Loader Lite: a new software tool for the ABI PRISM 3700 DNA sequencer.

Here we describe the development of a novel software tool entitled Loader Lite that generates plate records or sample sheetsfor the ABI PRISMs 3700 DNA sequencer. The major advantage of this program is that it enables the ongoing operation of sequencing instruments without reference to external network(s). The autonomous operation of sequencing instruments is critical if sample throughput is to be maintained during periods of network outage. Loader Lite employs a deliberate strategy of inputting anonymous tray barcodes at run time. After sequencing, the barcodes are reconciled with relevant project details by reference to a database. This software takes advantage of barcode scanning technology by creating plate records directly on the local computer, serving an individual sequencer, immediately before importing and linking. This real-time synthesis of the plate records at the point of loading all but eliminates loading errors. Loader Lite is user-friendly, fully configurable, and permits the running of partial or full 384-well sample trays, using any standard combinations of run modules, dye sets, mobility files, analysis modules, etc. The 96-well format is not supported; however, this capability will appear in subsequent versions that are currently under development. This application is designed as an added value, adjunct program to the regular ABI PRISM 3700 Data Collection software. We have successfully used Loader Lite over the past six months to load approximately 7 million sequencing reactions and believe its utility and functionality will prove to be attractive to the wider sequencing community.

OrCGDB: a database of genes involved in oral cancer.

The Oral Cancer Gene Database (OrCGDB; http://www.tumor-gene. org/Oral/oral.html) was developed to provide the biomedical community with easy access to the latest information on the genes involved in oral cancer. The information is stored in a relational database and accessed through a WWW interface. The OrCGDB is organized by gene name, which is linked to information describing properties of the gene. This information is stored as a collection of findings ('facts') that are entered by the database curator in a semi-structured format from information in primary publications using a WWW interface. These facts include causes of oncogenic activation, chromosomal localization of the gene, mutations associated with the gene, the biochemical identity and activity of the gene product, synonyms for the gene name and a variety of clinical information. Each fact is associated with a MEDLINE citation. The user can search the OrCGDB by gene name or by entering a textword. The OrCGDB is part of a larger WWW-based tumor gene database and represents a new approach to catalog and display the research literature.

Digital reviews in molecular biology: approaches to structured digital publication.

MOTIVATION: It is widely appreciated that it is no longer possible for biomedical research scientists to keep up with as much of what is published in their field as they ought. One solution to this problem is to increase the efficiency of information use by moving away from the classical browsing model for scientific information dissemination towards an information on demand model which would allow researchers to access information quickly and efficiently only as they need it. The most common approach to this goal has been to use information retrieval technology to improve access to text databases of biomedical information. We are interested in exploring an alternative; encoding this information for storage in structured databases for efficient retrieval. RESULTS: Two small databases described here are test beds for development of structured digital publication software; the Tumor Gene Database, containing information about genes which are the sites for cancer-causing mutations, and the Mammary Transgene Database, containing information about expression of transgenes in agriculturally important animals. Both have been successfully searched by users and edited by curators via the World Wide Web.

Immunohistochemical detection of somatostatin sst2a receptors in the lymphatic, smooth muscular, and peripheral nervous systems of the human gastrointestinal tract: facts and artifacts.

The cellular distribution of the somatostatin sst2A receptor protein was investigated in the lymphatic, smooth muscular, and nervous components of the human gastrointestinal tract using subtype-specific antibody R2-88 for immunohistochemical staining of cryostat and formalin-fixed, paraffin-embedded tissue sections. Germinal centers of intestinal lymphatic follicles were immunostained, exhibiting a predominantly plasma membrane localization of the receptor. Similarly, nerve fibers and cells in the submucosal and myenteric plexus were stained for sst2A. Antibody preabsorption with 100 nmol/L antigen peptide abolished staining in all of these tissues, and immunohistochemical staining correlated with the labeling observed after receptor autoradiography using the sst2-preferring radioligand 125I-[Tyr3]octreotide. Cytoplasmic immunostaining was detected in gastrointestinal smooth muscle cells and was inhibited by antibody pre-absorption with antigen peptide. However, 125I-[Tyr3]octreotide autoradiography was negative, and Western blots showed no band at the usual 70-90 kDa location for sst2A. Instead, a band was observed at 205 kDa. This band comigrated with the rabbit myosin standard, which was also stained with R2-88, although antibody sensitivity for myosin was less than 0.002% of that for the sst2A receptor. Rigorous computer-based sequence analysis demonstrated the peptide sequence chosen for antibody production was unique. Moreover, standard sequence alignment protocols were unable to identify the sequences in myosin responsible for the observed reactivity with the R2-88 antiserum. The observed cross-reactivity emphasizes the need for extensive controls to prove the specificity of immunostaining for such low abundance proteins as receptors even when the peptide sequence chosen for antibody production is unique. This study demonstrates for the first time the presence of specific sst2A receptor protein by immunohistochemistry in the human gastrointestinal lymphatic and nervous components, but not in gastrointestinal circular and longitudinal smooth muscle.

The breast cancer gene database: a collaborative information resource.

The Breast Cancer Gene Database (BCGD) is a compendium of molecular genetic data relating to genes involved in breast cancer, and which is freely available via the World Wide Web. The data in BCGD is extracted from the published biomedical research literature and stored as a collection of 'Facts', which in turn are collected into topical categories organized by gene. This organization facilitates quick searches and rapid retrievals of specific data such as gene characteristics, functions and role in oncogenesis, and is an important factor allowing for continuous updates. BCGD can be searched either by gene name or keyword. Data is deposited and retrieved from the database through a set of interactive Web forms, making it both platform-independent and universally accessible in facilitating worldwide collaborative authoring of the database. Data in BCGD is linked to other on-line resources such as Entrez, GeneCards and On-Line Mendelian Inheritance in Man. BCGD is located at http://mbcr.bcm.tmc.edu/ermb/bcgd/bcgd.html.

Frequent activation of the lck gene by promoter insertion and aberrant splicing in murine leukemia virus-induced rat lymphomas.

We have analysed DNA and RNA from 36 T-cell lymphomas induced in Fischer rats by Moloney murine leukemia virus for alterations affecting the structure or expression of the lck gene. At least five primary tumors (14%) have a proviral insertion upstream of lck. In at least four of the tumors, proviral insertion increases lck mRNA levels an average of eight-fold. Overexpression of lck results from transcription initiating in the viral promoter and extending into lck sequences. Three different structures of hybrid transcript were detected. In all three, the hybrid RNAs are spliced to a normal lck splice acceptor in the first exon of lck, resulting in removal of three out of frame ATG codons which would be expected to increase the translation efficiency of the hybrid message. In one tumor, the viral splice donor is used, in one tumor, proviral insertion generates a splice donor sequence one base pair downstream of the long terminal repeat boundary, and in two tumors, a cryptic splice donor in the upstream lck sequences is used. The significance of these unusual splicing patterns and of the higher frequency of proviral insertions adjacent to lck in rats relative to mice is discussed.

Effect of ras-gene transformation on the inhibition of NIH3T3 cell growth by pertussis toxin.

To investigate the relationship between the effects of a pertussis toxin-inhibitable class of G-proteins and the ras family of protooncogenes on cell growth, we isolated multiple cell lines transformed by oncogenic Hras or Nras genes and measured the ability of pertussis toxin to inhibit their growth rate. Although all of the cell lines were morphologically transformed and could grow in agar suspension, there was considerable variability in their resistance to pertussis toxin, ranging from cell lines completely resistant to pertussis toxin to cell lines as sensitive to pertussis toxin as the parental cells from which they derived. For those lines resistant to pertussis toxin, this resistance is not due to an inability of pertussis toxin to reach or react with its intracellular target; pertussis toxin could be shown to ADP-ribosylate the endogenous G-proteins of all lines tested regardless of whether it affected their growth rate. There was a strong correlation between the level of active ras protein expressed in the different lines and the degree of resistance to pertussis toxin (r = 0.80). Although the Hras-transformed cell lines were more resistant to pertussis toxin as a group than the Nras-transformed cell lines, we believe that this is not a primary difference between Nras and Hras, but, rather, is due to a higher average level of expression of ras in the cell lines receiving Hras. We suggest that the consequences of ras transformation vary with the concentration of oncogenic ras present in the cell, and that different assays or different properties of transformation show different sensitivities to the level of ras expression.(ABSTRACT TRUNCATED AT 250 WORDS)

A retrovirus vector which transduces a functional estrogen receptor gene at high efficiency.

A high titer retroviral vector containing the cDNA of human estrogen receptor (hER) was generated and used to transfer the hER gene into the rat 208F cell line. Southern blot analysis showed the integration of the provirus to be at a unique site and that the provirus was intact in the genome of recipient cells. The expression of the integrated hER gene in the infected rat cells was detected by Northern blot analysis and by a functional assay in which the hER gene product stimulated the production of a chloramphenicol acetyl transferase gene under the control of an estrogen-responsive element. These experiments demonstrate the feasibility of using a retroviral vector system to introduce a functional ER gene into cultured cells lacking this receptor.

Nucleotide sequence of the first exon of the rat c-myc gene: proviral insertions in murine leukemia virus-induced lymphomas do not affect exon 1.

We have previously reported that proviruses are integrated adjacent to the c-myc gene in rat thymomas induced by murine leukemia viruses. In order to characterize these insertions, we have isolated recombinant DNA clones from normal rat DNA containing all of the normal rat c-myc gene, and from two Moloney murine leukemia virus-induced lymphomas containing both proviral and adjacent rat c-myc sequences. We determined the DNA sequence of portions of the normal and one tumor-derived clone. The normal and tumor-derived exon 1 sequences are identical. By comparing our sequence to the sequences of mouse and human c-myc, we located the first exon of the rat c-myc gene. Analysis of the tumor-derived rat c-myc clones showed that proviral integration occurred approximately 1.4 kb upstream of exon 1 of c-myc in the case of one tumor and 0.55 kb upstream of c-myc exon 1 in the other. Thus, we conclude that the proviral insertions in these tumors did not affect the rat c-myc gene by altering the structure of the c-myc RNA. Consistent with this, the c-myc RNA present in a cell line derived from one of these tumors is identical in size to the normal c-myc RNA. Furthermore, the level of c-myc expression is not dramatically elevated in this cell line. Exon 1 of the rat c-myc gene contains no ATG start codons and contains multiple stop codons in all three reading frames, indicating that it, like the chicken and mouse exon 1 sequences, is noncoding. The extent of homology between our sequence of rat c-myc exon 1 and the published sequence of human c-myc exon 1 is similar to the extent of homology between the sequences of mouse and human c-myc exon 1. The rat and mouse c-myc exon 1 sequences differ from each other by about the amount predicted from the known divergence times of mice from rats. Exon 1 of c-myc is only slightly conserved, evolving at a rate similar to that seen for introns and pseudogenes.

Dsi-1, a region with frequent proviral insertions in Moloney murine leukemia virus-induced rat thymomas.

Dsi-1 is a region of chromosomal DNA that underwent proviral insertion in 3 of 24 Moloney murine leukemia virus-induced rat thymomas. In one of these tumors, a provirus is also integrated adjacent to the proto-oncogene c-myc. The proviruses in Dsi-1 have been characterized and appear to be complete. The proviruses were located within a 2-kilobase region that contained four prominent DNase I-hypersensitive sites. These hypersensitive sites were observed in Moloney murine leukemia virus-induced thymomas but not in NRK cells. The region of Dsi-1 immediately 3' to the insertions cross-hybridized with human and chicken DNA, indicating that it contains highly conserved sequences. No evidence could be found for the expression of this highly conserved region. Dsi-1 was mapped to mouse chromosome 4. This location demonstrates that Dsi-1 is different from 16 of the known proto-oncogenes (c-abl, c-erbA c-erbB, c-ets-1, c-ets-2, c-fes, c-fos, c-myb, c-myc, c-raf, A-raf, c-Ha-ras, c-Ki-ras, N-ras, c-sis, and c-src) and 12 cellular regions of tumor-associated integrations in retrovirus-induced tumors (c-erbB, Fis-1, int-1, int-2, Mis-1/pvt-1, Mlvi-1, Mlvi-2, c-mos, c-myb, c-myc, Pim-1, and c-Ha-ras). Hybridization experiments indicated that Dsi-1 is probably different from five additional proto-oncogenes (c-fgr, c-fms, c-mos, neu, and c-yes) and from two additional frequent integration regions (lck and Mlvi-3).

Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin.

Seven cellular loci with acceptor sites for retroviral integrations have been mapped for the presence of DNase I-hypersensitive sites in chromatin. Integrations in three of these loci, chicken c-erbB, rat c-myc, and a rat locus, dsi-1, had been selected for in retrovirus-induced tumors. Of the remaining four, two, designated dsi-3 and dsi-4, harbored acceptor sites for apparently unselected integrations of Moloney murine leukemia virus in a Moloney murine leukemia virus-induced thymoma, and two, designated C and F, harbored unselected acceptor sites for Moloney murine leukemia virus integrations in a rat fibroblast cell line. Each acceptor site mapped to within 500 base pairs of a DNase I-hypersensitive site. In the analyses of the unselected integrations, six hypersensitive sites were observed in 39 kilobases of DNA. The four acceptor sites in this DNA were localized between 0.05 and 0.43 kilobases of a hypersensitive site. The probability of this close association occurring by chance was calculated to be extremely low. Hypersensitive sites were mapped in cells representing the lineage in which integration had occurred as well as in an unrelated lineage. In six of the seven acceptor loci hypersensitive sites could not be detected in the unrelated lineage. Our results indicate that retroviruses preferentially integrate close to DNase I-hypersensitive sites and that many of these sites are expressed in some but not all cells.

Evidence for an early evolutionary origin and locus polymorphism of mouse VL30 DNA sequences.

The VL30 sequences of mouse DNA are a family of sequences with retrovirus-like structure which code for a 30S RNA transcript that can be packaged into the virions of murine leukemia viruses and thereby transmitted from cell to cell. A Southern blot analysis of these sequences revealed that multiple copies are present in the DNA of all mice examined, regardless of species or geographic origin. Considerable locus polymorphism was also apparent, and at least one of these polymorphisms appeared to reflect the differing chromosomal location of a complete VL30 sequence. These data indicated that VL30 elements are not recent additions to the mouse genome and suggested that the evolution of the VL30 multigene family has been accompanied by duplication and dispersion of VL30 sequences to diverse genomic sites. In addition, we reexamined the issue of genetic relatedness between mouse VL30 sequences and a physically similar family of virus-like elements in the rat genome. We found that many, if not all, rat and mouse VL30 loci contain regions of sequence homology. These data suggested that rodent VL30 sequences have evolved from a common ancestral sequence.

Most of the murine leukemia virus sequences in the DNA of NIH/swiss mice consist of two closely related proviruses, each repeated several times.

The structure of the endogenous murine leukemia virus (MuLV) sequences of NIH/Swiss mice was analyzed by restriction endonuclease digestion, gel electrophoresis, and hybridization to an MuLV nucleic acid probe. Digestion of mouse DNA with certain restriction endonucleases revealed two classes of fragments. A large number of fragments (about 30) were present at a relatively low concentration, indicating that each derived from a sequence present once in the mouse genome. A smaller number of fragments (one to five) were present at a much higher concentration and must have resulted from sequences present multiple times in the mouse genome. These results indicated that the endogenous MuLV sequences represent a family of dispersed repetitive sequences. Hybridization of these same digested mouse DNAs to nucleic acid probes representing different portions of the MuLV genome allowed construction of a map of the sites where restriction endonucleases cleave the endogenous MuLV sequences. Several independent recombinant DNA clones of endogenous MuLV sequences have been isolated from C3H mice (Roblin et al., J. Virol. 43:113-126, 1982). Analysis of these sequences shows that they have the structure of MuLV proviruses. The sites at which restriction endonucleases cleave within these proviruses appeared to be similar or identical to the sites at which these nucleases cleaved within the MuLV sequences of NIH/Swiss mice. This identity was confirmed by parallel electrophoresis. We conclude that the apparently complex pattern of endogenous MuLV sequences of NIH/Swiss mice consists largely of only two kinds of provirus, each repeated multiple times at dispersed sites in the mouse genome.

Continuing germ line integration of AKV proviruses during the breeding of AKR mice and derivative recombinant inbred strains.

The gel electrophoresis-hybridization technique of Southern was used to analyze genetically transmitted proviruses coding for the AKV strain of murine leukemia virus. We were able to identify the restriction endonuclease EcoRI fragments containing two previously unidentified, genetically transmitted AKV proviruses of AKR mice. Comparison of different sublines of AKR mice revealed considerable heterogeneity in their complement of germ line proviruses. This heterogeneity provides evidence that the provirus complement of AKR mice is not stable. Rather, the number of genetically transmitted proviruses increases during inbreeding. Examination of a series of sublines of the C3H strain indicated that this amplification is dependent on viremia. We estimate that, in viremic strains of mice, one new provirus becomes fixed in the germ line every 15 to 30 years.

Evidence for the Asiatic origin of endogenous AKR-type murine leukemia proviruses.

A restriction endonuclease cleavage map of the genome of AKV, the endogenous, ecotropic leukemia virus of AKR mice, has been derived. By using this map and analyzing DNA from congenic mice, we have defined four DNA fragments diagnostic for AKV proviruses. Analysis of DNAs from 10 strains of American laboratory mice revealed that all strains carrying inducible, ecotropic murine leukemia viruses yielded DNAs which contained the four DNA fragments diagnostic for AKV. Virus-negative strains lacked these fragments in their DNA. Screening DNA from 23 additional mice revealed that, among these mice, only mice from Asia gave rise to the DNA fragments diagnostic of an AKV provirus. We conclude that all of the endogenous ecotropic murine leukemia proviruses in American laboratory mice are closely related since they share a common set of restriction endonuclease cleavage sites. These proviruses appear to derive from the East Asian ancestors of these mouse strains. Analysis of DNA from six selected mice with an additional restriction endonuclease showed that greater than 97% of the nucleotide sequences in each provirus are contigous and that these endogenous proviruses are indistinguishable from proviruses introduced by exogenous infection.

Micro-complement fixation in Klebsiella classification.

The alkaline phosphatases of 29 strains of bacteria assigned by various authors to the genera Aerobacter, Klebsiella and Enterobacter were compared by the micro-complement fixation technique. On the basis of phosphatase resemblance, we recommend that all strains hitherto assigned to Aerobacter aerogenes and Enterobacter aerogenes be assigned to the genus Klebsiella.