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S Brenner

Publications and source records attributed to S Brenner.

At least 37 records · Page 2Linked to original sources
PubMed2000

Fugu: a compact vertebrate reference genome.

At 400 Mb, the Japanese pufferfish, Fugu rubripes, has the smallest vertebrate genome but has a similar gene repertoire to other vertebrates. Its genes are densely packed with short intergenic and intronic sequences devoid of repetitive elements. It likely has a mutational bias towards DNA elimination and is probably close to a 'minimal' vertebrate genome. As such it is a useful reference genome for gene discovery and gene validation in other vertebrates. Its usefulness in the discovery of conserved regulatory elements has already been demonstrated. The Fugu genome sequence is a good complement to genetic studies in other vertebrates.

Animals↗
PubMed2000

Hard cases (contd)

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Journal Article↗
PubMed2000

The bottom line

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Journal Article↗
PubMed2000

Characterization of the recombinase activating gene-1 and 2 locus in the Japanese pufferfish, Fugu rubripes.

The recombinase activating genes (RAG1 and RAG2) encode nuclear proteins that directly mediate the mechanism V(D)J recombination process that occurs in T- and B-lymphocytes. The expression of RAG1 and RAG2 is required for the proper development of maturing lymphocytes. To identify evolutionary conserved regulatory regions adjacent to both genes we isolated and sequenced a cosmid clone containing 43kb of genomic DNA of the Japanese pufferfish, Fugu rubripes. Fugu has a haploid genome of 400Mb and contains the same number of genes as the genome of higher vertebrates. With low abundance of repetitive DNA, the genome of the pufferfish has shown to be ideal for comparative genomics. We found three complete genes, RAG1, RAG2 and ACS (a possible homologue of the plant 1-aminocyclopropane-carboxylate synthase gene). There is also the 5' exon of a prohormone convertase gene, possibly PACE4. The genetic structure of both RAG1 and RAG2 is identical to that found in other fish, but the size of the intergenic region is smaller in Fugu. Expression analysis by RT-PCR shows the presence of RAG transcripts in kidney of adult Fugu. The human ACS was identified in a cosmid assigned to chromosome 11p11, which is close to the location of the RAGs (11p12). This indicates conservation of linkage between human and pufferfish.

Animals↗
PubMed2000

What lies ahead?

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Scientific Misconduct↗
PubMed2000

Hard cases.

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Journal Article↗
PubMed2000

In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs.

We describe a method for cloning nucleic acid molecules onto the surfaces of 5-micrometer microbeads rather than in biological hosts. A unique tag sequence is attached to each molecule, and the tagged library is amplified. Unique tagging of the molecules is achieved by sampling a small fraction (1%) of a very large repertoire of tag sequences. The resulting library is hybridized to microbeads that each carry approximately 10(6) strands complementary to one of the tags. About 10(5) copies of each molecule are collected on each microbead. Because such clones are segregated on microbeads, they can be operated on simultaneously and then assayed separately. To demonstrate the utility of this approach, we show how to label and extract microbeads bearing clones differentially expressed between two libraries by using a fluorescence-activated cell sorter (FACS). Because no prior information about the cloned molecules is required, this process is obviously useful where sequence databases are incomplete or nonexistent. More importantly, the process also permits the isolation of clones that are expressed only in given tissues or that are differentially expressed between normal and diseased states. Such clones then may be spotted on much more cost-effective, tissue- or disease-directed, low-density planar microarrays.

Cloning, Molecular↗
PubMed2000

Transperineal ultrasonography: new method to image the anorectal region.

PURPOSE: The aim of this preliminary study was to present an alternative method to assess the anal sphincters by ultrasonography using a conventional ultrasound surface probe by transperineal approach. METHODS: Transperineal ultrasonography was performed in 20 asymptomatic volunteers to assess the anal sphincters. Ultrasonographic findings were compared with conventional anal endosonography pictures available in the literature. RESULTS: Images of the anal sphincters obtained by transperineal ultrasound were found to be similar to those produced by conventional anal endosonography. Internal and external anal sphincters were easily demonstrated in addition to mucosal and submucosal layers. CONCLUSIONS: Transperineal ultrasonography is a new technique that enables imaging of anal sphincters and anal canal structures with potential application in functional and inflammatory anorectal disorders.

Adult↗
PubMed2000

Characterization of approximately 50 kb of the immunoglobulin VH locus of the Japanese pufferfish, Fugu rubripes.

The variable region of the immunoglobulin heavy chain is created by a somatic rearrangement of a limited number of germline genes. This mechanism of gene assembly [V(D)J recombination] has been found to take place only in jawed vertebrates (gnathostomes). To understand how this mechanism evolved and diversified it is necessary to study the genomic organization of the heavy-chain gene in different vertebrate lineages. Since there is scant sequence information on the VH locus in fish, shotgun sequencing of a cosmid clone containing part of the VH genomic region of the Japanese pufferfish, Fugu rubripes, was undertaken. Eight full-length VH genes were isolated and characterized. They have higher homology to trout genes, but show the same structural features as VHs found in other vertebrates. Two VH subgroups have been identified whose members are interspersed. The frequency of synonymous and nonsynonymous substitution for VH comparisons between family members was found to be higher in the complementarity-determining regions than in the framework regions. Finally, there are four other genes interspersed with the VH genes, one of which is the first full-length retrotransposon element characterized in vertebrates.

Amino Acid Sequence↗
PubMed2000

Comparative analysis of the PCOLCE region in Fugu rubripes using a new automated annotation tool.

The Japanese pufferfish Fugu rubripes with a genome of about 400 Mb is becoming increasingly recognized as a vertebrate model organism for comparative gene analysis (see Elgar 1996 for review). We have isolated and sequenced two Fugu cosmids spanning a genomic region of 66 kb containing the Fugu homolog to the human PCOLCE-I (Glöckner et al. 1998). We then examined if RUMMAGE-DP, a newly developed analysis tool for gene discovery which was designed for human and mouse genomic DNA, can be used for automatic annotation of Fugu genomic sequence. The exon prediction programs contained in RUMMAGE-DP performed better overall for the human sequence than for the Fugu contig. The GENSCAN program was the only exon prediction programme that performed equally well for both organisms. We show that RUMMAGE-DP is very useful in automatic analysis of Fugu sequences. Comparative analysis of the genomic structure of the PCOLCE-I genes in Fugu and human reveals that the exon/intron structure throughout the protein coding region is almost identical. We defined an additional domain based on the high degree of similarity of 26 aa between mammals and Fugu. The PCOLCE-I protein in both organisms contains two highly conserved CUB domains. Exons 6 and 7 are the only coding exons that differ in length between the two species. We assume that these exons do not code for any catalytic domain of the protein. Analysis of the remaining five Fugu genes within the 66 kb interval revealed no conserved synteny with the corresponding human 7q22 region.

Amino Acid Sequence↗
PubMed2000

Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.

We describe a novel sequencing approach that combines non-gel-based signature sequencing with in vitro cloning of millions of templates on separate 5 microm diameter microbeads. After constructing a microbead library of DNA templates by in vitro cloning, we assembled a planar array of a million template-containing microbeads in a flow cell at a density greater than 3x10(6) microbeads/cm2. Sequences of the free ends of the cloned templates on each microbead were then simultaneously analyzed using a fluorescence-based signature sequencing method that does not require DNA fragment separation. Signature sequences of 16-20 bases were obtained by repeated cycles of enzymatic cleavage with a type IIs restriction endonuclease, adaptor ligation, and sequence interrogation by encoded hybridization probes. The approach was validated by sequencing over 269,000 signatures from two cDNA libraries constructed from a fully sequenced strain of Saccharomyces cerevisiae, and by measuring gene expression levels in the human cell line THP-1. The approach provides an unprecedented depth of analysis permitting application of powerful statistical techniques for discovery of functional relationships among genes, whether known or unknown beforehand, or whether expressed at high or very low levels.

Cell Line↗
PubMed2000

In vitro tannin acantholysis.

BACKGROUND: Exogenous factors, such as certain drugs, may be involved in the induction of pemphigus. Other offenders sharing a similar chemical composition to these drugs may also play a role. Tannins with their considerable biologic activity were suggested as possible factors. To substantiate the role of tannins in the pathomechanism of pemphigus, the present study examined the acantholytic potential of tannins in vitro. METHODS: Normal human breast skin from patients without any bullous disease was cultured for 3 days in the presence of tannic acid at concentrations of 0.02, 0.05, 0.1, 0.25, 0.5, 1.0, and 2.0 mM. The effect of the tannic acid was microscopically examined in a blind fashion by three independent investigators. RESULTS: In addition to the cytotoxic effect, tannic acid caused marked acantholytic changes, with a clear suprabasal cleavage and intraepidermal acantholytic cells. The acantholytic changes were the most constant and specific effects. They were constantly observed at 1.0 and 2.0 mM, whereas lower concentrations showed changes only in some of the explants. The concentrations needed to exert this effect were notably low. There was a remarkable variability among the subjects who had provided the explants. CONCLUSIONS: The results suggest a possible role of tannin in the disease process of pemphigus. The tannin acantholytic potential was much greater than the potential of known acantholytic drugs, such as penicillamine and captopril. The interindividual variability in susceptibility to acantholysis may explain the variability in the individual potential for developing pemphigus.

Acantholysis↗