Increasing yield is one of the most important goals in crop breeding. Soybean （Glycine max L. Merr.）, one of the most economically important leguminous seed crops, provides the majority of plant proteins, and more t...Increasing yield is one of the most important goals in crop breeding. Soybean （Glycine max L. Merr.）, one of the most economically important leguminous seed crops, provides the majority of plant proteins, and more than a quarter of the world＇s food and animal feed （Graham and Vance, 2003）. The yield of soybean is finally determined by the number of seeds per unit area, which affected by many characters, such as height, branching number, photosynthesis, seed size, seed number. The number of seeds per pod is taken for one of the critical components that related to yield （You et al., 1995）.展开更多
Since the whole genome sequence of Arabidopsis thaliana ecotype Columbia (Col-0) was published in 2 000, the focus of genomics study had turned from structural genomics to functional genomics era[1]. In the post genom...Since the whole genome sequence of Arabidopsis thaliana ecotype Columbia (Col-0) was published in 2 000, the focus of genomics study had turned from structural genomics to functional genomics era[1]. In the post genomics era, mutants play an important role for gene function exploring. Therefore, acquiring various variants and studying on them are useful for understanding the mechanism of plant development and molecular design for plant breeding.展开更多
Gelatinization temperature (GT) is an important parameter for evaluating the cooking and eating quality of rice besides amylose content (AC). The inheritance of the genes affecting GT has been widely studied and is co...Gelatinization temperature (GT) is an important parameter for evaluating the cooking and eating quality of rice besides amylose content (AC). The inheritance of the genes affecting GT has been widely studied and is considered to be controlled by a major gene. Here, we report the map-based cloning of rice ALK that encodes the soluble starch synthase II (SSSII). Comparison between the DNA sequences from different rice varieties, together with the results obtained with digestion of the rice seeds in alkali solution, indicates that the base substitutions in coding se-quence of ALK may cause the alteration in GT.展开更多
IspH is a key enzyme in the last step of the methyI-D-erythritol-4-phosphate （MEP） pathway. Loss of function of IspH can often result in complete yellow or albino phenotype in many plants. Here, we report the charac...IspH is a key enzyme in the last step of the methyI-D-erythritol-4-phosphate （MEP） pathway. Loss of function of IspH can often result in complete yellow or albino phenotype in many plants. Here, we report the characterization of a recessive mutant of maize, zebra7 （zb7）, showing transverse green/yellow striped leaves in young plants. The yellow bands of the mutant have decreased levels of chlorophylls and carotenoids with delayed chloroplast development. Low temperature suppressed mutant phenotype, while alternate light/dark cycle or high temperature enlarged the yellow section. Map-based cloning demonstrated that zb7 encodes the IspH protein with a mis-sense mutation in a conserved region. Transgenic silencing of Zb7 in maize resulted in complete albino plantlets that are aborted in a few weeks, confirming that Zb7 is important in the early stages of maize chloroplast development. Zb7 is constitutively expressed and its expression subject to a 16-h light/8-h dark cycle regulation. Our results suggest that the less effective or unstable IspH in zb7 mutant, together with its diurnal expression, are mechanistically accounted for the zebra phenotype. The increased IspH mRNA in the leaves of zb7 at the late development stage may explain the restoration of mutant phenotype in mature stages.展开更多
The no-cloning theorem has sparked considerable interest in achieving high-fidelity approximate quantum cloning.Most of the previous studies mainly focused on the cloning of single particle states,and cloning schemes ...The no-cloning theorem has sparked considerable interest in achieving high-fidelity approximate quantum cloning.Most of the previous studies mainly focused on the cloning of single particle states,and cloning schemes used there are incapable of cloning quantum entangled states in multipartite systems.Few schemes were proposed for cloning multiparticle states,which consume more entanglement resources with loss of qubits,and the fidelity of the cloned state is relatively low.In this paper,cloning schemes for bipartite and tripartite entangled states based on photonic quantum walk and entanglement swapping are proposed.The results show that according to the proposed schemes,two high-fidelity(up to 0.75)cloned states can be obtained with less quantum resource consumption.Because of the simple cloning steps,few quantum resources and high fidelity,these schemes are both efficient and feasible.Moreover,this cloning machine eliminates the need for tracing out cloning machine,thereby minimizing resource waste.展开更多
Molecular cloning remains a cornerstone technique in genetic engineering and synthetic biology.In this study,we conducted a systematic comparative analysis between the classical cloning method and the Golden Gate asse...Molecular cloning remains a cornerstone technique in genetic engineering and synthetic biology.In this study,we conducted a systematic comparative analysis between the classical cloning method and the Golden Gate assembly technique,utilizing Escherichia coli as the model organism.Through polymerase chain reaction(PCR)amplification,restriction enzyme digestion,ligation,transformation,and Sanger sequencing,we assessed the operational efficiency and cloning fidelity of both strategies.Our results demonstrated that Golden Gate assembly,leveraging type IIS restriction enzymes and simultaneous ligation,significantly enhanced cloning efficiency and precision,particularly for seamless multi-fragment assembly.In contrast,the classical cloning approach maintained certain advantages in simplicity and robustness for specific experimental conditions.Challenges encountered during transformation and sequencing highlighted the critical impact of technical accuracy on experimental outcomes.This study underscores the importance of selecting appropriate cloning methodologies tailored to experimental objectives and laboratory capabilities,providing a foundation for optimized molecular cloning workflows in future synthetic biology and biotechnology applications.展开更多
[Objectives]This study was conducted to investigate the functional characteristics of the trxB gene in Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the trxB gene sequence of V.alginol...[Objectives]This study was conducted to investigate the functional characteristics of the trxB gene in Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the trxB gene sequence of V.alginolyticus for PCR cloning of its full-length sequence.Systematic bioinformatics analyses were conducted to predict the physicochemical properties,secondary structure,and tertiary structure of the encoded protein.[Results]The trxB gene is 960 bp in length,encoding 319 amino acid residues.The deduced protein has a predicted molecular weight of 34.32 kDa and an isoelectric point(pI)of 4.77.Analysis of the amino acid sequence revealed a distinct signal peptide cleavage site at the N-terminus,with no transmembrane domains.The functional sites are as follows:1 N-glycosylation site,1 cAMP-and cGMP-dependent protein kinase phosphorylation site,4 protein kinase C phosphorylation sites,7 casein kinase II phosphorylation sites,1 tyrosine kinase phosphorylation site,11 N-myristoylation sites,1 prenyl group binding site,3 microbody C-terminal targeting signal sites,and 1 xanthine nucleotide-disulfide oxidoreductase class II active site.Subcellular localization prediction indicated the highest probability(44.4%)for endoplasmic reticulum localization.The TrxB amino acid sequence of V.alginolyticus shares 97.2%-98.4%homology with other Vibrio species,and they were clustered within the same subgroup.Secondary structure prediction showed proportions of random coils(31.97%),alpha-helices(31.66%),extended strands(25.08%),and beta turns(11.29%).The tertiary structure model exhibited 88.68%similarity to template 5vt3.1.A.[Conclusions]This study elucidated the characterization of the TrxB protein in V.alginolyticus,laying a theoretical foundation for the development of outer membrane protein subunit vaccines against this pathogen.展开更多
[Objectives] To analyze the function of cobQ gene from Vibrio alginolyticus strain HY9901,and to provide a reference for exploring the possible mechanism of cobQ gene from V.alginolyticus.[Methods] A pair of primers w...[Objectives] To analyze the function of cobQ gene from Vibrio alginolyticus strain HY9901,and to provide a reference for exploring the possible mechanism of cobQ gene from V.alginolyticus.[Methods] A pair of primers were designed based on the sequence of the V.alginolyticus cobQ gene and used to amplify the full-length gene by PCR.[Results] The PCR amplification results indicated that the cobQ gene has a full length of 780 bp,encoding 259 amino acid residues.The deduced amino acid sequence predicts a molecular weight of approximately 28.83 kD and an isoelectric point of 9.21.Sequence analysis revealed no N-terminal signal peptide cleavage site,suggesting the absence of both a signal peptide and transmembrane regions in this protein.The amino acid sequence contains 2 N-terminal myristoylation sites,1 N-glycosylation site,1 glycosaminoglycan attachment site,4 microbody C-terminal targeting signal sites,3 casein kinase II phosphorylation sites,and 4 protein kinase C phosphorylation sites.Subcellular localization prediction showed that the CobQ protein is primarily localized in the cytoplasm(65.2%probability).Homology analysis demonstrated that the amino acid sequence of the cobQ gene from V.alginolyticus shares up to 99%homology with other Vibrio species,clustering within the same subclade as Vibrio parahaemolyticus,indicating close phylogenetic relationships.Secondary structure prediction revealed proportions ofα-helices,random coils,and extended strands as 44.40%,36.68%,and 18.92%,respectively.The tertiary structure model exhibited 87.62%similarity to the template A0A165XBE1.1.[Conclusions] In this study,the V.alginolyticus cobq gene was successfully cloned and its sequence was analyzed by bioinformatics.It is expected to lay a foundation for the subsequent study of the regulatory mechanism of its protein on the virulence of V.alginolyticus.展开更多
Somatic cell nuclear transfer(SCNT)has been successfully employed across various mammalian species,yet cloned animals consistently exhibit low pregnancy rates,primarily due to placental abnormalities such as hyperplas...Somatic cell nuclear transfer(SCNT)has been successfully employed across various mammalian species,yet cloned animals consistently exhibit low pregnancy rates,primarily due to placental abnormalities such as hyperplasia and hypertrophy.This study investigated the involvement of the Hippo signaling pathway in aberrant placentaldevelopmentinSCNT-inducedbovine pregnancies.SCNT-derived cattle exhibited placental hypertrophy,including enlarged abdominal circumference and altered placental cotyledon morphology.RNA sequencing analysis indicated significant dysregulation of Hippo signaling pathway genes in SCNT placentas.Coexpression of YAP1 and CCND1 was observed in cloned blastocysts,placental tissues,and bovine placental mesenchymal stem cells(bPMSCs).Manipulation of YAP1expression demonstrated the capacity to regulate bPMSC proliferation.Experimental assays confirmed the direct binding of YAP1 to CCND1,which subsequently promoted CCND1 expression in bPMSCs.Furthermore,inhibition of CDK6,a downstream target of CCND1,attenuated SCNT bPMSC proliferation.This study identified YAP1 as a key regulatory component within the Hippo signaling pathway that drives placental hyperplasia in cloned cattle through up-regulation of CCND1-CDK6 expression,facilitating cell cycle progression.These findings offer potential avenues for enhancing cloning efficiency,with implications for evolutionary biology and the conservation of valuable germplasm resources.展开更多
Heading date is one of the most important agronomic traits that directly affect rice yield and determines the regional adaptability in specific growing environments.As a short-day plant,rice can grow under long-day(LD...Heading date is one of the most important agronomic traits that directly affect rice yield and determines the regional adaptability in specific growing environments.As a short-day plant,rice can grow under long-day(LD)conditions due to the synergistic regulation of many photosensitive genes.Using a set of chromosome segment substitution lines(CSSLs)with the indica cultivar Huanghuazhan(HHZ)as the recipient parent and Basmati Surkh 89-15(BAS)as the donor parent,we identified a QTL locus.展开更多
This paper presents a very simple method to derive the explicit transformations of the optimal economical 1 to M phase-covariant cloning. The fidelity of clones reaches the theoretic bound [D＇Ar]ano G M and Macchiave...This paper presents a very simple method to derive the explicit transformations of the optimal economical 1 to M phase-covariant cloning. The fidelity of clones reaches the theoretic bound [D＇Ar]ano G M and Macchiavello C 2003 Phys. Rev. A 67 042306]. The derived transformations cover the previous contributions [Delgado Y, Lamata Let al, 2007 Phys. Rev. Lett. 98 150502] in which M must be odd.展开更多
A new scan matching method for mobile robot localization is presented, which takes line segment as the feature and matches the real scans in the given reference map by relationships of the directional-defined line seg...A new scan matching method for mobile robot localization is presented, which takes line segment as the feature and matches the real scans in the given reference map by relationships of the directional-defined line segments. The alignment was done by hierarchically identifying the multiple relationships and the result was recorded in a correspondence matrix, where the best match is defined and selected for localization. It is indicated that the searching algorithm of the best match can find the ambiguities and get rid of them. This method with less computational cost works well in occluded environment, and can correct the error in pose estimation without the need for the estimation itself. The efficiency, accuracy and robustness of this method were verified by experiments of localization in an occluded environment and a long-distance indoor navigation.展开更多
This work proposes a map-based control method to improve a vehicle's lateral stability, and the performance of the proposed method is compared with that of the conventional model-referenced control method. Model-r...This work proposes a map-based control method to improve a vehicle's lateral stability, and the performance of the proposed method is compared with that of the conventional model-referenced control method. Model-referenced control uses the sliding mode method to determine the compensated yaw moment; in contrast, the proposed map-based control uses the compensated yaw moment map acquired by vehicle stability analysis. The vehicle stability region is calculated by a topological method based on the trajectory reversal method. A 2-DOF vehicle model and Pacejka's tire model are used to evaluate the proposed map-based control method. The properties of model-referenced control and map-based control are compared under various road conditions and driving inputs. Model-referenced control uses a control input to satisfy the linear reference model, and it generates unnecessary tire lateral forces that may lead to worse performance than an uncontrolled vehicle with step steering input on a road with a low friction coefficient. However, map-based control determines a compensated yaw moment to maintain the vehicle within the stability region,so the typical responses of vehicle enable to converge rapidly. The simulation results with sine and step steering show that map-based control provides better the tracking responsibility and control performance than model-referenced control.展开更多
In this experiment, it was designed to carry out superovulation on the two cloned cattles, vitrification and transfer of the embryos recovered from them. First of all, it was carried out vitrification on embryos obt...In this experiment, it was designed to carry out superovulation on the two cloned cattles, vitrification and transfer of the embryos recovered from them. First of all, it was carried out vitrification on embryos obtained by IVF. Results showed that there were no significant differences between the blastocysts (obtained by IVF) vitrified in EPS10 and these in EPS20 on the resuscitative rate and the developmental rate. The hatched rate of the blastocysts vitrified in EPS10 (31.3%, 35/112) was significantly higher than that in EPS20 (12.2%, 13/107)(P<0.01), so EPS20 was selected as the vitrification solution to freeze the embryos recovered from the cloned cattle. After superovulation, six (four usable embryos) and ten (nine usable embryos) embryos were respectively recovered from Kangkang and Shuanghuang. Two embryos were selected from the recovered embryos of each cloned cattle to freeze in EPS20, subsequently thawed and transferred into luteal ipsilateral uterine horns of 4 Holstein recipient cows after synchronization of estrus, respectively. At last, one recipient cow (No. 9908) became pregnant and delivered one healthy calf (descendant of the cloned cattle-Shuangshuang). The results of this experi- ment show that the cloned cattle as well as common cattle had better response to the exotic FSH and better ability to multiovulation, the embryos recovered from the cloned cattle can be vitrificated.展开更多
The performance of the speaker recognition system declines when training and testing audio codecs are mismatched. In this paper, based on analyzing the effect of mismatched audio codecs in the linear prediction cepstr...The performance of the speaker recognition system declines when training and testing audio codecs are mismatched. In this paper, based on analyzing the effect of mismatched audio codecs in the linear prediction cepstrum coefficients, a method of MAP-based audio coding compensation for speaker recognition is proposed. The proposed method firstly sets a standard codec as a reference and trains the speaker models in this codec format, then learns the deviation distributions between the standard codec format and the other ones, next gets the current bias via using a small number adaptive data and the MAP-based adaptive technique, and then adjusts the model parameters by the type of coming audio codec format and its related bias. During the test, the features of the coming speaker are used to match with the adjusted model. The experimental result shows that the accuracy reached 82.4% with just one second adaptive data, which is higher 5.5% than that in the baseline system.展开更多
Gene synthesis has provided important contributions in various fields including genomics and medicine. Current genes are 7 - 30 cents depending on the assembly and sequencing methods performed. Demand for gene synthes...Gene synthesis has provided important contributions in various fields including genomics and medicine. Current genes are 7 - 30 cents depending on the assembly and sequencing methods performed. Demand for gene synthesis has been increasing for the past few decades, yet available methods remain expensive. A solution to this problem involves microchip-derived oligonucleotides (oligos), an oligo pool with a substantial number of oligo fragments. Microchips have been proposed as a tool for gene synthesis, but this approach has been criticized for its high error rate during sequencing. This study tests a possible cost-effective method for gene synthesis utilizing fragment assembly and golden gate assembly, which can be employed for quicker manufacturing and efficient execution of genes in the near future. The droplet method was tested in two trials to determine the viability of the method through the accuracy of the oligos sequenced. A preliminary research experiment was performed to determine the efficacy of oligo lengths ranging from two to four overlapping oligos through Gibson assembly. Of the three oligo lengths tested, only two fragment oligos were correctly sequenced. Two fragment oligos were used for the second experiment, which determined the efficacy of the droplet method in reducing gene synthesis cost and speed. The first trial utilized a high-fidelity polymerase and resulted in 3% correctly sequenced oligos, so the second trial utilized a non-high-fidelity polymerase, resulting in 8% correctly sequenced oligos. After calculating, the cost of gene synthesis lowers down to 0.8 cents/base. The final calculated cost of 0.8 cents/base is significantly cheaper than other manufacturing costs of 7 - 30 cents/base. Reducing the cost of gene synthesis provides new insight into the cost-effectiveness of present technologies and protocols and has the potential to benefit the fields of bioengineering and gene therapy.展开更多
PhoR is a histidine kinase in a two-component regulatory system that regulates phosphorus metabolic pathways and undertakes the key mission of information transmission in pathogenic bacteria.The full-length phoR gene ...PhoR is a histidine kinase in a two-component regulatory system that regulates phosphorus metabolic pathways and undertakes the key mission of information transmission in pathogenic bacteria.The full-length phoR gene was successfully cloned from the Vibrio alginolyticus HY9901 strain.A comprehensive analysis of the cloned gene was conducted using bioinformatics.Sequence analysis revealed that the total length of the phoR gene(GenBank accession No.:KJ958404.1)is 1299 bp,with the coding region containing a total of 432 amino acid residues.The phylogenetic tree of PhoR revealed that it belongs to the same subclade as V.diabolicus.The SMART program was employed for the purpose of functional domain prediction,which revealed that PhoR possesses three major functional domains:PAS(amino acids 98-166),HisKA(amino acids 205-272),and HATPase_c(amino acids 317-429).展开更多
At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software too...At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software tools were used to analyze and predict the gene family and this gene.There were 30 members of the cucumber F-box gene family.The coding region of the cucumber CsFK111 gene was full-length 1314 bp,which encoded 437 amino acids and was predicted to be located in the nucleus.The protein encoded by this gene was a non-transmembrane protein,and the prediction of the secondary structure showed thatβ-lamellar structure and irregular crimp were dominant.A comparison of the phylogenetic tree showed that it was closest to cantaloupe and belonged to the same branch.The results provided a basis for future study on the regulation mechanism of the CsFK111 gene on cucumber dwarfing and also laid a foundation for further study of FBK family proteins.展开更多
[Objectives]This study was conducted to understand the structure and function of MsrA protein.[Methods]With Vibrio alginolyticus HY9901 as the object of study,primers were designed to amplify the full-length gene of m...[Objectives]This study was conducted to understand the structure and function of MsrA protein.[Methods]With Vibrio alginolyticus HY9901 as the object of study,primers were designed to amplify the full-length gene of msrA,and its bioinformatics analysis was carried out.[Results]The full length of msrA gene was 639 bp,encoding 212 amino acids,and its theoretical molecular weight was about 23729.60 Da.The protein had a stable structure,and it was hydrophobic overall.The structure of signal peptides at the N terminal of the amino acid sequence was predicted,and it was found that there was no signal peptide cleavage site and no transmembrane region.The amino acid sequence of MsrA contained multiple signal binding sites.Protein subcellular localization showed that MsrA protein was most likely located in the cytoplasm.Homology analysis showed that MsrA of V.alginolyticus had high homology with other Vibrio species,and the highest homology with V.alginolyticus.In the prediction of functional domains,MsrA had the function of methionine sulfoxide reduction.In secondary structure prediction,MsrA contained random coils at a proportion of 46.70%,which was the highest.The similarity between the tertiary structure model of MsrA and template Q87SW6.1.A was 89.15%.PTM analysis showed that MsrA protein had many PTM modification sites such as phosphorylation and glycosylation sites.[Conclusions]This study provides some reference value for further study on the role of MsrA in bacterial antioxidant stress.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.31271297 and 31222042) "One-hundred talents" Startup Funds from Chinese Academy of SciencesNational Key Basic Research Program(No. 2009CB 118402)
文摘Increasing yield is one of the most important goals in crop breeding. Soybean （Glycine max L. Merr.）, one of the most economically important leguminous seed crops, provides the majority of plant proteins, and more than a quarter of the world＇s food and animal feed （Graham and Vance, 2003）. The yield of soybean is finally determined by the number of seeds per unit area, which affected by many characters, such as height, branching number, photosynthesis, seed size, seed number. The number of seeds per pod is taken for one of the critical components that related to yield （You et al., 1995）.
文摘Since the whole genome sequence of Arabidopsis thaliana ecotype Columbia (Col-0) was published in 2 000, the focus of genomics study had turned from structural genomics to functional genomics era[1]. In the post genomics era, mutants play an important role for gene function exploring. Therefore, acquiring various variants and studying on them are useful for understanding the mechanism of plant development and molecular design for plant breeding.
基金supported by the National Special Program for Research and Transgenic Plants(Grant No.JY03-A-07-01)Natural Science Foundation,Zhejiang Province.
文摘Gelatinization temperature (GT) is an important parameter for evaluating the cooking and eating quality of rice besides amylose content (AC). The inheritance of the genes affecting GT has been widely studied and is considered to be controlled by a major gene. Here, we report the map-based cloning of rice ALK that encodes the soluble starch synthase II (SSSII). Comparison between the DNA sequences from different rice varieties, together with the results obtained with digestion of the rice seeds in alkali solution, indicates that the base substitutions in coding se-quence of ALK may cause the alteration in GT.
文摘IspH is a key enzyme in the last step of the methyI-D-erythritol-4-phosphate （MEP） pathway. Loss of function of IspH can often result in complete yellow or albino phenotype in many plants. Here, we report the characterization of a recessive mutant of maize, zebra7 （zb7）, showing transverse green/yellow striped leaves in young plants. The yellow bands of the mutant have decreased levels of chlorophylls and carotenoids with delayed chloroplast development. Low temperature suppressed mutant phenotype, while alternate light/dark cycle or high temperature enlarged the yellow section. Map-based cloning demonstrated that zb7 encodes the IspH protein with a mis-sense mutation in a conserved region. Transgenic silencing of Zb7 in maize resulted in complete albino plantlets that are aborted in a few weeks, confirming that Zb7 is important in the early stages of maize chloroplast development. Zb7 is constitutively expressed and its expression subject to a 16-h light/8-h dark cycle regulation. Our results suggest that the less effective or unstable IspH in zb7 mutant, together with its diurnal expression, are mechanistically accounted for the zebra phenotype. The increased IspH mRNA in the leaves of zb7 at the late development stage may explain the restoration of mutant phenotype in mature stages.
文摘The no-cloning theorem has sparked considerable interest in achieving high-fidelity approximate quantum cloning.Most of the previous studies mainly focused on the cloning of single particle states,and cloning schemes used there are incapable of cloning quantum entangled states in multipartite systems.Few schemes were proposed for cloning multiparticle states,which consume more entanglement resources with loss of qubits,and the fidelity of the cloned state is relatively low.In this paper,cloning schemes for bipartite and tripartite entangled states based on photonic quantum walk and entanglement swapping are proposed.The results show that according to the proposed schemes,two high-fidelity(up to 0.75)cloned states can be obtained with less quantum resource consumption.Because of the simple cloning steps,few quantum resources and high fidelity,these schemes are both efficient and feasible.Moreover,this cloning machine eliminates the need for tracing out cloning machine,thereby minimizing resource waste.
文摘Molecular cloning remains a cornerstone technique in genetic engineering and synthetic biology.In this study,we conducted a systematic comparative analysis between the classical cloning method and the Golden Gate assembly technique,utilizing Escherichia coli as the model organism.Through polymerase chain reaction(PCR)amplification,restriction enzyme digestion,ligation,transformation,and Sanger sequencing,we assessed the operational efficiency and cloning fidelity of both strategies.Our results demonstrated that Golden Gate assembly,leveraging type IIS restriction enzymes and simultaneous ligation,significantly enhanced cloning efficiency and precision,particularly for seamless multi-fragment assembly.In contrast,the classical cloning approach maintained certain advantages in simplicity and robustness for specific experimental conditions.Challenges encountered during transformation and sequencing highlighted the critical impact of technical accuracy on experimental outcomes.This study underscores the importance of selecting appropriate cloning methodologies tailored to experimental objectives and laboratory capabilities,providing a foundation for optimized molecular cloning workflows in future synthetic biology and biotechnology applications.
基金Supported by Natural Science Foundation of Guangdong Province(2025A1515011061)Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean University+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘[Objectives]This study was conducted to investigate the functional characteristics of the trxB gene in Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the trxB gene sequence of V.alginolyticus for PCR cloning of its full-length sequence.Systematic bioinformatics analyses were conducted to predict the physicochemical properties,secondary structure,and tertiary structure of the encoded protein.[Results]The trxB gene is 960 bp in length,encoding 319 amino acid residues.The deduced protein has a predicted molecular weight of 34.32 kDa and an isoelectric point(pI)of 4.77.Analysis of the amino acid sequence revealed a distinct signal peptide cleavage site at the N-terminus,with no transmembrane domains.The functional sites are as follows:1 N-glycosylation site,1 cAMP-and cGMP-dependent protein kinase phosphorylation site,4 protein kinase C phosphorylation sites,7 casein kinase II phosphorylation sites,1 tyrosine kinase phosphorylation site,11 N-myristoylation sites,1 prenyl group binding site,3 microbody C-terminal targeting signal sites,and 1 xanthine nucleotide-disulfide oxidoreductase class II active site.Subcellular localization prediction indicated the highest probability(44.4%)for endoplasmic reticulum localization.The TrxB amino acid sequence of V.alginolyticus shares 97.2%-98.4%homology with other Vibrio species,and they were clustered within the same subgroup.Secondary structure prediction showed proportions of random coils(31.97%),alpha-helices(31.66%),extended strands(25.08%),and beta turns(11.29%).The tertiary structure model exhibited 88.68%similarity to template 5vt3.1.A.[Conclusions]This study elucidated the characterization of the TrxB protein in V.alginolyticus,laying a theoretical foundation for the development of outer membrane protein subunit vaccines against this pathogen.
基金Natural Science Foundation of Guangdong Province(2025A1515011061)Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean University+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘[Objectives] To analyze the function of cobQ gene from Vibrio alginolyticus strain HY9901,and to provide a reference for exploring the possible mechanism of cobQ gene from V.alginolyticus.[Methods] A pair of primers were designed based on the sequence of the V.alginolyticus cobQ gene and used to amplify the full-length gene by PCR.[Results] The PCR amplification results indicated that the cobQ gene has a full length of 780 bp,encoding 259 amino acid residues.The deduced amino acid sequence predicts a molecular weight of approximately 28.83 kD and an isoelectric point of 9.21.Sequence analysis revealed no N-terminal signal peptide cleavage site,suggesting the absence of both a signal peptide and transmembrane regions in this protein.The amino acid sequence contains 2 N-terminal myristoylation sites,1 N-glycosylation site,1 glycosaminoglycan attachment site,4 microbody C-terminal targeting signal sites,3 casein kinase II phosphorylation sites,and 4 protein kinase C phosphorylation sites.Subcellular localization prediction showed that the CobQ protein is primarily localized in the cytoplasm(65.2%probability).Homology analysis demonstrated that the amino acid sequence of the cobQ gene from V.alginolyticus shares up to 99%homology with other Vibrio species,clustering within the same subclade as Vibrio parahaemolyticus,indicating close phylogenetic relationships.Secondary structure prediction revealed proportions ofα-helices,random coils,and extended strands as 44.40%,36.68%,and 18.92%,respectively.The tertiary structure model exhibited 87.62%similarity to the template A0A165XBE1.1.[Conclusions] In this study,the V.alginolyticus cobq gene was successfully cloned and its sequence was analyzed by bioinformatics.It is expected to lay a foundation for the subsequent study of the regulatory mechanism of its protein on the virulence of V.alginolyticus.
基金supported by the National Natural Science Foundation of China (32060755)Natural Science Foundation of Inner Mongolia (2024MS03001)+7 种基金Inner Mongolia Autonomous Region Open Competition Projects (2022JBGS0018)Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region (NJYT23090)Inner Mongolia Autonomous Region Science and Technology Leading Team (2022LJRC0006)Inner Mongolia Autonomous Region Science and Technology Major Project (2021ZD0009)Major Agricultural Science and Technology Project of the Ministry of Agriculture and Rural Affairs (NK2022130203)Central Government Guides Local Science and Technology Development Funds (2022ZY0212)Inner Mongolia Autonomous Region High-level Talent Support ProgramInner Mongolia University Chief Scientist Program。
文摘Somatic cell nuclear transfer(SCNT)has been successfully employed across various mammalian species,yet cloned animals consistently exhibit low pregnancy rates,primarily due to placental abnormalities such as hyperplasia and hypertrophy.This study investigated the involvement of the Hippo signaling pathway in aberrant placentaldevelopmentinSCNT-inducedbovine pregnancies.SCNT-derived cattle exhibited placental hypertrophy,including enlarged abdominal circumference and altered placental cotyledon morphology.RNA sequencing analysis indicated significant dysregulation of Hippo signaling pathway genes in SCNT placentas.Coexpression of YAP1 and CCND1 was observed in cloned blastocysts,placental tissues,and bovine placental mesenchymal stem cells(bPMSCs).Manipulation of YAP1expression demonstrated the capacity to regulate bPMSC proliferation.Experimental assays confirmed the direct binding of YAP1 to CCND1,which subsequently promoted CCND1 expression in bPMSCs.Furthermore,inhibition of CDK6,a downstream target of CCND1,attenuated SCNT bPMSC proliferation.This study identified YAP1 as a key regulatory component within the Hippo signaling pathway that drives placental hyperplasia in cloned cattle through up-regulation of CCND1-CDK6 expression,facilitating cell cycle progression.These findings offer potential avenues for enhancing cloning efficiency,with implications for evolutionary biology and the conservation of valuable germplasm resources.
基金supported by the Zhejiang Provincial Natural Science Foundation of China(Grant Nos.LZ24C130004 and LQ24C130008)。
文摘Heading date is one of the most important agronomic traits that directly affect rice yield and determines the regional adaptability in specific growing environments.As a short-day plant,rice can grow under long-day(LD)conditions due to the synergistic regulation of many photosensitive genes.Using a set of chromosome segment substitution lines(CSSLs)with the indica cultivar Huanghuazhan(HHZ)as the recipient parent and Basmati Surkh 89-15(BAS)as the donor parent,we identified a QTL locus.
基金supported by the National Natural Science Foundation of China (Grant No 10674001)the Program of the Education Department of Anhui Province of China (Grant No KJ2007A002)
文摘This paper presents a very simple method to derive the explicit transformations of the optimal economical 1 to M phase-covariant cloning. The fidelity of clones reaches the theoretic bound [D＇Ar]ano G M and Macchiavello C 2003 Phys. Rev. A 67 042306]. The derived transformations cover the previous contributions [Delgado Y, Lamata Let al, 2007 Phys. Rev. Lett. 98 150502] in which M must be odd.
基金Sponsored by the National High Technology Research and Development Program of China(Grant No.2006AA040203)The National Natural Science Foundation of China(Grant No.60475032 and 60775062)the Program for New Century Excellent Talents in University(Grant No.NCET-07-0538)
文摘A new scan matching method for mobile robot localization is presented, which takes line segment as the feature and matches the real scans in the given reference map by relationships of the directional-defined line segments. The alignment was done by hierarchically identifying the multiple relationships and the result was recorded in a correspondence matrix, where the best match is defined and selected for localization. It is indicated that the searching algorithm of the best match can find the ambiguities and get rid of them. This method with less computational cost works well in occluded environment, and can correct the error in pose estimation without the need for the estimation itself. The efficiency, accuracy and robustness of this method were verified by experiments of localization in an occluded environment and a long-distance indoor navigation.
基金supported by a grant from Research year of Inje University in 2008(0001200811700)
文摘This work proposes a map-based control method to improve a vehicle's lateral stability, and the performance of the proposed method is compared with that of the conventional model-referenced control method. Model-referenced control uses the sliding mode method to determine the compensated yaw moment; in contrast, the proposed map-based control uses the compensated yaw moment map acquired by vehicle stability analysis. The vehicle stability region is calculated by a topological method based on the trajectory reversal method. A 2-DOF vehicle model and Pacejka's tire model are used to evaluate the proposed map-based control method. The properties of model-referenced control and map-based control are compared under various road conditions and driving inputs. Model-referenced control uses a control input to satisfy the linear reference model, and it generates unnecessary tire lateral forces that may lead to worse performance than an uncontrolled vehicle with step steering input on a road with a low friction coefficient. However, map-based control determines a compensated yaw moment to maintain the vehicle within the stability region,so the typical responses of vehicle enable to converge rapidly. The simulation results with sine and step steering show that map-based control provides better the tracking responsibility and control performance than model-referenced control.
文摘In this experiment, it was designed to carry out superovulation on the two cloned cattles, vitrification and transfer of the embryos recovered from them. First of all, it was carried out vitrification on embryos obtained by IVF. Results showed that there were no significant differences between the blastocysts (obtained by IVF) vitrified in EPS10 and these in EPS20 on the resuscitative rate and the developmental rate. The hatched rate of the blastocysts vitrified in EPS10 (31.3%, 35/112) was significantly higher than that in EPS20 (12.2%, 13/107)(P<0.01), so EPS20 was selected as the vitrification solution to freeze the embryos recovered from the cloned cattle. After superovulation, six (four usable embryos) and ten (nine usable embryos) embryos were respectively recovered from Kangkang and Shuanghuang. Two embryos were selected from the recovered embryos of each cloned cattle to freeze in EPS20, subsequently thawed and transferred into luteal ipsilateral uterine horns of 4 Holstein recipient cows after synchronization of estrus, respectively. At last, one recipient cow (No. 9908) became pregnant and delivered one healthy calf (descendant of the cloned cattle-Shuangshuang). The results of this experi- ment show that the cloned cattle as well as common cattle had better response to the exotic FSH and better ability to multiovulation, the embryos recovered from the cloned cattle can be vitrificated.
文摘The performance of the speaker recognition system declines when training and testing audio codecs are mismatched. In this paper, based on analyzing the effect of mismatched audio codecs in the linear prediction cepstrum coefficients, a method of MAP-based audio coding compensation for speaker recognition is proposed. The proposed method firstly sets a standard codec as a reference and trains the speaker models in this codec format, then learns the deviation distributions between the standard codec format and the other ones, next gets the current bias via using a small number adaptive data and the MAP-based adaptive technique, and then adjusts the model parameters by the type of coming audio codec format and its related bias. During the test, the features of the coming speaker are used to match with the adjusted model. The experimental result shows that the accuracy reached 82.4% with just one second adaptive data, which is higher 5.5% than that in the baseline system.
文摘Gene synthesis has provided important contributions in various fields including genomics and medicine. Current genes are 7 - 30 cents depending on the assembly and sequencing methods performed. Demand for gene synthesis has been increasing for the past few decades, yet available methods remain expensive. A solution to this problem involves microchip-derived oligonucleotides (oligos), an oligo pool with a substantial number of oligo fragments. Microchips have been proposed as a tool for gene synthesis, but this approach has been criticized for its high error rate during sequencing. This study tests a possible cost-effective method for gene synthesis utilizing fragment assembly and golden gate assembly, which can be employed for quicker manufacturing and efficient execution of genes in the near future. The droplet method was tested in two trials to determine the viability of the method through the accuracy of the oligos sequenced. A preliminary research experiment was performed to determine the efficacy of oligo lengths ranging from two to four overlapping oligos through Gibson assembly. Of the three oligo lengths tested, only two fragment oligos were correctly sequenced. Two fragment oligos were used for the second experiment, which determined the efficacy of the droplet method in reducing gene synthesis cost and speed. The first trial utilized a high-fidelity polymerase and resulted in 3% correctly sequenced oligos, so the second trial utilized a non-high-fidelity polymerase, resulting in 8% correctly sequenced oligos. After calculating, the cost of gene synthesis lowers down to 0.8 cents/base. The final calculated cost of 0.8 cents/base is significantly cheaper than other manufacturing costs of 7 - 30 cents/base. Reducing the cost of gene synthesis provides new insight into the cost-effectiveness of present technologies and protocols and has the potential to benefit the fields of bioengineering and gene therapy.
基金Supported by Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean UniversityNational Natural Science Foundation of China(32073015)+1 种基金Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802)Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007).
文摘PhoR is a histidine kinase in a two-component regulatory system that regulates phosphorus metabolic pathways and undertakes the key mission of information transmission in pathogenic bacteria.The full-length phoR gene was successfully cloned from the Vibrio alginolyticus HY9901 strain.A comprehensive analysis of the cloned gene was conducted using bioinformatics.Sequence analysis revealed that the total length of the phoR gene(GenBank accession No.:KJ958404.1)is 1299 bp,with the coding region containing a total of 432 amino acid residues.The phylogenetic tree of PhoR revealed that it belongs to the same subclade as V.diabolicus.The SMART program was employed for the purpose of functional domain prediction,which revealed that PhoR possesses three major functional domains:PAS(amino acids 98-166),HisKA(amino acids 205-272),and HATPase_c(amino acids 317-429).
基金Supported by the National Natural Science Foundation of China(32272724)the National Science Foundation of Heilongjiang Province,China(LH2019C033)。
文摘At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software tools were used to analyze and predict the gene family and this gene.There were 30 members of the cucumber F-box gene family.The coding region of the cucumber CsFK111 gene was full-length 1314 bp,which encoded 437 amino acids and was predicted to be located in the nucleus.The protein encoded by this gene was a non-transmembrane protein,and the prediction of the secondary structure showed thatβ-lamellar structure and irregular crimp were dominant.A comparison of the phylogenetic tree showed that it was closest to cantaloupe and belonged to the same branch.The results provided a basis for future study on the regulation mechanism of the CsFK111 gene on cucumber dwarfing and also laid a foundation for further study of FBK family proteins.
基金Supported National Natural Science Foundation of China(32073015)Undergraduate Training Program for Innovation and Entrepreneurship of Guangdong Ocean University(CXXL2024007)+2 种基金Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802)Postgraduate Education Innovation Program of Guangdong Ocean University(No.202446)Postgraduate Education Innovation Program of Guangdong Province(YJYH[2022]1).
文摘[Objectives]This study was conducted to understand the structure and function of MsrA protein.[Methods]With Vibrio alginolyticus HY9901 as the object of study,primers were designed to amplify the full-length gene of msrA,and its bioinformatics analysis was carried out.[Results]The full length of msrA gene was 639 bp,encoding 212 amino acids,and its theoretical molecular weight was about 23729.60 Da.The protein had a stable structure,and it was hydrophobic overall.The structure of signal peptides at the N terminal of the amino acid sequence was predicted,and it was found that there was no signal peptide cleavage site and no transmembrane region.The amino acid sequence of MsrA contained multiple signal binding sites.Protein subcellular localization showed that MsrA protein was most likely located in the cytoplasm.Homology analysis showed that MsrA of V.alginolyticus had high homology with other Vibrio species,and the highest homology with V.alginolyticus.In the prediction of functional domains,MsrA had the function of methionine sulfoxide reduction.In secondary structure prediction,MsrA contained random coils at a proportion of 46.70%,which was the highest.The similarity between the tertiary structure model of MsrA and template Q87SW6.1.A was 89.15%.PTM analysis showed that MsrA protein had many PTM modification sites such as phosphorylation and glycosylation sites.[Conclusions]This study provides some reference value for further study on the role of MsrA in bacterial antioxidant stress.
