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
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
[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
Cognitive impairment is a particularly severe non-motor symptom of Parkinson's disease that significantly diminishes the quality of life of affected individuals.Identifying reliable biomarkers for cognitive impair...Cognitive impairment is a particularly severe non-motor symptom of Parkinson's disease that significantly diminishes the quality of life of affected individuals.Identifying reliable biomarkers for cognitive impairment in Parkinson's disease is essential for early diagnosis,prognostic assessments,and the development of targeted therapies.This review aims to summarize recent advancements in biofluid biomarkers for cognitive impairment in Parkinson's disease,focusing on the detection of specific proteins,metabolites,and other biomarkers in blood,cerebrospinal fluid,and saliva.These biomarkers can shed light on the multifaceted etiology of cognitive impairment in Parkinson's disease,which includes protein misfolding,neurodegeneration,inflammation,and oxidative stress.The integration of biofluid biomarkers with neuroimaging and clinical data can facilitate the development of predictive models to enhance early diagnosis and monitor the progression of cognitive impairment in patients with Parkinson's disease.This comprehensive approach can improve the existing understanding of the mechanisms driving cognitive decline and support the development of targeted therapeutic strategies aimed at modifying the course of cognitive impairment in Parkinson's disease.Despite the promise of these biomarkers in characterizing the mechanisms underlying cognitive decline in Parkinson's disease,further research is necessary to validate their clinical utility and establish a standardized framework for early detection and monitoring of cognitive impairment in Parkinson's disease.展开更多
Objective Urine is a promising biomarker source for clinical proteomics studies.Regional physiological differences are common in multi-center clinical studies.In this study,we investigate whether significant differenc...Objective Urine is a promising biomarker source for clinical proteomics studies.Regional physiological differences are common in multi-center clinical studies.In this study,we investigate whether significant differences are present in the urinary proteomes of individuals from different regions in China.Methods In this study,morning urine samples were collected from healthy urban residents in three regions of China(Haikou,Xi’an and Xining)and urinary proteins were preserved using a membrane-based method(Urimem).The urine proteomes of 27 normal samples were analyzed using LC-MS/MS and compared among three regions.Functional annotation of the differential proteins among the three areas was analyzed using the DAVID online database,and pathway enrichment of the differential urinary proteins was analyzed using KEGG.Results We identified 1898 proteins from Urimem samples using label-free proteome quantification,of which 56 urine proteins were differentially expressed among the three regions(P<0.05).Hierarchical clustering analysis showed that inter-regional differences caused less significant changes in the urine proteome than intersex differences.After gender stratification,16 differential proteins were identified in male samples and 84 differential proteins were identified in female samples.Among these differential proteins,several proteins have been previously reported as urinary disease biomarkers.Conclusions Urimem will facilitate urinary protein storage for large-scale urine sample collection.Regional differences are a confounding factor influencing the urine proteome and should be considered in future multicenter biomarker studies.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
Although the biochemical dissection of parasitoid-host interactions is becoming well characterized, the molecular knowledge concerning them is minimal. In order to understand the molecular bases of the host immune res...Although the biochemical dissection of parasitoid-host interactions is becoming well characterized, the molecular knowledge concerning them is minimal. In order to understand the molecular bases of the host immune response to parasitoid attack, we explored the response of Papilio xuthus parasitized by the endoparasitic wasp Pteromalus puparum using proteomic approach. By examining the differential expression of plasma proteins in the parasitized and unparasitized host pupae by two-dimensional (2D) electrophoresis, 16 proteins were found to vary in relation to parasitization compared with unparasitized control samples. All of them were submitted to identification by mass spectrometry coupled with a database search. The modulated proteins were found to fall into the following functional groups: humoral or cellular immunity, detoxification, energy metabolism, and others. This study contributes insights into the molecular mechanism of the relationships between parasitoids and their host insects.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
In order to improve beef color and color stability, step-chilling （SC） was applied on excised bovine Iongissimus lumborum muscle, with chilling starting at 0-4℃ for 5 h, then holding the temperature at 12-18℃ for ...In order to improve beef color and color stability, step-chilling （SC） was applied on excised bovine Iongissimus lumborum muscle, with chilling starting at 0-4℃ for 5 h, then holding the temperature at 12-18℃ for 6 h, followed by 0-4℃ again until 24 h post-mortem, pH and temperature were measured during rigor on SC loins as well as those subjected to routine chilling （RC, 0-4℃, till 24 h post-mortem）. Color L＊, a＊, b＊ values, metmyoglobin （MetMb） content, MetMb reducing ability （MRA） and NADH content were determined on samples aged for 1, 7, and 14 d. Sarcoplasmic proteome analysis was only conducted on d 1 samples. The results showed muscles subjected to SC maintained a temperature at around 15℃ for 5 to 10 h post-mortem, and exhibited a slow temperature decline, but rapid pH decline. Beef steaks treated with SC had higher L＊, a＊, b＊ and chroma values than those of RC samples at 1 and 7 d chilled storage （0-4℃）, while showing no significant difference for a＊, b＊ and chroma values at d 14. The SC samples also exhibited a lower relative content of surface MetMb, higher MRA and NADH content, compared with RC beef steaks during storage, indicating the SC-treated beef showed an improved color stability. Eleven differential protein spots/nine proteins were identified by two-dimensional gel electrophoresis and mass spectrometry, and those proteins were mainly involved in redox, chaperone binding, metabolic and peroxidase activity. Oxidoreductases play a role in decreasing the oxidation-induced myoglobin oxidation and benefiting the production of NADH, and finally improving the colour of beef. Of these, pyruvate dehydrogenase E1 component subunit beta showed a positive correlation with color L＊, a＊, b＊ values and accounted for more than 60% of the variation in color values; this protein can be considered as a potential beef color biomarker. The present study provided valuable information for studies on the molecular mechanism of color improvement from step-chilling, as well as for identifying markers associated with beef color.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
Parasitism by the endoparasitoid wasp Pteromalus puparum causes alterations in the plasma proteins of Pieris rapae. Analysis of plasma proteins using a proteomic approach showed that seven proteins were differentially...Parasitism by the endoparasitoid wasp Pteromalus puparum causes alterations in the plasma proteins of Pieris rapae. Analysis of plasma proteins using a proteomic approach showed that seven proteins were differentially expressed in the host pupae after 24-h parasitism. They were masquerade-like serine proteinase homolog (MSPH), enolase (Eno), bilin-binding protein (BBP), imaginal disc growth factor (IDGF), ornithine decarboxylase (ODC), cellular retinoic acid binding protein (CRABP), and one unknown function protein. The full length cDNA sequences of MSPH, Eno, and BBP were successfully cloned using rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis indicated that the transcript levels of MSPH and BBP in the fat bodies of host pupae were inducible in response to the parasitism and their variations were consistent with translational changes of these genes after parasitism, while the transcript levels of Eno and IDGF were not affected by parasitism. This study will contribute to the better understanding of the molecular bases of parasitoid-induced host alterations associated with innate immune responses, detoxification, and energy metabolism.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
The diploid species Brassica rapa （genome AA） and B. oleracea （genome CC） were compared by full-scale proteome analyses of seedling. A total of 28.2% of the proteins was common to both species, indicating the exis...The diploid species Brassica rapa （genome AA） and B. oleracea （genome CC） were compared by full-scale proteome analyses of seedling. A total of 28.2% of the proteins was common to both species, indicating the existence of a basal or ubiquitous proteome. However, a number of discriminating proteins （32.0%） and specific proteins （39.8%） of the Brassica A and C genomes, respectively, were identified, which could represent potentially species-specific functions. Based on these A or C genome-specific proteins, a number of PCR-based markers to distinguish B. rapa and B. oleracea species were also developed.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 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.
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 Applied Basic Research Foundation of Yunnan Province,Nos.202301AS070045,202101AY070001-115(to XY and BL)National Natural Science Foundation of China,No.81960242(to XY)。
文摘Cognitive impairment is a particularly severe non-motor symptom of Parkinson's disease that significantly diminishes the quality of life of affected individuals.Identifying reliable biomarkers for cognitive impairment in Parkinson's disease is essential for early diagnosis,prognostic assessments,and the development of targeted therapies.This review aims to summarize recent advancements in biofluid biomarkers for cognitive impairment in Parkinson's disease,focusing on the detection of specific proteins,metabolites,and other biomarkers in blood,cerebrospinal fluid,and saliva.These biomarkers can shed light on the multifaceted etiology of cognitive impairment in Parkinson's disease,which includes protein misfolding,neurodegeneration,inflammation,and oxidative stress.The integration of biofluid biomarkers with neuroimaging and clinical data can facilitate the development of predictive models to enhance early diagnosis and monitor the progression of cognitive impairment in patients with Parkinson's disease.This comprehensive approach can improve the existing understanding of the mechanisms driving cognitive decline and support the development of targeted therapeutic strategies aimed at modifying the course of cognitive impairment in Parkinson's disease.Despite the promise of these biomarkers in characterizing the mechanisms underlying cognitive decline in Parkinson's disease,further research is necessary to validate their clinical utility and establish a standardized framework for early detection and monitoring of cognitive impairment in Parkinson's disease.
基金supported by the Key Basic Research Program of the Ministry of Science and Technology of China(No.2013FY114100)the National Key Research and Development Program of China(No.2018YFC0910202,2016YFC1306300)+3 种基金the Beijing Natural Science Foundation(No.7172076)the Beijing Cooperative Construction Project(No.110651103)Beijing Normal University(No.11100704)Peking Union Medical College Hospital(2016-2.27)
文摘Objective Urine is a promising biomarker source for clinical proteomics studies.Regional physiological differences are common in multi-center clinical studies.In this study,we investigate whether significant differences are present in the urinary proteomes of individuals from different regions in China.Methods In this study,morning urine samples were collected from healthy urban residents in three regions of China(Haikou,Xi’an and Xining)and urinary proteins were preserved using a membrane-based method(Urimem).The urine proteomes of 27 normal samples were analyzed using LC-MS/MS and compared among three regions.Functional annotation of the differential proteins among the three areas was analyzed using the DAVID online database,and pathway enrichment of the differential urinary proteins was analyzed using KEGG.Results We identified 1898 proteins from Urimem samples using label-free proteome quantification,of which 56 urine proteins were differentially expressed among the three regions(P<0.05).Hierarchical clustering analysis showed that inter-regional differences caused less significant changes in the urine proteome than intersex differences.After gender stratification,16 differential proteins were identified in male samples and 84 differential proteins were identified in female samples.Among these differential proteins,several proteins have been previously reported as urinary disease biomarkers.Conclusions Urimem will facilitate urinary protein storage for large-scale urine sample collection.Regional differences are a confounding factor influencing the urine proteome and should be considered in future multicenter biomarker studies.
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.
基金Project supported by the National Basic Research Program (973) of China (No. 2006CB102005)the National Natural Science Foundation of China (Nos. 30571251 and 30170626)+1 种基金the Program for New Cen-tury Excellent Talents in University of the Ministry of Education of China (No. NCET-05-0513)the Innovation Research Team Program of the Ministry of Education of China (No. IRT0535)
文摘Although the biochemical dissection of parasitoid-host interactions is becoming well characterized, the molecular knowledge concerning them is minimal. In order to understand the molecular bases of the host immune response to parasitoid attack, we explored the response of Papilio xuthus parasitized by the endoparasitic wasp Pteromalus puparum using proteomic approach. By examining the differential expression of plasma proteins in the parasitized and unparasitized host pupae by two-dimensional (2D) electrophoresis, 16 proteins were found to vary in relation to parasitization compared with unparasitized control samples. All of them were submitted to identification by mass spectrometry coupled with a database search. The modulated proteins were found to fall into the following functional groups: humoral or cellular immunity, detoxification, energy metabolism, and others. This study contributes insights into the molecular mechanism of the relationships between parasitoids and their host insects.
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supported by the earmarked fund for the China Agriculture Research System(beef)(CARS-37)the Special Fund for Innovation Team of Modern Agricultural Industrial Technology System in Shandong Province,China(SDAIT-09-09)the Funds of Shandong“Double Tops”Program,China(SYL2017XTTD12)
文摘In order to improve beef color and color stability, step-chilling （SC） was applied on excised bovine Iongissimus lumborum muscle, with chilling starting at 0-4℃ for 5 h, then holding the temperature at 12-18℃ for 6 h, followed by 0-4℃ again until 24 h post-mortem, pH and temperature were measured during rigor on SC loins as well as those subjected to routine chilling （RC, 0-4℃, till 24 h post-mortem）. Color L＊, a＊, b＊ values, metmyoglobin （MetMb） content, MetMb reducing ability （MRA） and NADH content were determined on samples aged for 1, 7, and 14 d. Sarcoplasmic proteome analysis was only conducted on d 1 samples. The results showed muscles subjected to SC maintained a temperature at around 15℃ for 5 to 10 h post-mortem, and exhibited a slow temperature decline, but rapid pH decline. Beef steaks treated with SC had higher L＊, a＊, b＊ and chroma values than those of RC samples at 1 and 7 d chilled storage （0-4℃）, while showing no significant difference for a＊, b＊ and chroma values at d 14. The SC samples also exhibited a lower relative content of surface MetMb, higher MRA and NADH content, compared with RC beef steaks during storage, indicating the SC-treated beef showed an improved color stability. Eleven differential protein spots/nine proteins were identified by two-dimensional gel electrophoresis and mass spectrometry, and those proteins were mainly involved in redox, chaperone binding, metabolic and peroxidase activity. Oxidoreductases play a role in decreasing the oxidation-induced myoglobin oxidation and benefiting the production of NADH, and finally improving the colour of beef. Of these, pyruvate dehydrogenase E1 component subunit beta showed a positive correlation with color L＊, a＊, b＊ values and accounted for more than 60% of the variation in color values; this protein can be considered as a potential beef color biomarker. The present study provided valuable information for studies on the molecular mechanism of color improvement from step-chilling, as well as for identifying markers associated with beef color.
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 the National Basic Research Program (973) of China (No. 2006CB102005)the National Natural Science Foundation of China (Nos. 30571251 and 30971959)+1 种基金the Zhejiang Provincial Natural Science Foundation of China (No. Z3090191)and the Program for New Century Excellent Talents in University of the Ministry of Education of China (No. NCET-05-0513)
文摘Parasitism by the endoparasitoid wasp Pteromalus puparum causes alterations in the plasma proteins of Pieris rapae. Analysis of plasma proteins using a proteomic approach showed that seven proteins were differentially expressed in the host pupae after 24-h parasitism. They were masquerade-like serine proteinase homolog (MSPH), enolase (Eno), bilin-binding protein (BBP), imaginal disc growth factor (IDGF), ornithine decarboxylase (ODC), cellular retinoic acid binding protein (CRABP), and one unknown function protein. The full length cDNA sequences of MSPH, Eno, and BBP were successfully cloned using rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis indicated that the transcript levels of MSPH and BBP in the fat bodies of host pupae were inducible in response to the parasitism and their variations were consistent with translational changes of these genes after parasitism, while the transcript levels of Eno and IDGF were not affected by parasitism. This study will contribute to the better understanding of the molecular bases of parasitoid-induced host alterations associated with innate immune responses, detoxification, and energy metabolism.
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 National Natural Science Foundation of China(No.30671166 and 30971812)the National Key Project 973(No.2006CB101603)
文摘The diploid species Brassica rapa （genome AA） and B. oleracea （genome CC） were compared by full-scale proteome analyses of seedling. A total of 28.2% of the proteins was common to both species, indicating the existence of a basal or ubiquitous proteome. However, a number of discriminating proteins （32.0%） and specific proteins （39.8%） of the Brassica A and C genomes, respectively, were identified, which could represent potentially species-specific functions. Based on these A or C genome-specific proteins, a number of PCR-based markers to distinguish B. rapa and B. oleracea species were also developed.
