A DNA recombinant database management system.

A set of computer programs is described which constitutes a clone database management system. Maintenance of the database and the stocks of material is designed to be under the control of one person or group of people, who may insert, delete or modify data entries, and who may interrogate the database as to which stocks are in need of checking. The system is organised in such a way that information is freely and speedily available to all users. Database entries may be accessed by name or key word.     

Portable file management system in FORTRAN

It has been generally considered that FORTRAN is inferior to MUMPS and other computer languages in its facility to manipulate files and that it is not satisfactorily competent to handle databases. However, it is our finding that FORTRAN is the most widely used language in patient data management systems discussed in recently published papers. Therefore, it now seems appropriate to review and evaluate the validity of this general belief. The objective of this study is to establish a file management system in FORTRAN 77 for use in the construction of a clinical database. Comparative study is conducted on several problems associated with file manipulation, that is, time requirement for file access and access methods for data retrieval.     

An integrated software system for microcomputer management of recombinant DNA data.

A database-oriented system (pCP123) is described for the manipulation of recombinant DNA data. This system was developed within the context of an integrated software package with spreadsheet, database, graphing and programming capabilities. The system includes two databases, one of sites and another of regions, coordinately handled by a series of macro-programs operated from four user-define menus. A distinctive feature of the system is the possibility of handling both ends of defined functional or structural regions in situations of simulated deletions or insertions.     

An improved version of the DNA Methylation database (MethDB)

Cytosine methylation is a characteristic property of prokaryotic and eukaryotic genomes. In the latter, it is indispensable for a healthy development of the organism and uncontrolled changes in the distribution of 5-methylcytosine (5mC) have been linked to severe disorders, in particular cancer. The growing scientific interest in DNA methylation has led to a considerable amount of data about this epigenetic phenomenon. In order to make these data readily available, we have established a dedicated database. The DNA Methylation database (MethDB) is currently the only public database for DNA methylation (http://www.methdb.net). This constantly growing database has become a key resource in the field of DNA methylation research. The database contains currently methylation patterns, profiles and total methylation content data for 46 species, 160 tissues and 72 phenotypes coming from a total of 6667 experiments (as of September 4, 2002). About 14% of the data have not been published elsewhere. These data can be conveniently searched and represented in different ways. Recently, we have included an on-line submission tool that permits the scientific public to directly enter new data into MethDB.     

An integrated proteome database for two-dimensional electrophoresis data analysis and laboratory information management system

We describe an integrated proteome database, termed Yonsei Proteome Research Center Proteome Database (YPRC-PDB) which can store, retrieve and analyze various information including two-dimensional electrophoresis (2-DE) images and associated spot information that were obtained during studies of hepatocellular carcinoma (HCC). YPRC-PDB is also designed to perform as a laboratory information management system that manages sample information, clinical background, conditions of both sample preparation and 2-DE, and entire sets of experimental results. It also features query system and data-mining applications, which are amenable to automatically analyze expression level changes of a specific protein and directly link to clinical information. The user interface is web-based, so that the results from other laboratories can be shared effectively. In particular, the master gel image query is equipped with a graphic tool that can easily identify the relationship between the specific pathological stage of HCC and expression levels of a potential marker protein on the master gel image. Thus, YPRC-PDB is a versatile integrated database suitable for subsequent analyses. The information in YPRC-PDB is updated easily and it is available to authorized users on the World Wide Web (http://yprcpdb.proteomix.org/ approximately damduck/).     

Principle of codification for quick comparisons with the entire biomolecule databanks and associated programs in FORTRAN 77.

We propose a new method for homology search of nucleic acids or proteins in databanks. All the possible subsequences of a specific length in a sequence are converted into a code and stored in an indexed file (hash-coding). This preliminary work of codifying an entire bank is rather long but it enables an immediate access to all the sequence fragments of a given type. With our method a strict homology pattern of twenty nucleotides can be found for example in the Los Alamos bank (GENBANK) in less than 2 seconds. We can also use this data storage to considerably speed up the non-strict homology search programs and to write a program to help in the selection of nucleic acid hybridization probes.     

介绍一种改良的冷却装置的垂直板电泳槽

介绍一种改良的带冷却装置的浸入式垂直板电泳槽。用不会变形的有机玻璃制作固定架及控制凝胶厚度的隔条,以代替市售的可压缩的U形橡胶套,以螺丝固定玻璃板,用医用硅胶管密封以完全分隔正负极电泳缓冲液。经试用于蛋白质及核酸电泳,效果甚佳。     

An improved procedure for measuring DNA replication with transient assays in eukaryotic cells

We describe an improved method for quantifying covalently closed circular DNAs replicated in eukaryotic cells. Normally, for such assays, plasmid DNAs transfected into animal cells must be extensively digested with restriction enzymes such as Dpnl and the products of digestion of the input DNA separated from the Dpnl-resistant (replicated) DNAs by electrophoresis. In the procedure described, the input, unreplicated DNA is nicked by light digestion with Dpnl and subsequently denatured and eliminated by S1 nuclease digestion. The replicated Dpnl-resistant DNA is detected by slot blot hybridization. Multiple samples can be rapidly assayed, with a considerable reduction in expense and labor.     

An improved recombinant mammalian cell expression system for human transforming growth factor-beta2 and -beta3 preparations

Transforming growth factor-beta2 and -beta3 (TGF-beta2 and -beta3) are important members of TGF-beta family which play important roles in the growth, maintenance, and repair processes of developing embryos, neonates, and adults. Preparation of large quantities of these two cytokines, which is necessary for structural studies and other applications, has proven to be extremely difficult. We have developed a novel Chinese hamster ovary cell-based expression system for high-level expression and high recovery of recombinant human TGF-beta2 and -beta3. In this system, we used a mammalian expression vector which contains a glutamine synthetase coding region for amplification, together with a modified TGF-beta2 or -beta3 open reading frame for expression. The leader peptide of TGF-beta2 or -beta3 was replaced by that from the V-J2-C region of a mouse immunoglobulin kappa-chain, and a poly-histidine tag was inserted immediately after the leader sequence to facilitate protein purification without changing the mature TGF-beta2 or -beta3 amino acid sequence. In addition, the extreme N-terminal cysteine residue of TGF-beta2 or -beta3 was replaced by a serine residue. The resulting expression constructs produced two stable cell clones expressing 10 mg of TGF-beta2 and 8 mg of TGF-beta3 per liter of spent medium. The purification scheme involved the use of two simple chromatographic steps with a typical yield of 5 mg of TGF-beta2 and 4 mg of TGF-beta3. This method represents a significant improvement over previously published methods and may be applicable to other TGF-beta superfamily members. We further confirmed that latent TGF-beta2 and -beta3 can be activated by proteolysis and glycolysis, which have not been reported before.     

Heterologous transfection with bacteriophage phiX174 DNA: and improved system.

A highly efficient and much more reproducible system for the heterologous transfection of several kinds of Gram-negative bacterial spheroplasts with bacteriophage phiX174 DNA was established. By mild washing of the speroplasts, the efficiency of transfection of all non-host heterologous bacterial species tested increased one or more orders of magnitude in producing the progeny phages and/or the infectious intermediates. Using the improved heterologous transfection systems, it has become clearer that a strong suppression system operates on the processes of phiX174 progeny phage production and not on those of phiX174 dougle-stranded replicative form DNA synthesis in the heterologous bacterial cells. Similar stimulatory effects of this washing procedure were observed in the homologous transfection. With this improved assay system, even less than 100 molecules of phage phiX174 DNA can be detected and the number of molecules can be determined with accuracy.     

An improved electroantennogram apparatus with a new automatic sample injection system

ABSTRACT. An improved electroantennogram (EAG) apparatus with a new automatic sample injection system, based on a cyclic timer connected to a 12VD.C. electrovalve, is described. The device is fully automatic and allows insertion of constant cyclic air puffs of the test compounds to the antenna at predetermined intervals.     

An efficient medical database system implementation with its tool and data structure consideration

The development of a new system for medical database application running on minicomputer under MUMPS system is described. Two kinds of data representation in global structure are briefly reviewed. The use of a subject oriented multi-dimensional data structure greatly simplifies database design and facilitates data manipulation, organization, selective retrieval and software development. It is concluded that the program generator approach can provide the flexibility necessary for various applications and future growth of computerized medical record system. The final system has been proven effective in practical operation. The future extension concerns the introduction of multi-microprocessor structure and logic representation is presented.     

An improved procedure for quantitating mitochondrial DNA in cultured mammalian cells

A new improved method that reproducibly measures small perturbations of mitochondrial DNA in populations of cells has been developed. It is based on first obtaining a cell count and then analyzing three aliquots of cells: one for total DNA per cell by fluorometry, one for total protein per cell and one for the amount of mitochondrial DNA per microgram of total cell DNA. To quantitate mitochondrial DNA, 0, 1, 2, and 3 nanograms of mouse mtDNA purified from a plasmid are added as internal standard DNA to four 1.0-microgram samples of purified total cell DNA containing an unknown amount of mitochondrial DNA (a sample set). Three sample sets are electrophoresed in an agarose gel devoid of ethidium bromide. Following Southern transfer to nitrocellulose and hybridization to purified 32P-labeled mouse mitochondrial DNA, an autoradiogram is prepared for use as a template to locate the mitochondrial DNA bands. These bands are cut out of the nitrocellulose filters, and their 32P-content is determined using a liquid scintillation counter. For each sample set, the counts per minute is plotted against the amount of mitochondrial DNA added. The plot is linear and the negative average of the values for the three intercepts on the x-axis yields the amount of nanograms of mitochondrial DNA per microgram of total cell DNA. The method is highly reproducible with a standard deviation of approximately 9 percent. The advantages of using this method over others that have been reported are discussed.     

An improved method for the detection and quantification of recombinant protein in transgenic plants

A sensitive method has been developed for the detection of recombinant protein produced as a result of gene transfer into plants. This method is based upon antibody binding, which is then visualized using enhanced chemiluminescence and recorded on x-ray film for long-term storage. The technique is simple, rapid and reliable and can be used to screen large numbers of transgenic plants. Several plant species have been successfully tested in this way for a range of recombinant proteins.     

An improved integrative transformation system for Pichia pastoris with DNA-polyethylenimine-dextran sulfate nanoparticles

Pichia pastoris is a suitable host for selecting mutant enzymes, since it can secret many gene products to the medium. However, poor transformation efficiency is often encountered. This makes it difficult to obtain a large number of transformants necessary to thoroughly cover a large library. We report here that pre-coating DNA with polyethyleneimine and dextran sulfate increased gene integration significantly in Pichia electroporation. This improvement on integrative efficiency has been proved in different voltage, resistance, cell phase, and DNA concentrations. The condensed DNA nanoparticles make Pichia available as a host for screening large libraries of random mutants.     

An improved system for expressing pancreatic ribonuclease in Escherichia coli

An improved method for expressing and purifying bovine pancreatic ribonuclease from a synthetic gene using the lambda promoter controlled by a temperature-sensitive repressor is described. The procedure involves isolation in the presence of a refolding buffer containing oxidized and reduced glutathione, under conditions where RNase can refold, but where proteases presumably do not. Yields are approx. 2 mg purified protein per 1 ferment.     

An improved method for the detection of genetic variations in DNA with denaturing gradient gel electrophoresis

We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that employment of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than that of DNA:DNA heteroduplexes originally developed by Lerman et al. (1986), because preparation of RNA probes is easier than that of DNA probes. Three different 32P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of mismatch(es) was detected as a difference in mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and 3 thalassemic human beta-globin genes. The results of the experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human beta-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was made in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for the detection of heritable variation and should be a powerful tool for the detection of fresh mutations in DNA, which occur outside the known restriction sites.