Oral immune regulation using colitis extracted proteins for treatment of Crohn's disease: Results of a phase Ⅰ clinical trial

AIM: To evaluate safety and possible efficacy of induction of oral immune regulation using colitis extracted proteins (CEP) in Crohn's disease (CD) subjects. METHODS: Ten CDs were treated orally with autologous CEP thrice weekly for 16 wk. Subjects were monitored for CDAI and IBDQ. Immune modulatory effect was assessed by T-lymphocyte FACS analysis, CEP-specific IFNγ ELISPOT assay and cytokine levels. RESULTS: Induction of oral immune regulation significantly ameliorated disease activity. All (10/10) subjects had clinical response (CDAI≤70) and 7/10 achieved clinical remission (CDAI≤150). Significant increase in mean IBDQ score was noted (134±9 vs 164±12). No treatment-related adverse events were noted. High levels of CEP-specific IFNγ spot forming colonies were detected in five subjects prior to treatment and in all five, a marked decrease was observed. The CD4+/CD8+ lymphocyte ratio and peripheral NKT cell numbers increased significantly, in 7/10 and in 5/10 subjects, respectively. Significant increase in serum IL-10 and IL-4 levels was observed in 7/10 subjects during treatment period. CONCLUSION: Immune regulation via oral administration of CEP is a safe and possibly effective treatment for subjects with moderate CD and may provide means of antigen-specific immune modulation.

Optimization of Two-Dimensional Gel Electrophoresis for Kenaf Leaf Proteins

To establish a suitable and effective protocol of protein extraction for two-dimensional gel electrophoresis （2-DE） analysis in kenaf leaf tissues, three extraction methods （trichloroacetic acid/acetone, urea/thiourea, and phenol extraction methods） were applied to the extraction of kenaf leaf protein. The results were compared in regard to protein extraction efficiency, sodiumdodecyl sulfate-polyacrylamide gel electrophoresis （SDS-PAGE）, and 2-DE gels. Furthermore, the 2-DE system was optimized for four aspects： the pH range of IPG （immobilized pH gradient） stripes, sampling methods, sample volumes, and concentration of polyacrylamide gels. The data presented showed that the phenol extraction method is the best method to perform 2-DE analysis of kenaf leaf protein. The protein extracted from phenol extraction method reached the purity of （26.40±0.859）%, showed （25.67±1.53） protein bands in one dimension SDS-PAGE gels, and （1 374±54.44） protein spots on 2-DE gels. The research also indicates that kenaf leaf protein spots were distributed mainly within the pH range of 4-8. More clear background with a better distribution effect and many protein spots could be obtained on 2-DE gels under the conditions of active rehydration loading, 24 cm IPG strips （linear pH gradient of 4-7）, 1.4 mg samples, and 12% SDS-PAGE gels.

Analysis of differentially expressed proteins in cancerous and normal colonic tissues

AIM： To identify and analyze the differentially expressed proteins in normal and cancerous tissues of four patients suffering from colon cancer. METHODS： Colon tissues （normal and cancerous） were homogenized and the proteins were extracted using three protein extraction buffers. The extraction buffers were used in an orderly sequence of increasing extraction strength for proteins with hydrophobic properties. The protein extracts were separated using the SDS-PAGE method and the images were captured and analyzed using Quantity One software. The target protein bands were subjected to in-gel digestion with trypsin and finally analyzed using an ESI-ion trap mass spectrometer. RESULTS： A total of 50 differentially expressed proteins in colonic cancerous and normal tissues were identified. CONCLUSION： Many of the identified proteins have been reported to be involved in the progression of similar or other types of cancers. However, some of the identified proteins have not been reported before. In addition, a number of hypothetical proteins were also identified.

Methodological approach to the isolation of functionally active proteins from the tissues of marine hydrobionts: an example of Adamussium colbecki

Enzymes from cold-adapted organisms have significant application potential. Because of their unique properties they have been found to be useful in various industries. Despite indisputable practical interest, cold active enzymes also represent a valuable model for fundamental research into protein folding and catalysis. Many investigators have focused their attention on marine hydrobionts, which are growing in importance as a promising source of enzymes. The nature of the source not only determines the availability and the cost of biomolecules of interest but also determines the choice of method for their extraction. A simple and convenient methodological approach of two-stage extraction of proteins has been tested on the Antarctic marine hydrobiont--Adamussium colbecki. This method extracts enough effective protein directly from primary raw materials, as well as when using leftover crude precipitates. The electrophoretic pattern of proteins showed the presence of molecules in a wide range of molecular weights in the samples of A. colbecki after the first and the second stage of extraction. The general proteolytic activity in the first and the second extracts were examined using a zymogram technique. Our experiments revealed that the second extract of A. colbecki contained thermo stable protease exhibiting a molecular weight of 95 kDa in a gelatin zymogram. Further biochemical assays, using different substrates, were conducted to partially identify the types of hydrolases present in the first and the second extracts. Our results revealed the presence of enzymes with collagenolytic and some amylolytic activities preserved in the second extracts. But no esterase or amidase trypsin-like activities were found in the second extract, in contrast to the first extract where this type of activity was significant.

Mass Spectrometry-based Deep Coverage Proteome:Evaluation of Cellular Protein Extraction Methods

The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.

Gut microbiota remodeling drived by dietary millet protein prevents the metabolic syndrome

Metabolic syndrome(Met S)is a chronic disease associated with the disturbance of gut microbiota homeostasis.Metabolites derived from gut microbes play essential roles in Met S prevention and therapy.Here,we focused on the inhibitory effect of the extract of millet bran protein(EMBP)on a high-fat diet(HFD)-induced Met S,aiming to identify gut microbiota and their metabolites that involve in the anti-Met S activity of EMBP.The obesity,chronic inflammation,insulin resistance in Met S mouse models were abolished after EMBP treatment.The protective mechanism of EMBP against HFD-induced Met S may depend on improved gut barrier function.Using microbiome analysis,we found that EMBP supplementation improved gut microbiome dysbiosis in Met S mice,specifically upregulating Bacteroides acidifaciens.The fecal microbiota transplantation(FMT)also demonstrated this phenomenon.In addition,metabolomic analysis showed that EMBP mediates metabolic profiling reprogramming in Met S mice.Notably,a microbiota-derived metabolite,gamma-aminobutyric acid(GABA),is enriched by EMBP.In addition,exogenous GABA treatment produced a similar protective effect to EMBP by improving NRF2-dependent gut barrier function to protect HFDinduced Met S.The results suggest that EMBP suppress host Met S by remodeling of gut microbiota as an effective candidate for next-generation medicine food dual purpose dietary supplement to intervene in MetS.

Proteomic Analysis of Stichopus japonicus and Evaluation of the Antiaging Properties of Its Peptide

The sea cucumber Stichopus japonicus is one of the"Eight Treasures of Seafood"and contains a number of bioactive components involved in multiple physiological and pharmacological functions.Proteins and peptides are generally considered to be responsible for these beneficial properties.In this study,a total of 3478 proteins and 17390 peptides were identified in Stichopus japonicus by proteomics methods.Among them,4 proteins were involved in 8 metabolic pathways,especially oxidative phosphorylation and cell senescence.Subsequently,lifespan assay and oxidative stress test were performed to investigate the peptides prepared from sea cucumber protein hydrolyzate using the aging model of Caenorhabditis elegans.The results of the anti-aging experiment demonstrated that high-dose peptides significantly prolonged the lifespan of nematodes(30.50%),and improved their capacity to inhibit oxidative stress.The results provide evidence supporting the development of bioactive proteins and peptides derived from Stichopus japonicus as functional foods and lay the foundation for the research of an anti-aging drug.

Study on Processing of Clear Banana Juice Using Hot Water Extraction Method

In this study, the effects of hot water temperature on clarity, total soluble solids, polyphenol oxidase （PPO） and color of banana juice during hot water ex-traction were discussed based on the theory in which heat treatment might induce the pectin and protein in banana pulp to form insoluble products. The results showed the hot water temperature had a significant effect on the formation of insol-uble polymers in banana pulp from pectin and protein. In 75 ℃ water, the pectin and protein in banana pulp were most inclined to form insoluble products. Under this condition, the clarity of banana juice was also highest. The light transmittance at 660 nm was close to 90%. In the banana juice, extracted by 75 ℃ water, the pectin and protein contents were lowest, and they were lower than 7.3 mg/100 ml and 12.9 mg/100 ml respectively. The 75 ℃ water could not inactivate completely the pectin in banana pulp due to its high heat resistance, Therefore, 0.05% L-cys-teine or ascorbic acid needed to be added into banana pulp to inhibit the browning of juice induced by residual PPO.

Antibacterial Activity of Bacillus subtilis and Properties of Protein Crude Extract

In order to get biological drugs with no resistance or toxic side effects and to reduce the use of antibiotics, a strain of Baci//us subtilis was isolated from animal intestine, and the isolate was identified by molecular biological method; in vitro an- tibacterial test of the isolate was performed using agar diffusion method; the optimal fermentation condition of the isoJate was screened by conventional culture method; the antibacterial crude protein of the isolate was extracted by saturated ammonium sulfate method; the physicochemical properties of antibacterial crude protein was de- tected by comparison method; The results showed that the isolate was B. subti/is, which had antibacterial effects on Staphy/ococcus aureus, streptococcus and swine erysipelas. The fermentation effect of the isolate was the best under the condition of temperature 30 ~C, pH 7, liquid volume 75 ml/250 ml, inoculation volume 20% and culture time 48 h. The antibacterial effect of the isolate was the best when extract- ed by 80% saturated ammonium sulfate. The antibacterial crude protein had strong resistance to heat and acid. Organic solvent and UV irradiation had some influences on antibacterial crude protein. Proteases had hydrolytic effects on antibacterial crude protein. The isolated B. subti/is can be used to prevent and control the diseases caused by S. aureus, streptococcus and swine erysipelas, and can regulate intesti- nal microecology by adding into expanded feeds.

Deep eutectic solvents and alkaline extraction of protein from seabuckthorn seed meal: a comparison study

Seabuckthorn seed meal(SSM) is a waste of oil extraction industry that rich in protein. In order to seek suitable protein extraction method, three different deep eutectic solvents(DESs)(including choline chlorideglycerol, choline chloride-oxalic acid and choline chloride-urea) were developed for extracting protein from SSM and compared with alkaline. Result indicated that alkaline could effectively extract 56.9% protein from SSM and its protein content was 73.1%, higher than DES at 31.0%-41.4% and 64.3%-67.5%, respectively. However, compared to alkali, DES led to a product with less β-sheet, more β-turn, more essential amino acids, higher total amino acid content, especially choline chloride-urea which extracted protein showing an integrated and similar protein weight distribution compared to SSM. Also, this protein extracted chloride-urea showed a highest digestibility in vitro(by pepsin)(54.2%). These results indicated that choline chloride-urea extraction is better than alkaline extraction for SSM.

Protein Extraction Methods for Two-Dimensional Electrophoresis from Baphicacanthus cusia(Nees)Bremek Leaves-A Medicinal Plant with High Contents of Interfering Compounds

Protein extraction is a critical step for two-dimensional electrophoresis （2-DE）. Different plant samples require different and adaptive protein extraction protocols. The leaves of medicinal plant, Baphicacanthus cusia （Nees） Bremek are notoriously recalcitrant to common protein extraction methods due to high levels of interfering compounds （especially the secondary metabolites and pigments）. This study was aimed to establish a routine procedure for the proteomic analysis ofB. cusia leaves, and a new protocol for the protein extraction was developed by optimizing trichloroacetic acid （TCA）/ acetone extraction method. The efficiency of this protocol was demonstrated by comparison with 3 published protein extraction methods （chloroform/acetone, Mg/NP-40, Tris-base/acetone）. The results showed that the optimized TCA/ acetone precipitation extraction method gave a relatively high protein yield （9.263 mg g^-1 fresh weight）, high-resolution separation, clear protein profiles, the highest proteins spots （1 31 t protein spots）, and displayed less contamination in 2- DE gels. Therefore, the results suggested that the optimized TCA/acetone method was the most effective among the 4 methods for B. cusia leaves.

SCREENING OF AGGLUTININS IN MARINE ALGAE FROM FUJIAN COAST OF CHINA

Thirty three species of marine algae belonging to Rhodophyta, Phaeophyta and Chlorophyta from the Fujian coast were examined for agglutinins with different animal and human erythrocytes. Protein extracts from 26 species were active against at least one type of the erythrocytes tested. There were 3 species ( Grateloupia imbricata, Ishige foliacea and Entermorpha prolifera ) whose extracts could agglutinate all the erythrocytes used. The lowest protein concentration required to produce erythrocyte agglutination varied remarkably, from 3.1 μg/ml to 500 μg/ml . The strongest activity was found in the agglutination of rabbit erythrocytes by Gloiopeltis furcata extract. Inhibition assays performed with nine mono and bisaccharides indicated that agglutinations of rabbit erythrocytes by extracts of 7 species were inhibited by one or more types of the sugars assayed. The agglutinating activity shown by extracts of most species was not affected when the test solution was heated to 90℃, but was lost at 95℃-100℃. A few extracts lost their activity at 60℃, 65℃ and 75 ℃, respectively.

A Cooperative Approach for the Extraction of Protein Motifs

By integrating the concept of cooperative approach, an extension of the fast annealing coevolutionary algorithm is presented in this paper. It outperformed the original algorithm in the domain of function optimization, especially in terms of convergence rate. It was also applied to a real optimization problem, protein motif extraction. And a satisfactory result has been obtained with the accuracy of prediction achieving 67.0%, which is in agreement with the result in the PROSITE database.

A Comparative Study of Soluble Protein Extractions of Populus deltoides × （ Trichocarpa × Deltoides） for 2-DE

Background： The disclosure of the poplar genome strengthens its position as well-established model organism. Populus has been subject of several proteome studies, but up to date no comparative study was performed on the extraction method of soluble proteins for this species. The extraction is the most critical step in two-dimensional gel electrophoresis and each extraction method has its advantages, disadvantages and limitations. Therefore protein extraction methods should be optimized for each tissue before starting an experimental setup. In prospect of future DIGE （Differential Gel electrophoresis） experiments for the investigation of the effects of cadmium and inoculation with plant growth promoting bacteria at the proteome level, the aim of this study was to optimize an extraction method for soluble proteins of poplar leaves and roots. Results： The acetone-phenol extraction method was found to be the most suited, rendering a high spot number and low background interference. During further optimization, several critical steps in the extraction method were revealed. Conclusion： Aiming to optimize the extraction of soluble leaf and root proteins of Populus deltoides × （trichocarpa× deltoides） compatible with DIGE analysis, a protocol rendering high reproducibility, low background interference and a high spot number was established, however no novel insights were acquired.

A Simple Procedure for Extraction of Surface Protein of Salmonella Serotypes and Escherichia coli Strains Isolated from Poultry and Pigs

Salmonella and E.coli possess different surface protein structures that can induce protective immune responses.Identification of these proteins capacitates development of diverse applications in prevention and diagnosis that contribute to effectively control disease-causing enterobacteria pathogens such as Salmonella and E.coli.A simple procedure for obtaining protein complexes of Salmonella serotypes and E.coli is performed in this study.A sonication process with heat treatment of whole bacteria induced the release of protein complexes.Concentration of the protein extract was quantified using protein quantification Kits-Rapid,and protein complex profile was obtained by SDS-PAGE(Sodium dodecyl sulfate polyacrylamide gel electrophoresis)and silver staining.The concentrations of protein ranged from 29.45 to 45.35μg/mL in the Salmonella protein extracts,and from 25.35 to 36.72μg/mL in the E.coli protein extracts.Six major groups of proteins from E.coli(YfiO,NipB,OmpF,YfgL,Talc,YaeT)and four major groups of proteins from Salmonella(Flagellin,OmpA,Porin,SEF21)were preliminarily determined by a simple procedure of extraction based on the molecular weight.

Overview on pulse proteins for future foods:ingredient development and novel applications

We are facing the challenge of climate change and food insecurity for a growing population.The current mode of animal protein production via animal agriculture is resource-intensive and unsustainable.Therefore,there is a need to find alternative sources of food protein that are environmentally sustainable.Plant-based proteins,specifically pulse-based proteins,provide a promising solution to the problem.This review aims to provide an overview and perspective on extraction,functionality,digestibility,sensory,and new food applications of pulse proteins.Two main methods,namely wet fractionation and dry fractionation are used to extract pulse-based proteins.As compared to dry fractionation,wet fractionation yields high purity protein,but the process alters the structure and function of the proteins.Various biochemical and physical techniques can be used to assist wet extraction process to increase protein yield and/or reduce extraction time.The main techno-functional properties of plant-based proteins determining their practical applicability are solubility,water/oil holding capacity(WHC/OHC),gelation,emulsification,foaming,and rheological properties.Nutritionally,pulse proteins are deficient in one or more essential amino acids.Strategies to overcome the deficiency are discussed.Volatile and non-volatile compounds inherent to pulses or developed during processing are mostly responsible for the off flavors in the extracted protein.Approaches to improve the pulse protein flavor and remove or modify off-flavors are discussed.Pulse-based protein ingredients have applications in bakery products,pasta,meat analogues,dairy alternatives,and beverages.Beyond these applications,there is a need to explore novel applications of pulse proteins in infant and children’s formula,beverages,breakfast cereals,flavor development,and extruded snack products,develop new applications such as personalized and precision nutrition and bioactive peptides,and employ innovative technologies such as 3D printing,extrusion,and artificial intelligence for pulse protein research.This review presents the current status,limitations,and future perspectives for developing pulse protein ingredients as future foods.This review aims to foster thinking and generate novel ideas for future research.

Adsorption and Desorption of Cry1Ab Proteins on Differently Textured Paddy Soils

In recent years, selected cry genes from Bacillus thuringiensis（Bt） encoding the production of Cry proteins（Bt toxins） have been engineered into crop plants（Bt-crops）. Through the cultivation of Bt crops and the application of Bt pesticides, Cry proteins could be introduced into arable soils. The interaction between the proteins and soils was analyzed in this study to investigate the affinity of Cry proteins in paddy soil ecosystems. Four Paddy soils were selected to represent different soil textures. Cry proteins were spiked in soils, and the amount of protein adsorbed was measured over 24 h. Desorption of Cry1Ab proteins from paddy soils was performed by washing with sterile Milli-Q water（H_2O_（MQ））, and subsequently extracted with an extraction buffer. The paddy soils had a strong affinity for Cry1Ab proteins. Most of the Cry1Ab proteins added（＆gt; 98%） were rapidly adsorbed on the paddy soils tested. More Cry1Ab proteins were adsorbed on non-sterile soils than on sterile soils. Less than 2% of the adsorbed Cry1Ab proteins were desorbed using H2 OMQ, while a considerable proportion of the adsorbed proteins could be desorbed with the buffer, ranging from 20% to 40%.The amount of proteins desorbed increased with the increases in the initial amount of Cry1Ab proteins added to the paddy soils. The concentration of Cry1Ab proteins desorbed from the paddy soils was higher for sterile soils than non-sterile ones. Our results indicate that Bt toxins released via the cultivation of Bt crops, the application of Bt pesticides can be adsorbed on paddy soils, and soil texture could impose an impact on the adsorption capability.

Comparison of alternative extraction methods for secretome profiling in human hepatocellular carcinoma cells

Secreted proteins are important sources for early detection and diagnosis of disease, and as such have received considerable attention. The extraction of low concentration proteins from large volumes of culture media, which are rich in salts and other compounds that interfere with most proteomics techniques, presents a problem for secretome studies. Ultrafiltration, precipitation, and dialysis are three major extraction methods that can be used to overcome this problem. The present study for the first time, compared the merits and shortcomings of these three methods, without bias. Centrifugal ultrafiltration provided the best extraction efficiency, and precipitation provided the highest number of identifiable proteins. The three methods yielded closely related, but different, information on the secretome; thus, they should be considered complementary or, at least, supplementary methods. Three hundred and sixty unique proteins were identified, including 211 potential secreted proteins. Compared with previous studies, this study also identified 42 new secreted proteins. The present study not only offers a reference for the selection of secretome extraction methods, but also expands the secretome database for the investigation of hepatocellular carcinoma.

Optimization of low-abundance protein extraction and abundant protein removal from defatted soybean meal

The aim of this study was to optimize the conditions for the extraction of low-abundance proteins（LAPs） and the removal of abundant proteins（APs; β-conglycinin and glycinin） from soybean meal.Single factor and orthogonal experiments were designed to determine the effects of four factors（isopropanol concentration, total extraction time, ultrasonic power, and ultrasonic time） on protein concentration in isopropanol extracts.Proteins in the isopropanol supernatant and the cold acetone precipitate of isopropanol were identified by sodium dodecyl sulfate polyacrylamide gel electrophoresis（SDS-PAGE） and matrix-assisted laser desorption/ionization-time of flight mass spectrometry（MALDI-TOF-MS）.The results showed that the optimal conditions were 50% isopropanol, ultrasonic pretreatment for 15 min at 350 W, and a total extraction time of 1 h.Under these conditions, the protein concentration in the isopropanol extracts reached 0.8081 g/L.Many LAPs were detected, including β-amylase, soybean agglutinin, soybean trypsin inhibitor, fumarylacetoacetase-like, phospholipase D alpha 1-like, oleosin, and even some unknown soybean proteins.The soybean APs（β-conglycinin and glycinin） were not found.The method may be useful for discovering new soybean proteins and extracting enough LAPs of soybean to allow further studies of their physiological effects on animals without the influence of APs.

Recent Advances in Protein Extraction and Chiral Separation of Biomolecules

Reverse micelles create unique environment in organic media. They are capable of solubilizing hydrophilic biomolecules （e.g., proteins, peptides, amino acids, and DNAs） in their aqueous interior. This feature brings about the practical use of biomaterials in organic media because reverse micelles solubilize them with the intrinsic activity. In this paper, we focus on recent two topics concerning protein extraction and chiral separation of biomolecules using liquid membranes. In the first topic, we present recent attempts to extract proteins from an aqueous solution into isooctane using reverse micelles, and some important operational parameters to achieve an efficient protein transfer are discussed. Furthermore, novel function of reverse micelles as a protein activation medium is introduced. In the reverse micellar phase, denatured proteins were completely reactivated in the reverse micellar solution. The reverse micellar technique is found to be a useful tool not only for protein separation but also for protein refolding. Furthermore, we found that a cyclic ligand carixarene has an extraction ability to set up optimum conditions for protein transfer. In the second topic, we have found that a supported liquid membrane （SLM） encapsulating enzymes shows high enantioselectivity （enantioselective excess value is over 96%） in the transport of racemic pharmaceutical compound ibuprofen. A different experiment also suggests that the α-chymotrypsin-catalyzed reactions droved the enantioselective transport of L-phenylalanine based on the enantioselectivity of the enzyme. The SLM encapsulating the surfactant-enzyme complex enabled the highly enantioselective separation of racemic mixtures. It can be envisioned that arrangement of appropriate enzymes in the SLM system will allow enantioselective separation of various useful organic compounds.