AFLP分析中多态性扩增产物的回收、克隆及鉴定

本研究在摸索和优化了水稻AFLP分析体系的基础上,发展了多态性AFLP产物的高效克隆方法。特异AFLP扩增产物直接从变性聚丙烯酰胺凝胶上分离纯化,再经过一至二轮PCR扩增,即可高效地克隆于pGEM-Teasy vector系统中。本实验利用该方法成功地克隆了水稻温敏核不育等位突变系546 0S和5460F间的4个多态性AFLP产物,Southern bloting分析证明其中3个产物在水稻基因组中为单拷贝序列,另一个为低拷贝序列。AFLP技术强有力的多态性检出能力再结合多态性扩增产物的高效克隆方法,为寻找与目标基因紧密连锁的分子标记提供了有力工具。 Abstracts:An efficient method for cloning DNA fragment from denaturing polyacrylamide gels was developed to allow the isolation of specific bands obtained from amplified fragment length polymorphism(AFLP)products.After isolation and purification from the thin denaturing polyacrylamide gels,specific AFLP products were successfully cloned after one or two rounds of PCR reamplification.Using this method 4 polymorphic AFLP products between a pair of rice allelic lines differing for thermo-sensitive genic male sterile(TGMS)ene were cloned and it was confirmed that 3 of the AFLP products represented single copy sequences and the other 1 represented low copy sequence in rice genome.     

有和无甘油的聚丙烯酰胺胶在检测突变时的差别

有文献报道在非变性的聚丙烯酰胺中加入甘油可提高SSCP检测的灵敏度。我们的实验结果建议研究者在进行SSCP筛查未知突变时最好采用不加甘油的非变性的聚丙烯酰胺胶,这既省力省钱,又灵敏。在判读SSCP胶时,千万不要看到在双链带位置有一条比正常迁移率慢的带就判定为插入突变。此时要判定突变的性质,最好测序。 Abstract：It was reported that glycerol in the non-denatured SSCP polyacrylamide gel could increase the sensibility of detecting mutation. We detected the mutation of PKD 1 gene in the patients with autosomal dominant polycystic kidney disease.PCR com bined with SSCP(single-strained conformation polymorphism),the non-denatured 10% polyacrylamide gel without glycerol or 10% polyacrylamide gel with 5% glycerol and DNA sequencing method were used.Our results showed that four single strand b ands were found in the non-denatured polyacrylamide gel without glycerol while t wo single strand bands were found in the polyacrylamide gel with glycerol in the same patient.Sequence showed there is a deletion of G in one DNA molecular and a G→A substitution in another DNA molecular in the patient with abnormal shift SSCP bands.Therefore, our experiment suggested that non-denat ured polyacrylamide gel was better than the polyacrylamide gel with glycerol in detection mutation,and it will save labor and money.It also suggeste d that one basedeletion can cause a slow double-strand DNA following the normal double strand band,which was caused by the heterogeneous DNA molecule formed bet ween the normal DNA strand and the one base deletion DNA strand with the protrud ing base.Our results suggest that when judging mutation in SSCP gel,it is not re liable to decide that mutation is inversion according to slow mobility in the ge l,and when the characteristic of mutation need to be judged,it must be sequenced .     

内蒙古蒙古族人群DYS413基因座的多态性分布

为 调查DYS413(YCAⅢ) 基因座在内蒙古蒙古族人群中的分布情况,为其应用于法医学和人类遗传学研究提供依据,采集了120例内蒙古蒙古族男性无关个体静脉血,EDTA抗凝,用酚-氯仿法抽提DNA,PCR扩增DYS413基因座,6%非变性聚丙烯酰胺凝胶电泳,1‰硝酸银(AgNO3)染色分型。 在120例内蒙古蒙古族男性人群中共检出30个不同的单倍型,其频率介于0.0007至0.01361之间,其HD(单倍型多样性)值为0.94054。表明DYS413基因座在内蒙古蒙古族人群中分布好,对法医学和人类遗传学研究具有重要价值。Abstract： In order to provide the evidence for the application of DYS413(YCAⅢ) locus in forensic medicine and population genetics by investigating its polymorphism in the Mongolians lived in the Inner Mongolia Autonomous Region, China, to collect 120 unrelated male Mongolians’ venous blood, who lived in the Inner Mongolia Autonomous Region, and the blood is anticoagulant with EDTA, then to extract DNA by using the method of phenol-chloroform and amplify the DYS413 locus with PCR. The products were separated with 6% non-denatured polyacrylamide/bisacrylamide gels(19:1) electrophoresis and stained with 1‰ nitrate of silver(AgNO3). There are total 30 different haplotypes in Mongolians, the frequencies are from 0.0007 to 0.01361, the HD(haplotype diversity) is 0.94054. It shows that DYS413 locus is high valuable in the application of forensic medicine and population genetics.     

紫孢侧耳、糙皮侧耳及其融合菌株的同工酶分析

采用聚丙烯酰胺凝胶垂直板电泳方法对紫孢侧耳、糙皮侧耳及其融合菌株的酯酶和过氧化物酶同工酶进行了分析。经多次试验,得到了两亲株和融合株恒定的同工酶谱, 在酶谱中融合菌株与亲株有明显差异,并表现出典型的双亲株互补酶带特征,从而证实融合菌株为两亲株基因重组之产物。 Abstract: After many repetitions,the patterns of esterase isozyme and peroxidase isozyme of Pleurotus sapidus,Pleurotus ostreatus and their fusant strains were obtained.There were differences among the parent strains and theirfusant strains in theirisozyme bands.Parental isozyme bands appeared in patterns of fusant strains.Itdemonstrated that fusant were recombinants of P.sapidus and P.ostreatus.     

Optimization of PCR protocol in microsatellite analysis with silver and SYBR® stains

Here we present the optimization of PCR conditions for microsatellite analysis of coniferous trees. The use of touchdown protocol for annealing resulted in a high success rate for optimization using fewer temperature profiles. The use of SYBR^￠ Green gel stain to detect PCR products in agarose gels was more sensitive than ethidium bromide. This is valuable for determining the success of PCR reactions and estimating the amount of PCR products formed—which is crucial in determining the dilution required to produce bands of similar intensity upon silver staining of the polyacrylamide gels. The use of SYBR^￠ Gold for staining polyacrylamide gels was not satisfactory in terms of the image quality produced. However, it was comparable to silver staining in terms of sensitivity, and could possibly be used in cases where the products are present as sharp single bands. In those cases, the use of SYBR^￠ Gold gel stain would save time and money for staining polyacrylamide gels.     

菠菜叶片中乙醇酸氧化酶3种同工酶的生化特性

By DEAE cellulose and Sepharose 6B chromatography, the proteins containing glycolate oxidase isozymes GOⅡ and GOⅢ were extracted from spinach green leaves. The protein containing GOⅡ showed two bands of 67±2 kD and 40±2 kD in SDS PAGE whose specific activity of glycolate oxidase was 33.4 U·mg -1 ·min -1 .It migrated towards cathode in Native PAGE in pH 8.3 buffer system. pI of GOⅡwas about 9.4 detected by IEF. The protein containing GOⅢ showed three bands of 67±2 kD, 40±2 kD and 38±2 kD in SDS PAGE whose specific activity of glycolate oxidase 14.4 U·mg -1 ·min -1 and could not migrate anywhere in the same Native PAGE. pI of GOⅢ was about 8.3 detected by IEF. The 40±2 kD might be the subunits of GOⅡ and GOⅢ. Antibodies of the protein containing GOⅡ and GOⅢ were prepared respectively. GOⅡ was very unstable and could change into GOⅢ artifact; GOⅢ was also unstable and could change into GOⅠartifact whose Mr ≈470 kD and pI ≈7.4 . This GOⅠ(specific activity: 9.8 U·mg -1 ·min -1 ), showing one 40±2 kD band in SDS PAGE, could be purified on another Sepharose 6B chromatography. The specific activity of GOⅡ decreased rapidly to about half of its original value and then was relatively stable when stored in 50% glycerol at -20℃. The results above explained why GOⅡ was extracted difficultly, and GOⅢ were easily confused with GOⅠ and GOⅡ.     

Purification and characterization of glyceraldehyde-3-phosphate dehydrogenase from European pilchard Sardina pilchardus

The NAD＋-dependent cytosolic glyceralehyde-3-phosphate dehydrogenase （GAPDH; EC 1.2.1.12） was purified from the skeletal muscle of European pilchard Sardina pilchardus and its physicochemical and kinetic properties were investigated. The purification method consisted of two steps, ammonium sulfate fractionation followed by Blue Sepharose CL-6B chromatography, resulting in an approximately 78-fold increase in specific activity and a final yield of approximately 25%. The Michaelis constants （Kin） for NAD＋ and D-glyceraldehyde-3-phosphate were 92.0 μM and 73.4 μM, respectively. The maximal velocity （Vmax） of the purified enzyme was estimated to be 37.6 U/mg. Under the assay conditions, the optimum pH and temperature were 8.0 and 30 ℃. The molecular weight of the purified enzyme was 37 kDa determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Non-denaturing polyacrylamide gels yielding a molecular weight of 154 kDa suggested that the enzyme is a homotetramer. Polyclonal antibodies against the purified enzyme were used to recognize the enzyme in different sardine tissues by Western blot analysis. The isoelectric point, obtained by an isoelectric focusing system in polyacrylamide slab gels, revealed only one GAPDH isoform （pI 7.9）.     

云南汉族人群D17S30位点扩增片段长度多态性A

应用PCR技术和小型聚丙烯酰胺凝胶电泳银染法, 对云南汉族人群D17S30位点扩增片段长度多态性进行了分析。在被检的105名无关个体中,共检出12个等位基因,41种基因型。等位基因频率范围在0.0048-0.2190之间,杂合度为83.81%,DP值为0.9647。观察的基因型分布符合Hardy-Weinber g定律。 Abstract:A study on amplified fragment length polymorphism(Amp-FLP)at locus D17S30 in Han nationality of Yunnan was carried out by using PCR followed by a high-resolution PAGE technique and silver staining.In a sample of 105 unrelated individuals,a total 12 different alleles and 41 genotypes were detected.The heterozygosity was 83.81% and the probability of discrimination(DP) was 0.9647.The distribution of observed genotypes obeyed the Hardy-Weinberg equilibrium.     

Identification of Contaminations Hiding Beneath the α- and β-Subunits of Partially Purified Nitrogenase MoFe Protein on the Sodium Dodecyl Sulfate Gel

To identify the unknown proteins that would contaminate the α- and β-subunits of nitrogenase MoFe protein on sodium dodecyl sulfate-polyacrylamide gel electrophoresis （SDS-PAGE）, the partially purified MoFe protein （Avl） preparation was obtained from Azotobacter vinelandii Lipmann OP by chroma- tography on DEAE-cellulose （DE52） and Sephacryl S-200 columns and analyzed by PAGE and matrix- assisted laser desorption/ionization time-of-flight （MALDI-TOF） mass spectrometry. The Av 1 preparation was shown to have two main bands at the position of the α- and β-subunits of crystalline Avl on the SDS gel. However, on the anoxic native PAGE, in addition to the Avl band, the preparation was shown to have three other main bands that migrated slower than Av 1. Of these three main bands, the protein with the fastest migration was identified as bacterioferritin elsewhere. The proteins on the other two bands, termed Upper and Middle, were suggested to be two different homopolymers with the same apparent subunit electrophoretic mobilities as the α- and β-subunits of Avl, respectively. By analysis of MALDI-TOF mass spectrometry, the Upper was identified as GroEL, which belongs to the heat shock protein 60 family, and the Middle was identified as glucose-6-phosphate isomerase （PGI）. In our preparation, anoxic native electrophoresis indicated that GroEL was composed of 14 identical subunits and that PGI was composed of 10 identical subunits. This is the first report of PGI, with so many subunits. The contaminating proteins in the Av 1 preparation, mainly GroEL and PGI, could be totally or partially removed from Av 1 if the shoulders and center of the elution peak were collected separately from the Sephacryl S-200 column and the center fraction was purified further by Q-Sepharose developed with an NaC1 concentration gradient. Thus, Avl with more than 90% purity was obtained. Obviously, this modified method is useful for the purification of mutant MoFe proteins with a high purity.     

Urinary proteins in four rodent species.

1. Mean urinary protein concentration levels are significantly higher in male Peromyscus leucopus than females (98.4 and 72.4 mg/dl). 2. Only females showed a significant correlation between weight and urinary protein concentration (r = 0.75 vs r = 0.03). 3. In intraspecific sexual electrophoretic comparisons of P. leucopus and P. maniculatus non-denatured urinary protein, four and two common bands were identified, respectively. Males of both species showed an extra protein band. 4. Four common electrophoretically separable denatured urinary protein bands were observed between 14,200 and 116,000 mol. wt in male and female P. leucopus and female P. gossypinus. Three of the four major protein bands were also found in P. maniculatus. Male Reithrodontomys megalotis pattern showed none of the major bands.     

The Freshwater Mussel (Elliptio complanata) as a Sentinel Species: Vitellogenin and Steroid Receptors

Freshwater mussels, Elliptio complanata were collected froma reference and pollutant-impacted pond on Cape Cod, MA. Glutathione-S-transferase(GST) activity was measured in gill, hepatopancreas and foot.In addition, content of seven heavy metals were measured inwhole bodies. GST activity was significantly elevated in hepatopancreasand foot, as was whole body cadmium level in animals from thecontaminated site suggesting that these animals have been exposedto organic and inorganic contaminants. Sodium dodecyl acrylamidegel electrophoresis (SDS-PAGE) analysis showed putative vitellogeninswith molecular weight 180 and 205 kDa bands only in the ovary.In non-denatured gel electrophoresis ovarian extracts revealedtwo higher molecular weight bands at 550 and 700 kDa, whichwere reproductive stage specific. Western blotting of SDS-PAGEand non-denatured gels using the anti-scallop yolk-protein antibodyconfirmed the presence of cross-reacting bands of the same molecularweights in the ovary but not other tissues. Although severalexperiments involving steroid hormone exposure were done, nosignificant changes in vitellogenin protein levels were observed.However, using an anti-human ERß antibody, ERßpositive bands were observed both in female foot, and the ovary.No cross reactivity with the antibody was observed in hepatopancreas.Additional studies are required to resolve questions of vitellogeninregulation and the role of (xeno)estrogens in bivalve molluscs.     

Multiple acid proteinases in the cellular slime mould Dictyostelium discoideum.

Proteinase activity in the cellular slime mould Dictyostelium discoideum has been analyzed by electrophoresis on polyacrylamide gels containing denatured hemoglobin. At least eight bands due to acid proteinases have been defined using extracts of myxamoebae, four bands A-D which move faster than the fifth and major band E, a minor band E' which moves just behind E and two slow bands G and H. Fruiting body formation was accompanied by the appearance of one new proteinase band F. The proteinases were present in extracts of both axenically-grown and bacterially-grown cells. Differences between the pH dependence and stability of the individual proteinases were detected. Inhibitor studies suggested that the faster proteinases A-D may be cathepsin B-like, whilst the slower enzymes E, E' and F do not fit readily into any known group of proteinases since they were sensitive to HgCl2 but not to other inhibitors of cathepsin B and not to inhibitors of cathepsin D-like proteinases under standard conditions. None of the proteinases was apparently formed during or after preparation of extracts and the proteinases could be re-run on polyacrylamide gels to give only the band expected from the first run. The bands are believed to reflect multiple proteinase activities within the cell.     

Purification of a Ciliary Neurotrophic Factor from Bovine Heart

A neurotrophic factor that promotes the survival of cholinergic parasympathetic ciliary neurons has been purified approximately 20,000-fold from bovine cardiac tissue under nondenaturing conditions using heparin-affinity chromatography. Up to 22 micrograms of purified factor having a specific activity of 4 X 10(5) trophic units/mg can be obtained from 250 g of heart muscle. Sodium dodecyl sulfate (SDS)-polyacrylamide gels of the purified material show a broad band that is sometimes resolvable into a closely spaced pair of bands of 22 and 23 kilodaltons. Partially purified factor can be resolved into two peaks of activity (pI 5.6 and 5.0) by high-resolution anion-exchange chromatography and chromatofocusing, although these procedures have not proved useful as purification methods because of the large losses of activity incurred. It is likely that these two peaks represent the two bands seen on SDS-polyacrylamide gels. The bovine cardiac factor(s) differs from similar factors purified from chick optic tissues and pig brain in that it is irreversibly denatured by SDS.     

Separation of the complementary strands of DNA fragments on polyacrylamide gels.

32P-labeled (in vivo) phiX174 RFI DNA was restricted by Hinc II. Three aliquots of the same digest: a) nondenatured, b) heat denatured, and c) denatured by 5 mM Me-HgOH were analyzed on 3-15% acrylamide gel gradients or on 3% gels with reduced N,N'-methylene-bis-acrylamide. The autoradiography of the gels showed that the nondenatured sample migrates two times faster than the denatured samples. After denaturation each original fragment appeared as a doublet. Using in vitro synthesized RFI DNA labeled only in negative strand with 32P we could identify the position of the negative strand in each denatured doublet. The single strand DNA fragments could be recovered from the gel slices on a semi-preparative scale by electrophoresis into dialysis tubing.     

Comparative analysis of proteins from the fibrous sheath and outer dense fibers of rat spermatozoa

The protein composition of the fibrous sheath (FS) and the outer dense fibers (ODF), two cytoskeletal components of the tail of spermatozoa, was compared by using polyacrylamide gel electrophoresis and immunochemistry applied to Western blots and to spermatozoa. Isolated FS and ODF, the purity of which were verified by electron microscopy (EM), were denatured and either run on sodium dodecyl sulfate-polyacrylamide gels or used to raise antibodies. The gels revealed at least 18 and 14 polypeptide bands for the FS and ODF, respectively. The major bands of the FS had molecular masses of 75, 27.5, and 14.4 kDa, whereas the major bands of the ODF-connecting piece had molecular masses of 32-26, 20, 14.4, 84, and 80 kDa. Several prominent FS and ODF bands were found to comigrate on gels, and the 14.4 kDa polypeptides had similar electrophoretic properties. Anti-FS serum reacted with the majority of Western blot-transferred FS polypeptides, but also cross-reacted strongly with a major 14.4 kDa ODF polypeptide and with less affinity to other major ODF polypeptides. Anti-ODF serum reacted with the majority of ODF polypeptides, but also cross-reacted strongly with a major 14.4 kDa FS polypeptide, and with less affinity to several other FS polypeptides including the 75 kDa band. Antibodies affinity-purified from the 14.4 kDa FS polypeptide only cross-reacted with the 14.4 kDa ODF polypeptide, whereas antibodies purified from the 14.4 kDa ODF polypeptide cross-reacted with 14.4, 27.5, 57, and 63 kDa FS polypeptides. The immunocross-reactions observed on Western blots were confirmed by immunocytochemical methods applied to spermatozoa. This study demonstrates that the FS and ODF, both composed of many polypeptides, several having similar molecular weights, are related cytoskeletal structures as they have epitopes in common, and both contain 14.4 kDa polypeptides with common antigenic and electrophoretic properties.     

Increase of inheritable polymorphisms of arbitrary primed PCR products on DGGE gels

Summary Single 10-mer primers of arbitrary sequence were used to amplify, by polymerase chain reaction (PCR), random genomic regions of two closely related hexaploid wheat cultivars. Polymorphic bands between the two genomes were visualized on both agarose and denaturing gradient gel electrophoresis (DGGE) gels. There was approximately a four-fold increase in inheritable polymorphisms when the PCR fragments were separated on DGGE gels.     

A zymogram method to detect endoglucanases fromBacillus subtilis,Myrothecium verrucaria andTrichoderma reesei

Summary A purified endoglucanase (Eg) fromBacillus subtilis and crude Eg preparations fromMyrothecium verrucaria andTrichoderma reesei were denatured by heat in the presence of SDS and separated by using SDS polyacrylamide gel electrophoresis. Eg zymogram activity bands were detected directly in carboxymethylcellulose-laden separating gels after enzyme renaturation. Denaturing zymogram analysis was a simple method for the separation and detection of Egs.     

An improved alkaline lysis method for minipreparation of plasmid DNA

This study is to improve the digestion pattern of miniprepped plasmid analyzed on gel. Frequently, some ambiguous DNA bands, which are suspected to be denatured DNA molecules, appear during electrophoresis of enzyme digested miniprepped plasmids. By employing Southern hybridization of two identical gels, one had been treated with denaturation-neutralization step and another without such treatment, we confirmed that many of these ambiguous DNA bands were single-stranded (SS) DNA molecules. The presence of SS DNA was due to the use of excess amount of NaOH during plasmid DNA purification with the conventional alkaline lysis method. We, therefore, modified the procedure and recommend that a half amount of NaOH (0.1N instead of 0.2N) should be used when isolating small quantity of plasmid DNA with the method.