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1.
Electron. j. biotechnol ; 52: 1-12, July. 2021. tab, ilus, graf
Article in English | LILACS | ID: biblio-1283167

ABSTRACT

BACKGROUND: Chronic lymphocytic leukaemia (CLL) is a neoplasm of B-cells characterized by variable prognosis. Exploring the proteome of CLL cells may provide insights into the disease. Therefore, eleven proteomics experiments were conducted on eleven primary CLL samples. RESULTS: We reported a CLL proteome consisting of 919 proteins (false discovery rate (FDR) 1%) whose identification was based on the sequencing of two or more distinct peptides (FDR of peptide sequencing 1%). Mass spectrometry-based protein identification was validated for four different proteins using Western blotting and specific antibodies in different CLL samples. Small sizes of nucleolin (~57 kDa and ~68 kDa) showed a potential association with good prognosis CLL cells (n = 8, p < 0.01). Compared with normal B-cells, CLL cells over-expressed thyroid hormone receptor-associated protein 3 (THRAP3; n = 9; p = 0.00007), which is implicated in cell proliferation; and heterochromatin protein 1-binding protein 3 (HP1BP3; n = 10; p = 0.0002), which promotes cell survival and tumourogenesis. A smaller form of HP1BP3, which may correspond to HP1BP3 isoform-2, was specifically identified in normal B-cells (n = 10; p = 0.0001). HP1BP3 and THRAP3 predicted poor prognosis of CLL (p 0.05). Consistently, THRAP3 and HP1BP3 were found to be associated with cancer-related pathways (p 0.05). CONCLUSIONS: Our findings add to the known proteome of CLL and confirm the prognostic importance of two novel cancer-associated proteins in this disease.


Subject(s)
Leukemia, Lymphocytic, Chronic, B-Cell , Biomarkers, Tumor/analysis , Mass Spectrometry , Transcription Factors/analysis , Nuclear Proteins/analysis , Blotting, Western , Chromatography, Liquid , Proteomics , DNA-Binding Proteins/analysis
2.
Int. braz. j. urol ; 47(3): 503-514, May-June 2021. tab
Article in English | LILACS | ID: biblio-1154498

ABSTRACT

ABSTRACT Purpose: Proteomic biomarkers have been emerging as alternative methods to the gold standard procedures of cystoscopy and urine cytology in the diagnosis and surveillance of bladder cancer (BC). This review aims to update the state of the art of proteomics research and diagnosis in BC. Materials and Methods: We reviewed the current literature related to BC research on urinary, tissue, blood and cell line proteomics, using the Pubmed database. Findings: Two urinary protein biomarkers are FDA-approved (NMP22® and BTA® tests), only if performed along with cystoscopy for surveillance after initial diagnosis, but not in the primary diagnostic setting due to high false-positive rates in case of infections, stones and hematuria. There are a great number of non-FDA approved proteins being studied, with good preliminary results; panels of proteins seem valuable tools to be refined in ongoing trials. Blood proteins are a bigger challenge, because of the complexity of the serum protein profile and the scarcity of blood proteomic studies in BC. Previous studies with the BC tissue proteome do not correlate well with the urinary proteome, likely due to the tumor heterogeneity. Cell line proteomic research helps in the understanding of basic mechanisms that drive BC development and progression; the main difficulty is culturing low-grade tumors in vitro, which represents the majority of BC tumors in clinical practice. Conclusion: Protein biomarkers have promising value in the diagnosis, surveillance and prognostic of BC. Urine is the most appropriate body fluid for biomarker research in BC due to its easiness of sampling, stability and enrichment of shed and secreted tumor-specific proteins. Panels of biomarkers may exhibit higher sensitivity than single proteins in the diagnosis of BC at larger populations due to clinical and tumor heterogeneity. Prospective clinical trials are warranted to validate the relevance of proteomic data in the clinical management of BC.


Subject(s)
Humans , Urinary Bladder Neoplasms/diagnosis , Biomarkers, Tumor , Prospective Studies , Sensitivity and Specificity , Cystoscopy , Proteomics
3.
Article in Chinese | WPRIM | ID: wpr-880039

ABSTRACT

OBJECTIVE@#To investigate the correlation between FOXP3, CD11c protein expression and the prognosis of patients with diffuse large B-cell lymphoma (DLBCL).@*METHODS@#This study included 48 patients with DLBCL who were admitted to Jiujiang No.1 People's Hospital and TCM-Integrated Hospital of Southern Medical University from January 2015 to January 2019. The DLBCL tissues removed during the operation were collected as test specimens. The expression of FOXP3 and CD11c protein were detected by immunohistochemistry. The deadline for postoperative follow-up was December 31, 2019, and the patient's short-term efficacy (complete remission, partial remission) and progression-free survival were recorded.@*RESULTS@#FOXP3 protein was positively expressed in the nucleus, mostly focally or diffusely distributed, the FOXP3@*CONCLUSION@#In some patients with DLBCL, FOXP3 and CD11c expresse positively, and the positive expression rate is related to the clinical stage and international prognostic index score. The positive expression of FOXP3 and CD11c indicate a good prognosis.


Subject(s)
Forkhead Transcription Factors , Humans , Immunohistochemistry , Lymphoma, Large B-Cell, Diffuse , Prognosis , Proteomics
4.
Chinese Journal of Biotechnology ; (12): 1526-1540, 2021.
Article in Chinese | WPRIM | ID: wpr-878653

ABSTRACT

Genome-scale metabolic network model (GSMM) is becoming an important tool for studying cellular metabolic characteristics, and remarkable advances in relevant theories and methods have been made. Recently, various constraint-based GSMMs that integrated genomic, transcriptomic, proteomic, and thermodynamic data have been developed. These developments, together with the theoretical breakthroughs, have greatly contributed to identification of target genes, systems metabolic engineering, drug discovery, understanding disease mechanism, and many others. This review summarizes how to incorporate transcriptomic, proteomic, and thermodynamic-constraints into GSMM, and illustrates the shortcomings and challenges of applying each of these methods. Finally, we illustrate how to develop and refine a fully integrated GSMM by incorporating transcriptomic, proteomic, and thermodynamic constraints, and discuss future perspectives of constraint-based GSMM.


Subject(s)
Genome/genetics , Metabolic Engineering , Metabolic Networks and Pathways/genetics , Models, Biological , Proteomics
5.
Chinese Journal of Biotechnology ; (12): 846-859, 2021.
Article in Chinese | WPRIM | ID: wpr-878600

ABSTRACT

Microbial oils are potential resources of fuels and food oils in the future. In recent years, with the rapid development of systems biology technology, understanding the physiological metabolism and lipid accumulation characteristics of oleaginous microorganisms from a global perspective has become a research focus. As an important tool for systems biology research, omics technology has been widely used to reveal the mechanism of high-efficiency production of oils by oleaginous microorganisms. This provides a basis for rational genetic modification and fermentation process control of oleaginous microorganisms. In this article, we summarize the application of omics technology in oleaginous microorganisms, introduced the commonly used sample pre-processing and data analysis methods for omics analysis of oleaginous microorganisms, reviewe the researches for revealing the mechanism of efficient lipid production by oleaginous microorganisms based on omics technologies including genomics, transcriptomics, proteomics (modification) and metabolomics (lipidomics), as well as mathematical models based on omics data. The future development and application of omics technology for microbial oil production are also proposed.


Subject(s)
Fermentation , Lipids , Metabolomics , Proteomics , Technology
6.
Chinese Journal of Biotechnology ; (12): 100-111, 2021.
Article in Chinese | WPRIM | ID: wpr-878546

ABSTRACT

The enrichment of tyrosine phosphorylation sites plays an important role in the study of tyrosine phosphoproteomics and the commonly used enrichment methods are antibody affinity enrichment and SH2 superbinder enrichment. In addition, in order to achieve large-scale identification of tyrosine phosphorylation sites, biological mass spectrometry and bioinformatics have been applied in tyrosine phosphoproteomics. In-depth coverage research of tyrosine phosphoproteomics, revealing the dysregulated kinases in cancer process, may help us understanding the occurrence and development process of cancer. According to literature reports, three quarters of the oncogenes are tyrosine kinase genes. Therefore, tyrosine kinase inhibitors have received more and more attention as anticancer drugs. The application of tyrosine phosphoproteomics technology can identify tyrosine kinases related to cancer and other major diseases, so as to help finding tyrosine kinase inhibitors. In short, tyrosine phosphoproteomics technology can be applied in biomedical fields such as tyrosine kinase identification, tyrosine kinase inhibitor research, and tyrosine phosphorylation signal pathway research.


Subject(s)
Biomedical Research , Mass Spectrometry , Phosphorylation , Proteomics , Tyrosine/metabolism
7.
Article in Chinese | WPRIM | ID: wpr-877608

ABSTRACT

OBJECTIVE@#To screen protein target in prevention and treatment with electroacupuncture (EA) for Alzheimer's disease (AD) and explore the potential mechanism of EA in prevention of AD.@*METHODS@#A total of 40 APP/PS1 transgenic young male mice, 1.5-month old, were randomized into an EA group and a model group, 20 mice in each one, and 20 C57BL/6J mice were chosen as the normal control group. After adaptive housing for 1 week, the mice in the EA group were stimulated with EA at "Baihui" (GV 20), "Fengfu" (GV 16) and "Shenshu" (BL 23), with intermittent wave, 10 Hz in frequency and 2 mA in electric intensity. EA was given once daily, 20 min each time. There was 1 day at interval after EA for 6 days each week. Totally, the intervention lasted for 16 weeks. On day 3 after the end of EA intervention, Morris water maze test was adopted to detect learning and memory abilities of mice in each group. After water maze test, the label-free method was used to measure the difference expressions in cerebral cortex and hippocampus. Using Western blot method, the expressions of guanylate binding protein beta 5 (GNB 5) and histone-H 3 in cerebral cortex and hippocampus were verified. Using immunohistochemical method, the expressions of amyloid beta protein (Aβ) in cerebral cortex and hippocampus were detected.@*RESULTS@#Compared with the normal control group, the escape latency (on day 2, 3 and 4) was prolonged, the frequency of crossing platform and the duration of platform stay were decreased in the mice of the model group (@*CONCLUSION@#The intervention with EA effectively prevents from the decline of learning and memory ability and the formation of Aβ senile plaques in cerebral cortex and hippocampus in young mouse models of AD after growing up. Besides, EA plays a regulatory function for protein expression differences induced by AD model.


Subject(s)
Alzheimer Disease/therapy , Amyloid beta-Peptides/genetics , Animals , Disease Models, Animal , Electroacupuncture , Hippocampus , Male , Mice , Mice, Inbred C57BL , Proteomics
8.
J. venom. anim. toxins incl. trop. dis ; 27: e20200177, 2021. tab, graf
Article in English | ID: biblio-1250255

ABSTRACT

The western Russell's viper (Daboia russelii) is widely distributed in South Asia, and geographical venom variation is anticipated among distant populations. Antivenoms used for Russell's viper envenomation are, however, raised typically against snakes from Southern India. The present study investigated and compared the venom proteomes of D. russelii from Sri Lanka (DrSL) and India (DrI), the immunorecognition of Indian VINS Polyvalent Antivenom (VPAV) and its efficacy in neutralizing the venom toxicity. Methods: The venoms of DrSL and DrI were decomplexed with C18 high-performance liquid chromatography and SDS-polyacrylamide gel electrophoresis under reducing conditions. The proteins fractionated were identified through nano-ESI-liquid chromatography-tandem mass spectrometry (LCMS/MS). The immunological studies were conducted with enzyme-linked immunosorbent assay. The neutralization of the venom procoagulant effect was evaluated in citrated human plasma. The neutralization of the venom lethality was assessed in vivo in mice adopting the WHO protocol. Results: DrSL and DrI venom proteomes showed comparable major protein families, with phospholipases A2 (PLA2) being the most abundant (> 60% of total venom proteins) and diverse (six protein forms identified). Both venoms were highly procoagulant and lethal (intravenous median lethal dose in mice, LD50 = 0.24 and 0.32 µg/g, for DrSL and DrI, respectively), while lacking hemorrhagic and anticoagulant activities. VPAV was immunoreactive toward DrSL and DrI venoms, indicating conserved protein antigenicity in the venoms. The high molecular weight venom proteins were, however, more effectively immunorecognized than small ones. VPAV was able to neutralize the coagulopathic and lethal effects of the venoms moderately. Conclusion: Considering that a large amount of venom can be injected by Russell's viper during envenomation, the potency of antivenom can be further improved for optimal neutralization and effective treatment. Region-specific venoms and key toxins may be incorporated into the immunization procedure during antivenom production.(AU)


Subject(s)
Animals , Poisons/toxicity , Antivenins/biosynthesis , Russell's Viper , Proteomics , Geographic Locations
9.
J. venom. anim. toxins incl. trop. dis ; 27: e20200105, 2021. tab, graf
Article in English | ID: biblio-1180822

ABSTRACT

Amphibians inhabit the terrestrial environment, a conquest achieved after several evolutionary steps, which were still insufficient to make them completely independent of the aquatic environment. These processes gave rise to many morphological and physiological changes, making their skin (and cutaneous secretion) rich in bioactive molecules. Among the tree frogs, the secretion is composed mainly of peptides; but alkaloids, proteins and steroids can also be found depending on the species. The most known class of biologically active molecules is the antimicrobial peptides (AMPs) that act against bacteria, fungi and protozoans. Although these molecules are well-studied among the hylids, AMPs ontogeny remains unknown. Therefore, we performed peptidomic and proteomic analyses of Pithecopus nordestinus (formerly Phyllomedusa nordestina) in order to evaluate the peptide content in post-metamorphosed juveniles and adult individuals. Methods: Cutaneous secretion of both life stages of individuals was obtained and analyzed by LC-MS/MS after reduction and alkylation of disulfide bonds or reduction, alkylation and hydrolysis by trypsin. Results: Differences in the TIC profile of juveniles and adults in both treatments were observed. Moreover, the proteomic data revealed known proteins and peptides, with slight differences in the composition, according to the life stage and the treatment. AMPs were identified, and bradykinin-potentiating peptides were observed in trypsin-treated samples, which suggests a protein source of such peptide (cryptide). Conclusion: In general, skin secretion contents were similar between juveniles and adults, varying in quantity, indicating that the different stages of life are reflected in the number of molecules and not on their diversity.(AU)


Subject(s)
Animals , Female , Peptides , Trypsin , Proteomics , Amphibians , Bodily Secretions , Hydrolysis
10.
Pesqui. vet. bras ; 41: e06129, 2021. tab
Article in English | ID: biblio-1180876

ABSTRACT

Mastitis occupies a prominent place among the diseases that affect dairy herds due to economic problems and public health. Staphylococcus spp. are infectious agents more involved in the etiology of caprine mastites, especially coagulase-negative Staphylococcus. Nineteen isolates of Staphylococcus spp. were obtained from subclinical caprine mastitis. All isolates were characterized by MALDI-TOF MS, being 47.36% (9/19) identified for S. epidermidis, 15.78% (3/19) for S. warneri, 10.52% (2/19) for S. aureus and S. caprae and 5.26% (1/19) for S. lugdunensis, S. simulans, and S. cohnii. All isolates characterized by MALDI-TOF were subjected a to polymerase chain reaction (PCR) for the 16S rRNA gene of Staphylococcus spp. to confirm the gender. After determining the species, tests for phenotypic detection of resistance to beta-lactams were carried out simple disk diffusion oxacillin, cefoxitin, penicillin G and amoxicillin + clavulanic acid, agar "screen" oxacillin and microdilution (MIC) cefoxitin. The disk diffusion test showed a strength of 58% (11/19) for penicillin G, 26.31% (5/19) for cefoxitin and 26.31% (5/19) for oxacillin. All strains were susceptible to amoxicillin + clavulanic acid and agar "screen" oxacillin. In the MIC, 63.15% (12/19) of the samples were cefoxitin resistant (MIC >4.0μg/ml). Then isolates were subjected to detection of the mecA resistance genes and regulators (mecl and mecRI), mecC and blaZ. Two samples of Staphylococcus epidermidis had the mecA gene. All isolates were negative for the mecA gene variant, mecl, mecRI, mecC and blaZ. These findings reinforce the importance of this group of microorganisms in the etiology of subclinical mastitis in goats and open perspectives for future research to investigate the epidemiology of the disease.(AU)


A mastite ocupa lugar de destaque entre as doenças que acometem o rebanho leiteiro, em virtude de problemas econômicos e de saúde pública. Staphylococcus spp. são os agentes infecciosos mais envolvidos na etiologia das mastites caprinas, principalmente Staphylococcus coagulase negativo. Dezenove isolados de Staphylococcus spp. foram obtidos a partir de mastite caprina subclínica. Todos os isolados foram caracterizados por MALDI-TOF MS, sendo 47,36% (9/19) identificadas como S. epidermidis, 15,78%(3/19) como S. warneri, 10,52% (2/19) como S. caprae e S. aureus e 5,26% (1/19) tanto para S. lugdunensis, como para S. simulans e S. cohnii. Todos os isolados caracterizados pelo MALDI-TOF foram submetidos a reação em cadeia da polimerase (PCR) para o gene 16rRNA de Staphylococcus spp. para a confirmação do gênero. Após a determinação da espécie, foram realizadas as provas para a detecção fenotípica de resistência aos beta-lactâmicos: difusão em disco simples de oxacilina, cefoxitina, penicilina G e amoxacilina +ácido clavulânico, ágar "screen" de oxacilina e microdiluição em caldo (MIC) de cefoxitina. O teste de difusão em disco demonstrou resistência de 58% (11/19) para penicilina G, 26,31% (5/19) para cefoxitina e 26,31% (5/19) para oxacilina. Todas as amostras foram sensíveis a amoxicilina + ácido clavulânico e ao ágar "screen" de oxacilina. Pelo MIC, 63,15% (12/19) das amostras foram resistentes a cefoxitina (MIC >4,0μg/ml). Em seguida os isolados foram submetidos a detecção dos genes de resistência mecA e seus reguladores (mecl e mecRI), mecC e blaZ. Duas amostras de S. epidermidis apresentaram o gene mecA. Todos os isolados foram negativos para a variante do gene mecA, mecl, mecRI, mecC e blaZ. Tais achados reforçam a importância deste grupo de microrganismos na etiologia da mastite subclínica em caprinos e abre perspectivas para futuras pesquisas para a investigação da epidemiologia da doença.(AU)


Subject(s)
Animals , Penicillin G , Staphylococcus , Ruminants , Goats , Proteomics , beta-Lactams , Mastitis , Polymerase Chain Reaction
11.
J. venom. anim. toxins incl. trop. dis ; 27: e20200125, 2021. tab, graf
Article in English | ID: biblio-1287096

ABSTRACT

Background Naja mandalayensis is a spitting cobra from Myanmar. To the best of our knowledge, no studies on this venom composition have been conducted so far. On the other hand, few envenomation descriptions state that it elicits mainly local inflammation in the victims' eyes, the preferred target of this spiting cobra. Symptoms would typically include burning and painful sensation, conjunctivitis, edema and temporary loss of vision. Methods We have performed a liquid-chromatography (C18-RP-HPLC) mass spectrometry (ESI-IT-TOF/MS) based approach in order to biochemically characterize N. mandalayensis venom. Results A wide variety of three-finger toxins (cardiotoxins) and metallopeptidases were detected. Less abundant, but still representative, were cysteine-rich secretory proteins, L-amino-acid oxidases, phospholipases A2, venom 5'-nucleotidase and a serine peptidase inhibitor. Other proteins were present, but were detected in a relatively small concentration. Conclusion The present study set the basis for a better comprehension of the envenomation from a molecular perspective and, by increasing the interest and information available for this species, allows future venom comparisons among cobras and their diverse venom proteins.(AU)


Subject(s)
Animals , Proteomics/classification , Elapid Venoms/enzymology
12.
Braz. j. med. biol. res ; 54(4): e9850, 2021. tab, graf
Article in English | LILACS | ID: biblio-1153545

ABSTRACT

Respiratory syncytial virus (RSV) infection is the main cause of lower respiratory tract infection in children. However, there is no effective treatment for RSV infection. Here, we aimed to identify potential biomarkers to aid in the treatment of RSV infection. Children in the acute and convalescence phases of RSV infection were recruited and proteomic analysis was performed to identify differentially expressed proteins (DEPs). Subsequently, promising candidate proteins were determined by functional enrichment and protein-protein interaction network analysis, and underwent further validation by western blot both in clinical and mouse model samples. Among the 79 DEPs identified in RSV patient samples, 4 proteins (BPGM, TPI1, PRDX2, and CFL1) were confirmed to be significantly upregulated during RSV infection. Functional analysis showed that BPGM and TPI1 were mainly involved in glycolysis, indicating an association between RSV infection and the glycolysis metabolic pathway. Our findings provide insights into the proteomic profile during RSV infection and indicated that BPGM, TPI1, PRDX2, and CFL1 may be potential therapeutic biomarkers or targets for the treatment of RSV infection.


Subject(s)
Humans , Child , Respiratory Syncytial Virus, Human , Respiratory Syncytial Virus Infections , Biomarkers , Proteomics
13.
Article in Chinese | WPRIM | ID: wpr-878925

ABSTRACT

To study the time-toxicity relationship and mechanism of Gardeniae Fructus extract on the hepatoxicity in rats. Rats were randomly divided into C group(0 day), D5 group(5 days), D12 group(12 days), D19 group(19 days), and D26 group(7 days recovery after 19 days of administration). The rats in normal group received normal saline through intragastric administration, and the rats in other groups received 10 g·kg~(-1 )Gardeniae Fructus extract through intragastric administration. After the final administration, the livers were collected. Hematoxylin-eosin staining was used to observe the histopathological changes in the liver tissue. Total liver proteins were extracted for proteomic analysis, detected by the Nano-ESI liquid-mass spectrometry system and identified by Protein Disco-very software. SIEVE software was used for relative quantitative and qualitative analysis of proteins. The protein-protein interaction network was constructed based on STRING. Cytoscape software was used for cluster analysis of differential proteins. Kyoto encyclopedia of genes and genomes(KEGG) database was used to perform enrichment signal pathway analysis. Pearson correlation analysis was performed for the screened differential protein expression and liver pathology degree score. The results showed that the severity of liver injury in D5, D12 and D19 groups was significantly higher than that in group C. The degree of liver damage in D5 group was slightly higher than that in D12 and D19 groups, with no significant difference between group D26 and group C. Totally 147 key differential proteins have been screened out by proteomics and mainly formed 6 clusters, involving in drug metabolism pathways, retinol metabolism pathways, proteasomes, amino acid biosynthesis pathways, and glycolysis/gluconeogenesis pathways. The results of Pearson correlation analysis indicated that differential protein expressions had a certain temporal relationship with the change of liver pathological degree. The above results indicated that the severity of liver damage caused by Gardeniae Fructus extract did not increase with time and would recover after drug with drawal. The above pathways may be related to the mechanism of liver injury induced by Gardeniae Fructus extract.


Subject(s)
Animals , Drugs, Chinese Herbal/toxicity , Fruit , Gardenia , Liver , Proteomics , Rats , Signal Transduction
14.
Article in Chinese | WPRIM | ID: wpr-878892

ABSTRACT

The rat osteoarthritis model was replicated by injection of sodium iodoacetate into the knee joint cavity, and the effects of Gancao Fuzi Decoction on rat osteoarthritis and the proteome of articular cartilage were investigated. Sixty SD rats weighing 230-250 g were randomly divided into normal group, model group, glucosamine sulfate group, and Gancao Fuzi Decoction high, medium and low dose groups. Osteoarthritis model was induced by intra-articular injection of sodium iodoacetate(3 mg on each leg) in all groups except the normal group. After modeling, each administration group was given intragastric administration for 1 month. During the administration period, joint pain test and joint width measurement were performed every week to observe the autonomous behavior of rats. Enzyme linked immunosorbent assay(ELISA) method was used to detect the contents of tumor necrosis factor-α(TNF-α), interleukin-1β(IL-1β), matrix metalloproteinase-3(MMP-3), and matrix metalloproteinase tissue inhibitor(TIMP-1) in rat joint lavage fluid. Hematoxylin-eosin(HE) staining was used to observe bone and joint morphology. Nano-LC-LTQ-Orbitrap system was used to detect arti-cular cartilage proteins. The results showed that, compared with the model group, Gancao Fuzi Decoction could significantly improve joint pain and joint swelling in osteoarthritis rats, significantly reduce the contents of TNF-α, IL-1β and MMP-3 in the joint cavity la-vage fluid, increase the content of TIMP-1, and relieve inflammatory diseases such as enlarged joint space, rough cartilage edge, different thickness of cartilage layer, and disordered arrangement of chondrocytes. After comparing the proteins between the groups, 273 differential proteins were screened out. KEGG analysis found that the above differential proteins involved 43 signaling pathways such as systemic lupus erythematosus, among which 11 signaling pathways were related to osteoarthritis. The above results indicated that Gancao Fuzi Decoction had a preventive effect on osteoarthritis, and its mechanism of action may be accomplished by regulating the protein expression of osteoarthritis-related signal pathways.


Subject(s)
Animals , Cartilage, Articular , Drugs, Chinese Herbal , Osteoarthritis/drug therapy , Plant Extracts , Proteomics , Rats , Rats, Sprague-Dawley
15.
Electron. j. biotechnol ; 48: 86-94, nov. 2020. tab, graf, ilus
Article in English | LILACS | ID: biblio-1254836

ABSTRACT

BACKGROUND: Chinese hamster ovary (CHO) cells are the workhorse for obtaining recombinant proteins. Proteomic studies of these cells intend to understand cell biology and obtain more productive and robust cell lines for therapeutic protein production in the pharmaceutical industry. Because of the great importance of precipitation methods for the processing of samples in proteomics, the acetone, methanol-chloroform (M/C), and trichloroacetic acid (TCA)-acetone protocols were compared for CHO cells in terms of protein recovery, band pattern resolution, and presence on SDS-PAGE. RESULTS: Higher recovery and similar band profile with cellular homogenates were obtained using acetone precipitation with ultrasonic bath cycles (104.18 ± 2.67%) or NaOH addition (103.12 ± 5.74%), compared to the other two protocols tested. TCA-acetone precipitates were difficult to solubilize, which negatively influenced recovery percentage (77.91 ± 8.79%) and band presence. M/C with ultrasonic homogenization showed an intermediate recovery between the other two protocols (94.22 ± 4.86%) without affecting protein pattern on SDS-PAGE. These precipitation methods affected the recovery of low MW proteins (< 15 kDa). CONCLUSIONS: These results help in the processing of samples of CHO cells for their proteomic study by means of an easily accessible, fast protocol, with an almost complete recovery of cellular proteins and the capture of the original complexity of the cellular composition. Acetone protocol could be incorporated to sample-preparation workflows in a straightforward manner and can probably be applied to other mammalian cell lines as well.


Subject(s)
Animals , Recombinant Proteins , CHO Cells , Proteomics/methods , Acetone , Chemical Precipitation , Solubility , Trichloroacetic Acid , Cell Separation , Chloroform , Cell Culture Techniques , Methanol , Electrophoresis, Polyacrylamide Gel
16.
Rev. colomb. anestesiol ; 48(3): 155-161, July-Sept. 2020. tab, graf
Article in English | LILACS, COLNAL | ID: biblio-1126297

ABSTRACT

Abstract Introduction: With the evolution of diagnostic techniques in traumatic brain injury (TBI), the study of neurological injury has made progress based on the concepts of primary and secondary injury, leading to the era of proteomics to understand the complex molecular events involved in the process. Objectives: This narrative review is intended to discuss the state of the art of the most frequently used biomarkers in TBI, their clinical utility, and the implications for therapeutic decision-making protocols. Materials and methods: In order to fulfill the objective of this paper, a literature review was conducted of the most important databases. Results: Several biomarkers have been studied as prognostic factors in patients with TBI. Learning about their sensitivity and specificity in neurological injury, and its post-trauma evolution over time, has been the goal of various papers in the past few years. Conclusion: Breakthroughs in the study of protein degradation make it necessary to broaden the spectrum and knowledge of new diagnostic methods in TBI. Further studies are needed to define the role of biomarkers and to promote protocols integrating specific values.


Resumen Introducción: Con la evolución de las técnicas diagnósticas en el trauma craneoencefálico, el estudio de la lesión neurológica ha progresado sobre los conceptos de lesión primaria y secundaria, para entrar así en la era de la proteómica y, con ella, entender los complejos eventos moleculares existentes en su proceso. Objetivos: En esta revisión narrativa se pretende presentar el estado actual de los biomarcadores que más se usan en lesión cerebral traumática, su utilidad clínica y las implicaciones en protocolos de decisión terapéutica. Materiales y métodos: Para dar respuesta al objetivo de este trabajo, se realizó una revisión de la literatura en las principales bases de datos. Resultados: Se han estudiado varios biomarcadores como factor pronóstico en pacientes con trauma craneoencefálico. Conocer su sensibilidad y especificidad para la lesión neurológica, así como su evolución en el tiempo tras el traumatismo, ha sido el objetivo de diversos trabajos en los últimos años. Conclusión: El avance en el estudio de los productos de degradación de las proteínas hace necesario ampliar el espectro y el conocimiento en el campo de los nuevos métodos diagnósticos en el trauma craneoencefálico. Se requieren más estudios para definir la función de los biomarcadores y proponer protocolos que integren valores específicos.


Subject(s)
Humans , Biomarkers , Soft Tissue Injuries , Brain Injuries, Traumatic , Prognosis , Biological Factors/administration & dosage , Proteomics
17.
Electron. j. biotechnol ; 47: 1-9, sept. 2020. graf, tab
Article in English | LILACS | ID: biblio-1224606

ABSTRACT

BACKGROUND: γ-Aminobutyric acid (GABA) bypasses the TCA cycle via GABA shunt, suggesting a relationship with respiration. However, little is known about its role in seed germination under salt conditions. RESULTS: In this study, exogenous GABA was shown to have almost no influence on mungbean seed germination, except 0.1 mM at 10 h, while it completely alleviated the inhibition of germination by salt treatment. Seed respiration was significantly inhibited by 0.1 and 0.5 mM GABA, but was evidently enhanced under salt treatment, whereas both were promoted by 1 mM GABA alone or with salt treatment. Mitochondrial respiration also showed a similar trend at 0.1 mM GABA. Moreover, proteomic analysis further showed that 43 annotated proteins were affected by exogenous GABA, even 0.1 mM under salt treatment, including complexes of the mitochondrial respiratory chain. CONCLUSIONS: Our study provides new evidence that GABA may act as a signal molecule in regulating respiration of mungbean seed germination in response to salt stress.


Subject(s)
Seeds/growth & development , Vigna , gamma-Aminobutyric Acid , Respiration , Stress, Physiological , Proteins , Germination , Proteomics , Salt Tolerance , Salt Stress
18.
Braz. dent. j ; 31(3): 319-336, May-June 2020. tab, graf
Article in English | LILACS, BBO | ID: biblio-1132301

ABSTRACT

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.


Subject(s)
Humans , Pulpitis , Dental Pulp , Pilot Projects , Proteomics
19.
Braz. j. med. biol. res ; 53(1): e9001, Jan. 2020. tab, graf
Article in English | LILACS | ID: biblio-1055477

ABSTRACT

Due to its various structures in bio-compounds, snake venom is the indisputable result of evolutionary stages of molecules with an increasingly complex structure, high specificity, and of great importance for medicine because of their potential. The present study proposed an underpinning examination of venom composition from nine species of venomous snakes using a useful and replicable methodology. The objective was the extension of the evaluation of protein fractions in the field up to 230 kDa to permit possible identification of some fractions that are insufficiently studied. The gel capillary electrophoresis method on the chip was performed using an Agilent 2100 bioassay with the 80 and 230-LabChip Protein kits. Interpretation of electrophoresis was performed using the Protein 2100 expert (Agilent) test software as follows: a) Protein 80 (peak size scale): 1.60, 3.5, 6.50, 15.00, 28.00, 46.00, 63.00, 95.00 kDa; b) Protein 230 (peak size scale): 4.50, 7.00, 15.00, 28.00, 46.00, 63.00, 95.00, 150.00, 240.00 kDa. The screening revealed the presence of compounds with a molecular weight greater than 80 kDa, in the case of Vipera aspis and Vipera xantina palestinae. For V. aspis, a 125 kDa molecular weight pro-coagulant protein was identified, known as being involved in the reduction of plasma clotting time without any direct activity in the fibrinogen coagulation process. The samples examined on the Protein 230-LabChip electrophoresis chip can be considered as a novelty with possible uses in medicine, requiring further approaches by advanced proteomics techniques to confirm the intimate structural features and biological properties of snake venoms.


Subject(s)
Animals , Viper Venoms/chemistry , Proteins/chemistry , Viperidae/classification , Viper Venoms/analysis , Proteins/isolation & purification , Proteins/analysis , Electrophoresis, Capillary , Proteome/classification , Proteome/chemistry , Proteomics/methods
20.
Article in English | WPRIM | ID: wpr-816620

ABSTRACT

BACKGROUND: Adrenal cortical carcinoma (ACC) is a rare cancer with a variable prognosis. Several prognostic factors of ACC have been previously reported, but a proteomic analysis has not yet been performed. This study aimed to investigate prognostic biomarkers for ACC using a proteomic approach.METHODS: We used reverse-phase protein array data from The Cancer Proteome Atlas, and identified differentially expressed proteins in metastatic ACCs. Multivariate Cox regression analysis adjusted by age and staging was used for survival analysis, and the C-index and category-free net reclassification improvement (cfNRI) were utilized to evaluate additive prognostic value.RESULTS: In 46 patients with ACC, cyclin B1, transferrin receptor (TfR1), and fibronectin were significantly overexpressed in patients with distant metastasis. In multivariate models, high expression of cyclin B1 and TfR1 was significantly associated with mortality (hazard ratio [HR], 6.13; 95% confidence interval [CI], 1.02 to 36.7; and HR, 6.59; 95% CI, 1.14 to 38.2; respectively), whereas high fibronectin expression was not (HR, 3.92; 95% CI, 0.75 to 20.4). Combinations of high cyclin B1/high TfR1, high cyclin B1/high fibronectin, and high TfR1/high fibronectin were strongly associated with mortality ([HR, 13.72; 95% CI, 1.89 to 99.66], [HR, 9.22; 95% CI, 1.34 to 63.55], and [HR, 18.59; 95% CI, 2.54 to 135.88], respectively). In reclassification analyses, cyclin B1, TfR1, fibronectin, and combinations thereof improved the prognostic performance (C-index, 0.78 to 0.82–0.86; cfNRI, all P values <0.05).CONCLUSION: In ACC patients, the overexpression of cyclin B1, TfR1, and fibronectin and combinations thereof were associated with poor prognosis.


Subject(s)
Adrenocortical Carcinoma , Biomarkers , Cyclin B1 , Cyclins , Fibronectins , Humans , Mortality , Neoplasm Metastasis , Prognosis , Protein Array Analysis , Proteome , Proteomics , Receptors, Transferrin , Transferrin
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