Tree peony(Paeonia suffruticosa Andrews)is a well-known ornamental plant with high economic value,but the short fluorescence is a key obstacle to its ornamental value and industry development.High temperature accelera...Tree peony(Paeonia suffruticosa Andrews)is a well-known ornamental plant with high economic value,but the short fluorescence is a key obstacle to its ornamental value and industry development.High temperature accelerates flower senescence and abscission,but the associated mechanisms are poorly understood.In this study,the tandem mass tag(TMT)proteome and label-free quantitative ubiquitome from tree peony cut flowers treated with 20℃for 0 h(RT0),20℃or 28℃for 60 h(RT60 or HT60)were examined based on morphological observation,respectively.Totally,6970 proteins and 1545 lysine ubiquitinated(Kub)sites in 844 proteins were identified.Hydrophilic residues(such as glutamate and aspartate)neighboring the Kub sites were in preference,and 36.01%of the Kub sites were located on the protein surface.The differentially expressed proteins(DEPs)and Kub-DEPs in HT60 vs RT60 were mainly enriched in ribosomal protein,protein biosynthesis,secondary metabolites biosynthesis,flavonoid metabolism,carbohydrate catabolism,and auxin biosynthesis and signaling revealed by GO and KEGG analysis,accompanying the increase of endogenous abscisic acid(ABA)accumulation and decrease of endogenous indoleacetic acid(IAA)level.Additionally,the expression patterns of six enzymes(SAMS,ACO,YUC,CHS,ANS and PFK)putatively with Kub modifications were analyzed by proteome and real-time quantitative RT-PCR.The cell-free degradation assays showed PsSAMS and PsACO proteins could be degraded via the 26 S proteasome system in tree peony flowers.Finally,a working model was proposed for the acceleration of flower senescence and abscission by high temperature.In summary,all results contributed to understanding the mechanism of flower senescence induced by high temperature and prolonging fluorescence in tree peony.展开更多
Muscle fibers are the main component of skeletal muscle and undergo maturation through the formation of myotubes.During early development,a population of skeletal muscle satellite cells(SSCs)proliferate into myoblasts...Muscle fibers are the main component of skeletal muscle and undergo maturation through the formation of myotubes.During early development,a population of skeletal muscle satellite cells(SSCs)proliferate into myoblasts.The myoblasts then undergo further differentiation and fusion events,leading to the development of myotubes.However,the mechanisms involved in the transition from SSCs to myotube formation remain unclear.In this study,we characterized changes in the proteomic and transcriptomic expression profiles of SSCs,myoblasts(differentiation for 2 d)and myotubes(differentiation for 10 d).Proteomic analysis identified SLMAP and STOM as potentially associated with myotube formation.In addition,some different changes in MyoD,MyoG,Myosin7 and Desmin occurred after silencing SLMAP and STOM,suggesting that they may affect changes in the myogenic marker.GO analysis indicated that the differentiation and migration factors SVIL,ENSCHIG00000026624(AQP1)and SERPINE1 enhanced the transition from SSCs to myoblasts,accompanied by changes in the apoptotic balance.In the myoblast vs.myotube group,candidates related to cell adhesion and signal transduction were highly expressed in the myotubes.Additionally,CCN2,TGFB1,MYL2 and MYL4 were identified as hub-candidates in this group.These data enhance our existing understanding of myotube formation during early development and repair.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
Background Spermatozoa interact with oviduct secretions before fertilization in vivo but the molecular players of this dialog and underlying dynamics remain largely unknown.Our objectives were to identify an exhaustiv...Background Spermatozoa interact with oviduct secretions before fertilization in vivo but the molecular players of this dialog and underlying dynamics remain largely unknown.Our objectives were to identify an exhaustive list of sperm-interacting proteins(SIPs)in the bovine oviduct fluid and to evaluate the impact of the oviduct anatomical region(isthmus vs.ampulla)and time relative to ovulation(pre-ovulatory vs.post-ovulatory)on SIPs number and abundance.Methods Pools of oviduct fluid(OF)from the pre-ovulatory ampulla,pre-ovulatory isthmus,post-ovulatory ampulla,and post-ovulatory isthmus in the side of ovulation were collected from the slaughterhouse.Frozen-thawed bull sperm were incubated with OF or phosphate-buffered saline(control)for 60 min at 38.5℃.After protein extraction and digestion,sperm and OF samples were analyzed by nanoLC-MS/MS and label-free protein quantification.Results A quantitative comparison between proteins identified in sperm and OF samples(2333 and 2471 proteins,respectively)allowed for the identification of 245 SIPs.The highest number(187)were found in the pre-ovulatory isthmus,i.e.,time and place of the sperm reservoir.In total,41 SIPs(17%)were differentially abundant between stages in a given region or between regions at a given stage and 76 SIPs(31%)were identified in only one region×stage condition.Functional analysis of SIPs predicted roles in cell response to stress,regulation of cell motility,fertilization,and early embryo development.Conclusion This study provides a comprehensive list of SIPs in the bovine oviduct and evidences dynamic spatiotemporal changes in sperm-oviduct interactions around ovulation time.Moreover,these data provide protein candidates to improve sperm conservation and in vitro fertilization media.展开更多
Staphylococcus aureus is a common marine foodborne pathogen.In this study,antibiotics ciprofloxacin and enrofloxacin were used to induce drug-resistance in S.aureus.The differentially expressed proteins(DEPs)were anal...Staphylococcus aureus is a common marine foodborne pathogen.In this study,antibiotics ciprofloxacin and enrofloxacin were used to induce drug-resistance in S.aureus.The differentially expressed proteins(DEPs)were analyzed and compared with those in the bacteria cultured without antibiotics.The primary proteomic alterations were in the levels of cell membrane components and proteins related to lysine and folic acid biosynthesis,which were all significantly up-regulated.The minimal inhibitory concentrations(MIC)for both test drugs were elevated to 10μg m L^(-1)following serial passaging.These results indicated that,for both ciprofloxacin and enrofloxacin,drug-resistance were developed even in the subinhibitory levels and the primary response was a major alteration in the cell membrane proteome.These changes were similar to those observed in S.aureus cultured with super-MIC levels of these antibiotics.The current study provides a theoretical basis for in-depth study of the related changes of marine foodborne pathogens in subinhibitory concentrations that are commonly found in situ.展开更多
Proteomic characterization of plasma is critical for the development of novel pharmacodynamic biomarkers.However,the vast dynamic range renders the profiling of proteomes extremely challenging.Here,we synthesized zeol...Proteomic characterization of plasma is critical for the development of novel pharmacodynamic biomarkers.However,the vast dynamic range renders the profiling of proteomes extremely challenging.Here,we synthesized zeolite NaY and developed a simple and rapid method to achieve comprehensive and deep profiling of the plasma proteome using the plasma protein corona formed on zeolite NaY.Specifically,zeolite NaY and plasma were co-incubated to form plasma protein corona on zeolite NaY(NaY-PPC),followed by conventional protein identification using liquid chromatography-tandem mass spectrometry.NaY was able to significantly enhance the detection of low-abundance plasma proteins,minimizing the“masking”effect caused by high-abundance proteins.The relative abundance of middleand low-abundance proteins increased substantially from 2.54%to 54.41%,and the top 20 highabundance proteins decreased from 83.63%to 25.77%.Notably,our method can quantify approximately 4000 plasma proteins with sensitivity up to pg/mL,compared to only about 600 proteins identified from untreated plasma samples.A pilot study based on plasma samples from 30 lung adenocarcinoma patients and 15 healthy subjects demonstrated that our method could successfully distinguish between healthy and disease states.In summary,this work provides an advantageous tool for the exploration of plasma proteomics and its translational applications.展开更多
Nitrogen(N)is one of the basic nutrients and signals for plant development and deficiency of it would always limit the productions of crops in the field.Quantitative research on expression of N-stress responsive prote...Nitrogen(N)is one of the basic nutrients and signals for plant development and deficiency of it would always limit the productions of crops in the field.Quantitative research on expression of N-stress responsive proteins on a proteome level remains elusive.In order to gain a deep insight into the proteins responding to nitrogen stress in rapeseed(Brassica napus L.),comparative proteomic analysis was performed to investigate changes of protein expression profiles from the root,stem and leaf under different N concentrations,respectively.More than 200 differential abundance proteins(DAPs)were detected and categorized into groups according to annotations,including“binding and catalytic activity”,“involved in primary metabolism and cellular processes”,“stress-response”and so on.Variation in chlorophyll(Chl)content and antioxidant activities further revealed that oxidative stress raised with the increase of N concentration.Bioinformatics analysis based on the expression level of total proteins suggested these DAPs might play important roles in adaptation to N-stress conditions.Generally,these results provides a new aspect into N-stress responding proteins in Brassica plants.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 protein peaks. In summary, these studies find a peak pattern that is able to distinguish the individuals with prostate cancer from those without the disease.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 screeni...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
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
In order to improve beef color and color stability,step-chilling(SC)was applied on excised bovine longissimus lumborum muscle,with chilling starting at 0–4℃ for 5 h,then holding the temperature at 12–18℃ for 6 h,f...In order to improve beef color and color stability,step-chilling(SC)was applied on excised bovine longissimus 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(MetM b)content,MetM b 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 MetM b,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
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 ...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
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
The phenomenon of sex dimorphism prevails among many fi sh species. It has attracted the general research interest due to its close relationship to fi sh growth and thus aquaculture productivity. In Chinese tongue sol...The phenomenon of sex dimorphism prevails among many fi sh species. It has attracted the general research interest due to its close relationship to fi sh growth and thus aquaculture productivity. In Chinese tongue sole ( Cynoglossus semilaevis ), 17β-estradiol (E2) can be used reportedly to induce the feminization of fi sh, although the detailed regulatory network remained elusive. We treated the tongue sole fry before sex diff erentiation with E2 (10 and 30 μg/L) to identify potential targets of E2 in Chinese tongue sole. The E2 treatment indeed induced genetic male fi sh sex-reversal to phenotypic female. Using an iTRAQ-based comparative proteomic analysis, 409 proteins that diff erentially expressed after E2 induction were identifi ed, including 259 up-regulated and 150 down-regulated proteins. Furthermore, 19 diff erentially expressed proteins identifi ed in the comparative proteomic analysis were selected to assess their transcription and eight of them exhibited the same tendency. Functions of the eight proteins included mainly nucleotide and protein binding. Interestingly, a far upstream element-binding protein 3-like isoform exhibited the signifi cant upregulation both at transcription and translation levels after E2 treatment. This work identifi ed a set of candidate proteins for E2 response and deepened our understanding of E2 regulatory mechanism.展开更多
Background:Implantation failure limits the success of in vitro fertilization and embryo transfer(IVF-ET).Wellorganized embryo-maternal crosstalk is essential for successful implantation.Previous studies mainly focused...Background:Implantation failure limits the success of in vitro fertilization and embryo transfer(IVF-ET).Wellorganized embryo-maternal crosstalk is essential for successful implantation.Previous studies mainly focused on the aberrant development of in vitro fertilized(IVF)embryos.In contrast,the mechanism of IVF-induced aberrant embryo-maternal crosstalk is not well defined.Results:In the present study,using ewes as the model,we profiled the proteome that features aberrant IVF embryo-maternal crosstalk following IVF-ET.By comparing in vivo(IVO)and IVF conceptuses,as well as matched endometrial caruncular(C)and intercaruncular(IC)areas,we filtered out 207,295,and 403 differentially expressed proteins(DEPs)in each comparison.Proteome functional analysis showed that the IVF conceptuses were characterized by the increased abundance of energy metabolism and proliferation-related proteins,and the decreased abundance of methyl metabolism-related proteins.In addition,IVF endometrial C areas showed the decreased abundance of endometrial remodeling and redox homeostasis-related proteins;while IC areas displayed the aberrant abundance of protein homeostasis and extracellular matrix(ECM)interaction-related proteins.Based on these observations,we propose a model depicting the disrupted embryo-maternal crosstalk following IVF-ET:Aberrant energy metabolism and redox homeostasis of IVF embryos,might lead to an aberrant endometrial response to conceptus-derived pregnancy signals,thus impairing maternal receptivity.In turn,the suboptimal uterine environment might stimulate a compensation effect of the IVF conceptuses,which was revealed as enhanced energy metabolism and over-proliferation.Conclusion:Systematic proteomic profiling provides insights to understand the mechanisms that underlie the aberrant IVF embryo-maternal crosstalk.This might be helpful to develop practical strategies to prevent implantation failure following IVF-ET.展开更多
Chronic denervation is one of the key factors that affect nerve regeneration.Chronic axotomy deteriorates the distal nerve stump,causes protein changes,and renders the microenvironment less permissive for regeneration...Chronic denervation is one of the key factors that affect nerve regeneration.Chronic axotomy deteriorates the distal nerve stump,causes protein changes,and renders the microenvironment less permissive for regeneration.Some of these factors/proteins have been individually studied.To better delineate the comprehensive protein expression profiles and identify proteins that contribute to or are associated with this detrimental effect,we carried out a proteomic analysis of the distal nerve using an established delayed rat sciatic nerve repair model.Four rats that received immediate repair after sciatic nerve transection served as control,whereas four rats in the experimental group(chronic denervation)had their sciatic nerve repaired after a 12-week delay.All the rats were sacrificed after 16 weeks to harvest the distal nerves for extracting proteins.Twenty-five micrograms of protein from each sample were fractionated in SDS-PAGE gels.NanoLC-MS/MS analysis was applied to the gels.Protein expression levels of nerves on the surgery side were compared to those on the contralateral side.Any protein with a P value of less than 0.05 and a fold change of 4 or higher was deemed differentially expressed.All the differentially expressed proteins in both groups were further stratified according to the biological processes.A PubMed search was also conducted to identify the differentially expressed proteins that have been reported to be either beneficial or detrimental to nerve regeneration.Ingenuity Pathway Analysis(IPA)software was used for pathway analysis.The results showed that 709 differentially expressed proteins were identified in the delayed repair group,with a bigger proportion of immune and inflammatory process-related proteins and a smaller proportion of proteins related to axon regeneration and lipid metabolism in comparison to the control group where 478 differentially expressed proteins were identified.The experimental group also had more beneficial proteins that were downregulated and more detrimental proteins that were upregulated.IPA revealed that protective pathways such as LXR/RXR,acute phase response,RAC,ERK/MAPK,CNTF,IL-6,and FGF signaling were inhibited in the delayed repair group,whereas three detrimental pathways,including the complement system,PTEN,and apoptosis signaling,were activated.An available database of the adult rodent sciatic nerve was used to assign protein changes to specific cell types.The poor regeneration seen in the delayed repair group could be associated with the down-regulation of beneficial proteins and up-regulation of detrimental proteins.The proteins and pathways identified in this study may offer clues for future studies to identify therapeutic targets.展开更多
Available reports have confirmed a link between bacterial infection and the progression of different types of cancers,including colon,lungs,and prostate cancer.Here we report the Chlamydia pneumonia proteins targeting...Available reports have confirmed a link between bacterial infection and the progression of different types of cancers,including colon,lungs,and prostate cancer.Here we report the Chlamydia pneumonia proteins targeting in endoplasmic reticulum(ER)using in-silico approaches and their possible role in lung cancer etiology.We predicted 48 proteins that target human ER,which may be associated with protein folding and protein-protein interactions during infection.The results showed C.pneumoniae proteins targeting human ER and their implications in lung cancer growth.These targeted proteins may be involved in competitive interactions between host and bacterial proteins,which may change the usual pathway functions and trigger the development of lung cancer.Moreover,C.pneumoniae unfolded protein accumulation in the human ER possibly induces ER stress,consequently activating the unfolded protein response(UPR),and providing a favorable microenvironment for cancer growth.The current study showed the C.pneumoniae protein targeting in ER of host cell and their implication in lung cancer growth.These results may help researchers better manage lung cancer and establish a molecular mechanism for C.pneumoniae lung cancer association.展开更多
Complement (C) activation-related hypersensitivity reactions (HSRs) represent an unsolved adverse immune effect of many i.v. administered “nanomedicines”, such as liposomal doxorubicin (Doxil/Caelyx). Because these ...Complement (C) activation-related hypersensitivity reactions (HSRs) represent an unsolved adverse immune effect of many i.v. administered “nanomedicines”, such as liposomal doxorubicin (Doxil/Caelyx). Because these pseudoallergic reactions can be severe or even lethal, it is an important clinical objective to find biomarkers for proneness for C activation by reactogenic nanoparticles that will allow the prediction of in vivo reactions by in vitro assays. With this goal in mind we identified a normal human blood donor who consistently showed high sensitivity to Caelyx-induced C activation in vitro, whose plasma (Caelyx sensitive plasma, CSP) was subjected to proteome profiling with a library of human plasma proteome specific mAbs. The chip (PlasmaScan-380TM) contained 380 non redundant (with respect to epitopes) mAbs. The analysis revealed 8 proteins that were differentially represented in CSP in comparison with Caelyx-insensitive control plasma. These proteins were identified by mass spectrometry and Western blot analyses to represent factor H (decreased in CSP), factor H related protein, serum amyloid P component, fibronectin, complement component C4, Apo B100, prothrombin and alpha-2-HS glycoprotein (all increased in CSP). Some of these protein changes are consistent with proneness for increased C activation, suggesting the potential use of this method in the search for biomarkers for liposome-induced or other types of nanomedicine-induced HSRs.展开更多
Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xin...Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.Results:Through transcriptome analysis in cotton leaves under salt stress for 0 h(T0),3 h(T3)and 12 h(T12),we identified 8436,11628 and 6311 differentially expressed genes(DEGs)in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.A total of 459 differentially expressed proteins(DEPs)were identified by proteomic analysis,of which 273,99 and 260 DEPs were identified in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.Metabolic pathways,biosynthesis of secondary metabolites,photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs.Detail analysis of the DEGs or DEPs revealed that complex signaling pathways,such as abscisic acid(ABA)and jasmonic acid(JA)signaling,calcium signaling,mitogen-activated protein kinase(MAPK)signaling cascade,transcription factors,activation of antioxidant and ion transporters,were participated in regulating salt response in cotton.Conclusions:Our research not only contributed to understand the mechanism of cotton response to salt stress,but also identified nine candidate genes,which might be useful for molecular breeding to improve salt-toleranee in cotton.展开更多
基金supported by National Natural Science Foundation of China(Grant Nos.32072614 and 31972452)Shandong Provincial Natural Science Foundation(Grant Nos.ZR2020MC146 and ZR2020QC160)Seed improvement project of Shandong Province(Grant No.2020LZGC011-1-4)。
文摘Tree peony(Paeonia suffruticosa Andrews)is a well-known ornamental plant with high economic value,but the short fluorescence is a key obstacle to its ornamental value and industry development.High temperature accelerates flower senescence and abscission,but the associated mechanisms are poorly understood.In this study,the tandem mass tag(TMT)proteome and label-free quantitative ubiquitome from tree peony cut flowers treated with 20℃for 0 h(RT0),20℃or 28℃for 60 h(RT60 or HT60)were examined based on morphological observation,respectively.Totally,6970 proteins and 1545 lysine ubiquitinated(Kub)sites in 844 proteins were identified.Hydrophilic residues(such as glutamate and aspartate)neighboring the Kub sites were in preference,and 36.01%of the Kub sites were located on the protein surface.The differentially expressed proteins(DEPs)and Kub-DEPs in HT60 vs RT60 were mainly enriched in ribosomal protein,protein biosynthesis,secondary metabolites biosynthesis,flavonoid metabolism,carbohydrate catabolism,and auxin biosynthesis and signaling revealed by GO and KEGG analysis,accompanying the increase of endogenous abscisic acid(ABA)accumulation and decrease of endogenous indoleacetic acid(IAA)level.Additionally,the expression patterns of six enzymes(SAMS,ACO,YUC,CHS,ANS and PFK)putatively with Kub modifications were analyzed by proteome and real-time quantitative RT-PCR.The cell-free degradation assays showed PsSAMS and PsACO proteins could be degraded via the 26 S proteasome system in tree peony flowers.Finally,a working model was proposed for the acceleration of flower senescence and abscission by high temperature.In summary,all results contributed to understanding the mechanism of flower senescence induced by high temperature and prolonging fluorescence in tree peony.
基金the National Natural Science Foundation of China(32172695)Natural Science Foundation of Anhui Province,China(2108085Y11)+1 种基金China Agriculture Research System(CARS-38)the Open Project of Anhui Key Laboratory of Embryonic Development and Reproductive Regulation,Anhui Provincial Department of Science and Technology,China(FSKFKT019D)。
文摘Muscle fibers are the main component of skeletal muscle and undergo maturation through the formation of myotubes.During early development,a population of skeletal muscle satellite cells(SSCs)proliferate into myoblasts.The myoblasts then undergo further differentiation and fusion events,leading to the development of myotubes.However,the mechanisms involved in the transition from SSCs to myotube formation remain unclear.In this study,we characterized changes in the proteomic and transcriptomic expression profiles of SSCs,myoblasts(differentiation for 2 d)and myotubes(differentiation for 10 d).Proteomic analysis identified SLMAP and STOM as potentially associated with myotube formation.In addition,some different changes in MyoD,MyoG,Myosin7 and Desmin occurred after silencing SLMAP and STOM,suggesting that they may affect changes in the myogenic marker.GO analysis indicated that the differentiation and migration factors SVIL,ENSCHIG00000026624(AQP1)and SERPINE1 enhanced the transition from SSCs to myoblasts,accompanied by changes in the apoptotic balance.In the myoblast vs.myotube group,candidates related to cell adhesion and signal transduction were highly expressed in the myotubes.Additionally,CCN2,TGFB1,MYL2 and MYL4 were identified as hub-candidates in this group.These data enhance our existing understanding of myotube formation during early development and repair.
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.
基金funded by INRAE and Agence Nationale de la Recherche under the grant number ANR-18-CE92-0049supported by grants from Biogenouest+1 种基金Infrastructures en Biologie Santéet Agronomie (IBiSA)Conseil Régional de Bretagne awarded to Protim proteomics core facility。
文摘Background Spermatozoa interact with oviduct secretions before fertilization in vivo but the molecular players of this dialog and underlying dynamics remain largely unknown.Our objectives were to identify an exhaustive list of sperm-interacting proteins(SIPs)in the bovine oviduct fluid and to evaluate the impact of the oviduct anatomical region(isthmus vs.ampulla)and time relative to ovulation(pre-ovulatory vs.post-ovulatory)on SIPs number and abundance.Methods Pools of oviduct fluid(OF)from the pre-ovulatory ampulla,pre-ovulatory isthmus,post-ovulatory ampulla,and post-ovulatory isthmus in the side of ovulation were collected from the slaughterhouse.Frozen-thawed bull sperm were incubated with OF or phosphate-buffered saline(control)for 60 min at 38.5℃.After protein extraction and digestion,sperm and OF samples were analyzed by nanoLC-MS/MS and label-free protein quantification.Results A quantitative comparison between proteins identified in sperm and OF samples(2333 and 2471 proteins,respectively)allowed for the identification of 245 SIPs.The highest number(187)were found in the pre-ovulatory isthmus,i.e.,time and place of the sperm reservoir.In total,41 SIPs(17%)were differentially abundant between stages in a given region or between regions at a given stage and 76 SIPs(31%)were identified in only one region×stage condition.Functional analysis of SIPs predicted roles in cell response to stress,regulation of cell motility,fertilization,and early embryo development.Conclusion This study provides a comprehensive list of SIPs in the bovine oviduct and evidences dynamic spatiotemporal changes in sperm-oviduct interactions around ovulation time.Moreover,these data provide protein candidates to improve sperm conservation and in vitro fertilization media.
基金funded by the Professional Innovation and Integration Project of Qingdao University(2020)。
文摘Staphylococcus aureus is a common marine foodborne pathogen.In this study,antibiotics ciprofloxacin and enrofloxacin were used to induce drug-resistance in S.aureus.The differentially expressed proteins(DEPs)were analyzed and compared with those in the bacteria cultured without antibiotics.The primary proteomic alterations were in the levels of cell membrane components and proteins related to lysine and folic acid biosynthesis,which were all significantly up-regulated.The minimal inhibitory concentrations(MIC)for both test drugs were elevated to 10μg m L^(-1)following serial passaging.These results indicated that,for both ciprofloxacin and enrofloxacin,drug-resistance were developed even in the subinhibitory levels and the primary response was a major alteration in the cell membrane proteome.These changes were similar to those observed in S.aureus cultured with super-MIC levels of these antibiotics.The current study provides a theoretical basis for in-depth study of the related changes of marine foodborne pathogens in subinhibitory concentrations that are commonly found in situ.
基金supported by the National Natural Science Foundation of China(Grant No:51773151)。
文摘Proteomic characterization of plasma is critical for the development of novel pharmacodynamic biomarkers.However,the vast dynamic range renders the profiling of proteomes extremely challenging.Here,we synthesized zeolite NaY and developed a simple and rapid method to achieve comprehensive and deep profiling of the plasma proteome using the plasma protein corona formed on zeolite NaY.Specifically,zeolite NaY and plasma were co-incubated to form plasma protein corona on zeolite NaY(NaY-PPC),followed by conventional protein identification using liquid chromatography-tandem mass spectrometry.NaY was able to significantly enhance the detection of low-abundance plasma proteins,minimizing the“masking”effect caused by high-abundance proteins.The relative abundance of middleand low-abundance proteins increased substantially from 2.54%to 54.41%,and the top 20 highabundance proteins decreased from 83.63%to 25.77%.Notably,our method can quantify approximately 4000 plasma proteins with sensitivity up to pg/mL,compared to only about 600 proteins identified from untreated plasma samples.A pilot study based on plasma samples from 30 lung adenocarcinoma patients and 15 healthy subjects demonstrated that our method could successfully distinguish between healthy and disease states.In summary,this work provides an advantageous tool for the exploration of plasma proteomics and its translational applications.
基金funded by Modern Agro-Industry Technology Research System of China(CARS-12)Independent Innovation Project of SAAS(2022ZZCX004)+5 种基金1+9 Open Competition Project of SAAS(1+9KJGG002,1+9KJGG001)the Accurate Identification Project of Crop Germplasm from Sichuan Provincial Finance DepartmentSichuan Science and Technology Program(2022ZDZX0015)Sichuan Crop Breeding Community(2021YFYZ0018)Disciplinary Construction Project for Modern Agriculture in SAAS(2021XKJS003)Chengdu Science and Technology Project(2021-YF09-00062-SN).
文摘Nitrogen(N)is one of the basic nutrients and signals for plant development and deficiency of it would always limit the productions of crops in the field.Quantitative research on expression of N-stress responsive proteins on a proteome level remains elusive.In order to gain a deep insight into the proteins responding to nitrogen stress in rapeseed(Brassica napus L.),comparative proteomic analysis was performed to investigate changes of protein expression profiles from the root,stem and leaf under different N concentrations,respectively.More than 200 differential abundance proteins(DAPs)were detected and categorized into groups according to annotations,including“binding and catalytic activity”,“involved in primary metabolism and cellular processes”,“stress-response”and so on.Variation in chlorophyll(Chl)content and antioxidant activities further revealed that oxidative stress raised with the increase of N concentration.Bioinformatics analysis based on the expression level of total proteins suggested these DAPs might play important roles in adaptation to N-stress conditions.Generally,these results provides a new aspect into N-stress responding proteins in Brassica plants.
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 protein peaks. In summary, these studies find a peak pattern that is able to distinguish the individuals with prostate cancer from those without the disease.
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 longissimus 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(MetM b)content,MetM b 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 MetM b,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 Natural Science Foundation of Shandong Province(No.ZR2014CQ053)the National Natural Science Foundation of China(No.31402293)the Taishan Scholar Climbing Program of Shandong Province,China
文摘The phenomenon of sex dimorphism prevails among many fi sh species. It has attracted the general research interest due to its close relationship to fi sh growth and thus aquaculture productivity. In Chinese tongue sole ( Cynoglossus semilaevis ), 17β-estradiol (E2) can be used reportedly to induce the feminization of fi sh, although the detailed regulatory network remained elusive. We treated the tongue sole fry before sex diff erentiation with E2 (10 and 30 μg/L) to identify potential targets of E2 in Chinese tongue sole. The E2 treatment indeed induced genetic male fi sh sex-reversal to phenotypic female. Using an iTRAQ-based comparative proteomic analysis, 409 proteins that diff erentially expressed after E2 induction were identifi ed, including 259 up-regulated and 150 down-regulated proteins. Furthermore, 19 diff erentially expressed proteins identifi ed in the comparative proteomic analysis were selected to assess their transcription and eight of them exhibited the same tendency. Functions of the eight proteins included mainly nucleotide and protein binding. Interestingly, a far upstream element-binding protein 3-like isoform exhibited the signifi cant upregulation both at transcription and translation levels after E2 treatment. This work identifi ed a set of candidate proteins for E2 response and deepened our understanding of E2 regulatory mechanism.
基金supported by the grants from National Key R&D Program(2017YFD0501901 and 2017YFD0501905)National Natural Science Foundation of China(No.3167246 and 31972573)+1 种基金National Support Program for Youth Top-notch Talentsthe Earmarked Fund for the Innovative Teams of Beijing Swine Industrialization Research Program.
文摘Background:Implantation failure limits the success of in vitro fertilization and embryo transfer(IVF-ET).Wellorganized embryo-maternal crosstalk is essential for successful implantation.Previous studies mainly focused on the aberrant development of in vitro fertilized(IVF)embryos.In contrast,the mechanism of IVF-induced aberrant embryo-maternal crosstalk is not well defined.Results:In the present study,using ewes as the model,we profiled the proteome that features aberrant IVF embryo-maternal crosstalk following IVF-ET.By comparing in vivo(IVO)and IVF conceptuses,as well as matched endometrial caruncular(C)and intercaruncular(IC)areas,we filtered out 207,295,and 403 differentially expressed proteins(DEPs)in each comparison.Proteome functional analysis showed that the IVF conceptuses were characterized by the increased abundance of energy metabolism and proliferation-related proteins,and the decreased abundance of methyl metabolism-related proteins.In addition,IVF endometrial C areas showed the decreased abundance of endometrial remodeling and redox homeostasis-related proteins;while IC areas displayed the aberrant abundance of protein homeostasis and extracellular matrix(ECM)interaction-related proteins.Based on these observations,we propose a model depicting the disrupted embryo-maternal crosstalk following IVF-ET:Aberrant energy metabolism and redox homeostasis of IVF embryos,might lead to an aberrant endometrial response to conceptus-derived pregnancy signals,thus impairing maternal receptivity.In turn,the suboptimal uterine environment might stimulate a compensation effect of the IVF conceptuses,which was revealed as enhanced energy metabolism and over-proliferation.Conclusion:Systematic proteomic profiling provides insights to understand the mechanisms that underlie the aberrant IVF embryo-maternal crosstalk.This might be helpful to develop practical strategies to prevent implantation failure following IVF-ET.
基金supported by Helene Houle Career Development Award in Neurologic Surgery Research and Fund for Mayo Clinic Center for Regenerative Medicine Program Director,Neuroregenerative Medicine,Mayo Clinic College of Medicine and Science.SG was supported by the Chinese Scholarship Council.
文摘Chronic denervation is one of the key factors that affect nerve regeneration.Chronic axotomy deteriorates the distal nerve stump,causes protein changes,and renders the microenvironment less permissive for regeneration.Some of these factors/proteins have been individually studied.To better delineate the comprehensive protein expression profiles and identify proteins that contribute to or are associated with this detrimental effect,we carried out a proteomic analysis of the distal nerve using an established delayed rat sciatic nerve repair model.Four rats that received immediate repair after sciatic nerve transection served as control,whereas four rats in the experimental group(chronic denervation)had their sciatic nerve repaired after a 12-week delay.All the rats were sacrificed after 16 weeks to harvest the distal nerves for extracting proteins.Twenty-five micrograms of protein from each sample were fractionated in SDS-PAGE gels.NanoLC-MS/MS analysis was applied to the gels.Protein expression levels of nerves on the surgery side were compared to those on the contralateral side.Any protein with a P value of less than 0.05 and a fold change of 4 or higher was deemed differentially expressed.All the differentially expressed proteins in both groups were further stratified according to the biological processes.A PubMed search was also conducted to identify the differentially expressed proteins that have been reported to be either beneficial or detrimental to nerve regeneration.Ingenuity Pathway Analysis(IPA)software was used for pathway analysis.The results showed that 709 differentially expressed proteins were identified in the delayed repair group,with a bigger proportion of immune and inflammatory process-related proteins and a smaller proportion of proteins related to axon regeneration and lipid metabolism in comparison to the control group where 478 differentially expressed proteins were identified.The experimental group also had more beneficial proteins that were downregulated and more detrimental proteins that were upregulated.IPA revealed that protective pathways such as LXR/RXR,acute phase response,RAC,ERK/MAPK,CNTF,IL-6,and FGF signaling were inhibited in the delayed repair group,whereas three detrimental pathways,including the complement system,PTEN,and apoptosis signaling,were activated.An available database of the adult rodent sciatic nerve was used to assign protein changes to specific cell types.The poor regeneration seen in the delayed repair group could be associated with the down-regulation of beneficial proteins and up-regulation of detrimental proteins.The proteins and pathways identified in this study may offer clues for future studies to identify therapeutic targets.
文摘Available reports have confirmed a link between bacterial infection and the progression of different types of cancers,including colon,lungs,and prostate cancer.Here we report the Chlamydia pneumonia proteins targeting in endoplasmic reticulum(ER)using in-silico approaches and their possible role in lung cancer etiology.We predicted 48 proteins that target human ER,which may be associated with protein folding and protein-protein interactions during infection.The results showed C.pneumoniae proteins targeting human ER and their implications in lung cancer growth.These targeted proteins may be involved in competitive interactions between host and bacterial proteins,which may change the usual pathway functions and trigger the development of lung cancer.Moreover,C.pneumoniae unfolded protein accumulation in the human ER possibly induces ER stress,consequently activating the unfolded protein response(UPR),and providing a favorable microenvironment for cancer growth.The current study showed the C.pneumoniae protein targeting in ER of host cell and their implication in lung cancer growth.These results may help researchers better manage lung cancer and establish a molecular mechanism for C.pneumoniae lung cancer association.
文摘Complement (C) activation-related hypersensitivity reactions (HSRs) represent an unsolved adverse immune effect of many i.v. administered “nanomedicines”, such as liposomal doxorubicin (Doxil/Caelyx). Because these pseudoallergic reactions can be severe or even lethal, it is an important clinical objective to find biomarkers for proneness for C activation by reactogenic nanoparticles that will allow the prediction of in vivo reactions by in vitro assays. With this goal in mind we identified a normal human blood donor who consistently showed high sensitivity to Caelyx-induced C activation in vitro, whose plasma (Caelyx sensitive plasma, CSP) was subjected to proteome profiling with a library of human plasma proteome specific mAbs. The chip (PlasmaScan-380TM) contained 380 non redundant (with respect to epitopes) mAbs. The analysis revealed 8 proteins that were differentially represented in CSP in comparison with Caelyx-insensitive control plasma. These proteins were identified by mass spectrometry and Western blot analyses to represent factor H (decreased in CSP), factor H related protein, serum amyloid P component, fibronectin, complement component C4, Apo B100, prothrombin and alpha-2-HS glycoprotein (all increased in CSP). Some of these protein changes are consistent with proneness for increased C activation, suggesting the potential use of this method in the search for biomarkers for liposome-induced or other types of nanomedicine-induced HSRs.
基金This work was supported by National R&D Project of Transgenic Crops of Ministry of Science and Technology of China(2016ZX08005–004-002).
文摘Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.Results:Through transcriptome analysis in cotton leaves under salt stress for 0 h(T0),3 h(T3)and 12 h(T12),we identified 8436,11628 and 6311 differentially expressed genes(DEGs)in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.A total of 459 differentially expressed proteins(DEPs)were identified by proteomic analysis,of which 273,99 and 260 DEPs were identified in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.Metabolic pathways,biosynthesis of secondary metabolites,photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs.Detail analysis of the DEGs or DEPs revealed that complex signaling pathways,such as abscisic acid(ABA)and jasmonic acid(JA)signaling,calcium signaling,mitogen-activated protein kinase(MAPK)signaling cascade,transcription factors,activation of antioxidant and ion transporters,were participated in regulating salt response in cotton.Conclusions:Our research not only contributed to understand the mechanism of cotton response to salt stress,but also identified nine candidate genes,which might be useful for molecular breeding to improve salt-toleranee in cotton.
