Existence of Pink1 antisense RNAs in mouse and their localization

PTEN-induced kinase 1 (PINK1), which is identified as the gene transactivated by the tumor suppressor PTEN, has been found to be one of the causative genes in Parkinson's disease (PD). In order to understand PD, rodent models containing affected Pink1 such as loss-of-function mutations have been exploited. Recently, natural antisense RNA of PINK1 has been demonstrated to be involved in the regulation of the PINK1 locus. However, no antisense RNAs of Pink1 except for human have been reported so far. Therefore, in the present study, while searching for the Pink1 antisense RNAs in mouse, we found that the antisense RNAs are transcribed from a mouse genomic region corresponding to the human region from which the antisense RNAs are produced. Further, we investigated the localization of the antisense RNAs in mouse brain using in situ hybridization; this demonstrated that the antisense RNAs were localized in the regions of brain where the Pink1 mRNA was found. In addition, the mRNA and antisense RNAs were found more densely in the hippocampus than in the other brain regions in newborn and 1-week-old mice, while those RNAs were found uniformly in the mouse brain regions of embryo day (E) 14, E17, and 8-weeks-old.

Localization of sense and antisense transcripts of Prdx2 gene in mouse tissues

Recently, it has been reported that antisense RNAs are transcribed from a large number of genes in various species including human and mouse. The Prdx2 gene, which is indicated to be involved in signal transduction related to platelet-derived growth factor as well as to protection from oxidizing agents, has been shown to produce sense and antisense transcripts. To obtain clues for possible roles of Prdx2 antisense transcripts, we have performed Northern blot analysis and in situ hybridization on tissues of 8-week-old C57BL/6J mice. The Northern blot analysis revealed that major parts of sense and antisense transcripts were poly(A-)-RNA. The analysis of the fractionated RNA of fibroblasts indicated that the poly(A-)-RNA would be localized in the cytoplasm of cells. The in situ hybridization demonstrated that the sense and antisense transcripts were localized in almost the same limited areas of brain, testis, and spleen. It also revealed that the sense and antisense transcripts coexisted in Purkinje cells. In thymus and stomach, the antisense transcripts were detected, but sense transcripts were not. When tissues of BALB/c mice were examined by in situ hybridization, the observations were essentially the same as those of C57BL/6J except that it appeared that the amounts of sense and antisense transcripts in testis of BALB/c were greater than those in C57BL/6J, and that the amounts of antisense transcripts in stomach of BALB/c were much smaller than those in C57BL/6J.

Systematic genome-wide approach to positional candidate cloning for identification of novel human disease genes

BACKGROUND

Recent large-scale genome projects afford a unique opportunity to identify many novel disease genes and thereby better understand the genetic basis of human disease. Functional Annotation of Mouse (FANTOM) 2, the largest mouse transcriptome project yet, provides a wealth of data on novel genes, splice variants and non-coding RNA, and provides a unique opportunity to identify novel human disease genes.

AIMS

To demonstrate the power of combining the FANTOM 2 cDNA dataset with a positional candidate approach and bioinformatics analysis to identify genes underlying human genetic disease.

RESULTS

By mapping all FANTOM 2 cDNA to the human genome, we were able to identify mouse clones that co-localised on the human genome with mapped but uncloned human disease loci. By this method we identified mouse and corresponding human genes mapping within the loci of 100 different human genetic diseases (mapped interval of <5 cM). Of particular interest was the elucidation through FANTOM 2 novel mouse gene data of candidate human genes for the following: (i) developmental -disorders: neural tube defect, Meckel syndrome, Wolf--Hirschhorn syndrome and keratosis follicularis spinulosa decalvans cum ophiasi; (ii) neurological disorders: benign familial infantile convulsions 3, early-onset cerebellar ataxia with retained tendon reflexes, infantile-onset spinocerebellar ataxia and vacuolar neuro-myopathy and (iii) cancer-related syndromes: tylosis with oesophageal cancer and low-grade B-cell chronic lymphatic leukaemia.

CONCLUSIONS

The FANTOM 2 data will dramatically accelerate efforts to identify genes underlying human disease. It will also facilitate the creation of transgenic mouse models to help elucidate the function of potential human disease genes.

Speculations on the role of natural antisense transcripts in mammalian X chromosome evolution

Recent comprehensive transcriptome analyses in mice have revealed tremendous numbers of natural antisense transcripts in a hitherto ignored category of genes in eukaryotes. We discuss the possible biological roles of these transcripts and their relationships with mammalian sex chromosome evolution. Of 60,770 full-length cDNA sequences, as many as 2,500 pairs of sense-antisense transcripts (SATs) with the potential to form RNA duplex via their complementary sequences have been identified. This high number of antisense transcripts indicates their generic roles in gene expression regulation. These SATs are almost evenly distributed along the chromosomes, with the exception of the X chromosome. The rate of occurrence of SATs on the X chromosome is one-third to one-half that on the autosomes, and this under-representation must be related to a property intrinsic to the X chromosome. Here we hypothesize that monoallelically expressed antisense RNA regulates its sense partner, but that this regulatory system cannot operate on the mammalian X chromosome, as the mammalian X chromosome is effectively in a hemizygous state in both sexes. Loss of such regulation may be involved in the evolution of the X chromosome itself.

Expression of the GLI2 oncogene and its isoforms in human basal cell carcinoma

BACKGROUND

Mutations of the patched (Ptc) gene, a developmental regulator implicated in the signalling pathway via sonic hedgehog (Shh) and smoothened (Smo), play an essential pathogenic role in the development of basal cell carcinomas (BCCs). We previously reported the upregulation of Shh signal transducers, including Ptc, Smo and hedgehog-interacting protein, in BCCs. In vertebrates, specific downstream effectors in the Shh signalling pathway include three zinc-finger transcription factors, Gli1, Gli2 and Gli3. Gli1 possesses only an activation domain, while Gli2 and Gli3 contain both activation and repression domains. It remains unclear which of these transcription factors are responsible for the development of BCCs.

OBJECTIVES

To examine the expression pattern of Gli2 mRNA by human BCCs in comparison with those by normal human skin and various skin tumours.

METHODS

We performed quantitative reverse transcriptase-polymerase chain reaction analyses with a series of samples from BCCs, other skin tumours and normal skin.

RESULTS

We found that Gli2 mRNA expression was enhanced in the BCCs we examined, whereas there was no significant increase in other skin tumours or normal skin. Of four spliced Gli2 isoforms designated Gli2alpha, beta, gamma and delta, the expression of Gli2beta mRNA was increased the most in BCCs.

CONCLUSIONS

As Gli2beta is an isoform spliced at the first splicing site containing a repression domain and consists of an intact activation domain, its overexpression may lead to the upregulation of the Shh signalling pathway, thereby inducing BCCs.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Expression of a sonic hedgehog signal transducer, hedgehog-interacting protein, by human basal cell carcinoma

BACKGROUND

Aberrant activation of the hedgehog pathway has been identified in various human tumours, including familial and sporadic basal cell carcinomas (BCCs). It has been postulated that binding of sonic hedgehog protein (SHH) to its receptor, patched protein (PTC), releases the inhibitory effect of PTC against smoothened protein (SMO), another protein of the SHH signalling pathway. The positive SMO signalling is not downregulated in BCCs because of the mutational inactivation of PTC. Recently, hedgehog-interacting protein (HIP) was found to bind to SHH directly and attenuate SHH signalling like PTC, while its expression was induced by SHH signals.

OBJECTIVES

To examine the expression patterns of HIP, SHH and PTC gene mRNA by human BCCs, in comparison with those by normal human skin and various skin tumours.

METHODS

We performed quantitative reverse transcriptase-polymerase chain reaction analyses with a series of samples from BCCs, other skin tumours and normal skin.

RESULTS

We found that the mRNA expression of both HIP and PTC genes was enhanced in all samples of BCCs, whereas none of the other skin tumours tested exhibited an increased level of such mRNAs as compared with normal skin. The transcription of the SHH gene, however, was at a baseline level in most BCCs.

CONCLUSIONS

These results indicate that both HIP and PTC gene expression are specifically involved in the development of BCCs, and that the production of HIP is linked with the expression of the PTC gene but not the SHH gene.

Computational analysis of full-length mouse cDNAs compared with human genome sequences

Although the sequencing of the human genome is complete, identification of encoded genes and determination of their structures remain a major challenge. In this report, we introduce a method that effectively uses full-length mouse cDNAs to complement efforts in carrying out these difficult tasks. A total of 61,227 RIKEN mouse cDNAs (21,076 full-length and 40,151 EST sequences containing certain redundancies) were aligned with the draft human sequences. We found 35,141 non-redundant genomic regions that showed a significant alignment with the mouse cDNAs. We analyzed the structures and compositional properties of the regions detected by the full-length cDNAs, including cross-species comparisons, and noted a systematic bias of GENSCAN against exons of small size and/or low GC-content. Of the cDNAs locating the 35,141 genomic regions, 3,217 did not match any sequences of the known human genes or ESTs. Among those 3,217 cDNAs, 1,141 did not show any significant similarity to any protein sequence in the GenBank non-redundant protein database and thus are candidates for novel genes.

Functional annotation of a full-length mouse cDNA collection

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

Anti-tumor immunity against CT26 colon tumor in mice immunized with plasmid DNA encoding beta-galactosidase fused to an envelope protein of endogenous retrovirus

Endogenous retroviral gene products have been recognized as being expressed in human cancerous tissues. However, these products have not been shown to be antigenic targets for T-cells, possibly due to immune tolerance. Since carcinogen-induced colon tumor CT26 expresses an envelope protein, gp70, of an endogenous ecotropic murine leukemia virus that is comparable to human tumor-associated antigens, we examined whether a DNA vaccine containing the gp70 gene induces protective immunity against CT26 cells. Injection of mice with plasmid DNA (pDNA) encoding gp70 alone failed to induce anti-gp70 antibody (Ab) or anti-CT26 cytotoxic T lymphocyte (CTL) responses. However, immunization with pDNA encoding the beta-galactosidase (beta-gal)/gp70 fusion protein induced anti-gp70 Ab and anti-CT26 CTL responses and conferred protective immunity against CT26 cells. These results indicate that beta-gal acts as an immunogenic carrier protein that helps in the induction of immune responses against the poorly immunogenic gp70. Considering these results, it is possible that potential tolerance to the endogenous retroviral gene products expressed by human tumors may be overcome by DNA vaccines that contain an endogenous retroviral gene fused to genes encoding immunogenic carrier proteins.

Facilitated diagnosis of CMT1A duplication in chromosome 17p11.2-12: analysis with a CMT1A-REP repeat probe and photostimulated luminescence imaging

Charcot-Marie-Tooth disease type 1A (CMT1A) is a common autosomal dominant demyelinating peripheral neuropathy. Most patients with CMT1A have been found to have a 1.5 megabase tandem DNA duplication in chromosome 17p11.2-12. Meiotic unequal crossover mediated by the CMT1A-REP repeat is a proposed mechanism for generation of the duplication in CMT1A and a reciprocal deletion seen in hereditary neuropathy with liability to pressure palsies. Testing for the CMT1A duplication is frequently the first step in the molecular diagnosis of patients with suspected inherited demyelinating neuropathy. We used a 1.0 kb EcoRI-PstI DNA fragment (pHK1.0P) from the proximal CMT1A-REP repeat as a probe for Southern blot analysis and detected increased gene dosage in CMT1A by determining measuring radioactivity ratios with a photostimulated luminescence imaging plate. We found that this method is useful for rapid diagnosis of the DNA duplication associated with CMT1A.

YAC/BAC-based physical and transcript mapping around the gracile axonal dystrophy (gad) locus identifies Uchl1, Pmx2b, Atp3a2, and Hip2 genes

We generated a yeast artificial chromosome (YAC)/bacterial artificial chromosome (BAC)-based physical and transcript map of a region containing the gracile axonal dystrophy (gad) locus on mouse chromosome 5. The YAC/BAC contig consists of 13 YAC and 49 BAC clones onto which 4 genes, 40 expressed sequence tags, and 7 new DNA polymorphisms were ordered. Using this physical map, we mapped Uchl1 encoding ubiquitin carboxyl-terminal hydrolase I, whose deletion has been determined to cause the gad mutation. We also mapped three other recently identified genes: Hip2, encoding Huntingtin interacting protein 2; Atp3a2, encoding a P-type ATPase; and Pmx2b, encoding PHOX2b.

Intragenic deletion in the gene encoding ubiquitin carboxy-terminal hydrolase in gad mice

The gracile axonal dystrophy (gad) mouse is an autosomal recessive mutant that shows sensory ataxia at an early stage, followed by motor ataxia at a later stage. Pathologically, the mutant is characterized by 'dying-back' type axonal degeneration and formation of spheroid bodies in nerve terminals. Recent pathological observations have associated brain ageing and neurodegenerative diseases with progressive accumulation of ubiquitinated protein conjugates. In gad mice, accumulation of amyloid beta-protein and ubiquitin-positive deposits occur retrogradely along the sensory and motor nervous systems. We previously reported that the gad mutation was transmitted by a gene on chromosome 5 (refs 10,11). Here we find that the gad mutation is caused by an in-frame deletion including exons 7 and 8 of Uchl1, encoding the ubiquitin carboxy-terminal hydrolase (UCH) isozyme (Uch-l1) selectively expressed in the nervous system and testis. The gad allele encodes a truncated Uch-l1 lacking a segment of 42 amino acids containing a catalytic residue. As Uch-l1 is thought to stimulate protein degradation by generating free monomeric ubiquitin, the gad mutation appears to affect protein turnover. Our data suggest that altered function of the ubiquitin system directly causes neurodegeneration. The gad mouse provides a useful model for investigating human neurodegenerative disorders.

Expression of sonic hedgehog signal transducers, patched and smoothened, in human basal cell carcinoma

In basal cell nevus syndrome (BCNS) patients, mutations of a gene, patched (ptc), which encodes a putative signal transducer of sonic hedgehog protein (SHH), were found and are thought to be one of the major causes of BCNS. The SHH signaling pathway is an important developmental pathway, and ptc protein (PTC) is a suppressive component serving as a receptor for the secreted SHH. Another transmembrane protein, smoothened (SMO), forms a complex with PTC and regulates this signaling pathway. Recent transgenic studies have strengthened the importance of the SHH signaling system in the etiology of basal cell carcinoma (BCC). In this study, we examined the expression patterns of mRNA for ptc and smo in two different BCC subtypes and normal skin. We found that the expressions of ptc and smo mRNA were enhanced in the tumor nests of the nodular BCC, especially at the advancing portions, but were under the detectable level in the superficial BCC cases examined, indicating that ptc and smo mRNA expressions might be associated with BCC tumor progression and divide the BCC histologic types into two subtypes, superficial and nodular types. In addition, no obvious signals for ptc and smo mRNA were detected in the normal human epidermis, appendages, or seborrheic keratosis, indicating that the abnormal proliferation of follicular epithelial cells caused by ptc, smo and/or other genetic changes, which also cause ptc and smo overexpressions, might result in BCC tumor formation.

Identification of a novel gene, OASIS, which encodes for a putative CREB/ATF family transcription factor in the long-term cultured astrocytes and gliotic tissue

Gliosis is a characteristic response of astrocytes to inflammation and trauma of the central nervous system (CNS). To study the mechanisms underlying gliosis, we performed differential display screening for genes specifically induced in long-term cultured astrocytes used as an in vitro gliosis model. We identified and characterized a gene (named OASIS, for old astrocyte specifically-induced substance) expressed in long-term cultured mouse astrocytes, or 'old astrocytes (OA)'. The OASIS gene encoded a putative transcription factor belonging to the cyclic AMP responsive element binding protein/activating transcription factor (CREB/ATF) gene family, with homology to box B-binding factor-2 (BBF-2), a Drosophila transcription factor. Its expression was developmentally regulated; OASIS mRNA was primarily expressed in the salivary gland and cartilage in the mouse embryo and it was transiently upregulated in the brain during postnatal two weeks. The expression became weaker in the adult brain. We also demonstrated that an expression of the OASIS mRNA was induced in response to the cryo-injury of the mouse cerebral cortex. The distribution pattern of the OASIS-positive cells in the injured cortex was very similar to that of the glial fibrillary acidic protein (GFAP)-positive cells. These results suggest that OASIS protein may play a role in gliotic events.

Eos: a novel member of the Ikaros gene family expressed predominantly in the developing nervous system

We identified a novel member of the Ikaros gene family, which has critical roles in the development of lymphoid lineages. This gene, which we named Eos, was expressed predominantly in the developing central and peripheral nervous system. Eos protein could interact with itself and Ikaros protein through its C-terminal portion in the yeast two hybrid assay. These findings suggested that Eos may have important roles in neural development similarly to the Ikaros family in the development of hemolymphoid tissue.

Dictyostelium discoideum nuclear plasmid Ddp5 is a chimera related to the Ddp1 and Ddp2 plasmid families

The 14,955-bp Dictyostelium discoideum nuclear plasmid Ddp5 contains six transcribed open reading frames. One of these is related to the rep gene of the Ddp2 plasmid, and the other five are related to genes present on the Ddp1 plasmid. The absence of a homolog of the Ddp1 G1 gene, coupled with the presence of the Ddp2 rep gene homolog and of a 1.6-kb inverted repeat analogous to the inverted repeats on members of the Ddp2 plasmid family, suggests that Ddp5 uses Ddp2-like replication and copy number control mechanisms and that it should be assigned to the Ddp2 plasmid family. Ddp5 carries genes homologous to the D1/D3 and D2 genes of the Ddp1 plasmid as well as the Ddp1 G2/G3/D4, G5/D6, and G6/G4/D5 genes. The products of the Ddp5 G2-like, G5-like, and G6-like genes are likely to be transcription factors regulating the expression of themselves and of the other Ddp5 genes. The D1-like and D2-like genes may confer a selective advantage to plasmid-bearing cells, because they can be deleted from plasmid-based shuttle vectors with no apparent effect on vector maintenance. Updated sequence information for the Ddp1 G5/D6, D1/D3, and D2 genes as well as the Dmp1 and Dmp2 G5-like genes is presented. The locations of introns in the G5-like and D1-like genes of Ddp5 and in the homologous genes of the Ddp1, Dmp1, and Dmp2 plasmids were identified. These introns all have GU at the 5' intron border and AG at the 3' intron border, are short (59 to 71 nucleotides), and are AT-rich. A conserved HHCC domain was identified in the G5 proteins; this is a putative zinc binding domain and may be involved in protein-DNA interaction.

Ornithine decarboxylase overexpression in mouse 10T1/2 fibroblasts: cellular transformation and invasion

BACKGROUND

Ornithine decarboxylase (ODC) plays a pivotal role in the synthesis of polyamines, a group of chemical compounds that are essential for cell growth. Recent reports have shown that ODC overexpression may be involved in malignant transformation of immortalized NIH 3T3 cells. We have demonstrated that ODC-overproducing mouse breast cancer cells are more invasive in vitro than control cells. However, little information is available concerning the relationship between ODC overexpression, tumor invasion, and metastasis and the signal transduction pathways involved in ODC-induced transformation and invasion.

PURPOSE

Our purpose was twofold: 1) to determine whether ODC overexpression is directly involved in tumor cell invasion and 2) to determine whether ODC overexpression induces mitogen-activated protein (MAP) kinase activities that are associated with cell growth and transformation.

METHODS

We transfected C3H clone 8 mouse 10T1/2 fibroblasts with an expression vector that carries a complementary DNA encoding rat ODC. Neomycin-resistant cells that overproduced ODC (4-6.5 times the control levels) were isolated. The transformed phenotype of these cells was determined by assessing colony formation and anchorage-independent growth in soft agar. The invasiveness of the cells was studied by means of an invasion assay that used Matrigel-coated filters in Boyden chambers. The MAP kinase activity of the cells was assayed by an in-gel kinase assay, using myelin basic protein as the substrate.

RESULTS

Overexpression of ODC induced not only cell transformation and anchorage-independent growth in soft agar but also invasiveness through a Matrigel-coated filter. The ODC-overproducing transfectants showed enhanced MAP kinase activity that paralleled the magnitude of cell invasiveness.

CONCLUSIONS

ODC plays a pivotal role not only in cell transformation but also in cancer cell invasion. ODC overexpression enhanced MAP kinase activity.

IMPLICATIONS

Our results demonstrate a connection between the polyamine/ODC and the MAP kinase signal transduction pathways and suggest that MAP kinase may play a pivotal role in ODC-induced cell transformation and invasion.

Locations of crossover breakpoints within the CMT1A-REP repeat in Japanese patients with CMT1A and HNPP

The crossover breakpoints for Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP) are located in the CMT1A-REP repeat flanking a 1.5-Mb region of chromosome 17p11.2-12. The precise locations of the breakpoints are heterogeneous, and we analyzed the relative frequency distribution of breakpoints in 33 unrelated Japanese CMT1A and 3 unrelated HNPP families. The CMT1A-REP repeat region was divided into five regions, A, B, C, D and E, based on restriction site differences between the proximal and distal CMT1A-REP repeats. The frequency distribution of breakpoints within the CMT1A-REP repeat in the Japanese patients was 3% in region A, .78% in B/C and 19% in D, which is similar to that in Caucasian patients. This result also indicates that an 8-kb region defined by region B/C is a recombinational hotspot within the CMT1A-REP repeat in Japanese patients.

Bucillamine induced pulmonary injury occurs with immunoglobulin decrease

We describe pulmonary involvement in 3 patients with rheumatoid arthritis treated with bucillamine. In all 3, synovitis was in remission. The common radiological characteristic was mottled dense infiltrates, in which were air bronchograms, in the bilateral central lung, sparing the periphery. Lung biopsies in 2 cases revealed organizing exudates in the alveolar ducts and alveoli, and cellular infiltration into alveoli and septa. Serum immunoglobulin (Ig) levels decreased markedly at the time of involvement. After discontinuation of bucillamine, lung injury resolved without exacerbation of synovitis and Ig levels increased. A mechanism involving decreased Ig concentration is suggested.

Primate origin of the CMT1A-REP repeat and analysis of a putative transposon-associated recombinational hotspot

The CMT1A-REP repeat on chromosome 17p11.2-12 is proposed to mediate misalignment and meiotic unequal crossover leading to a 1.5 Mb pair duplication associated with Charcot-Marie-Tooth neuropathy type 1A (CMT1A) and a reciprocal deletion associated with hereditary neuropathy with liability to pressure palsies (HNPP). Restriction enzyme endonuclease mapping indicated that the size of the CMT1A-REP repeat is approximately 24 kb and DNA sequence analysis determined that the repeat is flanked by inverted Alu sequences. Full length Alu sequences are present at the centromeric ends of the proximal and distal CMT1A-REP repeats and at the telomeric end of the distal repeat. A truncated Alu sequence is present at the telomeric end of the proximal repeat suggesting that the distal CMT1A-REP repeat is the progenitor copy. The crossover breakpoints for a series of unrelated CMT1A and HNPP patients were mapped using a variant SacI site found only in the proximal CMT1A-REP repeat. Seventy-six percent (66/85) of patients had breakpoints which mapped to a 3.2 kb interval, providing further evidence for a recombinational hotspot within the CMT1A-REP repeat. A mariner-like element was mapped within the CMT1A-REP repeat approximately 700 bp centromeric to the 3.2 kb interval containing the hotspot. Analysis of this sequence suggested that it does not encode a functional transposon. By Northern blot analysis a cloned fragment from the CMT1A-REP repeat containing the mariner-like sequence detected a 2.2 kb transcript only in testis. Two cDNA clones which contain the mariner-like element were isolated from a human testis cDNA library. These clones which are interrupted by Alu and other repeats appear to be non-functional versions of the transposon. The functional relationship of the mariner-like element to the recombinational hotspot remains unknown. The origin of the CMT1A-REP repeat was investigated through an analysis of homologous sequences in non-human primates. Southern blot analysis indicated that the chimpanzee has two copies of a CMT1A-REP-like sequence, whereas gorilla, orangutan, and gibbon have a single copy. A high degree of conservation amongst non-human primates for restriction fragments specific to the human distal CMT1A-REP repeat provides further evidence that the distal repeat is the progenitor copy. The mariner-like sequence was detected in association with the CMT1A-REP sequence in all primates studied suggesting that the mariner-like element was introduced into the progenitor CMT1A-REP sequence prior to emergence of the proximal and distal CMT1A-REP repeats. These observations suggest that CMT1A-REP sequence appeared as a repeat before the divergence of chimpanzee and human, but after gorilla and human around 6 to 7 million years ago.

Analysis of the CMT1A-REP repeat: mapping crossover breakpoints in CMT1A and HNPP

The CMT1A-REP repeat sequence flanks a 1.5 megabase pair (Mb) segment of chromosome 17p11.2-12 which is duplicated in Charcot-Marie-Tooth neuropathy type 1A (CMT1A) and deleted in hereditary neuropathy with liability to pressure palsies (HNPP). The CMT1A-REP repeat is proposed to mediate misalignment and unequal crossover resulting in reciprocal chromosomal rearrangements in CMT1A and HNPP. We have constructed a physical map of the proximal and distal CMT1A-REP repeats. Cloned fragments from CMT1A-REP repeat regions are used to determine the size of the repeats and assess regions of homology. The crossover breakpoints were mapped in series of 30 unrelated CMT1A patients and 22 unrelated HNPP patients. The CMT1A-REP repeat spans approximately 27 kilobase pairs and appears to be continuous. Locations of restriction enzyme sites are highly conserved for the proximal and distal CMT1A-REP repeats. All crossovers mapped within the CMT1A-REP repeat sequence and heterogeneity for breakpoint location demonstrated. Seventy-seven percent (40 to 52) of CMT1A and HNPP chromosomes contained breakpoints which mapped within a 7.9 kb interval, suggesting the presence of a possible 'hotspot'for recombination in CMT1A-REP. DNA sequence analysis for 4 kb of the interval containing the majority of crossovers revealed over 98% sequence identity between proximal and distal CMT1A-REP repeat sequences. Probes useful for molecular-based diagnosis of CMT1A and HNPP are described.

The replication origin position and its relationship to a negative trans-acting transcription regulator encoded by Dictyostelium discoideum nuclear plasmid Ddp1

The replication origin of the Dictyostelium discoideum plasmid Ddp1 was localized to a 543-bp region. This includes most of the AT-rich intergenic region between the G1 and G5/D6 genes containing both of their promoters and multiple copies of a TTTTGACT repeat. The G5/D6 gene, which lies adjacent to, and partially overlaps, the 543-bp origin region, encodes a trans-acting factor that negatively regulates transcription of the G4/D5 gene. Inactivation of the G5/D6 gene led to expression of a transcript (G6) 0.2 kb larger than the D5 transcript from the G4/D5 gene in vegetative and developing cells. The G5/D6 gene also regulates transcription of the G1, G2/G3/D4 and G5/D6 genes either alone or in concert with other Ddp1 gene products.

Plasmid maintenance functions encoded on Dictyostelium discoideum nuclear plasmid Ddp1

All of the plasmid-carried genes expressed during vegetative growth are essential for long-term maintenance of plasmid Ddp1 in the nucleus of Dictyostelium discoideum. Deletion of Ddp1 genes expressed only during development had no detectable effect on plasmid maintenance. Deletion of vegetatively expressed genes, either singly or in pairs, resulted in (i) a rapid loss of plasmid from cells grown in the absence of selection for plasmid retention, (ii) variation in the proportion of monomer to multimer forms of the plasmid molecules, and/or (iii) abnormalities in plasmid copy number. At least two plasmid-encoded gene products influence patterns of expression of plasmid genes.

Compatible Dictyostelium mucoroides nuclear plasmids Dmp1 and Dmp2 both belong to the Ddp1 plasmid family

Dictyostelium mucoroides plasmids Dmp1 and Dmp2 are naturally occurring compatible members of the Dictyostelium Ddp1 plasmid family found in the same wild isolate strain. The nucleotide sequences of Dmp1 (5983 bp) and Dmp2 (6018 bp) are 74% identical and each carries open reading frames (ORFs) similar to the G1 and G5 ORFs of the Dictyostelium discoideum plasmid Ddp1. The predicted protein product of the Ddp1 G1 ORF is 49% similar to that of the Dmp1 G1-like ORF and 52% similar to that of the Dmp2 G1-like ORF. For the G5 and G5-like ORFs the corresponding values are 47 and 43%, respectively. The G1 and G5 ORFs of Ddp1 are transcribed during both vegetative growth and development of the asexual fruiting body. The G1-like ORF of Dmp2 is expressed in vegetative and developing cells, while that of Dmp1 appears to be expressed mostly in developing cells. The G5-like ORFs of Dmp1 and Dmp2 are expressed in both vegetative and developing cells. Dmp1 and Dmp2 differ from Ddp1 in (1) lacking homologs for the Ddp1 G2/G3/D4, G4/D5, D1/D3, and D2 ORFs; (2) containing multiple copies of a 173 bp direct repeat; and (3) having a different orientation of the G1 ORF relative to the G5 ORF. These findings suggest that the basic replicon unit of the Ddp1 plasmid family is composed of an origin of replication coupled to G1-like and G5-like genes. The additional ORFs and direct repeat elements in Ddp1, Dmp1, and Dmp2 may provide accessory functions beneficial to plasmid maintenance. Shuttle vectors based on Dmp1 or Dmp2 replicate in D. discoideum transformants.

Nucleotide sequence of Ddp1, a high copy number nuclear plasmid of Dictyostelium discoideum

The complete nucleotide sequence of Ddp1, a high copy number 13.7-kbp endogenous nuclear plasmid of Dictyostelium discoideum is presented. Previous studies have shown nine transcripts which map to five different regions of Ddp1, suggesting alternative transcription initiation sites and/or post-transcriptional processing. The sequence presented here shows five long open reading frames corresponding to previously known transcribed regions, as well as an additional reading frame, in the region of the presumed origin of replication. Two of the predicted proteins from the Ddp1 reading frames have potential leader sequences and transmembrane domains, while the rest, if translated, would encode soluble proteins. One of these has both leucine zipper and zinc finger-like motifs. Sequences upstream of the reading frames show strong similarities to chromosomal promoter elements, suggesting that transcription of at least some of the plasmid-encoded genes is regulated by factors which regulate chromosomal transcription in this organism. The region containing the presumptive origin of replication contains the promoters of the major growth-specific gene, as well as a second gene; thus, the processes of transcription and replication of Ddp1 may be intimately linked. The origin-encompassing region has a long homopurine/homopyrimidine stretch, which is similar to sequences shown in vitro to be capable of forming a triple helix structure through Hoogsteen base pairing. Possible roles for these sequences and the products of the ORFs in plasmid maintenance are discussed.

Small circular plasmids of the eukaryote Dictyostelium purpureum define two novel plasmid families

Two novel groups of circular, nuclear plasmids were discovered in the simple eukaryote Dictyostelium purpureum. They define two new Dictyostelium plasmid families each containing three members: Dpp1A, Dpp1B, and Dpp2 in the Dpp1 family, and Dpp3, Dpp4, and Dpp5 in the Dpp3 family. These plasmids are among the smallest known, ranging in size from 1309 bp (Dpp1A and Dpp1B) to 1961 bp (Dpp4). Family members are very similar. The most distantly related members of the Dpp1 family (Dpp1A and Dpp2) are 89% identical, while the most distantly related members of the Dpp3 family (Dpp3 and Dpp4) are 91% identical. No sequence similarity is found between these plasmid families, or to any other known plasmid or chromosomal DNA sequence. A 72-bp inverted repeat present in one copy in Dpp1A and Dpp1B is tandemly repeated in Dpp2. The Dpp3 family contains a region of 102-160 nucleotides rich in short, overlapping direct sequence repeats. This region is present once in Dpp3 and Dpp5 and is tandemly repeated in Dpp4. The repeat structures in the Dpp1 and Dpp3 families are relatively rich in GC base pairs (29-41%) in comparison to the unique sequence regions of the plasmids (16-22%). The longest open reading frame (ORF) beginning with an AUG codon in these plasmids is 168 bp in the Dpp3 family, although longer ORFs without AUG start codons (up to 201 bp) also exist. Northern blot analysis did not detect any plasmid-specific transcripts in total RNA prepared from vegetative cells carrying Dpp1A or Dpp3.

[Immunoglobulin decrease accompanying adverse reactions with bucillamine]

Forty-two RA patients treated with Bucillamine (B) were divided into two groups with (n = 26) and without (n = 16) adverse reactions, and IgG, M, A and total protein concentration x globulin ratio (Ig) before and after B were compared. IgG did not differ before B administration, but was significantly lower in the adverse reactions group after B, and in each group it was significantly lower after B treatment with a much greater decrease demonstrated in the adverse reactions group. IgA before B did not differ either between the two groups or between before and after B administration in the non-adverse reaction group, but was significantly lower only after B in the adverse reaction group. IgM did not differ either before or after B treatment between the two groups, and was significantly lower following B administration in both groups. Ig showed results similar to IgA. In the adverse reaction group, IgG, A, M and Ig recovered following suspension of administration. It is concluded that the adverse reaction brought on by B administration might occur with the decrease in immunoglobulin.

Circadian variations of acute toxicity and blood and brain concentrations of inhaled toluene in rats

To investigate circadian variations in the acute toxicity of toluene, rats were exposed to it (2000 ppm or 4000 ppm) both in the dark (the animals' active phase) and the light (the inactive phase) for 4 hours. The performance decrements of rats were greater in the light phase than in the dark phase in all time zones of exposure to toluene. In the dark phase, the performance recovered almost to that pre-exposure, whereas a significant delay of recovery was noted in the light phase. The differences in the number of lever presses between exposure to 2000 ppm toluene and control (air) exposure were also greater in the light phase than in the dark phase. Significant differences according to the time of exposure were also found in toluene concentrations in blood and the brain. Both blood and brain concentrations in the light phase were higher than those in the dark phase at four hours after exposure to 2000 ppm toluene or at two hours after exposure to 4000 ppm toluene. These results suggest that there was a significant difference in circadian susceptibility after exposure to toluene, which might be caused by circadian differences in the pharmacokinetics of toluene in the light and dark phases.

DNA strand cleavage at 8-hydroxyguanine residues by hot piperidine treatment

The two findings indicate that 8-hydroxyguanine(8-OH-Gua) is a hot piperidine-sensitive lesion in DNA. These are cleavages of DNA containing 8-OH-Gua at the site of this residue and decomposition of 8-hydroxydeoxyguanosine when the DNA and nucleoside were treated in 1 M piperidine for 30 min at 90 degrees C. However, no cleavage was observed in DNA containing 8-hydroxyadenine or O6-methylguanine. 8-OH-Gua was found to be different from apurinic sites that are also alkali-labile lesions since the former was more resistant to alkali treatment. This property of 8-OH-Gua can be used as a check for the incorporation of this base into DNA after the synthesis of DNA containing 8-OH-Gua at a specific position or possibly can be one of the markers for the identification of 8-OH-Gua formed in DNA exposed to reactive oxygen species.

[A case of asymptomatic endobronchial lipoma followed for 4 years]

Bronchoscopy was performed on a 68-year-old male patient with pulmonary tuberculosis, and revealed a yellow smooth polypoid tumor in the lumen of the left upper division bronchus. The histopathological diagnosis of the biopsy specimen was endobronchial lipoma. Since the patient did not have any symptoms due to the lipoma, we performed treatment for tuberculosis and continued careful observation of the tumor. During the subsequent 4 years, the patient developed no complications such as obstructive pneumonia, and the size of the tumor under bronchoscopic observation did not change. Endobronchial lipoma is a very rare benign tumor. Almost all reported cases have undergone operation or endoscopic surgery. This case is the first that was followed over 4 years without surgical procedure. The findings of follow-up bronchoscopic examination suggest that the growth rate of endobronchial lipoma is very slow. Furthermore, we reviewed 36 cases of endobronchial lipoma in the Japanese literature, including our case. Smoking seems to have a strong relation to the occurrence of the tumor. It is noteworthy that 6 cases had separate malignancies, but the direct relationship between endobronchial lipoma and such malignancies is unclear.

Cigarette smoking induces formation of 8-hydroxydeoxyguanosine, one of the oxidative DNA damages in human peripheral leukocytes

Active oxygen species (AOS) such as O2- and H2O2 have been shown to be generated from both gas and tar phases of cigarette smoke and it has been suggested that they are involved in carcinogenesis due to cigarette smoking. Therefore, we investigated the effect of cigarette smoking on oxidative DNA damages in human peripheral blood cells using 8-hydroxydeoxy-guanosine (8-OH-dG) as a marker. From ten healthy male volunteers aged 20-22 years, 5 ml of blood was taken before and 10 minutes after smoking 2 cigarettes in 10 minutes. After lysis of blood cell membranes leukocyte DNA was isolated using a DNA extractor and 8-OH-dG levels were determined using high performance liquid chromatography (HPLC) with electrochemical detection. The mean levels of 8-OH-dG increased significantly (P less than 0.05) from 3.3 +/- 0.8/10(6) dG (mean +/- SD) to 5.1 +/- 2.5 after smoking. These results indicate that cigarette smoking induces oxidative DNA damage in peripheral blood cells in a relatively short time.

Decrease of serum triglyceride in normal rats fed with 2000 ppm aluminum diet for 67 days. I. Feeding young rats sucrose, lactose, milk, casein or soy-protein diets with addition of aluminum chloride

Aluminum (Al) compounds are widely used in drugs and food additives but the toxicity of such compounds is not known in detail except in patients with renal insufficiency (J. W. Coburn and A. C. Alfrey, 1986, Kidney Int. 29, Suppl. 18). In this experiment, toxicity of ingested Al was investigated in relation to nutritional conditions in normal rats having no renal insufficiency. Sucrose, lactose, milk, casein and soy-protein diets were prepared. As the Al source, aluminum chloride (AlCl3) was added to these diets at the level of 2000 micrograms/g (ppm). Male weanling Wistar rats were fed for 67 days without any Al effect on body weight gain. After a half-day starvation they were terminated. The significance of difference resulting from Al treatment was statistically tested between rats consuming diet with or without added Al. Serum Al concentrations did not exceed 20 ng/ml in any of the groups. Tibia Al concentration doubled in rats consuming added Al in every diet but lactose. Liver Al concentration increased significantly in the Sucrose, Milk, and Casein groups compared to each Control group consuming diet without addition of Al. No lactose effect on Al accumulation was observed. With Al treatment, anemia and hypophosphatemia were not observed, but a decrease in tibia weight was observed with every diet. Aluminum-dependent decreases in serum triglyceride (TG) concentration were also observed in all dietary groups, without any effect on serum cholesterol or phospholipid (P-lipid) concentrations.(ABSTRACT TRUNCATED AT 250 WORDS)

Decrease of serum triglyceride in normal rat fed with 2000 ppm aluminum diet for 67 days. II. Feeding young and adult rats a sucrose diet with addition of aluminum hydroxide and aluminum potassium sulfate

To confirm the hypotriglyceridemic effect of aluminum (Al), male weanling and adult Wistar rats were fed sucrose diets with the addition of aluminum hydroxide (Al(OH)3) or aluminum potassium sulfate (AlK(SO4)2) for 67 days. As in the foregoing report (C. Sugawara, N. Sugawara, H. Kiyosawa, and H. Miyake, Fundam. Appl. Toxicol. 10, 607-615), no Al-induced anemia or hypophosphatemia was observed and serum Al did not exceed 20 ng/ml. Serum triglyceride (TG) was decreased by aluminum. Serum TG was significantly correlated with the serum nonesterified fatty acid (NEFA) concentration in both the Young groups (R = 0.757, n = 22, p less than 0.01) and the Adult groups (R = 0.727, n = 19, p less than 0.01). Neither serum cholesterol nor phospholipids was affected by Al ingestion. Aluminum caused a decrease in hepatic glycogen in all groups, but the decrease was significant only in Adult groups. Glycerol tri[9,10(n)-3H]oleate was administered by gastric tube into rats fed for 81 days with experimental diets. In all the Al-treated groups serum 3H was significantly greater than in control groups at 3 hr after intubation. At 24 hr after intubation, serum 3H did not differ between Control and Al-treated groups. Total 3H at 24 hr found in serum, liver, and epididymal adipose tissue was not changed significantly by Al feeding. These effects were observed without measurable increase of Al in the serum.(ABSTRACT TRUNCATED AT 250 WORDS)

[Dietary vitamin intake and cancer]

We collected information on dietary intake from 9230 participants aged 40 years old or more by means of self-administered food frequency questionnaire in Fujieda city in order to conduct prospective study to examine the relationship between dietary VA, C and carotene intakes and subsequent risk of cancer in August 1985. To estimate VA, C, and carotene intakes from this questionnaire we multiplied food frequency scores for individual items (25 foods rich in VA, C, and carotene) by the nutrient contents of the standard portion, after adjustments were made for the seasonal availability of some foods.

Effect of skim milk and yogurt on serum lipids and development of sudanophilic lesions in cholesterol-fed rabbits

Three groups of male Japanese rabbits weighing about 2.7 kg each were given experimental diets consisting of high cholesterol food and fluid skim milk, yogurt, or water, and were bled every 4 wk to measure serum lipids. After 12 wk they were killed and concentrations of total cholesterol and atheromatous areas dyed with Oil Red O were determined in the aorta to evaluate the development of atherosclerosis. At 8 and 12 wk, the skim milk group showed significantly lower levels of serum total cholesterol, low-density lipoprotein cholesterol, and triglyceride than the control group. Although no significant difference between the yogurt and control groups in the concentration of serum lipids was observed, total cholesterol concentrations in the aorta were significantly lower in both the skim milk and the yogurt groups than in the control group. The atheromatous areas of the skim milk group (38 +/- 34%) were significantly smaller than those of the control group (75 +/- 25%). Significant difference, however, was not found between the yogurt group (51 +/- 22%) and the control group. Concentrations of total cholesterol in the liver did not differ among the three groups. These results suggest that skim milk may have a preventive effect on the development of atherosclerosis.

[A chronobiological study on toluene anesthesia in mice]

An experimental study of toluene exposure was performed on mice at various times of the day using the righting reflex and blood concentration as indicators. One hundred and sixty ICR mice were housed 8 mice per cage for 3 weeks with free access to food and water under a dark-light cycle consisting of alternate 12 hr periods of darkness and light: the dark period beginning at 7:00. The exposure was begun when the mice were 8 weeks old. They were exposed to 10,000 ppm of toluene for 40 min at 4:00, 10:00, 16:00 and 22:00, and they were sacrificed at the end of the exposure, after 3 min or after 30 min. The duration of anesthesia was 200.2 +/- 15.4 (sec) at 4:00, 361.1 +/- 21.5 (sec) at 10:00, 335.1 +/- 18.5 (sec) at 16:00 and 309.2 +/- 19.8 (sec) at 22:00. The duration of anesthesia at 4:00 was shorter than that of the other times of the day statistically (p less than 0.01). With regard to the toluene concentration in blood, there was no significant difference between those mice sacrificed at the end of exposure and those sacrificed after 3 min.

Case-control study of ovarian cancer in Japan

A case-control study of 80 women with ovarian epithelial carcinoma and 160 individually age-matched controls were conducted to assess various factors associated with the incidence of ovarian cancer in Hokkaido, Japan. Among the characteristics studied, the following factors were significantly greater in the cases than in the controls: (1) blood group A; (2) never married or married late in life; (3) more frequent surgery for retroflexion of the uterus; (4) less use of contraceptive appliances; and (5) less daily use of cosmetics. It was inferred from these observations that ovarian cancer patients had a genetic predisposition and dysfunctional ovaries. Gonadal dysfunction among ovarian cancer patients presumably explained not only altered personality and behavior patterns, but also facilitated the pituitary gonadotropin activity which has been suggested as increasing the incidence of the disease experimentally.

Effects of trichloroethylene exposure on hearing. An investigation of cochlear microphonics and action potential of the guinea pig

Four groups of guinea pigs with normal Preyer's reflex were exposed to trichloroethylene (TCE). Each group consisted of nine to 10 naive male albino Hartley guinea pigs of 9 weeks of age with a body weight of approximately 400 g. To test the suggestion that TCE causes damage to the cochlear system, a study was conducted involving four experiments. The results were as follows: No significant difference was observed between the intensity functions of the CM (4 kHz) and AP (7 kHz) potentials of the control groups and those of the TCE-exposed groups by analysis of variance. It was considered that there was no difference in the cochlear reaction to high frequency sound between guinea pig and man. It therefore might be suggested that acute exposure to TCE of a high concentration does not always induce dysfunction of the organ of Corti and the 8th nerve in man.