RNAs have important biological functions and the functions of RNAs are generally coupled to their structures, especiallytheir secondary structures. In this work, we have made a comprehensive evaluation of the performa...RNAs have important biological functions and the functions of RNAs are generally coupled to their structures, especiallytheir secondary structures. In this work, we have made a comprehensive evaluation of the performances of existingtop RNA secondary structure prediction methods, including five deep-learning (DL) based methods and five minimum freeenergy (MFE) based methods. First, we made a brief overview of these RNA secondary structure prediction methods.Afterwards, we built two rigorous test datasets consisting of RNAs with non-redundant sequences and comprehensivelyexamined the performances of the RNA secondary structure prediction methods through classifying the RNAs into differentlength ranges and different types. Our examination shows that the DL-based methods generally perform better thanthe MFE-based methods for RNAs with long lengths and complex structures, while the MFE-based methods can achievegood performance for small RNAs and some specialized MFE-based methods can achieve good prediction accuracy forpseudoknots. Finally, we provided some insights and perspectives in modeling RNA secondary structures.展开更多
Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational proper...Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.展开更多
The present study focuses on the analysis and description of lineaments interpreted as secondary structures to describe the nature of Senegalo Malian Discontinuity. These lineaments cross-cut the large north-south ori...The present study focuses on the analysis and description of lineaments interpreted as secondary structures to describe the nature of Senegalo Malian Discontinuity. These lineaments cross-cut the large north-south oriented transcurrent lithospheric structure known as the Senegalo Malian Discontinuity (SMD). Two lineaments were selected oriented NNE (N15˚ to N25˚), one at Dialafara and one at Sadiola. Four profiles on each lineament of these 2 zones, so that there were 2 on each side of the SMD. The ground data collected were processed using proper parameter and software. Some filters were applied to enhance the signal level. These ground data were later compared to the existing airborne magnetic data for consistency and accuracy using the upward continuation filter. The results show that the quality of ground data is good. In addition, the ground magnetic data show the presence of certain local anomalies that are not visible in the regional data. The analytical signal was also used to determine domain boundaries or possible contact zones. The contact zone can be highlighted on certain profiles such as L300 and L600. The study showed that the west and east sides of the SMD are not the same. Secondary structures become wide when approaching the SMD on both sides. They are also duplicated to the east of the SMD when we move progressively away. In the Dialafara area, the ground magnetic data intersect an interpreted fold. The results of this work confirm the presence of the secondary structures and their evolution in relation to the SMD. The relationships between the secondary structures in the Dailafara and Sadiola zones and their relations with the SMD are highlighted. The technique used in this study, is an important approach to better description and interpreting of regional structures using the secondary structures and proposing a structural model.展开更多
We have previously reported that the human ACAT1 gene produces a chimeric mRNA through the interchromosomal processing of two discontinuous RNAs transcribed from chromosomes 1 and 7. The chimeric mRNA uses AUG1397-139...We have previously reported that the human ACAT1 gene produces a chimeric mRNA through the interchromosomal processing of two discontinuous RNAs transcribed from chromosomes 1 and 7. The chimeric mRNA uses AUG1397-1399 and GGC1274-1276 as translation initiation codons to produce normal 50-kDa ACAT1 and a novel enzymatically active 56-kDa isoform, respectively, with the latter being authentically present in human cells, including human monocyte- derived macrophages. In this work, we report that RNA secondary structures located in the vicinity of the GGC1274-1276 codon are required for production of the 56-kDa isoform. The effects of the three predicted stem-loops （nt 1255-1268, 1286-1342 and 1355-1384） were tested individually by transfecting expression plasmids into cells that contained the wild-type, deleted or mutant stem-loop sequences linked to a partial ACAT1 AUG open reading frame （ORF） or to the ORFs of other genes. The expression patterns were monitored by western blot analyses. We found that the upstream stem-loop1255-1268 from chromosome 7 and downstream stem-loop1286-1342 from chromosome 1 were needed for production of the 56-kDa isoform, whereas the last stem-loop135s-1384 from chromosome 1 was dispensable. The results of experi- ments using both monocistronic and bicistronic vectors with a stable hairpin showed that translation initiation from the GGC1274-1276 codon was mediated by an internal ribosome entry site （IRES）. Further experiments revealed that translation initiation from the GGC1274-1276 codon requires the upstream AU-constituted RNA secondary structure and the downstream GC-rich structure. This mechanistic work provides further support for the biological significance of the chimeric nature of the human ACAT1 transcript.展开更多
The secondary structure is a fundamental feature of both non-coding RNAs(ncRNAs)and messenger RNAs(mRNAs).However,our understanding of the secondary structures of mRNAs,especially those of the coding regions,remains e...The secondary structure is a fundamental feature of both non-coding RNAs(ncRNAs)and messenger RNAs(mRNAs).However,our understanding of the secondary structures of mRNAs,especially those of the coding regions,remains elusive,likely due to translation and the lack of RNA-binding proteins that sustain the consensus structure like those binding to ncRNAs.Indeed,mRNAs have recently been found to adopt diverse alternative structures,but the overall functional significance remains untested.We hereby approach this problem by estimating the folding specificity,i.e.,the probability that a fragment of an mRNA folds back to the same partner once refolded.We show that the folding specificity of mRNAs is lower than that of ncRNAs and exhibits moderate evolutionary conservation.Notably,we find that specific rather than alternative folding is likely evolutionarily adaptive since specific folding is frequently associated with functionally important genes or sites within a gene.Additional analysis in combination with ribosome density suggests the ability to modulate ribosome movement as one potential functional advantage provided by specific folding.Our findings reveal a novel facet of the RNA structurome with important functional and evolutionary implications and indicate a potential method for distinguishing the mRNA secondary structures maintained by natural selection from molecular noise.展开更多
Calcium ions play an important role in the oxygen_evolving process of photosystem Ⅱ as demonstrated in many experiments. The changes of the secondary structures of PS Ⅱ induced by the depletion of Ca 2+ were reporte...Calcium ions play an important role in the oxygen_evolving process of photosystem Ⅱ as demonstrated in many experiments. The changes of the secondary structures of PS Ⅱ induced by the depletion of Ca 2+ were reported. The results indicated that the removal of Ca 2+ led to the transition of α helix to turns and sheet structures. While Ca 2+ was re_added to the media, only the structures changed to turns could be recovered. The protein conformational changes of PS Ⅱ during the donor side photoinhibition induced by the depletion of Ca 2+ were also studied. This showed that the protein conformational changes differed between the control and Ca 2+ _depleted samples in a short period of illumination (within 10 min). However, the changes became similar when the illumination time was increased.展开更多
Background:RNA secondary structures play a pivotal role in posttranscriptional regulation and the functions of non-coding RNAs,yet in vivo RNA secondary structures remain enigmatic.PARIS(Psoralen Analysis of RNA Inter...Background:RNA secondary structures play a pivotal role in posttranscriptional regulation and the functions of non-coding RNAs,yet in vivo RNA secondary structures remain enigmatic.PARIS(Psoralen Analysis of RNA Interactions and Structures)is a recently developed high-throughput sequencing-based approach that enables direct capture of RNA duplex structures in vivo.However,the existence of incompatible,fuzzy pairing information obstructs the integration of PARIS data with the existing tools for reconstructing RNA secondary structure models at the single-base resolution.Methods:We introduce IRIS,a method for predicting RNA secondary structure ensembles based on PARIS data.IRIS generates a large set of candidate RNA secondary structure models under the guidance of redistributed PARIS reads and then uses a Bayesian model to identify the optimal ensemble,according to both thermodynamic principles and PARIS data.Results:The predicted RNA structure ensembles by IRIS have been verified based on evolutionary conservation information and consistency with other experimental RNA structural data.HIS is implemented in Python and freely available at http://iris.zhanglab.net.Conclusion:IRIS capitalizes upon PARIS data to improve the prediction of in vivo RNA secondary structure ensembles.We expect that IRIS will enhance the application of the PARIS technology and shed more insight on in vivo RNA secondary structures.展开更多
Taking a widely contaminated yet abundant waste,such as poultry feathers,and extracting keratin from this struc-ture appears to be a real challenge whenever the preservation of the secondary structure of the protein i...Taking a widely contaminated yet abundant waste,such as poultry feathers,and extracting keratin from this struc-ture appears to be a real challenge whenever the preservation of the secondary structure of the protein is desired.This process would allow exploiting it in ways(e.g.,in the biomedicalfield)that are inspired by a structure that is primarily designed forflight,therefore capable specifically of withstandingflexure and lateral buckling,also with very low thicknesses.The preservation of the structure is based on disulfide crosslinks,and it is offered with pre-ference by some chemical treatments,mainly those based on ionic liquid and on a reduction process.However,the degree of preservation cannot always be precisely assessed;however,beyond chemical characterization,the forma-tion of homogeneous gels can also suggest that the process was successful in this sense.An extraction respectful of nature’s intentions,considering that the secondary structure builds up according to the very function of the feath-ers in the animal,can be deemed to be biomimetic.In particular,biomimetic extractions comply with the very characteristics the protein was designed for to serve in the specific environmental and mechanical situation in which it is inserted.This review tries to elucidate in which cases this aim is achieved and for which specific appli-cations a chicken feather keratin that has preserved its secondary structure can be suited.展开更多
[ Objective] The aim was to predict the secondary structure and B cell epitope of growth hormone （GH） protein from Acipenser sinensis. [Method] With the amino acid sequence of GH protein from A. sinensis as the base...[ Objective] The aim was to predict the secondary structure and B cell epitope of growth hormone （GH） protein from Acipenser sinensis. [Method] With the amino acid sequence of GH protein from A. sinensis as the base, the secondary structure of GH protein from A. sinensis was predicted by the method of Gamier-Robson, Chou-Fasman and Karpius-Schulz, and its cell epitope was predicted by the method of Kyte- Doolittle, Emini and Jameson-Wolf. [Result] The sections of 18 -23, 55 -55, 67 -73, 83 -86,112 -114,151 -157 and 209 -211 in the N terminal of GH protein molecule had softer structure and these sections could sway or fold to produce more complex tertiary structure. The sections of 19 -23, 51 -71,84 -95, 128 -139, 164 -176 and 189 -195 in the N terminal of GH protein could be the epitope of B cell and there were flexible regions in these sections or near these sections of GH protein molecule. So the dominant regions could be in these sections or near these sections. [ Conclusion] The research provided the basis for the preparation of monoctonal antibody of GH protein from A. sinensis and provided the reference for the discussion for the molecular regulation mechanism of A. sinensis.展开更多
Peptide amphiphiles with well-organized secondary structure are an important family of molecules that are known to assemble into a variety of nanostructures.In this work,we present three guanidiniocarbonylpyrrole(GCP)...Peptide amphiphiles with well-organized secondary structure are an important family of molecules that are known to assemble into a variety of nanostructures.In this work,we present three guanidiniocarbonylpyrrole(GCP)containing peptide amphiphiles,which show versatile morphology and secondary structure changes as a result of different chain lengths and in different concentration regimes.The random coil conformation,α-helix,andβ-sheet are obtained for peptide 1,peptide 2,and peptide 3,respectively under neutral aqueous conditions.Furthermore,all peptide amphiphiles can aggregate to form nanoparticles at low concentrations.However,at high concentrations,peptide 1 selfassembles into left-ha nded twisted helical fibers,while longer bamboo-like mo rphology can be obse rved exclusively for peptide 2.For peptide 3,freshly prepared samples show uniform spherical morphology,whereas an obvious morphological transition from original nanoparticles to disordered fibers was realized after incubating for one week.These fascinating morphology changes were determined by the combination of circular dichroism,dynamic light scattering,transmission electron microscopy,atomic force microscopy,and theoretical calculations.展开更多
[Objective] To examine the grammar model based on lexical substring exac- tion for RNA secondary structure prediction. [Method] By introducing cloud model into stochastic grammar model, a machine learning algorithm su...[Objective] To examine the grammar model based on lexical substring exac- tion for RNA secondary structure prediction. [Method] By introducing cloud model into stochastic grammar model, a machine learning algorithm suitable for the lexicalized stochastic grammar model was proposed. The word grid mode was used to extract and divide RNA sequence to acquire lexical substring, and the cloud classifier was used to search the maximum probability of each lemma which was marked as a certain sec- ondary structure type. Then, the lemma information was introduced into the training stochastic grammar process as prior information, realizing the prediction on the sec- ondary structure of RNA, and the method was tested by experiment. [Result] The experimental results showed that the prediction accuracy and searching speed of stochastic grammar cloud model were significantly improved from the prediction with simple stochastic grammar. [Conclusion] This study laid the foundation for the wide application of stochastic grammar model for RNA secondary structure prediction.展开更多
Aim To determine the secondary structure of insulin encapsulated withinliposome. Methods The secondary structure of native insulin, mixture of insulin with liposome(sample Ⅰ) and insulin encapsulated within liposome(...Aim To determine the secondary structure of insulin encapsulated withinliposome. Methods The secondary structure of native insulin, mixture of insulin with liposome(sample Ⅰ) and insulin encapsulated within liposome( sample Ⅱ) were determined by FTIR (FourierTransform Infrared) spectroscopy. Results The secondary structure of insulin encapsulated withinliposome(Ⅱ) are similar with the secondary structure of native insulin. The difference existed inthe amount of α-helices (from 36% of insulin to 31% of sample Ⅱ) and β-sheet(from 48% of insulinto 51% of sample Ⅱ). The content of α-helices and β-sheet of insulin in sample Ⅰ was found to bevery close to that of sample Ⅱ. The results revealed that the insulin encapsulated within liposomepossibly spread on the surface of liposome, without inserting into the liposome membrane.Conclusion The secondary structure of insulin encapsulated within liposome is similar with thenative insulin.展开更多
Proteolysis is one of the most important biochemical reactions during cheese ripening.Studies on the secondary structure of proteins during ripening would be helpful for characterizing protein changes for assessing ch...Proteolysis is one of the most important biochemical reactions during cheese ripening.Studies on the secondary structure of proteins during ripening would be helpful for characterizing protein changes for assessing cheese quality.Fourier transform infrared spectroscopy(FTIR),with self-deconvolution,second derivative analysis and band curve-fitting,was used to characterize the secondary structure of proteins in Cheddar cheese during ripening.The spectra of the amide I region showed great similarity,while the relative contents of the secondary structures underwent a series of changes.As ripening progressed,the α-helix content decreased and the β-sheet content increased.This structural shift was attributed to the strengthening of hydrogen bonds that resulted from hydrolysis of caseins.In summary,FTIR could provide the basis for rapid characterization of cheese that is undergoing ripening.展开更多
This study aimed to modify isolated and extracted peanut protein with hot alkali to study the impact of pH,heating temperature,processing time and other alkali liquor conditions on the molecular structure of the peanu...This study aimed to modify isolated and extracted peanut protein with hot alkali to study the impact of pH,heating temperature,processing time and other alkali liquor conditions on the molecular structure of the peanut.Curcumin was loaded in modified peanut protein.The results of the study are as follows:Within the alkaline range of 8<pH<12,the percentage of amino acid residue(AAR)and-turns first increased and then decreased with the increasing pH,and the percentage of AAR reached a maximum 5.21±0.33%when the pH was 11(p<0.01).The percentage of˛-helices andβ-sheets gradually decreased with increasing pH,while that of random coils gradually increased with increasing pH,reaching a maximum 11.24±0.87%when the pH was 11(p<0.05).Within the range of the heating temperature 75℃<T<95℃,the percentage of random coils andβ-sheets gradually increased with increasing heating temperature,while that of-helices and AAR gradually decreased with increasing heating temperature;they remained unchanged when the heating temperature was 90℃,and then decreased to(10.41±1.18%;p<0.01)and(4.02±2.12%;p<0.01),respectively.Within the range of 5 min<t<20 min,the percentage of random coils and AAR gradually increased with increasing heating time,while the percentage ofα-helices decreased from 11.83±1.04%to 10.75±2.34%with increased heating time(p<0.01).The optimum conditions for hot alkali modification of peanut protein as followed:heating temperature of 90℃,heating time of 20 min and a pH of alkali liquor of 11.Under these optimum conditions,the embedding rate of curcumin by the modified protein can reach 88.32±1.29%.展开更多
Based on the starch hydrolysis reaction accelerated by microwave irradiation with α-amylase, the circular dichroism （CD） and secondary structure changes of α-amylase under the condition of microwave irradiation an...Based on the starch hydrolysis reaction accelerated by microwave irradiation with α-amylase, the circular dichroism （CD） and secondary structure changes of α-amylase under the condition of microwave irradiation and water bath were studied by circular dichroism spectra. The results showed that, both the peak heights （at 2=193 nm） of the CD spectra of the samples treated by microwave irradiation and water bath reduced. The reduced rate by microwave irradiation ranged from 140% to 220%, while the reduced rate by water bath ranged from 60% to 140%. The peak of the sample treated by microwave irradiation for 60 min disappeared at λ=193 nm, while the sample showed a wake peak by water bath. The peak position by microwave irradiation emerged a blue shift in the range of 5-8 nm at λ=204 nm and λ=220 nm, while it emerged in the range of 3-5 nm by water bath. With time going on, the microwave irradiation and water bath have prompted the secondary structure of α-helix, β-sheet, β-turn and the mutual transformations of random coil, but the trends were different.展开更多
A novel method for the prediction of RNA secondary structure was proposed based on the particle swarm optimization（PSO）. PSO is known to be effective in solving many different types of optimization problems and know...A novel method for the prediction of RNA secondary structure was proposed based on the particle swarm optimization（PSO）. PSO is known to be effective in solving many different types of optimization problems and known for being able to approximate the global optimal results in the solution space. We designed an efficient objective function according to the minimum free energy, the number of selected stems and the average length of selected stems. We calculated how many legal stems there were in the sequence, and selected some of them to obtain an optimal result using PSO in the right of the objective function. A method based on the improved particle swarm optimization（IPSO） was proposed to predict RNA secondary structure, which consisted of three stages. The first stage was applied to encoding the source sequences, and to exploring all the legal stems. Then, a set of encoded stems were created in order to prepare input data for the second stage. In the second stage, IPSO was responsible for structure selection. At last, the optimal result was obtained from the secondary structures selected via IPSO. Nine sequences from the comparative RNA website were selected for the evaluation of the proposed method. Compared with other six methods, the proposed method decreased the complexity and enhanced the sensitivity and specificity on the basis of the experiment results.展开更多
The attenuated vaccine strains of CSFV have a 12-nucleotides （nt） insertion in the 3＇-UTR of genome as compared to that of CSFV virulent strains. In this study, we found a distinct heterogeneity in the 3＇-UTR of a...The attenuated vaccine strains of CSFV have a 12-nucleotides （nt） insertion in the 3＇-UTR of genome as compared to that of CSFV virulent strains. In this study, we found a distinct heterogeneity in the 3＇-UTR of attenuated Thiverval and HCLV strains. The longest 3＇-UTR of Thiverval strain was 259 base pairs （bp） with a 32-nt insertion, the shortest 3＇-UTR had only 233 bp with a 6-nt insertion. The longest 3＇-UTR of HCLV strain was 244 bp with a 17-nt insertion and the shortest 3＇ UTR was 235 bp with a 8-nt insertion. Compared with the published sequences of 3＇-UTR of vaccine and virulent strains, the 3＇-UTR of CSFV vaccine strains have two variable regions where insertion among the different vaccine strains were frequently found. The first is located between the second conservative TALk codon and the start of T-rich region where we found the variable length insertion in the same vaccine strain Thiveral or HCLV and the second is located between the end of T-rich region and the front of GAA eodon, however, a 4-nt deletion was found in this region in the virulent Shimen strain. These two regions may represent the ＂hot spot＂ for mutation. Modeling the secondary structures of the 3＇-UTR suggests that the T-rich insertion could result in the change of structure and free energy, thus affecting the stability of the 3＇-UTR structure. These findings will help to understand the mechanism of attenuated vaccines and improve vaccine safety, stability, and efficacy.展开更多
The morphology, bending property and secondary structure estimation of dog hair were investigated by scanning electron microscope( SEM),fiber compression bending analyzer,fiber frictional coefficient tester and Fourie...The morphology, bending property and secondary structure estimation of dog hair were investigated by scanning electron microscope( SEM),fiber compression bending analyzer,fiber frictional coefficient tester and Fourier transform infrared spectroscopy( FTIR). The SEM micrograph of hair indicated guard hair( GH),intermediate hair( IH) and underhair( UH) from dog hair fibers displayed considerable differences in the diameter,length,scale shape and medulla. In addition,the bending property of fibers were related to the diameter of fibers and the percentage and structure of medulla. The UH had the greatest frictional coefficient,while the guard hair had the largest bending rigidity in three kinds of hairs. The analysis of amide I region implied that there was an apparent variety in the secondary structure of hairs,mainly the percentage of α-helix and β-pleated sheet and β-turn structure. The X-ray diffraction results showed that the crystallinity of the UH was the lowest in the three kinds of fibers. The tensile behaviors of dog hair also indicated that the increase of β-pleated and β-turn structure caused the increase of the breaking strength.展开更多
We introduced a new method---duration Hidden Markov Model (dHMM) to predicate the secondary structure of Protein. In our study, we divide the basic second structure of protein into three parts: H (a-Helix), E (B-sheet...We introduced a new method---duration Hidden Markov Model (dHMM) to predicate the secondary structure of Protein. In our study, we divide the basic second structure of protein into three parts: H (a-Helix), E (B-sheet) and O (others, include coil and turn). HMM is a kind of probabilistic model which more thinking of the interaction between adjacent amino acids (these interaction were represented by transmit probability), and we use genetic algorithm to determine the model parameters. After improving on the model and fixed on the parameters of the model, we write a program HMMPS. Our example shows that HMM is a nice method for protein secondary structure prediction.展开更多
The algorithm based on combination learning usually is superior to a singleclassification algorithm on the task of protein secondary structure prediction. However,the assignment of the weight of the base classifier us...The algorithm based on combination learning usually is superior to a singleclassification algorithm on the task of protein secondary structure prediction. However,the assignment of the weight of the base classifier usually lacks decision-makingevidence. In this paper, we propose a protein secondary structure prediction method withdynamic self-adaptation combination strategy based on entropy, where the weights areassigned according to the entropy of posterior probabilities outputted by base classifiers.The higher entropy value means a lower weight for the base classifier. The final structureprediction is decided by the weighted combination of posterior probabilities. Extensiveexperiments on CB513 dataset demonstrates that the proposed method outperforms theexisting methods, which can effectively improve the prediction performance.展开更多
基金supported by grants from the National Science Foundation of China(Grant Nos.12375038 and 12075171 to ZJT,and 12205223 to YLT).
文摘RNAs have important biological functions and the functions of RNAs are generally coupled to their structures, especiallytheir secondary structures. In this work, we have made a comprehensive evaluation of the performances of existingtop RNA secondary structure prediction methods, including five deep-learning (DL) based methods and five minimum freeenergy (MFE) based methods. First, we made a brief overview of these RNA secondary structure prediction methods.Afterwards, we built two rigorous test datasets consisting of RNAs with non-redundant sequences and comprehensivelyexamined the performances of the RNA secondary structure prediction methods through classifying the RNAs into differentlength ranges and different types. Our examination shows that the DL-based methods generally perform better thanthe MFE-based methods for RNAs with long lengths and complex structures, while the MFE-based methods can achievegood performance for small RNAs and some specialized MFE-based methods can achieve good prediction accuracy forpseudoknots. Finally, we provided some insights and perspectives in modeling RNA secondary structures.
文摘Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.
文摘The present study focuses on the analysis and description of lineaments interpreted as secondary structures to describe the nature of Senegalo Malian Discontinuity. These lineaments cross-cut the large north-south oriented transcurrent lithospheric structure known as the Senegalo Malian Discontinuity (SMD). Two lineaments were selected oriented NNE (N15˚ to N25˚), one at Dialafara and one at Sadiola. Four profiles on each lineament of these 2 zones, so that there were 2 on each side of the SMD. The ground data collected were processed using proper parameter and software. Some filters were applied to enhance the signal level. These ground data were later compared to the existing airborne magnetic data for consistency and accuracy using the upward continuation filter. The results show that the quality of ground data is good. In addition, the ground magnetic data show the presence of certain local anomalies that are not visible in the regional data. The analytical signal was also used to determine domain boundaries or possible contact zones. The contact zone can be highlighted on certain profiles such as L300 and L600. The study showed that the west and east sides of the SMD are not the same. Secondary structures become wide when approaching the SMD on both sides. They are also duplicated to the east of the SMD when we move progressively away. In the Dialafara area, the ground magnetic data intersect an interpreted fold. The results of this work confirm the presence of the secondary structures and their evolution in relation to the SMD. The relationships between the secondary structures in the Dailafara and Sadiola zones and their relations with the SMD are highlighted. The technique used in this study, is an important approach to better description and interpreting of regional structures using the secondary structures and proposing a structural model.
文摘We have previously reported that the human ACAT1 gene produces a chimeric mRNA through the interchromosomal processing of two discontinuous RNAs transcribed from chromosomes 1 and 7. The chimeric mRNA uses AUG1397-1399 and GGC1274-1276 as translation initiation codons to produce normal 50-kDa ACAT1 and a novel enzymatically active 56-kDa isoform, respectively, with the latter being authentically present in human cells, including human monocyte- derived macrophages. In this work, we report that RNA secondary structures located in the vicinity of the GGC1274-1276 codon are required for production of the 56-kDa isoform. The effects of the three predicted stem-loops （nt 1255-1268, 1286-1342 and 1355-1384） were tested individually by transfecting expression plasmids into cells that contained the wild-type, deleted or mutant stem-loop sequences linked to a partial ACAT1 AUG open reading frame （ORF） or to the ORFs of other genes. The expression patterns were monitored by western blot analyses. We found that the upstream stem-loop1255-1268 from chromosome 7 and downstream stem-loop1286-1342 from chromosome 1 were needed for production of the 56-kDa isoform, whereas the last stem-loop135s-1384 from chromosome 1 was dispensable. The results of experi- ments using both monocistronic and bicistronic vectors with a stable hairpin showed that translation initiation from the GGC1274-1276 codon was mediated by an internal ribosome entry site （IRES）. Further experiments revealed that translation initiation from the GGC1274-1276 codon requires the upstream AU-constituted RNA secondary structure and the downstream GC-rich structure. This mechanistic work provides further support for the biological significance of the chimeric nature of the human ACAT1 transcript.
基金supported by the National Key Technology R&D Program of China(Grant Nos.2017YFA0103504 to XC,2018ZX10301402 to JRY)the National Natural Science Foundation of China(Grant Nos.31671320,31871320,and 81830103 to JRY)the start-up grants from the“100 Top Talents Program”of Sun Yat-sen University,China(Grant Nos.50000-18821112 to XC,50000-18821117 to JRY).
文摘The secondary structure is a fundamental feature of both non-coding RNAs(ncRNAs)and messenger RNAs(mRNAs).However,our understanding of the secondary structures of mRNAs,especially those of the coding regions,remains elusive,likely due to translation and the lack of RNA-binding proteins that sustain the consensus structure like those binding to ncRNAs.Indeed,mRNAs have recently been found to adopt diverse alternative structures,but the overall functional significance remains untested.We hereby approach this problem by estimating the folding specificity,i.e.,the probability that a fragment of an mRNA folds back to the same partner once refolded.We show that the folding specificity of mRNAs is lower than that of ncRNAs and exhibits moderate evolutionary conservation.Notably,we find that specific rather than alternative folding is likely evolutionarily adaptive since specific folding is frequently associated with functionally important genes or sites within a gene.Additional analysis in combination with ribosome density suggests the ability to modulate ribosome movement as one potential functional advantage provided by specific folding.Our findings reveal a novel facet of the RNA structurome with important functional and evolutionary implications and indicate a potential method for distinguishing the mRNA secondary structures maintained by natural selection from molecular noise.
文摘Calcium ions play an important role in the oxygen_evolving process of photosystem Ⅱ as demonstrated in many experiments. The changes of the secondary structures of PS Ⅱ induced by the depletion of Ca 2+ were reported. The results indicated that the removal of Ca 2+ led to the transition of α helix to turns and sheet structures. While Ca 2+ was re_added to the media, only the structures changed to turns could be recovered. The protein conformational changes of PS Ⅱ during the donor side photoinhibition induced by the depletion of Ca 2+ were also studied. This showed that the protein conformational changes differed between the control and Ca 2+ _depleted samples in a short period of illumination (within 10 min). However, the changes became similar when the illumination time was increased.
基金the Chinese Ministry of Science and Technology(No.2018YFA0107603 to Q.C.Z.)the National Natural Science Foundation ofChina(Nos.91740204 and 31761163007 to Q.C.Z.)+1 种基金the National Natural Science Foundation of China(No.61772197 to T.J.)the National Key Research and Development Program of China(No.2018YFC0910404 to T.J.)。
文摘Background:RNA secondary structures play a pivotal role in posttranscriptional regulation and the functions of non-coding RNAs,yet in vivo RNA secondary structures remain enigmatic.PARIS(Psoralen Analysis of RNA Interactions and Structures)is a recently developed high-throughput sequencing-based approach that enables direct capture of RNA duplex structures in vivo.However,the existence of incompatible,fuzzy pairing information obstructs the integration of PARIS data with the existing tools for reconstructing RNA secondary structure models at the single-base resolution.Methods:We introduce IRIS,a method for predicting RNA secondary structure ensembles based on PARIS data.IRIS generates a large set of candidate RNA secondary structure models under the guidance of redistributed PARIS reads and then uses a Bayesian model to identify the optimal ensemble,according to both thermodynamic principles and PARIS data.Results:The predicted RNA structure ensembles by IRIS have been verified based on evolutionary conservation information and consistency with other experimental RNA structural data.HIS is implemented in Python and freely available at http://iris.zhanglab.net.Conclusion:IRIS capitalizes upon PARIS data to improve the prediction of in vivo RNA secondary structure ensembles.We expect that IRIS will enhance the application of the PARIS technology and shed more insight on in vivo RNA secondary structures.
文摘Taking a widely contaminated yet abundant waste,such as poultry feathers,and extracting keratin from this struc-ture appears to be a real challenge whenever the preservation of the secondary structure of the protein is desired.This process would allow exploiting it in ways(e.g.,in the biomedicalfield)that are inspired by a structure that is primarily designed forflight,therefore capable specifically of withstandingflexure and lateral buckling,also with very low thicknesses.The preservation of the structure is based on disulfide crosslinks,and it is offered with pre-ference by some chemical treatments,mainly those based on ionic liquid and on a reduction process.However,the degree of preservation cannot always be precisely assessed;however,beyond chemical characterization,the forma-tion of homogeneous gels can also suggest that the process was successful in this sense.An extraction respectful of nature’s intentions,considering that the secondary structure builds up according to the very function of the feath-ers in the animal,can be deemed to be biomimetic.In particular,biomimetic extractions comply with the very characteristics the protein was designed for to serve in the specific environmental and mechanical situation in which it is inserted.This review tries to elucidate in which cases this aim is achieved and for which specific appli-cations a chicken feather keratin that has preserved its secondary structure can be suited.
文摘[ Objective] The aim was to predict the secondary structure and B cell epitope of growth hormone （GH） protein from Acipenser sinensis. [Method] With the amino acid sequence of GH protein from A. sinensis as the base, the secondary structure of GH protein from A. sinensis was predicted by the method of Gamier-Robson, Chou-Fasman and Karpius-Schulz, and its cell epitope was predicted by the method of Kyte- Doolittle, Emini and Jameson-Wolf. [Result] The sections of 18 -23, 55 -55, 67 -73, 83 -86,112 -114,151 -157 and 209 -211 in the N terminal of GH protein molecule had softer structure and these sections could sway or fold to produce more complex tertiary structure. The sections of 19 -23, 51 -71,84 -95, 128 -139, 164 -176 and 189 -195 in the N terminal of GH protein could be the epitope of B cell and there were flexible regions in these sections or near these sections of GH protein molecule. So the dominant regions could be in these sections or near these sections. [ Conclusion] The research provided the basis for the preparation of monoctonal antibody of GH protein from A. sinensis and provided the reference for the discussion for the molecular regulation mechanism of A. sinensis.
基金supported by the National Natural Science Foundation of China(No.21572101)the Natural Science Foundation of Jiangsu Province(No.BK20180055)+1 种基金Qinghai Provincial Key Laboratory of Tibetan Medicine Research(No.2017-ZJ-Y11)funding by the Fonds der Chemischen Industrie(Liebig-Fellowship)。
文摘Peptide amphiphiles with well-organized secondary structure are an important family of molecules that are known to assemble into a variety of nanostructures.In this work,we present three guanidiniocarbonylpyrrole(GCP)containing peptide amphiphiles,which show versatile morphology and secondary structure changes as a result of different chain lengths and in different concentration regimes.The random coil conformation,α-helix,andβ-sheet are obtained for peptide 1,peptide 2,and peptide 3,respectively under neutral aqueous conditions.Furthermore,all peptide amphiphiles can aggregate to form nanoparticles at low concentrations.However,at high concentrations,peptide 1 selfassembles into left-ha nded twisted helical fibers,while longer bamboo-like mo rphology can be obse rved exclusively for peptide 2.For peptide 3,freshly prepared samples show uniform spherical morphology,whereas an obvious morphological transition from original nanoparticles to disordered fibers was realized after incubating for one week.These fascinating morphology changes were determined by the combination of circular dichroism,dynamic light scattering,transmission electron microscopy,atomic force microscopy,and theoretical calculations.
基金Supported by the Science Foundation of Hengyang Normal University of China(09A36)~~
文摘[Objective] To examine the grammar model based on lexical substring exac- tion for RNA secondary structure prediction. [Method] By introducing cloud model into stochastic grammar model, a machine learning algorithm suitable for the lexicalized stochastic grammar model was proposed. The word grid mode was used to extract and divide RNA sequence to acquire lexical substring, and the cloud classifier was used to search the maximum probability of each lemma which was marked as a certain sec- ondary structure type. Then, the lemma information was introduced into the training stochastic grammar process as prior information, realizing the prediction on the sec- ondary structure of RNA, and the method was tested by experiment. [Result] The experimental results showed that the prediction accuracy and searching speed of stochastic grammar cloud model were significantly improved from the prediction with simple stochastic grammar. [Conclusion] This study laid the foundation for the wide application of stochastic grammar model for RNA secondary structure prediction.
文摘Aim To determine the secondary structure of insulin encapsulated withinliposome. Methods The secondary structure of native insulin, mixture of insulin with liposome(sample Ⅰ) and insulin encapsulated within liposome( sample Ⅱ) were determined by FTIR (FourierTransform Infrared) spectroscopy. Results The secondary structure of insulin encapsulated withinliposome(Ⅱ) are similar with the secondary structure of native insulin. The difference existed inthe amount of α-helices (from 36% of insulin to 31% of sample Ⅱ) and β-sheet(from 48% of insulinto 51% of sample Ⅱ). The content of α-helices and β-sheet of insulin in sample Ⅰ was found to bevery close to that of sample Ⅱ. The results revealed that the insulin encapsulated within liposomepossibly spread on the surface of liposome, without inserting into the liposome membrane.Conclusion The secondary structure of insulin encapsulated within liposome is similar with thenative insulin.
基金financially supported by Beijing Municipal Commission of Education Co-Constructed Programand Chinese Universities Scientific Fund(2009-4-25)
文摘Proteolysis is one of the most important biochemical reactions during cheese ripening.Studies on the secondary structure of proteins during ripening would be helpful for characterizing protein changes for assessing cheese quality.Fourier transform infrared spectroscopy(FTIR),with self-deconvolution,second derivative analysis and band curve-fitting,was used to characterize the secondary structure of proteins in Cheddar cheese during ripening.The spectra of the amide I region showed great similarity,while the relative contents of the secondary structures underwent a series of changes.As ripening progressed,the α-helix content decreased and the β-sheet content increased.This structural shift was attributed to the strengthening of hydrogen bonds that resulted from hydrolysis of caseins.In summary,FTIR could provide the basis for rapid characterization of cheese that is undergoing ripening.
基金financially supported by The foundation for young scientists of hubei province(grant number 610112246)the foundation for Doctoral startup project of Hubei University of Technology(grant number 337/338).
文摘This study aimed to modify isolated and extracted peanut protein with hot alkali to study the impact of pH,heating temperature,processing time and other alkali liquor conditions on the molecular structure of the peanut.Curcumin was loaded in modified peanut protein.The results of the study are as follows:Within the alkaline range of 8<pH<12,the percentage of amino acid residue(AAR)and-turns first increased and then decreased with the increasing pH,and the percentage of AAR reached a maximum 5.21±0.33%when the pH was 11(p<0.01).The percentage of˛-helices andβ-sheets gradually decreased with increasing pH,while that of random coils gradually increased with increasing pH,reaching a maximum 11.24±0.87%when the pH was 11(p<0.05).Within the range of the heating temperature 75℃<T<95℃,the percentage of random coils andβ-sheets gradually increased with increasing heating temperature,while that of-helices and AAR gradually decreased with increasing heating temperature;they remained unchanged when the heating temperature was 90℃,and then decreased to(10.41±1.18%;p<0.01)and(4.02±2.12%;p<0.01),respectively.Within the range of 5 min<t<20 min,the percentage of random coils and AAR gradually increased with increasing heating time,while the percentage ofα-helices decreased from 11.83±1.04%to 10.75±2.34%with increased heating time(p<0.01).The optimum conditions for hot alkali modification of peanut protein as followed:heating temperature of 90℃,heating time of 20 min and a pH of alkali liquor of 11.Under these optimum conditions,the embedding rate of curcumin by the modified protein can reach 88.32±1.29%.
基金Project(08A080) supported by the Scientific Research Fund of Hunan Provincial Education Department,China
文摘Based on the starch hydrolysis reaction accelerated by microwave irradiation with α-amylase, the circular dichroism （CD） and secondary structure changes of α-amylase under the condition of microwave irradiation and water bath were studied by circular dichroism spectra. The results showed that, both the peak heights （at 2=193 nm） of the CD spectra of the samples treated by microwave irradiation and water bath reduced. The reduced rate by microwave irradiation ranged from 140% to 220%, while the reduced rate by water bath ranged from 60% to 140%. The peak of the sample treated by microwave irradiation for 60 min disappeared at λ=193 nm, while the sample showed a wake peak by water bath. The peak position by microwave irradiation emerged a blue shift in the range of 5-8 nm at λ=204 nm and λ=220 nm, while it emerged in the range of 3-5 nm by water bath. With time going on, the microwave irradiation and water bath have prompted the secondary structure of α-helix, β-sheet, β-turn and the mutual transformations of random coil, but the trends were different.
基金Supported by the National Natural Science Foundation of China(No60971089)
文摘A novel method for the prediction of RNA secondary structure was proposed based on the particle swarm optimization（PSO）. PSO is known to be effective in solving many different types of optimization problems and known for being able to approximate the global optimal results in the solution space. We designed an efficient objective function according to the minimum free energy, the number of selected stems and the average length of selected stems. We calculated how many legal stems there were in the sequence, and selected some of them to obtain an optimal result using PSO in the right of the objective function. A method based on the improved particle swarm optimization（IPSO） was proposed to predict RNA secondary structure, which consisted of three stages. The first stage was applied to encoding the source sequences, and to exploring all the legal stems. Then, a set of encoded stems were created in order to prepare input data for the second stage. In the second stage, IPSO was responsible for structure selection. At last, the optimal result was obtained from the secondary structures selected via IPSO. Nine sequences from the comparative RNA website were selected for the evaluation of the proposed method. Compared with other six methods, the proposed method decreased the complexity and enhanced the sensitivity and specificity on the basis of the experiment results.
基金supported by the National Natural Science Foundation of China (30571377)the National High-Tech R&D Program of China (863 Program,2006AA10A204)
文摘The attenuated vaccine strains of CSFV have a 12-nucleotides （nt） insertion in the 3＇-UTR of genome as compared to that of CSFV virulent strains. In this study, we found a distinct heterogeneity in the 3＇-UTR of attenuated Thiverval and HCLV strains. The longest 3＇-UTR of Thiverval strain was 259 base pairs （bp） with a 32-nt insertion, the shortest 3＇-UTR had only 233 bp with a 6-nt insertion. The longest 3＇-UTR of HCLV strain was 244 bp with a 17-nt insertion and the shortest 3＇ UTR was 235 bp with a 8-nt insertion. Compared with the published sequences of 3＇-UTR of vaccine and virulent strains, the 3＇-UTR of CSFV vaccine strains have two variable regions where insertion among the different vaccine strains were frequently found. The first is located between the second conservative TALk codon and the start of T-rich region where we found the variable length insertion in the same vaccine strain Thiveral or HCLV and the second is located between the end of T-rich region and the front of GAA eodon, however, a 4-nt deletion was found in this region in the virulent Shimen strain. These two regions may represent the ＂hot spot＂ for mutation. Modeling the secondary structures of the 3＇-UTR suggests that the T-rich insertion could result in the change of structure and free energy, thus affecting the stability of the 3＇-UTR structure. These findings will help to understand the mechanism of attenuated vaccines and improve vaccine safety, stability, and efficacy.
基金the Fundamental Research Fund for the Central Universities,China(No.2232013D3-02)
文摘The morphology, bending property and secondary structure estimation of dog hair were investigated by scanning electron microscope( SEM),fiber compression bending analyzer,fiber frictional coefficient tester and Fourier transform infrared spectroscopy( FTIR). The SEM micrograph of hair indicated guard hair( GH),intermediate hair( IH) and underhair( UH) from dog hair fibers displayed considerable differences in the diameter,length,scale shape and medulla. In addition,the bending property of fibers were related to the diameter of fibers and the percentage and structure of medulla. The UH had the greatest frictional coefficient,while the guard hair had the largest bending rigidity in three kinds of hairs. The analysis of amide I region implied that there was an apparent variety in the secondary structure of hairs,mainly the percentage of α-helix and β-pleated sheet and β-turn structure. The X-ray diffraction results showed that the crystallinity of the UH was the lowest in the three kinds of fibers. The tensile behaviors of dog hair also indicated that the increase of β-pleated and β-turn structure caused the increase of the breaking strength.
基金Supported by the National Natural Science Foundation of China(30170214)
文摘We introduced a new method---duration Hidden Markov Model (dHMM) to predicate the secondary structure of Protein. In our study, we divide the basic second structure of protein into three parts: H (a-Helix), E (B-sheet) and O (others, include coil and turn). HMM is a kind of probabilistic model which more thinking of the interaction between adjacent amino acids (these interaction were represented by transmit probability), and we use genetic algorithm to determine the model parameters. After improving on the model and fixed on the parameters of the model, we write a program HMMPS. Our example shows that HMM is a nice method for protein secondary structure prediction.
文摘The algorithm based on combination learning usually is superior to a singleclassification algorithm on the task of protein secondary structure prediction. However,the assignment of the weight of the base classifier usually lacks decision-makingevidence. In this paper, we propose a protein secondary structure prediction method withdynamic self-adaptation combination strategy based on entropy, where the weights areassigned according to the entropy of posterior probabilities outputted by base classifiers.The higher entropy value means a lower weight for the base classifier. The final structureprediction is decided by the weighted combination of posterior probabilities. Extensiveexperiments on CB513 dataset demonstrates that the proposed method outperforms theexisting methods, which can effectively improve the prediction performance.
