Drivers of spatial structure in thinned forests

Background:As is widely known,an increasing number of forest areas were managed to preserve and enhance the health of forest ecosystems.However,previous research on forest management has often overlooked the importance of structure-based.Aims:Our objectives were to define the direction of structure-based forest management.Subsequently,we investigated the relationships between forest structure and the regeneration,growth,and mortality of trees under different thinning treatments.Ultimately,the drivers of forest structural change were explored.Methods:On the basis of 92 sites selected from northeastern China,with different recovery time (from 1 to 15years) and different thinning intensities (0–59.9%) since the last thinning.Principal component analysis (PCA)identified relationships among factors determining forest spatial structure.The structural equation model (SEM)was used to analyze the driving factors behind the changes in forest spatial structure after thinning.Results:Light thinning (0–20%trees removed) promoted forest regeneration,and heavy thinning (over 35% of trees removed) facilitated forest growth.However,only moderate thinning (20%–35%trees removed) created a reasonable spatial structure.While dead trees were clustered,and they were hardly affected by thinning intensity.Additionally,thinning intensity,recovery time,and altitude indirectly improve the spatial structure of the forest by influencing diameter at breast height (DBH) and canopy area.Conclusion:Creating larger DBH and canopy area through thinning will promote the formation of complex forest structures,which cultivates healthy and stable forests.

Study on the secondary structure and hydration effect of human serum albumin under acidic pH and ethanol perturbation with IR/NIR spectroscopy

Human serum albumin(HSA)is the most abundant protein in plasma and plays an essential physiological role in the human body.Ethanol precipitation is the most widely used way to obtain HSA,and pH and ethanol are crucial factors affecting the process.In this study,infrared(IR)spectroscopy and near-infrared(NIR)spectroscopy in combination with chemometrics were used to investigate the changes in the secondary structure and hydration of HSA at acidic pH(5.6-3.2)and isoelectric pH when ethanol concentration was varied from 0%to 40%as a perturbation.IR spectroscopy combined with the two-dimensional correlation spectroscopy(2DCOS)analysis for acid pH system proved that the secondary structure of HSA changed significantly when pH was around 4.5.What's more,the IR spectroscopy and 2DCOS analysis showed different secondary structure forms under different ethanol concentrations at the isoelectric pH.For the hydration effect analysis,NIR spectroscopy combined with the McCabe-Fisher method and aquaphotomics showed that the free hydrogen-bonded water fluctuates dynamically,with ethanol at 0-20%enhancing the hydrogen-bonded water clusters,while weak hydrogen-bonded water clusters were formed when the ethanol concentration increased continuously from 20%to 30%.These measurements provide new insights into the structural changes and changes in the hydration behavior of HSA,revealing the dynamic process of protein purification,and providing a theoretical basis for the selection of HSA alcoholic precipitation process parameters,as well as for further studies of complex biological systems.

Prediction of Secondary Structure and B Cell Epitope of GH Protein from Acipenser sinensis

[ 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.

DISTRIBUTIONS OF TRIPLET CODONS IN MESSENGER RNA SECONDARY STRUCTURES

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.

Grammar Model Based on Lexical Substring Extraction for RNA Secondary Structure Prediction

[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.

Dietary bamboo leaf flavonoids improve quality and microstructure of broiler meat by changing untargeted metabolome

Background Dietary bamboo leaf flavonoids(BLFs)are rarely used in poultry production,and it is unknown whether they influence meat texture profile,perceived color,or microstructure.Results A total of 720 one-day-old Arbor Acres broilers were supplemented with a basal diet with 20 mg bacitracin/kg,50 mg BLFs/kg,or 250 mg BLFs/kg or without additions.Data showed that the dietary BLFs significantly(P<0.05)changed growth performance and the texture profile.In particular,BLFs increased birds’average daily gain and average daily feed intake,decreased the feed:gain ratio and mortality rate,improved elasticity of breast meat,enhanced the gumminess of breast and leg meat,and decreased the hardness of breast meat.Moreover,a significant(P<0.05)increase in redness(a*)and chroma(c*)of breast meat and c*and water-holding capacity of leg meat was found in BLF-supplemented broilers compared with control broilers.In addition,BLFs supplementation significantly decreased(P<0.05)theβ-sheet ratio and serum malondialdehyde and increased theβ-turn ratio of protein secondary structure,superoxide dismutase,and glutathione peroxidase of breast meat and total antioxidant capacity and catalase of serum.Based on the analysis of untargeted metabolome,BLFs treatment considerably altered 14 metabolites of the breast meat,including flavonoids,amino acids,and organic acids,as well as phenolic and aromatic compounds.Conclusions Dietary BLFs supplementation could play a beneficial role in improving meat quality and sensory color in the poultry industry by changing protein secondary structures and modulating metabolites.

FTIR Characterization of the Secondary Structure of 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.

FTIR Analysis of Protein Secondary Structure in Cheddar Cheese during Ripening

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.

Sensitive and Label-Free Detection of Protein Secondary Structure by Amide Ⅲ Spectral Signals using Surface-Enhanced Raman Spectroscopy

Proteins and peptides perform a vital role in living systems, however it remains a challenge for accurate description of proteins at the molecular level. Despite that surface-enhanced Raman spectroscopy (SERS) can provide the intrinsic fingerprint information of samples with ultrahigh sensitivity, it suffers from the poor reproducibility and reliability. Herein, we demonstrate that the silver nanorod array fabricated by an oblique angle deposition method is a powerful substrate for SERS to probe the protein secondary structures without exogenous labels. With this method, the SERS signals of two typical proteins (lysozyme and cytochrome c) are successfully obtained. Additionally, by analyzing the spectral signals of the amide Ⅲ of protein backbone, the influence of concentration on the folding status of proteins has been elucidated. With the concentration increasing, the components of α-helix and β-sheet structures of lysozyme increase while the secondary structures of cytochrome c almost keep constant. The SERS method in this work offers an effective optical marker to characterize the structures of proteins.

A wide hybrid zone mediated by precipitation contributed to confused geographical structure of Scutiger boulengeri

Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology.In this study,we generated a time-calibrated phylogeny of Scutiger boulengeri,an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang(Tibet)Plateau(QTP).Based on three mitochondrial DNA(mt DNA)genes,eight clades were assigned to three deeply divergent lineages.Analysis of nuclear DNA(nu DNA)genes revealed three distinct clusters without geographic structure,indicating significantly high rates of gene flow.Coalescent theory framework analysis(approximate Bayesian computation model DIYABC and Migrate-N)suggested that divergence of the main intraspecific clusters was the result of hybridization after secondary contact in the Holocene around 0.59 million years ago(Ma).The ratio of mt DNA FST(fixation index)to nu DNA FST was 2.3,thus failing to show male-biased dispersal.Geographic cline analysis showed that a wide hybrid zone was initially established in southwestern China,without significant reproductive isolation but with strong introgression in S.boulengeri,suggesting high hybrid fitness.Furthermore,mt DNA genes exhibited isolation by distance(IBD)while nu DNA genes exhibited significant isolation by environment(IBE).Results suggested that mitonuclear discordance may have initially been caused by geographic isolation,followed by precipitation-mediated hybridization,producing a wide hybrid zone and geographic structure confusion of nu DNA genes in S.boulengeri.This study indicated that complicated historical processes may have led to specific genetic patterns,with a specific climate factor facilitating gene flow in the system.

RNA secondary structures located in the interchromosomal region of human ACAT1 chimeric mRNA are required to produce the 56-kDa isoform

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.

Compensation for secondary uncertainty in electro-hydraulic servo system by gain adaptive sliding mode variable structure control

Based on consideration of the differential relations between the immeasurable variables and measurable variables in electro-hydraulic servo system,adaptive dynamic recurrent fuzzy neural networks(ADRFNNs) were employed to identify the primary uncertainty and the mathematic model of the system was turned into an equivalent linear model with terms of secondary uncertainty.At the same time,gain adaptive sliding mode variable structure control(GASMVSC) was employed to synthesize the control effort.The results show that the unrealization problem caused by some system's immeasurable state variables in traditional fuzzy neural networks(TFNN) taking all state variables as its inputs is overcome.On the other hand,the identification by the ADRFNNs online with high accuracy and the adaptive function of the correction term's gain in the GASMVSC make the system possess strong robustness and improved steady accuracy,and the chattering phenomenon of the control effort is also suppressed effectively.

Inspections of Mobile Phone Microwaves Effects on Proteins Secondary Structure by Means of Fourier Transform Infrared Spectroscopy

In this study the effects of microwaves on the secondary structure of three typical proteins have been investigated. A set of samples of lysozyme, bovine serum albumin and myoglobin in D2O solutions were exposed for 8 hours to mobile phone microwaves at 900 MHz at a magnetic field intensity around 16 mA/m. The relative effects on the secondary structure of the proteins were studied by means of Fourier Transform Infrared Spectroscopy. An increase of the amide I band intensity in the secondary structure of the proteins was observed after the microwaves exposure. Furthermore, a weak shift of the amide I mode of bovine serum albumin and a heavier shift of the amide I of myoglobin occurred after the exposure. In addition, a clear increasing of the β-sheet components with respect to the α-helix content was observed in the spectra of bovine serum albumin and myoglobin after the exposure, suggesting the hypothesis of the formation of aggregates.

Prediction of RNA Secondary Structure Based on Particle Swarm Optimization

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.

Heterogeneity and Secondary Structure Analysis of 3' Untranslated Region in Classical Swine Fever Viruses

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.

Morphology,Bending Property and Secondary Structure Estimation of Dog Hair

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.

HMM in Predicting Protein Secondary Structure

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.

Impact of hot alkali modification conditions on secondary structure of peanut protein and embedding rate of curcumin

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%.

Effect of microwave irradiation on secondary structure of α-amylase by circular dichroism

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.

Neural Network Based on GA-BP Algorithm and its Application in the Protein Secondary Structure Prediction

The advantages and disadvantages of genetic algorithm and BP algorithm are introduced. A neural network based on GA-BP algorithm is proposed and applied in the prediction of protein secondary structure, which combines the advantages of BP and GA. The prediction and training on the neural network are made respectively based on 4 structure classifications of protein so as to get higher rate of predication---the highest prediction rate 75.65%,the average prediction rate 65.04%.