Gel Maps Research Articles

Rheological‐based digital approach for gel curve analysis of alcohol ethoxylates

AbstractMany surfactants, such as higher mole alcohol ethoxylates like C12‐15–7EO and C9‐11–8EO, when diluted in water, will form a gel at specific concentrations and temperatures. Gels can be highly viscous and semi‐solid and should be avoided since they take time and energy to disperse once formed. Historically, the creation of gel diagrams or maps for our technical product brochures primarily has depended on visual observation, leading to variable interpretations and inconsistent results over time. Also, completing a gel map for one surfactant grade requires a minimum of one day, due to testing many samples across various concentrations and temperatures. To improve objectivity, consistency, and speed in gel mapping, oscillatory rheology was utilized to identify gels using viscoelastic properties by testing samples prepared at various concentrations. The digitization of the gel mapping technique provides two significant benefits. It offers a rheological‐based approach giving a non‐subjective, digital gel map and it is faster than our visual‐based method. Furthermore, this digital method is consistent with our visual‐based method giving good discrimination between surfactant grades and reproducibility within batches of the same grade. This work also demonstrates the promising potential of utilizing machine learning algorithms to model the rheological behavior of gel maps effectively. R and Python, programming languages widely used for data analysis, graphing, and machine learning, were employed. Overall, the new digital approach presented yields several benefits for surfactant gel behavior study, including a reduction in subjectivity, faster data generation, and increased efficiency in the gel map analysis process.

In Silico Comparative Analysis of the Functional, Structural, and Evolutionary Properties of SARS-CoV-2 Variant Spike Proteins.

BackgroundA recent global outbreak of COVID-19 caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) created a pandemic and emerged as a potential threat to humanity. The analysis of virus genetic composition has revealed that the spike protein, one of the major structural proteins, facilitates the entry of the virus to host cells.ObjectiveThe spike protein has become the main target for prophylactics and therapeutics studies. Here, we compared the spike proteins of SARS-CoV-2 variants using bioinformatics tools.MethodsThe spike protein sequences of wild-type SARS-CoV-2 and its 6 variants—D614G, alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2), gamma (P.1), and omicron (B.1.1.529)—were retrieved from the NCBI database. The ClustalX program was used to sequence multiple alignment and perform mutational analysis. Several online bioinformatics tools were used to predict the physiological, immunological, and structural features of the spike proteins of SARS-CoV-2 variants. A phylogenetic tree was constructed using CLC software. Statistical analysis of the data was done using jamovi 2 software.ResultsMultiple sequence analysis revealed that the P681R mutation in the delta variant, which changed an amino acid from histidine (H) to arginine (R), made the protein more alkaline due to arginine’s high pKa value (12.5) compared to histidine’s (6.0). Physicochemical properties revealed the relatively higher isoelectric point (7.34) and aliphatic index (84.65) of the delta variant compared to other variants. Statistical analysis of the isoelectric point, antigenicity, and immunogenicity of all the variants revealed significant correlation, with P values ranging from <.007 to .04. The generation of a 2D gel map showed the separation of the delta spike protein from a grouping of the other variants. The phylogenetic tree of the spike proteins showed that the delta variant was close to and a mix of the Rousettus bat coronavirus and MERS-CoV.ConclusionsThe comparative analysis of SARS-CoV-2 variants revealed that the delta variant is more aliphatic in nature, which provides more stability to it and subsequently influences virus behavior.

Proteomic Determination of Low-Molecular-Weight Glutenin Subunit Composition in Aroona Near-Isogenic Lines and Standard Wheat Cultivars

The low-molecular weight glutenin subunit (LMW-GS) composition of wheat (Triticum aestivum) flour has important effects on end-use quality. However, assessing the contributions of each LMW-GS to flour quality remains challenging because of the complex LMW-GS composition and allelic variation among wheat cultivars. Therefore, accurate and reliable determination of LMW-GS alleles in germplasm remains an important challenge for wheat breeding. In this study, we used an optimized reversed-phase HPLC method and proteomics approach comprising 2-D gels coupled with liquid chromatography–tandem mass spectrometry (MS/MS) to discriminate individual LMW-GSs corresponding to alleles encoded by the Glu-A3, Glu-B3, and Glu-D3 loci in the ‘Aroona’ cultivar and 12 ‘Aroona’ near-isogenic lines (ARILs), which contain unique LMW-GS alleles in the same genetic background. The LMW-GS separation patterns for ‘Aroona’ and ARILs on chromatograms and 2-D gels were consistent with those from a set of 10 standard wheat cultivars for Glu-3. Furthermore, 12 previously uncharacterized spots in ‘Aroona’ and ARILs were excised from 2-D gels, digested with chymotrypsin, and subjected to MS/MS. We identified their gene haplotypes and created a 2-D gel map of LMW-GS alleles in the germplasm for breeding and screening for desirable LMW-GS alleles for wheat quality improvement.

Analysis of Two-Dimensional Gel Electrophoresis Map of Methicillin-Resistant &amp;lt;i&amp;gt;Staphylococcus aureus&amp;lt;/i&amp;gt; Treated with Acetone Extract from &amp;lt;i&amp;gt;Canarium odontophyllum&amp;lt;/i&amp;gt; Miq. Leaves

Methicillin-resistant Staphylococcus aureus (MRSA) infection is a global health concern that has caused severe health threats over the past decade. Leaves extract of C. odontophyllum has been proven previously as an anti MRSA agent. Proteomics provide a technique that used to analyze the differential of protein expression profile between untreated and treated MRSA with subinhibitory concentrations of acetone extract from C. odontophyllum leaves. This study aims to determine the optimum parameter for analysis of protein expression profile using two-dimension gels electrophoresis (2-DE) for MRSA protein after treatment with acetone extract from C. odontophyllum leaves. Comparison of the Protein Expression Profile (PEP) between the untreated and treated MRSA was analyzed using PDQuest software. The optimum condition for MRSA protein treated with acetone extract from C. odontophyllum leaves to produce the best resolution with greater spot distribution was as follows: 100 μg volume of MRSA protein that loaded after passive rehydration then was run until reaching 25 kVrhs during IEF using 17 cm IPG strip within ranges of pH 4 - 7. Analysis of protein expression from the 2-DE gel map shows that 9 protein spots up-regulated and 41 protein spots were down-regulated with more than 2-fold differences (p C. odontophyllum leave may provide an insight into the antimicrobial mechanism, which could lead to the identification of target protein for future novel therapeutic development against MRSA infections.

Prevalence of Acridine Immunization to Subsaharians Africans Blood Donors

To conduct a study project on the inactivation of pathogens in whole blood using acridine derivatives in Africa, in order to prevent the transmission of pathogens, it is important to look for possible immunization to acridine in the blood donor population. It is therefore important to undertake an estimate of the prevalence in the sub-Saharan population in order to guide the design of the clinical study that will use the INTERCEPT Red Blood System procedure on whole blood for transfusion. to define the starting point in the evaluation of the immunological safety and transfusion safety of the product treated by this process. The objective of this study is to determine the prevalence of AAA among blood donors in sub-Saharan Africa. We conducted a multicenter prospective descriptive study of 902 blood donors collected in Côte d'Ivoire, Benin and Cameroon over the period from June 2015 to January 2017. Blood samples were collected from voluntary blood donors, of any sex, aged between 18 and 65, having given their consent for the study and having participated in the medical consultation for the donation of blood. The samples were analyzed according to the technique of the RAI gel card of the company BIORAD after centrifugation and incubation using test red cells treated with S-303 and glutathione. In the case of positive RAI results, to confirm the presence of anti-acridine, the donor plasma should be incubated with S-300. S-300 is a degradation product of S-303. The donor serum and S-300 are then incubated with the same red test cells. S-300 binds to the antibody and produces a negative result in the gel map in the presence of anti-acridin antibodies. Of the 903 samples tested both at the Abidjan laboratory in Côte D'Ivoire and at the Frankfurt laboratory, we found 1 positive sample and 8 reactive samples (positive for anti-erythrocyte antibodies). Positive donor plasma was incubated with S-300 which is the degradation product of S-303. The result is always positive, whereas according to the instructions of the reference laboratory of Frankfurt, it should be negative in case of presence of Locustacan. The results on AAA testing among 903 donors in three sub-Saharan countries show the absence of AAA in the sample of subjects included in the study according to the hypothesis emitted from this study. This opens the door to the prospect of conducting a clinical study on the inactivation of pathogens by acridine derivatives.

Developmental expression and oxidative stress induction of proteome of glutathione S-transferases in Aedes albopictus (Diptera: Culicidae)

The combination of proteomic approach and affinity chromatography (GSTrap™ HP) has been used to identify and investigate the differential expression of GSTs under toxic challenge and during the course of development in Aedes albopictus. There were multiple isoforms of glutathione transferases (GSTs) expressed in the three developmental stages of Aedes albopictus. On a 2D gel map, the results indicate that there were 19 spots with a molecular mass in the range of 24–30kDa. Three types of GSTs were identified from the spots; namely GSTS1, GSTD1, and GST Theta. Spots identified as GSTS1 and GSTD1 were further designated as GSTS1–1 to GSTS1–5 and GSTD1–1 to GSTD1–13 respectively. Isoforms GSTD1–10, GSTD1–11, GSTD1–12, GSTD1–13, and GSTT were absent in the adult life stage. Isoenzymes GSTS1–3, GSTD1–2, and GSTD1–6 appeared as the major expressed isoforms in all the life stages. The effect of free radical generators such as hydrogen peroxide and paraquat on the expression of the GST isoforms in larvae mosquitoes was also investigated. Isoforms GSTD1–1, GSTD1–4, GSTS1–4, and GSTD1–12 had >1.5 fold increase when the larvae were challenged with both chemicals. GSTS1–3, GSTS1–4, GSTD1–1, GSTD1–2, GSTD1–3, GSTD1–6, and GSTD1–12 were significantly expressed (p<0.05) with >1.5 fold change when the larvae were challenged with hydrogen peroxide. On the contrary, different GST isoforms were responsive towards paraquat challenge. Those isoforms were GSTS1–2, GSTS1–4, GSTD1–1, GSTD1–5, GSTD1–9, GSTD1–11, GSTD1–12, and GSTT (with >1.5 fold change). The purified larvae GSTs seemed to have limited substrate specificities with the ability to only conjugate 1-chloro-2,4-dinitrobenzene (CDNB) and 1,2-dichloro-4-nitrobenzene (DCNB). The GSTs have however shown that they were capable of detoxifying lipid peroxidation products and possessing glutathione peroxidase activities.

Different Proteomics of Ca2+ on SA-induced Resistance to Botrytis cinerea in Tomato

This study aims to comprehensively study the effects of Ca2+ on the SA-induced resistance Botrytis cinerea in tomato through proteomics analysis. A proteomic approach was used to uncover the inducible proteins of tomato in the susceptible tomato cultivars ‘L402’ against Botrytis cinerea after salicylic acid (SA) and a combination treatment of CaCl2 and SA. The results showed that the use of combination treatment of CaCl2 and SA significantly enhanced tomato resistance against Botrytis cinerea. In total, 46 differentially expressed protein spots from 2-DE gel maps were detected, of which 41 were identified by mass spectrometry. All the identified proteins were categorized into eight groups according to their putative functions: defense response (14.00%), antioxidative protein (9.75%), photosynthesis (24.39%), molecular chaperone (4.88%), energy (17.01%), metabolism (21.95%), protein synthesis (4.88%) and signal transduction (0.2%). Of the proteins in the eight function groups, the effect of stress/defense and reactive oxygen species on Ca2+-regulated SA-induced resistance may be the most important one in induced resistance by RT-PCR. The expression level of pathogenesis-related proteins (PRs) and chitinase was upregulated by a combination treatment of CaCl2 and SA. The characterization of these proteins greatly helped to reveal the induced proteins involved in the regulation of Ca2+ on SA-induced resistance to Botrytis cinerea. In the combination treatment of CaCl2 and SA, the defense response and antioxidative protein were clearly upregulated much more than SA alone or the control treatment by the method of proteomics and RT-PCR. The present findings suggest that susceptible tomato cultivars treated by the combination treatment of CaCl2 and SA might possess a more sensitive SA signaling system or effective pathway than SA treatment alone. In addition, results indicated that SA could coordinate other cellular activities linked with photosynthesis and metabolism to facilitate defense response and recovery, indicating that the self-defense capability of tomato was improved by the combination treatment of CaCl2 and SA.

Identification and comparative proteomic study of quail and duck egg white protein using 2-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry analysis

A proteomic study of egg white proteins from 2 major poultry species, namely quail (Coturnix coturnix) and duck (Anas platyrhynchos), was performed with comparison to those of chicken (Gallus gallus) through 2-dimensional polyacrylamide gel electrophoresis (2-DE) analysis. By using matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS), 29 protein spots representing 10 different kinds of proteins as well as 17 protein spots designating 9 proteins were successfully identified in quail and duck egg white, respectively. This report suggested a closer relationship between quail and chicken egg white proteome patterns, whereas the duck egg white protein distribution on the 2-DE map was more distinct. In duck egg white, some well-known major proteins, such as ovomucoid, clusterin, extracellular fatty acid-binding protein precursor (ex-FABP), and prostaglandin D2 synthase (PG D2 synthase), were not detected, while two major protein spots identified as “deleted in malignant brain tumors 1” protein (DMBT1) and vitellogenin-2 were found specific to duck in the corresponding range on the 2-DE gel map. These interspecies diversities may be associated with the egg white protein functions in cell defense or regulating/supporting the embryonic development to adapt to the inhabiting environment or reproduction demand during long-term evolution. The findings of this work will give insight into the advantages involved in the application on egg white proteins from various egg sources, which may present novel beneficial properties in the food industry or related to human health.

Algorithms for Warping of 2-D PAGE Maps.

Software-based image analysis of 2-D PAGE maps is an important step for the investigation of proteome. Warping algorithms, which are employed to register spots among gels, are able to overcome the difficulties due to the low reproducibility of this analytical technique. Over the years, the research of new matching and warping mathematical methods has allowed the development of several routine applications of easy-to-use software. This chapter describes common and basic spatial transformations used for the alignment of protein spots present in different gel maps; some recently new approaches are also presented.

GENOCOP Algorithm and Hierarchical Grid Transformation for Image Warping of Two-Dimensional Gel Electrophoretic Maps.

Hierarchical grid transformation is a powerful hierarchical approach to 2-D map warping, able to model both global and local deformations. The algorithm can be stopped when a desired degree of accuracy in the images alignment is obtained. The deformed image is warped and aligned to the target image using a grid where the number of nodes increases in each step of the algorithm. The numerical optimization of the position of the nodes of the grid can be efficiently solved by genetic algorithms, ensuring the achievement of the optimal position of the nodes with a low computational cost with respect to other methods. Here, the optimization of the position of the nodes is carried out by GENOCOP (genetic algorithm for numerical optimization of constrained problems), refined by the following conjugate gradient optimization step. The modeling of the warped space is then achieved by a spline model where some constraints are introduced in the choice of the nodes that are moved. The whole procedure can be intended as an evolutionary method that models the deformation of the gel map at different levels of detail.

In vitro Growth and Multiplication of Pineapple under Different Duration of Sterilization and Different Concentrations of Benzylaminopurine and Sucrose

Objective:To analyze mechanism of multiple shoot of mutant.Method:The two-dimensional electrophoresis(2-DE) was employed to compare the global protein patterns between normal and mutant.The 2-De gel maps were evaluated qualitatively and quantitatively with the Image Master 2-DE analyzer;Results:The 59 expressed proteins in the mutant were different in quality and quantity from those in the normal,in which 35 spots increased and 20 spots decreased in quantity.Furthermore,4 spots were missing in mutant;Conclusion:The difference of maps of two stages might relate to multiple shoot of mutant.

Proteomic Differences between Listeria monocytogenes Isolates from Food and Clinical Environments.

Listeria monocytogenes is an organism associated with a wide range of foods. It causes listeriosis, a severe illness that mainly affects people with weakened immune systems. Proteomic profiles of three different L. monocytogenes isolates were studied using 1D SDS PAGE, 2DE and mass spectrometry. The protein banding patterns generated by 1D SDS PAGE of three strains of L. monocytogenes were found to be similar. Visual observations from 2DE gel maps revealed that certain spots appeared to have intensity differences. Key differences in proteins synthesis of three strains of L. monocytogenes were found using the PDQest TM 2DE Analysis software. Comparison showed that the clinical isolate (strain SB92/844) had 53.4% and 53.9% protein profile similarity with dairy isolate (strain V7) and seafood isolate (SB92/870), respectively. The identity of selected protein spots was achieved using MALDI-TOF and ion trap mass spectrometry. It was found that certain identified proteins (i.e., a major cold shock protein and superoxide dismutase) were expressed differently between two local strains of L. monocytogenes (SB92/844, SB92/870) and one strain from overseas (V7).

Differential proteome analysis of mature and germinated seeds of Magnolia sieboldii K. Koch

This is the first reported proteomic analysis to study the dormancy breaking of Magnolia sieboldii seeds. Our results provide a fundamental reference for further studies on the regulation of protein expression during seed germination. Magnolia sieboldii K. Koch is an ornamental tree. The deep dormancy of its seeds hinders its cultivation for economic purposes. The biochemical basis of the regulation of seed germination remains poorly understood. The present study aimed to identify differentially expressed proteins in germinated seeds of M. sieboldii using polyethylene glycol fractionation. In total, 59 differentially expressed protein spots from two-dimensional gel maps were detected, 33 of which were identified by mass spectrometry. They were assigned to eight functional classes on the basis of their putative biological functions: photosynthesis (3 %), chaperonin/heat shock protein (9 %), protein and amino acid synthesis (9 %), stress/defense (18 %), cytoskeleton structure (3 %), metabolism (18 %), hormone and polyamine (9 %) and storage proteins (31 %). Among the other functions, the effects of plant hormones on seed germination may be one of the most important functions in plant growth. Gibberellins and ethylene positively regulate seed germination. The activities of several hormone-associated proteins possibly influencing seed germination were increased. The characterization of these proteins will be of great help in identifying the molecular mechanism underlying seed germination.

Animal species milk identification by comparison of two-dimensional gel map profile and mass spectrometry approach

The aim of the current study was to present the primary protein profile of cow, goat, camel, yak and buffalo milk, along with binary mixtures of these milks through two-dimensional gel electrophoresis coupled with mass spectrometry for detection of specific milks in mixtures. Distributions of α-lactalbumin and/or β-lactoglobulin spots on gel maps were used to detect goat, camel, yak and buffalo milk adulterated with cow milk. Appearance of α-lactalbumin and β-lactoglobulin protein spots were helpful for detection of camel, yak and buffalo milk adulteration with goat milk. αS1-Casein from cow and goat milk was also used to determine camel milk adulteration. In particular, β-lactoglobulin from cow, goat, yak and buffalo milk, and α-lactalbumin from camel milk were useful to detect adulteration of specific milk mixtures at levels as low as 0.5%. These results highlight applicability of this method for characterisation of milk proteome and detection of specific milk in mixtures.

An effective protein extraction method for two‐dimensional electrophoresis in the anticancer herb Andrographis paniculata Nees.

Proteomic analysis of plants relies on high yields of pure protein. In plants, protein extraction and purification present a great challenge due to accumulation of a large amount of interfering substances, including polysaccharides, polyphenols, and secondary metabolites. Therefore, it is necessary to modify the extraction protocols. A study was conducted to compare four protein extraction and precipitation methods for proteomic analysis. The results showed significant differences in protein content among the four methods. The chloroform-trichloroacetic acid-acetone method using 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer provided the best results in terms of protein content, pellets, spot resolution, and intensity of unique spots detected. An overall of 83 qualitative or quantitative significant differential spots were found among the four methods. Based on the 2-DE gel map, the method is expected to benefit the development of high-level proteomic and biochemical studies of Andrographis paniculata, which may also be applied to other recalcitrant medicinal plant tissues.

Identification of up-regulated proteins potentially involved in the antagonism mechanism of Bacillus amyloliquefaciens G1

The use of Bacillus probiotics has been demonstrated as a promising method in the biocontrol of bacterial diseases in aquaculture. However, the molecular antibacterial mechanism of Bacillus still remains unclear. In order to explore the antibacterial mechanism of the potential antagonistic Bacillus amyloliquefaciens strain G1, comparative proteomics between B. amyloliquefaciens strain G1 and its non-antagonistic mutant strain was investigated. The 2-dimensional electrophoresis gel maps of their total extracted proteins were described and 42 different proteins were found to be highly expressed in strain G1 in comparison with those in the mutant strain. 35 of these up-regulated proteins were successfully identified using MALDI-TOF-TOF MS and databank analysis, and their biological functions were analyzed through the KEGG database. The increased expression of these proteins suggested that high levels of energy metabolism, biosynthesis and stress resistance could play important roles in strain G1's antagonism. To our knowledge, this is the first report on the proteins involved in the antagonism mechanism of B. amyloliquefaciens using a proteomic approach and the proteomic data also contribute to a better understanding of the molecular basis for the antagonism of B. amyloliquefaciens.

Differential expression analysis of proteins in neutrophils between clinical mastitis and healthy dairy cows

Neutrophils provide the first line of defense against invading pathogens and have been reported to play a key role in bovine mammary immune. To examine the differential expression of proteins in neutrophils between clinical mastitis and healthy dairy cows, a 2-dimensional electrophoresis gel map with high repeatability was constructed for bovine neutrophils. From this map, seven differentially expressed proteins were identified by MALDI-TOF MS which are believed to be involved in pathways such as cell metabolism, oxidative stress, and inflammatory reaction. The differentially expressed proteins identified in this study may provide the basis for bovine mastitis resistance breeding research.

Discovery of Potential Bladder Cancer Biomarkers by Comparative Urine Proteomics and Analysis

ObjectiveWe searched for bladder tumor markers by analyzing urine samples from patients with bladder cancer and from normal controls. MethodsProteins in urine samples of patients with bladder cancer and with normal controls were systematically examined by 2-dimensional electrophoresis combined with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The expression of the protein apolipoprotein A-I (apoA-I) was confirmed by Western blot analysis and further evaluated. ResultsWe successfully obtained the 2-dimensional electrophoresis gel maps of urinary proteins in patients with bladder cancer and in normal controls. Thirty differentially expressed protein spots were successfully matched by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Combined with the SWISS-PROT database, only 14 proteins (beta-2-microglobulin, fatty acid–binding protein adipocyte, gelsolin, isoform 1 of gelsolin, myoglobin, isoform 2 of fibrinogen alpha chain, apoA-I, prostaglandin D2 synthase 21 kDa [brain], protein AMBP, transthyretin, keratin type II cytoskeletal 1, type II cytoskeletal 8, putative uncharacterized protein ALB, putative uncharacterized protein MASP2 [fragment]) were identified, including 2 putative proteins. Furthermore, apoA-I was confirmed by Western blot analysis, and the high level of apoA-I was found in urine samples from patients with bladder tumors compared with normal controls. ConclusionsAnalysis of urinary proteome may be a feasible, noninvasive, and efficient strategy for searching for potential bladder tumor biomarkers. A significant relationship of expressed apoA-I was established between bladder cancer and normal controls. We concluded that 14 differential spots included the apoA-I and would be potential urinary biomarkers for the diagnosis and surveillance of bladder cancer.

Systematic Annotation and Bioinformatics Analyses of Large-Scale Oryza sativa Proteome

Much has been now recognized on the rice (Oryza sativa L.) proteomics by using the powerful experimental tool two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). 2D-PAGE can be utilized for monitoring global changes of quantitative protein expression in specific tissues under various conditions. However, systematic annotations of the protein spots generated by 2D-PAGE are still limited for rice. In this study, a new approach for Oryza sativa proteome annotation based on the 2D-gel maps was developed. Based on the publicly available 2D-PAGE data of rice, 11,201 gel spots were annotated accounting for 87.2% of the total spots on the gel maps. Gel spot alignments were performed for the annotated gel maps belonging to 23 rice tissues or organelles. In summary, 253 alignments between 23 tissues or organelles were performed, and 26,207 co-expressed proteins were identified using our analytical strategy. Large-scale bi-cluster analysis of 23 tissues/organelles proteomes of rice was carried out to detect novel functional proteins. Function and pathway analysis identified a number of common gene products with great potential in regulating specific physiological and biochemical events within various rice tissues/organelles. It also suggested that the tissue- or organelle-specific proteins might be responsible for the functional divergence of these tissues or organelles. Taken together, this study provides us new strategies and informative resources for rice proteome research based on 2D-PAGE data.

AUTOMATIC PROTEIN SPOTS QUANTIFICATION IN TWO-DIMENSIONAL GEL IMAGES

Two-dimensional (2D) polyacrylamide gel electrophoresis of proteins is a robust and reproducible technique. It is the most widely used separation tool in proteomics. Current efforts in the field are directed at development of tools for expanding the range of proteins accessible with 2D gels. Proteomics was built around the 2D gel. The idea that multiple proteins can be analyzed in parallel grew from 2D gel maps. Proteomics researchers needed to identify interested protein spots by examining the gel. This is time-consuming, labor-extensive, and error-prone process. It is desired that the computer can analyze the proteins automatically by first detecting then quantifying the protein spots in the 2D gel images. In our previous work, we presented a new technique for segmentation of 2D gel images using the fuzzy c-means (FCM) algorithm using the notion of fuzzy relations. In this paper, we will describe the new relational FCM (RFCM) algorithm and use it for automatic protein spots quantification. We will also use two methods to evaluate its performance: the unsupervised evaluation method and comparison with the expert spots quantification.