Factor properties and their structures are important themes in combinatorics on words.Let D be the infinite one-sided sequence over the alphabet{a,b}generated by the period-doubling substitutionσ(a)=ab andσ(b)=aa.In...Factor properties and their structures are important themes in combinatorics on words.Let D be the infinite one-sided sequence over the alphabet{a,b}generated by the period-doubling substitutionσ(a)=ab andσ(b)=aa.In this paper,we determine the derived sequence D_(ω)(D)for any factorω■D,and study some factor spectra using the structures of derived sequences.We also prove the reflexivity property of derived sequences.展开更多
Given a protein sequence, how can we identify whether it is a metalloprotein or not? If it is, which main functional class and subclasses it belongs to? This is an important biological question because they are closel...Given a protein sequence, how can we identify whether it is a metalloprotein or not? If it is, which main functional class and subclasses it belongs to? This is an important biological question because they are closely related to the biological function of an uncharacterized protein. Particularly, with the avalanche of protein sequences generated in the post genomic era and since conventional techniques are time consuming and expensive, it is highly desirable to develop an automated method by which one can get a fast and accurate answer to these questions. Here, a top-down predictor, called MetalloPred, is developed which consists of 3 level of hierarchical classification using cascade of neural networks from sequence derived features. The 1st layer of the prediction engine is for identifying a query protein as metalloprotein or not;the 2nd layer for the main functional class;and the 3rd layer for the sub-functional class. The overall success rates for all the three layers are higher than 60% that were obtained through rigorous cross-validation tests on the very stringent benchmark datasets in which none of the proteins has 30% sequence identity with any other in the same class or subclass. MetalloPred achieved good prediction accuracies and could nicely complement experimental approaches for identification of metal binding proteins. MetalloPred is freely available to be used in-house as a standalone and is accessible at http://www.juit.ac.in/assets/Metallopred/.展开更多
Non-coding RNAs(ncRNAs) are a type of RNA that is not translated into proteins. Transfer RNAs(tRNAs), a type of ncRNA, are the second most abundant type of RNA in cells. Recent studies have shown that tRNAs can be cle...Non-coding RNAs(ncRNAs) are a type of RNA that is not translated into proteins. Transfer RNAs(tRNAs), a type of ncRNA, are the second most abundant type of RNA in cells. Recent studies have shown that tRNAs can be cleaved into a heterogeneous population of ncRNAs with lengths of 18–40 nucleotides, known as tRNA-derived small RNAs(tsRNAs). There are two main types of tsRNA, based on their length and the number of cleavage sites that they contain: tRNA-derived fragments and tRNA-derived stress-induced RNAs. These RNA species were first considered to be byproducts of tRNA random cleavage. However, mounting evidence has demonstrated their critical functional roles as regulatory factors in the pathophysiological processes of various diseases, including neurological diseases. However, the underlying mechanisms by which tsRNAs affect specific cellular processes are largely unknown. Therefore, this study comprehensively summarizes the following points:(1) The biogenetics of tsRNA, including their discovery, classification, formation, and the roles of key enzymes.(2) The main biological functions of tsRNA, including its miRNA-like roles in gene expression regulation, protein translation regulation, regulation of various cellular activities, immune mediation, and response to stress.(3) The potential mechanisms of pathophysiological changes in neurological diseases that are regulated by tsRNA, including neurodegeneration and neurotrauma.(4) The identification of the functional diversity of tsRNA may provide valuable information regarding the physiological and pathophysiological mechanisms of neurological disorders, thus providing a new reference for the clinical treatment of neurological diseases. Research into tsRNAs in neurological diseases also has the following challenges: potential function and mechanism studies, how to accurately quantify expression, and the exact relationship between tsRNA and miRNA. These challenges require future research efforts.展开更多
Consider the canonical isomorphism between the positive part U+ of the quantum group Uq(g) and the Hall algebra H(Λ),where the semisimple Lie algebra g and the finite-dimensional hereditary algebra Λ share a Dynkin ...Consider the canonical isomorphism between the positive part U+ of the quantum group Uq(g) and the Hall algebra H(Λ),where the semisimple Lie algebra g and the finite-dimensional hereditary algebra Λ share a Dynkin diagram.Chen and Xiao have given two algorithms to decompose the root vectors into linear combinations of monomials of Chevalley generators of U+,respectively induced by the braid group action on the exceptional sequences of Λ-modules and the structure of the Auslander-Reiten quiver of Λ.In this paper,we obtain the corresponding algorithms for the derived Hall algebra DH(Λ),which was introduced by Toen.We show that both algorithms are applicable to the lattice algebra and Heisenberg double in the sense of Kapranov.All the new recursive formulae have the same flavor with the quantum Serre relations.展开更多
Based on the structure-activity relationships of RGD-containing peptides, a series of 1,3-dihydro-1,3-dioxo-2H-isoindole derivatives were synthesized. All of them were first reported. Their structures were confirmed b...Based on the structure-activity relationships of RGD-containing peptides, a series of 1,3-dihydro-1,3-dioxo-2H-isoindole derivatives were synthesized. All of them were first reported. Their structures were confirmed by spectral data and elemental analysis. Their ability to inhibit angiogenesis were evaluated in the chick embryo chorioallantoic membrane assay at 10-5 mol/L. Compounds 5b and 5e displayed obviously antiangiogenic activity.展开更多
Based on the structure-activity relationships and antiangiogenic mechanism of RGD-containing peptides, a series of 5-amino- 1,3-dihydro-1,3-dioxo-2H-isoindole derivatives were synthesized. The structures were characte...Based on the structure-activity relationships and antiangiogenic mechanism of RGD-containing peptides, a series of 5-amino- 1,3-dihydro-1,3-dioxo-2H-isoindole derivatives were synthesized. The structures were characterized by ^1H NMR, MS and elementary analysis. There ability to inhibit angiogenesis were evaluated by chick embryo chorioallantoic membrane assay at 10^-5 mol/L. Compounds 7a and 7b displayed obvious antiangiogenic activity.展开更多
The amino acid sequencing on mutation region of tumor necmeis factor a derivative 3a(rh-TNFaD3a).Methods: PCR was used to produce the TNF half molecule which contains the mutation "don in itS 5’ end.Then, a fusi...The amino acid sequencing on mutation region of tumor necmeis factor a derivative 3a(rh-TNFaD3a).Methods: PCR was used to produce the TNF half molecule which contains the mutation "don in itS 5’ end.Then, a fusion protein expression system was used to express the TNF half molecule. The fusion protein waspubbed by sanity chromatography and enzymatically cleaved by Xa factor protease to remove fusion vectorpeptide. Finally, the N-terminal amino acid sequencing was performed. Results and Conclusion: The site-specific artificial mutation of TNFαD3a was realized as expected: position 80 Ile→Ser, position 90 Lys→Hisand position 92 Asn→Val.展开更多
Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be a...Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.展开更多
基金supported by National Natural Science Foundation of China(11701024)the Fundamental Research Funds for the Central Universities(2019RC17)。
文摘Factor properties and their structures are important themes in combinatorics on words.Let D be the infinite one-sided sequence over the alphabet{a,b}generated by the period-doubling substitutionσ(a)=ab andσ(b)=aa.In this paper,we determine the derived sequence D_(ω)(D)for any factorω■D,and study some factor spectra using the structures of derived sequences.We also prove the reflexivity property of derived sequences.
文摘Given a protein sequence, how can we identify whether it is a metalloprotein or not? If it is, which main functional class and subclasses it belongs to? This is an important biological question because they are closely related to the biological function of an uncharacterized protein. Particularly, with the avalanche of protein sequences generated in the post genomic era and since conventional techniques are time consuming and expensive, it is highly desirable to develop an automated method by which one can get a fast and accurate answer to these questions. Here, a top-down predictor, called MetalloPred, is developed which consists of 3 level of hierarchical classification using cascade of neural networks from sequence derived features. The 1st layer of the prediction engine is for identifying a query protein as metalloprotein or not;the 2nd layer for the main functional class;and the 3rd layer for the sub-functional class. The overall success rates for all the three layers are higher than 60% that were obtained through rigorous cross-validation tests on the very stringent benchmark datasets in which none of the proteins has 30% sequence identity with any other in the same class or subclass. MetalloPred achieved good prediction accuracies and could nicely complement experimental approaches for identification of metal binding proteins. MetalloPred is freely available to be used in-house as a standalone and is accessible at http://www.juit.ac.in/assets/Metallopred/.
基金supported by the National Natural Science Foundation of China,No.81870979(to JJL),No.81271366(to MLY)the National Key R&D Program of China,No.2018YFF0301104(to JJL)+4 种基金the Special Fund for Basic Scientific Research of Central Public Research Institutes of China,No.2018CZ-1(to JJL)the Basic Scientific Research Foundation of China Rehabilitation Research Center,No.2018ZX-30(to FG)the Scientific Research Foundation of CRRC,No.2012C-1(to JJL)the Major Science and Technology Project of Beijing of China,No.D161100002816004(to JJL)the Special Capital Health Research and Development of China,No.2018-1-6011(to JJL)
文摘Non-coding RNAs(ncRNAs) are a type of RNA that is not translated into proteins. Transfer RNAs(tRNAs), a type of ncRNA, are the second most abundant type of RNA in cells. Recent studies have shown that tRNAs can be cleaved into a heterogeneous population of ncRNAs with lengths of 18–40 nucleotides, known as tRNA-derived small RNAs(tsRNAs). There are two main types of tsRNA, based on their length and the number of cleavage sites that they contain: tRNA-derived fragments and tRNA-derived stress-induced RNAs. These RNA species were first considered to be byproducts of tRNA random cleavage. However, mounting evidence has demonstrated their critical functional roles as regulatory factors in the pathophysiological processes of various diseases, including neurological diseases. However, the underlying mechanisms by which tsRNAs affect specific cellular processes are largely unknown. Therefore, this study comprehensively summarizes the following points:(1) The biogenetics of tsRNA, including their discovery, classification, formation, and the roles of key enzymes.(2) The main biological functions of tsRNA, including its miRNA-like roles in gene expression regulation, protein translation regulation, regulation of various cellular activities, immune mediation, and response to stress.(3) The potential mechanisms of pathophysiological changes in neurological diseases that are regulated by tsRNA, including neurodegeneration and neurotrauma.(4) The identification of the functional diversity of tsRNA may provide valuable information regarding the physiological and pathophysiological mechanisms of neurological disorders, thus providing a new reference for the clinical treatment of neurological diseases. Research into tsRNAs in neurological diseases also has the following challenges: potential function and mechanism studies, how to accurately quantify expression, and the exact relationship between tsRNA and miRNA. These challenges require future research efforts.
基金supported by National Natural Science Foundation of China(Grant No.10631010)National Key Basic Research Project of China (Grant No.2006CB805905)
文摘Consider the canonical isomorphism between the positive part U+ of the quantum group Uq(g) and the Hall algebra H(Λ),where the semisimple Lie algebra g and the finite-dimensional hereditary algebra Λ share a Dynkin diagram.Chen and Xiao have given two algorithms to decompose the root vectors into linear combinations of monomials of Chevalley generators of U+,respectively induced by the braid group action on the exceptional sequences of Λ-modules and the structure of the Auslander-Reiten quiver of Λ.In this paper,we obtain the corresponding algorithms for the derived Hall algebra DH(Λ),which was introduced by Toen.We show that both algorithms are applicable to the lattice algebra and Heisenberg double in the sense of Kapranov.All the new recursive formulae have the same flavor with the quantum Serre relations.
文摘Based on the structure-activity relationships of RGD-containing peptides, a series of 1,3-dihydro-1,3-dioxo-2H-isoindole derivatives were synthesized. All of them were first reported. Their structures were confirmed by spectral data and elemental analysis. Their ability to inhibit angiogenesis were evaluated in the chick embryo chorioallantoic membrane assay at 10-5 mol/L. Compounds 5b and 5e displayed obviously antiangiogenic activity.
文摘Based on the structure-activity relationships and antiangiogenic mechanism of RGD-containing peptides, a series of 5-amino- 1,3-dihydro-1,3-dioxo-2H-isoindole derivatives were synthesized. The structures were characterized by ^1H NMR, MS and elementary analysis. There ability to inhibit angiogenesis were evaluated by chick embryo chorioallantoic membrane assay at 10^-5 mol/L. Compounds 7a and 7b displayed obvious antiangiogenic activity.
文摘The amino acid sequencing on mutation region of tumor necmeis factor a derivative 3a(rh-TNFaD3a).Methods: PCR was used to produce the TNF half molecule which contains the mutation "don in itS 5’ end.Then, a fusion protein expression system was used to express the TNF half molecule. The fusion protein waspubbed by sanity chromatography and enzymatically cleaved by Xa factor protease to remove fusion vectorpeptide. Finally, the N-terminal amino acid sequencing was performed. Results and Conclusion: The site-specific artificial mutation of TNFαD3a was realized as expected: position 80 Ile→Ser, position 90 Lys→Hisand position 92 Asn→Val.
文摘Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.
