Comparative examination of soluble red muscle proteins of fifteen Sparidae species

Soluble red muscle proteins from the lateral line of 15 Sparidae species were analysed by isoelectric focusing. Species-specific patterns were found. The species-specific protein fractions could be correlated with different metabolic activities and with different growth indexes. More protein fractions were identified for Pagellus acarne (Risso) and Diplodus annularis (L.) than for the other 13 species. This would appear to be related to growth index. The existence of red muscle with a greater number of protein bands than white muscle was confirmed in almost all species. The similarity coefficients have shown that closely related species have similar patterns and, thus, higher similarity coefficients. The derived dendrogram agrees with previous classifications based on morphological information.     

Study of the soluble lens proteins from fifteen sparidae species

• 1.1. Soluble eye lens proteins of fifteen different Sparidae species were analysed.
• 2.2. Species-specific electrophoretic and isoelectric focusing patterns were found.
• 3.3. Significant differences in the distribution of β and γ-crystallin protein components were noted for all species.
• 4.4. These data suggest that the Sparidae family may be a heterogenenous taxonomic group encompassing considerable genetic diferences and with different evolutionary histories.

     

Two-dimensional polyacrylamide gel electrophoresis of membrane proteins

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is one of the most powerful separation techniques for complex protein solutions. The proteins are first separated according to their isoelectric point, driven by an electric field across a pH gradient. The pH gradient necessary for the separation according to isoelectric point (pL) is usually established by electrophoresing carrier ampholytes prior to and/or concomitantly with the sample. The second dimension is usually a separation according to molecular size. Mostly this separation is performed after complete denaturation of the proteins by sodium dodecyl sulfate and 2-mercaptoethanol (SDS-PAGE). This standard method has considerable disadvantages when relatively hydrophobic membrane proteins are to be separated: cathodic drift, resulting in nonreproducible separation, and the denaturation of the protein, mostly making it impossible to detect native properties of the proteins after separation (e.g., enzymatic activity, antigenicity, intact multimers, and so on). The protocols presented here take care of most of these obstacles. However, there is probably no universal procedure that can guarantee success at first try for any mixture of membrane proteins; some experimentation will be necessary for optimization. Two procedures are each presented: a denaturing (with urea) and a nondenaturing method for IEF in immobilized pH gradient gels using Immobilines, and a denaturing (with SDS and 2-mercaptoethanol) and a nondenaturing technique (with CHAPS) for the second dimension. Essential tips and tricks are presented to keep frustrations of the newcomer at a low level.     

Expression of myofibrillar proteins and parvalbumin isoforms in white muscle of dorada during development

Several polyacrylamide gel electrophoresis techniques were used to study developmental changes in myofibrillar protein composition and parvalbumin distribution in the myotomal muscle of Brycon moorei . Two myosin LC2 chains and two troponin I isoforms were successively detected. Up to four troponin T isoforms were synthesized. Slow red-muscle myofibrils from adult fish showed no common component (except actin) with larval, juvenile or adult fast white-muscle myofibrils. During growth of B. moorei , two classes of parvalbumin isoforms were sequentially expressed: larval PA I, PA IIa, and PA IIb and adult PA III. In adult fish, the content in Tn T-2 isoform decreased from the anterior to the posterior myomeres, in favour of Tn T-1 and Tn T-4. The parvalbumin content also diminished from the rostral to the caudal muscle. The fast rate of transition from larval to adult isoforms appeared to parallel the extremely fast growth of B. moorei . Sequential expression of these isoforms presumably reflected variations in the contractile properties of the muscle fibres, required by changes in physiological demands of the propulsive musculature.     

Biochemical characterisation of Australian strains of Echinococcus granulosus by isoelectric focusing of soluble proteins

The existence of three distinct strains of E. granulosus in Australia has been previously demonstrated on the basis of several criteria. In the present study, numerous isolates of E. granulosus from domestic and wild animal populations in different geographical areas of Australia were subjected to detailed biochemical analysis using isoelectric focusing of soluble proteins. Three different populations were recognised which corresponded to the three strains described previously, thus confirming their genetic distinction. One strain is common to all domestic intermediate hosts on the Australian mainland. Evidence is presented that humans and macropod marsupials are also susceptible to infection with this strain and that it is similar to E. granulosus occurring in sheep in New Zealand and the United Kingdom. The other two strains are confined to macropod marsupials on the Australian mainland and sheep in Tasmania respectively.     

Polyacrylamide gel electrophoresis: recovery of non-stained and stained proteins from gel slices

Following electrophoresis or isoelectric focusing in gels of polyacrylamide the protein band of interest is cut out and placed above a sucrose gradient column, containing carrier ampholytes (Pharmalyte). By electrophoresis, isoelectric focusing or displacement electrophoresis the proteins migrate out of the gel slice and into the isoelectric focusing column for concentration and further purification. From this column, the proteins can be withdrawn and their isoelectric points determined. Even after staining with Coomassie Brilliant Blue at least some proteins can be recovered by this technique and used for further analyses, for instance amino acid determinations. The focusing in a pH gradient by carrier ampholytes can be replaced by an electrophoresis in a conductivity gradient column. However, in comparison with isoelectric focusing, this concentration technique has the drawback of not permitting further purification of the eluted protein.     

The use of prontosil for the visualization of carbonic anhydrase bands in polyacrylamide gels. Application to the carbonic anhydrase isozymes of erythrocytes and white skeletal muscle of the rabbit

Prontosil, a carbonic anhydrase inhibitor of orange-red colour, is used to visualize carbonic anhydrase bands during isoelectric focusing in polyacrylamide gels. 5–60 ng of the sulfonamide Prontosil are added to the 100–200 μl samples before application to the gels. Bound Prontosil moves into the gel together with carbonic anhydrase and stains the enzyme bands formed there, while unbound Prontosil remains on top of the gels. The method is specific, no proteins other than carbonic anhydrase were observed to be stained, and it requires no special equippment. It was applied to chloroform/ethanol extracts of erythrolysates and while muscle homogenates from rabbits. Densitometric evaluation of the Prontosil-stained bands obtained with these extracts showed that rabbit red cells contain roughly equla amounts of carbonic anhydrase isoenzymes B and C while in rabbit white skeletal muscle isoenzyme C is predominant and little B enzyme occurs. These results confirm previous findings obtained by affinity chromatography of erythrolysates and muscle homogenates.     

Characterization of proteins in the human serum proteome.

This paper presents a multidimensional profile of the human serum proteome, produced by a two-dimensional protein fractionation system based on liquid chromatography followed by characterization with capillary electrophoresis (CE). The first-dimension separation was done by chromatofocusing over a pH range from 8.5 to 4.0, where proteins were separated by their isoelectric points (pI). In this dimension, fractions were collected based on pH. The first-dimension pI fractions were then resolved in the second dimension by high-resolution, reversed-phase chromatography with a gradient of trifluoroacetic acid (TFA) in acetonitrile and TFA in water. A selected protein fraction collected from the second dimension by time was characterized by CE for molecular-weight estimation and for presence of isoforms. Molecular-weight estimation was done by sodium dodecyl sulfate capillary gel electrophoresis, where proteins were separated in the range of 10,000-225,000 Da. Detection of isoforms was done by capillary isoelectric focusing over a pH range of 3-10. A selected second-dimension fraction that contained the putative serum iron-binding protein transferrin was analyzed by these two CE techniques for molecular-weight determination and the presence of isoforms. The combination of two-dimensional protein fractionation and CE characterization represents an advanced tool for proteomics.     

Optimization of the first dimension for separation by two-dimensional gel electrophoresis of basic proteins from human brain tissue

A major cause of poor resolution in the alkaline pH range of two-dimensional electrophoresis (2-DE) gels is unsatisfactory separation of basic proteins in the first dimension. We have compared methods for the separation of basic proteins in the isoelectric focusing dimension of human brain proteins. The combined use of anodic cup-loading and the hydroxyethyldisulphide containing solution (DeStreak) produced better resolution in both analytical and micropreparative protein loaded 2-DE gels than the other methods investigated.     

The sensitivity of isoelectric focusing and electrophoresis in the detection of sequence differences in proteins

Fourteen myoglobins of known sequence were examined by isoelectric focusing with and without urea. The 14 sequences formed six distinct mobility classes on gels without urea and three classes on those with urea. For these proteins, isoelectric focusing provides no advantage over single, nonequilibrium, nondenaturing gels in the total number of distinguishable mobility classes. Only major charge differences, resulting from the changes in the total numbers of acidic and basic amino acids, can be detected on gels with urea, indicating that denaturation by urea alters proteins so that small differences in ionization are eliminated.We thank the Department of Biology, University of Utah, for financial support.     

Additional microsatellites for Sparus aurata and cross‐species amplification within the Sparidae family

Six new microsatellite loci were isolated and characterized in 32 individuals from a farm population of gilthead seabream (Sparus aurata). Expected heterozygosity at all loci was high, ranging from 0.835 to 0.958 with between 10 and 27 alleles per locus. A multiplex polymerase chain reaction protocol was developed using four of the loci. Cross‐species amplification of the loci was tested in six species of the Sparidae family and four loci were successfully amplified in two or more related species.     

Isoelectric focusing following by electrophoresis of proteins for visualizing their titration curves by zymogram and immunofixation

After isoelectric focusing followed by electrophoresis at right angles in the same gel slab, it is possible to visualize the titration curve of proteins by zymograms or immunofixation even of an unpurified sample. This information can be very useful for the selection of the proper purification strategy by charge-dependent methods, e.g. ion-exchange chromatography, zone and disc electrophoresis and isotachophoresis. The titration curve also gives information on the stability of the protein as a function of the prevailing pH of the medium, in the pH 3-10 range. A region of instability is found for most proteins in acidic conditions, below pH 4.5, while most proteins are stable in the alkaline pH region, at least up to pH 10. The best method for developing zymograms and immunoprints appears to pH 10. The best method for developing zymograms and immunoprints appears to be the 'sandwich technique', by which a thin agarose slab, cast on an hydrophilic polyester sheet, and impregnated with appropriate reagents, is left in contact with a polyacrylamide gel thin layer used to generate the titration curves.     

Seed proteins and systematics of Tripsacum

The genus Tripsacum (Gramineae) is distributed between the latitude 42°N and 24°S in the New World. It is divided into two sections. Section Tripsacum includes 11 species with T. dectyloides (L) L. extending across the range of the genus. Section Fasciculata includes five Meso-American species with T. lanceolatum Rupr. ex Fourn. extending into southern Arizona. The genus displays considerable diversity in seed proteins. Variation patterns are of limited use in distinguishing sections, but are species and habitat specific. Protein data are particularly useful in subspecific classification, and consistently distinguish diploid from polyploid races of T. zopilotense Hern. and Randolph and T. bravum Gray. The tetraploid ectotype of T. bravum deserves specific rank and the robust ecotype of T. dactyloides var. meridonate de Wet and Timothy deserves varietal rank.     

二氢叶酸还原酶结合底物的去除

分析了应用氨甲蝶呤（MTX-Agarose）亲和层析法提纯的鸡肝二氢叶酸还原酶的组成和性质.建立了用平面粒度胶等电聚焦法去除与酶紧密结合底物的方法．讨论了结合底物对酶构象研究的影响,并指出,用未完全去除结合底物的酶研究酶在变性过程构象变化会得到错误的结论．     

Mapping of alkaline proteins in bovine skeletal muscle

In agricultural sciences, proteomics has become the new hope for analyzing the meat quality traits that are closely related to the skeletal muscle traits. 2-DE muscle maps of many species have been recently reported and used to find molecular markers of meat quality traits. However, one limitation of 2-DE based analyses is due to the limited alkaline protein separation. Considering this problem, there is a need to use recent advances that have markedly improved the 2-DE based analysis of alkaline proteins. Hence, the present study provides additional information concerning the alkaline proteome of bovine skeletal muscle by using an appropriate protocol to characterize proteins over the entire range of pH 7-11. A total of 32 distinct gene products corresponding to 60 protein spots were identified by PMF and grouped in seven categories according to their main function. This 2-D map will contribute to muscle proteome studies since a significant portion of proteins is in the alkaline pH range.     

Comparative electrophoretic studies of muscle and eye lens proteins in freshwater fish of Iraq

Muscle myogens and eye lens proteins have been studied in ten species of freshwater fish from Iraq. The electrophoretic analysis revealed that the muscle myogens can be considered as a good taxonomic criterion to differentiate the family Mugilidae from the Cyprinodontidae and Cyprinidae, but not between the families Poeciliidae and Cyprinodontidae. Within the Cyprinidae the muscle myogens can be used to diferentiate Barbus grypus from the remaining species of this family. Eye lens proteins are not considered a good taxonomic criterion to differentiate the members of the four families studied, but can distinguish B. belawayei and B. grypus from the other Cyprinid species.     

Electrophoretic variation of seed proteins among U.S. populations of Tripsacum dactyloides Var. dactyloides

Accessions from across the range of Tripsacum dectyloides in the US. were assayed electrophoretically for interpopulation variation in seed proteins. Clustering of isoelectric focusing patterns for Tris-HCl and water-soluble proteins revealed high levels of homogeneity. Preliminary resultswith alcohol-soluble proteins, in contrast, showed this fraction to be intrinsically much more variable. Divergent functional roles of the protein fractions themselves could account for this observed difference in variation and are discussed in the paper.     

High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae

Recently, 454 sequencing has emerged as a popular method for isolating microsatellites owing to cost-effectiveness and time saving. In this study, repeat-enriched libraries from two southern African endemic sparids (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX sequenced. From these, 7370 sequences containing repeats (SCRs) were identified. A brief survey of 23 studies showed a significant difference between the number of SCRs when enrichment was performed first before 454 sequencing. We designed primers for 302 unique fragments containing more than five repeat units and suitable flanking regions. A fraction (<11%) of these loci were characterized with 18 polymorphic microsatellite loci (nine in each of the focal species) being described. Sanger sequencing of alleles confirmed that size variation was because of differences in the number of tandem repeats. However, a case of homoplasy and sequencing errors in the 454 sequencing were identified. These newly developed and four previously isolated loci were successfully used to identify polymorphic markers in nine other economically important species, representative of sparid diversity. The combination of newly developed markers with data from previous sparid cross-species studies showed a significant negative correlation between genetic divergence to focal species and microsatellite transferability. The high level of transferability we described (48% amplification success and 32% polymorphism) suggests that the 302 microsatellite loci identified represent an excellent resource for future studies on sparids. Microsatellite marker development should commonly include tests of transferability to reduce costs and increase feasibility of population genetics studies in nonmodel organisms.     

A simple and reliable method for the drying of polyacrylamide slab gels

A simple method for the drying of polyacrylamide slab gels is described. 2-mm thick gels with gradients of 5–20% acrylamide dry without complications. The dried gels are transparent permitting transmission densitometry and fluorography.     

Immunological relationships and a genetic interpretation of major and minor acidic proteins in human parotid saliva

Isoelectric focusing was performed on parotid salivas selected for their electrophoretic phenotypes of proline-rich acidic salivary proteins. Fractions encompassing narrow pH regions were pooled and examined by polyacrylamide gel electrophoresis. Isoelectric focusing yielded partial purification of major and minor acidic proline-rich proteins which were subsequently compared by immunoelectrophoresis and double immunodiffusion against goat anti-human parotid saliva. Cross-reactivity without spurring between all fractions containing major Pr proteins in both immunoelectrophoresis and double immunodiffusion suggests that these proteins are immunologically very similar or identical.This study was supported in part by an award from the American Cancer Society Institutional Grant IN-88F to Fels Research Institute.