Large-scale proteomics studies can refine our understanding of health and disease and enable precision medicine.Here,we provide a detailed atlas of 2,920 plasma proteins linking to diseases(406 prevalent and 660 incid...Large-scale proteomics studies can refine our understanding of health and disease and enable precision medicine.Here,we provide a detailed atlas of 2,920 plasma proteins linking to diseases(406 prevalent and 660 incident)and 986 health-related traits in 53,026 individuals(median follow-up:14.8 years)from the UK Biobank,representing the most comprehensive proteome profiles to date.This atlas revealed 168,100 protein-disease associations and 554,488 protein-trait associations.Over 650 proteins were shared among at least 50 diseases,and over 1,000 showed sex and age heterogeneity.Furthermore,proteins demonstrated promising potential in disease discrimination(area under the curve[AUC]>0.80 in 183 diseases).Finally,integrating protein quantitative trait locus data determined 474 causal proteins,providing 37 drug-repurposing opportunities and 26 promising targets with favorable safety profiles.These results provide an open-access comprehensive proteome-phenome resource(https://proteome-phenome-atlas.com/)to help elucidate the biological mechanisms of diseases and accelerate the development of disease biomarkers,prediction models,and therapeutic targets.展开更多
Cryptocaryon irritans is the parasite responsible for“white spot disease”in the yellowfin seabream Acanthopagrus latus,which has caused significant losses to the aquaculture industry.This experiment investigated the...Cryptocaryon irritans is the parasite responsible for“white spot disease”in the yellowfin seabream Acanthopagrus latus,which has caused significant losses to the aquaculture industry.This experiment investigated the changes in the morphology,transcriptome,and proteome of gill tissue in yellowfin seabream infected with C.irritans,aiming to provide foundational data for further understanding the pathogenic mechanisms and control measures against this parasite.The main findings were as follows,after C.irritans infection,the structure of gill tissue in yellowfin seabream was damaged,with microvessels ruptured,some cells proliferating,and large amounts of mucus infiltrating.Transcriptome analysis revealed a total of 4299 differentially expressed genes,with 2367 up-regulated and 1932down-regulated.Further bioinformatics analysis of all differentially expressed genes identified nine immune-related genes,cox-2,mcama,tbx21,dcn,tnfb,cd74a,illb,ppib,and cd4-1 in A.latus.The reliability of the transcriptome data was validated by real time q PCR,which showed the same trend as the RNA-seq results.Proteome analysis found365 differential proteins,with 180 proteins up-regulated and 185 proteins down-regulated.Bioinformatics analysis identified three immune-related proteins,Myll,Gapdh,and Actn3b.These findings indicated that C.irritans disrupted the structure of gill tissue,impeded gas exchange and led to asphyxiation and death in affected fish.Transcriptome and proteome analyses showed that the expression of immune-related genes and proteins in yellowfin seabream,involved not only inflammatory responses and the activation and migration of immune cells but also potentially participated in tissue repair and defense regulation.These findings highlighted the complex immune regulatory network in response to C.irritans infection,offering references for prevention and control of white spot disease in yellowfin seabream.展开更多
Soil cadmium pollution has increasingly become a serious problem for crop production,which drastically attenuates plant growth and food safety.Although N6-methyladenosine(m^(6)A)methylation is crucial for plant respon...Soil cadmium pollution has increasingly become a serious problem for crop production,which drastically attenuates plant growth and food safety.Although N6-methyladenosine(m^(6)A)methylation is crucial for plant response to various stresses,the regulatory mechanism underlying m^(6)A modification during cadmium(Cd)stress remains unclear.This study investigated the physiological responses,transcriptome-wide m^(6)A methylome,and proteome changes in tomato roots exposed to 50 μmol·L^(-1)CdCl2.Excess Cd restricted plant growth,altered the antioxidant system and disrupted mineral nutrient absorption.We identified a negative correlation between m^(6)A levels and gene transcription for that 150 out of 198 differentially expressed genes(DEGs)were hypomethylated but mRNA up-regulated.Cd stress also enhanced translational efficiency,particularly for differentially abundant proteins(DAPs).Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis revealed that differentially m^(6)A modified genes(DMGs),DEGs,and DAPs were commonly enriched in phenylpropanoid biosynthesis,glutathione metabolism,and ABC transporters,reflecting cell wall barriers,chelation,and transport of Cd,respectively.Finally,we confirmed the Cd-transport activity of eight putative metal transporters identified in DMGs,DEGs,or DAPs by yeast complementaion experiments,and pharmacologically investigated the effect of m^(6)A modification on their expression.Treatment with the m^(6)A methylation inhibitor 3-deazaneplanocin A(3-DA)reduced SlIRT1/2 expression and increased SlNRAMP3/SlZIP4 expression,while the m^(6)A demethylase inhibitor meclofenamic acid(MA)treatment decreased SlNRAMP3 expression but elevated SlIRT2 expression under Cd stress.Our findings provide novel insights into the interplay between m^(6)A modification,transcription,and translation under Cd stress and the associated plant stress response.展开更多
[Objective] The research aimed to establish the two-dimensional electrophoresis（2-DE）technology which was suitable for the rapeseed proteome research.[Method] Xiangyou 17 was as the material.The sample preparation m...[Objective] The research aimed to establish the two-dimensional electrophoresis（2-DE）technology which was suitable for the rapeseed proteome research.[Method] Xiangyou 17 was as the material.The sample preparation method,gel concentration and loading amount,etc.in 2-DE technology were optimized.[Result] The best extraction method of total protein of rapeseed was TCA-acetone method,and the protein spots on 2-DE map were the most.When IPG strip（pH 3-10）and 12% gel were used,and the loading amount was 250 μg,the two-dimensional electrophoresis map with the clear background,good repeatability and high protein spot resolution was obtained.[Conclusion] The research laid the foundation for carrying out the rapeseed proteomics research.展开更多
Background The objective was to characterize the colostrum proteome of primiparous Holstein cows in association with immunoglobulin G(IgG)content.Immediately after calving,colostrum samples were collected from 18 cows...Background The objective was to characterize the colostrum proteome of primiparous Holstein cows in association with immunoglobulin G(IgG)content.Immediately after calving,colostrum samples were collected from 18 cows to measure IgG concentration.Based on colostrum IgG content,samples were classified through cluster analysis and were identified as poor,average,and excellent quality.The proteome was assessed with quantitative shotgun proteomics;abundance data were compared among the colostrum types;enrichment analysis of metabolic processes and proteins classes was performed as well.We also tested correlations between this proteome and blood globulin level of cows and passive immunity level of calves.Results On average,428 proteins were identified per sample,which belonged mainly to cellular process,biological regulation,response to stimulus,metabolic process,and immune system process.Most abundant proteins were complement C3(Q2UVX4),alpha-S1-casein(P02662),Ig-like domain-containing protein(A0A3Q1M032),albumin(A0A140T897),polymeric immunoglobulin receptor(P81265),lactotransferrrin(P24627),and IGHG1*01(X167014).Colostrum of excellent quality had greater(P<0.05)abundance of serpin A3-7(A2I7N3),complement factorl(A0A3Q1 MIF4),lipocalin/cytosolic fatty-acid binding domain-containing protein(A0A3Q1 MRQ2),complement C3(E1B805),complement component 4 binding protein alpha(A0AAF6ZHP5),and complement component C6(F1MM86).However,colostrum of excellent quality had lower(P<0.05)abundance of HGF activator(E1BCW0),alpha-S1-casein(P02662),and xanthine dehydrogenase/oxidase(P80457).This resulted in enrichment of the biological processes predominantly for complement activation alternative pathway,complement activation,complement activation classical pathway,humoral immune response,leukocyte mediated immunity,and negative regulation of endopeptidase activity in excellent-quality colostrum.Additionally,some colostrum proteins were found to be correlated with the blood globulin level of cows and with the passive immunity level of calves(P<0.05;r≥0.57).Conclusions This study provides new insights into the bovine colostrum proteome,demonstrating associations between IgG levels and the abundance of other proteins,as well as the enrichment of metabolic processes related to innate immune response.Thus,results suggest that the colostrum proteomic profile is associated with the content of IgG.Future research should deeply explore the association of these findings with pre-calving nutrition status and blood composition of the cow,and with passive immunity transfer to the calf.展开更多
This manuscript examines the utility, utilizing the Ciphergen Protein Biosystem II, to develop a fingerprint for the diagnosis of prostate cancer. The investigators compared samples from control individuals as well as...This manuscript examines the utility, utilizing the Ciphergen Protein Biosystem II, to develop a fingerprint for the diagnosis of prostate cancer. The investigators compared samples from control individuals as well as those with prostate cancer. In doing so, they utilize several chip platforms on which to examine the resulting展开更多
AIM： To isolate and identify the biological characteristics of human colon cancer stem cells （SW1116 cells） and further study their proteome. METHODS： SW1116 cells were isolated and cultured with a serum-free medi...AIM： To isolate and identify the biological characteristics of human colon cancer stem cells （SW1116 cells） and further study their proteome. METHODS： SW1116 cells were isolated and cultured with a serum-free medium （SFM）. Sphere formation was assayed to observe the formation of colon cancer stem cell spheres. SW1116 cells were inoculated into a serum-containing medium for observing their differentiation characteristics. Proliferation curve and cross-resistance of SWl116 cells to different drugs were detected by MTT. Percentage of SP cells in SW1116 cells was detected with Hoechst33342 staining. Telomerase activity in SW1116cells was checked by polymerase chain reaction （PCR）-enzyme linked immunosorbent assay. Expressions of stem cell relevant genes and proteins were detected by reverse transcription-PCR and Western blot, respectively. Total protein was isolated from SW1116 cells by two-dimensional gel electrophoresis （2-DE） and differentially expressed proteins were identified by tandem mass spectrometry （MALDI-TOF/TOF）. RESULTS： The isolated SW1116 cells presented as spheroid and suspension growths in SFM with a strong self-renewal, proliferation, differentiation and drug-resistance ability. The percentage of SP cells in SW1116 cells was 38.9%. The SW1116 cells co-expressed the CD133 and CD29 proteins. The telomerase activity in SW1116 cells was increased. The expressions of different stem cell relevant genes and proteins were detected. The proteomic analysis showed that the 26 protein spots were differently expressed in SW1116 cells and 10 protein spots were identified as ubiquitin fusion- degradation l-like protein, nuclear chloride channel protein, tubulin 13, Raichu404X, stratifin, F-actin cap- ping protein α-1 subunit, eukaryotic translation elongation factor 1 delta isoform 2, hypothetical protein, glyceraldehyde-3-phosphate dehydrogenase and guanine nucleotide binding protein 13 polypeptide 2-like 1, respectively. CONCLUSION： SW1116 cells are biologically characterized by self-renewal, proliferation and differentiation, and the differently expressed proteins in SW1116 cells may be essential for isolating cancer stem cells.展开更多
Background： Early pregnancy failure has a profound impact on both human reproductive health and animal production. 2/3 pregnancy failures occur during the peri-implantation period; however, the underlying mechanism（...Background： Early pregnancy failure has a profound impact on both human reproductive health and animal production. 2/3 pregnancy failures occur during the peri-implantation period; however, the underlying mechanism（s） remains unclear. Well-organized modification of the endometrium to a receptive state is critical to establish pregnancy Aberrant endometrial modification during implantation is thought to be largely responsible for early pregnancy loss. Result： In this study, using well-managed recipient ewes that received embryo transfer as model, we compared the endometrial proteome between pregnant and non-pregnant ewes during implantation period. After embryo transfer, recipients were assigned as pregnant or non-pregnant ewes according to the presence or absence of an elongated conceptus at Day 17 of pregnancy. By comparing the endometrial proteomic profiles between pregnant and non-pregnant ewes, we identified 94 and 257 differentially expressed proteins （DEPs） in the endometrial caruncular and intercaruncular areas, respectively. Functional analysis showed that the DEPs were mainly associated with immune response, nutrient transport and utilization, as well as proteasome-mediated proteolysis. Conclusion： These analysis imply that dysfunction of these biological processes or pathways of DEP in the endometrium is highly associated with early pregnancy loss. In addition, many proteins that are essential for the establishment of pregnancy showed dysregulation in the endometrium of non-pregnant ewes. These proteins, as potential candidates, may contribute to early pregnancy loss.展开更多
Objective To identify potential serum biomarkers for distinguishing between latent tuberculosis infection（LTBI） and active tuberculosis（TB）. Methods A proteome microarray containing 4,262 antigens was used for scr...Objective To identify potential serum biomarkers for distinguishing between latent tuberculosis infection（LTBI） and active tuberculosis（TB）. Methods A proteome microarray containing 4,262 antigens was used for screening serum biomarkers of 40 serum samples from patients with LTBI and active TB at the systems level. The interaction network and functional classification of differentially expressed antigens were analyzed using STRING 10.0 and the TB database, respectively. Enzyme-linked immunosorbent assays（ELISA） were used to validate candidate antigens further using 279 samples. The diagnostic performances of candidate antigens were evaluated by receiver operating characteristic curve（ROC） analysis. Both antigen combination and logistic regression analysis were used to improve diagnostic ability. Results Microarray results showed that levels of 152 Mycobacterium tuberculosis（Mtb）-antigenspecific IgG were significantly higher in active TB patients than in LTBI patients（P 〈 0.05）, and these differentially expressed antigens showed stronger associations with each other and were involved in various biological processes. Eleven candidate antigens were further validated using ELISA and showed consistent results in microarray analysis. ROC analysis showed that antigens Rv2031 c, Rv1408, and Rv2421 c had higher areas under the curve（AUCs） of 0.8520, 0.8152, and 0.7970, respectively. In addition, both antigen combination and logistic regression analysis improved the diagnostic ability. Conclusion Several antigens have the potential to serve as serum biomarkers for discrimination between LTBI and active TB.展开更多
To evaluate the response of alfalfa to water deficit （WD） stress, WD-induced candidates were investigated through a proteomic approach. Alfalfa seedlings were exposed to WD stress for 12 and 15 days respectively, fo...To evaluate the response of alfalfa to water deficit （WD） stress, WD-induced candidates were investigated through a proteomic approach. Alfalfa seedlings were exposed to WD stress for 12 and 15 days respectively, followed by 3 days re-watering. Water deficit increased H202 content, lipid peroxidation, DPPH （1,1-diphenyl-2-picrylhydrazyl）-radical scavenging activity, and the free proline level in alfalfa roots. Root proteins were extracted and separated by two-dimentional polyacrylamide gel electrophoresis （2-DE）. A total of 49 WD-responsive proteins were identified in alfalfa roots; 25 proteins were reproducibly found to be up-regulated and 24 were down-regulated. Two proteins, namely cytosolic ascorbate peroxidase （APx2） and putative F-box protein were newly detected on 2-DE maps of WD-treated plants. We identified several proteins including agamous-like 65, albumin b-32, inward rectifying potassium channel, and auxin-independent growth promoter. The identified proteins are involved in a variety of cellular functions including calcium signaling, abacisic acid （ABA） biosynthesis, reactive oxygen species （ROS） regulation, transcription/translation, antioxidant/detoxification/stress defense, energy metabolism, signal transduction, and storage. These results indicate the potential candidates were responsible for adaptive response in alfalfa roots.展开更多
Background:Immunological stress decreases feed intake,suppresses growth and induces economic losses.However,the underlying molecular mechanism remains unclear.Label-free liquid chromatography and mass spectrometry(LC-...Background:Immunological stress decreases feed intake,suppresses growth and induces economic losses.However,the underlying molecular mechanism remains unclear.Label-free liquid chromatography and mass spectrometry(LC-MS)proteomics techniques were employed to investigate effects of immune stress on the hepatic proteome changes of Arbor Acres broilers(Gallus Gallus domesticus)challenged with Escherichia coli lipopolysaccharide(LPS).Results:Proteomic analysis indicated that 111 proteins were differentially expressed in the liver of broiler chickens from the immune stress group.Of these,28 proteins were down-regulated,and 83 proteins were up-regulated in the immune stress group.Enrichment analysis showed that immune stress upregulated the expression of hepatic proteins involved in defense function,amino acid catabolism,ion transport,wound healing,and hormone secretion.Furthermore,immune stress increased valine,leucine and isoleucine degradation pathways.Conclusion:The data suggests that growth depression of broiler chickens induced by immune stress is triggered by hepatic proteome alterations,and provides a new insight into the mechanism by which immune challenge impairs poultry production.展开更多
Objective： To establish the two-dimensional electrophoresis profiles with high resolution and reproducibility from human lung squamous carcinoma tissue and paired normal tumor-adjacent bronchial epithelial tissue, an...Objective： To establish the two-dimensional electrophoresis profiles with high resolution and reproducibility from human lung squamous carcinoma tissue and paired normal tumor-adjacent bronchial epithelial tissue, and to identify differential expression tumor-associated proteins by using proteome analysis. Methods： Comparative proteome analysis with 20 human lung squamous carcinoma tissues and the paired normal bronchial epithelial tissues adjacent to tumors was carried out. The total proteins of human lung squamous carcinoma tissue and paired normal tumor-adjacent bronchial epithelial tissue were separated by means of immobilized pH gradient-based two-dimensional gel electrophoresis （2-DE） and silver staining. The differential expression proteins were analyzed and then identified by matrix-assisted laser desorption/ionization time of flight mass spectrometry （MALDI-TOF-MS）. Results： （1） Well-resolved, reproducible 2-DE patterns of human lung squamous carcinoma and adjacent normal bronchial epithelial tissues were obtained. For tumor tissue, average spots of 3 gels were 1567±46, and 1436±54 spots were matched with an average matching rate of 91.6%. For control, average spots of 3 gels were 1349±58, and 1228±35 spots were matched with an average matching rate of 91.03%. The average position deviation of matched spots was 0.924±0.128 mm in IEF direction, and 1.022±0.205 mm in SDS-PAGE direction; （2） A total of 1178±56 spots were matched between the eleetrophoretie maps of 20 human lung squamous carcinoma tissues and paired normal tumor-adjacent bronchial epithelial tissues. Seventy-six differentially expressed proteins were screened; （3） Sixty-eight differential proteins were identified by PMF, some proteins were the products of oneogenes, and others involved in the regulation of cell cycle and signal transduetion; （4） In order to validate the reliability of the identified results, the expression of 3 proteins mdm2, c-jun and EGFR, which was correlated with lung squamous carcinoma, was detected by immunohistoehemieal staining and Western blot analysis. The results revealed that mdm2, c-jun and EGFR were up-regulated in lung squamous carcinomas, whereas they were down-regulated in adjacent normal bronchial epithelial tissues, normal lung tissues and inflammatory pseudotumor, which was consistent with our proteome analysis results. Conclusion： The well-resolved, reproducible 2-DE patterns of human lung squamous carcinoma and adjacent normal bronchial epithelial tissues were established and 68 differential proteins were characterized by applying comparative proteome analysis successfully. These results will provide scientific foundation for screening the molecular biomarker used to diagnose and treat lung squamous carcinoma, as well as to improve the patient＇s prognosis and provide new clue for the research of lung squamous carcinogenic mechanism.展开更多
The inhibitory effect of gadolinium on Sinorhizobium fredii USDA 205 was studied on a global scale using twodimensional gel electrophoresis and MALDI-TOF MS. The results indicated that 22 proteins were significantly a...The inhibitory effect of gadolinium on Sinorhizobium fredii USDA 205 was studied on a global scale using twodimensional gel electrophoresis and MALDI-TOF MS. The results indicated that 22 proteins were significantly affected by 1 mmol · L^-1 Gd^3 ＋ treatment when compared with an untreated control. Among these proteins, nine were up-regulated and thirteen were down-regulated. The differently expressed proteins were classified into 8 functional categories based on their functions, including transporters, proteins for cellular defence, and proteins involved in metabolism.展开更多
OBJECTIVE:To evaluate the extent of vascular endothelial dysfunction and preliminary identify serum protein biomarkers associated with obese individuals at risk for cardiovascular disease(CVD).METHODS:Fifteen obese vo...OBJECTIVE:To evaluate the extent of vascular endothelial dysfunction and preliminary identify serum protein biomarkers associated with obese individuals at risk for cardiovascular disease(CVD).METHODS:Fifteen obese volunteers with the phlegmdampness constitution or balanced constitution were recruited for this study respectively.The clinical baseline data was collected,and the vascular endothelial function was evaluated using the EndoPAT?.Blood samples were collected for the serum proteome analysis.The differences in the serum protein expression levels between the two groups were detected and the protein interaction network analysis,correlation analysis,receiver operating characteristic(ROC)curve analysis,and random forest model investigation were conducted.RESULTS:There were no statistical differences found in the baseline data.For vascular endothelial function,the reactive hyperemia index(RHI)of the phlegm-dampness constitution obese group was significantly lower than that of the balanced constitution obese group(1.46±0.30 vs 2.82±0.78,P<0.0001),indicating vascular endothelial dysfunction.There are 66 differentially expressed serum proteins between the two groups.apolipoprotein A2(Apo A2),angiotensin-converting enzyme 2(ACE-2),interleukin-33(IL-33),and forkhead box P3(FoxP3)showed significant differences and area under curve values of their ROC curves were greater than 0.7 and correlated significantly with RHI.CONCLUSION:Vascular endothelial dysfunction was present in the phlegm-dampness constitution obese group.Thus,alterations in the expression levels of key serum proteins,including Apo A2,ACE-2,IL-33,and Fox P3 could serve as potential biomarkers in the obese population at risk of CVD.展开更多
Strain EDP3 was isolated from an industrial-activated sludge. It belonged to the gamma group of Pro-teobacteria with an identity of 97.0% to Acinetobacter calcoaceticus according to the 16S rRNA gene sequences. It can...Strain EDP3 was isolated from an industrial-activated sludge. It belonged to the gamma group of Pro-teobacteria with an identity of 97.0% to Acinetobacter calcoaceticus according to the 16S rRNA gene sequences. It can tolerate up to 1000mg·L^-1 phenol at room temperature with a much longer lag phase. This indicates that higher phenol concentration has induced some physiological and genotypic changes in the bacterium. The aim of this study is, therefore, to investigate these responses to phenol concentration variations in strain EDP3. Proteome analysis is conducted by means of a two-dimensional polyacrylamide gel electrophoresis （2D PAGE） and matrix-assisted laser desorption ionization time of flight mass spectrometry （MALDI-TOF-MS） was conducted to obtain a deeper insight into the adaptive responses inside the bacterium. Comparative analysis of the proteome profiles of strain EDP3. grown in 400mg·L^-1 and 1000mg·L^-1 phenol allowed us to identify that among all the proteins up-regulated under the higher phenol concentration, oxidative stress proteins were dominant. The synthesis of a heat shock protein, 60000 chaperonin GroEL, was also amplified. In addition, the expression of one membrane protein, adenosine 5＇-triphosphate （ATP）-binding cassette （ABC） type sugar transporter, was found up-regulated. The inhibition of adenosine 5＇-triphosphate （ATP） and RNA/protein synthesis was also observed.展开更多
Bryum argenteum Hedw. is a desiccation tolerant bryophyte and belongs to one of the most important components of the biological soil crusts （BSCs） found in the deserts of Central Asia. Limited information is availab...Bryum argenteum Hedw. is a desiccation tolerant bryophyte and belongs to one of the most important components of the biological soil crusts （BSCs） found in the deserts of Central Asia. Limited information is available on rehydration-responsive proteins in desiccation tolerant plants. As a complement to our previous research analyzing the rehydration transcriptome, we present a parallel quantitative proteomic effort to study rehydration-responsive proteins. Bryophyte gametophores were desiccated （Dry） and rehydrated for 2 h （R2） and 24 h （R24）. Proteins from Dry, R2 and R24 gametophores were labeled by isobaric tags for relative and absolute quantitation （iTRAQ） to determine the relative abundance of rehydration-responsive proteins. A total of 5503 non-redundant protein sequences were identified and 4772 （86.7%） protein sequences were annotated using Gene Ontology （GO） terms and Pfam classifications. Upon rehydration 239 proteins were elevated and 461 proteins were reduced as compared to the desiccated protein sample. Differentially up-regulated proteins were classified into a number of categories including reactive oxygen species scavenging enzymes, detoxifying enzymes, Late Embryogenesis Abundant （LEA） proteins, heat shock proteins, proteasome components and proteases, and photosynthesis and translation related proteins. Furthermore, the results of the correlation between transcriptome and proteome revealed the discordant changes in the expression between protein and mRNA.展开更多
This study is to compare the protein composition of the high royal jelly producing bee （A. m. ligustica） with that of Carniolian bee （A. m. carnica） during their worker larval developmental stage. The experiment w...This study is to compare the protein composition of the high royal jelly producing bee （A. m. ligustica） with that of Carniolian bee （A. m. carnica） during their worker larval developmental stage. The experiment was carried out by two- dimensional gel electrophoresis. The results showed that significant higher numbers of total proteins （283） were detected in larvae of high royal jelly producing bees （Jelly bee） than those of Carniolian bees （152） on 2-d-old larvae. Among them, 110 proteins were presented on both strains of bee larvae, whereas 173 proteins were specific to larvae of Jelly bees, and 42 proteins were exclusive to Carniolian larvae. However, on the 4th d, a significant higher number of total proteins （290） were detected in larvae of Jelly bees than those of Carniolian bees （240）, 163 proteins resolved to both bee larvae, and 127 proteins were specific to Jelly bees and 77 proteins to Camiolian bees. Until the 6th d, also a significant higher number of total proteins （236） were detected in larvae of Jelly bees than those of Carniolian bees （180）, 132 proteins were constantly expressed in two bee larvae, whereas 104 and 48 proteins are unique to Jelly bee and Carniolian bee larvae, respectively. We tentatively concluded that the metabolic rate and gene expression of Jelly bees larvae is higher than those of Carniolian bees based proteins detected as total proteins and proteins specific to each stage of two strains of bee larvae. Proteins constantly expressed on 3 stages of larval development with some significant differences between two bee strains, and proteins unique to each stage expressed differences in term of quality and quantity, indicating that larval development needed house keeping and specific proteins to regulate its growth at different development phage, but the expression mold is different between two strains of larval development.展开更多
The large yellow croaker(Larimichthys crocea)is an important mariculture fish in China.Farmed large yellow croaker undergo periods of fasting to adapt to the environment or to improve meat quality.To better understand...The large yellow croaker(Larimichthys crocea)is an important mariculture fish in China.Farmed large yellow croaker undergo periods of fasting to adapt to the environment or to improve meat quality.To better understand the physiological responses of their muscle tissues to fasting stresses,we analyzed the transcriptomes and proteome s of both normally-fed and fasting fish groups and identified 7578 differentially expressed genes(DEGs)and 297 differentially expressed proteins(DEPs)among them.Gene ontology and KEGG analysis showed that the enriched biological pathways were mainly involved in various synthetic and catabolic pathways,especially the protein metabolism.Based on the omics data,nine DEGs related to muscle composition(CAN3,MYL3,and TNNC2),growth(MSTN and MYF5),autophagy(TSC2 and ULK1),and the ubiquitin proteasome pathway(PRS6 B and UCHL3)were examined using qPCR.In response to fasting stress,MYL3 and TNNC2 were significantly downregulated,while genes associated with autophagy and the ubiquitin proteasome pathway were significantly upregulated.In re sponse to fasting stres s,MYL3,TNNC2,and MYF5 positively correlated with muscle growth were significantly downregulated,while inhibiting growth MSTN and genes associated with autophagy and the ubiquitin proteasome pathways were significantly upregulated.These results clarify the effects of fasting on metabolic changes in their muscle components and growth at the molecular level.展开更多
Objective： To investigate the pathogenic properties of Helicobacterpylori by comparing the proteome map of H. pylori clinical strains. Methods： Two wild-type H. pylori strains, YN8 （isolated from biopsy tissue of a...Objective： To investigate the pathogenic properties of Helicobacterpylori by comparing the proteome map of H. pylori clinical strains. Methods： Two wild-type H. pylori strains, YN8 （isolated from biopsy tissue of a gastric cancer patient） and YN14 （isolated from biopsy tissue of a gastritis and duodenal ulcer patient）, were used. Proteomic analysis, using a pH range of 3-10 and 5-8, was performed. The individual proteins were identified by quadrupole time-of-flight （Q-TOF） mass spectrometer and protein database search. Results： Variation in spot patterns directed towards differential protein expression levels was observed between the strains. The gel revealed prominent proteins with several protein ＂families＂. The comparison of protein expressions of the two strains reveals a high variability. Differentially present or absent spots were observed. Nine differentially expressed protein spots identified by Q-TOF included adenosine triphosphate （ATP）-binding protein, disulfide oxidoreductase B （DsbB）-Iike protein, N utilization substance A （NusA）, ATP-dependent protease binding subunit/heat shock protein, hydantoin utilization protein A, seryl-tRNA synthetase, molybdenum ABC transporter ModD, and hypothetical proteins. Conclusions： This study suggests that H. pylori strains express/repress protein variation, not only in terms of the virulence proteins, but also in terms of physiological proteins, when they infect a human host. The difference of protein expression levels between H. pylori strains isolated from gastric cancer and gastritis may be the initiator of inflammation, and result in the different clinical presentation. In this preliminary study, we report seven differential proteins between strains, with molecule weights from approximately 10 kDa to approximately 40 kDa. Further studies are needed to investigate those proteins and their function associated with H. pylori colonization and adaptation to host environment stress.展开更多
Phosphorus(P) deficiency limits the growth,development,and productivity of rice.To better understand the underlying mechanisms in P-deficiency tolerance and the role of Pup1 QTL in enhancing P use efficiency(PUE) for ...Phosphorus(P) deficiency limits the growth,development,and productivity of rice.To better understand the underlying mechanisms in P-deficiency tolerance and the role of Pup1 QTL in enhancing P use efficiency(PUE) for the development of P-efficient rice cultivars,a pair of contrasting rice genotypes(Pusa-44 and NIL-23) was applied to investigate the morpho-physio-biochemical and proteomic variation under P-starvation stress.The rice genotypes were grown hydroponically in a PusaRich medium with adequate P(16 mg/kg,+P) or without P(0 mg/kg,-P) for 30 d.P-starvation manifested a significant reductions in root and shoot biomass,shoot length,leaf area,total chlorophyll,and P,nitrogen and starch contents,as well as protein kinase activity.The stress increased root-to-shoot biomass ratio,root length,sucrose content,and acid phosphatase activity,particularly in the P-tolerant genotype(NIL-23).Comparative proteome analysis revealed several P metabolism-associated proteins(including OsCDPKs,OsMAPKs,OsCPKs,OsLecRK2,and OsSAPks) to be expressed in the shoot of NIL-23,indicating that multiple protein kinases were involved in P-starvation/deficiency tolerance.Moreover,the up-regulated expression of OsrbcL,OsABCG32,OsSUS5,OsPoll-like B,and ClpC2 proteins in the shoot,and OsACA9,OsACA8,OsSPS2F,OsPP2C15,and OsBiP3 in the root of NIL-23,indicated their role in P-starvation stress control through the Pup1 QTL. Thus,our findings indicated that-P stress-responsive proteins,in conjunction with morpho-physio-biochemical modulations,improved PUE and made NIL-23 a P-deficiency tolerant genotype due to the introgression of the Pup1 QTL in the Pusa-44 background.展开更多
文摘Large-scale proteomics studies can refine our understanding of health and disease and enable precision medicine.Here,we provide a detailed atlas of 2,920 plasma proteins linking to diseases(406 prevalent and 660 incident)and 986 health-related traits in 53,026 individuals(median follow-up:14.8 years)from the UK Biobank,representing the most comprehensive proteome profiles to date.This atlas revealed 168,100 protein-disease associations and 554,488 protein-trait associations.Over 650 proteins were shared among at least 50 diseases,and over 1,000 showed sex and age heterogeneity.Furthermore,proteins demonstrated promising potential in disease discrimination(area under the curve[AUC]>0.80 in 183 diseases).Finally,integrating protein quantitative trait locus data determined 474 causal proteins,providing 37 drug-repurposing opportunities and 26 promising targets with favorable safety profiles.These results provide an open-access comprehensive proteome-phenome resource(https://proteome-phenome-atlas.com/)to help elucidate the biological mechanisms of diseases and accelerate the development of disease biomarkers,prediction models,and therapeutic targets.
基金Fujian Province Science and Technology Plan Project under contract No.2023N0011Xiamen Municipal Bureau of Marine Development Project under contract No.S24258。
文摘Cryptocaryon irritans is the parasite responsible for“white spot disease”in the yellowfin seabream Acanthopagrus latus,which has caused significant losses to the aquaculture industry.This experiment investigated the changes in the morphology,transcriptome,and proteome of gill tissue in yellowfin seabream infected with C.irritans,aiming to provide foundational data for further understanding the pathogenic mechanisms and control measures against this parasite.The main findings were as follows,after C.irritans infection,the structure of gill tissue in yellowfin seabream was damaged,with microvessels ruptured,some cells proliferating,and large amounts of mucus infiltrating.Transcriptome analysis revealed a total of 4299 differentially expressed genes,with 2367 up-regulated and 1932down-regulated.Further bioinformatics analysis of all differentially expressed genes identified nine immune-related genes,cox-2,mcama,tbx21,dcn,tnfb,cd74a,illb,ppib,and cd4-1 in A.latus.The reliability of the transcriptome data was validated by real time q PCR,which showed the same trend as the RNA-seq results.Proteome analysis found365 differential proteins,with 180 proteins up-regulated and 185 proteins down-regulated.Bioinformatics analysis identified three immune-related proteins,Myll,Gapdh,and Actn3b.These findings indicated that C.irritans disrupted the structure of gill tissue,impeded gas exchange and led to asphyxiation and death in affected fish.Transcriptome and proteome analyses showed that the expression of immune-related genes and proteins in yellowfin seabream,involved not only inflammatory responses and the activation and migration of immune cells but also potentially participated in tissue repair and defense regulation.These findings highlighted the complex immune regulatory network in response to C.irritans infection,offering references for prevention and control of white spot disease in yellowfin seabream.
基金supported by the National Natural Science Foundation of China(Grant No.32002113)the Natural Science Research Project of Jiangsu Higher Education Institutions(Grant No.19KJB210001)+7 种基金the Natural Science Foundation of Jiangsu Province(Grant No.BK20190958)the Key Research and Development Program of Zhejiang Province(Grant No.2021C02052)National Key Research and Development Program of China(Grant Nos.2018YFD1000800,2017YFE0114500)Zhejiang Provincial major Agricultural Science and Technology Projects of New Varieties Breeding(2021C02065)China Agriculture Research System of MOF and MARA(Grant No.CARS-23-G44)the Ministry of Science and Technology of the People’s Republic of China(Grant No.DL2022026004L)the National Natural Science Foundation of China(Grant No.31950410555)the Innovative Research Team(Science and Technology)in the University of Henan Province(Grant No.23IRTSTHN024).
文摘Soil cadmium pollution has increasingly become a serious problem for crop production,which drastically attenuates plant growth and food safety.Although N6-methyladenosine(m^(6)A)methylation is crucial for plant response to various stresses,the regulatory mechanism underlying m^(6)A modification during cadmium(Cd)stress remains unclear.This study investigated the physiological responses,transcriptome-wide m^(6)A methylome,and proteome changes in tomato roots exposed to 50 μmol·L^(-1)CdCl2.Excess Cd restricted plant growth,altered the antioxidant system and disrupted mineral nutrient absorption.We identified a negative correlation between m^(6)A levels and gene transcription for that 150 out of 198 differentially expressed genes(DEGs)were hypomethylated but mRNA up-regulated.Cd stress also enhanced translational efficiency,particularly for differentially abundant proteins(DAPs).Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis revealed that differentially m^(6)A modified genes(DMGs),DEGs,and DAPs were commonly enriched in phenylpropanoid biosynthesis,glutathione metabolism,and ABC transporters,reflecting cell wall barriers,chelation,and transport of Cd,respectively.Finally,we confirmed the Cd-transport activity of eight putative metal transporters identified in DMGs,DEGs,or DAPs by yeast complementaion experiments,and pharmacologically investigated the effect of m^(6)A modification on their expression.Treatment with the m^(6)A methylation inhibitor 3-deazaneplanocin A(3-DA)reduced SlIRT1/2 expression and increased SlNRAMP3/SlZIP4 expression,while the m^(6)A demethylase inhibitor meclofenamic acid(MA)treatment decreased SlNRAMP3 expression but elevated SlIRT2 expression under Cd stress.Our findings provide novel insights into the interplay between m^(6)A modification,transcription,and translation under Cd stress and the associated plant stress response.
基金Supported by National 863 Project(2010AA101503)National Science and Technology Support Planning Item(2006BAD05A12)Student Innovation Fund Item of Hefei University of Technology(XS2010100)~~
文摘[Objective] The research aimed to establish the two-dimensional electrophoresis（2-DE）technology which was suitable for the rapeseed proteome research.[Method] Xiangyou 17 was as the material.The sample preparation method,gel concentration and loading amount,etc.in 2-DE technology were optimized.[Result] The best extraction method of total protein of rapeseed was TCA-acetone method,and the protein spots on 2-DE map were the most.When IPG strip（pH 3-10）and 12% gel were used,and the loading amount was 250 μg,the two-dimensional electrophoresis map with the clear background,good repeatability and high protein spot resolution was obtained.[Conclusion] The research laid the foundation for carrying out the rapeseed proteomics research.
基金supported by Austrian Federal Ministry for Digital and Economic Affairsthe National Foundation for Research,Technology and Developmentsupported using resources of the Vet Core Facility(Mass Spectrometry)of the University of Veterinary Medicine Vienna。
文摘Background The objective was to characterize the colostrum proteome of primiparous Holstein cows in association with immunoglobulin G(IgG)content.Immediately after calving,colostrum samples were collected from 18 cows to measure IgG concentration.Based on colostrum IgG content,samples were classified through cluster analysis and were identified as poor,average,and excellent quality.The proteome was assessed with quantitative shotgun proteomics;abundance data were compared among the colostrum types;enrichment analysis of metabolic processes and proteins classes was performed as well.We also tested correlations between this proteome and blood globulin level of cows and passive immunity level of calves.Results On average,428 proteins were identified per sample,which belonged mainly to cellular process,biological regulation,response to stimulus,metabolic process,and immune system process.Most abundant proteins were complement C3(Q2UVX4),alpha-S1-casein(P02662),Ig-like domain-containing protein(A0A3Q1M032),albumin(A0A140T897),polymeric immunoglobulin receptor(P81265),lactotransferrrin(P24627),and IGHG1*01(X167014).Colostrum of excellent quality had greater(P<0.05)abundance of serpin A3-7(A2I7N3),complement factorl(A0A3Q1 MIF4),lipocalin/cytosolic fatty-acid binding domain-containing protein(A0A3Q1 MRQ2),complement C3(E1B805),complement component 4 binding protein alpha(A0AAF6ZHP5),and complement component C6(F1MM86).However,colostrum of excellent quality had lower(P<0.05)abundance of HGF activator(E1BCW0),alpha-S1-casein(P02662),and xanthine dehydrogenase/oxidase(P80457).This resulted in enrichment of the biological processes predominantly for complement activation alternative pathway,complement activation,complement activation classical pathway,humoral immune response,leukocyte mediated immunity,and negative regulation of endopeptidase activity in excellent-quality colostrum.Additionally,some colostrum proteins were found to be correlated with the blood globulin level of cows and with the passive immunity level of calves(P<0.05;r≥0.57).Conclusions This study provides new insights into the bovine colostrum proteome,demonstrating associations between IgG levels and the abundance of other proteins,as well as the enrichment of metabolic processes related to innate immune response.Thus,results suggest that the colostrum proteomic profile is associated with the content of IgG.Future research should deeply explore the association of these findings with pre-calving nutrition status and blood composition of the cow,and with passive immunity transfer to the calf.
文摘This manuscript examines the utility, utilizing the Ciphergen Protein Biosystem II, to develop a fingerprint for the diagnosis of prostate cancer. The investigators compared samples from control individuals as well as those with prostate cancer. In doing so, they utilize several chip platforms on which to examine the resulting
基金Supported by Medical Guidance Project of Shanghai Science Committee (No. 10411961800)Youth Science Fund of Fudan University (No. 08FQ49)
文摘AIM： To isolate and identify the biological characteristics of human colon cancer stem cells （SW1116 cells） and further study their proteome. METHODS： SW1116 cells were isolated and cultured with a serum-free medium （SFM）. Sphere formation was assayed to observe the formation of colon cancer stem cell spheres. SW1116 cells were inoculated into a serum-containing medium for observing their differentiation characteristics. Proliferation curve and cross-resistance of SWl116 cells to different drugs were detected by MTT. Percentage of SP cells in SW1116 cells was detected with Hoechst33342 staining. Telomerase activity in SW1116cells was checked by polymerase chain reaction （PCR）-enzyme linked immunosorbent assay. Expressions of stem cell relevant genes and proteins were detected by reverse transcription-PCR and Western blot, respectively. Total protein was isolated from SW1116 cells by two-dimensional gel electrophoresis （2-DE） and differentially expressed proteins were identified by tandem mass spectrometry （MALDI-TOF/TOF）. RESULTS： The isolated SW1116 cells presented as spheroid and suspension growths in SFM with a strong self-renewal, proliferation, differentiation and drug-resistance ability. The percentage of SP cells in SW1116 cells was 38.9%. The SW1116 cells co-expressed the CD133 and CD29 proteins. The telomerase activity in SW1116 cells was increased. The expressions of different stem cell relevant genes and proteins were detected. The proteomic analysis showed that the 26 protein spots were differently expressed in SW1116 cells and 10 protein spots were identified as ubiquitin fusion- degradation l-like protein, nuclear chloride channel protein, tubulin 13, Raichu404X, stratifin, F-actin cap- ping protein α-1 subunit, eukaryotic translation elongation factor 1 delta isoform 2, hypothetical protein, glyceraldehyde-3-phosphate dehydrogenase and guanine nucleotide binding protein 13 polypeptide 2-like 1, respectively. CONCLUSION： SW1116 cells are biologically characterized by self-renewal, proliferation and differentiation, and the differently expressed proteins in SW1116 cells may be essential for isolating cancer stem cells.
基金supported by grants from the National High-Tech R&D Program (Nos.2011AA100303,2013AA102506)the National Key Technology R&D Program(Nos.2011BAD19B01,2011BAD19B03,2011BAD19B04)
文摘Background： Early pregnancy failure has a profound impact on both human reproductive health and animal production. 2/3 pregnancy failures occur during the peri-implantation period; however, the underlying mechanism（s） remains unclear. Well-organized modification of the endometrium to a receptive state is critical to establish pregnancy Aberrant endometrial modification during implantation is thought to be largely responsible for early pregnancy loss. Result： In this study, using well-managed recipient ewes that received embryo transfer as model, we compared the endometrial proteome between pregnant and non-pregnant ewes during implantation period. After embryo transfer, recipients were assigned as pregnant or non-pregnant ewes according to the presence or absence of an elongated conceptus at Day 17 of pregnancy. By comparing the endometrial proteomic profiles between pregnant and non-pregnant ewes, we identified 94 and 257 differentially expressed proteins （DEPs） in the endometrial caruncular and intercaruncular areas, respectively. Functional analysis showed that the DEPs were mainly associated with immune response, nutrient transport and utilization, as well as proteasome-mediated proteolysis. Conclusion： These analysis imply that dysfunction of these biological processes or pathways of DEP in the endometrium is highly associated with early pregnancy loss. In addition, many proteins that are essential for the establishment of pregnancy showed dysregulation in the endometrium of non-pregnant ewes. These proteins, as potential candidates, may contribute to early pregnancy loss.
基金supported by the Natural Science Foundation of China[No:81470091]Beijing Municipal Administration of Hospitals Ascent Plan[DFL20151501]
文摘Objective To identify potential serum biomarkers for distinguishing between latent tuberculosis infection（LTBI） and active tuberculosis（TB）. Methods A proteome microarray containing 4,262 antigens was used for screening serum biomarkers of 40 serum samples from patients with LTBI and active TB at the systems level. The interaction network and functional classification of differentially expressed antigens were analyzed using STRING 10.0 and the TB database, respectively. Enzyme-linked immunosorbent assays（ELISA） were used to validate candidate antigens further using 279 samples. The diagnostic performances of candidate antigens were evaluated by receiver operating characteristic curve（ROC） analysis. Both antigen combination and logistic regression analysis were used to improve diagnostic ability. Results Microarray results showed that levels of 152 Mycobacterium tuberculosis（Mtb）-antigenspecific IgG were significantly higher in active TB patients than in LTBI patients（P 〈 0.05）, and these differentially expressed antigens showed stronger associations with each other and were involved in various biological processes. Eleven candidate antigens were further validated using ELISA and showed consistent results in microarray analysis. ROC analysis showed that antigens Rv2031 c, Rv1408, and Rv2421 c had higher areas under the curve（AUCs） of 0.8520, 0.8152, and 0.7970, respectively. In addition, both antigen combination and logistic regression analysis improved the diagnostic ability. Conclusion Several antigens have the potential to serve as serum biomarkers for discrimination between LTBI and active TB.
基金supported by the National Research Foundation of Korea (NRF) Grant (NRF-2011-616-F00013)supported by post-doctoral grantsupported by the scholarship from BK21Plus program, Ministry of Education, Republic of Korea
文摘To evaluate the response of alfalfa to water deficit （WD） stress, WD-induced candidates were investigated through a proteomic approach. Alfalfa seedlings were exposed to WD stress for 12 and 15 days respectively, followed by 3 days re-watering. Water deficit increased H202 content, lipid peroxidation, DPPH （1,1-diphenyl-2-picrylhydrazyl）-radical scavenging activity, and the free proline level in alfalfa roots. Root proteins were extracted and separated by two-dimentional polyacrylamide gel electrophoresis （2-DE）. A total of 49 WD-responsive proteins were identified in alfalfa roots; 25 proteins were reproducibly found to be up-regulated and 24 were down-regulated. Two proteins, namely cytosolic ascorbate peroxidase （APx2） and putative F-box protein were newly detected on 2-DE maps of WD-treated plants. We identified several proteins including agamous-like 65, albumin b-32, inward rectifying potassium channel, and auxin-independent growth promoter. The identified proteins are involved in a variety of cellular functions including calcium signaling, abacisic acid （ABA） biosynthesis, reactive oxygen species （ROS） regulation, transcription/translation, antioxidant/detoxification/stress defense, energy metabolism, signal transduction, and storage. These results indicate the potential candidates were responsible for adaptive response in alfalfa roots.
基金Sponsored by National Natural Science Foundation of China(grant no.31101731)National Key Research and Development Program of China(No.2018YFD0500600)The Agricultural Science and Technology Innovation Program(ASTIP).
文摘Background:Immunological stress decreases feed intake,suppresses growth and induces economic losses.However,the underlying molecular mechanism remains unclear.Label-free liquid chromatography and mass spectrometry(LC-MS)proteomics techniques were employed to investigate effects of immune stress on the hepatic proteome changes of Arbor Acres broilers(Gallus Gallus domesticus)challenged with Escherichia coli lipopolysaccharide(LPS).Results:Proteomic analysis indicated that 111 proteins were differentially expressed in the liver of broiler chickens from the immune stress group.Of these,28 proteins were down-regulated,and 83 proteins were up-regulated in the immune stress group.Enrichment analysis showed that immune stress upregulated the expression of hepatic proteins involved in defense function,amino acid catabolism,ion transport,wound healing,and hormone secretion.Furthermore,immune stress increased valine,leucine and isoleucine degradation pathways.Conclusion:The data suggests that growth depression of broiler chickens induced by immune stress is triggered by hepatic proteome alterations,and provides a new insight into the mechanism by which immune challenge impairs poultry production.
文摘Objective： To establish the two-dimensional electrophoresis profiles with high resolution and reproducibility from human lung squamous carcinoma tissue and paired normal tumor-adjacent bronchial epithelial tissue, and to identify differential expression tumor-associated proteins by using proteome analysis. Methods： Comparative proteome analysis with 20 human lung squamous carcinoma tissues and the paired normal bronchial epithelial tissues adjacent to tumors was carried out. The total proteins of human lung squamous carcinoma tissue and paired normal tumor-adjacent bronchial epithelial tissue were separated by means of immobilized pH gradient-based two-dimensional gel electrophoresis （2-DE） and silver staining. The differential expression proteins were analyzed and then identified by matrix-assisted laser desorption/ionization time of flight mass spectrometry （MALDI-TOF-MS）. Results： （1） Well-resolved, reproducible 2-DE patterns of human lung squamous carcinoma and adjacent normal bronchial epithelial tissues were obtained. For tumor tissue, average spots of 3 gels were 1567±46, and 1436±54 spots were matched with an average matching rate of 91.6%. For control, average spots of 3 gels were 1349±58, and 1228±35 spots were matched with an average matching rate of 91.03%. The average position deviation of matched spots was 0.924±0.128 mm in IEF direction, and 1.022±0.205 mm in SDS-PAGE direction; （2） A total of 1178±56 spots were matched between the eleetrophoretie maps of 20 human lung squamous carcinoma tissues and paired normal tumor-adjacent bronchial epithelial tissues. Seventy-six differentially expressed proteins were screened; （3） Sixty-eight differential proteins were identified by PMF, some proteins were the products of oneogenes, and others involved in the regulation of cell cycle and signal transduetion; （4） In order to validate the reliability of the identified results, the expression of 3 proteins mdm2, c-jun and EGFR, which was correlated with lung squamous carcinoma, was detected by immunohistoehemieal staining and Western blot analysis. The results revealed that mdm2, c-jun and EGFR were up-regulated in lung squamous carcinomas, whereas they were down-regulated in adjacent normal bronchial epithelial tissues, normal lung tissues and inflammatory pseudotumor, which was consistent with our proteome analysis results. Conclusion： The well-resolved, reproducible 2-DE patterns of human lung squamous carcinoma and adjacent normal bronchial epithelial tissues were established and 68 differential proteins were characterized by applying comparative proteome analysis successfully. These results will provide scientific foundation for screening the molecular biomarker used to diagnose and treat lung squamous carcinoma, as well as to improve the patient＇s prognosis and provide new clue for the research of lung squamous carcinogenic mechanism.
基金Project supported by the National Natural Science Foundation of China (G2001CB108902 ,2004CB418506)
文摘The inhibitory effect of gadolinium on Sinorhizobium fredii USDA 205 was studied on a global scale using twodimensional gel electrophoresis and MALDI-TOF MS. The results indicated that 22 proteins were significantly affected by 1 mmol · L^-1 Gd^3 ＋ treatment when compared with an untreated control. Among these proteins, nine were up-regulated and thirteen were down-regulated. The differently expressed proteins were classified into 8 functional categories based on their functions, including transporters, proteins for cellular defence, and proteins involved in metabolism.
基金Supported by General Program of National Natural Science of China:Qigui Slimming Prescription Upgrades the Activating Ability of the Phlegm-Dampness Constitution to Improve Obesity by Regulating the Thermogenesis Axis of Clostridium Enterica-PhytosphingosineSph K/S1P-Ca^(2+) Cycle(No.82374308)National Key Research and Development Program:Development of Dietary Intervention Series for the Elderly with Decreased Functionality(No.2022YFC2010104)National Nonprofit Institute Research Grant for Institute of Basic Theory for Chinese Medicine,CACMS:Methylation of Gut Microbiota-Host DNA Reveals the Mechanism of Promoting PhlegmDampness Constitution to Prevent Metabolic Diseases(No.YZ-202151)。
文摘OBJECTIVE:To evaluate the extent of vascular endothelial dysfunction and preliminary identify serum protein biomarkers associated with obese individuals at risk for cardiovascular disease(CVD).METHODS:Fifteen obese volunteers with the phlegmdampness constitution or balanced constitution were recruited for this study respectively.The clinical baseline data was collected,and the vascular endothelial function was evaluated using the EndoPAT?.Blood samples were collected for the serum proteome analysis.The differences in the serum protein expression levels between the two groups were detected and the protein interaction network analysis,correlation analysis,receiver operating characteristic(ROC)curve analysis,and random forest model investigation were conducted.RESULTS:There were no statistical differences found in the baseline data.For vascular endothelial function,the reactive hyperemia index(RHI)of the phlegm-dampness constitution obese group was significantly lower than that of the balanced constitution obese group(1.46±0.30 vs 2.82±0.78,P<0.0001),indicating vascular endothelial dysfunction.There are 66 differentially expressed serum proteins between the two groups.apolipoprotein A2(Apo A2),angiotensin-converting enzyme 2(ACE-2),interleukin-33(IL-33),and forkhead box P3(FoxP3)showed significant differences and area under curve values of their ROC curves were greater than 0.7 and correlated significantly with RHI.CONCLUSION:Vascular endothelial dysfunction was present in the phlegm-dampness constitution obese group.Thus,alterations in the expression levels of key serum proteins,including Apo A2,ACE-2,IL-33,and Fox P3 could serve as potential biomarkers in the obese population at risk of CVD.
文摘Strain EDP3 was isolated from an industrial-activated sludge. It belonged to the gamma group of Pro-teobacteria with an identity of 97.0% to Acinetobacter calcoaceticus according to the 16S rRNA gene sequences. It can tolerate up to 1000mg·L^-1 phenol at room temperature with a much longer lag phase. This indicates that higher phenol concentration has induced some physiological and genotypic changes in the bacterium. The aim of this study is, therefore, to investigate these responses to phenol concentration variations in strain EDP3. Proteome analysis is conducted by means of a two-dimensional polyacrylamide gel electrophoresis （2D PAGE） and matrix-assisted laser desorption ionization time of flight mass spectrometry （MALDI-TOF-MS） was conducted to obtain a deeper insight into the adaptive responses inside the bacterium. Comparative analysis of the proteome profiles of strain EDP3. grown in 400mg·L^-1 and 1000mg·L^-1 phenol allowed us to identify that among all the proteins up-regulated under the higher phenol concentration, oxidative stress proteins were dominant. The synthesis of a heat shock protein, 60000 chaperonin GroEL, was also amplified. In addition, the expression of one membrane protein, adenosine 5＇-triphosphate （ATP）-binding cassette （ABC） type sugar transporter, was found up-regulated. The inhibition of adenosine 5＇-triphosphate （ATP） and RNA/protein synthesis was also observed.
基金supported by the Scientific Service Project of Chinese Academy of Sciences (TSS-2015-014-FW-4-3)the National Science Foundation of China-Xinjiang Talent Youth Project (U1403302)
文摘Bryum argenteum Hedw. is a desiccation tolerant bryophyte and belongs to one of the most important components of the biological soil crusts （BSCs） found in the deserts of Central Asia. Limited information is available on rehydration-responsive proteins in desiccation tolerant plants. As a complement to our previous research analyzing the rehydration transcriptome, we present a parallel quantitative proteomic effort to study rehydration-responsive proteins. Bryophyte gametophores were desiccated （Dry） and rehydrated for 2 h （R2） and 24 h （R24）. Proteins from Dry, R2 and R24 gametophores were labeled by isobaric tags for relative and absolute quantitation （iTRAQ） to determine the relative abundance of rehydration-responsive proteins. A total of 5503 non-redundant protein sequences were identified and 4772 （86.7%） protein sequences were annotated using Gene Ontology （GO） terms and Pfam classifications. Upon rehydration 239 proteins were elevated and 461 proteins were reduced as compared to the desiccated protein sample. Differentially up-regulated proteins were classified into a number of categories including reactive oxygen species scavenging enzymes, detoxifying enzymes, Late Embryogenesis Abundant （LEA） proteins, heat shock proteins, proteasome components and proteases, and photosynthesis and translation related proteins. Furthermore, the results of the correlation between transcriptome and proteome revealed the discordant changes in the expression between protein and mRNA.
基金supported by a special fund of Technical Production System of the National Beekeeping Industry,China (NYCYTX-43)the National Natural Science Foundation of China (30972148)Special Scientific and Research Found for Public Welfare Industry,China (nyhyzx07-041)
文摘This study is to compare the protein composition of the high royal jelly producing bee （A. m. ligustica） with that of Carniolian bee （A. m. carnica） during their worker larval developmental stage. The experiment was carried out by two- dimensional gel electrophoresis. The results showed that significant higher numbers of total proteins （283） were detected in larvae of high royal jelly producing bees （Jelly bee） than those of Carniolian bees （152） on 2-d-old larvae. Among them, 110 proteins were presented on both strains of bee larvae, whereas 173 proteins were specific to larvae of Jelly bees, and 42 proteins were exclusive to Carniolian larvae. However, on the 4th d, a significant higher number of total proteins （290） were detected in larvae of Jelly bees than those of Carniolian bees （240）, 163 proteins resolved to both bee larvae, and 127 proteins were specific to Jelly bees and 77 proteins to Camiolian bees. Until the 6th d, also a significant higher number of total proteins （236） were detected in larvae of Jelly bees than those of Carniolian bees （180）, 132 proteins were constantly expressed in two bee larvae, whereas 104 and 48 proteins are unique to Jelly bee and Carniolian bee larvae, respectively. We tentatively concluded that the metabolic rate and gene expression of Jelly bees larvae is higher than those of Carniolian bees based proteins detected as total proteins and proteins specific to each stage of two strains of bee larvae. Proteins constantly expressed on 3 stages of larval development with some significant differences between two bee strains, and proteins unique to each stage expressed differences in term of quality and quantity, indicating that larval development needed house keeping and specific proteins to regulate its growth at different development phage, but the expression mold is different between two strains of larval development.
基金the Agricultural Major Project of Ningbo Municipality(No.2015 C110005)the K.C.Wong Magna Fund in Ningbo University。
文摘The large yellow croaker(Larimichthys crocea)is an important mariculture fish in China.Farmed large yellow croaker undergo periods of fasting to adapt to the environment or to improve meat quality.To better understand the physiological responses of their muscle tissues to fasting stresses,we analyzed the transcriptomes and proteome s of both normally-fed and fasting fish groups and identified 7578 differentially expressed genes(DEGs)and 297 differentially expressed proteins(DEPs)among them.Gene ontology and KEGG analysis showed that the enriched biological pathways were mainly involved in various synthetic and catabolic pathways,especially the protein metabolism.Based on the omics data,nine DEGs related to muscle composition(CAN3,MYL3,and TNNC2),growth(MSTN and MYF5),autophagy(TSC2 and ULK1),and the ubiquitin proteasome pathway(PRS6 B and UCHL3)were examined using qPCR.In response to fasting stress,MYL3 and TNNC2 were significantly downregulated,while genes associated with autophagy and the ubiquitin proteasome pathway were significantly upregulated.In re sponse to fasting stres s,MYL3,TNNC2,and MYF5 positively correlated with muscle growth were significantly downregulated,while inhibiting growth MSTN and genes associated with autophagy and the ubiquitin proteasome pathways were significantly upregulated.These results clarify the effects of fasting on metabolic changes in their muscle components and growth at the molecular level.
基金supported by the National Natural Science Foundation of China (No. 30770980)the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry (2008)
文摘Objective： To investigate the pathogenic properties of Helicobacterpylori by comparing the proteome map of H. pylori clinical strains. Methods： Two wild-type H. pylori strains, YN8 （isolated from biopsy tissue of a gastric cancer patient） and YN14 （isolated from biopsy tissue of a gastritis and duodenal ulcer patient）, were used. Proteomic analysis, using a pH range of 3-10 and 5-8, was performed. The individual proteins were identified by quadrupole time-of-flight （Q-TOF） mass spectrometer and protein database search. Results： Variation in spot patterns directed towards differential protein expression levels was observed between the strains. The gel revealed prominent proteins with several protein ＂families＂. The comparison of protein expressions of the two strains reveals a high variability. Differentially present or absent spots were observed. Nine differentially expressed protein spots identified by Q-TOF included adenosine triphosphate （ATP）-binding protein, disulfide oxidoreductase B （DsbB）-Iike protein, N utilization substance A （NusA）, ATP-dependent protease binding subunit/heat shock protein, hydantoin utilization protein A, seryl-tRNA synthetase, molybdenum ABC transporter ModD, and hypothetical proteins. Conclusions： This study suggests that H. pylori strains express/repress protein variation, not only in terms of the virulence proteins, but also in terms of physiological proteins, when they infect a human host. The difference of protein expression levels between H. pylori strains isolated from gastric cancer and gastritis may be the initiator of inflammation, and result in the different clinical presentation. In this preliminary study, we report seven differential proteins between strains, with molecule weights from approximately 10 kDa to approximately 40 kDa. Further studies are needed to investigate those proteins and their function associated with H. pylori colonization and adaptation to host environment stress.
基金The study was funded by the financial support received from the Centre of Advanced Agricultural Science and Technology-National Agricultural Higher Education Project jointly funded by the World Bank and ICAR(Grant No.8776-IN-P151072).
文摘Phosphorus(P) deficiency limits the growth,development,and productivity of rice.To better understand the underlying mechanisms in P-deficiency tolerance and the role of Pup1 QTL in enhancing P use efficiency(PUE) for the development of P-efficient rice cultivars,a pair of contrasting rice genotypes(Pusa-44 and NIL-23) was applied to investigate the morpho-physio-biochemical and proteomic variation under P-starvation stress.The rice genotypes were grown hydroponically in a PusaRich medium with adequate P(16 mg/kg,+P) or without P(0 mg/kg,-P) for 30 d.P-starvation manifested a significant reductions in root and shoot biomass,shoot length,leaf area,total chlorophyll,and P,nitrogen and starch contents,as well as protein kinase activity.The stress increased root-to-shoot biomass ratio,root length,sucrose content,and acid phosphatase activity,particularly in the P-tolerant genotype(NIL-23).Comparative proteome analysis revealed several P metabolism-associated proteins(including OsCDPKs,OsMAPKs,OsCPKs,OsLecRK2,and OsSAPks) to be expressed in the shoot of NIL-23,indicating that multiple protein kinases were involved in P-starvation/deficiency tolerance.Moreover,the up-regulated expression of OsrbcL,OsABCG32,OsSUS5,OsPoll-like B,and ClpC2 proteins in the shoot,and OsACA9,OsACA8,OsSPS2F,OsPP2C15,and OsBiP3 in the root of NIL-23,indicated their role in P-starvation stress control through the Pup1 QTL. Thus,our findings indicated that-P stress-responsive proteins,in conjunction with morpho-physio-biochemical modulations,improved PUE and made NIL-23 a P-deficiency tolerant genotype due to the introgression of the Pup1 QTL in the Pusa-44 background.
