A highly efficient protein corona-based proteomic analysis strategy for the discovery of pharmacodynamic biomarkers / 药物分析学报

The composition of serum is extremely complex,which complicates the discovery of new pharmaco-dynamic biomarkers via serum proteome for disease prediction and diagnosis.Recently,nanoparticles have been reported to efficiently reduce the proportion of high-abundance proteins and enrich low-abundance proteins in serum.Here,we synthesized a silica-coated iron oxide nanoparticle and devel-oped a highly efficient and reproducible protein corona(PC)-based proteomic analysis strategy to improve the range of serum proteomic analysis.We identified 1,070 proteins with a median coefficient of variation of 12.56％using PC-based proteomic analysis,which was twice the number of proteins iden-tified by direct digestion.There were also more biological processes enriched with these proteins.We applied this strategy to identify more pharmacodynamic biomarkers on collagen-induced arthritis(CIA)rat model treated with methotrexate(MTX).The bioinformatic results indicated that 485 differentially expressed proteins(DEPs)were found in CIA rats,of which 323 DEPs recovered to near normal levels after treatment with MTX.This strategy can not only help enhance our understanding of the mechanisms of disease and drug action through serum proteomics studies,but also provide more pharmacodynamic biomarkers for disease prediction,diagnosis,and treatment.

Cambios en el perfil protéico de E. coli O157:H7 frente al tratamiento con Ib-M1 e IONP@Ib-M1 / Changes in the protein profile of E. coli O157: H7 against treatment with Ib-M1 and IONP@Ib-M1 / Identificação de alterações no perfil protetor de E. coli O157: H7 contra o tratamento com Ib-M1 e IONP@Ib-M1

Resumen Escherichia coli 0157:H7 es una bacteria patógena reconocida por su capacidad de resistencia a diversos antibióticos; razón por la cual, se generan complicaciones en el tratamiento de infecciones producidas por esta bacteria. El péptido Ib-M1 y el bioconjugado I0NP@Ib-M1 han surgido como una nueva alternativa antimicrobiana contra E. coli 0157:H7. El mecanismo de acción de Ib-Mi e I0NP@Ib-M1 contra esta bacteria aún es desconocido; por lo tanto, el objetivo de esta investigación fue identificar el cambio en el perfil de proteínas de E. coli 0157:H7 luego del tratamiento con Ib-M1 e I0NP@ Ib-M1 como primer paso para determinar su mecanismo de acción. Para esto, se llevó a cabo la obtención de proteínas, posteriormente se realizó una electroforesis bidimensional para finalmente realizar la determinación de la variabilidad de los perfiles proteicos. Una vez obtenidos estos perfiles, se llevó a cabo un análisis de varianza (AN0VA). Se identificaron 72 proteínas expresadas diferencialmente, las cuales pueden relacionarse con el efecto sobre el crecimiento de la bacteria en presencia de Ib-M1 e I0NP@Ib-M. Estas proteínas se encuentran involucradas en procesos de transferencia de grupos acilo (proteína Yhbs), translocación de lipoproteínas (proteína LolA) y transporte de aminoácidos (proteína GpmA), entre otros.

Abstract Escherichia coli 0157: H7 is a pathogenic bacterium which is recognized for the ability to resist multiple antibiotics; accordingly, complications occur in the treatment of infections caused by this bacterium. The Ib-M1 peptide and the I0NP @ Ib-M1 bioconjugate have emerged as a new antimicrobial alternatives against E. coli 0157: H7. The mechanism of action of Ib-M1 and I0NP @ Ib-M1 against this bacterium is still unknown; therefore, the goal of this research was to identify the change in the proteins profile of E. coli 0157: H7 after treatment with Ib-M1 and I0NP @ Ib-M1 as a first step to determine its mechanism of action. For this, the proteins were obtained first, and then a two-dimensional electrophoresis was performed to finally determine the variability of the protein profiles. 0nce the protein profiles were obtained, an analysis of variance (AN0VA) was carried out. 72 differentially expressed proteins were identified, which can be connected to the effect on the bacterium's growth in the presence of Ib-M1 and I0NP @ Ib-M. These proteins are involved in acyl groups transfer processes (Yhbs protein), lipoprotein translocation (LolA protein) and amino acid transport (GpmA protein), among others.

Resumo Escherichia coli O157: H7 é uma bactéria patogênica reconhecida por sua capacidade de resistir a vários antibióticos; razão pela qual, complicações são geradas no tratamento de infecções produzidas por essa bactéria. O peptídeo Ib-M1 livre e imobilizado em nanopartículas magnéticas de óxido de ferro (IONP @ Ib-M1) surgiu como uma nova alternativa antimicrobiana contra E. coli O157: H7 e isolados clínicos desta bactéria. O mecanismo de ação de Ib-M1 e IONP @ Ib-M1 contra E. coli O157: H7 ainda é desconhecido; Portanto, o objetivo desta pesquisa foi identificar a alteração no perfil proteico de E. coli O157: H7 após o tratamento com Ib-M1 e IONP @ Ib-M1 como um primeiro passo para determinar seu mecanismo de ação. Para isso, foi realizada a obtenção das proteínas, posteriormente foi realizada uma eletroforese bidimensional para finalmente determinar a variabilidade dos perfis protéicos. Uma vez obtidos os perfis de proteínas, foi realizada uma análise de variância (ANOVA). Os resultados mostram a identificação de proteínas expressas diferencialmente e que estão envolvidas em processos de transferência de grupos acila (proteína Yhbs), translocação de lipoproteínas (proteína LolA) e transporte de aminoácidos (proteína GpmA), entre outros.

Proteomic analysis of lung injuries induced by paraquat in mice / 中华急诊医学杂志

Objective:To explore the molecular mechanism of paraquat (PQ)-induced lung injuries.Methods:Male C57BL/6 mice aged 6 to 8 weeks were randomly divided into four groups. Mice in the experimental groups (three groups, nine rats in each group) were intraperitoneally injected with 40 mg/kg PQ to establish an infection model, and mice in the control group ( n=9) were intraperitoneally injected with the same dose of saline. Mice were sacrificed at day 2, 7 and 14 after PQ administration. Pathological changes of lung tissues from mice model were observed by Hematoxylin-eosin staining. The expression of different proteins in the lung tissues at different time points were detected and identified by tandem mass spectrometry tag technology (TMT), and the functional analysis was performed. Results:Compared with the control group, there were 91 (69 up and 22 down), 160 (103 up and 57 down) and 78 (45 up and 33 down) proteins in the PQ-2 d, 7 d, and 14 d groups, respectively, and there was significant difference of protein expression . The subcellular localization analysis showed that compared with the control group, the differentially-expressed proteins in the PQ-2 d and -7 d groups were mainly distributed in the extracellular space, while in the PQ-14 d group were mainly distributed in the nuclear. GO analysis showed that compared with the control group, the differentially-expressed proteins in the PQ-2 d and PQ-7 d groups were mainly involved in humoral immunity and coagulation-related reactions, while in the PQ-14 d group were mainly involved in chemotactic and regulatory responses such as neutrophil aggregation. The KEGG signaling pathway analysis showed that the complement and coagulation cascades was the most important pathway in the PQ-2d and PQ-7 d groups, while metabolism of xenobiotics by cytochrome P450 was the most important pathway in the PQ-14 d group.Conclusions:It is the first time that TMT was used to analyze PQ-induced lung injuries in mice model at different time points. This study demonstrates the molecular mechanism of PQ-induced lung injuries at protein levels, and elucidates that humoral immunity and complement-coagulation pathways charge the main role of PQ-induced lung injuries. This study may provide an important theoretical basis for further research and clinical treatment.

Comparative analysis of the proteomic profile of the dental pulp in different conditions. a pilot study

Abstract This study aimed to quantitatively compare the difference in protein expression in the progression of pulp pathogenesis, as well as to describe the biological functions of proteins identified in pulp tissue. Samples were obtained from six patients treated at the Araçatuba School of Dentistry and were divided into three groups: normal pulp - from teeth extracted for orthodontic indication; inflamed pulp and necrotic pulp - from patients diagnosed with irreversible pulpitis and chronic apical periodontitis, respectively. After previous proteomic preparation, dental pulp samples were processed for label-free quantitative proteomic analysis in a nanoACQUITY UPLC-Xevo QTof MS system. The difference in expression between the groups was calculated using the Protein Lynx Global Service software using the Monte Carlo algorithm. A total of 465 human proteins were identified in all groups. The most expressed proteins in the inflamed pulp group in relation to the normal pulp group were hemoglobin, peroxiredoxins and immunoglobulins, whereas the less expressed were the tubulins. Expression levels of albumins, immunoglobulins and alpha-2-macroglobulin were higher in the necrotic pulp group than in the inflamed pulp group. As for the qualitative analysis, the most prevalent protein functions in the normal pulp group were metabolic and energetic pathways; in the inflamed pulp group: cellular communication and signal transduction; and regulation and repair of DNA/RNA, while in the necrotic pulp group proteins were associated with the immune response. Thus, proteomic analysis showed quantitative and qualitative differences in protein expression in different types of pulp conditions.

Resumo Este estudo teve como objetivo comparar quantitativamente a diferença da expressão de proteínas na progressão da patogênese pulpar, bem como descrever as funções biológicas das proteínas identificadas no tecido pulpar. As amostras foram obtidas de seis pacientes atendidos na Faculdade de Odontologia de Araçatuba e divididas em três grupos: polpa normal - dentes extraídos por indicação ortodôntica; polpa inflamada e polpa necrótica - pacientes diagnosticados com pulpite irreversível e periodontite apical crônica, respectivamente. Após o preparo proteômico prévio, as amostras de polpa dentária foram processadas para análise proteômica quantitativa livre de marcadores em um sistema nanoACQUITY UPLC-Xevo QTof MS. A diferença de expressão entre os grupos foi calculada usando o software Protein Lynx Global Service através do algoritmo de Monte Carlo. Um total de 465 proteínas humanas foram identificadas em todos os grupos. As proteínas mais expressas no grupo polpa inflamada em relação ao grupo polpa normal foram hemoglobinas, peroxirredoxinas e imunoglobulinas, enquanto as menos expressas foram as tubulinas. Os níveis de expressão de albuminas, imunoglobulinas e alfa-2-macroglobulina foram maiores no grupo polpa necrótica do que no grupo de polpa inflamada. Quanto à análise qualitativa, as funções proteicas mais prevalentes no grupo polpa normal foram vias metabólicas e energéticas; no grupo polpa inflamada: comunicação celular e transdução de sinal; e regulação e reparo de DNA / RNA, enquanto no grupo polpa necrótica as proteínas foram associadas à resposta imune. Assim, a análise proteômica mostrou diferenças quantitativas e qualitativas na expressão de proteínas em diferentes tipos de condições pulpares.

Extracellular vesicles in infectious diseases caused by protozoan parasites in buffaloes

Extracellular vesicles (EVs) are small membrane-bound vesicles of growing interest in vetetinary parasitology. The aim of the present report was to provide the first isolation, quantification and protein characterization of EVs from buffalo (Bubalus bubalis) sera infected with Theileria spp. Methods: Infected animals were identified through optical microscopy and PCR. EVs were isolated from buffalo sera by size-exclusion chromatography and characterized using western blotting analysis, nanoparticle tracking analysis and transmission electron microscopy. Subsequently, the proteins from isolated vesicles were characterized by mass spectrometry. Results: EVs from buffalo sera have shown sizes in the 124-140 nm range and 306 proteins were characterized. The protein-protein interaction analysis has evidenced biological processes and molecular function associated with signal transduction, binding, regulation of metabolic processes, transport, catalytic activity and response to acute stress. Five proteins have been shown to be differentially expressed between the control group and that infected with Theileria spp., all acting in the oxidative stress pathway. Conclusions: EVs from buffaloes infected with Theileria spp. were successfully isolated and characterized. This is an advance in the knowledge of host-parasite relationship that contributes to the understanding of host immune response and theileriosis evasion mechanisms. These findings may pave the way for searching new EVs candidate-markers for a better production of safe biological products derived from buffaloes.(AU)

Systematic analysis of protein expression in Candida albicans exposed to farnesol / 中华医学杂志(英文版)

Background@#The phenotypic switching of Candida spp. plays an important role in the development of vulvovaginal candidiasis (VVC). Farnesol, as a quorum-sensing molecule in Candida albicans, has the ability to prevent yeast-to-hyphal conversion in vitro. However, the mechanism underlying this ability is unclear. This study aimed to investigate changes in protein levels to better understand how farnesol impacts processes contributing to VVC.@*Methods@#The isobaric tag for relative and absolute quantitation technique was used to detect protein expression in C. albicans strain SC5314 (ATCC MYA-2876) with or without farnesol exposure. Proteins with a threshold fold change greater than 1.5 were screened and considered differentially expressed proteins. All the altered proteins were analyzed using Gene Ontology annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, and metabolic pathway annotation.@*Results@#Between the farnesol-exposed group and the farnesol-unexposd group, we detected 297 altered proteins among all 2047 tested proteins based on a threshold fold change of more than 1.5 (P < 0.05). Eighty-seven of the 297 altered proteins exhibited metabolic enzyme activity and participated in 85 metabolic pathways according to KEGG pathway analysis. Most of these metabolic pathways were associated with central carbon metabolism processes. In the sterol synthesis pathway, which involves the synthesis of farnesol, ERG25 (methylsterol monooxygenase) and ERG4 (delta 24(24(1))-sterol reductase) were both down-regulated in the farnesol-exposed group. All six altered proteases associated with the oxidative phosphorylation process were down-regulated in the farnesol-exposed group relative to the farnesol-unexposed group.@*Conclusions@#The mechanisms underlying farnesol-induced phenotype switching involves the adjustment of metabolic activities and epigenetic modification. Exogenous farnesol had an evident, but non-deterministic effect on the synthesis of ergosterol. The potential drug activity of farnesol warrants further investigation.

Comparison of gel-aided sample preparation (GASP) and two in-solution digestion workflows for proteomic analysis using Saccharomyces cerevisiae lysate

Abstracts@#Using Saccharomyces cerevisiae lysate, two in-solution trypsin digestions (chloroform-methanol-water precipitation and RapiGest) were compared to the recently reported gel-aided sample preparation (GASP) workflow. Our proteomic results showed that GASP afforded the highest number of overall protein identifications and peptide spectrum matches without systematic bias towards peptide or protein size.

Quantitative proteomic research of biological basis of Buyang Huanwu decoction therapy for cerebral infarction combined with Qi-deficiency and blood-stasis syndrome / 中国中药杂志

Chinese medicine Buyang Huanwu decoction (BYHW) is widely used in treating cerebral infarction combined with Qi-deficiency and blood-stasis syndrome, but the pharmacological basis is still not clear. This study aims to uncover the biological basis of BYHW therapy for cerebral infarction combined with Qi-deficiency and blood-stasis syndrome using label-free proteomic technology. Using Qi deficiency and blood stasis rat cerebral infarction model as the research object, the protein expression of rat brain tissue was compared among the sham operation group, the model group and the drug group. Quantitative analysis of the 3 groups of tissue samples detected 3 959, 3 996 and 4 055 proteins in the sham operation group, the model group and the drug group, respectively. Take model group as the control group, 391 proteins were identified to be upregulated or downregulated for more than 2 folds. Biological analysis and functional enrichment of the differentially expressed proteins revealed that BYHW may treat cerebral infarction combined with Qi-deficiency and blood-stasis syndrome through energy metabolism, nervous system and several signal pathways. This study preliminarily revealed the pharmacological mechanism of BYHW at the protein level, and provided a molecular basis for clinical treatment and traditional Chinese medicine research on cerebral infarction combined with Qi-deficiency and blood-stasis syndrome.

Avaliação da inervação entérica e análise proteômica do intestino delgado de ratos expostos à dose aguda ou crônica de fluoreto / Evaluation of enteric innervation and proteomic analysis of the small intestine of rats exposed to acute or chronic fluoride dose

O trato gastrointestinal (TGI) é a principal rota de exposição ao fluoreto (F) e o seu mais importante sítio de absorção. Acredita-se que a toxicidade do F comprometa a fisiologia do intestino, devido à relevante sintomatologia gastrointestinal relatada em consequência da exposição excessiva ao F. A função intestinal é controlada por uma complexa rede neuronal interligada e incorporada à parede deste órgão, denominada Sistema Nervoso Entérico (SNE). Embora os efeitos tóxicos do F sobre o Sistema Nervoso Central sejam descritos na literatura, não há estudos relacionados à sua toxicidade sobre o SNE. Neste estudo realizado em ratos, foi avaliado o efeito da exposição aguda ou crônica ao F, sobre a população geral de neurônios entéricos e sobre as subpopulações que expressam os principais neurotransmissores entéricos: Acetilcolina (ACh), Óxido Nítrico (NO), Peptídeo Vasoativo Intestinal (VIP), Peptídeo Relacionado ao Gene da Calcitonina (CGRP) e Substância P (SP). Os animais foram divididos em 5 grupos: 3 destinados à exposição crônica (0 ppm, 10 ppm ou 50 ppm de F na água de beber) e 2 à exposição aguda (0 ou 25 mgF/Kg por gavagem gástrica). Foram coletados os 3 segmentos do intestino delgado (duodeno, jejuno e íleo) e processados para a detecção da HuC/D, ChAT, nNOS, VIP, CGRP e SP, através de técnicas de imunofluorescência, no plexo mioentérico. Foram obtidas imagens para a realização da análise quantitativa dos neurônios da população geral (HuC/D) e nitrérgicos (imunorreativos à nNOS); e morfométrica dos neurônios imunorreativos à HuC/D ou nNOS; e das varicosidades imunorreativas à ChAT, VIP, CGRP ou SP. Amostras dos 3 segmentos intestinais foram preparadas e coradas em Hematoxilina e Eosina para análise histológica da morfologia básica. O segmento intestinal considerado mais afetado na análise morfométrica da população geral de neurônios, o duodeno, foi selecionado para a realização da análise proteômica, com o objetivo de oferecer o seu perfil proteico...

The gastrointestinal tract (GIT) is the main route of fluoride (F) exposure, and the most important site of its absorption. It is believed that F toxicity compromises the intestine physiology, due to the relevant gastrointestinal symptomatology reported in consequence to excessive exposure. The intestinal function is controlled by a complex neuronal net, which is interconnected and embedded in the wall of this organ, named Enteric Nervous System (ENS). Although the toxic effects of F on the Central Nervous system are described in the literature, there are no studies related to its toxicity on the ENS. Therefore, in this study performed in rats, the effects of chronic and acute F exposure were evaluated, on the general population of enteric neurons and on the subpopulations that express the main enteric neurotransmitters: Acetylcholine (Ach), Nitric Oxide (NO), Vasoactive Intestinal Peptide (VIP), Calcitonin gene related peptide (CGRP), and Substance P (SP). The animals were divided into 5 groups: 3 designed to the chronic exposure (0 ppm, 10 ppm ou 50 ppm de F in the drinking water) and 2 to the acute exposure (0 ou 25 mgF/Kg - gastric gavage). Three intestinal segments were collected (duodenum, jejunum, and ileum) and processed for the immunofluorescence techniques to detect HuC/D, ChAT, nNOS, VIP, CGRP and SP, on the myenteric plexus. Images were obtained for the quantitative analysis of the general population of neurons (HuC/D immunoreactive) and the nitrergic neurons (nNOS immunoreactive), for the morphometric analysis of the general population and nitrergic neurons and also for the immunoreactive varicosities to ChAT, VIP, CGRP or SP. Samples of the 3 intestinal segments were prepared and stained with hematoxylin and eosin for histological analysis of the basic morphology. Duodenum, the intestinal segment considered the most affected in the morphological analysis of the general population of neurons, was selected for the proteomic analysis...

Avaliação da inervação entérica e análise proteômica do intestino delgado de ratos expostos à dose aguda ou crônica de fluoreto / Evaluation of enteric innervation and proteomic analysis of the small intestine of rats exposed to acute or chronic fluoride dose

O trato gastrointestinal (TGI) é a principal rota de exposição ao fluoreto (F) e o seu mais importante sítio de absorção. Acredita-se que a toxicidade do F comprometa a fisiologia do intestino, devido à relevante sintomatologia gastrointestinal relatada em consequência da exposição excessiva ao F. A função intestinal é controlada por uma complexa rede neuronal interligada e incorporada à parede deste órgão, denominada Sistema Nervoso Entérico (SNE). Embora os efeitos tóxicos do F sobre o Sistema Nervoso Central sejam descritos na literatura, não há estudos relacionados à sua toxicidade sobre o SNE. Neste estudo realizado em ratos, foi avaliado o efeito da exposição aguda ou crônica ao F, sobre a população geral de neurônios entéricos e sobre as subpopulações que expressam os principais neurotransmissores entéricos: Acetilcolina (ACh), Óxido Nítrico (NO), Peptídeo Vasoativo Intestinal (VIP), Peptídeo Relacionado ao Gene da Calcitonina (CGRP) e Substância P (SP). Os animais foram divididos em 5 grupos: 3 destinados à exposição crônica (0 ppm, 10 ppm ou 50 ppm de F na água de beber) e 2 à exposição aguda (0 ou 25 mgF/Kg por gavagem gástrica). Foram coletados os 3 segmentos do intestino delgado (duodeno, jejuno e íleo) e processados para a detecção da HuC/D, ChAT, nNOS, VIP, CGRP e SP, através de técnicas de imunofluorescência, no plexo mioentérico. Foram obtidas imagens para a realização da análise quantitativa dos neurônios da população geral (HuC/D) e nitrérgicos (imunorreativos à nNOS); e morfométrica dos neurônios imunorreativos à HuC/D ou nNOS; e das varicosidades imunorreativas à ChAT, VIP, CGRP ou SP. Amostras dos 3 segmentos intestinais foram preparadas e coradas em Hematoxilina e Eosina para análise histológica da morfologia básica. O segmento intestinal considerado mais afetado na análise morfométrica da população geral de neurônios, o duodeno, foi selecionado para a realização da análise proteômica, com o objetivo de oferecer o seu perfil proteico...

The gastrointestinal tract (GIT) is the main route of fluoride (F) exposure, and the most important site of its absorption. It is believed that F toxicity compromises the intestine physiology, due to the relevant gastrointestinal symptomatology reported in consequence to excessive exposure. The intestinal function is controlled by a complex neuronal net, which is interconnected and embedded in the wall of this organ, named Enteric Nervous System (ENS). Although the toxic effects of F on the Central Nervous system are described in the literature, there are no studies related to its toxicity on the ENS. Therefore, in this study performed in rats, the effects of chronic and acute F exposure were evaluated, on the general population of enteric neurons and on the subpopulations that express the main enteric neurotransmitters: Acetylcholine (Ach), Nitric Oxide (NO), Vasoactive Intestinal Peptide (VIP), Calcitonin gene related peptide (CGRP), and Substance P (SP). The animals were divided into 5 groups: 3 designed to the chronic exposure (0 ppm, 10 ppm ou 50 ppm de F in the drinking water) and 2 to the acute exposure (0 ou 25 mgF/Kg - gastric gavage). Three intestinal segments were collected (duodenum, jejunum, and ileum) and processed for the immunofluorescence techniques to detect HuC/D, ChAT, nNOS, VIP, CGRP and SP, on the myenteric plexus. Images were obtained for the quantitative analysis of the general population of neurons (HuC/D immunoreactive) and the nitrergic neurons (nNOS immunoreactive), for the morphometric analysis of the general population and nitrergic neurons and also for the immunoreactive varicosities to ChAT, VIP, CGRP or SP. Samples of the 3 intestinal segments were prepared and stained with hematoxylin and eosin for histological analysis of the basic morphology. Duodenum, the intestinal segment considered the most affected in the morphological analysis of the general population of neurons, was selected for the proteomic analysis...

Differentially Expressed Proteins in Nitric Oxide-Stimulated NIH/3T3 Fibroblasts: Implications for Inhibiting Cancer Development

PURPOSE: Recent evidence shows that nitric oxide (NO) may exhibit both pro-cancer and anti-cancer activities. The present study aimed to determine the differentially expressed proteins in NO-treated NIH/3T3 fibroblasts in order to investigate whether NO induces proteins with pro-cancer or anti-cancer effects. MATERIALS AND METHODS: The cells were treated with 300 microM of an NO donor 3,3-bis-(aminoethyl)-1-hydroxy-2-oxo-1-triazene (NOC-18) for 12 h. The changed protein patterns, which were separated by two-dimensional electrophoresis using pH gradients of 4-7, were conclusively identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis of the peptide digests. RESULTS: Seventeen differentially expressed proteins were identified in NOC-18-treated cells. Nine proteins [vinculin protein, keratin 19, ubiquitous tropomodulin, F-actin capping protein (alpha1 subunit), tropomyosin 3, 26S proteasome-associated pad1 homolog, T-complex protein 1 (epsilon subunit) N(G)-dimethylarginine dimethylaminohydrolase, and heat shock protein 90] were increased and eight proteins (heat shock protein 70, glucosidase II, lamin B1, calreticulin, nucleophosmin 1, microtubule-associated protein retinitis pigmentosa/end binding family member 1, 150 kD oxygen-regulated protein precursor, and heat shock 70-related protein albino or pale green 2) were decreased by NOC-18 in the cells. Thirteen proteins are related to the suppression of cancer cell proliferation, invasion, and metastasis while two proteins (heat shock protein 90 and N(G)-dimethylarginine dimethylaminohydrolase) are related to carcinogenesis. The functions of 150 kD oxygen-regulated protein precursor and T-complex protein 1 (epsilon subunit) are unknown in relation to carcinogenesis. CONCLUSION: Most proteins differentially expressed by NOC-18 are involved in inhibiting cancer development.

Annexin A5 as a New Potential Biomarker for Cisplatin-Induced Toxicity in Human Kidney Epithelial Cells

Cisplatin is a member of platinum-containing anti-cancer drugs that causes cross-linking of DNA and ultimately cancer cell apoptosis. The therapeutic function of cisplatin on various types of cancers has been widely reported but the side effects have been discovered together and nephrotoxicity has been regarded as major side effect of cisplatin. To select candidates for new sensitive nephrotoxicity biomarker, we performed proteomic analysis using 2-DE/MALDI-TOF-MS followed by cisplatin treatment in human kidney cell line, HK-2 cells, and compared the results to the gene profi le from microarray composed of genes changed in expression by cisplatin from formerly reported article. Annexin A5 has been selected to be the most potential candidate and it has been identifi ed using Western blot, RT-PCR and cell viability assay whether annexin A5 is available to be a sensitive nephrotoxic biomarker. Treatment with cisplatin on HK-2 cells caused the increase of annexin A5 expression in protein and mRNA levels. Overexpression of annexin A5 blocked HK-2 cell proliferation, indicating correlation between annexin A5 and renal cell toxicity. Taken together, these results suggest the possibility of annexin A5 as a new biomarker for cisplatin-mediated nephrotoxicity.

Bone tuberculosis in Roman Period Pannonia (western Hungary)

The purpose of this study was to analyse a skeleton (adult female, 25-30 years) that presented evidence of tuberculous spondylitis. The skeleton, dated from the Roman Period (III-VI centuries), was excavated near the town of Győr, in western Hungary. The skeleton was examined by gross observation supplemented with mycolic acid and proteomic analyses using MALDI-TOF/TOF tandem mass spectrometry. The biomolecular analyses supported the morphological diagnosis.

Hazardous effects of fried potato chips on the development of retina in albino rats

<p><b>OBJECTIVE</b>To evaluate the hazardous effects of fried potato chips upon the retina of two developmental stages of the albino rats aged 7 and 14 days from parturition.</p><p><b>METHODS</b>PREGNANT RATS WERE ARRANGED INTO TWO GROUPS: control pregnant rats and consequently their delivered newborns until reaching 7 and 14 days old from parturition and fried potato chips group in which pregnant rats at the 6th day of gestation maintained on diet formed of fried potato chips supplied from the market mixed with standard diet at a concentration of 50% per each till 7 and 14 post-partum. Three fold integrated approaches were adopted, namely, histological, ultrastructural and proteomic analysis.</p><p><b>RESULTS</b>Histological examination of the retina of the experimental offsprings revealed many histopathological changes, including massive degeneration, vacuolization and cell loss in the ganglion cell layer, as well as general reduction in retinal size. At the ultrastructural level, the retina of experimental offsprings exhibited number of deformities, including ill differentiated and degenerated nuclear layer, malformed and vacuolated pigment epithelium with vesiculated and fragmented rough endoplasmic reticulum, degenerated outer segment of photoreceptors, as well as swollen choriocapillaris and loss of neuronal cells. Proteomic analysis of retina of the two experimental developmental stages showed variations in the expressed proteins as a result of intoxication which illustrated the adverse toxic effects of fried potato chips upon the retina.</p><p><b>CONCLUSIONS</b>It can be concluded that the effect of fried potato chips on the development of retina in rats may be due to the presence of acrylamide or its metabolite.</p>

Spinal Cord Injury Markedly Altered Protein Expression Patterns in the Affected Rat Urinary Bladder during Healing Stages

The influence of spinal cord injury (SCI) on protein expression in the rat urinary bladder was assessed by proteomic analysis at different time intervals post-injury. After contusion SCI between T9 and T10, bladder tissues were processed by 2-DE and MALDI-TOF/MS at 6 hr to 28 days after SCI to identify proteins involved in the healing process of SCI-induced neurogenic bladder. Approximately 1,000 spots from the bladder of SCI and sham groups were visualized and identified. At one day after SCI, the expression levels of three protein were increased, and seven spots were down-regulated, including heat shock protein 27 (Hsp27) and heat shock protein 20 (Hsp20). Fifteen spots such as S100-A11 were differentially expressed seven days post-injury, and seven proteins including transgelin had altered expression patterns 28 days after injury. Of the proteins with altered expression levels, transgelin, S100-A11, Hsp27 and Hsp20 were continuously and variably expressed throughout the entire post-SCI recovery of the bladder. The identified proteins at each time point belong to eight functional categories. The altered expression patterns identified by 2-DE of transgelin and S100-A11 were verified by Western blot. Transgelin and protein S100-A11 may be candidates for protein biomarkers in the bladder healing process after SCI.

Proteomic analysis of cytosolic proteins associated with petite mutations in Candida glabrata

The incidence of superficial or deep-seated infections due to Candida glabrata has increased markedly, probably because of the low intrinsic susceptibility of this microorganism to azole antifungals and its relatively high propensity to acquire azole resistance. To determine changes in the C. glabrata proteome associated with petite mutations, cytosolic extracts from an azole-resistant petite mutant of C. glabrata induced by exposure to ethidium bromide, and from its azole-susceptible parent isolate were compared by two-dimensional polyacrylamide gel electrophoresis. Proteins of interest were identified by peptide mass fingerprinting or sequence tagging using a matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometer. Tryptic peptides from a total of 160 Coomassie-positive spots were analyzed for each strain. Sixty-five different proteins were identified in the cytosolic extracts of the parent strain and 58 in the petite mutant. Among the proteins identified, 10 were higher in the mutant strain, whereas 23 were lower compared to the parent strain. The results revealed a significant decrease in the enzymes associated with the metabolic rate of mutant cells such as aconitase, transaldolase, and pyruvate kinase, and changes in the levels of specific heat shock proteins. Moreover, transketolase, aconitase and catalase activity measurements decreased significantly in the ethidium bromide-induced petite mutant. These data may be useful for designing experiments to obtain a better understanding of the nuclear response to impairment of mitochondrial function associated with this mutation in C. glabrata.

Proteomic Analyses of the Shrimp White Spot Syndrome Virus / 中国病毒学·英文版

White spot syndrome virus (WSSV), a unique member within the virus family Nimaviridae, is the most notorious aquatic virus infecting shrimp and other crustaceans and has caused enormous economic losses in the shrimp farming industry worldwide. Therefore, a comprehensive understanding of WSSV morphogenesis, structural proteins, and replication is essential for developing prevention measures of this serious parasite. The viral genome is approximately 300kb and contains more than 180 open reading frames (ORF). However, most of proteins encoded by these ORF have not been characterized. Due to the importance of WSSV structural proteins in the composition of the virion structure, infection process and interaction with host cells, knowledge of structural proteins is essential to understanding WSSV entry and infection as well as for exploring effective prevention measures. This review article summarizes mainly current investigations on WSSV structural proteins including the relative quantities, localization, function and protein-protein interactions. Traditional proteomic studies of 1D or 2D gel electrophoresis separations and mass spectrometry (MS) followed by database searches have identified a total of 39 structural proteins. Shotgun proteomics and iTRAQ were initiated to identify more structural proteins. To date, it is estimated that WSSV is assembled by at least 59 structural proteins, among them 35 are defined as the envelope fraction (including tegument proteins) and 9 as nucleocapsid proteins. Furthermore, the interaction within several major structural proteins has also been investigated. This identitification and characterization of WSSV protein components should help in the understanding of the viral assembly process and elucidate the roles of several major structural proteins.

Proteomic Analysis of DJ-1 Expression in the Muscles of Spastic Cerebral Palsy Patients / 대한정형외과연구학회지

PURPOSE: Using proteomic analysis, this study was performed to see the characteristics of proteins expression in the muscles of spastic cerebral palsy patients. MATERIALS AND METHODS: We studied twelve specimens from six patients with spastic cerebral palsy, three patients with myelomeningocele, and three normal people who underwent orthopaedic surgeries due to trauma. We studied the extracted proteins showing differences in the two-dimensional electrophoresis, and the prominent thirteen proteins were re-evaluated by proteomics and the reverse transcriptional polymerase chain reaction, which was to clarify the relationship between gene and protein expression. RESULTS: Among fifteen proteins, six proteins were found to be higher in normal people, and nine were found to be higher in the groups of patients by spot histogram. The results of proteomic analysis with MALDI-TOF for fifteen proteins showed that the expression of DJ-1 was related to cerebral palsy. CONCLUSION: This study shows that strong expression of DJ-1 is related to spasticity and cerebral palsy. We showed for the first time the possibility of any relationship between spastic condition and DJ-1 expression.