Rapid, accurate and serotype independent pipeline for in silico epitope mapping of SARS-CoV-2 antigens: a combined machine learning and Chou’s pseudo amino acid composition method

Here,a new integrated machine learning and Chou’s pseudo amino acid composition method has been proposed for in silico epitope mapping of severe acute respiratorysyndrome-like coronavirus antigens.For this,a training dataset including 266 linear B-cell epitopes,1,267 T-cell epitopes and 1,280 non-epitopes were prepared.The epitope sequences were then converted to numerical vectors using Chou’s pseudo amino acid composition method.The vectors were then introduced to the support vector machine,random forest,artificial neural network,and K-nearest neighbor algorithms for the classification process.The algorithm with the highest performance was selected for the epitope mapping procedure.Based on the obtained results,the random forest algorithm was the most accurate classifier with an accuracy of 0.934 followed by K-nearest neighbor,artificial neural network,and support vector machine respectively.Furthermore,the efficacies of predicted epitopes by the trained random forest algorithm were assessed through their antigenicity potential as well as affinity to human B cell receptor and MHC-I/II alleles using the VaxiJen score and molecular docking,respectively.It was also clear that the predicted epitopes especially the B-cell epitopes had high antigenicity potentials and good affinities to the protein targets.According to the results,the suggested method can be considered for developing specific epitope predictor software as well as an accelerator pipeline for designing serotype independent vaccine against the virus.

Protein Content and Amino Acid Composition in Grains of Wheat-Related Species

The protein content and amino acid composition for 17 wheat-related species （WRS） and three common wheats （control） were determined and analyzed, and the essential amino acids （EAAs） in WRS were evaluated according to FAO/WHO amino acid recommendations. The results showed that the mean protein content for WRS was 16.67%, which was 23.21% higher than that for the control. The mean contents （g 100 g^-1 protein） of most amino acids for WRS were lysine 2.74%, threonine 2.83%, phenylalanine 4.17%, isoleucine 3.42%, valine 3.90%, histidine 2.81%, glutamic acid 29.96%, proline 9.12%, glycine 3.59%, alanine 3.37%, and cysteine 1.57%, which were higher than those for the control. The contents of the other 6 amino acids for WRS were lower than those for the control. The materials （Triticum monococcum L., Triticum carthlicum Nevski, and Triticum turgidum L.） contained relatively high concentration of the most deficient EAAs （lysine, threonine, and methionine）. Comparing with FAO/WHO amino acid recommendations, the amino acid scores （AAS） of lysine （49.8%）, threonine （70.7%）, and sulfur-containing amino acids （74.8%） were the lowest, which were considered as the main limiting amino acids in WRS. It was observed that the materials with Triticum urartu Turn. （AA） and Aegilops speltoides Tausch. （SS） genomes had relatively high contents of protein and EAA. The contents of protein （16.91%）, phenylalanine （4.78%）, isoleucine （3.53%）, leucine （6.16%）, and valine （4.09%） for the diploid materials were higher than those for the other materials. These results will provide some information for selecting parents in breeding about nutrient quality and utilization of fine gene in wheat.

The Significant and Profound Impacts of Chou’s Pseudo Amino Acid Composition or PseAAC

In this short review paper, the significant and profound impacts of the Pseudo Amino Acid Composition or PseAAC have been briefly presented with crystal clear convincingness.

Study on Amino Acid Composition of HSP70 and the Level of Plasma Free Amino Acids of Workers with Long-term Exposure to Harmful factors

In order to know the practical value of heat stress protein 70 (HSP70) and to know the changes of plasma free amino acids of workers with the induction of HSP70 by harmful factors, the amino acid composition of major HSP, HSP70 purified from the heated cultured human leukemia cancer cell line K562, rabbit liver, rat liver and heart, and mouse liver with two-step procedures of DE52-cel-lulose ion exchange chromatography and affinity chromatography on ATP-agarose was examined. The level of plasma free amino acids of workers with long-term exposure to heat, carbon monoxide and the combined effect of both heat and carbon monoxide was also investigated. The results showed that the three richest amino acids in HSP70 of all origins were Gly, Glu and Asp, except that of rat heart which was rich in Gly, Phe and Glu. Additionally, Lys, Val, Leu and Ala were also found very rich in HSP70 of all origins. Compared with controls, the most of plasma free amino acids tended to increase and free methionine and trypto-phan were increased significantly (P<0. 05) after a long-term exposure to heat, carbon monoxide, and both. These findings suggested that further studies need to be done to find the substances or drugs which induce the synthesis of HSP70 and reduce the inhibition of synthesis of normal proteins for the purpose of protecting people with exposure to harmful factors against the damage of the factors.

Comparative Analysis of Amino Acid Composition in the Head, Muscle and Tail of Fresh African Cat Fish (Clarias gariepinus)

Consumption of seafood has increased globally over the past 50 years, from an average of 9.9 kg per capital in the 1960s to over 20 kg in 2016. In Nigeria, African catfish (Clarias gariepinus) has gained more attention in terms of farming and consumption compared to other seafood. This project was carried out to determine the level of amino acid composition in the head, muscle and tail of catfish so as to enlighten the public about their choice on the part of catfish to be eaten. Eight different sets of fresh catfish with a mean ± standard deviation of 15.6 kg ± 1.89, which were collected from a local fish pound in Ado-Ekiti, Nigeria, were used for the analysis. Extraction and evaluation of the amino acid composition were carried out using standard analytical techniques. The results obtained showed that high values of amino acids were observed in the fresh catfish (g/100g protein): 13.27 - 13.87 (Glu), 8.76 - 10.39 (Asp), 7.20 - 9.15 (Leu), 7.00 - 8.26 (Lys) and a low value in (Cys), 1.27 - 1.38. The total amino acids had a range of 89.16 - 92.12 g/100g. The coefficient of variation percent (CV %) for all the parameters determined were all generally low with values of 0.74 (observed for Ser) and 39.41 (observed for Pro). Total essential amino acid with histidine values ranged from 38.64 - 42.91 g/100g (CV % = 5.66). It was also observed that the concentrations (g/100g) of amino acids in the muscle of fresh catfish (92.12) are higher than that of the tail (91.98) and that of the head (89.16). There is no appreciable variation in the amino composition of the head, muscle and tail of catfish as the values observed were found to be statistically insignificant (p > 0.05). Therefore, it could be posited that the amino acid in the muscle, tail and head of African catfish would therefore be enough to prevent malnutrition in children and in adults who feed solely on any part of this fish as a main source of protein.

Flavonoids and Amino Acids Analysis of the Fruits of Cornus mas L. Introduced in Uzbekistan

Cornelian cherry is used in the food and pharmaceutical industry as an ornament, in traditional medicine, and in the manufacture of household items. It is widely used in medicine for the prevention and treatment of many diseases. Therefore, it is important to research the chemical composition of these species. In the article, based on our research, the analysis of the quantitative calculation of flavonoids and amino acids of the fruits of the “Elegant” and “Svetlyachok” cherry varieties was carried out. It was found that the amount of amino acids in the fruits of Cornus mas L., introduced in Uzbekistan, is higher in the variety “Svetlyachok” 2.643235 mg/g. In “Elegant” variety it was 1.794235 mg/g. The amount of 4 different flavonoids in the fruit was also determined. It has been established that the Elegant variety has a high concentration of lutein and rutin, and the svetlyachok has a high concentration of apigenin and quercetin.

SuccSite:Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites

Protein succinylation is a biochemical reaction in which a succinyl group(-CO-CH2-CH2-CO-)is attached to the lysine residue of a protein molecule.Lysine succinylation plays important regulatory roles in living cells.However,studies in this field are limited by the difficulty in experimentally identifying the substrate site specificity of lysine succinylation.To facilitate this process,several tools have been proposed for the computational identification of succinylated lysine sites.In this study,we developed an approach to investigate the substrate specificity of lysine succinylated sites based on amino acid composition.Using experimentally verified lysine succinylated sites collected from public resources,the significant differences in position-specific amino acid composition between succinylated and non-succinylated sites were represented using the Two Sample Logo program.These findings enabled the adoption of an effective machine learning method,support vector machine,to train a predictive model with not only the amino acid composition,but also the composition of k-spaced amino acid pairs.After the selection of the best model using a ten-fold crossvalidation approach,the selected model significantly outperformed existing tools based on an independent dataset manually extracted from published research articles.Finally,the selected model was used to develop a web-based tool,SuccSite,to aid the study of protein succinylation.Two proteins were used as case studies on the website to demonstrate the effective prediction of succinylation sites.We will regularly update SuccSite by integrating more experimental datasets.SuccSite is freely accessible at http://csb.cse.yzu.edu.tw/SuccSite/.

The characterization of acid and pepsin soluble collagen from ovine bones (Ujumuqin sheep)

Ovine bones are the major by-products after slaughtered. The present study was conducted to extract and characterize acid soluble collagens （ASC） and pepsin soluble collagens （PSC） from ovine bones （Ujumuqin sheep）. Ovine bones collagen were identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis （SDS-PAGE） and liquid chromatography-tan- dem mass spectrometry （LC-MS/MS） as type I collagen. The results of Fourier transform infrared （FTIR） spectra analysis testified the existence of triple superhelical structure in both ASC and PSC, showing pepsin did not disrupt the triple helical structure of ovine bones collagen. Glycine, accounting for one-third of total amino acids, was the major amino acid for ovine bones collagen. Higher imino acid content was responsible for higher thermal denaturation temperature of ovine bones collagen compared to fish collagens. The isoelectric point of ASC was lower than PSC due to the higher content of acidic amino acids. Therefore, this study provides the potential reference for collagen extraction and application of ovine bones by-procduct.

Nutrient Composition of Different Foxtail Millet Seeds

Ten millet cultivars from China and abroad were analyzed for their crude fat, amylose and amylopectin, crude protein and amino acid content. A wide variation was observed in amylopectin contain, ranging from 54.47% to 69.26%, while amylose content ranged from 11.26% to 23.22%. The average crude fat in all cultivates was 3.46%, and most cultivates ranged from 3.1% to 3.7%. Protein contents ranged from 8.61% to 15.54% with a mean value of 11.94%. For amino acid composition, the ten cultivates were particularly rich in leucine, and the mean was 34.57 mg/g. The millet cultivars were also high in glycine, glutamic acid and cysteine. Millet was known to be limiting in the essential amino lysine, and the mean was 5.18 mg/g. Other amino acids, tyrosine, histidine and arginine were also very low in the ten cultivars. In general, significant nutrient composition differences were observed between the different millet cultivars, and A2 （a kind of mother line of the hybrid millet） and hybrid millet registered a higher level of protein and amino acid composition which would be useful in millet breeding.

Science Letters:EHPred: an SVM-based method for epoxide hydrolases recognition and classification

A two-layer method based on support vector machines (SVMs) has been developed to distinguish epoxide hydrolases (EHs) from other enzymes and to classify its subfamilies using its primary protein sequences. SVM classifiers were built using three different feature vectors extracted from the primary sequence of EHs: the amino acid composition (AAC), the dipeptide composition (DPC), and the pseudo-amino acid composition (PAAC). Validated by 5-fold cross tests, the first layer SVM clas- sifier can differentiate EHs and non-EHs with an accuracy of 94.2% and has a Matthew’s correlation coefficient (MCC) of 0.84. Using 2-fold cross validation, PAAC-based second layer SVM can further classify EH subfamilies with an overall accuracy of 90.7% and MCC of 0.87 as compared to AAC (80.0%) and DPC (84.9%). A program called EHPred has also been developed to assist readers to recognize EHs and to classify their subfamilies using primary protein sequences with greater accuracy.

Dietary guanidinoacetic acid supplementation improves water holding capacity and lowers free amino acid concentration of fresh meat in finishing pigs fed with various dietary protein levels

The current study was carried out to detect the effect of dietary guanidinoacetic acid(GAA)supplementation on carcass characteristics and meat quality in finishing pigs fed different dietary crude protein(CP)levels.Sixty-four barrows with an initial body weight of 73.05±2.34 kg were randomly allocated into 1 of 4 dietary treatments in a 2(100%vs.125%NRC CP level)×2(0 vs.300 mg/kg GAA)factorial arrangement(n=7).The feeding trial lasted for 49 d.GAA supplementation significantly reduced drip loss(P=0.01),free water distribution(T23peak area ratio)(P=0.05)and the concentrations of free alanine,threonine,methionine and isoleucine(P<0.05);but increased total glycine content(P=0.03)in the longissimus dorsi muscle of finishing pigs regardless of the dietary CP levels.Furthermore,primary myogenic cell differentiation system was employed to investigate the influence of inclusion of GAA on free amino acid concentrations in myotubes(n=4)and validate the finding in the animal feeding trial.We found that GAA inclusion in culture medium also decreased intracellular concentrations of free alanine,threonine,methionine,isoleucine,valine and proline in differentiated primary myogenic cells in vitro(P<0.05).Meanwhile,relative to diets with 100%NRC CP level,the intake of diets with 125%NRC CP level improved sarcoplasmic protein solubility,increased the contents of carnosine and total free amino acids as well as flavor amino acids in the longissimus dorsi muscle and decreased backfat thickness at the 6-7th ribs in pigs(P<0.05).In addition,we observed that the impact of dietary GAA supplementation on the last rib fat thickness,shear force,and free lysine content in the longissimus dorsi muscle was dependent on dietary CP levels(P<0.05).Collectively,dietary GAA supplementation can reduce drip loss,decrease the concentrations of free amino acids and flavor amino acids of fresh meat independent of dietary CP levels.

Structural Prediction of Membrane Protein:Application to Known Structures

Membrane proteins are embedded in the lipid bilayer,which creates a suitable environment for their actions. It is important to decide which tpye it belongs to because it is closely relevant to its biological function and its interaction process with other molecules in a biological system. Membrane proteins have different types. The function of a membrane protein is closely correlated with the type it belongs to. In this study,on the basis of the concept of pseudo amino acid (PseAA) composition originally introduced by Chou,the value of approximate entropy (ApEn) of the query membrane protein was used to integrate the complementary information. By fusing fifteen powerful individual fuzzy K-nearest neighbor ( FKNN) classifiers,an ensemble classifier was presented. Each basic classifier was trained in PseAA composition of membrane protein sequences with different parameters. The results of experiments demonstrate it is efficient for the structural prediction of membrane proteins.

Comparative Analysis of Nutritional Components in Muscles between Wild and Cultured Masu Salmon Oncorhynchus masou

In this paper,approximate nutritional components and amino acid content were determined in muscles of female wild population(WP)with body weight of 2500-3000 g and female cultured population(CP)with body weight of 750-1250 g masu salmon Oncorhynchus masou in the gonadal development stage IV by conventional method.The results showed that there were significantly higher crude protein and significantly lower crude fat in fresh muscle of WP than that in CP(P<0.05),but not significant differences in the contents of moisture and crude ash between WP and CP(P>0.05).Eighteen kinds of amino acids were detected in muscles of WP and CP,with higher total content of amino acids(TAA),essential amino acids(EAA)and four kinds of delicious amino acids(DAA)in WP than those in CP(P<0.05).The amino acid score(AAS)and chemical score(CS)revealed that the first limiting amino acid was tryptophan in two populations,with essential amino acid index(EAAI)of 75.59%in WP and 70.77%in CP.The findings indicated that the amino acid contents in muscles of CP are lower than that of WP,but the amino acid nutritional value evaluation indicators of both populations are very close,and both have high nutritional value.

Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues

Although the function of tRNAs in the translational process is well established,it remains controversial whether tRNA abundance is tightly associated with translational efficiency(TE)in mammals.Moreover,how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed.Here,we measured both tRNA expression using demethylase-tRNA sequencing(DM-tRNA-seq)and TE of mRNAs using ribosome-tagging sequencing(RiboTag-seq)in the brain,heart,and testis of mice.Remarkable variation in the expression of tRNA isodecoders was observed among different tissues.When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons,we observed an expected reduction in the variation of anticodon expression across all samples,an unexpected smaller variation of anticodon usage bias,and an unexpected larger variation of tRNA isotype expression at amino acid level.Regardless of whether or not they share the same anticodons,the isodecoders encoding the same amino acids are co-expressed across different tissues.Based on the expression of tRNAs and the TE of mRNAs,we find that the tRNA adaptation index(tAI)and TE are significantly correlated in the same tissues but not between tissues;and tRNA expression and the amino acid composition of translating peptides are positively correlated in the same tissues but not between tissues.We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms.This study provides a resource for tRNA and translation studies,as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.

Prediction of Protein Structural Classes Using the Theory of Increment of Diversity and Support Vector Machine

Based on the concept of the pseudo amino acid composition （PseAAC）, protein structural classes are predicted by using an approach of increment of diversity combined with support vector machine （ID-SVM）, in which the dipeptide amino acid composition of proteins is used as the source of diversity. Jackknife test shows that total prediction accuracy is 96.6% and higher than that given by other approaches. Besides, the specificity （Sp） and the Matthew＇s correlation coefficient （MCC） are also calculated for each protein structural class, the Sp is more than 88%, the MCC is higher than 92%, and the higher MCC and Sp imply that it is credible to use ID-SVM model predicting protein structural class. The results indicate that： 1 the choice of the source of diversity is reasonable, 2 the predictive performance of IDSVM is excellent, and3 the amino acid sequences of proteins contain information of protein structural classes.

Antioxidant and free radical-scavenging activities of black soybean peptides (BSP)

The antioxidant and free radical-scavenging activities of black soybean peptides(BSP)fractions(Fra-Ⅰ,Fra-Ⅱ,Fra-Ⅲ)were investigated using reducing power and DPPH·/superoxide/hydroxyl radical-scavenging assay.The reducing power activity of Fra-Ⅲwas closer to that of BHT but lower than that of ascorbic acid.Fra-Ⅲshowed the strongest scavenging activity against free radicals.The radical-scavenging effect was in a dose-dependent manner and the IC50 values for DPPH·,superoxide and hydroxyl radicals were found to be 1.873,1.684 and 1.735 mg/mL,respectively.Amino acid analysis showed that Fra-Ⅲhad high hydrophobic amino acids(HAA)content and hydrophobicity.The molecular weight distribution of Fra-Ⅲwas found to vary from 100 to 1,000 Da mainly.The antioxidant activity of Fra-Ⅲis clearly related to the amino acid composition,the content of HAA and the molecular mass.The present study suggests that BSP with low molecular weight are useful nutritional antioxidant and potential functional factor for anti-aging.

Prediction of Protein Homo-Oligomer Types by Using IB1 Algorithm

Protein homo-oligomers play an important role in various vital activities. Successful prediction of protein homo-oligomers directly from primary sequence is very beneficial to understand their protein function. In this paper, a total of 14 238 homo-oligomeric protein sequences are predicted by IB1 algorithm. 10-fold cross-validation test is applied to test the predictive capability of the proposed method. The predictive results show that overall prediction accuracy is 90.46%, which is at least 9% higher than that of previous results; furthermore,the sensitivity and Matthew＇s correlation coefficient for each class of homo-oligomers are also improved significantly. The results show that IB1 algorithm is effective and feasible,and very suitable for predicting protein homo-oligomer types.