An overview of the BioExtract Server: a distributed, Web-based system for genomic analysis.

Genome research is becoming increasingly dependent on access to multiple, distributed data sources, and bioinformatic tools. The importance of integration across distributed databases and Web services will continue to grow as the number of requisite resources expands. Use of bioinformatic workflows has seen considerable growth in recent years as scientific research becomes increasingly dependent on the analysis of large sets of data and the use of distributed resources. The BioExtract Server (http://bioextract.org) is a Web-based system designed to aid researchers in the analysis of distributed genomic data by providing a platform to facilitate the creation of bioinformatic workflows. Scientific workflows are created within the system by recording the analytic tasks preformed by researchers. These steps may include querying multiple data sources, saving query results as searchable data extracts, and executing local and Web-accessible analytic tools. The series of recorded tasks can be saved as a computational workflow simply by providing a name and description.

Spliceosomal proteins in plants.

The spliceosome is a large nuclear structure consisting of dynamically interacting RNAs and proteins. This chapter briefly reviews some of the known components and their interactions. Large-scale proteomics and gene expression studies may be required to unravel the many intricate mechanisms involved in splice site recognition and selection.

Multi-query sequence BLAST output examination with MuSeqBox.

SUMMARY: MuSeqBox is a program to parse BLAST output and store attributes of BLAST hits in tabular form. The user can apply a number of selection criteria to filter out hits with particular attributes. MuSeqBox provides a powerful annotation tool for large sets of query sequences that are simultaneously compared against a database with any of the standard stand-alone or network-client BLAST programs. We discuss such application to the problem of annotation and analysis of EST collections. AVAILABILITY: The program was written in standard C++ and is freely available to noncommercial users by request from the authors. The program is also available over the web at http://bioinformatics.iastate.edu/bioinformatics2go/mb/MuSeqBox.html.

Optimal spliced alignment of homologous cDNA to a genomic DNA template.

MOTIVATION: Supplementary cDNA or EST evidence is often decisive for discriminating between alternative gene predictions derived from computational sequence inspection by any of a number of requisite programs. Without additional experimental effort, this approach must rely on the occurrence of cognate ESTs for the gene under consideration in available, generally incomplete, EST collections for the given species. In some cases, particular exon assignments can be supported by sequence matching even if the cDNA or EST is produced from non-cognate genomic DNA, including different loci of a gene family or homologous loci from different species. However, marginally significant sequence matching alone can also be misleading. We sought to develop an algorithm that would simultaneously score for predicted intrinsic splice site strength and sequence matching between the genomic DNA template and a related cDNA or EST. In this case, weakly predicted splice sites may be chosen for the optimal scoring spliced alignment on the basis of surrounding sequence matching. Strongly predicted splice sites will enter the optimal spliced alignment even without strong sequence matching. RESULTS: We designed a novel algorithm that produces the optimal spliced alignment of a genomic DNA with a cDNA or EST based on scoring for both sequence matching and intrinsic splice site strength. By example, we demonstrate that this combined approach appears to improve gene prediction accuracy compared with current methods that rely only on either search by content and signal or on sequence similarity. AVAILABILITY: The algorithm is available as a C subroutine and is implemented in the SplicePredictor and GeneSeqer programs. The source code is available via anonymous ftp from ftp. zmdb.iastate.edu. Both programs are also implemented as a Web service at http://gremlin1.zool.iastate.edu/cgi-bin/s p.cgiand http://gremlin1.zool.iastate.edu/cgi-bin/g s.cgi, respectively. CONTACT: vbrendel@iastate.edu

Immunity to murine breast cancer cells modified to express MUC-1, a human breast cancer antigen, in transgenic mice tolerant to human MUC-1.

The high incidence of breast cancer in women and the severity of the disease have stimulated a need for improved and novel forms of therapy. The product of the MUC-1 gene has been identified as a breast cancer-associated antigen in breast cancer patients. The gene has been cloned and sequenced. Transgenic mice were prepared that express human mucin and are naturally tolerant to the molecule, providing a unique opportunity to investigate immunotherapeutic strategies in experimental animals that might eventually be applied to breast cancer patients. A cell line (410.4) derived from a mouse mammary adenocarcinoma that arose in a BALB/c mouse was transduced with a retroviral vector (R1-MUC1-pEMSVscribe) that encoded MUC-1. After confirmation of the expression of human mucin, the cells (E3) were further modified by transduction with retroviral vectors encoding interleukin (IL)-2, IL-4, IL-12, or IFN-gamma to evaluate the effect of cytokine-secretion on the immunogenic properties of the cells in the MUC-1 transgenic mice. The results indicated that modification of the breast cancer cells to secrete IL-12 reduced and at times eliminated the tumorigenic growth properties of the cells. Under similar circumstances, progressively growing tumors formed in MUC-1 transgenic mice that received injections of unmodified E3 cells or with E3 cells modified to secrete IL-2, IL-4, or IFN-gamma. Immunity to breast cancer developed in MUC-1 transgenic mice that had rejected IL-12-secreting E3 cells because the animals were resistant to challenge with (non-cytokine-secreting) E3 cells. In vitro analyses confirmed the presence of T cell-mediated cytotoxicity toward the breast cancer cells in MUC-1 transgenic mice immunized with the IL-12-secreting cells. Our data obtained in a unique animal model system point toward an analogous form of therapy for breast cancer patients.

Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring.

Gene identification in genomic DNA from eukaryotes is complicated by the vast combinatorial possibilities of potential exon assemblies. If the gene encodes a protein that is closely related to known proteins, gene identification is aided by matching similarity of potential translation products to those target proteins. The genomic DNA and protein sequences can be aligned directly by scoring the implied residues of in-frame nucleotide triplets against the protein residues in conventional ways, while allowing for long gaps in the alignment corresponding to introns in the genomic DNA. We describe a novel method for such spliced alignment. The method derives an optimal alignment based on scoring for both sequence similarity of the predicted gene product to the protein sequence and intrinsic splice site strength of the predicted introns. Application of the method to a representative set of 50 known genes from Arabidopsis thaliana showed significant improvement in prediction accuracy compared to previous spliced alignment methods. The method is also more accurate than ab initio gene prediction methods, provided sufficiently close target proteins are available. In view of the fast growth of public sequence repositories, we argue that close targets will be available for the majority of novel genes, making spliced alignment an excellent practical tool for high-throughput automated genome annotation.

Gene discovery using the maize genome database ZmDB.

Zea mays DataBase (ZmDB) is a repository and analysis tool for sequence, expression and phenotype data of the major crop plant maize. The data accessible in ZmDB are mostly generated in a large collaborative project of maize gene discovery, sequencing and phenotypic analysis using a transposon tagging strategy and expressed sequence tag (EST) sequencing. ESTs constitute most of the current content. Database search tools, convenient links to external databases, and novel sequence analysis programs for spliced alignment are provided and together serve as an efficient protocol for gene discovery by sequence inspection. ZmDB can be accessed at http://zmdb. iastate.edu. ZmDB also provides web-based ordering of materials generated in the project, including EST and genomic DNA clones, seeds of mutant plants and microarrays of amplified EST and genomic DNA sequences.

Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor.

Accumulation of red phlobaphene pigments in sorghum grain pericarp is under the control of the Y gene. A mutable allele of Y, designated as y-cs (y-candystripe), produces a variegated pericarp phenotype. Using probes from the maize p1 gene that cross-hybridize with the sorghum Y gene, we isolated the y-cs allele containing a large insertion element. Our results show that the Y gene is a member of the MYB-transcription factor family. The insertion element, named Candystripe1 (Cs1), is present in the second intron of the Y gene and shares features of the CACTA superfamily of transposons. Cs1 is 23,018 bp in size and is bordered by 20-bp terminal inverted repeat sequences. It generated a 3-bp target site duplication upon insertion within the Y gene and excised from y-cs, leaving a 2-bp footprint in two cases analyzed. Reinsertion of the excised copy of Cs1 was identified by Southern hybridization in the genome of each of seven red pericarp revertant lines tested. Cs1 is the first active transposable element isolated from sorghum. Our analysis suggests that Cs1-homologous sequences are present in low copy number in sorghum and other grasses, including sudangrass, maize, rice, teosinte, and sugarcane. The low copy number and high transposition frequency of Cs1 imply that this transposon could prove to be an efficient gene isolation tool in sorghum.

Immunity to breast cancer in mice immunized with X-irradiated breast cancer cells modified to secrete IL-12.

A mouse mammary adenocarcinoma cell line (410.4) originating in a BALB/c mouse, was transduced with a retroviral vector (TGF-mIL-12-Neo) that encoded murine IL-12. After confirmation of IL-12-secretion, the cells were tested for their tumorigenic properties in BALB/c mice. The results indicated that unlike other tumors modified for cytokine secretion, modification of 410.4 cells to secrete IL-12 (410.4-IL-12 cells) failed to eliminate the cells' neoplastic growth properties. Progressively growing tumors of 410.4-IL-12 cells invariably formed in syngeneic BALB/c mice and led, eventually, to the animals' death. However, the cells' immunogenic properties were preserved as indicated by the finding that immunizations with 410.4-IL-12 cells, inactivated before injection by X-irradiation, resulted in potent, long-term immunity toward unmodified 410.4 cells and protected the mice against the malignant proliferation of the breast cancer cells. We conclude that modification of 410.4 cells for IL-12-secretion augmented the response of syngeneic BALB/c mice to weakly immunogenic tumor-associated antigens expressed by the cells. The increase in the cells' immunogenic properties, however, was insufficient to prevent tumor growth in the mice. The results point toward the immunotherapeutic potential of X-irradiated tumor cells modified for the secretion of immune augmenting cytokines.

Treatment of breast cancer with fibroblasts transfected with DNA from breast cancer cells.

This investigation was based on the hypothesis that weakly immunogenic, breast cancer-associated Ags, the products of mutant or dysregulated genes in the malignant cells, will be expressed in a highly immunogenic form by semiallogeneic IL-2-secreting fibroblasts transfected with DNA from breast cancer cells. (Classic studies indicate that transfection of genomic DNA can stably alter both the genotype and the phenotype of the cells that take up the exogenous DNA.) To investigate this question, we transfected LM mouse fibroblasts (H-2k) modified to secrete IL-2 with genomic DNA from a breast adenocarcinoma that arose spontaneously in a C3H/He mouse (H-2k). To increase their nonspecific immunogenic properties, the fibroblasts were also modified before transfection to express allogeneic MHC determinants (H-2Kb). Afterward, the IL-2-secreting semiallogeneic cells were cotransfected with DNA from the spontaneous breast neoplasm, along with a plasmid (pHyg) conferring resistance to hygromycin. Pooled colonies of hygromycin-resistant cells were then tested in C3H/He mice for their immunotherapeutic properties against the growth of the breast neoplasm. The results indicated that tumor-bearing mice immunized with the transfected cells survived significantly longer than mice in various control groups. Similar beneficial effects were seen in C57BL/6 mice injected with a syngeneic breast carcinoma cell line (EO771) and semiallogeneic, IL-2-secreting fibroblasts transfected with DNA from EO771 cells. The immunity was mediated by CD8+ T cells since immunized mice depleted of CD8+ cells failed to resist tumor growth.

Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors.

Human immunodeficiency virus type 1 (HIV-1) amino acid substitutions observed during antiretroviral drug therapy may be caused by drug selection, non-drug-related evolution, or sampling error introduced by the sequencing process. We analyzed HIV-1 sequences from 371 untreated patients and from 178 patients receiving a single protease inhibitor. Amino acid substitution patterns during treatment were compared with inferred substitution patterns arising evolutionarily without treatment. Our results suggest that most treatment-associated amino acid substitutions are caused by selective drug pressure, including substitutions not previously associated with drug resistance.

Test of the combinatorial model of intron recognition in a native maize gene.

Previous studies have established that splice site selection and splicing efficiency in plants depend strongly on local compositional contrast consisting of high exon G+C content relative to high intron U content. The combinatorial model of plant intron recognition posits that splice site sequences as well as local intron and exon sequences contribute to splice site selection and splicing efficiency. Most of the previous studies used synthetic or chimeric constructs, often tested in heterologous hosts. To perform a more critical test of the combinatorial model in a native context, the single intron of the maize Bronze2 gene and its flanking exons were modified by site-directed mutagenesis. Splicing efficiency was tested in maize protoplasts. Results show that a higher U content in the flanking 5' exon, whether close to or distant from the 5' splice site, did not modify splicing efficiency. Decreasing exon G+C content dramatically impaired splicing. Increasing intron G+C content or decreasing intron U content adversely impacted splicing. In all constructs splicing occurred exclusively at the original 5' and 3' splice sites. These results are consistent with the hypothesis that exon G+C content and intron U content contribute separate but complementary aspects of intron definition in the native Bz2 transcript.

Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA.

Prediction of splice site selection and efficiency from sequence inspection is of fundamental interest (testing the current knowledge of requisite sequence features) and practical importance (genome annotation, design of mutant or transgenic organisms). In plants, the dominant variables affecting splice site selection and efficiency include the degree of matching to the extended splice site consensus and the local gradient of U- and G+C-composition (introns being U-rich and exons G+C-rich). We present a novel method for splice site prediction, which was particularly trained for maize and Arabidopsis thaliana. The method extends our previous algorithm based on logitlinear models by considering three variables simultaneously: intrinsic splice site strength, local optimality and fit with respect to the overall splice pattern prediction. We show that the method considerably improves prediction specificity without compromising the high degree of sensitivity required in gene prediction algorithms. Applications to gene identification are illustrated for Arabidopsis and suggest that successful methods must combine scoring for splice sites, coding potential and similarity with potential homologs in non-trivial ways. A WWW version of the SplicePredictor program is available at http:/gnomic.stanford.edu/volker/SplicePredi ctor.html/

GeneGenerator--a flexible algorithm for gene prediction and its application to maize sequences.

MOTIVATION: We developed GeneGenerator because of the need for a tool to predict gene structure without knowing in advance how to score potential exons and introns in order to obtain the best results, pertinent in particular to less well-studied organisms for which suitable training sets are small. GeneGenerator is a very flexible algorithm which for a given genomic sequence generates a number of feasible gene structures satisfying user-defined constraints. The specific implementation described in detail requires minimum scoring for translation start and donor and acceptor splice sites according to previously trained logitlinear models. In addition, potential exons and introns are required to exceed specified minimal lengths and threshold scores for coding or non-coding potential derived as log-likelihood ratios of appropriate Markov sequence models. RESULTS: A database of 46 non-redundant genomic sequences from maize is used for illustration. It is shown that the correct gene structures do not always maximize the considered target function. However, in most cases, the correct or nearly correct structures are found in a small set of high-scoring structures. A critical review of the generated structures sometimes allows the choices to be narrowed by considering additional variables such as predicted splice site strength or local optimality of splice site scores. Summary statistics for prediction accuracy over all 46 maize genes are derived under cross-validation and non-cross-validation training conditions for the Markov sequence models. The algorithm achieved exon sensitivity of 0.81 and specificity of 0.75 on an independent set of 14 novel maize genomic segments. AVAILABILITY: GeneGenerator runs under Borland-Pascal 7.0 using MS-DOS and C on UNIX work stations. The source code is available upon request. CONTACT: jkleffe@euler.grumed.fu-berlin-de

Immunization with interleukin-2-secreting allogeneic cells transfected with DNA from mouse melanoma cells induces immune responses that prolong the lives of mice with melanoma.

Altered genes in tumor cells specify tumor-associated antigens. Because genetic instability is a characteristic of the malignant cell phenotype, a large number of different, altered genes may be present in a population of neoplastic cells, specifying an array of undefined tumor-associated determinants. We hypothesized that immunogenic cells transfected with DNA from malignant cells will include cells that specify tumor-associated antigens. To test this question, we deliberately mutagenized a population of B16 melanoma cells (H-2b) by ultraviolet-B irradiation. DNA from the surviving cells was used to transfect LM cells (H-2k), a mouse fibroblast cell line modified previously to secrete interleukin-2. The transfected allogeneic cells were then tested for their immunogenic properties in C57BL/6J mice (H-2b) syngeneic with the melanoma. Mice injected with a mixture of the mutagenized B16 cells and the transfected cells survived significantly longer than untreated mice injected with the mutagenized B16 cells alone. Mice injected with a mixture of mutagenized B16 cells and cells transfected with DNA from unirradiated B16 cells died in shorter intervals. Based on the results of cytotoxicity assays performed in vitro, the cellular immune responses of greatest magnitude were directed toward the type of cell from which the DNA was obtained.

Sustained expression of high levels of human factor IX from human cells implanted within an immunoisolation device into athymic rodents.

Immunoisolation of allogeneic cells within a membrane-bound device is a unique approach for gene therapy. We employed an immunoisolation device that protects allograft, but not xenograft, cells from destruction, to implant a human fibroblast line (MSU 1.2) in athymic rodents. Cells, transduced with the MFG-human factor IX retroviral vector, and expressing 0.9 microg/10(6) cells/day in vitro, were implanted in rats (four 40-microl devices, each containing 2 x 10(7) cells, two subcutaneously, two in epididymal fat) and in mice (two 20-microl devices, each containing 2 x 10(6) cells, subcutaneously). Plasma factor IX levels increased for 50 days, reaching maxima of 203 ng/ml (rat) and 597 ng/ml (mouse), and both continued at greater than 100 ng/ml for more than 140 days. A clone derived from the transduced cells, making 5 microg of factor IX/10(6) cells/day, was implanted within a device (one 20-microl device containing 2.5 x 10(6) cells), or without a device (1 x 10(7) cells implanted freely), either subcutaneously or in epididymal fat. The freely implanted cells expressed transiently, reaching more than 100 ng/ml in each site by day 4, but dropped to zero by day 20 (subcutaneous) or day 90 (epididymal fat). In devices, levels gradually increased to 100 ng/ml (subcutaneous) or 300 ng/ml (epididymal fat), remaining high for more than 100 days. These results show long-term, high-level expression of a human protein: (1) when cells are implanted within a cell transplantation device, but not when the cells are freely implanted, and (2) from a transgene driven by a viral promoter. An alloprotective device will enable the use of cloned cell lines that can be subjected to stringent quality control assessment that is impossible to achieve with autologous approaches.

U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize.

Using a large set of plant gene sequences we compared individual introns to their flanking exons. Both Zea mays and Arabidopsis thaliana introns are U-rich but display no apparent bias for A. We identified fifteen 11-mer U-rich motifs as frequent elements of maize introns, and these are virtually absent from exons. By mutagenesis, we show that the single U-rich motif in the Bronze2 intron of maize plays a key role in intron processing in vivo.

Resistance to melanoma in mice immunized with semiallogeneic fibroblasts transfected with DNA from mouse melanoma cells.

Tumor-associated Ags (TAA) that characterize a population of malignant cells are recognized by CTLs in the context of determinants specified by the MHC class I locus. Nevertheless, most progressively growing neoplasms do not induce antitumor immune responses that can control tumor cell growth. The TAA may be insufficiently antigenic. We found previously that immunization of mice with a cellular immunogen prepared by transfecting tumor DNA into allogeneic mouse fibroblasts resulted in strong antitumor immune responses that were specific for the type of tumor from which the DNA was obtained. Since the fibroblasts differed at the MHC from the immunized mice, we postulated that the immunogenic properties of the allogeneic transfected cells might be enhanced if the cells were modified to express syngeneic class I determinants. In a mouse melanoma model system, the H-2Kb gene was introduced into LM mouse fibroblasts (H-2k). Afterward, the cells were transfected with DNA from B16 melanoma cells (H-2b). The transfected cells were tested for their immunotherapeutic properties in C57BL/6J mice (H-2b) with melanoma. Mice with melanoma treated solely by immunization with the semiallogeneic transfected cells developed strong, long-term resistance to the growth of the tumor. In some instances, the mice survived indefinitely. Intact rather than disrupted transfected cells were required to induce the antimelanoma response, consistent with direct presentation of TAA by the transfected cells. The augmented resistance to melanoma in mice treated with the semiallogeneic transfected cells points toward an analogous form of therapy for cancer patients.

Prediction of splice sites in plant pre-mRNA from sequence properties.

Heterologous introns are often inaccurately or inefficiently processed in higher plants. The precise features that distinguish the process of pre-mRNA splicing in plants from splicing in yeast and mammals are unclear. One contributing factor is the prominent base compositional contrast between U-rich plant introns and flanking G + C-rich exons. Inclusion of this contrast factor in recently developed statistical methods for splice site prediction from sequence inspection significantly improved prediction accuracy. We applied the prediction tools to re-analyze experimental data on splice site selection and splicing efficiency for native and more than 170 mutated plant introns. In almost all cases, the experimentally determined preferred sites correspond to the highest scoring sites predicted by the model. In native genes, about 90% of splice sites are the locally highest scoring sites within the bounds of the flanking exon and intron. We propose that, in most cases, local context (about 50 bases upstream and downstream from a potential intron end) is sufficient to account for intrinsic splice site strength, and that competition for transacting factors determines splice site selection in vivo. We suggest that computer-aided splice site prediction can be a powerful tool for experimental design and interpretation.

Co-expression of immunogenic determinants by the same cellular immunogen is required for the optimum immunotherapeutic benefit in mice with melanoma.

Tumor-associated T cell epitopes are recognized by T cells in the context of determinants specified by class I loci. Since the rejection of foreign histocompatibility antigens is known to enhance tumor immunity, immunization with a cellular vaccine that combined the expression of both syngeneic and allogeneic class I determinants could have important immunological advantages over a vaccine that expressed either syngeneic or allogeneic determinants alone. To investigate this question in a mouse melanoma model system, we tested the immunotherapeutic properties of B16 melanoma x LM fibroblast hybrid cells in C57BL/6J mice with melanoma. Like C57BL/6J mice, B16 cells expressed H-2Kb class I determinants and (antibody-defined) melanoma-associated antigens. LM cells, of C3H mouse origin, formed H-2Kk determinants along with B7.1, a co-stimulatory molecule that can activate T cells. The B16 x LM hybrid cells co-expressed H-2Kb and H-2Kk class I determinants, B7.1 and the melanoma-associated antigens. C57BL/6J mice with melanoma, immunized with the semi-allogeneic hybrid cells, developed CD8-mediated melanoma immunity and survived significantly (P < 0.005) longer than mice with melanoma immunized with a mixture of the parental cell types. The failure of melanoma immunity to develop in mice injected with the mixture of parental cells indicated that co-expression of the immunogenic determinants by the same cellular immunogen was necessary for an optimum immunotherapeutic effect. Augmented immunity to melanoma in mice immunized with the semi-allogeneic hybrid cells points toward an analogous form of therapy for patients with melanoma.