bluuebunny/crossref_metadata_2025 huggingface dataset:
Generation of mouse chromosome painting probes by DOP-PCR amplification of microdissected meiotic chromosomes
Authors: Xiao Y. , Darroudi F. , Kuipers A.G.J. , de Jong J.H. , de Boer P. , Natarajan A.T.
Published: May 2008

We describe here the development of four sets of painting probes for mouse chromosomes 1 and 13, 2 and 8, 6 and 15, and X and Y by degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) amplification of 10–20 copies of microdissected male meiotic chromosomes. The XY probe was obtained from the X-Y bivalent of diakinesis/metaphase I complements of mice with a normal karyotype, whereas the other probes were derived from tri- or quadrivalents in diakinesis/metaphase I of two reciprocal translocations, T(1;13)70H and T(2;8)2Wa, and one inversion heterozygote carrying a small deletion, In(6;15)Rb1A1d de1615 1Wa. The specificity of these probes was established by fluorescence in situ hybridization (FISH) to meiotic and mitotic metaphase complements. The chromosomes painted by these probes could be identified by single or multicolor FISH.
In vivo cytogenetic damage revealed by FISH analysis of micronuclei in uncultured human T lymphocytes
Authors: Surrallés J. , Falck G. , Norppa H.
Published: May 2008

FISH analysis of micronuclei in uncultured human T lymphocytes provides a convenient new possibility to assess structural and numerical chromosome damage in vivo. In women, T-cell micronuclei mostly contained whole chromosomes (71.6 %), especially the X chromosome (28.5%). Cell culture (72 h) enhanced the frequency of micronuclei harboring sacentric fragments 2.9 fold and the X chromosome 1.5 fold. X-chromosome-positive micronuclei were particularly prevalent (42.0%) in binucleate cells produced by cytochalasin B, a cytokinesis inhibitor used to identify cells that have divided in vitro. This was explained by a decrease in autosome-containing and an increase in X-positive micronuclei.
Application of micro-FISH to delineate deletions
Authors: Engelen J.J.M. , Albrechts J.C.M. , Loots W.J.G. , Hollanders-Crombach B.H.T.M. , Hamers A.J.H. , Geraedts J.P.M.
Published: May 2008

Microdissection combined with fluorescence in situ hybridization (micro-FISH) was used to visualize deletions in rearranged human chromosomes and in a de novo translocation. In each experiment five copies of a structurally aberrant chromosome or of the two chromosomes involved in the de novo translocation were isolated by microdissection and amplified using DOP-PCR. The PCR products were then used as probes for FISH to metaphase chromosomes of three patients. After reverse chromosome painting, the structurally aberrant chromosomes were completely painted, and the region deleted in the aberrant chromosomes was visible in the normal chromosomes. The smallest deletion that could be demonstrated this way was a microdeletion of ∼6 × 106 bp, which is frequently reported in Angelman and Prader-Willi syndromes.
Complementary replication R- and G-band patterns induced by cell blocking at the R-band/G-band transition, a possible regulatory checkpoint within the S phase of the cell cycle
Authors: Fetni R. , Drouin R. , Richer C.-L. , Lemieux N.
Published: May 2008

The characteristic band patterns of replication banding (dynamic banding) were analyzed. High-resolution (550–1,250 bands per haploid genome) G- and R-band patterns were obtained after 5-bromo-2’-deoxyuridine (BrdU) incorporation during early or late S phase. Thymidine-BrdU permutation culture methods, which arrest DNA synthesis at the R-band/G-band transition, allow complementary BrdU substitution. The RBI (R bands by BrdU using immunological staining) and GBI (G bands by BrdU using immunological staining) band patterns were complementary for all chromosomes. There was no overlapping, and every part of each chromosome was positively stained by one of the two banding procedures. Cornparative analysis of RBG (R bands by BrdU using Giemsa staining) and RBI band patterns, as well as GBG (G bands by BrdU using Giemsa staining) and GBI band patterns, showed good congruency, displaying a very good band-for-band match. The congruency and complementarity found for these band patterns show that high concentrations of both thymidine and BrdU blocked S-phase progression near the R-band to G-band replication transition within the S phase. They also prove that BrdU incorporation is complementary and, therefore, demonstrate the existence of the R/G transition; a possible regulatory checkpoint within the S phase of the cell cycle.
Genomic localization of the human gene encoding Dr1, a negative modulator of transcription of class II and class III genes
Authors: Purrello M. , Di Pietro C. , Rapisarda A. , Viola A. , Corsaro C. , Motta S. , Grzeschik K.-H. , Sichel G.
Published: May 2008

Dr1 is a nuclear protein of 19 kDa that exists in the nucleoplasm as a homotetramer. By binding to TBP (the DNA-binding subunit of TFIID, and also a subunit of SL1 and TFIIIB), the protein blocks class II and class III preinitiation complex assembly, thus repressing the activity of the corresponding promoters. Since transcription of class I genes is unaffected by Drl, it has been proposed that the protein may coordinate the expression of class I, class II and class III genes. By somatic cell genetics and fluorescence in situ hybridization, we have localized the gene (DRl), present in the genome of higher eukaryotes as a single copy, to human chromosome region 1p21→p13. The nucleotide sequence conservation of the coding segment of the gene, as determined by Noah’s ark blot analysis, and its ubiquitous transcription suggest that Drl has an important biological role, which could be related to the negative control of cell proliferation.
Isolation of 45 exon-like fragments from 8p22→p21.3, a region that is commonly deleted in hepatocellular, colorectal, and non-small cell lung carcinomas
Authors: Chinen K. , Isomura M. , Izawa K. , Fujiwara Y. , Ohata H. , Iwamasa T. , Nakamura Y.
Published: May 2008

The loss of heterozygosity that is frequently observed at chromosome 8p22→p21.3 in hepatocellular carcinomas (HCC), colorectal cancers (CRC), prostate cancers (PRC), and non-small cell lung cancers (NSCLC), suggests the presence there of one or more tumor suppressor genes associated with development and/or progression of these types of carcinomas. We have constructed a cosmid contig map of the target region by means of Southern hybridization and have isolated 45 exon-like fragments by exon amplification, using cosmid clones derived from three yeast artificial chromosomes (YACs). The map and the exon-like fragments reported here will be useful resources for isolation of the putative tumor suppressor gene(s) as well as other novel genes located in the 8p22→p21.3 region.
Molecular analysis of the genomic structure of the human Y chromosome in the euchromatic part of its long arm (Yq11)
Authors: Kirsch S. , Keil R. , Edelmann A. , Henegariu O. , Hirschmann P. , LePaslier D. , Vogt P.H.
Published: May 2008

Conventional methods of long range restriction mapping for analysis of the genomic DNA structure failed in Yql 1, because single-copy DNA probes for blot hybridization analyses are rare and the rate of DNA methylation is high in this Y region. Numerous repetitive sequence blocks of unknown extensions are scattered throughout Yql 1 and a patchwork of X-Y homologous DNA blocks were found by different investigators. Therefore, our approach towards a molecular analysis of this Y region reduced this complexity by performing first its molecular analysis in YAC clones mapping to Yq11. YACs contain only a part of the whole Yq11 DNA structure. In this paper, we present our first results of this approach based on quantitative blot analysis of 51 DNA loci in 67 YAC clones. The YACs were isolated from the three CEPH libraries and mapped to a contig of 13 Mb from proximal to distal Yq11 with aid of a detailed interval map. In distal Yq11, our analysis revealed the presence of local amplification events of different DNA domains. A model of their possible arrangement is presented.
Isolation of cosmids corresponding to the chromosome breakpoints of a de novo autosomal translocation, t(6;19)(p21;q13.1), in a patient with multicystic renal dysplasia
Authors: Groenen P.M.A. , Garcia E. , Thoelen R. , Aly M. , Schoenmakers E.F.P.M. , Devriendt K. , Fryns J.P. , Van de Ven W.J.M.
Published: May 2008

Hydronephrosis caused by pelvi-ureteric junction obstruction (PUJO) is a frequent urological malformation assumed to result from a deficient development of the ureteric bud. The exact etiology of pelvi-ureteric junction stenosis is unknown, but there is convincing evidence for a genetic cause, with linkage analysis predicting a hereditary hydronephrosis locus on chromosome 6p. We encountered a patient with a de novo autosomal t(6;19)(p21;q13.1) and attendant bilateral multicystic renal dysplasia (MRD), bilateral PUJO resulting in massive hydronephrosis, and an associated von Mayer-Rokitansky-Küster disorder. On the basis of the presumption that in this patient the putative hydronephrosis gene might be disrupted by the translocation, we sought to isolate DNA from the breakpoint regions as the initial step in a strategy to identify genes affected by the t(6;19). Using sequential rounds of fiuorescence in situ hybridization (FISH) with cosmids selected from a detailed integrated map of the long arm of chromosome 19, we have identified a cosmid clone that spans the breakpoint. The position of the breakpoint was further localized by Southern blot analysis. Using a vectorette PCR approach, rearranged DNA fragments were isolated and, by comparative nucleotide sequence analysis, these were shown to contain ectopic sequences. A cosmid clone containing these ectopic sequences was isolated and shown by CASH (chromosome assignment using somatic cell hybrids) and FISH (fluorescence in situ hybridization) analysis to map to the short arm of chromosome 6 and to span the breakpoint found in the MRD patient. The isolated cosmid clones are useful reagents for analysis of other MRD patients and for the search for genes at or flanking the breakpoints.
A pseudogene for the human ribosomal protein L5 (RPL5P1) maps within an intron of the SNRPN transcription unit on human chromosome 15
Authors: Buiting K. , Kaya-Westerloh S. , Horsthemke B.
Published: May 2008

The ribosomal protein genes are members of multigene families, most of which are processed pseudogenes. Here we report that an intronless pseudogene for the L5 ribosomal protein maps within an intron of the SNRPN transcription unit on human chromosome 15. The pseudogene (RPL5P1) shares 95% sequence homology with the L5 mRNA, has a poly (A) stretch and is flanked by direct repeats.
Assignment of the human proprotein convertase gene PCSK5 to chromosome 9q21.3
Authors: van de Loo J.-W.H.P. , Creemers J.W.M. , Kas K. , Roebroek A.J.M. , Van de Ven W.J.M.
Published: May 2008

The human PCSK5 gene, which encodes a subtilisin-like proprotein processing enzyme, has been mapped by analysis of somatic cell hybrids and YAC clones as well as fluorescence in situ hybridization to chromosome 9q21.3 near markers D9S175 and D9S276.
A novel multicolor hybridization scheme applied to localization of a transcribed sequence (D10S170/H4) and deletion mapping in the thyroid cancer cell line TPC-1
Authors: Jossart G.H. , O’Brien B. , Cheng J.F. , Tong Q. , Jhiang S.M. , Duh Q. , Clark O.H. , Weier H.-U.G.
Published: May 2008

The sequence-tagged site (STS) D10S170, also referred to as H4, is a gene of unknown function. Its 5’ end was found fused to the catalytic domain of the RET protooncogene to generate RET/PTC1, the most common form of PTC onco-genes in human papillary thyroid carcinoma. This gene has previously been assigned to a very large genomic region, 10q11.22→q22.1. Here, we describe the application of a novel hybridization scheme to the physical and genetic mapping of D10S170. First, we selected a homologous large-insert DNA clone from a human P1 library by filter hybridization and confirmed its authenticity by Southern blot analysis. Triple-color fluorescence in situ hybridization (FISH) experiments mapped this clone to 10q21.2→q21.3. “Binning” experiments were performed using a quadruple-color FISH approach aimed toward placing the gene in a genetic interval defined by differentially labeled P1 DNA probes containing known polymorphic markers. We found that multicolor FISH greatly expedites chromosomal mapping. Finally, we applied our FISH approach to determine the extent of deletion involving this locus (D10S170) in a papillary thyroid cancer cell line, TPC-1.
AZT induces high frequency, rapid amplification of centromeric DNA
Authors: Parra I. , Flores C. , Adrian D. , Windle B.
Published: May 2008

The reverse transcriptase inhibitor 3’-azido-deoxythymidine (AZT) has previously been shown to be incorporated into specific regions near the telomeres and centromeres of Chinese hamster ovary cell chromosomes. Our investigation of the effects of AZT on chromosome stability has led to the discovery of a high frequency amplification of telomere-like centromeric DNA. The amplified structures, when analyzed cytogenetically, appear as tandem arrays of tightly clustered blocks of centromeric repeats containing telomeric sequences (TTAGGG)n. There were 5–13 blocks of amplified DNA per structure. These structures form rapidly within one or two cell cycles and can be observed with an incidence as high as 2%. Because the amplification was so rapid, we tested whether the amplification structures could be the result of aberrant overreplication by analyzing BrdU incorporation. Our results indicate that the amplified DNA does not undergo abnormal replication during its formation, but appears to form from existing centromeric regions. We propose a model that involves the excision of multiple centromeric DNA regions from other chromosomes and their relocalization to a new site.
Genomic organization and mapping of the human HEP-COP gene (COPA) to 1q
Authors: Quek H.H. , Chow V.T.K.
Published: May 2008

In eukaryotic cells, protein transport between the endoplasmic reticulum and Golgi compartments is mediated in part by non-clathrin-coated vesicular coat proteins (COP). Seven COP subunits have been recognized, and represent components of a complex known as coatomer. We have previously isolated the cDNA of the human homolog of α-COP, designated HEP-COP and given the official gene symbol COPA. Here we report the genomic organization of COPA, which contains 33 exons ranging in size from 67 to 611 bp. Mapped by PCR and cycle sequencing, all the exon-intron junctions conformed with the GT-AG rule, the 32 introns ranging from about 80 bp to 4 kbp, with the genomic DNA of COPA estimated to span ∼ 37 kb. Southern blot analysis of genomic DNAs of nine eukaryotic species, from human to yeast, revealed identical signals totaling 36 kb each for man and monkey only. Using 5’ RACE and primer extension analysis, the putative transcriptional start site was localized to 466 nucleotides upstream of the translation initiation codon. Comprising a 126-nucleotide 5’ untranscribed genomic sequence and a 466-nucleotide 5’ noncoding cDNA sequence, the 592-nucleotide 5’ CpG island lacked TATA and CAAT boxes but displayed a high G+C content, was enriched for CpG dinucleotides, and contained a potential Spl-binding site, i.e., features compatible with a housekeeping gene. COPA was mapped by fluorescence in situ hybridization to chromosome region 1q23→q25.
The spreading of metaphases is a slow process which leads to a stretching of chromosomes
Authors: Hliscs R. , Mühlig P. , Claussen U.
Published: May 2008

In routine chromosome harvesting of blood lymphocytes it is well accepted that metaphase spreads are obtained from fixed mitotic cells which burst on the surface of slides during the dropping procedure. For confirmation and clarification, fixed mitotic cells were dropped onto coverslips and observed under an inverted microscope during the evaporation of the fixative. Fixed mitotic cells in the metaphase stage first stick onto the surface of the coverslip without changing their three-dimensional shape and they do not burst. Thereafter, when evaporation of the fixative occurs, they slowly flatten until they are spread. This slow process leads to a stretching of chromosomes which may be a prerequisite for high resolution banding patterns. Confocal laser scanning microscopic measurements of the length, thickness, and width of chromosomes after (i) short term evaporation of the fixative, (ii) evaporation of the fixative under routine harvesting conditions and (iii) a prolonged evaporation, confirmed the stretching of chromosomes. The humidity, the temperature, and the drying time of the fixative influence the dynamic flow of the remaining fixative on the slide. This dynamic flow leads to an intensive wash of the fixed mitotic cells with increasing concentrations of acetic acid which is primarily responsible for the better quality of the metaphase spread.
Cellular localization and chromosome mapping of a novel candidate tumor suppressor gene (ING1)
Authors: Garkavtsev I. , Demetrick D. , Riabowol K.
Published: May 2008

A novel gene called ING1 encoding a 33-kDa protein that is an inhibitor of cell growth and a candidate tumor suppressor has been recently isolated (Garkavtsev et al., 1996). Here we show, using indirect immunofluorescence, that the protein (p331NG1) is located in the nucleus, which is consistent with its proposed role as a growth regulator. In addition, we show that a genomic probe to human ING1 localizes to chromosome 13 at q33→q34 by fluorescence in situ hybridization. This candidate tumor suppressor gene is located near a chromosome region which has been reported to be a site for translocation and deletion in gastric cancers and head and neck squamous carcinomas.
The origin of human chromosome 18 from a human/ape ancestor
Authors: McConkey E.H.
Published: May 2008

Karyotype analysis by previous investigators demonstrated that human chromosome 18 differs from homologous chromosomes in the great apes by a pericentric inversion. The present study uses fluorescence in situ hybridization on human and pygmy chimpanzee chromosomes to confirm the inversion and to delimit the regions where the breakpoints must have occurred in the human/ape ancestor.
Preferential induction of chromosome 1 multibranched figures and whole-arm deletions in a human pro-B cell line treated with 5-azacytidine or 5-azadeoxycytidine
Authors: Hernandez R. , Frady A. , Zhang X.-Y. , Varela M. , Ehrlich M.
Published: May 2008

5-Azacytidine (azaCR) causes genomic demethylation and decondensation of juxtacentromeric heterochromatin in chromosomes 1, 9, and 16. We determined the karyotypes of a pro-B cell line (FLEB14) treated with azaCR or its deoxynucleoside analog (azaCdR). About 80% of the induced rearrangements were in chromosome 1, and almost 90% of these involved its pericentromeric region. Multibranched figures with up to seven chromosome 1 arms, as well as whole-arm deletions of this chromosome, were the predominant anomalies, often with one normal homolog of chromosome 1 present. Isochromosomes 1 and fusions in the pericentromeric regions of chromosomes 1 and 16 or chromosomes 1 and 9 were also seen. The overlap of the spectrum of chromosomal rearrangements in azaCR- or azaCdR-treated FLEB14 cells and in mitogen-stimulated lymphocytes from patients with a rare genetic disease (ICF) associated with localized DNA hypomethylation supports the hypothesis that the DNA demethyiating activity of azaCR is essential for the induction of these pericentromeric rearrangements. These studies may help elucidate the overrepresentation of chromosome 1 pericentromeric rearrangements in many types of cancer cells.
Pulsed-field gel electrophoresis and FISH mapping of chromosome 9q22: placement of a novel zinc finger gene within the NBCCS and ESS1 region
Authors: Levanat S. , Chidambaram A. , Wicking C. , Bray-Ward P. , Pressman C. , Toftgard R. , Gailani M.R. , Myers J.C. , Wainwright B. , Dean M. , Bale A.E.
Published: May 2008

Chromosome 9q22 is a gene-rich region to which several human disease loci have been mapped. Pulsed field gel electrophoresis (PFGE) and FISH were used to determine the order of and distance between 12 chromosome 9q22 markers flanked by D9S196 and D9S180. D9S780 and XPA were within 190 kb of each other and hybridized to the same 460-kb NotI fragment as D9S180. ZNF169, a novel kruppel-type gene, and D9S280 shared several PFGE fragments indicating that they are not more than 300 kb apart. Interphase FISH showed that COL15A1 lies distal to the region bounded by D9S180 and D9S196 and that ZNF169 is adjacent to D9S196. Based on the restriction fragment lengths in this region and estimates from FISH, the distance from D9S180 to D9S196 is not less than 2 Mb.
Loss of heterozygosity analysis in a human fibrosarcoma cell line
Authors: Gupta P.K. , Shao C. , Zhu Y. , Sahota A. , Tischfield J.A.
Published: May 2008

Loss of heterozygosity (LOH) is an important event in tumor formation. We have used polymorphic microsatellite repeat markers to identify and characterize LOH in spontaneous mutants of a human cell line, MR 12–1, that is heterozygous for the adenine phosphoribosyltransferase gene (APRT+/–) located on chromosome 16q24.3. Initially, clones without extensive LOH (which are likely derived as a consequence of intragenic point mutations) and clones with multilocus LOH (which are likely due to major chromosome alterations) were identified. Clones with major regions of LOH were further characterized by assaying additional informative microsatellite markers. Analysis of 20 spontaneously-arising, independent APRT–/– clones from MR12-1 demonstrated that nine of the mutants retained both copies of APRT and 11 had undergone multilocus genetic alterations. The nature of LOH in four of the latter clones has been examined in detail by karyotype and fluorescence in situ hybridization analysis (Shao et al., 1996). These data demonstrate that LOH of chromosome 16 may be due to mitotic recombination, interstitial or partial deletion, or to more complex mechanisms. LOH in these clones may be a consequence of events similar to those observed in many tumors.
Assignment of the chicken MAX gene to chromosome 5p by fluorescence in situ hybridization
Authors: Nanda I. , Peters M.A. , Taparowsky E.J. , Sperling K. , Schmid M.
Published: May 2008

It has been shown that the protein encoded by the MAX gene plays an important role in the physiological activity of Myc oncoproteins. In this study, we determined the chromosome location of the chicken MAX gene,via fluorescence in situ hybridization. Hybridization of two biotinylated cloned fragments of 5.7 kb and 12.0 kb derived from the chicken MAX locus localized the gene to chromosome 5p. It is the third gene marker to be assigned to this telocentric macrochromosome. Since the MAX sequence is highly conserved both at the nucleotide and at the amino acid level in a wide range of vertebrate species, our data may provide evidence for the existence of a segmental homology between human and chicken chromosomes.
A high resolution GBG-banded karyotype of the Atlantic bottlenose dolphin, Tursiops truncatus: generation of an ideogram, and NOR localization by fluorescence in situ hybridization
Authors: Bielec P.E. , Riggs P.K. , Womack J.E. , Busbee D.L
Published: May 2008

A high resolution karyotype was prepared using GBG-banded chromosomes from kidney epithelial cell lines of the Atlantic bottlenose dolphin, Tursiops truncatus. The karyotype was used to generate a banded ideogram of T. truncatus that will facilitate cytogenetic analyses essential for comparison of dolphin chromosomes with those of potentially related terrestrial vertebrates. Fluorescence in situ hybridization analysis of the karyotype using a rodent (Geomys bursarius) 28S ribosomal DNA (rDNA) probe allowed localization of four nucleolar organizer (NOR) regions to the short arms of two chromosome pairs. FISH mapping, using DNA probes, is dependent on a pre-existing banded ideogram, and provides the means to initiate physical mapping of the dolphin genome.
In situ hybridisation mapping of genomic clones for five human respiratory chain complex I genes
Authors: Dunbar D.R. , Shibasaki Y. , Dobbie L. , Andersson B. , Brookes A.J.
Published: May 2008

Using human and bovine short cDNA sequences as probes we screened human cosmid and P1 libraries for components of the complex I multi-subunit enzyme of oxidative phosphorylation. We isolated genomic recombinants encoding d-B8 (gene NDUFA2), d-B14 (gene NDUFA6), d-B14.5a (gene NDUFA7), cI-ASHI (gene NDUFB8) and d-23kD (gene NDUFS8). Genomic versions of these genes have not been previously cloned in the human although they are represented as anonymous entries in public cDNA databases. By using the derived genomic clones for in situ hybridisation studies we determined the following chromosome locations: NDUFA2, 5q31; NDUFA6, 21q22; NDUFA7, 20pl3; NDUFB8, 12q21; NDUFS8, 3q28.
Molecular cloning and mapping of a human cDNA (PA2G4) that encodes a protein highly homologous to the mouse cell cycle protein P38-2G4
Authors: Lamartine J. , Seri M. , Cinti R. , Heitzmann F. , Creaven M. , Radomski N. , Jost E. , Lenoir G.M. , Romeo G. , Sylla B.S.
Published: May 2008

We have identified a novel human gene with strong homology to the mouse Pa2g4 cell cycle gene. This novel gene (called PA2G4) belongs to a gene family with members in several chromosome regions: 3q24-q25, 6q22, 9q21, 12q13, 18q12, 20p12 and Xq25. A composite cDNA of 1697 nucleotides was isolated. The sequence of this cDNA predicts a protein of 394 amino acids. The deduced amino acid sequence of this human protein shows very strong homology to the mouse protein p38–2G4. The cDNA analyzed probably corresponds to a functional copy found at 12q13.
Fertility investigations in the F1 hybrid and backcross progeny of cattle (Bos taurus) and yak (B. grunniens) in Mongolia
Authors: Tumennasan Kh. , Tuya Ts. , Hotta Y. , Takase H. , Speed R.M. , Chandley A.C.
Published: May 2008

Investigations conducted in Mongolia into the sterility of the male khainag, an F1 hybrid animal resulting from crossing cattle (Bos tαurus, 2n = 60) with yaks (B. grunniens, 2n = 60), are reported. Reduced numbers of spermatogonia appear to characterise the testicular tubules of the khainag, and despite the identical cytological appearance of the two parental karyotypes, synaptic anomalies are seen at meiotic prophase in primary spermatocytes. The female khainag is fertile and can be backcrossed to cattle or yak bulls to produce a B1 backcross animal, the ortoom. Further backcrossing of ortoom females to cattle or yaks will yield a B2 backcross animal, the usanguzee. The impression is gained of better meiotic pairing in the backross animals than in the khainag. The “Haldane Rule” is followed perfectly by the cattle × yak hybrid; namely, sterility is confined to the male.
Monosomy 6 in human cultured fibroblast-like cells after long-term stimulation with acidic fibroblast growth factor (FGF1)
Authors: Krone W. , Kehrer-Sawatzki H.. , Siegel A. , Röck H. , Götz H.
Published: May 2008

Long-term exposure to fibroblast growth factor type 1 (FGFl) of fibroblast-like cells derived from neurofibromas of patients with neurofibromatosis type 1, from angiofibromas of patients with tuberous sclerosis, and from foreskin of unaffected donors resulted in the outgrowth of monosomy 6 in 7 out of 14 cell lines examined. After their initial detection by cytogenetic analysis, the proportion of cells which had lost one chromosome 6 was monitored by FISH using α-satellite probes specific for chromosome 6 and 7, and by PCR analysis of polymorphic microsatellite markers. Monosomy 6 exceeding baseline levels developed only in cultures exposed to FGF1, and the emergence of monosomic cells could not be correlated with a given donor’s genotype. During serial culture, the proportion of monosomic cells increased to over 90 % in 5 of the 7 affected strains. A conspicuous change of cellular morphology from spindle-shaped to more epithelial-type cells was noted in monosomic cultures, even though none of them converted to a permanent cell line during the observation period. We conclude that long-term exposure of human fibroblast-like cell strains to FGFl results in the emergence of monosomy 6 in 50% of the cultures so treated. A selective advantage for such monosomic cells is the most likely explanation for their steady increase during serial culture.
T4 DNA ligase reduces chromosome damage and enhances cell survival in CHO cells treated with bleomycin
Authors: Ortiz T. , Flores M.J. , Piñero J. , Cortés F.
Published: May 2008

The effect of DNA ligase from T4 phage on the modulation of the damage induced by bleomycin was studied. CH06 cells were electroporated with either bleomycin alone or bleomycin plus T4 DNA ligase, and both cytogenetic and clonogenic assays were carried out in parallel. Our results show that T4 DNA ligase is able to decrease the frequency of chromosome aberrations in bleomycin-treated cells while increasing cell survival.
Molecular cloning of CISH, chromosome assignment to 3p21.3, and analysis of expression in fetal and adult tissues
Authors: Uchida K. , Yoshimura A. , Inazawa J. , Yanagisawa K. , Osada H. , Masuda A. , Saito T. , Takahashi T. , Miyajima A. , Takahashi T.
Published: May 2008

The murine cytokine inducible SH2-containing (Cis) protein gene (Cish) was recently cloned and shown to have a growth inhibitory function. We have isolated cDNAs coding for its human homologue (CISH) and assigned the gene to 3p21.3 by fluorescence in situ hybridization. Northern blot analysis showed CISH expression in various epithelial tissues including lung and kidney, in which tumors frequently exhibit 3p21.3 deletions.
Chromosomes of Brants’ whistling rat and genome conservation in the Otomyinae revealed by G-banding and fluorescence in situ hybridization
Authors: Rambau R.V. , Harrison W.R. , Elder F.F.B. , Robinson T.J.
Published: May 2008

Conventional G- and C-banding were used to describe the chromosomes of the whistling rat, Parotomys brantsii. This species has a diploid number of 42 chromosomes. C-banding showed that large blocks of pericentromeric hete-rochromatin or entirely heterochromatic short arms characterize most chromosomes. G-banding and fluorescence in situ hybridization (FISH) incorporating two laboratory mouse chromosome paints were used to compare the genomes of P. brantsii, the bush karoo rat (Otomys unisulcatus; 2n = 28), and the vlei rat (O. irroratus; 2n = 28–31). The FISH results showed that sequences corresponding to mouse chromosome 2 are conserved as a single chromosome in O. irroratus but are found on two separate chromosomes in P. brantsii and O. unisulcatus. In contrast, a mouse chromosome 6 paint showed hybridization to single chromosomes in all three species examined. When taken together, the FISH and cytogenetic results produce two important findings: (1) previously undetected homoeologies between the two Otomys species can be identified and (2) a high proportion of conserved chromosomes exists between P. brantsii and O. unisulcatus. This, in conjunction with previously reported allozyme and immunoblot data, raises serious questions about the validity of the current generic taxonomy of the Otomyinae.
Localization of 18S+28S and 5S ribosomal RNA genes in the dog by fluorescence in situ hybridization
Authors: Mäkinen A. , Zijlstra C. , de Haan N.A. , Mellink C.H.M. , Bosma A.A.
Published: May 2008

The gene clusters encoding 18S+28S and 5S rRNA in the dog (Canis familiaris) have been localized by using GTG-banding and fluorescence in situ hybridization. The 18S+28S rDNA maps to chromosome regions 7q2.5→q2.7, 17q17, qter of a medium-sized, not yet numbered autosome, and Yql.2→q13. Our data show that there is one cluster of 5S rDNA in the dog, which maps to chromosome region 4q1.4.
Extensive Nucleolus Organizer Region polymorphism in Gymnotus carapo (Gymnotoidei, Gymnotidae)
Authors: Fernandes-Matioli F.M.C. , Almeida-Toledo L.F. , Toledo-Filho S.A.
Published: May 2008

An investigation was conducted on six populations of Gymnotus carapo from the Upper Parana river system in Brazil. A wide variability of the NOR-bearing chromosomes was found involving paracentric inversions in the heterochromatic regions associated with NORs, resulting in 5 NOR chromosome phenotypes. The distribution of the distinct NOR phenotypes varied both inter and intrapopulationally. Results obtained using an exact test revealed that the six populations are in Hardy-Weinberg equilibrium. Although NOR size polymorphism is quite a common occurrence in fish karyotypes, this is the first description of a balanced polymorphism involving 3 different NOR chromosomes in 5 combinations.
Novel COL4A5/COL4A6 deletions and further characterization of the diffuse leiomyomatosis-Alport syndrome (DL-AS) locus define the DL critical region
Authors: Heidet L. , Cohen-Solal L. , Boye E. , Thorner P. , Kemper M.J. , David A. , Larget Piet L. , Zhou J. , Flinter F. , Zhang X. , Gubler M.C , Antignac C.
Published: May 2008

Diffuse leiomyomatosis (DL) with Alport syndrome (AS) has been shown to be associated with contiguous gene deletions of the COL4A5 and COL4A6 genes, with the COL4A6 breakpoint of the deletions invariably located in the large intron 2 of the gene. We describe four YAC clones covering the locus and a refined restriction map of the entire COL4A6 gene. These resources have allowed us to make a precise estimate of the size of COL4A6 introns 2 and 3, as well as the size of the gene itself. We also describe five novel deletions which, in conjunction with previous reports, allow the definition of a 90-kb critical region in which to search for a gene or other entity involved in the pathogenesis of DL.
Reciprocal chromosome painting between human and prosimians (Eulemur macaco macaco and E. fulvus mayottensis)
Authors: Müller S. , O’Brien P.C.M. , Ferguson-Smith M.A. , Wienberg J.
Published: May 2008

We used fluorescence in situ hybridisation to delineate the homology between the human karyotype and those of two lemur species (Eulemur macaco macaco and E. fulvus mayottensis). Human and lemur chromosome-specific probes were established by bivariate fluorescence-activated flow sorting (FACS) and subsequent degenerate oligonucleotide-primed PCR (DOP-PCR). Reciprocal painting of human probes to lemur chromosomes and vice versa allowed a detailed analysis of the interchromosomal rearrangements that had occurred during the evolution of these species. The results indicate that the genomes of both species have undergone only a few translocations during more that 45 million years of lemur and human evolution. The synteny of homologs to human chromosomes 3, 9, 11, 13, 14, 17, 18, 20, 21, X, and Y was found to be conserved in the two lemur species. Taking non-primate mammals as the outgroup for primates, ancestral conditions for various primate chromosomes were identified and distinguished from derived forms. Lemur chromosome painting probes were also used for cross-species hybridization between the two lemur species. The results support an earlier assumption, made on the basis of chromosome banding, that the karyotypes of the two species have evolved exclusively by Robertsonian transformations. All probes derived from E. f. mayottensis chromosomes specific for homologs involved in rearrangements in E. m. macaco exclusively painted entire chromosome arms. The results further indicate that E. f. mayottensis most probably has a more ancestral karyotype than E. m. macaco. Probes derived from prosimians will be useful in comparing the karyotypes of other lower primates, which will improve our understanding of early primate genome evolution.
Comparative linkage mapping of genes on sheep chromosome 3 provides evidence of chromosomal rearrangements in the evolution of the Bovidae
Authors: Jenkins Z.A. , Henry H.M. , Galloway S.M. , Dodds K.G. , Montgomery G.W.
Published: May 2008

Three genes—parathyroid hormone-like hormone (PTHLH), insulin-like growth factor 1 (IGF1), and retinoic acid receptor γ (RARG)—have been mapped to sheep (Ovis aries) chromosome 3 (OAR 3). The order and genetic distances between loci on OAR 3 are similar to those on cattle (Bos taurus) chromosome 5, as expected from their close evolutionary relationship. The OAR 3 linkage map shows conserved synteny with human chromosome 12, but there are at least two rearrangements in gene order between the species.
Localization by fluorescence in situ hybridization (FISH) of human mitochondrial polymerase γ (POLG) to human chromosome band 15q24→q26, and of mouse mitochondrial polymerase γ (Polg) to mouse chromosome band 7E, with confirmation by direct sequence analysis of bacterial artificial chromosomes (BACs)
Authors: Zullo S.J. , Butler L , Zahorchak R.J. , Macville M. , Wilkes C. , Merril C.R.
Published: May 2008

Cloned cDNAs for the human mitochondrial DNA polymerase γ (POLG) were identified by homology with the yeast mitochondrial DNA polymerase catalytic subunit (MIP). Fluorescence in situ hybridization (FISH) of human and mouse bacterial artificial chromosomes (BACs), hybridized by radioactively labeled POLG cDNAs, mapped to human chromosome band 15q24→q26, as well as to mouse chromosome band 7E. Direct sequencing of the BAC DNA without subcloning confirmed the presence of both human POLG and mouse mitochondrial DNA polymerase γ (Polg) in the respective BACs.
Assignment of mouse Gfra1, the homologue of a new human HSCR candidate gene, to the telomeric region of mouse Chromosome 19
Authors: Puliti A. , Cinti R. , Seri M. , Ceccherini I. , Romeo G.
Published: May 2008

Glial cell line-derived neurotrophic factor (Gdnf) and its alpha receptor (Gfra1) interact with the Ret receptor triggering its tyrosine kinase activity. As Gdnf and Ret have been linked to the development of Hirschsprung disease (HSCR), it seems likely that Gfra1 could also be a susceptibility gene for HSCR. A further HSCR candidate gene is represented by the human homologue of the Dom (Dominant megacolon) mouse mutation, mapped to Chr 15, for which the gene has not yet been identified. In order to test if Gfra1 could be the Dom gene or if it represents a new possible HSCR locus we have undertaken the mapping of the mouse Gfra1. Using specific PCR primers on a somatic cell hybrid mapping panel and fluorescence in situ hybridization with an expressed sequence tag (EST) cDNA clone corresponding to the mouse Gfra1, we mapped the gene to mouse chromosome 19D2-D3, a region with known homology with human chromosome 10q24→q26.
Swine centromeric DNA repeats revealed by primed in situ (PRINS) labeling
Authors: Rogel-Gaillard C. , Hayes H. , Coullin P. , Chardon P. , Vaiman M.
Published: May 2008

In swine, distinct centromeric satellite DNA families have been described that correspond to either all the meta-centric chromosomes except the Y (Mel) or all the acrocentric chromosomes (Ac2). Using primed in situ (PRINS) labeling, we show here that primers derived from various sequences specifically label the centromeres of different subgroups of chromosomes. Among five primers derived from centromeric sequences of acrocentric chromosomes reported to be very homogeneous, four recognize all the acrocentric chromosomes, whereas one labels prominently chromosome 17. For the metacentric chromosomes, six primers have been derived from several divergent sequences. Among these primers, two recognize all the metacentric chromosomes except 5, 10, and 12. Three other primers label small subsets of metacentric chromosomes, including the X and one or two additional chromosomes. The last primer is specific to chromosome 1. These preliminary results suggest that it should be possible to define specific primers for almost every swine chromosome. Already, some of the primers reported here permit a distinction between swine chromosomes difficult to differentiate without banding, such as the X chromosome and chromosome 9. Therefore, the PRINS technique using centromeric motifs constitutes an additional tool for cytogenetic studies in swine.
Assignment of TCF1, TGM1, CALM1, CKB, THBS1 B2M, and FES in Ateles paniscus chamek (Platyrrhini, Primates)
Authors: Moreira M.A.M. , Canavez F. , Parham P. , Seuánez H.N.
Published: May 2008

Regional assignment of five markers to chromosome 2 of Ateles paniscus chamek (APC) confirmed a syntenic association similar to human (HSA) 12q + 14q + 15q. TCF1 was allocated to a shortest region of overlap (SRO) in APC 2p and found to be syntenic to PEPB, while TGM1, CALM1, THBS1, and B2M were assigned to APC 2q, being syntenic to NP, HEXA, and MPI. Conversely, markers close to HSA 14qter (CKB) and HSA 15qter (FES-IDH2) were relocated to other Ateles syntenic groups. Karyotypic comparisons showed an evident homoeology between APC 2p and HSA 12q, whereas APC 2q was similar to an HSA 14qter::HSA 15qter fusion product.
Cloning and characterization of BAI2 and BAI3, novel genes homologous to brain-specific angiogenesis inhibitor 1 (BAI1)
Authors: Shiratsuchi T. , Nishimori H. , Ichise H. , Nakamura Y. , Tokino T.
Published: May 2008

We have identified two novel human genes homologous to BAH (brain-specific angiogenesis inhibitor 1), an angiogenesis inhibitor that is a candidate for involvement in development of glioblastoma. Like BAH, these two genes, designated BAI2 and BAD, were specifically expressed in brain, and are likely to be expressed in the same type of cells. However, in spite of similar tissue specificity among the three BAI genes, only BAH is transcriptionally regulated by p53. BAD expression was absent in two of nine glioblastoma cell lines examined and was significantly reduced in three of the remaining seven. These data suggest that members of this novel gene family may play important roles in suppression of glioblastoma. BAH, BAI2 and BAI3 were mapped to 8q24, 1p35 and 6q12, respectively.
Cloning, expression and mapping of a novel RING-finger gene (RNF5), a human homologue of a putative zinc-finger gene from Caenorhabditis elegans
Authors: Kyushioki H. , Kuga Y. , Suzuki M. , Takahashi E. , Horie M..
Published: May 2008

The RING-finger is a unique zinc-chelating domain involved in mediating protein-protein interactions. The extensive sequence homology within the RING-finger domain allowed us to clone a novel member of the RING-finger family of genes. This cDNA clone, designated RNF5 (Ring-finger protein 5), contained an open reading frame of 540 nucleotides. Its predicted amino acid sequence revealed significant homology to a hypothetical protein encoded by Caenorhabditis elegans cosmid C16C10.7. The expression of RNF5 was detected in a variety of human tissues. The RNF5 gene was mapped by fluorescence in situ hybridization to chromosome 6p21.31. Radiation hybrid mapping further assigned RNF5 to a region proximal to the major histocompatibility complex (MHC) on chromosome 6. RNF5 is the third RING-finger gene identified in the region proximal to MHC raising the possibility that the RING-finger family of genes may exist as a cluster in this region.
The nature of G-bands analyzed by chromosome stretching
Authors: Hliscs R. , Mühlig P. , Claussen U.
Published: May 2008

To investigate the nature of G-banding, chromosome stretching was performed on chromosome 6 at the 400-band level of normal human lymphocytes that had been cultivated and harvested using standard techniques. The GTG-banding patterns of five stretched chromosomes 6 were compared microscopically with each other and found to be identical at the 1,400-band level. A high-resolution ideogram at the 1,400-band level was constructed. The banding pattern at this level appeared to be very regular, with all dark bands at the 400-band level splitting into three to six dark subbands. While the dark subbands observed at the 1,400-band level seem to derive solely from the dark bands seen at the 400-band level, light bands visible at the 400-band level do not split into sub-bands, which is in contrast to the published (ISCN, 1995) ideograms. The splitting process, which was analyzed on the video monitor in more detail, shows that chromosome stretching is due mainly to the appearance of light subbands flanked by dark subbands. To shed more light on this phenomenon, the staining intensity of the dark bands and their subbands was measured while the chromosomes were stretched from the 400- to the 1,400-band level. At first, staining intensity was found to diminish in inverse proportion to the elongation of the chromosome, but then remained relatively unaffected until the dark subbands were gradually split up. After stretching to the 1,400-band level, these dark subbands were followed by newly appearing small light subbands, which were about the same size as the stretched light bands visible at the 400-band level. The results indicate that, in general, the light bands of human chromosomes are the preferentially stretched chromosome regions and that the resolution-dependent characteristic banding pattern of human chromosomes is mainly based on a fixed hierarchy of the stretchability of chromosomes.
Biochemical-Genetic Factors of Taste-Polymorphism and their Relation to Salivary Thyroid Metabolism in Health and Mental Retardation
Authors: Fischer R. , Griffin F. , England S. , Pasamanick B.
Published: May 2008

Differences in biochemical reactivity between the saliva of “tasters” and “non-tasters” of phenylthiourea (PTC) 1-methyl-2-mercapto-imidazol, 6-n-pro-pylthiouracil (PROP) as well as a whole series of chemically related thiocarbamide type antithyroid compounds are described. The influence of (salivary) thyroid metabolites on taste thresholds for the thioureas as well as quinine is also discussed. A relationship between taste thresholds for bitterness and food selectivity is reported and shown that parents of mongoloid children are characterized by high taste thresholds for quinine.
Robots with Bad Accents: Living with Synthetic Speech
Authors: Böhlen Marc
Published: May 2008

Synthetic speech technologies have a profound impact on how we think about and interact with computers. This text discusses parts I and II of the “Make Language Project,” a trilogy on the cultural fallout of machine generated speech as a conduit for reconsidering prejudices in synthetic speech production and humanoid robot design.
A Cultural History of the Hologram
Authors: Johnston Sean F.
Published: May 2008

The hologram, the novel imaging medium conceived in 1947, underwent a series of technical mutations over the following 50 years. Those successive adaptations altered the form of the medium, broadened its imaging capabilities and promoted wider perceptions of its functions and possibilities. Appropriated by disparate technical communities and presented to varied audiences, the hologram and its cultural meanings evolved dramatically. This paper relates the fluidity of the form, function and meaning of the hologram to its distinct creators and users.
Physics of Aesthetics: A Meeting of Science, Art and Thought in Barcelona
Authors: Perelló Josep , Altaió Vicenç
Published: May 2008

The Physics of Aesthetics conference in Barcelona introduced the paradigms of the liveliest aspects of physics. One hundred years after Einstein's annus mirabilis, physics continues making progress, and the authors participated with internationally well-known scientists in drawing the outline of its more attractive face. Universal questions naturally arose, relating to the limits of our perception, the design of matter and the narrative of the complexity surrounding us. Local non-scientist personalities helped to distill aesthetics from the contemporary tendencies of this scientific discipline.
Riddles in Fundamental Physics
Authors: Gaumé Luis Álvarez
Published: May 2008

Scientific understanding of natural phenomena should be a legitimate part of aesthetic theory, as this understanding involves the beauty of insight into the inner workings of nature. This insight is not always easy to communicate. Despite the huge progress made during the 20th century, fundamental physics now faces puzzles and paradoxes involving the infinitely small (the frontier of high energies) and the infinitely large (the overall structure of the observed universe). Working in basic science is fascinating but difficult. Discoveries happen not in a linear manner but just as they do in the creation of a work of art.