality of the weight coefficients of the AVs. The AV filter with orthogonal AVs and optimal weight coefficients has the best performance, but requires considerable computational complexity and suffers from the numerical unstable operation. In order to reduce its computational load while keeping the superior performance, several low complexity algorithms are proposed to efficiently calculate the AVs and their weight coefficients. The diagonal loading technique is also introduced to solve the numerical unstability problem without complexity increase. The performance of the three types of AV filters is also compared through their application to Direct Sequence Code Division Multiple Access (DS-CDM A) systems for interference suppression.
文摘With the support from the National Natural Science Foundation of China,Prof.Huang Yanyi(黄岩谊)led a team at Peking University to demonstrate a novel approach,which combined fluorogenic sequencingby-synthesis(SBS)chemistry with an information theory-based error-correction coding scheme to
基金supported by the National Natural Science Foundation of China under Grant No.11171366"the Fundamental Research Funds for the Central Universities"South-Central University for Nationalities under Grant No.CZY12014
文摘The weight hierarchy of a linear[n;k;q]code C over GF(q) is the sequence(d_1,d_2,…,d_k)where d_r is the smallest support of any r-dimensional subcode of C. "Determining all possible weight hierarchies of general linear codes" is a basic theoretical issue and has important scientific significance in communication system.However,it is impossible for g-ary linear codes of dimension k when q and k are slightly larger,then a reasonable formulation of the problem is modified as: "Determine almost all weight hierarchies of general g-ary linear codes of dimension k".In this paper,based on the finite projective geometry method,the authors study g-ary linear codes of dimension 5 in class IV,and find new necessary conditions of their weight hierarchies,and classify their weight hierarchies into6 subclasses.The authors also develop and improve the method of the subspace set,thus determine almost all weight hierarchies of 5-dimensional linear codes in class IV.It opens the way to determine the weight hierarchies of the rest two of 5-dimensional codes(classes III and VI),and break through the difficulties.Furthermore,the new necessary conditions show that original necessary conditions of the weight hierarchies of k-dimensional codes were not enough(not most tight nor best),so,it is important to excogitate further new necessary conditions for attacking and solving the fc-dimensional problem.