1
|
Singh H, Jakhar R, Kirar M, Sehrawat N. A systematic evaluation of sample preparation and 2-D gel electrophoresis protocol for mosquito proteomic profiling. MethodsX 2024; 12:102677. [PMID: 38660035 PMCID: PMC11041838 DOI: 10.1016/j.mex.2024.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/24/2024] [Indexed: 04/26/2024] Open
Abstract
-Mosquito act as the carrier insect to transfer pathogens into hosts for various vector-borne diseases.To identify the pathogenesis causing determinant, comprehensive knowledge of the protein expression in different tissues and physiological conditions is very important. The most widely used technique is 2-D gel electrophoresis to study the protein expression in mosquitoes. 2-D gel electrophoresis is the multistep process to resolve intact protein with similar molecular weight. It is also useful to separate post-translational modified protein, which are not distinguished through shotgun proteomic analysis. Here, we optimized the protocol for 2-D gel electrophoresis that can effectively resolve the protein in mosquitoes and some other insects, to target immunogenic protein to fight against the vector borne disease. The optimized 2-D protocol helps to resolve complex proteomic data which is very difficult to analyze in mosquitoes.The updated protocol improved the protein solubility, resolution and visualization that help in comparative analysis of protein expression.
Collapse
Affiliation(s)
- Hitesh Singh
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Renu Jakhar
- Indira Gandhi University, Meerpur, Rewari, Haryana, India
| | - Manisha Kirar
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Neelam Sehrawat
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
| |
Collapse
|
2
|
Hlozáková TK, Gálová Z, Šliková S, Leišová-Svobodová L, Beinhauer J, Dyčka F, Šebela M, Zetochová E, Gregová E. Molecular Characterization of Novel x-Type HMW Glutenin Subunit 1B × 6.5 in Wheat. Plants (Basel) 2021; 10:plants10102108. [PMID: 34685917 PMCID: PMC8541187 DOI: 10.3390/plants10102108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/29/2022]
Abstract
A novel high molecular weight glutenin subunit encoded by the Glu-1B locus was identified in the French genotype Bagou, which we named 1B × 6.5. This subunit differed in SDS-PAGE from well-known 1B × 6 and 1B × 7 subunits, which are also encoded at this locus. Subunit 1B × 6.5 has a theoretical molecular weight of 88,322.83 Da, which is more mobile than 1B × 6 subunit, and isoelectric point (pI) of about 8.7, which is lower than that for 1B × 6 subunit. The specific primers were designed to amplify and sequence 2476 bp of the Glu-1B locus from genotype Bagou. A high level of similarity was found between the sequence encoding 1B × 6.5 and other x-type encoding alleles of this locus.
Collapse
Affiliation(s)
- Tímea Kuťka Hlozáková
- Faculty of Biotechnology and Food Science, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (T.K.H.); (Z.G.)
| | - Zdenka Gálová
- Faculty of Biotechnology and Food Science, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (T.K.H.); (Z.G.)
| | - Svetlana Šliková
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská Cesta 122, 921 01 Piešťany, Slovakia; (S.Š.); (E.Z.)
| | | | - Jana Beinhauer
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 27, 783 71 Olomouc, Czech Republic; (J.B.); (F.D.); (M.Š.)
| | - Filip Dyčka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 27, 783 71 Olomouc, Czech Republic; (J.B.); (F.D.); (M.Š.)
| | - Marek Šebela
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 27, 783 71 Olomouc, Czech Republic; (J.B.); (F.D.); (M.Š.)
| | - Erika Zetochová
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská Cesta 122, 921 01 Piešťany, Slovakia; (S.Š.); (E.Z.)
| | - Edita Gregová
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská Cesta 122, 921 01 Piešťany, Slovakia; (S.Š.); (E.Z.)
- Correspondence:
| |
Collapse
|
3
|
Almeida J, Roma-Rodrigues C, Mahmoud AG, Guedes da Silva MFC, Pombeiro AJL, Martins LMDRS, Baptista PV, Fernandes AR. Structural characterization and biological properties of silver(I) tris(pyrazolyl)methane sulfonate. J Inorg Biochem 2019; 199:110789. [PMID: 31357066 DOI: 10.1016/j.jinorgbio.2019.110789] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 11/24/2022]
Abstract
The water-soluble 1D helical coordination polymer [Ag(Tpms)]n (1) [Tpms = tris(pyrazolyl)methane sulfonate, -O3SC(pz)3; pz = pyrazolyl] was synthesized and fully characterized, its single-crystal X-ray diffraction analysis revealing the ligand acting as a bridging chelate N3-donor ligand. The antiproliferative potential of 1 was performed on two human tumour cell lines, A2780 and HCT116, and in normal fibroblasts, with a much higher effect in the former cell line (IC50 of 0.04 μM) as compared to the latter cell line and to normal fibroblasts. Compound 1 does not alter cell cycle progression but interferes with the adherence of A2780 cells triggering cell apoptosis. Apoptosis appears to occur via the extrinsic pathway (no changes in mitochondria membrane potential, reactive oxygen species (ROS) and pro-apoptotic (B-cell lymphoma 2 (BCL-2) associated protein (BAX))/anti-apoptotic (BCL-2) ratio) being this hypothesis also supported by the presence of silver mainly in the supernatants of A2780 cells. Results also indicated that cell death via autophagy was triggered. Proteomic analysis allowed us to confirm that compound 1 is able to induce a stress response in A2780 cells that is related with its antiproliferative activity and the trigger of apoptosis.
Collapse
|
4
|
Starkova TY, Artamonova TO, Ermakova VV, Chikhirzhina EV, Khodorkovskii MA, Tomilin AN. The Profile of Post-translational Modifications of Histone H1 in Chromatin of Mouse Embryonic Stem Cells. Acta Naturae 2019; 11:82-91. [PMID: 31413884 PMCID: PMC6643340 DOI: 10.32607/20758251-2019-11-2-82-91] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 01/10/2023] Open
Abstract
Linker histone H1 is one of the main chromatin proteins which plays an important role in organizing eukaryotic DNA into a compact structure. There is data indicating that cell type-specific post-translational modifications of H1 modulate chromatin activity. Here, we compared histone H1 variants from NIH/3T3, mouse embryonic fibroblasts (MEFs), and mouse embryonic stem (ES) cells using matrix-assisted laser desorption/ ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS). We found significant differences in the nature and positions of the post-translational modifications (PTMs) of H1.3-H1.5 variants in ES cells compared to differentiated cells. For instance, methylation of K75 in the H1.2-1.4 variants; methylation of K108, K148, K151, K152 K154, K155, K160, K161, K179, and K185 in H1.1, as well as of K168 in H1.2; phosphorylation of S129, T146, T149, S159, S163, and S180 in H1.1, T180 in H1.2, and T155 in H1.3 were identified exclusively in ES cells. The H1.0 and H1.2 variants in ES cells were characterized by an enhanced acetylation and overall reduced expression levels. Most of the acetylation sites of the H1.0 and H1.2 variants from ES cells were located within their C-terminal tails known to be involved in the stabilization of the condensed chromatin. These data may be used for further studies aimed at analyzing the functional role played by the revealed histone H1 PTMs in the self-renewal and differentiation of pluripotent stem cells.
Collapse
Affiliation(s)
- T. Yu. Starkova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - T. O. Artamonova
- Peter the Great St.Petersburg Polytechnic University, Politekhnicheskaya Str. 29, St. Petersburg, 195251 , Russia
| | - V. V. Ermakova
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - E. V. Chikhirzhina
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
| | - M. A. Khodorkovskii
- Peter the Great St.Petersburg Polytechnic University, Politekhnicheskaya Str. 29, St. Petersburg, 195251 , Russia
| | - A. N. Tomilin
- Institute of Cytology of the Russian Academy of Sciences, Laboratory of Molecular Biology of Stem Cells, Tikhoretsky Ave. 4, St. Petersburg, 194064, Russia
- Saint Petersburg State University, 13B Universitetskaya Emb., St. Petersburg, 199034, Russia
| |
Collapse
|
5
|
Hou X, Liu R, Huang C, Jiang L, Zhou Y, Chen Q. Cyclophilin A was revealed as a candidate marker for human oral submucous fibrosis by proteomic analysis. Cancer Biomark 2018; 20:345-356. [PMID: 28826174 DOI: 10.3233/cbm-170142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Oral submucous fibrosis (OSF) is a chronic insidious disease which predisposes to oral cancer. Understanding the molecular markers for OSF is critical for diagnosis and treatment of oral cancer. In this study, the proteins expression profile of OSF tissues was compared to normal mucous tissues by 2 dimensional electrophoresis (2-DE). The 2-DE images were analyzed through cut, spot detection and match analysis using mass spectrometry (MS). Differentially expressed genes were identified as candidates. RT-PCR, Western Blot and immunohistochemistry were performed to validate the difference in expression of the candidates between OSF and normal mucous tissues. The shRNA targeted to the candidates were then transfected by Lipofectamine2000 to the 3T3 cells to study gene function. Cell proliferation and apoptosis were measured by MTT, clonogenic formation, PI and TUNEL staining. From the proteomic analysis, 94 of the 182 selected spots with differential expression were identified by MS analysis and Cyclophilin A (CYPA) was determined to be the OSF-associated protein candidate. The significant differences in expression between OSF and normal tissues were verified and confirmed by RT-PCR, Western blot and Immunohistochemical analysis. Inhibition of CYPA expression by RNA interference suggested its potential activities involved in cell proliferation and apoptosis process. In conclusion, these results indicated a novel molecular mechanism of OSF pathogenesis and demonstrated CYPA as a potential biomarker and gene intervention targets of OSF. These data may help the development for therapeutics of oral cancer.
Collapse
Affiliation(s)
- Xiaohui Hou
- Laboratory of Oral Biomedical Science and Translational Medicine, School of Stomatology, Tongji University, Shanghai 200072, China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Rui Liu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Canhua Huang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Lu Jiang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| |
Collapse
|
6
|
Abstract
Naja ashei is an African spitting cobra species closely related to N. mossambica and N. nigricollis. It is known that the venom of N. ashei, like that of other African spitting cobras, mainly has cytotoxic effects, however data about its specific protein composition are not yet available. Thus, an attempt was made to determine the venom proteome of N. ashei with the use of 2-D electrophoresis and MALDI ToF/ToF (Matrix-Assisted Laser Desorption/Ionization Time of Flight) mass spectrometry techniques. Our investigation revealed that the main components of analysed venom are 3FTxs (Three-Finger Toxins) and PLA₂s (Phospholipases A₂). Additionally the presence of cysteine-rich venom proteins, 5'-nucleotidase and metalloproteinases has also been confirmed. The most interesting fact derived from this study is that the venom of N. ashei includes proteins not described previously in other African spitting cobras-cobra venom factor and venom nerve growth factor. To our knowledge, there are currently no other reports concerning this venom composition and we believe that our results will significantly increase interest in research of this species.
Collapse
Affiliation(s)
- Konrad Kamil Hus
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959 Rzeszow, Poland.
| | - Justyna Buczkowicz
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959 Rzeszow, Poland.
| | - Vladimír Petrilla
- Department of Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Kosice, Slovakia.
- Zoological Department, Zoological Garden Košice, Široká 31, 040 06 Košice-Kavečany, Slovakia.
| | - Monika Petrillová
- Department of General Education Subjects, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Kosice, Slovakia.
| | - Andrzej Łyskowski
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959 Rzeszow, Poland.
| | - Jaroslav Legáth
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959 Rzeszow, Poland.
- Department of Pharmacology and Toxicology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Kosice, Slovakia.
| | - Aleksandra Bocian
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6, 35-959 Rzeszow, Poland.
| |
Collapse
|
7
|
Menezes EB, de Oliveira RV, van Tilburg MF, Barbosa EA, Nascimento NV, Velho ALMCS, Moreno FB, Moreira RA, Monteiro-Moreira ACO, Carvalho GMC, Ramos AF, Memili E, Moura AA. Proteomic analysis of seminal plasma from locally-adapted "Curraleiro Pé-Duro bulls" (Bos taurus): identifying biomarkers involved in sperm physiology in endangered animals for conservation of biodiversity. Anim Reprod Sci 2017. [PMID: 28625714 DOI: 10.1016/j.anireprosci.2017.05.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The present study was aimed at evaluating the seminal plasma proteins and sperm parameters of Curraleiro Pé-Duro bulls. Semen was collected from 10 bulls by electroejaculation, and sperm parameters were evaluated in fresh and frozen-thawed semen. Seminal plasma proteins were analyzed by 2-D SDS-PAGE and mass spectrophotometry. Tools in computational biology were used to generate bioinformatic knowledge and evaluate gene ontology, protein-protein interactions, phylogenetic trees and multiple sequence alignments. Sperm motility in fresh and frozen-thawed semen was 78.8±1.8% and 21.2±1.6%, respectively. Pearson's correlations were evaluated (p<0.05). Sperm motility and vigor in fresh semen were correlated with clusterin, TIMP2 and cathepsin S (r=0.64-0.71) and sperm defects were related to inhibitor of carbonic anhydrase and BSP 5 (r=0.78-0.80). Clusterin, BSP 5, alpha-enolase, creatine kinase M-type, glyceraldehyde-3-phosphate dehydrogenase, BSP 3, albumin, and 5'-nucleotidase and legumain were correlated with acrosome intact live sperm (r=0.80-0.64). Associations were detected between sperm vigor and spermadhesin 1 (r=-0.89), and between sperm defects in fresh semen and spermadhesin 1 and clusterin (r=-0.81). Sperm motility in frozen-thawed semen was associated with BSP 1, spermadhesin 1, clusterin and spermadhesin Z13 (r=0.64-0.85). The percent of motile sperm after freeze-thawing was negatively correlated (r=-0.64) with the amount of spermadhesin 1 in the seminal plasma. Based on in silico analysis, TIMP2 interacted with BSP1, BSP3, BSP5 and metalloproteinases. Molecular functions of proteins associated with sperm parameters were binding, catalytic activity and enzymatic regulation. Amino acid sequences of spermadhesin 1 and BSP 1 from Bos taurus, and other domestic species were similar. Phylogenetic tree analysis demonstrated that clusterin from Bos taurus was related to Ovis aries and domains of clusterin, spermadhesin 1, BSP 1 and inhibitor of carbonic anhydrase were conserved as well. In summary, specific seminal proteins are associated with sperm parameters of locally-adapted bulls. Use of the endangered mammalian as a model may assist in understanding aspects of evolutionary adaptations and could improve assisted reproductive biotechnologies.
Collapse
Affiliation(s)
- E B Menezes
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, 39762, USA; Department of Animal Science, Federal University of Ceara, Fortaleza, Ceara, 60455760, Brazil
| | - R V de Oliveira
- Department of Animal Production - Animal Science Institute, Federal Rural University of Rio de Janeiro, Seropedica, Rio de Janeiro, 23890000, Brazil
| | - M F van Tilburg
- Department of Biology, State University of Ceara, Fortaleza, Ceara, 60714-903, Brazil
| | - E A Barbosa
- Embrapa Genetic Resources and Biotechnology, Brasilia, Brazilian Federal District, 70770901, Brazil
| | - N V Nascimento
- Embrapa Genetic Resources and Biotechnology, Brasilia, Brazilian Federal District, 70770901, Brazil
| | - A L M C S Velho
- Department of Animal Science, Federal University of Ceara, Fortaleza, Ceara, 60455760, Brazil
| | - F B Moreno
- School of Pharmacy, The University of Fortaleza, Fortaleza, Ceara, Brazil, 60811905
| | - R A Moreira
- School of Pharmacy, The University of Fortaleza, Fortaleza, Ceara, Brazil, 60811905
| | | | | | - A F Ramos
- Embrapa Genetic Resources and Biotechnology, Brasilia, Brazilian Federal District, 70770901, Brazil
| | - E Memili
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, 39762, USA
| | - A A Moura
- Department of Animal Science, Federal University of Ceara, Fortaleza, Ceara, 60455760, Brazil.
| |
Collapse
|
8
|
Ura B, Scrimin F, Franchin C, Arrigoni G, Licastro D, Monasta L, Ricci G. Identification of proteins with different abundance associated with cell migration and proliferation in leiomyoma interstitial fluid by proteomics. Oncol Lett 2017; 13:3912-3920. [PMID: 28521489 DOI: 10.3892/ol.2017.5943] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/26/2017] [Indexed: 11/06/2022] Open
Abstract
Uterine leiomyoma is the most common female reproductive tract benign tumor. Little is known about protein composition and changes in the leiomyoma interstitial fluid (IF). The present study focused on changes in protein abundance in the IF of leiomyoma. Leiomyoma IFs and adjacent myometrial IFs were obtained and analyzed by two-dimensional electrophoresis (2-DE) coupled with mass spectrometry and western blotting for 2-DE data validation. A total of 25 unique proteins were observed to change significantly (P<0.05). Of these proteins with different abundance, 22 had not been previously identified in leiomyoma IF. In silico analysis predicted that three of these proteins were secreted via classical mechanisms, while 22 were secreted via non-classical mechanisms. Ingenuity Pathway Analysis identified 17 proteins associated with cellular migration and proliferation. Among these, phosphoglycerate mutase 1 had not been previously associated with leiomyoma. The abundance of seven proteins was further validated by western blotting. A comparative proteomic approach identified a number of proteins associated with cellular migration and proliferation, with changes in abundance in IF likely to be involved in tumor development. Further studies will be required to investigate the role of these proteins in leiomyoma IF and their possible association with tumor development and growth.
Collapse
Affiliation(s)
- Blendi Ura
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I-34137 Trieste, Italy
| | - Federica Scrimin
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I-34137 Trieste, Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, I-35122 Padova, Italy.,Proteomics Center, University of Padua and Padua Hospital, I-35129 Padova, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, I-35122 Padova, Italy.,Proteomics Center, University of Padua and Padua Hospital, I-35129 Padova, Italy
| | - Danilo Licastro
- Consortium for Molecular Biomedicine Genomics, Area Science Park, Basovizza, I-34149 Trieste, Italy
| | - Lorenzo Monasta
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I-34137 Trieste, Italy
| | - Giuseppe Ricci
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I-34137 Trieste, Italy.,Department of Medical, Surgery and Health Sciences, University of Trieste, I-34128 Trieste, Italy
| |
Collapse
|
9
|
Rodrigues RC, Haddad N, Tresse O. Methods for Proteome Analysis of Campylobacter jejuni Using 2-D Electrophoresis. Methods Mol Biol 2017; 1512:233-244. [PMID: 27885611 DOI: 10.1007/978-1-4939-6536-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This chapter describes protocols used for two-dimensional electrophoretic analysis of the proteome or subproteome of Campylobacter jejuni, a major human food-borne pathogen. The following protocols, adapted to Campylobacter strains, include all the steps from cultivation to gel-support protein separation.
Collapse
Affiliation(s)
- Ramila C Rodrigues
- INRA, UMR 1014 Secalim, Nantes, F-44307, France
- LUNAM Université Oniris, Nantes, F-44307, France
| | - Nabila Haddad
- INRA, UMR 1014 Secalim, Nantes, F-44307, France
- LUNAM Université Oniris, Nantes, F-44307, France
| | - Odile Tresse
- INRA, UMR 1014 Secalim, Nantes, F-44307, France.
- LUNAM Université Oniris, Nantes, F-44307, France.
| |
Collapse
|
10
|
van Tilburg MF, Sousa SD, Ferreira de Melo RB, Moreno FB, Monteiro-Moreira AC, Moreira RA, de Alencar Moura A. Proteome of the rete testis fluid from tropically-adapted Morada Nova rams. Anim Reprod Sci 2016; 176:20-31. [PMID: 27908670 DOI: 10.1016/j.anireprosci.2016.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/06/2016] [Accepted: 11/17/2016] [Indexed: 01/25/2023]
Abstract
The rete testis has a close relationship with sperm development and may have other functions besides serving as an intercalated channel. The aim of this study was to identify and characterize the proteins of rete testis fluid (RTF) from tropically-adapted Morada Nova rams. Testicles obtained from six Morada Nova rams were dissected and the head of the epididymis was separated to access the efferent ducts. Rete testis fluid was obtained by gentle massage of the testis. The fluid was centrifuged to remove cell debris and sperm. RTF samples (containing 400μg protein) were separated by 2-D SDS-PAGE and gels, analyzed using PDQuest software (Bio Rad, USA). Proteins were identified using tandem mass spectrometry. Gene ontology and protein network were analyzed using the software tool for searching annotations of proteins (STRAP) and STRING database. Gels had, on average, 227±13.5 spots and 51% of the proteins were found above 40kDa, corresponding to 65% of the intensity of all spots detected. Based on gene ontology analysis, the most common biological processes associated with RTF proteins were regulation (24.3%) and cellular process (23.3%). Binding (27.3%) and catalytic activity (19.3%) corresponded to the most frequent molecular functions. Albumin, clusterin, serotransferrin, immunoglobulin gamma-1 chain and alpha-2-HS-glycoprotein were the most abundant proteins in the ram rete testis fluid. In conclusion, proteins identified in the ram rete testis fluid are linked to several physiological processes associated with sperm protection and spermatogenesis.
Collapse
Affiliation(s)
| | | | | | - Frederico B Moreno
- Department of Pharmacy, The University of Fortaleza, Fortaleza, Ceará, Brazil
| | | | - Renato A Moreira
- Department of Pharmacy, The University of Fortaleza, Fortaleza, Ceará, Brazil
| | | |
Collapse
|
11
|
Das S, Krishnan P, Mishra V, Kumar R, Ramakrishnan B, Singh NK. Proteomic changes in rice leaves grown under open field high temperature stress conditions. Mol Biol Rep 2015; 42:1545-58. [PMID: 26323334 DOI: 10.1007/s11033-015-3923-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 08/25/2015] [Indexed: 12/18/2022]
Abstract
The interactive effect of temperature with other climatic and soil factors has profound influences on the growth and development of rice. The responses of rice to high temperatures under field conditions are more important than those under the controlled conditions. To understand the genes associated with high temperature stress response in general and tolerance in particular, the expression of all those genes associated with adaptation and tolerance in rice requires proteomic analysis. High temperature stress-tolerant cv. N22 was subjected to 28/18 °C (control) and 42/32 °C (high temperature stress) at flowering stage. The plants were grown in the field under the free air temperature increment condition. The proteomic changes in rice leaves due to high temperature stress were discussed. The proteomes of leaves had about 3000 protein spots, reproducibly detected on 2-dimensional electrophoretic gels with 573 proteins differentially expressed between the control and the high temperature treatments. Putative physiological functions suggested five categories such as growth (15.4%), heat shock proteins (7.7%), regulatory proteins (26.9%), redox homeostasis proteins (11.5%) and energy and metabolism (38.5%) related proteins. The results of the present study suggest that cv. N22, an agronomically recognized temperature tolerant rice cultivar copes with high temperature stress in a complex manner. Several functional proteins play important roles in its responses. The predicted climate change events necessitate more studies using this cultivar under different simulated ecological conditions to identify proteomic changes and the associated genes to be used as biomarkers and to gain a better understanding on the biochemical pathways involved in tolerance.
Collapse
|
12
|
Oliveira CHA, Silva AM, Silva LM, van Tilburg MF, Fernandes CCL, Moura AA, Moreno FBMB, Monteiro-Moreira ACO, Moreira RA, Bezerra FJ, Rondina D. Meat quality assessment from young goats fed for long periods with castor de-oiled cake. Meat Sci 2015; 106:16-24. [PMID: 25866931 DOI: 10.1016/j.meatsci.2015.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 10/02/2014] [Accepted: 03/01/2015] [Indexed: 10/23/2022]
Abstract
Diet can influence both the qualitative and quantitative traits of ruminant meat. This study evaluated the effects of castor de-oiled cake on the meat of mixed-breed male goat kids. After 165days of diet treatment, no alterations (p>0.05) were observed in the in vivo performance, anatomic components, dissection and proximate composition of the Longissimus dorsi muscle, as well as in the color and pH of the carcasses. However, diet had an effect (p<0.05) on energy metabolites, fatty acid profile, and expression of certain proteins of the Longissimus dorsi muscle. To conclude, this study showed that the establishment of castor de-oiled cake diet for a long period to goats led to alterations in meat quality, without compromising its consumption qualities.
Collapse
Affiliation(s)
- C H A Oliveira
- Department of Veterinary Medicine, State University of Ceará, CEP: 60740-000 Fortaleza, Ceará, Brazil
| | - A M Silva
- Department of Veterinary Medicine, State University of Ceará, CEP: 60740-000 Fortaleza, Ceará, Brazil
| | - L M Silva
- Department of Veterinary Medicine, State University of Ceará, CEP: 60740-000 Fortaleza, Ceará, Brazil
| | - M F van Tilburg
- Department of Animal Science, Federal University of Ceará, CEP: 60356-000 Fortaleza, Ceará, Brazil
| | - C C L Fernandes
- Department of Veterinary Medicine, State University of Ceará, CEP: 60740-000 Fortaleza, Ceará, Brazil
| | - A A Moura
- Department of Animal Science, Federal University of Ceará, CEP: 60356-000 Fortaleza, Ceará, Brazil
| | - F B M B Moreno
- Department of Biochemistry, Federal University of Ceará, CEP: 60356-000, Fortaleza, Ceará, Brazil
| | - A C O Monteiro-Moreira
- Department of Pharmacy, University of Fortaleza, Ceará, CEP: 60811-905, Fortaleza, Ceará, Brazil
| | - R A Moreira
- Department of Pharmacy, University of Fortaleza, Ceará, CEP: 60811-905, Fortaleza, Ceará, Brazil
| | - F J Bezerra
- Department of Nutrition, University of Fortaleza, Ceará, CEP: 60811-905, Fortaleza, Ceará, Brazil
| | - D Rondina
- Department of Veterinary Medicine, State University of Ceará, CEP: 60740-000 Fortaleza, Ceará, Brazil.
| |
Collapse
|
13
|
Pavlíková N, Bartoňová I, Balušíková K, Kopperova D, Halada P, Kovář J. Differentially expressed proteins in human MCF-7 breast cancer cells sensitive and resistant to paclitaxel. Exp Cell Res 2014; 333:1-10. [PMID: 25557873 DOI: 10.1016/j.yexcr.2014.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 10/24/2022]
Abstract
Resistance of cancer cells to chemotherapeutic agents is one of the main causes of treatment failure. In order to detect proteins potentially involved in the mechanism of resistance to taxanes, we assessed differences in protein expression in MCF-7 breast cancer cells that are sensitive to paclitaxel and in the same cells with acquired resistance to paclitaxel (established in our lab). Proteins were separated using two-dimensional electrophoresis. Changes in their expression were determined and proteins with altered expression were identified using mass spectrometry. Changes in their expression were confirmed using western blot analysis. With these techniques, we found three proteins expressed differently in resistant MCF-7 cells, i.e., thyroid hormone-interacting protein 6 (TRIP6; upregulated to 650%), heat shock protein 27 (HSP27; downregulated to 50%) and cathepsin D (downregulated to 28%). Silencing of TRIP6 expression by specific siRNA leads to decreased number of grown resistant MCF-7 cells. In the present study we have pointed at some new directions in the studies of the mechanism of resistance to paclitaxel in breast cancer cells.
Collapse
Affiliation(s)
- Nela Pavlíková
- Department of Cell & Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Irena Bartoňová
- Department of Cell & Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kamila Balušíková
- Department of Cell & Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Dana Kopperova
- Department of Cell & Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Petr Halada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology,v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kovář
- Department of Cell & Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| |
Collapse
|
14
|
Yang Y, Luo Y, Li X, Yi Y. Differential expression analysis of Golgi apparatus proteomes in hepatocellular carcinomas and the surrounding liver tissues. Hepatol Res 2014; 44:542-50. [PMID: 23621634 DOI: 10.1111/hepr.12151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 04/18/2013] [Accepted: 04/23/2013] [Indexed: 02/08/2023]
Abstract
AIM Hepatocellular carcinoma (HCC) is the sixth most common malignancy worldwide. Liver is the largest human digestive gland with abundant Golgi apparatus involved in cell division, migration and apoptosis and others. METHODS In the present study, Golgi apparatus of HCC and the surrounding liver tissues were isolated by sucrose density gradient centrifugation and identified by electron microscopy and enzymology methods. Using 2-D gel electrophoresis and mass spectrometry, 17 differentially expressed protein of Golgi apparatus in HCC and the surrounding liver tissue were screened and identified in the Mascot database. RESULTS Of those differentially expressed proteins, six were upregulated and 11 were downregulated, some of them were related to the biological processes such as protein sorting, glycosylation, cell cycle regulation, transcription regulation and Golgi integrity. One protein, annexin A5, was verified to be upregulated in HCC by western blot. CONCLUSION The differentially expressed proteins may provide new insight into HCC biology and potential diagnostic and therapeutic biomarkers.
Collapse
Affiliation(s)
- Yaying Yang
- Department of Pathology, Molecular Medicine and Tumor Center, China
| | | | | | | |
Collapse
|
15
|
Abstract
Human individuals differ from one another in almost all of their genes due to single nucleotide polymorphisms (SNPs). When the maternal and the paternal genomes become combined in a F1 individual, the two alleles of each gene represent arbitrary combinations. In consequence, individuals show high variability in protein expression. Furthermore, within a proteome, the proteins form networks of protein-protein interactions. These networks differ between individuals in robustness against genetic or/and environmental perturbation due to polymorphisms, which differ in type and composition between individuals, and modify the arrangement of proteins in the proteomic network. As a general conclusion, the robustness of a human individual against diseases may depend on the structure and expression of the protein-protein interaction network that varies in its functional efficiency between individuals due to "network-polymorphisms". This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
Collapse
Affiliation(s)
- Stefanie Forler
- Institute for Medical Genetics and Human Genetics, Charité - University Medicine Berlin, Germany
| | - Oliver Klein
- Institute for Medical Genetics and Human Genetics, Charité - University Medicine Berlin, Germany; Core Unit Proteomics, Berlin-Brandenburg Center for Regenerative Therapies, Charité - University Medicine Berlin, Germany
| | - Joachim Klose
- Institute for Medical Genetics and Human Genetics, Charité - University Medicine Berlin, Germany; Core Unit Proteomics, Berlin-Brandenburg Center for Regenerative Therapies, Charité - University Medicine Berlin, Germany.
| |
Collapse
|
16
|
Abstract
The post-translational modification of protein by acetylation has been emerging as a prevalent modification in enzymes that catalyze intermediary metabolism. However, the dynamics of protein acetylation during adipocyte differentiation that involves a major shift in cellular metabolism is not known. In this study, we investigated the temporal changes in acetylation during adipocyte differentiation. Almost all acetylated proteins identified showed a sequential change in acetylation during the differentiation process. While the majority of the acetylated proteins showed a sequential upregulation during adipocyte differentiation, in a few proteins a sequential downregulation of protein acetylation was also observed. Our findings suggest that a wide-ranging temporal change in protein acetylation occurs during adipocyte differentiation including differentially expressed proteins signifying an important role in adipocyte differentiation.
Collapse
|
17
|
Kuczyńska A, Kosmala A, Surma M, Adamski T. Identification of tillering node proteins differentially accumulated in barley recombinant inbred lines with different juvenile growth habits. Int J Mol Sci 2012; 13:10410-10423. [PMID: 22949870 PMCID: PMC3431868 DOI: 10.3390/ijms130810410] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/08/2012] [Accepted: 08/14/2012] [Indexed: 12/03/2022] Open
Abstract
Barley (Hordeum vulgare L.) is an important cereal crop grown for both the feed and malting industries. The allelic dwarfing gene sdw1/denso has been used throughout the world to develop commercial barley varieties. Proteomic analysis offers a new approach to identify a broad spectrum of genes that are expressed in the living system. Two-dimensional electrophoresis and mass spectrometry were applied to investigate changes in protein abundance associated with different juvenile growth habit as effect of the denso locus in barley homozygous lines derived from a Maresi × Pomo cross combination. A total of 31 protein spots were revealed that demonstrate quantitative differences in protein abundance between the analyzed plants with different juvenile growth habit, and these protein spots were selected to be identified by mass spectrometry. Identification was successful for 27 spots, and functional annotations of proteins revealed that most of them are involved in metabolism and disease/defense-related processes. Functions of the identified proteins and their probable influence on the growth habit in barley are discussed.
Collapse
Affiliation(s)
- Anetta Kuczyńska
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +48-61-65-50-224; Fax: +48-61-65-50-301
| | | | | | | |
Collapse
|
18
|
Casadei L, Vallorani L, Gioacchini AM, Guescini M, Burattini S, D'Emilio A, Biagiotti L, Falcieri E, Stocchi V. Proteomics-based investigation in C2C12 myoblast differentiation. Eur J Histochem 2012; 53:e31. [PMID: 22073363 PMCID: PMC3167332 DOI: 10.4081/ejh.2009.e31] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2009] [Indexed: 11/23/2022] Open
Abstract
Skeletal muscle cell differentiation is a multistage process extensively studied over the years. Even if great improvements have been achieved in defining biological process underlying myogenesis, many molecular mechanisms need still to be clarified. To further highlight this process, we studied cells at undifferentiated, intermediate and highly differentiated stages, and we analyzed, for each condition, morphological and proteomic changes. We also identified the proteins that showed statistical significant changes by a ESI-Q-TOF mass spectrometer. This work provides further evidence of the involvement of particular proteins in skeletal muscle development. Furthermore, the high level of expression of many heat shock proteins, suggests a relationship between differentiation and cellular stress. Intriguingly, the discovery of myogenesis-correlated proteins, known to play a role in apoptosis, suggests a link between differentiation and this type of cell death.
Collapse
Affiliation(s)
- L Casadei
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino "Carlo Bo", Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Bruno JG. Development of a membrane-bound random DNA sequence combinatorial array recognition surface (CARS). J Biomol Tech 2010; 21:35-43. [PMID: 20357981 PMCID: PMC2841992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A partially overlapping population of random sequence 60mer DNA molecules consisting of many concatamers of varied lengths was spatially separated in one and two dimensions by electrophoresis in polyacrylamide and transferred to nitrocellulose membranes. The spatially separated library serves as a potential sensor interface on which many different molecular recognition events or target analyte-binding patterns may emerge, thereby theoretically representing a "universal sensor" surface. The separated DNA library has been referred to as a DNA combinatorial array recognition surface or "CARS." After UV baking and various fluorescence staining or fluorescent probe interactions, the one-dimensional (1-D) and 2-D membrane-bound CARS were digitally photographed and subjected to image analysis with National Institutes of Health Image-Java software. Image analysis demonstrated relatively consistent and more similar spatial fluorescence patterns within CARS analyte treatment groups but noteworthy pattern differences before and after analyte addition and between different analyte treatments. Taken together, these data suggest a potential role for CARS as a novel, inexpensive, self-assembling universal molecular recognition surface that could be coupled to sophisticated Bayesian or other pattern recognition algorithms to classify analytes or make specific identifications, much like the senses of smell or taste.
Collapse
Affiliation(s)
- John G Bruno
- Operational Technologies Corporation, San Antonio, Texas 78229, USA.
| |
Collapse
|