1
|
Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
Collapse
Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
| |
Collapse
|
2
|
Andrews WT, Bickner AN, Tobias F, Ryan KA, Bruening ML, Hummon AB. Electroblotting through Enzymatic Membranes to Enhance Molecular Tissue Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1689-1699. [PMID: 34110793 PMCID: PMC9241434 DOI: 10.1021/jasms.1c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
MALDI-TOF mass spectrometry imaging (MSI) is a powerful tool for studying biomolecule localization in tissue. Protein distributions in tissue provide important histological information; however, large proteins exhibit a high limit of detection in MALDI-MS when compared to their corresponding smaller proteolytic peptides. As a result, several techniques have emerged to digest proteins into more detectable peptides for imaging. Digestion is typically accomplished through trypsin deposition on the tissue, but this technique increases the complexity of the tissue microenvironment, which can limit the number of detectable species. This proof-of-principle study explores tryptic tissue digestion during electroblotting through a trypsin-containing membrane. This approach actively extracts and enzymatically digests proteins from mouse brain tissue sections while simultaneously reducing the complexity of the tissue microenvironment (compared to trypsin deposition on the surface) to obtain an increased number of detectable peptide fragments. The method does not greatly compromise spatial location or require expensive devices to uniformly deposit trypsin on tissue. Using electrodigestion through membranes, we detected and tentatively identified several tryptic peptides that were not observed after on-tissue digestion. Moreover, the use of pepsin rather than trypsin in digestion membranes allows extraction and digestion at low pH to detect peptides from a complementary subset of tissue proteins. Future studies will aim to further improve the method, including changing the substrate membrane to increase spatial resolution and the number of detected peptides.
Collapse
Affiliation(s)
| | | | - Fernando Tobias
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | | | | | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
3
|
Bickner AN, Champion MM, Hummon AB, Bruening ML. Electroblotting through a tryptic membrane for LC-MS/MS analysis of proteins separated in electrophoretic gels. Analyst 2021; 145:7724-7735. [PMID: 33000802 DOI: 10.1039/d0an01380c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Digestion of proteins separated via sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) remains a popular method for protein identification using mass-spectrometry based proteomics. Although robust and routine, the in-gel digestion procedure is laborious and time-consuming. Electroblotting to a capture membrane prior to digestion reduces preparation steps but requires on-membrane digestion that yields fewer peptides than in-gel digestion. This paper develops direct electroblotting through a trypsin-containing membrane to a capture membrane to simplify extraction and digestion of proteins separated by SDS-PAGE. Subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) identifies the extracted peptides. Analysis of peptides from different capture membrane pieces shows that electrodigestion does not greatly disturb the spatial resolution of a standard protein mixture separated by SDS-PAGE. Electrodigestion of an Escherichia coli (E. coli) cell lysate requires four hours of total sample preparation and results in only 13% fewer protein identifications than in-gel digestion, which can take 24 h. Compared to simple electroblotting and protein digestion on a poly(vinylidene difluoride) (PVDF) capture membrane, adding a trypsin membrane to the electroblot increases the number of protein identifications by 22%. Additionally, electrodigestion experiments using capture membranes coated with polyelectrolyte layers identify a higher fraction of small proteolytic peptides than capture on PVDF or in-gel digestion.
Collapse
Affiliation(s)
- A N Bickner
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, Indiana 46556, USA.
| | | | | | | |
Collapse
|
4
|
Hattan SJ, Du J, Parker KC. Bifunctional Glass Membrane Designed to Interface SDS-PAGE Separations of Proteins with the Detection of Peptides by Mass Spectrometry. Anal Chem 2015; 87:3685-93. [DOI: 10.1021/ac503980x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen J. Hattan
- SimulTOF Systems, 60 Union Avenue, Sudbury, Massachusetts 01776, United States
| | - Jie Du
- Toxikon Corporation, 15 Wiggins Avenue, Bedford, Massachusetts 01730, United States
| | - Kenneth C. Parker
- SimulTOF Systems, 60 Union Avenue, Sudbury, Massachusetts 01776, United States
| |
Collapse
|
5
|
Škrášková K, Heeren RM. A review of complementary separation methods and matrix assisted laser desorption ionization-mass spectrometry imaging: Lowering sample complexity. J Chromatogr A 2013; 1319:1-13. [DOI: 10.1016/j.chroma.2013.10.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
6
|
Abstract
The complementary disciplines of genomics and proteomics offer better insights into the molecular mechanisms of diseases. While genomics hunts for defining our static genetic substrate, proteomics explores the structure and function of proteins expressed by a cell or tissue type under specified conditions. In the past decade, proteomics has been revolutionized by the application of techniques such as two-dimensional gel electrophoresis (2DGE), mass spectrometry (MS), and protein arrays. These techniques have tremendous potential for biomarker development, target validation, diagnosis, prognosis, and optimization of treatment in medical care, especially in the field of islet and diabetes research. This chapter will highlight the contributions of proteomic technologies toward the dissection of complex network of signaling molecules regulating islet function, the identification of potential biomarkers, and the understanding of mechanisms involved in the pathogenesis of diabetes.
Collapse
|
7
|
Affiliation(s)
- Kamila Chughtai
- FOM-Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Ron M.A. Heeren
- FOM-Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| |
Collapse
|
8
|
Lisitsa AV, Petushkova NA, Thiele H, Moshkovskii SA, Zgoda VG, Karuzina II, Chernobrovkin AL, Skipenko OG, Archakov AI. Application of slicing of one-dimensional gels with subsequent slice-by-slice mass spectrometry for the proteomic profiling of human liver cytochromes P450. J Proteome Res 2010; 9:95-103. [PMID: 19722723 DOI: 10.1021/pr900262z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Sequential thin slicing of one-dimensional electrophoresis gels followed by slice-by-slice mass spectrometry to allow protein identification was used to produce a proteomic map for cytochromes P450. Parallel MALDI-TOF-MS and LC-MS/MS analyses were performed. Combination of the two MS methods increased the quality of protein identification. We have proposed an efficient approach to obtain a comprehensive profile of drug-metabolizing enzymes in the liver that can be used to differentiate between polymorphic variants of cytochromes P450.
Collapse
Affiliation(s)
- Andrey V Lisitsa
- Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, Russia
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Kaletaş BK, van der Wiel IM, Stauber J, Lennard J. Dekker, Güzel C, Kros JM, Luider TM, Heeren RMA. Sample preparation issues for tissue imaging by imaging MS. Proteomics 2009; 9:2622-33. [DOI: 10.1002/pmic.200800364] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
10
|
Nebrich G, Herrmann M, Hartl D, Diedrich M, Kreitler T, Wierling C, Klose J, Giavalisco P, Zabel C, Mao L. PROTEOMER: A workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics. Proteomics 2009; 9:1795-808. [DOI: 10.1002/pmic.200800522] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
11
|
Lebedev AT, Zaikin VG. Organic mass spectrometry at the beginning of the 21st century. JOURNAL OF ANALYTICAL CHEMISTRY 2008. [DOI: 10.1134/s1061934808120022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Vaezzadeh AR, Simicevic J, Chauvet A, François P, Zimmermann-Ivol CG, Lescuyer P, Deshusses JPM, Hochstrasser DF. Imaging mass spectrometry using peptide isoelectric focusing. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:2667-2676. [PMID: 18677718 DOI: 10.1002/rcm.3658] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Imaging Mass Spectrometry (IMS) has emerged as a powerful technique in the field of proteomics. The use of Immobilized pH Gradient-IsoElectric Focusing (IPG-IEF) is also a new trend, as the first dimension of separation, in shotgun proteomics. We report a combination of these two outstanding technologies. This approach is based on the separation of shotgun-produced peptides by IPG-IEF. The peptides are then transferred by capillarity to a capture membrane, which is then scanned by the mass spectrometer to generate MS images. This high-throughput methodology allows a preview of the sample to be obtained in a single day. We report the application of this new pipeline for differential comparison of the membrane proteome of two different strains of Staphylococcus aureus bacteria in a proof-of-principle experiment.
Collapse
Affiliation(s)
- Ali R Vaezzadeh
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Geneva University, 1 rue Michel Servet, 1211 Geneva, Switzerland.
| | | | | | | | | | | | | | | |
Collapse
|
13
|
|
14
|
Cui H, Dutta P, Ivory CF. Isotachophoresis of proteins in a networked microfluidic chip: Experiment and 2-D simulation. Electrophoresis 2007; 28:1138-45. [PMID: 17330226 DOI: 10.1002/elps.200600525] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This paper reports both the experimental application and 2-D simulation of ITP of proteins in a networked microfluidic chip. Experiments demonstrate that a mixture of three fluorescent proteins can be concentrated and stacked into adjacent zones of pure protein under a constant voltage of 100 V over a 2 cm long microchannel. Measurements of the isotachophoretic velocity of the moving zones demonstrates that, during ITP under a constant voltage, the zone velocity decreases as more of the channel is occupied by the terminating electrolyte. A 2-D ITP model based on the Nernst-Planck equations illustrates the stacking and separation features of ITP using simulations of three virtual proteins. The self-sharpening behavior of ITP zones dispersed by a T-junction is clearly demonstrated both by experiment and by simulation. Comparison of 2-D simulations of ITP and zone electrophoresis (ZE) confirms that ZE lacks the ability to resharpen protein zones after they pass through a T-junction.
Collapse
Affiliation(s)
- Huanchun Cui
- School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164-2710, USA
| | | | | |
Collapse
|
15
|
Groseclose MR, Andersson M, Hardesty WM, Caprioli RM. Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:254-62. [PMID: 17230433 DOI: 10.1002/jms.1177] [Citation(s) in RCA: 231] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
A novel method for on-tissue identification of proteins in spatially discrete regions is described using tryptic digestion followed by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) with MS/MS analysis. IMS is first used to reveal the protein and peptide spatial distribution in a tissue section and then a serial section is robotically spotted with small volumes of trypsin solution to carry out in situ protease digestion. After hydrolysis, 2,5-Dihydroxybenzoic acid (DHB) matrix solution is applied to the digested spots, with subsequent analysis by IMS to reveal the spatial distribution of the various tryptic fragments. Sequence determination of the tryptic fragments is performed using on-tissue MALDI MS/MS analysis directly from the individual digest spots. This protocol enables protein identification directly from tissue while preserving the spatial integrity of the tissue sample. The procedure is demonstrated with the identification of several proteins in the coronal sections of a rat brain.
Collapse
Affiliation(s)
- M Reid Groseclose
- Mass Spectrometry Research Center, Department of Chemistry, Vanderbilt University, 465 21st Avenue South, Medical Research Building 3, Room 9160, Nashville, Tennessee 37232-8575, USA
| | | | | | | |
Collapse
|
16
|
Petushkova NA, Kanaeva IP, Lisitsa AV, Sheremetyeva GF, Zgoda VG, Samenkova NF, Karuzina II, Archakov AI. Characterization of human liver cytochromes P450 by combining the biochemical and proteomic approaches. Toxicol In Vitro 2006; 20:966-74. [PMID: 16533590 DOI: 10.1016/j.tiv.2006.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 12/05/2005] [Accepted: 01/05/2006] [Indexed: 01/28/2023]
Abstract
Highly purified human liver microsomes were processed by a combination of the biochemical and proteomic methods. Microsomes were purified from the morphologically normal liver tissue obtained from the resected and discarded masses of surrounding liver upon surgical treatment for hemangioma (control) or hepatic metastases arising from colon cancer (pathology). Proteins of each sample were separated by two-dimensional (2-DE) and one-dimensional electrophoresis (1-DE); selected gel regions were excised, in-gel digested and analyzed by matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry. Analysis of collected fingerprints has revealed a total of 13 microsomal membrane proteins involved in the biotransformation of xenobiotics. These were disulfide isomerase, flavine monooxygenase, NADPH-cytochrome P450 reductase and 10 cytochrome P450 forms, namely: CYPs 1B1, 2A6, 2E1, 2C8, 2C9, 2C10, 2D6, 3A4, 4A11, 4F2. These same samples were characterized by the enzymatic assays using the marker substrates for CYPs 1A, 2B, 3A4, 2C and 2E1. Correlations between mass spectrometric data and enzymatic activities were investigated to demonstrate the manner in which the functional and structural aspects of proteomics meet each other in the field of cytochromes P450.
Collapse
Affiliation(s)
- N A Petushkova
- V.N. Orekchovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya St., 10, 119121 Moscow, Russia.
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Thiede B, Kretschmer A, Rudel T. Quantitative proteome analysis of CD95 (Fas/Apo-1)-induced apoptosis by stable isotope labeling with amino acids in cell culture, 2-DE and MALDI-MS. Proteomics 2006; 6:614-22. [PMID: 16342138 DOI: 10.1002/pmic.200500120] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteome analysis of Jurkat T cells induced to undergo apoptosis by CD95 (Fas/Apo-1) treatment was performed to identify modified proteins. We used stable isotope labeling with amino acids in cell culture (SILAC) using leucine to identify proteins of apoptotic and control Jurkat T cells by 2-DE and MALDI-MS. Out of 224 spots analyzed, we quantified 213 spots with 3.5 leucine-containing peptide pairs on average; 28 proteins with a relative abundance of higher than 1.5 were found. Five new modified proteins including calcyclin binding protein, cytosolic acyl coenzyme A thioester hydrolase, heterogeneous ribonucleoprotein M, replication factor C 37-kDa subunit, and tropomyosin 4 chain were identified as being modified in response to apoptosis. In comparison to differential proteome analysis via silver-stained 2-D gels and PMF of total Jurkat T cell lysates, 15 additional apoptosis-modified proteins were identified though 8 proteins were not found. The described approach using SILAC instead of silver staining for relative quantification was simpler to perform regarding the number of required 2-D gels, that cumbersome gel comparisons were avoided, and more apoptosis-modified proteins were identified, but with a higher demand on data interpretation of the mass spectra obtained.
Collapse
Affiliation(s)
- Bernd Thiede
- Max Planck Institute for Infection Biology, Department Molecular Biology, Berlin, Germany
| | | | | |
Collapse
|
18
|
Chen YC, Wang PW, Pan TL, Wallace CG, Chen CJ. Proteomic analysis of Down's syndrome patients with gout. Clin Chim Acta 2006; 369:89-94. [PMID: 16500633 DOI: 10.1016/j.cca.2006.01.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 01/16/2006] [Accepted: 01/16/2006] [Indexed: 11/26/2022]
Abstract
BACKGROUND In this study, the expression of hypoxanthine-guanine phosphoribosyl transferase (HPRT) in Down's syndrome patients with gout (DS/G) was determined, and possible underlying mechanisms of gout were characterized using proteomic tools. METHODS Serum was obtained from DS/G, healthy controls and gout patients (without DS), recruited from the rheumatology clinic. Baseline enzyme assays were recorded and RT-PCR used to identify HPRT gene expression. 2-D electrophoresis and mass spectrometry were utilized to determine a plausible explanation concerning the mechanisms leading to increased uric acid levels in DS patients. RESULTS Two DS patients were diagnosed with gouty arthritis. Their HPRT enzyme activity was slightly lower than that of normal controls. HPRT expression was also slightly decreased in DS/G patients compared with controls. Serum protein profiles of these two DS/G patients revealed that haptoglobin alpha chain and apolipoprotein A1 (ApoA1) were both significantly down-regulated. Protein expression was validated by immunoblot. CONCLUSION Our results revealed that low levels of haptoglobin in the two DS/G patients were related to renal dysfunction may have affected uric acid excretion and caused gout. However, decreased ApoA1 revealed a positive correlation between defective lipid metabolism and gouty arthritis in DS/G patients.
Collapse
Affiliation(s)
- Ying-Chou Chen
- Department of Rheumatology, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | | | | | | | | |
Collapse
|
19
|
Thadikkaran L, Crettaz D, Siegenthaler MA, Gallot D, Sapin V, Iozzo RV, Queloz PA, Schneider P, Tissot JD. The role of proteomics in the assessment of premature rupture of fetal membranes. Clin Chim Acta 2005; 360:27-36. [PMID: 15970282 DOI: 10.1016/j.cccn.2005.04.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 04/05/2005] [Accepted: 04/15/2005] [Indexed: 12/24/2022]
Abstract
The presence and integrity of amniotic fluid is fundamental for the normal development of the human fetus during pregnancy. Its production rate changes throughout pregnancy and is mainly related to the functions of the different fetal, placental and amniotic compartments. Premature rupture of the membranes (PROM) occurs in about 5% of deliveries, with complications such as infection and preterm birth. The management of patients with PROM, regardless of gestational age, remains controversial, and it is therefore important to develop new biological tests in order to achieve accurate diagnoses by identifying the presence of specific amniotic fluid markers in vaginal environment. We recently showed the usefulness of amniotic fluid proteomics in identifying a series of peptides that were absent from the corresponding maternal plasma. Several peptides corresponded to fragments of plasma proteins. Two peptides, absent from plasma samples of pregnant women, were identified in amniotic fluid. They corresponded to the COOH-terminal parts of perlecan (SwissProt: P98160) and of agrin (SwissProt: O00468) protein cores, two major heparan sulfate proteoglycans of basement membranes. In this review we will discuss modern proteomic strategies that may improve the laboratory assessment of PROM, and will focus on some of the biochemical characteristics of agrin and perlecan fragments identified in amniotic fluid.
Collapse
Affiliation(s)
- Lynne Thadikkaran
- Service Régional Vaudois de Transfusion sanguine, Rue du Bugnon 27, CH-1005 Lausanne, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Ranganath RM. Harnessing the developmental potential of nucellar cells: barriers and opportunities. Trends Biotechnol 2005; 22:504-10. [PMID: 15450743 DOI: 10.1016/j.tibtech.2004.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Angiosperm nucellar cells can either use or avoid meiosis in vivo, depending on the developmental context. This unique ability contrasts with the conditions required in vitro, either for a reconstituted oocyte to avoid meiosis and produce clones by somatic cell nuclear transfer (SCNT), or for mammalian stem cells to undergo meiosis and produce synthetic sex cells (gametes). Current biotechnological initiatives to harness the potential of nucellar cells are based on the transfer of apomixis genes to sexual crop plants with the aim of producing clones through seeds. The elusive genetic basis of apomixis compels us to examine whether this process involves epigenetic factors. The elegant and versatile developmental platform available in nucellar cells should be explored as a genome-scale science and compared with mammalian stem cell biology for a holistic understanding of developmental programming and reprogramming in eukaryotes.
Collapse
Affiliation(s)
- R M Ranganath
- Cytogenetics and Developmental Biology Laboratory, Department of Botany, Bangalore University, Jnanabharathi Campus, Bangalore 560056, India.
| |
Collapse
|
21
|
Abstract
In biomedical research, the discovery of new biomarkers and new drugs demands analytical techniques with high sensitivity together with increased throughput. The possibility to localize or to follow changes in organisms at the molecular level by imaging component distributions of specific tissues, is of prime importance to unravel biochemical pathways and develop new treatments and drugs. Established molecular imaging techniques such as MRI and PET are already widely used, however their need for molecular probes to report the presence of the analytes of interest precludes the simultaneous exploration of different biomolecules. Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI MSI) takes full advantage of the high sensitivity of mass spectrometry instrumentation but also of the ability of the latter to simultaneously detect a wide range of compounds, almost regardless from their nature and mass. To perform MALDI MSI, sections of biological tissues are introduced in an MALDI MS instrument, where the UV pulsed laser of the MALDI source is used to raster over a selected area while acquiring mass spectra of the ablated ions at every image point. From this array of spectra, hundreds of analyte-specific images can be generated based on the selected masses. MALDI MSI can be used to track biomarkers such as peptides or proteins but also to map drug/tissue interactions. In this paper, an overview of the possibilities of MSI will be given. As an example, MSI on brain tissue sections for the study of Alzheimer's disease (AD) will be shown. Mapping of amyloid peptides as a new approach for drug lead optimization will be presented. Target identification thanks to MSI will be introduced and the last part will be dedicated to the molecular scanner approach, which gives access to high-mass range by combining tissue blotting and digestion in a one-step process.
Collapse
Affiliation(s)
- Tatiana C Rohner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Lichtstrasse 35, CH-4002 Basel, Switzerland
| | | | | |
Collapse
|