bluuebunny/crossref_metadata_2025 huggingface dataset:
Recombination nodules and axial equalization in the ZW pairs of the Peking duck and the Guinea fowl
Authors: Solari A.J. , Pigozzi M.I.
Published: May 2008

The meiotic Z and W chromosomes of the Guinea fowl (Numida meleagris) and the Peking duck {Anas platyrhynchos) show features similar to those described previously for 3 species of Phasianidae: chicken, Japanese quail and bobwhite quail. Axial equalization in the gonosomes of the Peking duck involves lengthening of the W axis along with shortening of the Z axis. A single recombination nodule is constantly found in the synaptic, terminal region of the ZW pairs stained with phosphotungstic acid. The localization of this nodule is significantly different in these two species, but the length of synaptonemal complex harboring the nodules is not significantly different. Based on the phylogenetic distance between the observed species, the present data support the hypothesis that the presence of a pseudoautosomal region is a general property of ZW pairs in carinate birds.
Cloning and characterization of a fish centromeric satellite DNA
Authors: Garrido-Ramos M.A. , Jamilena M. , Lozano R. , Ruiz Rejón C. , Ruiz Rejón M.
Published: May 2008

A highly repetitive DNA sequence family from the genome of Spams aurata has been cloned and characterized. The family is composed of repeat units of 186 bp in length, and it accounts for 2% of the fish genome. Data from Southern blots and in situ hybridization demonstrate that repeating units are tandemly arranged at the centromeres of all the chromosomes in this species. The repetitive sequence is AT rich (67%) and is characterized by short stretches of consecutive AT base pairs and by short direct and inverted repeats. Sequence analysis of six cloned monomers of the family reveals some variation among clones at random positions and also distinguishes two subfamilies of repeats that differ in a highly divergent block of 31 bp. These two subfamilies do not seem to be located in separate domains but occur together in the centromere of each chromosome pair. The presence of this repeat family in the genome of other Sparidae species, some of which are relatively distant from S. aurata, indicates that this repetitive sequence could be an important component of the centromere in this fish family.
Chimpanzee Rh-like blood group genes map to chromosome region 1p36.1→p34.2 by in situ hybridization
Authors: Calvas P. , Blancher A. , Depétris D. , Salvignol I. , Chérif-Zahar B. , Mattéi M.-G.
Published: May 2008

A human Rh cDNA probe was used to map the Rh-like genes in the chimpanzee. The data gathered made it possible to uniquely localize these genes to chimpanzee chromosome region 1p36.1→p34.2. This chromosomal localization is homologous to the location of the Rh genes in the human genome.
A method for simultaneous detection of fluorescent G-bands and in situ hybridization signals
Authors: Hirai M. , Suto Y. , Kanoh M..
Published: May 2008

Improved techniques for detecting in situ hybridization signals on fluorescent G-bands are described. Prior to hybridization of biotinylated DNA probes, chromosomes with replication G-bands were treated with formaldehyde and denatured with an alkaline solution. These steps preserve chromosome morphology well, and enable us to simultaneously demonstrate fluorescein hybridization signals and G-banded chromosomes stained with propidium iodide. This method is useful for precise chromosomal localization of DNA markers.
B-chromosome systems in the greater glider, Petauroides volans (Marsupialia: Pseudocheiridae)
Authors: McQuade L.R. , Hill R.J. , Francis D.
Published: May 2008

B chromosomes, despite their common occurrence throughout the animal and plant kingdoms, have not been investigated extensively at the molecular level. While the majority of B chromosomes occurring in animals have been described as heterochromatic, only a few researchers have examined the DNA of these chromosomes beyond this gross cytological level. This is the case in the largest of the gliding marsupial possums, the greater glider, Petauroides volans. To examine the molecular composition and localization of B-chromosome DNA sequences in P. volans, a combination of micromanipulation and the polymerase chain reaction was used in this study to isolate and then amplify the DNA of the B chromosomes. Localization of the isolated B-chromosome sequences to metaphase chromosomes was investigated using fluorescence in situ hybridization. The B chromosomes in this species are shown to be composed of a heterogeneous mixture of sequences, some of which are unique to the B chromosomes, while others exhibit homology to the centromeric regions of the autosomal complement.
Isolation of rat chromosome-specific paint probes by bivariate flow sorting followed by degenerate oligonucleotide primed-PCR
Authors: Hoebee B. , de Stoppelaar J.M. , Suijkerbuijk R.F. , Monard S.
Published: May 2008

The flow karyotype of rat chromosomes was determined by dual beam flow cytometry. Eighteen fractions were sorted and subsequently amplified by degenerate oligonucleotide primed-PCR as described by Telenius et al. (1992a, 1992b). The PCR products were labeled and used as probes for fluorescence in situ hybridization on rat fibroblast metaphases. The amplified chromosomes were detectable as bright chromosome paints and in most cases the signal was evenly distributed along the whole chromosome except for the centromeric region in half of the chromosomes. The results show that chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, X and Y can be sorted as individual fractions, whereas chromosomes 11, 13, 14,15 and chromosomes 16, 17 and 18 are clustered together in the flow karyotype.
Localization of two genes encoding plasma membrane Ca2+ ATPases isoforms 2 (ATP2B2) and 3 (ATP2B3) to human chromosomes 3p26→p25 and Xq28, respectively
Authors: Wang M.G. , Yi H. , Hilfiker H. , Carafoli E. , Strehler E.E. , McBride O.W.
Published: May 2008

The plasma membrane Ca2+ ATPases (PMCA) represent a highly conserved, widely dispersed, multigene family in eukaryotes consisting of at least four functional genes. The genes for PMCA isoforms 1 and 4 (ATP2B1 and ATP2B4) have been previously localized to human chromosomes 12q21→ q23 and 1q25→q32, respectively. Based upon results of fluorescence in situ hybridization (FISH), analysis of somatic cell hybrids, and genetic linkage analyses, we now report localization of ATP2B3 (PMCA isoform 3) to human chromosome Xq28, and confirm the recent localization of ATP2B2 (PMCA isoform 2) to chromosome 3p26→p25. In contrast to ATP2B1 and ATP2B4, recent studies have suggested tissue specific regulation of expression of both ATP2B2 and ATP2B3 particularly in the nervous system. The genes for several neurological and neuromuscular diseases have been assigned to the distal portion of Xq, and ATP2B3 is a candidate gene for these diseases.
Evidence that metacentric and submetacentric chromosomes in canine tumors can result from telomeric fusions
Authors: Reimann N. , Rogalla P. , Kazmierczak B. , Bonk U. , Nolte I. , Grzonka T. , Bartnitzke S. , Bullerdiek J.
Published: May 2008

We have hypothesized that metacentric and submetacentric chromosomes frequently observed in malignant canine tumors are a result of telomeric fusions. Therefore cells from a canine mammary pleomorphic adenoma were transformed with a plasmid containing the SV40 ‘early region’, known to cause telomeric associations. Compared with non-transformed adenoma cells, the cells had a higher proliferative capacity and expressed the large SV40-T-antigen. Karyotype studies showed the conversion from a normal to an aberrant karyotype with an increase of bi-armed chromosomes resulting from fusions of acrocentric chromosomes. In addition, the length of the telomeric repeats (TTAGGG) was determined for an early and a late passage of the transformed cells by Southern hybridization. The length of the telomeric repeats was apparently longer in the 5th than in the 38th passage. In situ hybridization with a telomere-specific DNA revealed interstitial telomeric repeats in the bi-armed chromosomes. We have concluded that these findings reflect the clonal expansion of head-to-head-telomeric fusions of canine acrocentric chromosomes leading to dicentric chromosomes with a very short distance between the two centromeres. Our results support the idea that the apparent centric fusions that have been described in some canine tumors may in fact be the cytogenetic products of head-to-head-telomeric fusions.
Geographical variation of heterochromatin in Ctenomys flamarioni (Rodentia-Octodontidae) and its cytogenetic relationships with other species of the genus
Authors: de Freitas T.R.O.
Published: May 2008

The first karyotype analysis of Ctenomys flamarioni, based on a sample of 46 specimens collected along the geographical range of this species, is reported. All specimens exhibited a diploid number of 48 but varied in autosomal arm number from a low of 50 to a high of 78. The amount of constitutive heterochromatin also varied with the species’ geographical distribution. Comparison of G-band patterns showed a strong relationship between the karyotype of this species and those belonging to the Argentinian mendocinus group.
A panel of subchromosomal painting libraries representing over 300 regions of the human genome
Authors: Antonacci R. , Marzella R. , Finelli P. , Lonoce A. , Forabosco A. , Archidiacono N. , Rocchi M.
Published: May 2008

DNA samples from about 100 human-hamster somatic cell hybrids, previously characterized by conventional banding techniques, were amplified with dual-Alu PCR. The products were then used as probes in FISH experiments on normal human metaphases for an accurate cytogenetic characterization of the human material retained in each hybrid. In addition to entire chromosomes, most hybrids were found to contain one or a few chromosome fragments, as a result of rearrangements that had occurred in vitro. Forty additional primary hybrids, in which conventional cytogenetic analysis failed to reveal any complete human chromosome, contained many human chromosome fragments. More than 300 chromosome fragments were scored and their precise chromosomal location recorded. We show data indicating that subchromosomal painting libraries generated from these hybrids can be favorably used in the fine characterization of chromosomal rearrangements encountered in clinical cytogenetics or in tumor cytogenetics, and in tracking chromosomal changes that occurred in primate evolution.
A novel type of unstable homogeneously staining region with a head-to-tail arrangement: spontaneous decay and reintegration of DNA elements into a plethora of new chromosomal sites
Authors: Koehler U. , Abken H. , Grummt F. , Wienberg J. , Weidle U.H.
Published: May 2008

After transfection of amplification-promoting DNA elements into mammalian cells, homogeneously staining regions (HSRs) are formed by high copy numbers of transfected DNA arranged in head-to-tail polymers. Here, we wanted to evaluate the stability of this type of HSR during prolonged cultivation of transfected cells in selective medium. Thymidine kinase-deficient mouse L cells were transfected with pAPR4tk DNA harboring the amplification-promoting element 4 (APR4) linked to the gene for thymidine kinase (TK) or, alternatively, transfected with a DNA construct (pAPR4t-PA) carrying, in addition, the expression cassette for human tissue-type plasminogen activator (t-PA). After transfection, one or two HSRs per cell were formed that disintegrated spontaneously after 25–40 wk of continuous cultivation in the presence of selective HAT (hypoxanthine-aminopterin-thymidine) medium. Unexpectedly, plasmid DNA reinserted into a plethora of new chromosomal sites, as revealed by in situ hybridization and Southern blot analysis. Coincidently, secretion of t-PA decreased to 10–20% of its original level. After transfection of pAPR4tk DNA lacking the t-PA expression cassette, HSR decay and reintegration of plasmid constructs into multiple chromosomal sites were also observed, whereas the ptk vector without an amplification-promoting DNA element did not form an HSR after transfection. We conclude that, in contrast to the pattern of known structures with head-to-tail arrangements, the HSR formed by amplification-promoting DNA elements represents a novel type of HSR that disintegrates by transposition into a plethora of new chromosomal integration sites. This process is mediated by the amplification-promoting DNA element itself and can be observed even when selective pressure is maintained.
Chromosomal painting shows that “marked chromosomes” in lesser apes and Old World monkeys are not homologous and evolved by convergence
Authors: Stanyon R. , Arnold N. , Koehler U. , Bigoni F. , Wienberg J.
Published: May 2008

Cytogeneticists have long held that the single pair of metacentric, NOR-bearing “marked chromosomes” in lesser apes (Hylobatidae) and Old World monkeys (Cercopithecidae) are homologous. Hylobatids have sometimes been excluded from Hominoidea (great apes and humans) and phylogenetically allied with the lower primates, primarily on the basis of this shared “trait.” However, in situ hybridization of human chromosome-specific DNA probes to chromosomes of Hylobates lar, H. syndactylus, H. concolor, Cercopithecus aethiops, Macaco, fuscata, Colobus guereza, and Presbytis cristata showed that the so-called “marked chromosomes” in Hylobatidae and Cercopithecidae evolved by convergence. Therefore, “marked chromosomes” cannot be used to exclude gibbons from Hominoidea or to link Hylobatidae with monkeys. Chromosomal painting is a powerful tool to resolve problems of chromosomal homology and helps eliminate phylogenetic errors due to confusing convergence with homology. Chromosomal painting improves the confidence in using cytogenetic data for evolutionary studies, especially in phytogeny and taxonomy.
Cloning and chromosomal localization of the human and murine genes for the T-cell transcription factors NFATc and NFATp
Authors: Li X. , Ho S.N. , Luna J. , Giacalone J. , Thomas D.J. , Timmerman L.A. , Crabtree G.R. , Francke U.
Published: May 2008

The nuclear factor of activated T cells (NFAT) is a transcription factor complex involved in the activation of cytokines and cell surface molecules associated with coordinating the actions of different cells required for an immune response. Two different genes have recently been cloned that encode proteins capable of functioning as the pre-existing (p) and cytosolic (c) component of the NFAT transcription complex, NFATc of human and NFATp of murine origin (Northrop et al., 1994; McCaffrey et al., 1993b). We report here the partial cDNA cloning of the murine homolog of NFATc and the human homolog of NFATp, and the chromosomal localization of both genes in both species to conserved syntenic regions. Through the use of mapping panels of human × Chinese hamster and mouse × rodent cells hybrids, the NFATc genes were mapped to human and mouse chromosomes 18. By analyzing a chromosome 18 radiation hybrid panel, the human NFATc gene was localized to the q terminus, closely linked to STS marker D18S497. The murine Nfatc gene was sublocalized to chromosome band 18E4 by FISH. The NFATp genes were mapped by somatic cell hybrid analysis to human chromosome 20 and mouse chromosome 2. Human NFATp was assigned to chromosome region 20ql3.2→ql3.3 by FISH. Based on the conserved syntenic region on human chromosome 20 and mouse chromosome 2, murine Nfatp is predicted to reside in the vicinity of a mutant locus wasted. Homozygous wst/wst mice display a phenotype reminiscent of severe combined immune deficiency or ataxia telangiectasia, disorders that could therefore be considered candidates for NFATp mutations.
Incidence of low-fluorescence α satellite region on chromosome 21 escaping detection of aneuploidy at interphase by FISH
Authors: Bossuyt P.J. , Van Tienen M.-N. , De Gruyter L. , Smets V. , Dumon J. , Wauters J.G.
Published: May 2008

Aneuploidy detection for chromosome 21 by fluorescence in situ hybridization (FISH) to inteφhase nuclei using a probe specific for the alphoid DNA sequences D21Z1/D13Z1 should be avoided. An extreme heteromorphism, resulting in misdiagnosis if inteφhase FISH is the only test employed, may be far more frequent (4/101) than expected.
Assignment of the tenascin gene (HXB) to swine chromosome 1q21.1→q21.3 by fluorescence in situ hybridization
Authors: Awata T. , Yamakuchi H. , Kumagai M. , Yasue H.
Published: May 2008

The chromosomal location of the swine tenascin gene (HXB) was determined by fluorescence in situ hybridization and simultaneous R-banding. Swine tenascin cDNA was labeled with biotin, and used as a probe. Hybridization was detected by the FITC-labeled streptavidin/biotinylated anti-streptavidin antibody system. The signals revealed that the tenascin gene is localized on swine chromosome 1q21.1→q21.3.
X-linked juvenile retinoschisis (RS) maps between DXS987 and DXS443
Authors: Weber B.H.F. , Janocha S. , Vogt G. , Sander S. , Ewing C.C. , Roesch M. , Gibson A.
Published: May 2008

X-linked juvenile retinoschisis (RS) has previously been localized to a 7–8 cM interval between markers at (DXS43, DXS207) and (DXS274, DXS41). Our analysis of more than 300 meioses in two multigeneration RS families identified eight recombinant RS chromosomes and narrowed the RS locus to an interval between DXS987 and DXS443. Our data suggest the following order of loci: Xpter – DXS207 -DXS987 – ([DXS418 – DXS999], RS) – DXS443 – DXS365 – DXS274 – Xcen.
Assignment of CD38, the gene encoding human leukocyte antigen CD38 (ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase), to chromosome 4p15
Authors: Nakagawara K. , Mori M. , Takasawa S. , Nata K. , Takamura T. , Berlova A. , Tohgo A. , Karasawa T. , Yonekura H. , Takeuchi T. , Okamoto H.
Published: May 2008

CD38 has been used as a phenotype marker of lymphocyte differentiation. Recently, we have demonstrated that cyclic ADP-ribose can be synthesized and hydrolyzed by CD38 and acts as a second messenger in insulin secretion from pancreatic β-cells. We have mapped the CD38 gene to human chromosome 4p15 by fluorescence in situ hybridization.
Chromosomal assignment of the heparin-binding cytokine genes MDK and PTN in mouse and man
Authors: O’Hara B. , Jenkins N.A. , Gilbert D.J. , Copeland N.G. , Shows T.B. , Eddy R.L. , Böhlen P. , Kovesdi I.
Published: May 2008

MDK and PTN are two members of a family of heparin-binding cytokines thought to be involved in a number of developmental processes. The locations for these genes were determined in man and mouse using somatic cell hybrid analysis and interspecific backcross analysis. Human MDK was mapped to 11p13→p11. MDK in the mouse (Mdk) was mapped to a syntenic region of mouse Chromosome 2. A pseudogene of Mdk was mapped to mouse Chromosome 11. The closely related human gene PTN was mapped to a separate location on human chromosome region 7q22 →qter.
Expression and chromosomal localization of cDNA clones from an enriched human retinal pigment epithelial (RPE) cell line library: identification of two RPE-specific genes
Authors: Agarwal N. , Swaroop A. , Zheng K. , Liou J.-d. , O’Rourke K. , Graves K.A. , Gieser L. , Del Monte M. , Yang-Feng T.L.
Published: May 2008

We have previously constructed an enriched cDNA library from a human retinal pigment epithelium (RPE) cell line and generated expressed sequence tags (ESTs) from novel clones. Here, we report the analysis of expression of 14 cDNAs and identify two clones, AA1 and AA28, that appear to be specifically expressed in RPE but not in any other tissue tested. We have also localized 15 novel cDNAs (including the two RPE-specific cDNAs) to human chromosomes using in situ hybridization or in conjunction with somatic cell hybrid analysis. The cDNAs were mapped to the following chromosomal regions:1p35→p33, 1q41→q42 (two clones), 3q11.2→q13.1, 3q24→q25, 4q13→q21, 6q22→q23, 7q34→q36, 10q23→ q24, 11q23→q24, 15q25→q26, 19p13.3, 20p13, 21q11.2→ q21, and 21q22.2→q22.3. The genetic and functional analysis of the two RPE-specific genes should contribute to a better understanding of RPE function. Chromosomal localization of RPE cDNAs will be valuable in identifying candidate genes for inherited diseases involving RPE dysfunction and aid in establishing the expression map of the human genome.
Confirmation of 9q34 as the chromosomal site of the human lipocalin LCN1 gene
Authors: Herzog H. , Baumgartner M. , Holzfeind P. , Redl B.
Published: May 2008

The gene encoding the lipocalin LCN1 was previously assigned to human chromosome 8q24 by fluorescence in situ hybridization of a genomic DNA fragment and to 9q34 by in situ hybridization of a radiolabeled cDNA fragment of LCN1. To resolve this discrepancy, we used hamster × human hybrid cells for polymerase chain reaction experiments. These investigations confirmed the localization of LCN1 on chromosome 9.
Chromosomal mapping of the genes for the human cell cycle proteins cyclin C (CCNC), cyclin E (CCNE), p21 (CDKN1) and KAP (CDKN3)
Authors: Demetrick D.J. , Matsumoto S. , Hannon G.J. , Okamoto K. , Xiong Y. , Zhang H. , Beach D.H.
Published: May 2008

Many gene products associated with the cdk cell cycle kinases are thought to regulate the active kinase complex and thus regulate the transition points of the cell cycle. Genes encoding these proteins may potentially function as oncogenes or tumor suppressor genes. We describe the chromosomal mapping by FISH of the genes for several cdk-associated proteins including human CCNC (cyclin C) to 6q21 CCNE (cyclin E) to 19q12→q13, CDKN1 (p21) to 6p21.2 and CDKN3 (KAP to 14q22). Some of these sites are near chromosomal translocations or LOH sites common to a variety of human tumors. The potential role for each of these genes in neoplasia is discussed.
Generation and molecular cytogenetic characterization of a radiation-reduction hybrid panel for human chromosome 6
Authors: Pappas G.J. , Thompson E. , Burgess A. , Greenwood A. , Trent J.M.
Published: May 2008

A neoR marked chromosome-6 containing hybrid (D113 JA) was used to generate a panel of 15 radiation-reduced hybrid cell lines. The panel was constructed by irradiating microcells isolated from D113JA at 800 or 8000 rads, providing different levels of chromosome 6 retention. These hybrids have been systematically analyzed using interspersed repetitive elements, previously assigned markers for chromosome 6, and fluorescent in situ hybridization (FISH). As expected, G418 selection has favored the retention of fragments near the insertion site of the neoR gene (6q16). The panel as constituted provides an important resource for regional assignment of molecular markers, especially to regions on 6q.
FISH analyses of a newly established thyroid tumor cell line showing a t(1;19)(p35 or p36.1;q13) reveal that the breakpoint lies between 19q13.3–13.4 and 19q13.4
Authors: Belge G. , Garcia E. , de Jong P. , Bartnitzke S. , Bullerdiek J.
Published: May 2008

Translocations involving the long arm of human chromosome 19 are specific chromosomal alterations found in a subset of benign thyroid tumors. In the present communication we describe the establishment of an SV40-transformed cell line derived from a thyroid adenoma with a t(1;19)(p35 or p36.1;q13). Cytogenetic studies were carried out on this cell line, using a series of cosmids mapping along the long arm of chromosome 19. In situ hybridization with probes for RYR1, ATP1A3, BCKDHA, ERCCl, POLDl, and TRPT revealed that only TRPT mapped distal to the breakpoint of the translocation. The results indicated that the breakpoint is located between POLD1 and TRPT at the boundary between chromosome bands 19q13.3 and 19q13.4.
Mechanisms of the origin of a G-positive band within the secondary constriction region of human chromosome 9
Authors: Macera M.J. , Verma R.S. , Conte R.A. , Bialer M.G. , Klein V.R.
Published: May 2008

We report on a so-called rare variant where a G-positive band was sandwiched within the secondary constriction (qh) region of chromosome 9 and is apparently different from previous cases when characterized by the fluorescence in situ hybridization technique. The major differences included duplication of β-satellite and satellite III DNA sequences and bands 9q 13q21.1, without duplication or inversion of the alphoid sequences. Based on the reported cases, at least four types of variations can be accounted for. A variety of mechanisms have been proposed to describe the origin of a G-positive band within the 9qh region, which appears to be similar when studied by routine cytogenetic techniques but differs by molecular methods. It is hypothesized that the clinical consequences depend upon the size of the G-positive band(s) duplicated, and a genetic inactivation mechanism might have some sort of influence during the so-called heterochromatinization process. It appears that heterochromatin, once thought to be composed of junk DNA, may have some role after all in suppression of gene(s) and/or spreading of inactivation, if genes are embedded within the heterochromatic region. Apparently, the mixture of different types of DNA creating patches of genetic debris have become a fundamental hidden treasure, where genetically active chromatin could be inactivated without dire consequences. The variable nature of heterochromatin has resulted in cytogenetic heteromorphisms of a number of human chromosomes. Their characterization by molecular techniques is becoming imperative, because fetal wastage have occurred in many situations where variant chromosomes were wrongly identified as chromosomal abnormalities.
Generation and characterization of a human chromosome 6-specific hncDNA library from a somatic cell hybrid
Authors: Piontek K. , Müller H.W. , Fischer U. , Götten E. , Batzer M.A. , Meltzer P.S. , Trent J.M. , Meese E.
Published: May 2008

Chromosome specific cDNA libraries are a useful source of candidate genes for disorders which have been linked to particular chromosomes. Here, we report the generation of a cDNA library made from a somatic cell hybrid retaining chromosome 6 as its only human component. In order to ascertain the chromosomal location of cDNAs the library was amplified by inter-Alu-PCR and used as probe for competitive in situ suppression (CISS). To identify human specific cDNA clones the library was screened with PD39, a highly human specific Alu consensus probe. Out of 350,000 clones 360 were found to hybridize with PD39. Nucleotide sequences were determined for 40 clones with inserts larger than 500 basepairs (bp) and a sequence comparison was performed at the National Center for Biotechnology Information using BLASTN. One clone was shown to be identical to Manganese Superoxide Dismutase (MnSOD/SOD2) which has previously been assigned to chromosome 6q25. Localization of 11 clones was determined using PCR and clone-specific primer pairs on a hybrid mapping panel DNA set. Two PCR-localized clones and five additional clones were localized by fluorescence in situ hybridization. Transcripts for five clones were identified by RT-PCR. The generation of chromosome 6-specific hncDNAs from a somatic cell hybrid should aid in the identification of disease-associated genes localized on this chromosome.
Mapping of the human TATA-binding protein gene (TBP) to chromosome 6qter
Authors: Rosen D.R. , Trofatter J.A. , Brown Jr. RH.
Published: May 2008

TATA-binding protein (TBP) is a general transcription factor involved in transcriptional initiation. We have used oligonucleotide primers flanking a polymorphic stretch of 38 glutamine codons in the 5’ coding region of the TBP gene to genetically map this gene. We report the location of the human TBP gene to be at 6qter.
Direct microdissection and microcloning of a translocation breakpoint region, t(1;11) (q42.2;q21), associated with schizophrenia
Authors: Muir W.J. , Gosden C.M. , Brookes A.J. , Fantes J. , Evans K.L. , Maguire S.M. , Stevenson B. , Boyle S. , Blackwood D.H.R. , St Clair D.M. , Porteous D.J. , Weith A.
Published: May 2008

We describe the generation of large-fragment microclone libraries from the chromosomal breakpoint of a reciprocal balanced translocation linked to schizophrenia. The abnormality was visible under the phase-contrast microscope, allowing direct dissection from unstained, unhanded met-phases. Two separate microdissection experiments yielded 443 and 672 recombinants, respectively. Following complete EcoRl digestion, inserts with an average size of 0.3 kb (range, 0.2–3 kb) were obtained in the first experiment and 1.5 kb (range, 0.15–6.5 kb) in the second. FISH analysis of pooled clones “painted” back onto the derivative chromosome and assignment of microclones to somatic cell hybrids confirmed the fidelity of the method. Microdissection of chromosome regions identified by karyotype rearrangements in unstained, unhanded metaphases is a potentially powerful tool for positional cloning.
A human 12p-derived cosmid hybridizing to subsets of human and chimpanzee telomeres
Authors: Höglund M. , Mitelman F. , Mandahl N.
Published: May 2008

The chromosomal locations of a cosmid-linking clone, CLN12–43, isolated from band 12p13 in man and containing subtelomeric repeat sequences, were determined by FISH. The cosmid hybridized to the telomeres of 3q, 6p, 9p, 12p, 15q, 19p, 20p, and 20q at high frequency and showed variable hybridization to 1p, 6q, and 9q. Two interstitial loci were detected, one at bands 2q13→q14 and the other at band 12q1 3. The former corresponds to the fusion point of chimpanzee chromosomes 12 and 13, resulting in the human chromosome 2, whereas the latter may represent a similar but more ancient fusion event. The cLN12-43 cosmid was also shown to hybridize to a set of chimpanzee telomeres.
Clarification of dubious karyotypes in Hodgkin’s disease by simultaneous fluorescence immunophenotyping and interphase cytogenetics (FICTION)
Authors: Weber-Matthiesen K. , Deerberg J. , Poetsch M. , Grote W. , Schlegelberger B.
Published: May 2008

Cytogenetic studies on Hodgkin’s disease (HD) typically reveal very complex karyotypes with a variety of numerical and structural abnormalities. The confusing thing is that about 10% of cases contain relatively discrete chromosome aberrations, for example a simple trisomy or loss of one single chromosome. Whether these karyotypes really correspond to Hodgkin and Reed-Sternberg (HRS) cells is uncertain. They could, for example, represent early stages in the evolution of the karyotype of the pathognomonic HRS cells. On the other hand, they could be artificial events that occur during the cytogenetic procedure. In our experience, isolated loss of the Y chromosome is the most frequent finding of this type. This aberration is usually considered to be a preparation artifact. However, if one takes into account that in HD up to 50% of male cases with complex karyotypes also lack the Y chromosome, a possible relation to HRS cells must be considered. The technique of simultaneous fluorescence immunophenotyping and interphase cytogenetic analysis (referred to as FICTION) is a powerful tool for studying the nature of cytogenetically abnormal cells. With the FICTION technique we studied four cases of HD in which the chromosome analysis had shown only the loss of the Y chromosome. Our aim was to clarify whether these karyotypes corresponded to the CD30-positive HRS cells. In two cases we found that HRS cells actually lacked the Y chromosome. There was strong evidence, however, that the HRS cells additionally had other chromosome aberrations and thus could not correspond to the cytogenetically determined karyotypes.
Isolation and mapping of a human gene (PDCD2) that is highly homologous to Rp8, a rat gene associated with programmed cell death
Authors: Kawakami T. , Furukawa Y. , Sudo K. , Saito H. , Takami S. , Takahashi E. , Nakamura Y.
Published: May 2008

From a human fetal lung cDNA library we isolated and characterized a human cDNA highly homologous to Rp8, a rat gene associated with programmed cell death. This cDNA, termed PDCD2 (programmed cell death-2), contained an open reading frame of 1032 nucleotides encoding 344 amino acids; it revealed 81% identity in DNA sequence and 83% identity in amino acid sequence with rat Rp8. The gene represented by PDCD2 was expressed in all human tissues examined. We assigned the PDCD2 locus to chromosomal band 6q27 by fluorescence in situ hybridization (FISH).
High-resolution mapping of SNCA encoding α-synuclein, the non-Aβ component of Alzheimer’s disease amyloid precursor, to human chromosome 4q21.3→q22 by fluorescence in situ hybridization
Authors: Shibasaki Y. , Baillie D.A.M. , St. Clair D. , Brookes A.J.
Published: May 2008

The human α-synuclein gene (SNCA) was previously identified as the non-Aβ component of Alzheimer’s disease amyloid precursor (NACP). A cosmid clone containing this gene has been isolated and mapped by FISH and high-resolution fluorescence banding to human chromosome 4q21.3→q22.
Localization of PURA, the gene encoding the sequence-specific single-stranded-DNA-binding protein Purα, to chromosome band 5q31
Authors: Ma Z.-W. , Pejovic T. , Najfeld V. , Ward D.C. , Johnson E.M.
Published: May 2008

Purα (PurA) is a sequence-specific single-stranded-DNA-binding protein implicated in control of both DNA replication and transcription. We have localized the Purα gene (PURA) to human chromosome band 5q31 by fluorescence in situ hybridization with a 16-kb genomic probe together with hybridization of a cDNA probe to blots of DNA from human-hamster cell lines containing individual human chromosomes. Sequences with homology to the PURA locus are also present at 6ql4. The 5q31 locus is frequently deleted in myelogenous leukemias and other cancers.
Chromosome end associations, telomeres and telomerase activity in ataxia telangiectasia cells
Authors: Pandita T.K. , Pathak S. , Geard C.R.
Published: May 2008

Cells derived from individuals with ataxia telangiectasia (AT) show enhanced spontaneous levels of chromosomal abnormalities and are sensitive to ionizing radiations and radiomimetic drugs, as evidenced by decreased survival and increased chromosome aberration frequencies at mitosis when compared with normal cell lines. The higher base line frequencies of chromosome aberrations in part involve chromosome end-to-end associations as seen at metaphase. Since telomeres of tumor cells and aging tissues are often reduced in length, chromosome end associations may be due to loss of telomeric repeats. We studied the chromosome behavior and telomeres of two ataxia telangiectasia lymphoblastoid cell lines compared to two normal control cell lines. The ataxia telangiectasia cell lines showed higher frequencies of chromosome end associations both at metaphase and in interphase, determined in prematurely condensed chromosomes of G1 and G2 cells. They also showed higher frequencies of chromosomal breaks at metaphase and fewer telomeric signals determined using fluorescent in situ hybridization with a (TTAGGG)n probe. The frequency of telomeric repeats was variable in the ataxia telangiectasia cell lines (4.3 and 8.2 kb) compared to the normal cell lines (9.6 and 12 kb) and an inverse correlation between telomere length and chromosome end associations was observed. Both ataxia telangiectasia cell lines showed more robust telomerase activity than the normal cell lines, precluding defective enzymatic capacity as the basis for the chromosome end associations. It is possible that chromatin structure in the form of telomere-nuclear matrix interactions are variant in ataxia telangiectasia cells negatively influencing telomerase function and contributing to telomere associations.
The lymphoid proliferation-associated gene EPAG maps to human chromosome region Xq21→q22
Authors: Dizikes G.J. , Bennett J.S. , Metz R.J. , Nawrocki J.F.
Published: May 2008

Using Southern blot and fluorescence in situ hybridization analyses, we have shown that the novel human gene EPAG, expressed in association with the mitogenic active tion of T and B cells in peripheral blood, maps to chromosome region Xq21→q22. These data establish EPAG as a candidate gene in X-linked disorders.
In situ hybridization mapping of a 500-kDa calcium-sensing protein gene (LRP2) to human chromosome region 2q31→q32.1 and porcine chromosome region 15q22→q24
Authors: Chowdhary B.P. , Lundgren S. , Johansson M. , Hjälm G. , Åkerström G. , Gustavsson I. , Rask L.
Published: May 2008

Recently, a 500-kDa protein, with homology to the rat Gp330 glycoprotein, was found to be expressed on the surface of human parathyroid, placental cytotrophoblast, and renal proximal tubule cells. The protein has been implicated to function as a sensor of extracellular calcium on parathyroid and placental cytotrophoblast cells. We report here in situ hybridization mapping of the corresponding gene, designated as low-density lipoprotein receptor related protein-2 and symbolized as LRP2, to human chromosome region 2q31→q32.1 and porcine chromosome region 15q22→q24. The results are discussed in a comparative mapping context.
Meiotic segregation of the X and Y chromosomes and chromosome 1 analyzed by three-color FISH in human interphase spermatozoa
Authors: Chevret E. , Rousseaux S. , Monteil M. , Pelletier R. , Cozzi J. , Sèle B.
Published: May 2008

Meiotic segregation of the X and Y chromosomes and chromosome 1 was analyzed by three-color fluorescence in situ hybridization (FISH) in 94,575 human interphase spermatozoa from four control subjects. More than 99% of the sperm cells were labeled. The proportions of X- and Y-bearing sperm were estimated to be 49.83% and 48.30%, respectively. The disomy rates were 0.04%, 0.009%, and 0.20% for the X and Y chromosomes and chromosome 1, respectively. Hyperhaploidy with an extra gonosome was found in 0.34% of spermatozoa, due to nondisjunction during meiosis I. The frequency of diploidy was 0.11 % at meiosis I and 0.036% at meiosis II. Cohybridization of one autosomal and two gonosomal probes, in three-color FISH in interphase spermatozoa, seems to accurately discriminate diploidies from disomies, as well as the meiotic origin of gonosomal aneuploidies in sperm cells.
High-resolution mapping of 10 unique DNA sequences to human chromosome 3 subregions by in situ hybridization
Authors: Atchison L. , Atchison M.L. , Cannizzaro L.A.
Published: May 2008

Ten single-copy DNA probes derived from a human chromosome 3-specific genomic library were mapped by in situ hybridization to subregions of this chromosome. Seven sequences were assigned to subregions of 3q and two sequences were assigned to subregions of 3p. One single-copy DNA probe was assigned to the centromeric region of chromosome 3 by Southern blot analysis of DNA isolated from a somatic cell hybrid containing centromeric sequences of this chromosome. These DNA clones mapped by in situ hybridization can provide useful landmarks for mapping various disease loci on chromosome 3. They may also be useful for the generation of physical and genetic maps.
Isolation, characterization and chromosomal assignment of human colligin-2 gene (CBP2)
Authors: Ikegawa S. , Sudo K. , Okui K. , Nakamura Y.
Published: May 2008

Colligin, a collagen-binding glycoprotein localized to endoplasmic reticulum, belongs to the serpin superfamily. Colligin has been identified and cloned in a number of species including mouse, rat, chicken, and human. We have isolated and characterized a full-length human cDNA clone that encodes a 418-amino-acid peptide that is highly homologous (97 % identity) to the previously reported human colligin gene, and have named this new member of the colligin family human colligin-2. The expression of the colligin-2 gene (CBP2) is ubiquitous among all normal human tissues except for brain and peripheral leukocytes. We have mapped this novel gene to chromosome llql3.5 by fluorescent in situ hybridization (FISH) using a cosmid clone containing the entire coding sequence and the 3’ non-coding sequence.
Assignment of the mouse homologue of a human MEN1 candidate gene, phospholipase C-β3 (Plcb3), to chromosome region 19B by FISH
Authors: Gobl A.E. , Chowdhary B.P. , Shu W. , Eriksson L. , Larsson C. , Weber G. , Öberg K. , Skogseid B.
Published: May 2008

A recent study using comparative mapping analysis suggests that the proximal segment of mouse chromosome 19 contains the mouse homologs of the human multiple endocrine neoplasia type 1 (MENl) flanking markers proximal to the locus. We have recently shown that phospholipase C-β3 (PLCB3) is a candidate gene for the MENl syndrome. In the present investigation we used fluorescence in situ hybridization with a genomic DNA clone for mouse Plcb3, and mapped the locus to chromosome region 19B. This is in agreement with the comparative mapping of the MENl flanking markers in mouse.
Mapping segmental imbalances using comparative genomic hybridization and eigenanalysis
Authors: Haddad B. , Antonacci R. , Rizzu P. , Lindsay E.A. , Hughes M.R. , Smith L.C. , Knapp R.D. , Baldini A.
Published: May 2008

We have tested a new approach to comparative genomic hybridization (CGH) analysis using digital ratio images and eigenanalysis, which allows the recognition of consistent patterns along the chromosomes and discards random (background noise) patterns. We have performed test experiments using genomic DNAs from a patient with a duplication, another with a deletion of a chromosome segment, and a prostate cancer biopsy. Image ratio analysis was performed, and ratio images of the relevant chromosome were subjected to eigenanalysis. The results showed a high-contrast enhancement of the regions corresponding to the unbalanced genomic segment, with clearly defined limits between normal and abnormal fluorescence ratios. The combination of digital ratio images and eigenanalysis allowed the precise mapping of unbalanced regions consistent with other methods of analysis. Because there is no limit to the number of chromosomes that can be analyzed at any one time, the method has the potential of increasing the sensitivity of CGH by reducing the noise component.
Mapping the X chromosome breakpoint in two papillary renal cell carcinoma cell lines with a t(X;1)(p11.2;q21.2)and the first report of a female case
Authors: Shipley J.M. , Birdsall S. , Clark J. , Crew J. , Gill S. , Linehan M. , Gnarra J. , Fisher S. , Craig I.W. , Cooper C.S.
Published: May 2008

A t(X;1)(p11.2;q21.2) has been reported in cases of papillary renal cell tumors arising in males. In this study two cell lines derived from this tumor type have been used to indicate the breakpoint region on the X chromosome. Both cell lines have the translocation in addition to other rearrangements and one is derived from the first female case to be reported with the t(X;1)(p11.2;q21.2). Fluorescence in situ hybridization (FISH) has been used to position YACs belonging to contigs in the Xp11.2 region relative to the breakpoint. When considered together with detailed mapping information from the Xp11.2 region the position of the breakpoint in both cell lines was suggested as follows: Xpter→Xp11.23 – OATL1 – GATA1 – WAS – TFE3 – SYP – t(X;1) – DXS255 – CLCN5 – DXS146 – OATL2 – Xp11.22→Xcen. The breakpoint was determined to lie in an uncloned region between SYP and a YAC called FTDM/1 which extends 1 Mb distal to DXS255. These results are contrary to the conclusion from previous FISH studies that the breakpoint was near the OATL2 locus, but are consistent with, and considerably refine, the position that had been established by molecular analysis.
A new reciprocal translocation (7q+;15q–) in the domestic pig
Authors: Konfortova G.D. , Miller N.G.A. , Tucker E.M.
Published: May 2008

A reciprocal translocation was identified in a phenotypically normal Large White boar. Chromosome preparations from the carrier were studied by flow sorting, chromosome painting and G-banding. The flow karyotype displayed one additional clearly distinguishable peak, while in situ hybridization and G-banding showed two abnormal chromosomes involved in the translocation. All the results suggested that the translocation involved chromosomes 7 and 15 and the karyotype investigated was 38, XY, rcp(7;15)(q24;q12). The parents and three full sibs of the carrier had normal karyotypes. It would seem that the translocation had arisen de novo.
Molecular analysis of a novel subtelomeric repeat with polymorphic chromosomal distribution
Authors: Martin-Gallardo A. , Lamerdin J. , Sopapan P. , Friedman C. , Fertitta A.L. , Garcia E. , Carrano A. , Negorev D. , Macina R.A. , Trask B.J. , Riethman H.C.
Published: May 2008

DNA from a 50-kb yeast artificial chromosome (YAC) containing one human telomere was characterized. Cloned sequences from the centromeric end of this YAC (designated yRM2001) localized to several human chromosomes by somatic hybrid panel mapping. The telomeric end of the YAC contained both (TTAGGG)n sequences and the previously characterized TelBam3.4 subterminal repeat element. A novel low-copy repeat element (designated HC1103) mapped 19 kb from the telomeric end of the YAC. This repeat was shown by fluorescence in situ hybridization to be present in several sub-telomeric regions (3q, 12p, 15q, 19p, and 20p) and at an interstitial site (2q13→q14) in all individuals studied, but to be polymorphically distributed at several other telomeres. The YAC vector-insert EcoRl cloning site was positioned 50 kb to 70 kb from chromosome termini in human genomic DNA using RecA-assisted restriction endonuclease (RARE) cleavage analysis. Our results suggest that the DNA segment cloned in yRM2001 contains a novel block of low-copy DNA consistently present at some human telomeres, but polymorphically distributed at others.
The gene for the APC-binding protein β-catenin (CTNNB1) maps to chromosome 3p22, a region frequently altered in human malignancies
Authors: Trent J.M. , Wiltshire R. , Su L.-K. , Nicolaides N.C. , Vogelstein B. , Kinzler K.W.
Published: May 2008

β-Catenin is one of the E-cadherin associated proteins involved in the process of cellular adhesion. It has recently been shown to interact with the APC protein whose gene is known to be mutated in the germline of familial adenomatous polyposis patients. This interaction implies that β-catenin is a potential regulator of the APC gene. The localization of the human β-catenin gene (CTNNB1) to chromosome 3p22, by fluorescent in situ hybridization (FISH), has linked the gene to a region that is frequently altered in several human malignancies. The location of the gene and the protein interactions suggest the importance of β-catenin in the etiology of various human cancers.
The rat Prm3 gene is an intronless member of the protamine gene cluster and is expressed in haploid male germ cells
Authors: Schlüter G. , Engel W.
Published: May 2008

We have cloned and sequenced the cDNA of a novel gene from the rat protamine gene cluster. This gene, preliminarily referred to as Prm3, is intronless and resides between the genes for protamine 2 and transition protein 2. Prm3 is transcribed from the same strand as these genes and is expressed in haploid stages of spermatogenesis. The 410-bp-long cDNA possesses an ORF, coding for a putative 104-amino acid polypeptide with a high content of glutamic acid.
Assignment of the glucose transporter 1 gene (SLC2A1) to swine chromosome 6q34→qter
Authors: Kusumoto H. , Yasue H.
Published: May 2008

A cosmid clone containing the glucose transporter gene (SLC2A1) was selected from a cosmid library of swine genomic fragments by colony hybridization using the cDNA of swine glucose transporter as a probe. The genomic fragment thus cloned was partially sequenced, and the sequence was compared first with the sequence of the cDNA and then with the reported rat genomic sequence. The sequence homology and exon/intron structure indicated that the genomic fragment contained at least part of SLC2A1. The fragment, together with vector DNA, was then labeled by biotin and used as a probe for in situ hybridization on swine chromosome spreads. Hybridization was visualized by the FITC-labeled streptavidin/biotinylated anti-streptavidin system together with the R-band pattern of chromosomes. The fluorescence signals revealed that SLC2A1 is localized on swine chromosome 6q34→qter.