Sequence organization of porcine DNA.

The sequence organization of porcine DNA isolated from thyroid has been analyzed by hydroxylapatite (HAP) chromatography. The reassociation of 0.4 kilobase (Kb) DNA fragments shows, besides the presence of 5% inverted repeat sequences (foldback DNA), that 45% of the genome is represented by high (10%) and intermediate (35%) repetitive components, whereas the remaining 50% is unique sequences. 30% of the unique sequences consists of 1,000 nucleotide fragments interspersed with repetitive elements 400 nucleotides in length. The remaining 20% is longer unique sequences (10,000 nucleotides) apparently not linked to repetitive elements.     

Inverted repeat sequences in the drosophila genome

The properties of inverted repeat (foldback) sequences in Drosophila melanogaster DNA have been studied by HAP chromatography and electron microscope methods. Electron microscope observations show that there is a broad distribution of lengths of the duplex regions of the inverted repeats from very short to greater than 15 kb, with number and weight average values of 1.35 kb and 5.0 kb respectively. About 20% of the inverted repeats are separated by a single-strand spacer with lengths too short to observe, but the other 80% have spacers, P, with lengths ranging from 0.5 kb to greater than 30 kb. The number average and weight average spacer lengths for the total sample are 2.7 kb and 6.1 kb. With respect to the lengths of the spacers, P, between inverted repeats, the Drosophila genome differs from that of most organisms which have been studied where the spacers P are mostly too short to be measured. EM and HAP studies suggest that the average center-to-center spacing between sets of inverted repeats is 40–80 kb. The HAP studies show that there is a broad range of thermal stabilities for the duplexes formed by reassociation of inverted repeat sequences. Kinetic analysis shows that all of the frequency components of the Drosophila genome are present in the inverted repeats, the loops P, and the flanking sequences. There is a somewhat larger proportion of middle repetitive DNA in those inverted repeat duplexes which are resistant to digestion by Mung Bean Endonuclease I. These enzyme resistant duplexes comprise about 3% of the entire genome. It is estimated that there are approximately 2000–4000 inverted repeat pairs in the entire genome.     

Studies on the Organisation of the Chicken Genome and its Expression during Myogenesis in vitro

DNA from the chicken genome was analysed both by isopycnic centrifugation in cesium salt density gradients and by reassociation analysis using hydroxyapatite (HAP) chromatography. Centrifugation in neutral CsCl revealed a single non-Gaussian band skewed toward the heavy side, but no discrete satellite components. In heavy metal (Ag⁺ or Hg⁺⁺)-Cs₂SO₄ gradients, 4–8 satellite bands were revealed, comprising 5–9% of the total DNA. Purification of the satellites and recentrifugation in neutral CsCl demonstrated that 80–90% of this DNA would band in the shoulder, with the remainder in the main band. These satellites can account at most for 30% of the heavy shoulder DNA, thus most of the heavy shoulder DNA must be of lower repetition frequencies.
Reassociation analyses of chicken DNA demonstrated that the complexity of the non-repetitive DNA is 9.49 × 10⁸ nucleotide pairs, equivalent to about 90% of the haploid genome. Repetitive DNA comprises only 8–10% of the genome and has the following composition, relative to total DNA: 3.7% intermediate repetitive, 1.9% highly repetitive, and 3.9%"zero-time binding" DNA. This unusually low repetitive DNA content may be related to the small genome size of chickens, relative to other vertebrates, and to the presence of many microchromosomes in the chicken karyotype.
Total cell RNA extracted from prefusion myoblasts, post-fusion myotubes, and myoblasts grown in BrdU was incubated in large excess with ³H-TdR labelled non-repetitive DNA and the resulting hybrids assayed by HAP chromatography. The amount of non-repetitive DNA represented in the RNA was found to increase from 7–8% in the myoblast stage to 10–11% in myotubes. An even smaller proportion, about 5%, is represented in the RNA of myoblasts prevented from differentiating by growth in BrdU.     

Role of Type 1 Fimbriae in the Adhesion of Escherichia coli to Salivary Mucin and Secretory Immunoglobulin A

Saliva is known to modulate the adhesion of bacteria in the oral cavity. The present work was performed to assess the effect of salivary components on the adhesion of Escherichia coli to a model oral surface. Several genetically engineered E. coli strains were used to examine the role of type 1 fimbriation in the interaction of these strains with salivary components in solution or adsorbed to hydroxyapatite. High (MG1) and low (MG2) molecular weight salivary mucins, and secretory immunoglobulin A (sIgA), were found to interact with the surface of E. coli, and these interactions were independent of the expression of fimbriae or capsule. In contrast, fimbriated strains of E. coli adhered to a greater extent to saliva-coated synthetic hydroxyapatite (HAP) than did nonfimbriated strains. Testing of salivary components separated by gel filtration chromatography revealed that only high-molecular-weight components promoted adhesion of E. coli to HAP. Additional studies found that purified MG2 and sIgA promoted the adhesion of E. coli to HAP. Expression of type 1 fimbriae enhanced adhesion, while mannose inhibited adhesion of fimbriated strains, to saliva-coated HAP and to HAP coated with MG2 and sIgA. We conclude that salivary MG2 and sIgA may provide receptors for the adhesion of type 1 fimbriated E. coli to oral surfaces. Received: 10 February 1996 / Accepted: 11 March 1996     

The reassociation curve of human DNA amended

The reassociation kinetics of human DNA was studied, utilizing S1 nuclease digestion in aqueous dioxane and hydroxyapatite chromatography for isolating renatured DNA. The percentage of DNA reassociated at C0t = 10(-3) was 5--7% and that at C0t = 18 000 was about 85%, C0t being the product of the molar concentration of DNA and the reassociation period in s. The shape of the amended reassociation curve was roughly that of a rectangular hyperbola. It showed pronounced differences from the curves obtained by direct hydroxyapatite chromatography of reassociated DNA. The S1 nuclease-dioxane procedure offered two advantages over the conventional method. It was applicable to the study of reassociation with high molecular weight DNA, and the reassociated DNA so obtained was devoid of low-melting strands. The analysis of the new data took into account the possible effects of the diploid condition on the reassociation rate of DNA, the source of the DNA used in this study being placental tissue. The new reassociation profile was compared to ideal second-order reassociation curves calculated for the human genome (2.5 . 10(9) nucleotide pairs), and for a genome twice this size, containing various proportions of single-copy sequences. The results showed that approximately 85--90% of th total DNA may consist of unique sequences. This estimate is considerably higher than those reported previously.     

Preparative isolation and study of the reassociation kinetics of a T2 phage DNA fraction containing readily melting regions]

A DNA fraction comprising 6% of total DNA and containing readily-melting regions is isolated from phage T2 DNA using preparative chromatography on MAK columns at T congruent to T m--3 degrees C. Two denaturation regions, differing in the stability for 7 degrees, were observed on this DNA melting curve. A sharp increase of the reassociation rate at initial moments under reassociation temperatures T r approximately less than m --25 degrees C was observed. Thermodynamic characteristics obtained under the repeated melting of DNA fragments after reassociation confirm the fact, that under these reassociation temperatures the incorporation of readily-melting regions into spiral duplexes takes place.     

两种亨廷顿蛋白相关蛋白1异构体—HAP1A和HAP1B在大鼠脊髓灰质内的分布特征

目的明确2种亨廷顿蛋白相关蛋白1(huntingtin-associated protein 1,HAP1)异构体—HAP1A和HAP1B在大鼠脊髓灰质内的分布特征。方法提取重组表达的谷胱甘肽S-转移酶(GST)-HAP1AC末端融合蛋白和GST-HAP1BC末端融合蛋白,免疫兔和豚鼠制备分别抗HAP1A和HAP1B特异性多克隆抗体,并采用免疫印迹技术对其特异性和效价进行鉴定和检测;用免疫组织化学技术检测HAP1A和HAP1B在大鼠脊髓灰质内的分布和定位特征。结果成功制备了分别特异性识别HAP1A和HAP1B的高效价多克隆抗体,应用这些抗体进行的免疫组织化学ABC法检测显示,HAP1A与HAP1B在大鼠脊髓灰质内的分布区域相似,二者均在大鼠脊髓灰质RexedⅠ-Ⅹ层表达,在RexedⅠ、Ⅱ层表达最强,中央管周围灰质(RexedX层)其次,在RexedⅢ-Ⅵ层表达水平较低,在脊髓前角(RexedⅦ-Ⅸ层)只有极微弱的或无阳性表达。HAP1A免疫反应产物主要定位在Stigmoid小体,在神经元胞质和近端突起内只有极少的弥散反应产物;HAP1B免疫反应性较强,其免疫反应产物弥散、均匀分布在神经元核周质和近端突起内,也定位在Stigmoid小体上。免疫荧光双重标记显示,约有80%的Stigmoid小体既表达HAP1A也表达HAP1B,其余的Stigmoid小体仅表达HAP1A。结论 HAP1A和HAP1B蛋白在大鼠脊髓灰质内具有相同的区域分布模式,但在神经元内的定位具有明显区别,提示二者可能具有不同的功能。     

DNA changes during sequential leaf senescence of tobacco (Nicotiana tabacum)

Age related DNA changes in tobacco (Nicotiana tabacum) leaf nuclei were investigated by Feulgen cytophotometry, thermal denaturation, renaturation, and DNA-DNA hybridization studies during sequential leaf senescence. Cytophotometric Feulgen-DNA comparison measurements between young and senescing nuclei displayed 18% reduction in Feulgen-DNA values, with a corresponding decrease in nuclear area in senescing nuclei. Hydrolysis kinetics indicated that the loss was not due to compactness of the DNA as the curves for older nuclei were consistently lower than curves generated from younger nuclei. DNA loss in senescing nuclei was associated with a decrease in euchromatin or shift from euchromatin to facultative heterochromatin. Purified DNA from young and senescing leaf nuclei did not display different thermal profiles nor did hydroxylapatite chromatography reassociation curves. DNA-DNA hybridization in free solution from young and senescing leaf DNA performed by a Gilford thermo-programmer system indicated that DNA of senescing tobacco nuclei reassociated more slowly than DNA from young nuclei and the mixture of young and senescing leaf DNA displayed intermediate reassociation values. The study indicates that the DNA changes during senescence involve a complex phenomenon which includes the possibility of small single strand nicks undetectable by thermal denaturation, and a loss of small double strand fragments which were detectable only by precise DNA-DNA free solution reassociation and not by hydroxylapatite chromatography reassociation.     

A method of equalizing the level of DNA sequences of varying amount in a heterogeneous DNA mixture]

A method for the equalization of double-stranded DNA concentrations in the mixture which may be used for equalizing double-stranded cDNA concentrations involves thermal denaturation of the double-stranded DNA mixture followed by reassociation. The initial reassociation rate is Vi = Ki.(single-stranded DNA)2, and by the end of the process the concentrations of the unreassociated molecules for different DNAs should be approximately equal. Using hydroxylapatite chromatography one can separate single-stranded DNAs from double-stranded DNAs and carry out complete single-stranded DNAs reassociation. The new ratio of different double-stranded DNA concentrations would be almost 1.     

HAP-1在慢性复合应激大鼠肾上腺的表达

目的探讨慢性复合应激大鼠肾上腺髓质细胞亨廷顿蛋白相关蛋白1(Huntingtin-associated protein 1,HAP-1)表达的变化及其意义。方法36只大鼠随机分为两组:慢性复合应激组和对照组。应激组动物进行6周的垂直旋转、睡眠剥夺、捆绑(6h/d)和夜间光照等慢性复合性应激试验;实验结束后,所有动物采用免疫组织化学、Western-blot以及RT-PCR等方法检测肾上腺髓质细胞内HAP-1蛋白和mRNA水平的变化。结果与对照组相比,慢性复合应激组的大鼠肾上腺髓质中HAP-1的表达明显增强(P<0.05),HAP-1 mRNA水平明显升高(P<0.05)。结论6周慢性复合性应激大鼠HAP-1在肾上腺髓质区的表达加强,mRNA水平提高。提示HAP-1在慢性复合应激促进肾上腺功能中可能发挥一定作用。     

Hook-associated proteins essential for flagellar filament formation in Salmonella typhimurium.

The hooks of the flagella of Salmonella typhimurium were purified by a newly developed method, using a flaL mutant without a filament, and the hook components were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. As a result, we detected three protein species in addition to hook protein. We call these three proteins hook-associated proteins (HAPs). Their molecular weights were 59,000 for HAP1, 53,000 for HAP2, and 31,000 for HAP3. The HAP1/hook protein/HAP3/HAP2 molar ratio, calculated from their relative amounts and their molecular weights, was 1:10:1.1:0.53. The compositions of HAPs were analyzed in the hooks from the other filamentless mutants which were defective in H1 H2, flaV, flaU, or flaW. Hooks from the H1 H2 mutant had the same HAP composition as hooks from the flaL mutant. Hooks from the flaV mutants contained HAP1 and HAP3. Hooks from the flaU mutants contained HAP1. Hooks from the flaW mutants contained a very small amount of HAP3. From these results, the process of hook morphogenesis and the genes responsible for each step were postulated. Electron micrographs of hooks from the filamentless mutants showed that hooks which contained all three HAPs had a sharp clawlike tip, whereas hooks lacking any HAP had a flat tip. Electron micrographs of hooks treated with antibody against the hook protein showed that each claw-shaped end was not covered with antibody. These results strongly suggest that all three HAPs or at least some of them are located at the claw-shaped end and play an essential role in filament formation.     

Reassociation kinetics of three satellite components of calf thymus DNA.

Using absorption measurements the reassociation kinetics of three satellite DNA components isolated from calf thymus was studied under various conditions. A different method using CsC1 density gradient determinations particularly suited for kinetic analysis of mixtures was also used and shown to give similar results. Reassociation rate constants were corrected for mismatching during strand reassociation using data obtained by kinetic analysis of fractions of the 1.714 g/cm-3 satellite component. The values of corrected as well as uncorrected complexities were calculated and compared with results of other methods. They were shown to be compatible with the concept of sequence repetition at various levels.     

The effects of serum and human albumin on calcium hydroxyapatite crystal growth.

The effects of potential serum inhibitors upon the growth of calcium hydroxyapatite (HAP) crystals were studied in vivo using a pH-stat system. Whole serum caused a marked decrease in crystal growth in a dose-dependent manner. At a protein concentration of 13 micrograms/ml, whole serum reduced the initial rate of crystal growth from 84 mumol of KOH/h to 48 mumol of KOH/h. Serum components were separated by ultrafiltration (10,000 Da cut-off). The high-molecular-mass fraction containing serum proteins gave an initial rate of crystal growth of 48 mumol of KOH/h compared with 64 mumol of KOH/h given by the low-molecular-mass components. Thus, two-thirds of the inhibitory activity was associated with proteins and other serum macromolecules, whilst the remainder of the activity was associated with the low-molecular-mass components. Albumin-depleted serum showed an initial rate of crystal growth of 59 mumol of KOH/h, whilst albumin purified by affinity chromatography gave an initial rate of crystal growth of 56 mumol of KOH/h at the same protein concentration. Albumin, therefore, not only accounts for half of the protein concentration in serum, but also contributes half of the inhibitory activity of the high-molecular-mass fraction. Heat denaturation of albumin dramatically enhanced the inhibition of HAP seeded growth with the initial rate of crystal growth falling to 27 mumol of KOH/h after treatment compared with 62 mumol of KOH/h before denaturation. Isoelectric focusing indicated that the tertiary and secondary structure, and hence the distribution of surface charge of albumin, are altered by heat denaturation. Gels showed a mixture of species with isoelectric points ranging from 6.0 to 5.0 compared with the native protein value of 4.7. These data suggest that adsorption of serum proteins to the growing HAP crystals is one mechanism of growth inhibition. It is also clear that the most abundant serum protein, albumin, is an important mediator of this process.     

禁食促进下丘脑中摄食相关核团HAP1的表达

目的探讨下丘脑中的亨廷顿蛋白相关蛋白1（huntingtin-associated protein 1,HAP1）是否与摄食有关。方法免疫印迹法检测禁食对大鼠下丘脑HAP1表达的影响,RT-PCR法检测禁食对大鼠下丘脑HAP1 mRNA表达的影响,免疫组织化学染色法观察禁食对下丘脑与摄食调节有关核团内HAP1表达的影响。结果免疫印记分析和RT-PCR检测显示,与正常进食的大鼠比较,禁食1d、2d、3d、4d后大鼠下丘脑HAP1表达逐渐增多;免疫组织化学研究表明,弓状核、背内侧核、外侧下丘脑区内HAP1的表达在禁食后显著增多,而禁食对腹内侧核HAP1的表达无明显影响。结论下丘脑中的HAP1与摄食有关,可能参与了食欲的调节。     

慢性复合应激对大鼠胰腺HAP1表达的影响

目的探讨慢性复合应激大鼠胰腺内胰岛内分泌细胞HAP1表达的变化及其意义。方法36只大鼠随机分为两组:慢性复合应激组和正常对照组。应激组动物无规律交替暴露于垂直旋转、睡眠剥夺、捆绑(6h/d)和夜间光照等慢性复合性应激,共6周;实验结束后,采用免疫组织化学和Western-blot等方法检测两组大鼠胰腺胰岛内分泌细胞内HAP1蛋白表达的变化。结果HAP1在大鼠胰腺内选择性表达于胰岛内分泌细胞中。与对照组相比,慢性复合应激组大鼠胰腺HAP1的表达明显增强(P<0.05)。结论6周慢性复合性应激可使大鼠胰腺中胰岛内分泌细胞的HAP1表达加强,提示HAP-1在慢性复合应激促进胰腺内分泌功能中可能发挥一定作用。     

DNA sequence organization in the genome of Nicotiana tabacum

The genome of Nicotiana tabacum was investigated by DNA/DNA reassociation for its spectrum of DNA repetition components and pattern of DNA sequence organization. The reassociation of 300 nucleotide DNA fragments analyzed by hydroxyapatite chromatography reveals the presence of three major classes of DNA differing in reiteration frequency. Each class of DNA was isolated and characterized with respect to kinetic homogeneity and thermal properties on melting. These measurements demonstrate that the genome of N. tabacum has a 1C DNA content of 1.65 pg and that DNA sequences are represented an average of 12,400, 252, and 1 times each. — The organization of the DNA sequences in the N. tabacum genome was determined from the reassociation kinetics of long DNA fragments as well as S1 nuclease resistance and hyperchromicity measurements on DNA fragments after annealing to C₀t values at which only repetitive DNA sequences will reassociate. At least 55% of the total DNA sequences are organized in a short period interspersion pattern consisting of an alternation of single copy sequences, averaging 1400 nucleotides, with short repetitive elements approximately 300 nucleotides in length. Another 25% of the genome contains long repetitive DNA sequences having a minimal genomic length of 1500 nucleotides. These repetitive DNA sequences are much less divergent than the short interspersed DNA sequence elements. These results indicate that the pattern of DNA sequence organization in the tobacco genome bears remarkable similarity to that found in the genomes of most animal species investigated to date.     

Distribution of repetitious sequences in chick nuclear DNA

By an improved method of hydroxylapatite chromatography, the reassociated sequences of chick nuclear DNA were isolated, and their base composition analysed. By increasing the amount of reassociation, the G + C content of the renatured sequences decreased progressively to reach a mean value corresponding to that of the total DNA. In order to study the distribution of the families, or group of families having different amount of reassociation, DNA was fractionated by CsC1 density gradient centrifugation. Fractions having different G + C content were obtained, and their reassociation rates analysed. At high C(o)t value of renaturation (C(o)t=50) the amount of reassociated sequences included in the high or in the low buoyant density DNA fractions was approximately the same, but their G + C content was as expected different. At lower C(o)t values of renaturation (between C(o)t of 0.2 and the C(o)t of 10), the results indicated an heterogeneity of the repeated sequences in the A + T rich DNA fractions, as compared to the G + C rich ones.     

High diversity in DNA of soil bacteria.

Soil bacterium DNA was isolated by minor modifications of previously described methods. After purification on hydroxyapatite and precipitation with cetylpyridinium bromide, the DNA was sheared in a French press to give fragments with an average molecular mass of 420,000 daltons. After repeated hydroxyapatite purification and precipitation with cetylpyridinium bromide, high-pressure liquid chromatography analysis showed the presence of 2.1% RNA or less, whereas 5-methylcytosine made up 2.9% of the total deoxycytidine content. No other unusual bases could be detected. The hyperchromicity was 31 to 36%, and the melting curve in 1 X SSC (0.15 M NaCl plus 0.015 M sodium citrate) corresponded to 58.3 mol% G+C. High-pressure liquid chromatography analysis of two DNA samples gave 58.6 and 60.8 mol% G+C. The heterogeneity of the DNA was determined by reassociation of single-stranded DNA, measured spectrophotometrically. Owing to the high complexity of the DNA, the reassociation had to be carried out in 6 X SSC with 30% dimethyl sulfoxide added. Cuvettes with a 1-mm light path were used, and the A275 was read. DNA concentrations as high as 950 micrograms ml-1 could be used, and the reassociation rate of Escherichia coli DNA was increased about 4.3-fold compared with standard conditions. C0t1/2 values were determined relative to that for E. coli DNA, whereas calf thymus DNA was reassociated for comparison. Our results show that the major part of DNA isolated from the bacterial fraction of soil is very heterogeneous, with a C0t1/2 about 4,600, corresponding to about 4,000 completely different genomes of standard soil bacteria.(ABSTRACT TRUNCATED AT 250 WORDS)     

High diversity in DNA of soil bacteria

Soil bacterium DNA was isolated by minor modifications of previously described methods. After purification on hydroxyapatite and precipitation with cetylpyridinium bromide, the DNA was sheared in a French press to give fragments with an average molecular mass of 420,000 daltons. After repeated hydroxyapatite purification and precipitation with cetylpyridinium bromide, high-pressure liquid chromatography analysis showed the presence of 2.1% RNA or less, whereas 5-methylcytosine made up 2.9% of the total deoxycytidine content. No other unusual bases could be detected. The hyperchromicity was 31 to 36%, and the melting curve in 1 X SSC (0.15 M NaCl plus 0.015 M sodium citrate) corresponded to 58.3 mol% G+C. High-pressure liquid chromatography analysis of two DNA samples gave 58.6 and 60.8 mol% G+C. The heterogeneity of the DNA was determined by reassociation of single-stranded DNA, measured spectrophotometrically. Owing to the high complexity of the DNA, the reassociation had to be carried out in 6 X SSC with 30% dimethyl sulfoxide added. Cuvettes with a 1-mm light path were used, and the A275 was read. DNA concentrations as high as 950 micrograms ml-1 could be used, and the reassociation rate of Escherichia coli DNA was increased about 4.3-fold compared with standard conditions. C0t1/2 values were determined relative to that for E. coli DNA, whereas calf thymus DNA was reassociated for comparison. Our results show that the major part of DNA isolated from the bacterial fraction of soil is very heterogeneous, with a C0t1/2 about 4,600, corresponding to about 4,000 completely different genomes of standard soil bacteria.(ABSTRACT TRUNCATED AT 250 WORDS)     

Reversibility of coated vesicle dissociation

The dissociation of the coated vesicles to clathrin and uncoated vesicles and their reassociation have been studied under various conditions. The extent of reassociation is pH dependent and increases slightly with increasing concentrations of the components. Unlike the self-association of clathrin which is strongly salt dependent, the reassociation of clathrin and uncoated vesicles is practically independent of salt concentration. The coated vesicle gradually loses its coat with increasing pH, and the dissociation process is not an all or none reaction. Ca2+ inhibits dissociation of the coated vesicles and enhances the reassociation of clathrin and uncoated vesicles. Our results show that, although many conditions result in reassociation of protein and lipid vesicle, few conditions result in vesicles of both the same size and composition as native coated vesicles.