Biomedical subjects

D Frisch

Publications and source records attributed to D Frisch.

12 recordsLinked to original sources

PubMed2001

A framework for sequencing the rice genome.

Rice is an important food crop and a model plant for other cereal genomes. The Clemson University Genomics Institute framework project, begun two years ago in anticipation of the now ongoing international effort to sequence the rice genome, is nearing completion. Two bacterial artificial chromosome (BAC) libraries have been constructed from the Oryza sativa cultivar Nipponbare. Over 100,000 BAC end sequences have been generated from these libraries and, at a current total of 28 Mbp, represent 6.5% of the total rice genome sequence. This sequence information has allowed us to draw first conclusions about unique and redundant rice genomic sequences. In addition, more than 60,000 clones (19 genome equivalents) have been successfully fingerprinted and assembled into contigs using FPC software. Many of these contigs have been anchored to the rice chromosomes using a variety of techniques. Hybridization experiments have shown these contigs to be very robust. Contig assembly and hybridization experiments have revealed some surprising insights into the organization of the rice genome, which will have significant repercussions for the sequencing effort. Integration of BAC end sequence data with anchored contig information has provided unexpected revelations on sequence organization at the chromosomal level.

Chromosome Mapping↗

PubMed2001

Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2).

Utilizing improved methods, two bacterial artificial chromosome (BAC) libraries were constructed for the multidisease-resistant line of melon MR-1. The HindIII library consists of 177 microtiter plates in a 384-well format, while the EcoRI library consists of 222 microtiter plates. Approximately 95.6% of the HindIII library clones contain nuclear DNA inserts with an average size of 118 kb, providing a coverage of 15.4 genome equivalents. Similarly, 96% of the EcoRI library clones contain nuclear DNA inserts with an average size of 114 kb, providing a coverage of 18.7 genome equivalents. Both libraries were evaluated for contamination with high-copy vector, empty pIndigoBac536 vector, and organellar DNA sequences. High-density filters were screened with two genetic markers FM and AM that co-segregate with Fom-2, a gene conferring resistance to races 0 and 1 of Fusarium wilt. Fourteen and 18 candidate BAC clones were identified for the FM and AM probes, respectively, from the HindIII library, while 34 were identified for the AM probe from filters A, B, and C of the EcoRI library.

Chromosomes, Artificial, Bacterial↗

PubMed2000

Physical mapping of the barley stem rust resistance gene rpg4.

The barley stem rust resistance gene rpg4 was physically and genetically localized on two overlapping BAC clones covering an estimated 300-kb region of the long arm of barley chromosome 7(5H). Initially, our target was mapped within a 6.0-cM region between the previously described flanking markers MWG740 and ABG391. This region was then saturated by integrating new markers from several existing barley and rice maps and by using BAC libraries of barley cv. Morex and rice cv. Nipponbare. Physical/genetic distances in the vicinity of rpg4 were found to be 1.0 Mb/cM, which is lower than the average for barley (4 Mb/cM) and lower than that determined by translocation breakpoint mapping (1.8 Mb/cM). Synteny at high resolution levels has been established between the region of barley chromosome 7(5H) containing the rpg4 locus and the subtelomeric region of rice chromosome 3 between markers S16474 and E10757. This 1.7-cM segment of the rice genome was covered by two overlapping BAC clones, about 250 kb of total length. In barley the markers S16474 and E10757 genetically delimit rpg4, lying 0.6 cM distal and 0.4 cM proximal to the locus, respectively.

Blotting, Southern↗

PubMed2000

Rice transposable elements: a survey of 73,000 sequence-tagged-connectors.

As part of an international effort to sequence the rice genome, the Clemson University Genomics Institute is developing a sequence-tagged-connector (STC) framework. This framework includes the generation of deep-coverage BAC libraries from O. sativa ssp. japonica c.v. Nipponbare and the sequencing of both ends of the genomic DNA insert of the BAC clones. Here, we report a survey of the transposable elements (TE) in >73,000 STCs. A total of 6848 STCs were found homologous to regions of known TE sequences (E<10(-5)) by FASTX search of STCs against a set of 1358 TE protein sequences obtained from GenBank. Of these TE-containing STCs (TE-STCs), 88% (6027) are related to retroelements and the remaining are transposase homologs. Nearly all DNA transposons known previously in plants were present in the STCs, including maize Ac/Ds, En/Spm, Mutator, and mariner-like elements. In addition, 2746 STCs were found to contain regions homologous to known miniature inverted-repeat transposable elements (MITEs). The distribution of these MITEs in regions near genes was confirmed by EST comparisons to MITE-containing STCs, and our results showed that the association of MITEs with known EST transcripts varies by MITE type. Unlike the biased distribution of retroelements in maize, we found no evidence for the presence of gene islands when we correlated TE-STCs with a physical map of the CUGI BAC library. These analyses of TEs in nearly 50 Mb of rice genomic DNA provide an interesting and informative preview of the rice genome.

Arabidopsis↗

PubMed1994

Beyond expected utility: rethinking behavioral decision research.

Much research in psychology has evaluated the quality of people's decisions by comparisons with subjective expected utility (SEU) theory. This article suggests that typical arguments made for the status of utility theory as normative do not justify its use by psychologists as a standard by which to evaluate decision quality. It is argued that to evaluate decision quality, researchers need to identify those decision processes that tend to lead to desirable outcomes. It is contended that a good decision-making process must be concerned with how (and whether) decision makers evaluate potential consequences of decisions, the extent to which they accurately identify all relevant consequences, and the way in which they make final choices. Research that bears on these issues is reviewed.

Behavior↗

PubMed1993

Lectin-binding patterns in the embryonic human paraxial mesenchyme.

The paraxial mesenchyme in seven human embryos aged between Carnegie stages 12 and 17 was studied by lectin histochemistry with the lectins AIA, Con A, GSA II, LFA, LTA, PNA, RCA I, SBA, SNA, WGA. The paraxial mesenchyme was found to be segmented into sclerotomes by intersegmental vessels and from late stage 12 by intrasclerotomal clefts dividing each sclerotome into a cranial and caudal half. The lectins Con A, GSA II, LFA, LTA, SBA and SNA did not react at all in the paraxial mesenchyme. Staining for AIA, PNA, RCA I and WGA was found in the developing sclerotomes. However, no differences in the staining pattern between the two sclerotomal halves could be seen. It was striking that in contrast to the chick embryo no differences in binding for PNA between the cranial and caudal sclerotomal parts was observed. These findings reveal that PNA-binding sites do not play the same functional role in segmented axonal outgrowth and neural crest immigration into cranial sclerotomal halves in the human embryo, as found in chick embryonic development. Beginning with the stage 16-embryo, the already condensed caudal sclerotomal halves express Con A-, RCA- and PNA-binding sites. The staining for PNA in particular marked the differentiation of chondrogenous structures developing in this half. From the late stage 12 or stage 13, the walls of intersegmental and other vessels showed binding sites for AIA, PNA, RCA I, SNA and WGA.

Embryonic and Fetal Development↗

PubMed1974