Elastic behaviors of protein-like chains are investigated by Pruned-Enriched-Rosenbluth method and modified orientation-dependent monomer-monomer interactions model. The protein-like chain is pulled away from the attr...Elastic behaviors of protein-like chains are investigated by Pruned-Enriched-Rosenbluth method and modified orientation-dependent monomer-monomer interactions model. The protein-like chain is pulled away from the attractive surface slowly with elastic force acting on it. Strong adsorption interaction and no adsorption interaction are both considered. We calculate the characteristic ratio and shape factor of protein-like chains in the process of elongation. The conformation change of the protein-like chain is well depicted. The shape of chain changes from “rod” to “sphere” at the beginning of elongation. Then, the shape changes from “sphere” to “rod”. In the end, the shape becomes a “sphere” as the chain leaves away from the surface. In the meantime, we discuss average Helmoholtz free energy per bond, average energy per bond, average adsorbed energy per bond, average α-helical energy per bond, average β-sheet energy per bond and average contact energy per bond. On the other hand, elastic force is also studied. It is found that elastic force has a long plateau during the tensile elongation when there exists adsorption interaction. This result is consistent with SMFS experiment of general polymers. Energy contribution to elastic force and contact energy contribution to elastic force are both discussed. These investigations can provide some insights into the elastic behaviors of adsorbed protein chains.展开更多
The effect of channel-protein interaction on the translocation of a protein-like chain through a finite channel under certain electric field was studied by using dynamical Monte Carlo simulations. The interior behavio...The effect of channel-protein interaction on the translocation of a protein-like chain through a finite channel under certain electric field was studied by using dynamical Monte Carlo simulations. The interior behavior of chain conformation under different interactions was investigated, such as the number of monomers outside of channel nout, monomers inside of channel nm, mean-square radius of gyration 〈 S2 〉 and the average energy 〈U〉. It shows that with strong attractive interaction, the translocation is more difficult than moderate interaction. At the same time, the dependence of translocation time with different interactions shows that moderate repulsive interaction （εcp = 0.5） accelerates the translocation. Although the waiting time for successful translocation of εep = 1.0 is the longest, the average translocation time is not very large. It is far smaller than that of εep = -1.0. The probability distributions of translocation time p（t＇） and the probability distributions of three duration times p（t1＇）, p（t2＇） and p（t3＇） were all discussed. Log-normal distributions are found. All these findings will strengthen the understanding of protein translocation.展开更多
MicroRNAs(miRNAs)are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation in plants and animals by targeting messenger RNAs(mRNAs)for cleavage or repressing translation ...MicroRNAs(miRNAs)are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation in plants and animals by targeting messenger RNAs(mRNAs)for cleavage or repressing translation of specific mRNAs.The first miRNA identified in plants,miRNA156(miR156),targets the SQUAMOSA promoter-binding protein-like(SPL)transcription factors,which play critical roles in plant phase transition,flower and plant architecture,and fruit development.We identified multiple copies of MIR156 and SPL in the rice,Brachypodium,sorghum,maize,and foxtail millet genomes.Sequence and chromosomal synteny analysis showed that both MIR156s and SPLs are conserved across species in the grass family.Analysis of expression data of the SPLs in eleven juvenile and adult rice tissues revealed that four non-miR156-targeted genes were highly expressed and three miR156-targeted genes were only slightly expressed in all tissues/developmental stages.The remaining SPLs were highly expressed in the juvenile stage,but their expression was lower in the adult stage.It has been proposed that under strong selective pressure,non-miR156-targeted mRNA may be able to re-structure to form a miRNAresponsive element.In our analysis,some non-miR156-targeted SPLs(SPL5/8/10)had gene structure and gene expression patterns similar to those of miR156-targeted genes,suggesting that they could diversify into miR156-targeted genes.DNA methylation profiles of SPLs and MIR156s in different rice tissues showed diverse methylation patterns,and hypomethylation of non-CG sites was observed in rice endosperm.Our findings suggested that MIR156s and SPLs had different origination and evolutionary mechanisms:the SPLs appear to have resulted from vertical evolution,whereas MIR156s appear to have resulted from strong evolutionary selection on mature sequences.展开更多
BACKGROUND It is not uncommon to develop viral encephalitis.Epidemic Japanese B encephalitis infection combined with contactin-associated protein-like 2(CASPR-2)antibody-positive autoimmune encephalitis has not been r...BACKGROUND It is not uncommon to develop viral encephalitis.Epidemic Japanese B encephalitis infection combined with contactin-associated protein-like 2(CASPR-2)antibody-positive autoimmune encephalitis has not been reported at present.In clinical work,we need to consider more options.CASE SUMMARY A 32-year-old male worker presented with headache,fever and call-unresponsive presentation.Complete cranial magnetic resonance image showed symmetrical abnormal signals in bilateral medial temporal lobe,bilateral thalamus and basal ganglia.Improved lumbar puncture showed that cerebrospinal fluid protein and cell count increased significantly.Viral encephalitis was considered,and the patient's consciousness still increased rapidly after antiviral treatment.Further detection of Cerebrospinal fluid Japanese B encephalitis virus Polymerase Chain Reaction positive,serum autoimmune encephalitis antibody showed CASPR-2 antibody positive(1:320),the patient's condition gradually improved after plasma exchange treatment.3 mo later,the serum CASPR-2 antibody was negative and the patient's condition was stable.CONCLUSION This article reports the world’s first case of Epidemic Japanese B encephalitis infection combined with CASPR-2 antibody-positive autoimmune encephalitis,with a view to raising awareness.展开更多
Objective： To clone and construct the recombinant plasmid containing ATP synthase lipid-binding protein-like protein gene of Schistosomajaponicum,（SjAslp） and transfer it into mammalian cells to express the objecti...Objective： To clone and construct the recombinant plasmid containing ATP synthase lipid-binding protein-like protein gene of Schistosomajaponicum,（SjAslp） and transfer it into mammalian cells to express the objective protein. Methods： By polymerase chain reaction （PCR） technique, SjAslp was amplified from the constructed recombinant plasmid pBCSK＋/SjAslp, and inserted into cloning vector pUCm-T. Then, SjAslp was subcloned into an eukaryotic expression vector pcDNA3.1（＋）. After identifying it by PCR, restrictive enzymes digestion and DNA sequencing, the recombinant plasmid was transfected into HeLa cells using electroporation, and the expression of the recombinant protein was analyzed by immunocytochemical assay. Results： The specific gene fragment of 558 bp was successfully amplified. The DNA vaccine of SjAslp was successfully constructed. Immunocytochemical assay showed that SjAslp was expressed in the cytoplasm of HeLa cells. Conclusion： SjAslp gene can be expressed in eukaryotic system, which lays the foundation for development of the SjAslp DNA vaccine against schitosomiasis.展开更多
We study the translocation of a protein-like chain through a finite cylindrical channel using the pruned-enriched Rosenbluth method （PERM） and the modified orientation-dependent monomer-monomer interaction （ODI） m...We study the translocation of a protein-like chain through a finite cylindrical channel using the pruned-enriched Rosenbluth method （PERM） and the modified orientation-dependent monomer-monomer interaction （ODI） model. Attractive channels （εcp = -2.0, -1.0, -0.5）, repulsive chanaels （εcp： 0.5, 1.0, 2.0）, and a neutral channel （εcp =- 0） are discussed. The results of the chain dimension and the energy show that Z0 ： 1.0 is an important case to distinguish the types of the channels. For the strong attractive channel, more contacts form during the process of translocation. It is also found that an external force is needed to drive the chain outside of the channel with the strong attraction. While for the neutral, the repulsive, and the weak attractive channels, the translocation is spontaneous.展开更多
The conformational properties and elastic behaviors of protein-like single chains in the process of tensileelongation were investigated by means of Monte Carlo method.The sequences of protein-like single chains contai...The conformational properties and elastic behaviors of protein-like single chains in the process of tensileelongation were investigated by means of Monte Carlo method.The sequences of protein-like single chains contain two typesof residues:hydrophobic(H)and hydrophilic(P).The average conformations and thermodynamics statistical properties ofprotein-like single chains with various elongation ratio λ were calculated.It was found that the mean-square end-to-enddistance<R^2>(?).increases with elongation ratio λ.The tensor eigenvalues ratio of<L_2~2>:<L_1~2>decreases with elongationratio λ for short(HP)_x protein-like polymers,however,the ratio of<L_3~2>:<L_1~2>increases with elongation ratio λ,especially for long (H)_x sequence.Average energy per bond increases with elongation ratio λ,especially for (H)_xprotein-like single chains.Helmholtz free energy per bond also increases with elongation ratio λ.Elastic force(f),energycontribution to force(f_U)and entropy contribution to force(fs)for different protein-like single chains were also calculated.These investigations may provide some insights into elastic behaviors of proteins.展开更多
BACKGROUND Rearrangements of the anaplastic lymphoma kinase(ALK)gene(ALK-positive)represent an oncogenic driver in approximately 3%-5%of non-small-lung cancer(NSCLC)patients.Sarcoidosis is a multisystem disease,and it...BACKGROUND Rearrangements of the anaplastic lymphoma kinase(ALK)gene(ALK-positive)represent an oncogenic driver in approximately 3%-5%of non-small-lung cancer(NSCLC)patients.Sarcoidosis is a multisystem disease,and its reported incidence in Asia is 1 or less per 100000 people per year.The co-occurrence of sarcoidosis and ALK-positive NSCLC is rare,and ALK-positive lung cancer is likely to spread quickly.Therefore,the co-occurrence of sarcoidosis is more easily misdiagnosed as metastatic lung cancer by radiological examination.CASE SUMMARY A 50-year-old man had a nodule in the left superior lobe,many small nodules in left superior and right lungs,and enlarged bilateral hilar,mediastinal,and right supraclavicular lymph nodes.Computed tomography-guided pulmonary biopsy of the nodule in the left superior lobe revealed echinoderm microtubuleassociated protein-like 4 gene-ALK positive NSCLC with concomitant noncaseating granuloma.This patient was treated with crizotinib.Thirty days later,a chest computed tomography scan revealed a dramatic decrease in the size of the left superior lobe nodule;however,the lesions in the right lung progressed.The right supraclavicular lymph nodes showed granulomas,and no tumor cells were identified in the specimens. The angiotensin-converting enzyme level was high.After 1 wk of methylprednisolone treatment, a significant response of all lesionswas revealed. Following radical resection of the lung cancer, noncaseatinggranulomas were observed in both lung tissues and lymph nodes, which resultedin a diagnosis of echinoderm microtubule-associated protein-like 4-ALK positiveNSCLC accompanied with sarcoidosis.CONCLUSIONOur experience illustrates that pathological evidence is needed to confirmmetastatic disease, especially when some suspected metastatic lesions arenegative for malignancy.展开更多
The proper flowering time of rose(Rosa hybrida)is vital for the market value of this horticultural crop,but the mechanism regulating this trait is largely unclear.Here,we found that the transcription factor SQUAMOSA P...The proper flowering time of rose(Rosa hybrida)is vital for the market value of this horticultural crop,but the mechanism regulating this trait is largely unclear.Here,we found that the transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE4(RhSPL4)positively regulates flowering time in rose.Transient silencing or overexpression transgenic rose plants of RhSPL4 exhibited delayed or early flowering,respectively.Analysis of transcriptome data from transgenic lines overexpressing RhSPL4 compared to the wild type indicated that differentially expressed genes were significantly enriched in the circadian rhythm pathway.Among the proteins encoded by these genes,RhSPL4 binds to the promoter of PSEUDO-RESPONSE REGULATOR 5-LIKE(RhPRR5L),as revealed in yeast one-hybrid,dual-Luciferase/Renilla luciferase reporter,chromatin immunoprecipitation-quantitative PCR and electrophoretic mobility shift assay.Furthermore,RhSPL4 specifically binds to the478 to441 bp region of the RhPRR5L promoter and activates its transcription.The silencing of RhPRR5L delayed flowering time in rose,resembling the phenotype of RhSPL4-silenced plants.Together,these results indicate that the RhSPL4-RhPRR5L module positively regulates flowering time in rose,laying the foundation for the genetic improvement of flowering time in this important horticultural crop.展开更多
基金ACKNOWLEDGMENT This work was supported by the National Natural Science Foundation of China （No.20904047）.
文摘Elastic behaviors of protein-like chains are investigated by Pruned-Enriched-Rosenbluth method and modified orientation-dependent monomer-monomer interactions model. The protein-like chain is pulled away from the attractive surface slowly with elastic force acting on it. Strong adsorption interaction and no adsorption interaction are both considered. We calculate the characteristic ratio and shape factor of protein-like chains in the process of elongation. The conformation change of the protein-like chain is well depicted. The shape of chain changes from “rod” to “sphere” at the beginning of elongation. Then, the shape changes from “sphere” to “rod”. In the end, the shape becomes a “sphere” as the chain leaves away from the surface. In the meantime, we discuss average Helmoholtz free energy per bond, average energy per bond, average adsorbed energy per bond, average α-helical energy per bond, average β-sheet energy per bond and average contact energy per bond. On the other hand, elastic force is also studied. It is found that elastic force has a long plateau during the tensile elongation when there exists adsorption interaction. This result is consistent with SMFS experiment of general polymers. Energy contribution to elastic force and contact energy contribution to elastic force are both discussed. These investigations can provide some insights into the elastic behaviors of adsorbed protein chains.
基金supported by the National Natural Science Foundation of China(No.20904047)
文摘The effect of channel-protein interaction on the translocation of a protein-like chain through a finite channel under certain electric field was studied by using dynamical Monte Carlo simulations. The interior behavior of chain conformation under different interactions was investigated, such as the number of monomers outside of channel nout, monomers inside of channel nm, mean-square radius of gyration 〈 S2 〉 and the average energy 〈U〉. It shows that with strong attractive interaction, the translocation is more difficult than moderate interaction. At the same time, the dependence of translocation time with different interactions shows that moderate repulsive interaction （εcp = 0.5） accelerates the translocation. Although the waiting time for successful translocation of εep = 1.0 is the longest, the average translocation time is not very large. It is far smaller than that of εep = -1.0. The probability distributions of translocation time p（t＇） and the probability distributions of three duration times p（t1＇）, p（t2＇） and p（t3＇） were all discussed. Log-normal distributions are found. All these findings will strengthen the understanding of protein translocation.
基金This work was supported by the National Natural Science Foundation of China(No.31901515).
文摘MicroRNAs(miRNAs)are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation in plants and animals by targeting messenger RNAs(mRNAs)for cleavage or repressing translation of specific mRNAs.The first miRNA identified in plants,miRNA156(miR156),targets the SQUAMOSA promoter-binding protein-like(SPL)transcription factors,which play critical roles in plant phase transition,flower and plant architecture,and fruit development.We identified multiple copies of MIR156 and SPL in the rice,Brachypodium,sorghum,maize,and foxtail millet genomes.Sequence and chromosomal synteny analysis showed that both MIR156s and SPLs are conserved across species in the grass family.Analysis of expression data of the SPLs in eleven juvenile and adult rice tissues revealed that four non-miR156-targeted genes were highly expressed and three miR156-targeted genes were only slightly expressed in all tissues/developmental stages.The remaining SPLs were highly expressed in the juvenile stage,but their expression was lower in the adult stage.It has been proposed that under strong selective pressure,non-miR156-targeted mRNA may be able to re-structure to form a miRNAresponsive element.In our analysis,some non-miR156-targeted SPLs(SPL5/8/10)had gene structure and gene expression patterns similar to those of miR156-targeted genes,suggesting that they could diversify into miR156-targeted genes.DNA methylation profiles of SPLs and MIR156s in different rice tissues showed diverse methylation patterns,and hypomethylation of non-CG sites was observed in rice endosperm.Our findings suggested that MIR156s and SPLs had different origination and evolutionary mechanisms:the SPLs appear to have resulted from vertical evolution,whereas MIR156s appear to have resulted from strong evolutionary selection on mature sequences.
文摘BACKGROUND It is not uncommon to develop viral encephalitis.Epidemic Japanese B encephalitis infection combined with contactin-associated protein-like 2(CASPR-2)antibody-positive autoimmune encephalitis has not been reported at present.In clinical work,we need to consider more options.CASE SUMMARY A 32-year-old male worker presented with headache,fever and call-unresponsive presentation.Complete cranial magnetic resonance image showed symmetrical abnormal signals in bilateral medial temporal lobe,bilateral thalamus and basal ganglia.Improved lumbar puncture showed that cerebrospinal fluid protein and cell count increased significantly.Viral encephalitis was considered,and the patient's consciousness still increased rapidly after antiviral treatment.Further detection of Cerebrospinal fluid Japanese B encephalitis virus Polymerase Chain Reaction positive,serum autoimmune encephalitis antibody showed CASPR-2 antibody positive(1:320),the patient's condition gradually improved after plasma exchange treatment.3 mo later,the serum CASPR-2 antibody was negative and the patient's condition was stable.CONCLUSION This article reports the world’s first case of Epidemic Japanese B encephalitis infection combined with CASPR-2 antibody-positive autoimmune encephalitis,with a view to raising awareness.
基金the Scientific Research Foundation of Education Committee of Hunan (07C713 and 07C708)
文摘Objective： To clone and construct the recombinant plasmid containing ATP synthase lipid-binding protein-like protein gene of Schistosomajaponicum,（SjAslp） and transfer it into mammalian cells to express the objective protein. Methods： By polymerase chain reaction （PCR） technique, SjAslp was amplified from the constructed recombinant plasmid pBCSK＋/SjAslp, and inserted into cloning vector pUCm-T. Then, SjAslp was subcloned into an eukaryotic expression vector pcDNA3.1（＋）. After identifying it by PCR, restrictive enzymes digestion and DNA sequencing, the recombinant plasmid was transfected into HeLa cells using electroporation, and the expression of the recombinant protein was analyzed by immunocytochemical assay. Results： The specific gene fragment of 558 bp was successfully amplified. The DNA vaccine of SjAslp was successfully constructed. Immunocytochemical assay showed that SjAslp was expressed in the cytoplasm of HeLa cells. Conclusion： SjAslp gene can be expressed in eukaryotic system, which lays the foundation for development of the SjAslp DNA vaccine against schitosomiasis.
基金Project supported by the National Natural Science Foundation of China （Grant No. 20904047）, the Science and Technology Planning Project of Zhejiang Province, China （Grant No. 20100022）, and the Natural Science Foundation of Zhejiang Province, China （Grant No. Y6110304）.
文摘We study the translocation of a protein-like chain through a finite cylindrical channel using the pruned-enriched Rosenbluth method （PERM） and the modified orientation-dependent monomer-monomer interaction （ODI） model. Attractive channels （εcp = -2.0, -1.0, -0.5）, repulsive chanaels （εcp： 0.5, 1.0, 2.0）, and a neutral channel （εcp =- 0） are discussed. The results of the chain dimension and the energy show that Z0 ： 1.0 is an important case to distinguish the types of the channels. For the strong attractive channel, more contacts form during the process of translocation. It is also found that an external force is needed to drive the chain outside of the channel with the strong attraction. While for the neutral, the repulsive, and the weak attractive channels, the translocation is spontaneous.
基金The research was financially supported by the National Natural Science Foundation of China(Nos.20174036,20274040)the Natural Science Foundation of Zhejiang Province(No.R404047).
文摘The conformational properties and elastic behaviors of protein-like single chains in the process of tensileelongation were investigated by means of Monte Carlo method.The sequences of protein-like single chains contain two typesof residues:hydrophobic(H)and hydrophilic(P).The average conformations and thermodynamics statistical properties ofprotein-like single chains with various elongation ratio λ were calculated.It was found that the mean-square end-to-enddistance<R^2>(?).increases with elongation ratio λ.The tensor eigenvalues ratio of<L_2~2>:<L_1~2>decreases with elongationratio λ for short(HP)_x protein-like polymers,however,the ratio of<L_3~2>:<L_1~2>increases with elongation ratio λ,especially for long (H)_x sequence.Average energy per bond increases with elongation ratio λ,especially for (H)_xprotein-like single chains.Helmholtz free energy per bond also increases with elongation ratio λ.Elastic force(f),energycontribution to force(f_U)and entropy contribution to force(fs)for different protein-like single chains were also calculated.These investigations may provide some insights into elastic behaviors of proteins.
基金The Zhejiang Provincial Natural Science Foundation of China,No.LQ17H160005.
文摘BACKGROUND Rearrangements of the anaplastic lymphoma kinase(ALK)gene(ALK-positive)represent an oncogenic driver in approximately 3%-5%of non-small-lung cancer(NSCLC)patients.Sarcoidosis is a multisystem disease,and its reported incidence in Asia is 1 or less per 100000 people per year.The co-occurrence of sarcoidosis and ALK-positive NSCLC is rare,and ALK-positive lung cancer is likely to spread quickly.Therefore,the co-occurrence of sarcoidosis is more easily misdiagnosed as metastatic lung cancer by radiological examination.CASE SUMMARY A 50-year-old man had a nodule in the left superior lobe,many small nodules in left superior and right lungs,and enlarged bilateral hilar,mediastinal,and right supraclavicular lymph nodes.Computed tomography-guided pulmonary biopsy of the nodule in the left superior lobe revealed echinoderm microtubuleassociated protein-like 4 gene-ALK positive NSCLC with concomitant noncaseating granuloma.This patient was treated with crizotinib.Thirty days later,a chest computed tomography scan revealed a dramatic decrease in the size of the left superior lobe nodule;however,the lesions in the right lung progressed.The right supraclavicular lymph nodes showed granulomas,and no tumor cells were identified in the specimens. The angiotensin-converting enzyme level was high.After 1 wk of methylprednisolone treatment, a significant response of all lesionswas revealed. Following radical resection of the lung cancer, noncaseatinggranulomas were observed in both lung tissues and lymph nodes, which resultedin a diagnosis of echinoderm microtubule-associated protein-like 4-ALK positiveNSCLC accompanied with sarcoidosis.CONCLUSIONOur experience illustrates that pathological evidence is needed to confirmmetastatic disease, especially when some suspected metastatic lesions arenegative for malignancy.
基金supported by Yunnan Province Agricultural Joint Key Project(Grant No.202401BD070001-016)the National Natural Science Foundation of China(Grant No.32202530)+3 种基金Talent Introduction and Training Project of Yunnan Academy of Agricultural Sciences(Grant No.2024RCYP-09)Fundamental Research Project(Grant No.202401CF070046)Xingdian Talent support program(XDYC-QNRC-2023-0457)Yunnan Technology Innovation Center of Flower Technique.
文摘The proper flowering time of rose(Rosa hybrida)is vital for the market value of this horticultural crop,but the mechanism regulating this trait is largely unclear.Here,we found that the transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE4(RhSPL4)positively regulates flowering time in rose.Transient silencing or overexpression transgenic rose plants of RhSPL4 exhibited delayed or early flowering,respectively.Analysis of transcriptome data from transgenic lines overexpressing RhSPL4 compared to the wild type indicated that differentially expressed genes were significantly enriched in the circadian rhythm pathway.Among the proteins encoded by these genes,RhSPL4 binds to the promoter of PSEUDO-RESPONSE REGULATOR 5-LIKE(RhPRR5L),as revealed in yeast one-hybrid,dual-Luciferase/Renilla luciferase reporter,chromatin immunoprecipitation-quantitative PCR and electrophoretic mobility shift assay.Furthermore,RhSPL4 specifically binds to the478 to441 bp region of the RhPRR5L promoter and activates its transcription.The silencing of RhPRR5L delayed flowering time in rose,resembling the phenotype of RhSPL4-silenced plants.Together,these results indicate that the RhSPL4-RhPRR5L module positively regulates flowering time in rose,laying the foundation for the genetic improvement of flowering time in this important horticultural crop.
