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...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.展开更多
In this study,a total of 36 blackcurrant(Ribes nigrum L.)cultivars grown in the Northeast of China were selected,including 12 cultivars introduced from Russia,10 from Poland and the rest from local areas.The physicoch...In this study,a total of 36 blackcurrant(Ribes nigrum L.)cultivars grown in the Northeast of China were selected,including 12 cultivars introduced from Russia,10 from Poland and the rest from local areas.The physicochemical properties and amino acid compositions of these varieties were studied,and the geographical origins of blackcurrants were tracked by multivariate statistical analysis.A total of 23 amino acids were detected in all cultivars,which were rich in glutamine,glutamate,aspartate,asparagine,α-alanine,γ-aminobutyric acid,valine and serine.The content of the total amino acids in these cultivars was from 31.21 mg•100 g-1 to 319.40 mg•100 g-1.Stepwise linear discriminant analysis(SLDA)was introduced to perform satisfactory categorization for blackcurrant cultivars,which achieved a success rate of 88.9%for the identification of geographical origins.These results suggested that the compositions of amino acids in blackcurrants could effectively predict geographical origins.展开更多
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.
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 attentio...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.展开更多
A total of 14 parts of beef cuts were used to determine the amino acid composition in drought-master beef. Droughtmaster beef is a cross breed tropical cattle with 50% Shorthorn and 50% Brahman cattle. The most abunda...A total of 14 parts of beef cuts were used to determine the amino acid composition in drought-master beef. Droughtmaster beef is a cross breed tropical cattle with 50% Shorthorn and 50% Brahman cattle. The most abundant type of amino acid in droughtmaster beef was glutamic acid, followed by aspartic acid, lysine, leucine and arginine. The flank cut of beef was found to contain higher amount of total amino acids followed by top side and short rib cut of beef. The amino acid composition of droughtmaster beef indicates that beef is a good source of dietary protein for human.展开更多
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 ...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-cellulose 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 car bon 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展开更多
The carbonaceous chondrites are intriguing and unique in the sense that they are the only rocks that provide pristine records of the early solar nebular processes. We report here results of a detailed mineralogical, c...The carbonaceous chondrites are intriguing and unique in the sense that they are the only rocks that provide pristine records of the early solar nebular processes. We report here results of a detailed mineralogical, chemical, amino acid and isotopic studies of a recently observed fall at Mukundpura, near Jaipur in Rajasthan, India. Abundance of olivines in this meteorite is low and of serpentine minerals is high. FeO/SiO_2 = 1.05 in its Poorly Characterized Phases(PCP) is similar to that observed in other CM2.0 chondrites. The water content of ～9.8 wt.% is similar to that found in many other CM chondrites.Microscopic examination of matrix shows that its terrestrial weathering grade is WO but aqueous parent body alteration is high, as reflected in low abundance of identifiable chondrules and abundant remnants of chondrules(～7%). Thus, most of the chondrules formed initially have been significantly altered or dissolved by aqueous alterations on their parent bodies. The measured bulk carbon(2.3%) and nitrogen content and their isotopic(δ^(13)C =-5.5‰, δ^(15)N = 23.6%0) composition is consistent with CM2.0 classification probably bordering CM1. Several amino acids such as Alanine, Serine, Proline, Valine, Threonine,Leucine, Isoleucine, Asparagine and Histamine are present. Tyrosine and Tryptophan may occur in trace amounts which could not be precisely determined. All these data show that Mukundpura chondrite lies at the boundary of CM2.0 and CM1 type carbonaceous chondrites making it one of the most primitive chondrites.展开更多
The study of the nutritive value of Cowpea (Vigna ungiculata L.) legume seed is needed, as this legume is a food source in many developing countries. Whole Cowpea Flour (WCF), Dehulled Defatted Cowpea Flour (DDCF), an...The study of the nutritive value of Cowpea (Vigna ungiculata L.) legume seed is needed, as this legume is a food source in many developing countries. Whole Cowpea Flour (WCF), Dehulled Defatted Cowpea Flour (DDCF), and Cowpea Protein Isolates (CPI) prepared using Isoelectric method (CPII) and using Micellization method (CPIM) are studied. In proximate analysis, the protein content of WCF, DDCF, CPIA and CPIB was found to be 22.3, 26.7, 750 and 76.0 g/100 g, respectively. Net protein value (NPV) was 17.62 for DDCF. Chemical score was 0.66% for DDCF and 112%, 104% for CPII and CPIM, respectively. The first limiting amino acid was cystine for DDCF and threonine for CPII and CPIM. Methionine was found to be the most concentrated essential amino acid in both CPII and CPIM;values were 27.22 and 30.60 g/16 g N, respectively, while lysine was the most abundant essential amino acid in DDCF (4.28 g/16 g N). Essential amino acids of CPIi and CPIM were 22.99 and 15.78 g/16 g N respectively, higher than FAO/WHO reference.展开更多
The amino acid composition of α and β structural class of proteins from five species, Escherichia coli, Thermotoga maritima, Thermus thermophilus, yeast, and humans were investigated. Amino acid residues of proteins...The amino acid composition of α and β structural class of proteins from five species, Escherichia coli, Thermotoga maritima, Thermus thermophilus, yeast, and humans were investigated. Amino acid residues of proteins were classified into interior or surface residues based on the relative accessible surface area. The hydrophobic Leu, Ala, Val, and Ile residues were rich in interior residues, and hydrophilic Glu, Lys, Asp, and Arg were rich in surface residues both in α and β proteins. The amino acid composition of α proteins was different from that of β proteins in five species, and the difference was derived from the different contents of their interior residues between α and β proteins. α-helix content of α proteins was rich in interior residues than surface ones. Similarly, β-sheet content of β proteins was rich in interior residues than surface ones. The content of Leu residues was very high, approximately 20%, in interior residues of α proteins. This result suggested that the Leu residue plays an important role in the folding of α proteins.展开更多
The composition of tightly bound exopolymeric substances (EPS) obtained from biofilm and plan- ktonic cell subpopulations of Stenotrophomonas maltophilia 5426 UKM was analyzed to study an impact of mild steel presence...The composition of tightly bound exopolymeric substances (EPS) obtained from biofilm and plan- ktonic cell subpopulations of Stenotrophomonas maltophilia 5426 UKM was analyzed to study an impact of mild steel presence in the cultivation medium. The overall protein production was found to increase in the presence of a steel coupon. Some amino acids such as lysine, valine, iso-leucine, tyrosine and phenylalanine were found to be secreted in higher amounts in the presence of mild steel, while its absence leads to an increase of arginine, asparagine, serine, glutamine, proline, glycine, cysteine, leucine, methionine production levels. Biofilm cells EPS contained more arginine, glycine, cysteine, valine, methionine and leucine, comparing to EPS of planktonic cells. The chang- es of tightly bound EPS aggregation around the cells induced in the presence of steel coupons were revealed by transmission electron microscopy. The results suggested the transition of S. maltophilia 5426 UKM cells from planktonic to biofilm lifestyle to be a complex process involving more than a single step.展开更多
Purpose: Special nutrients have an impact on common cold infections. In this trial we have investigated the effectiveness of the specific amino acid composition “aminoplus? immun” on the occurrence, duration and sev...Purpose: Special nutrients have an impact on common cold infections. In this trial we have investigated the effectiveness of the specific amino acid composition “aminoplus? immun” on the occurrence, duration and severity of common cold. Material and Methods: Our study is a controlled, randomised completely masked trial comparing genuine trial remedy versus placebo in parallel groups. Eligible subjects were people with recurrent and chronic infections of the ear, nose and pharyngeal area. The treatment period was 90 days. The primary outcome was the mean number of days that the patients had symptoms of infections. Results: From Oct. 2009 to Feb. 2010 a total of 145 patients were recruited, of whom 119 had no major protocol violation and were valid for assessment. Two thirds of the patients were female. The mean age of the patients was 45 years. 65% of participants had come into contact with many people and thereby an increased risk of infection. On average the patients had 11.1 infections during the 12 months before the study. Compliance for the intake of the study preparation was 98.9%. Due to randomisation, the groups were very similar and balanced. The primary and all 6 secondary outcome variables showed a clear superiority of the investigated amino acid composition over placebo (p Conclusion: The specific composition “aminoplus? immun is effective in preventing recurrent and chronic infections of the ear, nose and upper respiratory tract.展开更多
Protein remote homology detection is a key problem in bioinformatics. Currently, the discriminative methods, such as Support Vector Machine (SVM), can achieve the best performance. The most efficient approach to impro...Protein remote homology detection is a key problem in bioinformatics. Currently, the discriminative methods, such as Support Vector Machine (SVM), can achieve the best performance. The most efficient approach to improve the performance of the SVM-based methods is to find a general protein representation method that is able to convert proteins with different lengths into fixed length vectors and captures the different properties of the proteins for the discrimination. The bottleneck of designing the protein representation method is that native proteins have different lengths. Motivated by the success of the pseudo amino acid composition (PseAAC) proposed by Chou, we applied this approach for protein remote homology detection. Some new indices derived from the amino acid index (AAIndex) database are incorporated into the PseAAC to improve the generalization ability of this method. Our experiments on a well-known benchmark show this method achieves superior or comparable performance with current state-of-the-art methods.展开更多
The significant demand for high quality food has motivated us to adopt appropriate processing methods to improve the food nutritional quality and flavors.In this study,the effects of five drying methods,namely,pulsed ...The significant demand for high quality food has motivated us to adopt appropriate processing methods to improve the food nutritional quality and flavors.In this study,the effects of five drying methods,namely,pulsed vacuum drying(PVD),freeze drying(FD),infrared drying(IRD),hot-air drying(HAD)and sun drying(SD)on free amino acids(FAAs),α-dicarbonyl compounds(α-DCs)and volatile compounds(VOCs)in rape bee pollen(RBP)were determined.The results showed that FD significantly released the essential amino acids(EAAs)compared with fresh samples while SD caused the highest loss.Glucosone was the dominantα-DCs in RBP and the highest loss was observed after PVD.Aldehydes were the dominant volatiles of RBP and SD samples contained more new volatile substances(especially aldehydes)than the other four drying methods.Comprehensively,FD and PVD would be potential methods to effectively reduce the quality deterioration of RBP in the drying process.展开更多
Background Two studies were designed to determine standard ileal crude protein(CP)and amino acid(AA)digestibility of soybean meal(SBM)from different origins fed to non-pregnant and pregnant sows.Seven solvent-extracte...Background Two studies were designed to determine standard ileal crude protein(CP)and amino acid(AA)digestibility of soybean meal(SBM)from different origins fed to non-pregnant and pregnant sows.Seven solvent-extracted SBMs from soybeans produced in the USA,Brazil,and China were selected.In Exp.1,eight different diets were created:a nitrogen(N)-free diet and 7 experimental diets containing SBM from different origins as the only N source.Eight non-pregnant,multiparous sows were arranged in an 8×8 Latin square design(8 periods and 8 diets).In Exp.2,the diet formula was the same as in Exp.1.Eight gestating sows(parity 3)were assigned to 4 different diets in a replicated 4×3 Youden square design(three periods and four diets)in mid-gestation and again in late-gestation stages.Results When fed to non-pregnant and late-gestating sows,the standardized ileal digestibility(SID)of CP and most AAs from different SBM were not significantly different(P>0.05).When fed to mid-gestating sows,the SID values for Arg,His,Lys,Phe,Cys,Gly,Ser,and Tyr in SBM 1 were lower than in SBM 4 and 5(P<0.05),whereas SID for Leu from SBM 5 was higher than in SBM 1 and 4(P<0.05).SID values for Ile,Ala,and Asp from SBM 4 were lower than in SBM 1 and 5(P<0.05).Sows had significantly greater SID values for Lys,Ala,and Asp during mid-gestation when compared with late-gestation stages(P<0.05).Mid-gestating sows had greater SID value for Val and lower SID value for Tyr when compared with non-pregnant and late-gestating sows(P<0.01),whereas non-pregnant sows had significantly greater SID value for Met when compared with gestating sows(P<0.01).Conclusions When fed to mid-gestating sows,the SID values for most AAs varied among SBM samples.The SID values for Lys,Met,Val,Ala,Asp,and Tyr in SBM were affected by sow gestation stages.Our findings provide a cornerstone for accurate SBM use in sow diets.展开更多
Solution processability significantly advances the development of highly-efficient perovskite solar cells.However,the precursor solution tends to undergo irreversible degradation reactions,impairing the device perform...Solution processability significantly advances the development of highly-efficient perovskite solar cells.However,the precursor solution tends to undergo irreversible degradation reactions,impairing the device performance and reproducibility.Here,we utilize a reductive natural amino acid,Nacetylcysteine(NALC),to stabilize the precursor solution for printable carbon-based hole-conductorfree mesoscopic perovskite solar cells.We find that I_(2) can be generated in the aged solution containing methylammonium iodide(MI) in an inert atmosphere and speed up the MA-FA^(+)(formamidinium) reaction which produces large-size cations and hinders the formation of perovskite phase.NALC effectively stabilizes the precursor via its sulfhydryl group which reduces I_(2) back to I^(-)and provides H^(+).The NALC-stabilized precursor which is aged for 1440 h leads to devices with a power conversion efficiency equivalent to 98% of that for devices prepared with the fresh precursor.Furthermore,NALC improves the device power conversion efficiency from 16.16% to 18.41% along with enhanced stability under atmospheric conditions by modifying grain boundaries in perovskite films and reducing associated defects.展开更多
AIM:To explore the correlation of gut microbiota and the metabolites with the progression of diabetic retinopathy(DR)and provide a novel strategy to elucidate the pathological mechanism of DR.METHODS:The fecal samples...AIM:To explore the correlation of gut microbiota and the metabolites with the progression of diabetic retinopathy(DR)and provide a novel strategy to elucidate the pathological mechanism of DR.METHODS:The fecal samples from 32 type 2 diabetes patients with proliferative retinopathy(PDR),23 with nonproliferative retinopathy(NPDR),27 without retinopathy(DM),and 29 from the sex-,age-and BMI-matched healthy controls(29 HC)were analyzed by 16S rDNA gene sequencing.Sixty fecal samples from PDR,DM,and HC groups were assayed by untargeted metabolomics.Fecal metabolites were measured using liquid chromatographymass spectrometry(LC-MS)analysis.Associations between gut microbiota and fecal metabolites were analyzed.RESULTS:A cluster of 2 microbiome and 12 metabolites accompanied with the severity of DR,and the close correlation of the disease progression with PDR-related microbiome and metabolites were found.To be specific,the structure of gut microbiota differed in four groups.Diversity and richness of gut microbiota were significantly lower in PDR and NPDR groups,than those in DM and HC groups.A cluster of microbiome enriched in PDR group,including Pseudomonas,Ruminococcaceae-UCG-002,Ruminococcaceae-UCG-005,Christensenellaceae-R-7,was observed.Functional analysis showed that the glucose and nicotinate degradations were significantly higher in PDR group than those in HC group.Arginine,serine,ornithine,and arachidonic acid were significantly enriched in PDR group,while proline was enriched in HC group.Functional analysis illustrated that arginine biosynthesis,lysine degradation,histidine catabolism,central carbon catabolism in cancer,D-arginine and D-ornithine catabolism were elevated in PDR group.Correlation analysis revealed that Ruminococcaceae-UCG-002 and Christensenellaceae-R-7 were positively associated with L-arginine,ornithine levels in fecal samples.CONCLUSION:This study elaborates the different microbiota structure in the gut from four groups.The relative abundance of Ruminococcaceae-UCG-002 and Parabacteroides are associated with the severity of DR.Amino acid and fatty acid catabolism is especially disordered in PDR group.This may help provide a novel diagnostic parameter for DR,especially PDR.展开更多
BACKGROUND The lack of specific predictors for type-2 diabetes mellitus(T2DM)severely impacts early intervention/prevention efforts.Elevated branched-chain amino acids(BCAAs:Isoleucine,leucine,valine)and aromatic amin...BACKGROUND The lack of specific predictors for type-2 diabetes mellitus(T2DM)severely impacts early intervention/prevention efforts.Elevated branched-chain amino acids(BCAAs:Isoleucine,leucine,valine)and aromatic amino acids(AAAs:Tyrosine,tryptophan,phenylalanine)show high sensitivity and specificity in predicting diabetes in animals and predict T2DM 10-19 years before T2DM onset in clinical studies.However,improvement is needed to support its clinical utility.AIM To evaluate the effects of body mass index(BMI)and sex on BCAAs/AAAs in new-onset T2DM individuals with varying body weight.METHODS Ninety-seven new-onset T2DM patients(<12 mo)differing in BMI[normal weight(NW),n=33,BMI=22.23±1.60;overweight,n=42,BMI=25.9±1.07;obesity(OB),n=22,BMI=31.23±2.31]from the First People’s Hospital of Yunnan Province,Kunming,China,were studied.One-way and 2-way ANOVAs were conducted to determine the effects of BMI and sex on BCAAs/AAAs.RESULTS Fasting serum AAAs,BCAAs,glutamate,and alanine were greater and high-density lipoprotein(HDL)was lower(P<0.05,each)in OB-T2DM patients than in NW-T2DM patients,especially in male OB-T2DM patients.Arginine,histidine,leucine,methionine,and lysine were greater in male patients than in female patients.Moreover,histidine,alanine,glutamate,lysine,valine,methionine,leucine,isoleucine,tyrosine,phenylalanine,and tryptophan were significantly correlated with abdominal adiposity,body weight and BMI,whereas isoleucine,leucine and phenylalanine were negatively correlated with HDL.CONCLUSION Heterogeneously elevated amino acids,especially BCAAs/AAAs,across new-onset T2DM patients in differing BMI categories revealed a potentially skewed prediction of T2DM development.The higher BCAA/AAA levels in obese T2DM patients would support T2DM prediction in obese individuals,whereas the lower levels of BCAAs/AAAs in NW-T2DM individuals may underestimate T2DM risk in NW individuals.This potentially skewed T2DM prediction should be considered when BCAAs/AAAs are to be used as the T2DM predictor.展开更多
The composition and concentration of dissolved free amino acid(DFAA)of seawater samples collected in May 2016 from the surface to the hadal zone of the northern region of the Yap Trench were analyzed by pre-column der...The composition and concentration of dissolved free amino acid(DFAA)of seawater samples collected in May 2016 from the surface to the hadal zone of the northern region of the Yap Trench were analyzed by pre-column derivatization of o-phthalaldehyde.Results show that the average concentration of DFAA in the study area was 0.47±0.36μmol/L.In different sampling stations,the concentrations of DFAA with water depth showed complex variation patterns.At the sediment-seawater interface,the concentrations of DFAA in the western side of the trench were obviously higher than that in its eastern side.In the study area,there were no significant correlations between the concentrations of DFAA and the environmental parameters such as concentrations of chlorophyll a(Chl a),dissolved oxygen(DO),pH,and dissolved inorganic nitrogen(DIN),indicating that the concentrations of DFAA in seawater of the trench are affected by many factors,such as photosynthesis,respiration,temperature,pressure,illumination,and circulation.The dominant DFAA are similar in different water layers of sampling stations,including aspartic acid(Asp),glutamic acid(Glu),glycine(Gly),and serine(Ser).The composition of different amino acids,and the relative abundance of acidic,basic,and neutral amino acids might be related to the sources and consumption of various amino acids.Nine pairs of amino acids in the DFAA showed significantly positive relationship by correlation matrix analysis,suggesting that they might share similar biogeochemical processes.The degradation index(DI)of the DFAA in seawater of the Yap Trench could reflect the degradation,source,and freshness of DFAA in the trench to some extents.This is a preliminary study of amino acids from sea surface to hadal zone in the ocean,more works shall be done in different trenches to reveal their biogeochemical characte ristics in extreme marine environme nts.展开更多
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...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.展开更多
文摘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.
基金Supported by the National Natural Science Foundation of China(32172521)the Natural Science Fund Joint Guidance Project of Heilongjiang Province(LH2019C031)+1 种基金Postdoctoral Scientific Research Development Fund of Heilongjiang Province,China(LBH-Q16020)the Natural Science Fund Project of Heilongjiang Province(SS2021C001)。
文摘In this study,a total of 36 blackcurrant(Ribes nigrum L.)cultivars grown in the Northeast of China were selected,including 12 cultivars introduced from Russia,10 from Poland and the rest from local areas.The physicochemical properties and amino acid compositions of these varieties were studied,and the geographical origins of blackcurrants were tracked by multivariate statistical analysis.A total of 23 amino acids were detected in all cultivars,which were rich in glutamine,glutamate,aspartate,asparagine,α-alanine,γ-aminobutyric acid,valine and serine.The content of the total amino acids in these cultivars was from 31.21 mg•100 g-1 to 319.40 mg•100 g-1.Stepwise linear discriminant analysis(SLDA)was introduced to perform satisfactory categorization for blackcurrant cultivars,which achieved a success rate of 88.9%for the identification of geographical origins.These results suggested that the compositions of amino acids in blackcurrants could effectively predict geographical origins.
文摘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.
文摘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.
基金supported by the National Natural Science Foundation of China(30671270)the National 863 Program of China(2006AA 10Z1E9)the Project for Improved Variety of Shandong Provice,China(Lu Nong Liang Zhong Zi[2006]No.6).
文摘A total of 14 parts of beef cuts were used to determine the amino acid composition in drought-master beef. Droughtmaster beef is a cross breed tropical cattle with 50% Shorthorn and 50% Brahman cattle. The most abundant type of amino acid in droughtmaster beef was glutamic acid, followed by aspartic acid, lysine, leucine and arginine. The flank cut of beef was found to contain higher amount of total amino acids followed by top side and short rib cut of beef. The amino acid composition of droughtmaster beef indicates that beef is a good source of dietary protein for human.
基金This project was supported by the grants from National Natural Science Foundation of China (No.38850662) the Research Fund of Ministry of Health, China (No.0688-203)
文摘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-cellulose 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 car bon 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
基金carried out with the support of MOES-PMN and PLANEX (Physical Research Laboratory, Ahmedabad) programs
文摘The carbonaceous chondrites are intriguing and unique in the sense that they are the only rocks that provide pristine records of the early solar nebular processes. We report here results of a detailed mineralogical, chemical, amino acid and isotopic studies of a recently observed fall at Mukundpura, near Jaipur in Rajasthan, India. Abundance of olivines in this meteorite is low and of serpentine minerals is high. FeO/SiO_2 = 1.05 in its Poorly Characterized Phases(PCP) is similar to that observed in other CM2.0 chondrites. The water content of ～9.8 wt.% is similar to that found in many other CM chondrites.Microscopic examination of matrix shows that its terrestrial weathering grade is WO but aqueous parent body alteration is high, as reflected in low abundance of identifiable chondrules and abundant remnants of chondrules(～7%). Thus, most of the chondrules formed initially have been significantly altered or dissolved by aqueous alterations on their parent bodies. The measured bulk carbon(2.3%) and nitrogen content and their isotopic(δ^(13)C =-5.5‰, δ^(15)N = 23.6%0) composition is consistent with CM2.0 classification probably bordering CM1. Several amino acids such as Alanine, Serine, Proline, Valine, Threonine,Leucine, Isoleucine, Asparagine and Histamine are present. Tyrosine and Tryptophan may occur in trace amounts which could not be precisely determined. All these data show that Mukundpura chondrite lies at the boundary of CM2.0 and CM1 type carbonaceous chondrites making it one of the most primitive chondrites.
文摘The study of the nutritive value of Cowpea (Vigna ungiculata L.) legume seed is needed, as this legume is a food source in many developing countries. Whole Cowpea Flour (WCF), Dehulled Defatted Cowpea Flour (DDCF), and Cowpea Protein Isolates (CPI) prepared using Isoelectric method (CPII) and using Micellization method (CPIM) are studied. In proximate analysis, the protein content of WCF, DDCF, CPIA and CPIB was found to be 22.3, 26.7, 750 and 76.0 g/100 g, respectively. Net protein value (NPV) was 17.62 for DDCF. Chemical score was 0.66% for DDCF and 112%, 104% for CPII and CPIM, respectively. The first limiting amino acid was cystine for DDCF and threonine for CPII and CPIM. Methionine was found to be the most concentrated essential amino acid in both CPII and CPIM;values were 27.22 and 30.60 g/16 g N, respectively, while lysine was the most abundant essential amino acid in DDCF (4.28 g/16 g N). Essential amino acids of CPIi and CPIM were 22.99 and 15.78 g/16 g N respectively, higher than FAO/WHO reference.
文摘The amino acid composition of α and β structural class of proteins from five species, Escherichia coli, Thermotoga maritima, Thermus thermophilus, yeast, and humans were investigated. Amino acid residues of proteins were classified into interior or surface residues based on the relative accessible surface area. The hydrophobic Leu, Ala, Val, and Ile residues were rich in interior residues, and hydrophilic Glu, Lys, Asp, and Arg were rich in surface residues both in α and β proteins. The amino acid composition of α proteins was different from that of β proteins in five species, and the difference was derived from the different contents of their interior residues between α and β proteins. α-helix content of α proteins was rich in interior residues than surface ones. Similarly, β-sheet content of β proteins was rich in interior residues than surface ones. The content of Leu residues was very high, approximately 20%, in interior residues of α proteins. This result suggested that the Leu residue plays an important role in the folding of α proteins.
文摘The composition of tightly bound exopolymeric substances (EPS) obtained from biofilm and plan- ktonic cell subpopulations of Stenotrophomonas maltophilia 5426 UKM was analyzed to study an impact of mild steel presence in the cultivation medium. The overall protein production was found to increase in the presence of a steel coupon. Some amino acids such as lysine, valine, iso-leucine, tyrosine and phenylalanine were found to be secreted in higher amounts in the presence of mild steel, while its absence leads to an increase of arginine, asparagine, serine, glutamine, proline, glycine, cysteine, leucine, methionine production levels. Biofilm cells EPS contained more arginine, glycine, cysteine, valine, methionine and leucine, comparing to EPS of planktonic cells. The chang- es of tightly bound EPS aggregation around the cells induced in the presence of steel coupons were revealed by transmission electron microscopy. The results suggested the transition of S. maltophilia 5426 UKM cells from planktonic to biofilm lifestyle to be a complex process involving more than a single step.
文摘Purpose: Special nutrients have an impact on common cold infections. In this trial we have investigated the effectiveness of the specific amino acid composition “aminoplus? immun” on the occurrence, duration and severity of common cold. Material and Methods: Our study is a controlled, randomised completely masked trial comparing genuine trial remedy versus placebo in parallel groups. Eligible subjects were people with recurrent and chronic infections of the ear, nose and pharyngeal area. The treatment period was 90 days. The primary outcome was the mean number of days that the patients had symptoms of infections. Results: From Oct. 2009 to Feb. 2010 a total of 145 patients were recruited, of whom 119 had no major protocol violation and were valid for assessment. Two thirds of the patients were female. The mean age of the patients was 45 years. 65% of participants had come into contact with many people and thereby an increased risk of infection. On average the patients had 11.1 infections during the 12 months before the study. Compliance for the intake of the study preparation was 98.9%. Due to randomisation, the groups were very similar and balanced. The primary and all 6 secondary outcome variables showed a clear superiority of the investigated amino acid composition over placebo (p Conclusion: The specific composition “aminoplus? immun is effective in preventing recurrent and chronic infections of the ear, nose and upper respiratory tract.
文摘Protein remote homology detection is a key problem in bioinformatics. Currently, the discriminative methods, such as Support Vector Machine (SVM), can achieve the best performance. The most efficient approach to improve the performance of the SVM-based methods is to find a general protein representation method that is able to convert proteins with different lengths into fixed length vectors and captures the different properties of the proteins for the discrimination. The bottleneck of designing the protein representation method is that native proteins have different lengths. Motivated by the success of the pseudo amino acid composition (PseAAC) proposed by Chou, we applied this approach for protein remote homology detection. Some new indices derived from the amino acid index (AAIndex) database are incorporated into the PseAAC to improve the generalization ability of this method. Our experiments on a well-known benchmark show this method achieves superior or comparable performance with current state-of-the-art methods.
基金supported by National Natural Science Foundation of China(Nos.31871861 and 31501548)The Apicultural Industry Technology System(NCYTI-43-KXJ17)The Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-ASTIP-2015-IAR)。
文摘The significant demand for high quality food has motivated us to adopt appropriate processing methods to improve the food nutritional quality and flavors.In this study,the effects of five drying methods,namely,pulsed vacuum drying(PVD),freeze drying(FD),infrared drying(IRD),hot-air drying(HAD)and sun drying(SD)on free amino acids(FAAs),α-dicarbonyl compounds(α-DCs)and volatile compounds(VOCs)in rape bee pollen(RBP)were determined.The results showed that FD significantly released the essential amino acids(EAAs)compared with fresh samples while SD caused the highest loss.Glucosone was the dominantα-DCs in RBP and the highest loss was observed after PVD.Aldehydes were the dominant volatiles of RBP and SD samples contained more new volatile substances(especially aldehydes)than the other four drying methods.Comprehensively,FD and PVD would be potential methods to effectively reduce the quality deterioration of RBP in the drying process.
基金funded by the National Key R&D Program of China(No.2021YFD1300202)the nutritional value evaluation and parameter establishment of protein feedstuffs for sowsthe Ministry of Agriculture and Rural Affairs of the People’s Republic of China(125D0203-16190295)the Major Scientific and Technological Special Project of Sichuan Province(No.2021ZDZX0009)。
文摘Background Two studies were designed to determine standard ileal crude protein(CP)and amino acid(AA)digestibility of soybean meal(SBM)from different origins fed to non-pregnant and pregnant sows.Seven solvent-extracted SBMs from soybeans produced in the USA,Brazil,and China were selected.In Exp.1,eight different diets were created:a nitrogen(N)-free diet and 7 experimental diets containing SBM from different origins as the only N source.Eight non-pregnant,multiparous sows were arranged in an 8×8 Latin square design(8 periods and 8 diets).In Exp.2,the diet formula was the same as in Exp.1.Eight gestating sows(parity 3)were assigned to 4 different diets in a replicated 4×3 Youden square design(three periods and four diets)in mid-gestation and again in late-gestation stages.Results When fed to non-pregnant and late-gestating sows,the standardized ileal digestibility(SID)of CP and most AAs from different SBM were not significantly different(P>0.05).When fed to mid-gestating sows,the SID values for Arg,His,Lys,Phe,Cys,Gly,Ser,and Tyr in SBM 1 were lower than in SBM 4 and 5(P<0.05),whereas SID for Leu from SBM 5 was higher than in SBM 1 and 4(P<0.05).SID values for Ile,Ala,and Asp from SBM 4 were lower than in SBM 1 and 5(P<0.05).Sows had significantly greater SID values for Lys,Ala,and Asp during mid-gestation when compared with late-gestation stages(P<0.05).Mid-gestating sows had greater SID value for Val and lower SID value for Tyr when compared with non-pregnant and late-gestating sows(P<0.01),whereas non-pregnant sows had significantly greater SID value for Met when compared with gestating sows(P<0.01).Conclusions When fed to mid-gestating sows,the SID values for most AAs varied among SBM samples.The SID values for Lys,Met,Val,Ala,Asp,and Tyr in SBM were affected by sow gestation stages.Our findings provide a cornerstone for accurate SBM use in sow diets.
基金financial support from the National Natural Science Foundation of China(grant nos.52172198,51902117,and 91733301)。
文摘Solution processability significantly advances the development of highly-efficient perovskite solar cells.However,the precursor solution tends to undergo irreversible degradation reactions,impairing the device performance and reproducibility.Here,we utilize a reductive natural amino acid,Nacetylcysteine(NALC),to stabilize the precursor solution for printable carbon-based hole-conductorfree mesoscopic perovskite solar cells.We find that I_(2) can be generated in the aged solution containing methylammonium iodide(MI) in an inert atmosphere and speed up the MA-FA^(+)(formamidinium) reaction which produces large-size cations and hinders the formation of perovskite phase.NALC effectively stabilizes the precursor via its sulfhydryl group which reduces I_(2) back to I^(-)and provides H^(+).The NALC-stabilized precursor which is aged for 1440 h leads to devices with a power conversion efficiency equivalent to 98% of that for devices prepared with the fresh precursor.Furthermore,NALC improves the device power conversion efficiency from 16.16% to 18.41% along with enhanced stability under atmospheric conditions by modifying grain boundaries in perovskite films and reducing associated defects.
文摘AIM:To explore the correlation of gut microbiota and the metabolites with the progression of diabetic retinopathy(DR)and provide a novel strategy to elucidate the pathological mechanism of DR.METHODS:The fecal samples from 32 type 2 diabetes patients with proliferative retinopathy(PDR),23 with nonproliferative retinopathy(NPDR),27 without retinopathy(DM),and 29 from the sex-,age-and BMI-matched healthy controls(29 HC)were analyzed by 16S rDNA gene sequencing.Sixty fecal samples from PDR,DM,and HC groups were assayed by untargeted metabolomics.Fecal metabolites were measured using liquid chromatographymass spectrometry(LC-MS)analysis.Associations between gut microbiota and fecal metabolites were analyzed.RESULTS:A cluster of 2 microbiome and 12 metabolites accompanied with the severity of DR,and the close correlation of the disease progression with PDR-related microbiome and metabolites were found.To be specific,the structure of gut microbiota differed in four groups.Diversity and richness of gut microbiota were significantly lower in PDR and NPDR groups,than those in DM and HC groups.A cluster of microbiome enriched in PDR group,including Pseudomonas,Ruminococcaceae-UCG-002,Ruminococcaceae-UCG-005,Christensenellaceae-R-7,was observed.Functional analysis showed that the glucose and nicotinate degradations were significantly higher in PDR group than those in HC group.Arginine,serine,ornithine,and arachidonic acid were significantly enriched in PDR group,while proline was enriched in HC group.Functional analysis illustrated that arginine biosynthesis,lysine degradation,histidine catabolism,central carbon catabolism in cancer,D-arginine and D-ornithine catabolism were elevated in PDR group.Correlation analysis revealed that Ruminococcaceae-UCG-002 and Christensenellaceae-R-7 were positively associated with L-arginine,ornithine levels in fecal samples.CONCLUSION:This study elaborates the different microbiota structure in the gut from four groups.The relative abundance of Ruminococcaceae-UCG-002 and Parabacteroides are associated with the severity of DR.Amino acid and fatty acid catabolism is especially disordered in PDR group.This may help provide a novel diagnostic parameter for DR,especially PDR.
基金Supported by the Open Project Grant for Clinical Medical Center of Yunnan Province,No.2019LCZXKF-NM03Medical Leader Training Grant,No.L-201624and Yunnan Province Ten Thousand Talents:“Medical Expert”grant,No.YNWR-MY-2019-020.
文摘BACKGROUND The lack of specific predictors for type-2 diabetes mellitus(T2DM)severely impacts early intervention/prevention efforts.Elevated branched-chain amino acids(BCAAs:Isoleucine,leucine,valine)and aromatic amino acids(AAAs:Tyrosine,tryptophan,phenylalanine)show high sensitivity and specificity in predicting diabetes in animals and predict T2DM 10-19 years before T2DM onset in clinical studies.However,improvement is needed to support its clinical utility.AIM To evaluate the effects of body mass index(BMI)and sex on BCAAs/AAAs in new-onset T2DM individuals with varying body weight.METHODS Ninety-seven new-onset T2DM patients(<12 mo)differing in BMI[normal weight(NW),n=33,BMI=22.23±1.60;overweight,n=42,BMI=25.9±1.07;obesity(OB),n=22,BMI=31.23±2.31]from the First People’s Hospital of Yunnan Province,Kunming,China,were studied.One-way and 2-way ANOVAs were conducted to determine the effects of BMI and sex on BCAAs/AAAs.RESULTS Fasting serum AAAs,BCAAs,glutamate,and alanine were greater and high-density lipoprotein(HDL)was lower(P<0.05,each)in OB-T2DM patients than in NW-T2DM patients,especially in male OB-T2DM patients.Arginine,histidine,leucine,methionine,and lysine were greater in male patients than in female patients.Moreover,histidine,alanine,glutamate,lysine,valine,methionine,leucine,isoleucine,tyrosine,phenylalanine,and tryptophan were significantly correlated with abdominal adiposity,body weight and BMI,whereas isoleucine,leucine and phenylalanine were negatively correlated with HDL.CONCLUSION Heterogeneously elevated amino acids,especially BCAAs/AAAs,across new-onset T2DM patients in differing BMI categories revealed a potentially skewed prediction of T2DM development.The higher BCAA/AAA levels in obese T2DM patients would support T2DM prediction in obese individuals,whereas the lower levels of BCAAs/AAAs in NW-T2DM individuals may underestimate T2DM risk in NW individuals.This potentially skewed T2DM prediction should be considered when BCAAs/AAAs are to be used as the T2DM predictor.
基金Supported by the Natural National Science Foundation of China(Nos.42076040,41676067)the National Basic Research Program of China(973 Program)(No.2015CB755904)the 111 Project(No.B13030)。
文摘The composition and concentration of dissolved free amino acid(DFAA)of seawater samples collected in May 2016 from the surface to the hadal zone of the northern region of the Yap Trench were analyzed by pre-column derivatization of o-phthalaldehyde.Results show that the average concentration of DFAA in the study area was 0.47±0.36μmol/L.In different sampling stations,the concentrations of DFAA with water depth showed complex variation patterns.At the sediment-seawater interface,the concentrations of DFAA in the western side of the trench were obviously higher than that in its eastern side.In the study area,there were no significant correlations between the concentrations of DFAA and the environmental parameters such as concentrations of chlorophyll a(Chl a),dissolved oxygen(DO),pH,and dissolved inorganic nitrogen(DIN),indicating that the concentrations of DFAA in seawater of the trench are affected by many factors,such as photosynthesis,respiration,temperature,pressure,illumination,and circulation.The dominant DFAA are similar in different water layers of sampling stations,including aspartic acid(Asp),glutamic acid(Glu),glycine(Gly),and serine(Ser).The composition of different amino acids,and the relative abundance of acidic,basic,and neutral amino acids might be related to the sources and consumption of various amino acids.Nine pairs of amino acids in the DFAA showed significantly positive relationship by correlation matrix analysis,suggesting that they might share similar biogeochemical processes.The degradation index(DI)of the DFAA in seawater of the Yap Trench could reflect the degradation,source,and freshness of DFAA in the trench to some extents.This is a preliminary study of amino acids from sea surface to hadal zone in the ocean,more works shall be done in different trenches to reveal their biogeochemical characte ristics in extreme marine environme nts.
文摘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.
