Preparative Scale,High Resolution Purification of Low Molecular Weight DNA Fragments

Abstract

A commercially available continuous electro elution system has been used to separate and purify low molecular weight DNA fragments from polyacrylamide gels. This method has several advantages over previously reported methods for the recovery of DNA fragments from polyacrylamide gels. This technique, which gives very high recovery rates (80–95%), can be carried out on a relatively large scale and in a way that is not labour intensive. Data are presented for the purification of DNA fragments with molecular weights in the range 1–4 ± 10 (200–700 base-pairs), although the method is also applicable to larger molecular weight DNA fragments, RNAs and proteins.     

具有原核基因启动子活性的蓖麻蚕染色体DNA片段

利用大肠杆菌启动子克隆载体pHE5,研究了蓖麻蚕染色体的Hind Ⅲ酶解片段在大肠杆菌中作为四环素抗性基因启动子的功能作用。蓖麻蚕染色体的Hind Ⅲ片段与pHE5重组,在大约10~6个重组子中获得953株启动子重组体。测定了这些含有重组质粒的菌株抗四环素能力,其中有4株在平板上抗四环素水平超过225微克/毫升。对其中pARP201的插入片段进行了限制性图谱分析和启动子活性区域的缺失定位,证明了pARP-DB(由pARP201衍生而来)中的约0.5kb的外源插入片段具有完整的原核启动子功能。我们分析了这段DNA的部分核苷酸顺序,发现它与原核基因启动子极其相似。     

Ds因子在烟草染色体插入位点旁邻顺序的克隆

用ＮｅｓｔｅｄＰＣＲ 方法从含Ｄｓ 因子的转基因烟草ＤＮＡ 中克隆了Ｄｓ 因子在烟草染色体插入位点的９ 个旁邻ＤＮＡ 片段,以这些片段作探针,和野生型烟草的ＤＮＡ 进行Ｓｏｕｔｈｅｒｎ 杂交,以检测这些片段在烟草基因组中的拷贝数,结果表明它们都属于烟草染色体上的低拷贝ＤＮＡ。另外,对这些ＤＮＡ 片段进行核苷酸序列测定,并将它们的顺序与Ｇｅｎｂａｎｋ 数据库中已有的核苷酸序列相比较,其中长度为１２８ 核苷酸的片段１ 和荷兰芹的４ＣＬ２ 基因的一个区段有５７ ．８ ％ 同源性,而另一长度为１６９ 核苷酸的片段３ 和百合中的反转座子的一个区段有６０ ．９ ％ 的同源性。这都表明Ｄｓ 因子在异源植物烟草中插入染色体单拷贝基因的机率很高,这对转座子标签法克隆基因是非常有利的。     

Efficiency and Stability of High Molecular Weight DNA Transformation: an Analysis in Tomato

The efficiency of the binary bacterial artificial chromosome (BIBAC) vector for Agrobacterium-mediated stable transfer of high molecular weight DNA into plants was tested in tomato. Several variables affecting transformation efficiency were examined including insert size, Agrobacterium genetic background, and the presence of additional copies of the virG, virE1 and virE2 genes. It was found that a helper plasmid containing extra copies of virG was an absolute requirement for obtaining tomato transformants with the BIBAC. MOG101 with the virG helper plasmid was found to be the most efficient strain for transfer of high molecular weight DNA (150kb). Selected high molecular weight DNA transformants were advanced several generations (up to the R4) to assess T-DNA stability. This analysis showed that the T-DNA was stably maintained and inherited through several meioses regardless of whether it was in the hemizygous or homozygous state. Expression of a selectable marker gene within the T-DNA was also examined through several generations and no gene silencing was observed. Thus, the BIBAC is a useful system for transfer of large DNA fragments into the plant genome.     

High Molecular Weight Protease in Rumen Ciliate Protozoa

Mixed rumen ciliate protozoa (mainly Entodiniinae) from goats have two kinds of protease; one has a pH optimum of 3.0, the other is active at neutral or alkaline pH. The protease active at neutral or alkaline pH was partially purified from the supernatant after centrifugation of sonicated mixed rumen ciliate protozoa. The supernatant was chromatographed on Bio-Gel A-1.5m and a partially purified protease was obtained. This protease had a molecular weight of more than 400,000. When the sonicated protozoa were heated at 55°C for 15min, the active peak from the Bio-Gel A-1.5m column was shifted to a lower molecular weight, 27,000. The high molecular weight protease was strongly activated by high temprature and SDS, and inhibited by E-64 c. The protease degraded many proteins including those found in rumen bacteria. These findings suggest that rumen ciliate protozoa have high molecular weight protease that plays a role in the digestion of feed and bacterial protein.     

High Molecular Weight Mucin-like Glycoprotein in Bovine Milk

We purified an enzyme hydrolyzing 2-sulfo-α-L-fucopyranose pyridylaminated 2-sulfo-α-L-fucopyranosyl-(1→2)-fucose from the acetone powder of the digestive tract of a sea urchin. The enzyme was purified 307-fold with an overall recovery of 1.63% by ammonium sulfate precipitation, cation exchange chromatography, and gel filtration chromatography. The enzyme is useful for the structural analysis of sulfated fucan.     

植物大片段 DNA 的研究进展

植物大片段 DNA 的研究成为了基因组学研究的一个重要方面．对它的研究得益于容纳大片段 DNA 片段载体的发展．对构建植物大片段 DNA 的载体、植物大片段 DNA 的提取方法、植物大片段 DNA 的主要应用领域的最新进展进行了介绍．     

In VivoAddition of Telomeric Repeats to Foreign DNA Generates Extrachromosomal DNAs in the Taxol-Producing FungusPestalotiopsis microspora

Transformation of the taxol-producing filamentous fungusPestalotiopsis microsporawith a plasmid containing the bacterial hygromycin resistance gene fused toAspergillusregulatory sequences resulted in thein vivoformation of extrachromosomal DNAs with telomeric repeats in the majority of transformants. Repeats of the telomeric sequence 5′-TTAGGG-3′ were appended to nontelomeric transforming DNA termini. No fungal sequences other than telomeric repeats were detected in extrachromosomal DNAs. Transformants contained three to six different sizes or conformational forms of extrachromosomal DNAs. The DNAs showed no change in size or internal structure during 6 months of growth with selection, but were lost after 20 days of growth without selection. Transformation of wild-typeP. microsporawith a PCR-amplified extrachromosomal DNA having terminal telomeric repeats produced up to 50-fold more transformants than the original transformation vector. The addition of telomeric repeats to foreign DNA is unusual among fungi and may have important adaptive or developmental implications.     

Molecular phylogeny of Dipterocarpaceae in Indonesia based on chloroplast DNA

In order to construct a molecular phylogeny of Indonesian Dipterocarpoideae (Dipterocarpaceae), PCR-RFLP of the chloroplast regions rbcL, petB, psbA, psaA, and trnL-F was performed with seven restriction enzymes in 129 samples including 58 species from nine genera. In the strict consensus tree with Monotes kerstingii as outgroup Indonesian Dipterocarpaceae were divided into two major clades. One clade (bootstrap value=71) consisted of Upuna, Cotylelobium, Anisoptera, Vatica, Dipterocarpus (tribe Dipterocarpeae, bootstrap value=83) and Dryobalanops (tribe Shoreae, bootstrap value=99) in a basal position. The second clade consisted of Hopea, Parashorea, and Shorea (tribe Shoreae) with 95% bootstrap support. Tribe Dipterocarpeae is monophyletic, tribe Shoreae is polyphyletic since Dryobalanops is sister to tribe Dipterocarpeae. In the neighbour-joining tree the sister group position of Dryobalanops to tribe Dipterocarpeae is not supported by the bootstrap analysis. Alternatively, we used Upuna borneensis as outgroup. The effect of outgroup selection on tree topology, taxonomic classification and the interpretation of character evolution is discussed.     

DNA分子标记在药用植物中的应用

对DNA分子标记技术在药用植物鉴定、中药质量标准化、遗传图谱构建和近缘物种进化关系等方面的研究进展进行了综述,并展望了分子标记技术在药用植物研究中的发展前景。     

植物钾营养高效分子遗传机制

钾是植物生长发育所必需的矿质营养元素之一。不同种类植物的钾营养效率存在差异,已有证据表明这种差异是受遗传基因控制的。植物细胞依靠细胞膜上的各种钾转运体和通道蛋白吸收和转运钾离子,这些膜蛋白的活性调控是植物钾营养效率调控的关键和基础。本文对植物钾营养高效性状分子遗传机制以及相关基因的分子功能和调控机制的研究进展进行了简要评述,并讨论了改善作物钾营养高效性状的可能途径。     

小麦高分子量麦谷蛋白亚基的遗传变异与小麦加工品质改良

高分子量麦谷蛋白亚基（HMW-GS）是小麦胚乳中一种具有多态性的蛋白质组分,在面团中它们可以通过相互之间或与低分子量麦谷蛋白亚基（LMw-Gs）之间形成二硫键来组成麦谷蛋白多聚体。由于其在小麦面粉加工所需的粘性和弹力方面具有极其重要的作用,过去几十年间在小麦加工品质相关蛋白研究方面的工作大多数集中在高分子量麦谷蛋白亚基上。近几年在高分子量麦谷蛋白亚基及其编码基因的鉴定、基因的遗传变异以及不同变异在小麦加工品质中的作用方面进行了大量研究。本文对近几年在HMW-GS领域的研究进展进行综述并且重点讨论HMW-GS的变异及其对小麦品质育种的重要意义。     

Molecular Dynamics Simulation in Solvent of the Estrogen Receptor Protein DNA Binding Domain in Complex with a Non-Consensus Estrogen Response Element DNA Sequence

Abstract

We investigated protein/DNA interactions, using molecular dynamics simulations computed between a 10 Angstom water layer model of the estrogen receptor (ER) protein DNA binding domain (DBD) amino acids and DNA of a non-consensus estrogen response element (ERE) consisting of 29 nucleotide base pairs. This ERE nucleotide sequence occurs naturally upstream of the Xenopus laevis Vitelligenin AI gene. The ER DBD is encoded by three exons. Namely, exons 2 and 3 which encode the two zinc binding motifs and a sequence of exon 4 which encodes a predicted alpha helix. We generated a computer model of the ER DBD using atomic coordinates derived from the average of 30 nuclear magnetic resonance (NMR) spectroscopy coordinate sets. Amino acids on the carboxyl end of the ER DBD were disordered in both X-ray crystallography and NMR determinations and no coordinates were reported. This disordered region includes 10 amino acids of a predicted alpha helix encoded in exon 4 at the exon 3/4 splice junction. These amino acids are known to be important in DNA binding and are also believed to function as a nuclear translocation signal sequence for the ER protein. We generated a computer model of the predicted alpha helix consisting of the 10 amino acids encoded in exon 4 and attached this helix to the carboxyl end of the ER DBD at the exon 3/4 splice junction site. We docked the ER DBD model within the DNA major groove halfsites of the 29 base pair non-consensus ERE and flanking nucleotides. We constructed a solvated model with the ER DBD/ERE complex surrounded by a ten Angstrom water layer and conducted molecular dynamics simulations. Hydrogen bonding interactions were monitored. In addition, van der Waals and electrostatic interaction energies were calculated. Amino acids of the ER DBD DNA recognition helix formed both direct and water mediated hydrogen bonds at cognate codon-anticodon nucleotide base and backbone sites within the ERE DNA right major groove halfsite. Amino acids of the ER DBD exon 4 encoded predicted alpha helix formed direct and water mediated H-bonds with base and backbone sites of their cognate codon-anticodon nucleotides within the minor grooves flanking the ERE DNA major groove halfsites. These interactions together induced bending of the DNA into the protein.     

Knockout of Nuclear High Molecular Weight FGF2 Isoforms in Mice Modulates Bone and Phosphate Homeostasis

We previously reported that targeted overexpression of the fibroblast growth factor 2 (FGF2) high molecular weight (HMW) isoforms in osteoblastic lineage cells in mice resulted in phenotypic changes, including dwarfism, rickets, osteomalacia, hypophosphatemia, increased serum parathyroid hormone, and increased levels of the phosphatonin FGF23 in serum and bone. This study examined the effects of genetically knocking out the FGF2HMW isoforms (HMWKO) on bone and phosphate homeostasis. HMWKO mice were not dwarfed and had significantly increased bone mineral density and bone mineral content in femurs and lumbar vertebrae when compared with the wild-type (WT) littermates. Micro-computed tomography analysis of femurs revealed increased trabecular bone volume, thickness, number, and connective tissue density with decreased trabecular spacing compared with WT. In addition, there was significantly decreased cortical porosity and increased cortical thickness and sub-periosteal area in femurs of HMWKO. Histomorphometric analysis demonstrated increased osteoblast activity and diminished osteoclast activity in the HMWKO. In vitro bone marrow stromal cell cultures showed there was a significant increase in alkaline phosphatase-positive colony number at 1 week in HMWKO. At 3 weeks of culture, the mineralized area was also significantly increased. There was increased expression of osteoblast differentiation marker genes and reduced expression of genes associated with impaired mineralization, including a significant reduction in Fgf23 and Sost mRNA. Normal serum phosphate and parathyroid hormone were observed in HMWKO mice. This study demonstrates a significant negative impact of HMWFGF2 on biological functions in bone and phosphate homeostasis in mice.     

Oral Administration of High Molecular Weight Hyaluronan (900 kDa) Controls Immune System via Toll-like Receptor 4 in the Intestinal Epithelium

Low molecular weight hyaluronan enhances or induces inflammation through toll-like receptor 4 (TLR-4).However, the effects of high molecular weight hyaluronan (HA900) on TLR-4 are unknown. In this study, HA900 (900 kDa) was administered orally to MRL-lpr/lpr mice, a Th-1-type autoimmune disease model. Lymphoaccumulation of double-negative T cells, which is enhanced by proinflammatory cytokines, was suppressed by HA900 treatment. Cytokine array analysis showed that HA900 treatment enhanced production of interleukin-10, an anti-inflammatory cytokine, and down-regulated chemokine production. HA900 colocalized with TLR-4 on the luminal surface of epithelial cells in the large intestine. These cells are parts of the immune system and express cytokines. DNA array analysis of the tissue from the large intestine showed that HA900 treatment up-regulated suppressor of cytokine signaling 3 (SOCS3) expression and down-regulated pleiotrophin expression. Treatment of cultured double-negative T cells from MRL-lpr/lpr mice with pleiotrophin rescued these cells. SOCS3, which is known to suppress inflammation, was enhanced by HA900 treatment. In TLR-4 knockdown HT29 cells (a cell line derived from large intestinal cells), HA900 did not bind to HT29 cells and did not up-regulate SOCS3 expression. Our results suggest that oral administration of HA900 modulates Th-1-type autoimmune disease and inflammation by up-regulating SOCS3 expression and down-regulating pleiotrophin expression via TLR-4 in intestinal epithelial cells.     

Dynamics of Phosphorylation and Assembly of the High Molecular Weight Neurofilament Subunit in NB2a/d1 Neuroblastoma

In neuronal systems thus far studied, newly synthesized neurofilament subunits rapidly associate with the Triton-insoluble cytoskeleton and subsequently undergo extensive phosphorylation. However, in the present study we demonstrate by biochemical and immunological criteria that NB2a/d1 neuroblastoma cells also contain Triton-soluble, extensively phosphorylated 200-kDa high molecular weight neurofilament subunits (NF-H). High-speed centrifugation (100,000 g) of the Triton-soluble fraction for 1 h sedimented some, but not all, soluble NF-H subunits; immunoelectron microscopic analyses of the resulting pellet indicated that a portion of the NF-H subunits in this fraction are assembled into (Triton-soluble) neurofilaments. When cells were pulse labeled for 15 min with [35S]methionine, radiolabel was first associated with the Triton-soluble 200-kDa NF-H variants. Because only extensively phosphorylated NF-H subunits migrate at 200 kDa, whereas hypophosphorylated subunits migrate instead at 160 kDa, these findings suggest that some newly synthesized subunits were phosphorylated before they polymerized. In pulse-chase analyses, radiolabeled 200-kDa NF-H migrated into the 100,000 g particulate fraction of Triton-soluble extracts before its arrival in the Triton-insoluble cytoskeleton. Undifferentiated cells, which do not possess axonal neurites and lack a significant amount of Triton-insoluble, extensively phosphorylated NF-H, contain a sizeable pool of Triton-soluble extensively phosphorylated NF-H subunits and polymers. We interpret these data to indicate that the integration of newly synthesized NF-H into the cytoskeleton occurs in a progression of distinct stages, and that assembly of NF-H into neurofilaments and integration into the Triton-insoluble cytoskeleton are not prerequisites for the incorporation of certain phosphate groups on these polypeptides.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular characterization and chromosomal localization of two families of satellite DNA in Prochilodus lineatus (Pisces,Prochilodontidae), a species with B chromosomes

Prochilodus lineatus, an abundant species in the Mogi-Guaçu river basin, represents a large part of the region's fishing potential. Karyotypic analyses based on classic cytogenetic techniques have revealed the presence of 54 meta-submetacentric type chromosomes, together with the occurrence of small supernumerary chromosomes with intra and interindividual variations. This paper describes the genomic organization of two families of satellite DNA in the P. lineatus genome. The chromosomal localization these two repetitive DNA families through fluorescence in situ hybridization (FISH) demonstrated that the SATH1 satellite DNA family, composed of approximately 900 bp, was located in the pericentromeric region of a group of chromosomes of the standard complement, as well as on all the B chromosomes. The SATH2 satellite family has a monomeric unit of 441 bp and was located in the pericentromeric regions of some chromosomes of the standard complement, but was absent in the B chromosomes. Double FISH analyses showed that these two families participate jointly in the pericentromeric organization of several chromosomes of this species. The data obtained in this study support the hypothesis that the B chromosomes derive from chromosomes of the standard complement, which are carriers of the SATH1 satellite DNA.     

Integrated Application of Physiological and Molecular Methods to Forecast Determinative Morphogenetic Events in Tissue Cultured Tobacco (<Emphasis Type="Italic">Nicotiana tabacum</Emphasis> L. cv Samsun) Leaf Discs

The purpose of this study was to search for physiological parameters that provide an early indication of the morphogenetic response of leaf disc explants to different tissue culture-level manipulations in order to design an accelerated optimisation process for this technology. Tobacco (Nicotiana tabacum L. cv. Samsun) was chosen as model in our studies, because this is still one of the most widely used species in experimental plant biology and detailed knowledge is available from its tissue culture system. Large numbers of physiological markers at the whole plant level (rates of photosynthesis and respiration) and cellular level ‘fitness’ (degree of DNA methylation) were measured together with the concentrations of the most abundant metabolites in photosynthetic carbohydrate metabolism, ATP and protein synthesis in leaf discs induced either for callus development or for shoot differentiation. As a result of the above examinations, we are able to show that the efficiency of photosynthesis, the rate of respiration and the degree of DNA methylation can be used as early markers for the changes that precede the appearance of in vitro morphogenesis. By examining these parameters, we were able to predict early ontogenesis (within 48 h) and the optimal concentrations of growth regulators needed to achieve either shoot differentiation or callus development. Collaborator via a fellowship under the OECD Co-operative Research Programme: Biological Resource Management for Sustainable Agriculture Systems     

Molecular identification of fecal pollution sources in water supplies by host-specific fecal DNA markers and Terminal Restriction Fragment Length Polymorphism profiles of 16S rRNA gene

Specific fecal DNA markers were investigated for major pollution sources, cow, human, and pig, and occurrence of the identified markers was analyzed in river waters using Terminal Restriction Fragment Length Polymorphism (T-RFLP) techniques and sequencing of 16S rDNA of Bacteroides-Prevotella. The unique and specific DNA markers for cow and human were identified as a 222 bp and 60 bp peak in HaeIII T-RFLP profiles, respectively, and the pig-specific marker was not identified but the unique T-RFLP profile of pig could be used as a substitution. Human-specific marker was detected in most of the river waters tested (92.1%) and T-RFLP profiles of river waters were shown to be similar to those of human feces. Cluster analysis of T-RFLP data showed that the fecal sources were multiple (human plus cow and human plus dairy cow) in most of the river waters. The phylogenetic analysis for the clones recovered from the fecal and water samples showed that the clones from cow formed a discreet cluster from those of other sources. The other clones from human, pig, and river water formed two groups all together. The results of this study could be used to identify and control the fecal pollution source in the bodies of water in Korea.