Conserved linkage between the puffer fish (Fugu rubripes) and human genes for platelet-derived growth factor receptor and macrophage colony-stimulating factor receptor

We have cloned and sequenced the teleost homologs of the human genes encoding platelet-derived growth factor receptor-beta (PDGFR beta) and macrophage colony-stimulating factor 1 receptor (CSFIR) from the puffer fish Fugu rubripes. The Fugu PDGFR beta and CSFIR genes each consist of 21 coding exons similar to the human CSFI gene, but are considerably smaller than their human counterparts because of the smaller introns. Furthermore, the two Fugu genes are linked tandemly in a head-to-tail array similar to their human homologs with 2.2 kb of intergenic sequence. Amino acid sequences of the Fugu and human PDGFR beta and CSFIR genes show an overall homology of 45% and 39%, respectively, with the kinase domains showing a much higher degree of conservation. Dot-matrix analysis revealed several short stretches of conserved sequences in the 3' untranslated regions of the PDGFR beta genes and the adjacent promoter regions of the CSFIR genes. These conserved sequences may have a role in the regulation of expression of either or both of these closely linked genes.

The tuberin (TSC2), autosomal dominant polycystic kidney disease (PKD1), and somatostatin type V receptor (SSTR5) genes form a synteny group in the Fugu genome

The tuberous sclerosis 2 (TSC2) and polycystic kidney disease 1 (PKD1) genes are adjacent on human chromosome 16p13.3 and form part of a conserved synteny group with mouse chromosome 17. We have determined that the PKD1 gene is evolutionarily conserved, single copy, and linked to TSC2 in the Fugu genome. A short cosmid contig has been identified containing both genes based on hybridization, exon trapping, and random sequence data. In addition sequences homologous to the somatostatin type V receptor (SSTR5) were identified 5' to PKD1, defining a larger syntenic region, as this gene has also been mapped to human chromosome 16p13.3. As in mammalian genomes, the Fugu TSC2 and PKD1 genes are adjacent in a tail-to-tail orientation.

Penicillamine-induced bullous dermatoses

The successful therapeutic use of D-penicillamine (DPA) has been hindered by its many adverse effects. Autoimmune bullous syndromes are among the less common adverse DPA reactions; they are not dose dependent and appear late in the treatment of diseases of altered immunity, most often rheumatoid arthritis. The majority of the DPA-induced bullous syndromes belong to the pemphigus spectrum, usually pemphigus foliaceus or erythematosus, have a lower prevalence of demonstrable tissue-fixed or circulating antibodies than spontaneously occurring pemphigus, display abnormal direct immunofluorescent patterns, and have a generally favorable prognosis. However, many cases do exhibit a full-blown chronic disease, unaffected by DPA withdrawal. DPA-induced cicatricial pemphigoid is a severe disease of both mucous and cutaneous involvement with a prognosis similar to the spontaneous disease. Cases of DPA-induced epidermolysis bullosa acquisita and DPA-induced bullous pemphigoid were not sufficiently substantiated by immunofluorescence or immunoprecipitation criteria.

Molecular cloning of the novel human G protein-coupled receptor (GPCR) gene mapped on chromosome 9

A novel human GPCR gene was cloned by PCR with degenerate primers designed from cannabinoid type 1 receptor (CB1) sequences and a full-length clone was isolated by screening of a human genomic DNA library. This gene, termed EDG-3, is highly homologous (51.9 % overall and 69.2 % in seven transmembrane regions) to human EDG-1, 47.9 % to rat AGR16 but only 28.0 % to human CB1 receptor. The Northern hybridization analysis showed that a 2.8 kb transcript of EDG-3 is abundantly expressed in the heart followed by placenta, kidney and liver. The EDG-3 gene was mapped on the human chromosome 9q22.1-q22.2 by fluorescence in situ hybridization analysis. Although the ligand and physiological role of this receptor is unknown, this gene may be a new member of the EDG family.

Genomic organization of the fungus Phycomyces

The fungus Phycomyces blakesleeanus has a relatively small genome, 30 megabases (Mb), with a low guanine and cytosine (G + C) content, 35%; the coding sequences cloned to date all have a G + C content of about 50%. In order to investigate the organization of the genome of this fungus, we have cloned and sequenced 251 DNA fragments. One hundred and twenty-six clones were obtained by digestion with MspI (target sequence 5'-CCGG-3') and 125 random clones were obtained by sonication. The average length of sequence obtained was about 200 base pairs (bp) and the total length was about 50 kilobases (kb). The G + C content is not homogeneous throughout the genome: sequences obtained after digestion with MspI have an average of 5% more G + C content than the random fragments, and are enriched in coding sequences. Fourteen MspI fragments show similarities to known proteins and 21 encode ribosomal RNA (rRNA). By contrast, only three of the random fragments are similar to known proteins and only one to a rRNA. We conclude that the Phycomyces genome is composed of G + C-rich genes surrounded by G + C-poor areas. Two clones have similarities to the transposase of the transposon Tc1 from Caenorhabditis elegans. This result suggests the presence of a high copy number of a Tc1-like transposable element in the Phycomyces genome. Another clone was similar to the transposon Tx1 from Xenopus laevis. A novel repetitive nt sequence has been characterized; about 5% of the total genome is a repetition of any of two consensus sequences of 31 bp named PrA1 and PrA2.

Surface display of proteins on bacteriophage lambda heads

We have developed plasmid and phage vectors for the display of foreign proteins on the surface of bacteriophage lambda capsid by modifying the D gene which encodes the major head protein gpD. The vectors have multiple cloning sites, and permit colour selection and conditional chain termination for recombinants. Displayed proteins can be fused to either the N or C terminus of gpD by a peptide linker. The conditional chain termination scheme, via a host Escherichia coli suppressor activity, allows the fusion and assembly of homomultimeric proteins as well as control of the number of fusion proteins per phage particle. We have successfully displayed beta-lactamase, IgG-binding domains of the Staphylococcus aureus protein A, and beta-galactosidase by cloning the genes into the vector. The constructs express functionally active proteins fused to gpD that assemble into phage particles. These results suggest that gpD may be fused to many other peptides and proteins at their N or C terminus and the fusion products may be accessible on the surface of bacteriophage lambda particles.

The conserved role of Krox-20 in directing Hox gene expression during vertebrate hindbrain segmentation

Transient segmentation in the hindbrain is a fundamental morphogenetic phenomenon in the vertebrate embryo, and the restricted expression of subsets of Hox genes in the developing rhombomeric units and their derivatives is linked with regional specification. Here we show that patterning of the vertebrate hindbrain involves the direct upregulation of the chicken and pufferfish group 2 paralogous genes, Hoxb-2 and Hoxa-2, in rhombomeres 3 and 5 (r3 and r5) by the zinc finger gene Krox-20. We identified evolutionarily conserved r3/r5 enhancers that contain high affinity Krox-20. binding sites capable of mediating transactivation by Krox-20. In addition to conservation of binding sites critical for Krox-20 activity in the chicken Hoxa-2 and pufferfish Hoxb-2 genes, the r3/r5 enhancers are also characterized by the presence of a number of identical motifs likely to be involved in cooperative interactions with Krox-20 during the process of hindbrain patterning in vertebrates.

A functional role for some Fugu introns larger than the typical short ones: the example of the gene coding for ribosomal protein S7 and snoRNA U17

The compact genome of Fugu rubripes, with its very small introns, appears to be particularly suitable to study intron-encoded functions. We have analyzed the Fugu gene for ribosomal protein S7 (formerly S8, see Note), whose Xenopus homolog contains in its introns the coding sequences for the small nucleolar RNA U17. Except for intron length, the organization of the Fugu S7 gene is very similar to that of the Xenopus counterpart. The total length of the Fugu S7 gene is 3930 bp, compared with 12691 bp for Xenopus. This length difference is uniquely due to smaller introns. Although short, the six introns are longer than the approximately 100 bp size of most Fugu introns, as they host U17 RNA coding sequences. While four of the six U17 sequences are 'canonical', the remaining two represent diverged U17 pseudocopies. In fact, microinjection in Xenopus oocytes of in vitro synthesized Fugu transcripts containing the 'canonical' U17f sequence results in efficient production of mature U17 RNA, while injection of a transcript containing the U17 psi b sequence does not.

Translocation events in the evolution of aminoacyl-tRNA synthetases

We have characterized hisS, the gene encoding the histidyl-tRNA synthetase (HisRS) from the tetraodontoid fish Fugu rubripes. The hisS gene is about 3.5 kbp long and contains 13 exons and 12 introns of 172 bp, on average. The Fugu hisS gene encodes a putative protein of 519 amino acids with the three motifs identified as signatures of class 2 aminoacyl-tRNA synthetases. A model for the shifting of intron 8 between Fugu and hamster is proposed based on the successive appearance of a cryptic splicing site followed by an insertion mutation that created a new acceptor site. In addition, sequence comparisons suggest that the hisS gene has undergone a translocation through the first intron. As a result, the Fugu HisRS has an N-terminal sequence markedly different from that in the human and hamster enzymes. We propose that similar events have been responsible for variations at the N-terminal end of other aminoacyl-tRNA synthetases. Our analysis suggests that this involves exchanges through introns of two exons encoding an ancestral 32-amino acid motif.

Molecular cloning of two cannabinoid type 1-like receptor genes from the puffer fish Fugu rubripes

The puffer fish, Fugu rubripes (Fugu), has been proposed as a model vertebrate genome. We have characterized two putative G-protein-coupled receptor encoding genes, FCB1A and FCB1B, obtained by degenerate PCR and low-stringency hybridization of a Fugu genomic library. These two genes show high homology to the human cannabinoid receptor type 1 (HCB1), but very low homology to the type 2 receptor. The amino acid sequences of the FCB1A and FCB1B genes are 66.2% identical, and the homology of each gene to HCB1 is 72.2 and 59.0%, respectively. The transcripts of both the FCB1A and the FCB1B receptors are abundant in the brain. No type 2 receptor could be cloned from Fugu. These data suggest that although two cannabinoid receptor-like genes are found in the puffer fish, both show similarity to the type 1 receptor found in human.

Isolation, characterization and evolution of nine pufferfish (Fugu rubripes) actin genes

The Japanese pufferfish Fugu rubripes (Fugu) has a small genome of about 400 Mb. Nine different actin genes have been isolated and sequenced from a genomic library constructed from this teleost. The six muscle-type actin genes include two alpha-skeletal actins, three alpha-cardiac actins and an alpha-anomalous (testis type) actin, and the three cytoplasmic actins include two beta-cytoplasmic actins and a beta-cytoplasmic (vascular type) actin. The two skeletal muscle actin genes have identical genomic organization, but differ by five amino acid residues. The three cardiac actin genes code for the same protein but differ in their nucleotide sequences and genomic organization. beta-Cytoplasmic actin1 differs by three amino acids from beta-cytoplasmic actin2. The alpha-anomalous (testis type) and beta-cytoplasmic (vascular type) actins are novel vertebrate actins. The amino acid sequence of alpha-anomalous (testis type) actin is the most divergent of all the known vertebrate actins and transcripts of this gene are abundant in the testis. The beta-cytoplasmic (vascular type) actin gene has eight introns, similar to mammalian smooth muscle actins, and is expressed in vascular tissues such as the gills, kidney and skin. Several known regulatory elements are found in the 5' flanking sequences and the first intron of various Fugu actin genes. The intron patterns of the various Fugu actins seem to be the result of loss of certain introns from a common ancestral gene.

Interaction between cAMP-dependent protein kinase catalytic subunit and peptide inhibitors analyzed with lambda repressor fusions

The lambda phage repressor is currently used as a genetic tool to analyze homodimeric interactions in Escherichia coli. We have applied this system to detect the interaction that takes place within an enzyme-protein inhibitor complex. The sequences encoding the catalytic subunit of the cAMP-dependent protein kinase and the active portion of the natural thermostable protein kinase inhibitor have been fused to the carboxy terminus of the repressor DNA binding domain and introduced into compatible plasmids. Co-expression of the two gene fusions in E. coli lead to the formation of heterodimers that confer a high level of protection from lambda phage infection. The level of lambda immunity depends specifically upon the amino acid sequence of the interacting proteins, as a single amino acid substitution in the inhibitor peptide (Phe10-Ala) restores the sensitivity phenotype.

Cloning and functional expression of cDNAs encoding human and rat pancreatic polypeptide receptors

PCR was used to isolate nucleotide sequences that may encode novel members of the neuropeptide Y receptor family. By use of a PCR product as a hybridization probe, a full-length human cDNA was isolated that encodes a 375-aa protein with a predicted membrane topology identifying it as a member of the G-protein-coupled receptor superfamily. After stable transfection of the cDNA into human embryonic kidney 293 cells, the receptor exhibited high affinity (Kd = 2.8 nM) for 125I-labeled human pancreatic polypeptide (PP). Competition binding studies in whole cells indicated the following rank order of potency: human PP = bovine PP > or = human [Pro34]peptide YY > rat PP > human peptide YY = human neuropeptide Y. Northern blot analysis revealed that human PP receptor mRNA is most abundantly expressed in skeletal muscle and, to a lesser extent, in lung and brain tissue. A rat cDNA clone encoding a high-affinity PP receptor that is 74% identical to the human PP receptor at the amino acid level was also isolated. These receptor clones will be useful in elucidating the functional role of PP and designing selective PP receptor agonists and antagonists.

Inhibition of proliferation of psoriatic and healthy fibroblasts in cell culture by selected Dead-sea salts

The effect of five selected minerals abundant in the Dead-sea brine was studied on proliferation of fibroblasts grown from psoriatic and healthy skin biopsy specimens in cell culture. The reason for carrying out this study was looking for the mechanism of the antiproliferative effect of selective Dead-sea minerals in improving the psoriatic condition. Psoriatic skin shave biopsy specimens (both from involved and uninvolved areas of the body) as well as healthy skin (obtained from amputated limbs) were incubated in tissue culture, and their outgrowing fibroblasts were used for this study. The number of cells and their cyclic AMP content were used as parameters for cell division and for proving the selective involvement of magnesium salts in the antiproliferative effect. It is shown that the inhibitory effects of magnesium bromide and magnesium chloride on cell growth were significantly stronger than those of their corresponding potassium salts or of sodium chloride. These results were obtained with both psoriatic and healthy skin fibroblasts, indicating that the inhibitory effect of the selected Dead-sea minerals is present in healthy and psoriatic skin cells.

Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes)

As the Human Genome Project advances, it is clear that the emphasis will switch from accumulation of data to their interpretation. Comparative genomics provides a powerful way in which to analyse sequence data. Indeed, there is already a long list of 'model' organisms, which allow comparative analyses in a variety of ways. The very small vertebrate genome of the pufferfish provides a simple and economical way of comparing sequence data from mammals and fish, representing a large evolutionary divergence and so permitting the identification of essential elements that are still present in both species. These elements include genes and the associated machinery that controls their expression; elements that, in many cases, have survived the test of time.

Treatment of Kaposi's sarcoma

The classic form of Kaposi's sarcoma (KS) is a rare multifocal neoplasm, as described by Kaposi in 1872. One hundred nine years after Kaposi's first description of the disease, the interest in all aspects of this disease escalated because of the emergence of human immunodeficiency virus (HIV), which is frequently accompanied by KS. This prompted zealous research, as reflected by numerous reports. Despite recent important discoveries, we are still far from understanding the pathogenesis of the disease and the mechanism of action of its various treatment modalities. As of today, treatment consists of most of the old modalities, some old ones in an updated improved version, and some new and experimental therapies. Our purpose is to focus on recent or novel data and to mention available treatments and their advantages, disadvantages, and side effects. We will also speculate on future directions.

Supplemental tests in the evaluation of occupational hand dermatitis in soldiers

BACKGROUND

Hand dermatitis in soldiers is a considerable problem. The purpose of the study was to evaluate appropriate screening tests to improve the diagnosis of hand dermatitis in soldiers.

MATERIALS AND METHODS

A group of 111 soldiers with occupational dermatitis from contact with fuels and oils underwent "tailored patch tests" with allergens relevant to their field of work and their environment. The control group consisted of 24 soldiers with various jobs similar to those of civilian life, who had not been exposed to oils and fuels. Seventy-three civilian patients, attending the clinic for patch testing, were also included. Twenty soldiers, who had a history of intensive contact with oil and fuels, but no contact dermatitis, and who were admitted because of various skin diseases (fungal infections, acne, etc.) also underwent the supplemental testing and served as an additional control group.

RESULTS

Of the soldiers, 31 (29%) showed one or more positive skin tests of the oil series and 30 patients of this group one or more positive reactions to the standard patch tests trays. No patient of the control groups had a positive test to the oil series.

CONCLUSIONS

Our results show the value of the supplementary tests as a first-step screening test for detection of oil allergy in soldiers and automobile-mechanics or in workers handling other gasoline- or diesel-powered engineering equipment. The test method appears to be practical, easy to perform, reliable and giving clear and accurate results, with a negligible rate of false positive reactions.