bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of aneuploidy in human sperm by fluorescence in situ hybridization (FISH): different frequencies in fresh and stored sperm nuclei
Authors: Martin R.H. , Chan K. , Ko E. , Rademaker A.W.
Published: May 2008

Fluorescence in situ hybridization (FISH) with chromosome-specific repetitive DNA probes provides a new method for rapid detection of aneuploidy in human sperm. There is widespread interest in this technique for basic research, as well as for screening men exposed to potential aneugens. A number of laboratories have reported a wide range in the frequency of aneuploidy for chromosomes in human sperm, suggesting that FISH may not reflect the true frequency accurately. We have serendipitously discovered that the length of time that fixed frozen sperm nuclei are stored affects both the hybridization efficiency and disomy frequency of individual chromosomes. This may explain some of the variation in the aneuploidy frequencies observed among laboratories.
Assignments of 37 YAC clones to R-banded chromosomes by fluorescent in situ hybridization
Authors: Slim R. , Machavoine C. , Bernheim A.
Published: May 2008

Fluorescent in situ hybridization was used to assign 37 yeast artificial chromosomes (YACs) from the CEPH (Centre d’Etude du Polymorphisme Humain) libraries to R-banded metaphases stained with propidium iodide. The use of the whole yeast DNA as probe, allows rapid mapping and characterization of YAC clones. Of 37 YAC clones, 11 were found cytogenetically chimeric (30%). The YAC clones reported in this study can be used to isolate and characterize targeted regions involved in genetic diseases and cancer breakpoints.
Chromosome assignment of the human glutathione S-transferase μ3 gene (GSTM3) to chromosome 1 by gene specific polymerase chain reaction
Authors: Gough A.C. , Zhong S. , Wolf C.R. , Spurr N.K.
Published: May 2008

Oligonucleotide primers specific for exons 4 and 5 sequences were used to amplify a unique 199-bp fragment in the human GSTM3 gene. Using DNA from a panel of somatic cell hybrids we assigned the GSTM3 locus to chromosome 1p.
Isolation and mapping of 328 new cosmid markers on human chromosome 8: construction of a high-resolution cytogenetic map of chromosome 8 with 416 markers
Authors: Nakamura Y. , Okui K. , Takahashi E. , Koyama K.
Published: May 2008

We have determined the chromosomal localizations of newly isolated cosmids by fluorescent in situ hybridization (FISH) on prometaphase R-banded chromosomes and have constructed a high-resolution cytogenetic map for human chromosome 8 with 416 cosmid markers, including 328 new markers and 88 reported previously. Of the 416 markers, 229 were mapped to the long arm of chromosome 8, 181 to the short arm, and 6 to the centromere. Although the clones were scattered throughout the chromosome, they were concentrated in R-positive bands. Since the estimated physical length of chromosome 8 is 135 Mb, the overall average distance between loci is 320 kb, but the average separation of loci on R-positive bands is nearly 130–200 kb. This cytogenetic map will serve as a resource for efforts to characterize chromosomal and molecular aberrations involved in cancers, to clone genes associated with hereditary diseases, and to construct a detailed physical map of large electrophoretic fragments and/or contiguous cosmids and yeast artificial chromosomes.
Chromosome banding in Amphibia
Authors: Schmid M. , Klett R.
Published: May 2008

Replication banding patterns were induced in the chromosomes of Gastrotheca riobambae by treating cell cultures with 5-bromodeoxyuridine (BrdU) and deoxythymidine (dT). In particular, the time sequence of replication of the highly differentiated XY/XX sex chromosomes was meticulously analyzed throughout the S phase. In the homogametic female, BrdU/dT labeling revealed no evidence of asynchronous replication between euchromatic regions in the XX pair. Minor replication asynchronies between the two X chromosomes were restricted to the heterochromatic C-bands. These results are further proof that dosage compensation in Amphibia for X- or Z-linked genes does not occur by inactivation of one of the two (XX or ZZ) sex chromosomes in the cells of homogametic individuals. In the very large and almost completely heterochromatic Y chromosome of G. riobambae, the various C-bands comprise at least three different structural categories, resulting in a complex pattern of early- and late-replicating bands along the Y chromosome.
High resolution ordering of DNA markers by multi-color fluorescent in situ hybridization of prophase chromosomes
Authors: Inazawa J. , Ariyama T. , Tokino T. , Tanigami A. , Nakamura Y. , Abe T.
Published: May 2008

To improve resolution for physical ordering of adjacent DNA loci, prophase chromosomes were used for multi-color fluorescent in situ hybridization (FISH). The prophase chromosomes were prepared from cultured lymphocytes by a thymidine synchronization, bromodeoxyuridine release technique and then treating the synchronized cultures with topoisomerase II inhibitors ICRF154 or ICRF193. Almost all mitotic figures exhibited highly elongated prophase chromosomes without significant reduction of the mitotic index. Using multi-color FISH with these prophase chromosomes, we were able to distinguish signals for loci separated by as little as 50 kb, and determine their orientation. Furthermore, using this prophase ordering system, we confirmed the linear order and defined the orientation of seven cosmid markers within a 360-kb region surrounding D1OS102, a locus that is closely linked to the disease locus in families segregating an allele causing multiple endocrine neoplasia IIA (MEN2A). This prophase FISH system, by rapidly and precisely providing the linear order of loci that are very close, can expedite construction of fine cytogenetic maps and contribute to positional-cloning studies in which the precise ordering of DNA loci in a target region is critical.
Increased FISH efficiency using APC probes generated by direct incorporation of labeled nucleotides by PCR
Authors: Richard F. , Vogt N. , Muleris M. , Malfoy B. , Dutrillaux B.
Published: May 2008

Probes of various sizes from the adenomatous polyposis coli gene (APC) were directly biotinylated by polymerase chain reaction (PCR) from genomic DNA. PCR labeling gave high efficiency in detection of fluorescence in situ hybridization (FISH) signals. Probes as small as 250 base pairs could be visualized through a fluorescence microscope without any image processing.
Mapping of the gene coding for a paraneoplastic encephalomyelitis antigen (HuD) to human chromosome site 1p34
Authors: Muresu R. , Baldini A. , Gress T. , Posner J.B. , Furneaux H.M. , Siniscalco M.
Published: May 2008

A cDNA clone coding for a human brain protein (HuD), which is highly homologous to the Drosophila neuronal determination protein Elav and elicits antibody formation in a high proportion of patients with paraneoplastic encephalomyelitis, was used to isolate a λ phage recombinant clone, including a large fragment of the relevant human genomic region. The fragment proved to be an efficient probe for the precise subregional mapping of the gene by molecular in situ hybridization onto extended human prometaphase chromosomes. Analysis of banded metaphases with clear hybridization signals pointed unequivocally to the localization of the HuD gene to human chromosome band 1p34.
Digitized and differentially shaded human chromosome ideograms for genomic applications
Authors: Francke Uta
Published: May 2008

Human chromosome ideograms that depict 850 bands, numbered in agreement with ISCN (1981) nomenclature but based on actual measurements of band sizes and differentiated by five shades of staining intensity, have been digitized using commercially available graphics software. They provide for more accurate estimates of distances within chromosome arms, DNA content of chromosome bands and correlation between cytogenetic, molecular and genetic linkage maps than the standard ISCN ideograms.
The human gene for water channel aquaporin 1 (AQP1) is localized on chromosome 7p15→p14
Authors: Deen P.M.T. , Weghuis D.O. , Geurts van Kessel A. , Wieringa B. , van Os C.H.
Published: May 2008

The chromosomal localization of the gene encoding aquaporin 1 (previously called CHIP28), which acts as a water channel in erythrocytes and in the renal proximal tubules and descending limbs of Henle, was determined. Southern blot hybridizations on chromosomal DNA of a panel of 25 different human × rodent hybrid cell lines localized the aquaporin 1 gene to human chromosome 7. Additionally, in situ hybridization on R-banded metaphase chromosomes sublocalized the aquaporin 1 gene (AQP1) to 7p15→p14, and some sequence-tagged sites in this region were identified.
Demonstration of the X-linkage and order of the genes GLA, G6PD, HPRT, and PGK in two vole species of the genus Microtus
Authors: Nesterova T.B. , Mazurok N.A. , Matveeva N.M. , Shilov A.G. , Yantsen E.I. , Ginsburg E.Kh. , Goss S.J. , Zakian S.M.
Published: May 2008

Using a variety of genetic methods, it is shown in this paper that the genes GLA, G6PD, HPRT, and PGK are X-linked in the vole Microtus subarvalis. The order of these genes has been investigated in two vole species, M. subarvalis and M. kirgisorum, by using the mapping technique of Goss and Harris (1977a, b), which depends on the analysis of γ-ray-induced gene segregation. The experimental data were processed with the computer programme RHMAP (Ginsburg et al., 1993). The analysis indicated that the correct gene order in M. subarvalis is PGK-HPRT-G6PD-GLA, and the same gene order was found to be the most probable for M. kirgisorum. The relative distances between the genes in the two vole species are apparently the same. The RHMAP programme has also been applied to data previously reported for the same set of X-linked genes in the American mink (Zhdanova et al., 1988), the Australian marsupial Planigale maculata (Dobrovic and Graves, 1986), and man. The evolutionary conservation of the linear order of these X-linked genes in different mammalian taxa is discussed.
Assignment of the human skeletal muscle alpha actin gene (ACTA1) to 1q42 by fluorescence in situ hybridisation
Authors: Akkari P.A. , Eyre H.J. , Wilton S.D. , Callen D.F. , Lane S.A. , Meredith C. , Kedes L. , Laing N.G.
Published: May 2008

The human skeletal muscle alpha actin gene (ACTAl) has previously been localized to 1p21→qter using somatic cell hybrids and a specific probe from the 3’ untranslated region of the gene. Using fluorescence in situ hybridization the localization has been confirmed and the ACTAl gene precisely mapped to 1q42.
Intragenic reorganization of RB1 in a complex (4;13) rearrangement demonstrated by FISH
Authors: Rosenberg C. , Janson M. , Nordeskjöld M. , Børresen A.L. , Vianna-Morgante A.M.
Published: May 2008

Reciprocal chromosome translocations with no apparent loss of material are the most common de novo structural rearrangements in man. The large majority of these cases have been characterized cytogenetically but very few have been investigated at the molecular level. Using fluorescence in situ hybridization (FISH) we have studied the organization of the tumor supressor gene RB1 in a patient with retinoblastoma and a rearrangement between chromosomes 4 and 13. In addition to the hybridization signal on the normal chromosome 13, three distinct sites of hybridization of RB1 probes on the translocated chromosomes were detected. These findings show that a complex rearrangement occurred involving at least three breaks on chromosome 13, two of them in the RB1 gene. This also demonstrates that FISH, which offers resolution between that of fine molecular methods and classical cytogenetics, is a valuable tool for investigating organization of sequences at breakpoints of chromosomal rearrangements.
The RAP1GA1 locus for human Rap1-GTPase activating protein 1 maps to chromosome 1p36.1→p35
Authors: Weiss J. , Rubinfeld B. , Polakis P.G. , McCormick F. , Cavenee W.K. , Arden K.C.
Published: May 2008

Using a panel of somatic cell hybrids we have mapped the locus for Rap1-GTPase activating protein 1 (RAP1GA1) to human chromosome 1. Fluorescence in situ hybridization experiments independently confirmed the chromosomal localization and refined it to 1p36.1→p35.
Multicolour fluorescence in situ hybridisation to order small, single-copy probes on metaphase chromosomes
Authors: Heppell-Parton A.C. , Albertson D.G. , Fishpool R. , Rabbitts P.H.
Published: May 2008

In constructing complete human chromosome maps, the relative order of markers and their precise chromosomal location will be combined. Multicolour in situ hybridisation, in which two probes are simultaneously hybridised to chromosomes and subsequently distinguished, potentially will provide both types of information. Using this technique, we have produced an ordered map of eight human chromosome 3 DNA markers, using small, single-copy probes that can detect target sequences ranging in size from 4 kb to as little as 500 bp.
The fucosyltransferase locus FUT1 maps distal to apolipoprotein loci E and C2 on human chromosome 19
Authors: Rouquier S. , Giorgi D. , Bergmann A. , Brandriff B. , Lennon G.
Published: May 2008

The location of the fucosyltransferase locus FUT1 relative to the apolipoprotein E/C2 loci on human chromosome 19 has remained unclear. We determined by a combination of physical mapping and fluorescence in situ hybridization that this fucosyltransferase gene maps distal to the apolipoprotein loci.
Chromosomal mapping of human CDK2, CDK4, and CDK5 cell cycle kinase genes
Authors: Demetrick D.J. , Zhang H. , Beach D.H.
Published: May 2008

Cyclin dependent kinases (CDK’s) are kinases that interact with cyclins and regulate cell division. Genomic clones encoding human CDK2, CDK4, and CDK5 were obtained and mapped to their respective chromosomal loci using fluorescence in situ hybridization on human lymphocyte metaphase spreads. Interestingly, CDK2 and CDK4 were located at the same position, 12q13, and CDK5 was mapped to 7q36. 12q13 has been shown to be associated with chromosome alterations such as amplifications and translocations in solid tumors. 7q36 does not appear to be a major site of chromosome alterations in tumors. As CDK2 and CDK4 appear to be important in regulating the human cell cycle, it is possible that the alterations of the 12q13 locus in tumors may involve changes in the regulation of CDK2 and CDK4 genes.
Regional assignment of the human immunoglobulin processed pseudogene Cε3 (IGHEP2) to 9p24.2→p24.1 by fluorescence in situ hybridization
Authors: Tanabe H. , Ishida T. , Ueda S. , Sofuni T. , Mizusawa H.
Published: May 2008

The human immunoglobulin processed pseudogene CΕ3 (IGHEP2), which was assigned to chromosome 9 by somatic cell hybrid analysis, has not been regionally localized as yet. In this study, using fluorescence in situ hybridization (FISH) combined with conventional QFQ-, RBG- or GTG-banding, IGHEP2 was assigned to the p terminus region of chromosome 9, at band 9p24.2→p24.1. This result suggests that the CΕ3 gene is a novel telomeric DNA marker useful not only for constructing the physical map of human chromosome 9 but also for cytogenetic analyses such as cryptic translocations. In addition, comparative mapping of this gene in other catarrhine primates would contribute to investigations of human and other primate karyotype evolution.
A mammalian homologue of Drosophila heterochromatin protein 1 (HP1) is a component of constitutive heterochromatin
Authors: Wreggett K.A. , Hill F. , James P.S. , Hutchings A. , Butcher G.W. , Singh P.B.
Published: May 2008

The Drosophila HP1 gene contains a highly conserved sequence, the chromobox, which can be used to isolate HP1-like genes from both mouse (M31 and M32) and man (HSM1) (Singh et al., 1991). Here we report that a monoclonal antibody (MoAb) raised against the M31 protein recognises a 26-kDa protein in murine and human nuclear extracts and localises to large masses of condensed chromatin within murine interphase nuclei, some of which are associated with the nucleoli. At metaphase, the MoAb binds to the centromeres of both human and murine chromosomes. The evolutionary conservation of this chromosomal localisation indicates that the M31 protein is likely to be important in the packaging of mammalian chromosomal DNA into constitutive heterochromatin.
Localization of the CAMKG gene encoding γ isoforms of multifunctional calcium/calmodulin-dependent protein kinase (CaM kinase) to human chromosome 10 band q22 and mouse chromosome 14
Authors: Li X. , Nghiem P. , Schulman H. , Francke U.
Published: May 2008

Multifunctional calcium/calmodulin-dependent protein kinase (CaM kinase) is an enzyme mediating calcium-dependent signal transduction pathways. CaM kinase exists in a variety of isoforms, each with a distinct tissue-specific expression pattern, that enables the kinase to regulate multiple functions in mammalian systems. Here we report the chromosomal localization of the previously cloned human γ-CaM kinase gene (CAMKG). By using a mapping panel of human × Chinese hamster somatic cell hybrid lines and fluorescence in situ hybridization, we have assigned human CAMKG to chromosome 10q22. We have partially cloned the murine γ-CaM kinase gene and mapped it Camkg to mouse chromosome 14 by analyzing a panel of mouse × rodent somatic cell hybrid lines. A recessive gene, asa, implicated in the control of autoimmune response, is located within the predicted region for Camkg.
Cell-cycle-stage specificity of the methotrexate block as resolved by X-ray-induced chromosome damage
Authors: Richardson V.B. , Littlefield L.G. , Sayer A.M. , Peterson P.T.
Published: May 2008

Radiation-induced chromosome aberrations were used as biomarkers to compare G₀, mid-G1, and methotrexate (MTX)-arrested lymphocytes. The ratio of chromosome-type to chromatid-type aberrations in MTX-arrested cells was consistent with that predicted when postreplicative chromosomes are exposed to ionizing radiation and supports the premise that MTX arrests cells in late S/G2 of the cell cycle.
Assignment of the human gene encoding the epidermal serine proteinase inhibitor SKALP (PI3) to chromosome region 20q12→q13
Authors: Molhuizen H.O.F. , Zeeuwen P.L.J.M. , OIde Weghuis D. , Geurts van Kessel A. , Schalkwijk J.
Published: May 2008

Recently we isolated a cDNA clone corresponding to an epidermal serine proteinase inhibitor named SKALP (skin-derived antileukoproteinase). Here we report the chromosomal localization of the human gene encoding SKALP by Southern blot analysis of a panel of human × hamster hybrid cell lines and by nonradioactive in situ hybridization on R-banded human lymphocyte chromosome spreads. The SKALP-encoding gene has been assigned the approved symbol P13 by the Human Gene Mapping nomenclature committee.
Refined localization of the asparagine synthetase gene (ASNS) to chromosome 7, region q21.3, and characterization of the somatic cell hybrid line 4AF/106/K015
Authors: Heng H.H.Q. , Shi X-M. , Scherer S.W. , Andrulis I.L. , Tsui L.-C.
Published: May 2008

We have mapped the asparagine synthetase gene (ASNS) to 7q21.3 by fluorescence in situ hybridization. While this study refined the localization of the gene, it also revealed a rearrangement in a somatic cell hybrid line which was used in previous ASNS mapping. Using additional probes from other regions of human chromosome 7, we showed that this cell line (4AF/106/K015) contained a rearranged chromosome 7 in which a segment of the long arm was apparently duplicated and inserted into the short arm. Caution should be used therefore when interpreting data obtained from this cell line for gene mapping studies.
Fast, sensitive multicolor detection of nucleic acids in situ by PRimed IN Situ labeling (PRINS)
Authors: Hindkjær J. , Koch J. , Terkelsen C. , Brandt C.A. , Kølvraa S. , Bolund L.
Published: May 2008

PRimed IN Situ labeling (PRINS) has become an alternative to traditional fluorescence in situ hybridization (FISH) methods for detection of nucleic acids in situ. PRINS is based on sequence-specific annealing in situ of an unlabeled DNA probe. The probe serves as a primer for chain elongation in situ, catalyzed by a suitable .DNA polymerase that uses labeled nucleotides as substrate. The fact that the probe is unlabeled means that high probe concentrations can be utilized, making the hybridization very fast. We describe here a fast method for detection of three different target sequences visualized in different colors with PRINS. An advantage, relative to FISH, is that even probes with different melting temperatures can be detected in the same metaphase with optimal stringency for each probe.
Chromosomal localization of the human AHR locus encoding the structural gene for the Ah receptor to 7p21→p15
Authors: Le Beau M.M. , Carver L.A. , Espinosa, III R. , Schmidt J.V. , Bradfield C.A.
Published: May 2008

The AHR locus encodes the structural gene for the Ah receptor, a ligand activated transcription factor that regulates the expression of a number of enzymes involved in the metabolism of chemical carcinogens and that appears to mediate the tumor promoting properties of compounds such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Using polymerase chain reaction (PCR), we amplified exon-10 and intron-D of the AHR gene from human genomic DNA. By using PCR analysis of somatic cell hybrids and fluorescence in situ hybridization of metaphase cells, we localized AHR to human chromosome 7, bands p21→pl5. This mapping data should prove useful in determining the role that the AHR locus plays in human cancer incidence and in the identification of human populations with altered susceptibilities to the toxic/carcinogenic effects of planar aromatic hydrocarbons.
A radiation hybrid map of human chromosome 18
Authors: Francke U. , Chang E. , Comeau K. , Geigl E.-M. , Giacalone J. , Li X. , Luna J. , Moon A. , Welch S. , Wilgenbus P.
Published: May 2008

A human × Chinese hamster (CH) somatic cell hybrid subclone deficient in HPRT and containing only human chromosome 18 was irradiated with 7000 rad and fused to a thymidine kinase deficient CH cell line. Radiation-rescued hybrid cell lines, selected in HAT medium, were analyzed for human DNA with human interspersed-repeat sequence primers. Size and number of human chromosome fragments retained in a subset of hybrids were determined by FISH. A panel of 98 radiation hybrids (RH) was selected and analyzed for 90 chromosome 18-specific STSs by PCR, and for the D18Z1 centromeric marker by Southern blotting. STSs were developed from previously mapped RFLP loci and from published sequences. In addition, 32 novel STSs were generated from an 18-specific lambda library and from 18-specific YACs previously localized to chromosome bands by FISH. Marker retention frequency varied from 8–65 % with an average of 24%. In selected RH the STS typing data were correlated with the chromosome 18 regions retained using ‘reverse FISH’ of IRS-PCR products from the RH to normal metaphase chromosomes. The order and intermarker distances of loci were determined using two-point and multipoint maximum likelihood methods. The resulting RH map covers most of chromosome 18 with four groups of tightly linked markers and three regions of loosely linked markers, one around the centromere and two on the long arm. More than a third of the markers are polymorphic and allow integration with the linkage map. This RH map provides a framework for establishing a clone contig of the entire chromosome 18.
Chromosomal mapping of mouse 5S rRNA genes by direct R-banding fluorescence in situ hybridization
Authors: Matsuda Y. , Moriwaki K. , Chapman V.M. , Hoi-Sen Y. , Akbarzadeh J. , Suzuki H.
Published: May 2008

The mouse 5S rRNA gene was mapped by direct R-banding fluorescence in situ hybridization (FISH) with biotinylated probes. Two genomic fragments amplified by PCR from total genomic DNA of BALB/c mice and Mus spretus, a 0.16-kb fragment that included the 121 -bp 5S rRNA gene and a 1.6-kb fragment that included the whole spacer region, were used for chromosomal mapping of the 5S rRNA gene. Both fragments hybridized to a single locus on a pair of autosomal chromosomes of BALB/c mice. The major cluster of mouse 5S rRNA genes was assigned to the most terminal R-negative to R-positive bands of the E region of mouse Chromosome 8, which is homologous to the linkage of the 5S rRNA gene on the long arm of human chromosome 1. The location of the 5S rRNA gene was mapped in five laboratory strains, in wild mice of six Mus musculus subspecies (domesticus, brevirostris, musculus, bactrianus, castaneus, and molossinus) derived from 10 separate localities, and in four different Mus species (spretus, hortulanus, spicilegus, and caroli), using FISH. The 5S rRNA cluster mapped to the same position on the chromosomes of all mouse species and subspecies studied. These results suggest that the location of the mouse 5S rRNA gene on the distal telomeric region of Chromosome 8 is evolutionarily conserved. In comparison, the chromosomal assignments of centromeric 18S-28S rRNA genes are highly variable among the different M. musculus subspecies and Mus species.
Chromosomal localization and sequences of the murine Brn-3 family of developmental control genes
Authors: Theil T. , Zechner U. , Klett C. , Adolph S. , Möröy T.
Published: May 2008

The POU proteins BRN-3a, -3b and -3c are transcription factors encoded by separate genes that are differentially expressed during neural development. Comparison of genomic and cDNA sequences revealed similar exon/intron structures for Brn-3a and -3c genes, whereas the Brn-3b gene appeared to contain an intronless coding region. Fluorescence in situ hybridization experiments with mouse chromosomes showed that Brn-3a maps to mouse chromosome 14E1-3, Brn-3b to XF1-5 and Brn-3c to 18B3-E1.
Expression level of Rps4 mRNA in 39, X mice and 40, XX mice
Authors: Omoe K. , Endo A.
Published: May 2008

Contrary to the effects of X-chromosome monosomy in humans (Turner syndrome), XO mice are fertile and anatomically normal. The human RPS4X gene encodes ribosomal protein S4 and escapes X-chromosome inactivation, and its haploinsufficiency has been suspected to contribute to Turner syndrome. Therefore, we compared the expression level of mRNA of Rps4 (the mouse homolog of RPS4X) between XX and XO mice using Northern blot analysis. The XO/XX ratio of Rps4 mRNA obtained from Northern blot analysis was 0.9. There was no difference in the expression level of Rps4 mRNA between XX and XO mice. The difference in the KPS4/Rps4 transcription pattern between humans and mice may contribute, at least in part, to the phenotypic difference in monosomy X between humans and mice.
Chromosomal assignments of the genes for the calcineurin Aα (Calna1) and Aβ subunits (Calna2) in the rat
Authors: Yamada T. , Kim J.K. , Muramatsu Y. , Serikawa T. , Matsumoto K.
Published: May 2008

Chromosomal assignments of the genes for the calcineurin Aα (Calnal) and Aβ (Cαlnα2) subunits in the rat genome were performed by polymerase chain reaction/single-strand conformation polymorphism (PCR/SSCP) analysis of somatic cell hybrid DNAs. Both genes, Cαlnαl and Cαlnαl, were assigned to rat chromosome 15.
Chromosomal assignment of the gene for rat protein phosphatase 1γ1 (Ppp1cc)
Authors: Muramatsu Y. , Yamada T. , Yamada J. , Serikawa T. , Matsumoto K.
Published: May 2008

The gene for rat protein phosphatase 1γ1 (Ppp1cc) was assigned to rat chromosome 12 by analyzing somatic cell hybrid DNAs with the polymerase chain reaction, using primers specific for the rat gene.
The RBA-banded karyotype of the fallow deer (Dama dama L.)
Authors: Lioi M.B. , Scarfi M.R. , Di Berardino D.
Published: May 2008

High resolution RBA-banding patterns of Dama dama prometaphase chromosomes and their ideograms are presented as models for the definition of the standard RBA-banded karyotype of the species. The haploid set of RBA-banded prometaphase chromosomes, including the X and Y gonosomes, has revealed 527 bands, of which 191 are R-positive, 254 are R-negative and 82 are intermediate.
Clarification of chromosome nomenclature in the sheep (Ovis aries)
Authors: Ansari H.A. , Bosma A.A. , Bunch T.D. , Long S.E. , Popescu C.P.
Published: May 2008

In gene mapping, it is obviously essential that gene assignment errors are minimized. Recently, confusion has arisen in sheep gene mapping, as a result of contradictions in chromosome nomenclature. The purpose of this brief communication, prepared by the International Sheep Karyotype Standardization Committee, is to minimize any further confusion that may arise, while new sheep standard Q, G and R karyotypes and ideograms are being prepared. This paper reviews the history of previous sheep karyotype standards, explains the errors that have been detected and presents a correlation table so that, whichever nomenclature is used, the exact chromosome can be identified.
A new marker (NGFB) on pig chromosome 4, isolated by using a consensus sequence conserved among species
Authors: Lahbib-Mansais Y. , Mellink C. , Yerle M. , Gellin J.
Published: May 2008

The nerve growth factor β gene (NGFB) belongs to a conserved syntenic group on human chromosome 1 and mouse Chromosome 3. The objective of this study was the isolation of a part of the porcine NGFB gene and its use as a genetic and physical marker in the pig genome. On the basis of a nucleotide sequence comparison among different species, NGFB-specific primers were chosen to amplify the corresponding porcine sequence by PCR. A pig genomic DNA fragment of 763 bp was isolated, and its DNA sequence, containing the complete coding sequence of mature NGFB, was determined. It was demonstrated that pig NGFB is largely homologous with NGFB of other species (mouse, cattle, chicken) and especially with human NGFB; the isolated clone shows 91% nucleotide and 99 % translated amino acid sequence identity to the human NGFB sequence. The porcine DNA clone allowed us to identify an RFLP marker for genetic mapping in pigs and was used to map the NGFB gene to pig chromosome region 4q1.6→q2.3 by radioactive in situ hybridization. Previously, we had localized to the same chromosome another member of this syntenic group, the gene encoding α1 Na+, K+ ATPase (ATP1A1). These results show that a portion of the homologous region between human chromosome 1 and mouse Chromosome 3 is also conserved on pig chromosome 4.
Cloning of the entire FL11 gene, disrupted by the Ewing’s Sarcoma translocation breakpoint on 11q24, in a yeast artificial chromosome
Authors: Selleri L. , Giovannini M. , Romo A. , Zucman J. , Delattre O. , Thomas G. , Evans G.A.
Published: May 2008

FLU (Friend leukemia virus integration 1), a member of the Ets gene family, is disrupted on llq24 by the Ewing’s Sarcoma (ES) and Peripheral Neuroepithelioma (PNE) t(11;22)(q24;q12) translocation. ES and PNE are Primitive Neuroectodermal Tumors (PNETs) and the consistent translocation t(11;22)(q24;q12) can be used for differential diagnosis. In PNETs the 3’ part of human FLU is translocated from 11q24 to 22q12, where it is juxtaposed to the 5’ end of the Ewing’s Sarcoma gene (EWS). A fusion transcript, resulting in a chimeric protein, is generated. Here, we present the isolation and detailed characterization of a 250-kb colinear YAC, B45C11, which encompasses the ES and PNE breakpoint on 11q24, as shown by FISSH on ES and PNE chromosomes and interphase nuclei. This YAC represents a new reagent for potential use in rapid differential diagnosis by FISSH on tumor biopsies and on paraffin embedded samples, particularly when DNA and/or RNA are not available for molecular analysis. YAC B45C11, which spans 250 kb of contiguous DNA around the ES and PNE breakpoint, contains the entire FLU gene. Three potential HpaII-tiny-fragment (HTF) islands are revealed within the YAC. One of these islands appears to be associated with the 5’ end of FLU, which extends over approximately 120 kb of DNA on 1 lq24. In addition, we demonstrate that YAC B45C11 contains other transcribed sequences in addition to FLU, by “cross-species” Northern blot hybridizations, which suggests the presence of additional genes in the immediate vicinity of the ES breakpoint on 1 lq24.
New Robertsonian translocation chromosomes in domestic sheep (Ovis aries)
Authors: Pearce P.D. , Ansari H.A. , Maher D.W. , Malcolm A.A. , Stewart-Scott I.A. , Broad T.E.
Published: May 2008

We report two new Robertsonian centric fusions, designated t4and t5, in New Zealand Romney sheep. Q- and G-banding studies show that sheep chromosomes 5 and 8 are fused in t4 and that chromosomes 8 and 22 are fused in t5. The presence of large blocks of centromeric heterochromatin in t4 and t5suggests that the fusions may be of recent origin.
Localization of a putative human brain sodium channel gene (SCN1A) to chromosome band 2q24
Authors: Malo M.S. , Blanchard B.J. , Andresen J.M. , Srivastava K. , Chen X.-N. , Li X. , Wang Jabs E. , Korenberg J.R. , Ingram V.M.
Published: May 2008

We have identified four putative human sodium channel gene sequences, 55 bp each, using the polymerase chain reaction (PCR) on total human placental DNA with primers specific for the cDNA sequence of the rat brain sodium channel Iα (Scn1a) gene. One of these sequences was extended bidirectionally by genomic inverse-PCR to obtain a 1.6-kb fragment. Sequencing of this 1,556-bp fragment showed a 282-bp complete exon, which has 95% and 94% homology at the nucleotide and amino acid levels, respectively, with the rat Scn1a gene. We putatively assign this sequence as belonging to the gene coding the α-subunit of a human brain type I sodium channel (SCN1A). PCR on human × rodent somatic cell hybrids with primers derived from SCN1A localized this gene to chromosome 2. Fluorescence in situ hybridization to human metaphase chromosomes sublocalized the gene to chromosome band 2q24.
Molecular cytogenetic characterization of two types of chromosome 9 variants
Authors: Wang J.-C.C. , Miller W.A.
Published: May 2008

Structural variations in the pericentromeric region of chromosome 9 are common. Molecular cytogenetic characterization of two types of rare variants, each studied in two families, are reported. For convenience, the variants are designated as types 2 and 3. Type 2 variants contain an additional G-positive band in the short arm near the centromere. Type 3 variants have heterochromatin both above and below the centromere in addition to having an additional G-positive band in the short arm immediately distal to the heterochromatin. Fluorescence in situ hybridization using α-satellite and D9Z5 β-satellite probes revealed two clear hybridization signals in type 3 variants, one corresponding to the position of the centromere and the other to the position of the additional G-positive band. Results of type 2 variants are less conclusive, probably due to the close proximity of the additional band to the centromere, but are suggestive of additional hybridization in proximal 9p. Our finding suggests that the type 3 variant, and possibly the type 2 variant, may represent dicentric chromosomes that are functionally stable and phenotypically inconsequential.
Localization of the gene encoding human phosphatidylinositol transfer protein (PITPN) to 17p13.3: a gene showing homology to the Drosophila retinal degeneration B gene (rdgB)
Authors: Fitzgibbon J. , Pilz A. , Gayther S. , Appukuttan B. , Dulai K.S. , Delhanty J.D.A. , Helmkamp Jr. G.M. , Yarbrough L.R. , Hunt D.M.
Published: May 2008

The human gene for phosphatidylinositol transfer protein (PITPN) has previously been shown to share sequence and functional homology to part of the Drosophila retinal degeneration B gene (rdgB). In view of the possible involvement of the PITPN locus in the etiology of retinal disease, the gene has been mapped to human chromosome 17p13.3 and mouse Chromosome 11.
Precise localization of the genes for glucose phosphate isomerase (GPI), calcium release channel (CRC), hormone-sensitive lipase (LIPE), and growth hormone (GH) in pigs, using nonradioactive in situ hybridization
Authors: Chowdhary B.P. , Thomsen P.D. , Harbitz I. , Landset M. , Gustavsson I.
Published: May 2008

Fluorescence in situ hybridization (FISH) was applied, using genomic DNA clones, to precisely localize the genes for GPI, CRC, LIPE, and GH on pig chromosomes. The porcine CRC gene was localized to band 6q12 using both genomic and cDNA clones. The GPI and LIPE genes, which are closely linked to the CRC gene, were also mapped to the same band (6q12), using genomic lambda clones. The mapping data are a refinement of earlier findings, wherein radioactive in situ hybridi zation was used and the assignments included boththe short and long arms. Results of the present study clearly exclude the short arm as the location for the three genes. Further, using a genomic cosmid clone, the GH gene was mapped to band 12p14. Compared to the earlier assignments, which included almost the entire short arm of the chromosome due to the use of radioactive in situ hybridization, the present FISH findings provide a band-specific localization for the gene. A modified, simpler version of the posthybridization trypsin/ EDTA banding method is also presented.
Cytogenetic analysis of gilthead seabream Sparus aurata (Pisces, Perciformes), a deletion affecting the NOR in a hatchery stock
Authors: Garrido-Ramos M.A. , Jamilena M. , Lozano R. , Cárdenas S. , Ruiz Rejón C. , Ruiz Rejón M.
Published: May 2008

We have cytogenetically characterized a hatchery stock of gilthead seabream, Sparus aurata. The study included larvae, juveniles and adults. In S. αurαtα (diploid chromosome number 2n = 48), a pair of NORs is located at the ends of the short arms of the first submetacentric pair of chromosomes. In this stock we discovered a polymorphism which affects the NORs, and, by means of several cytogenetic and molecular techniques, we demonstrate that this polymorphism is due to the complete deletion of one of the two NORs in a high number of individuals. The significance of these cytogenetic characteristics for this species are discussed since they may be the source of aquaculture problems.
Mapping the human pulmonary surfactant-associated protein B gene (SFTP3) to chromosome 2p12→p11.2
Authors: Vamvakopoulos N.C. , Modi W.S. , Floros J.
Published: May 2008

Pulmonary surfactant, a lipoprotein complex is essential for normal lung function. The non-serum surfactant-associated proteins, SP-A, SP-B, and SP-C, play important roles in the biology of pulmonary surfactant. We have mapped the human SP-B gene (SFTP3) to chromosome 2, band 2p12→p11.2 by fluorescent in situ hybridization.
A region-specific microdissection library for human chromosome 2p23→p21 and the analysis of an interstitial deletion of 2p21
Authors: Kao F.T. , Yu J. , Qi J. , Tong S. , Muenke M.
Published: May 2008

A region-specific library of human chromosome 2p23→p21 was constructed using microdissection and micro-cloning techniques. Analysis of 94 single-copy microclones from the library showed that 64% were derived from the dissected region. Ten microclones were further mapped to the 2p21 region using a patient with an interstitial deletion of 2p21 and displaying holoprosencephaly, an abnormal embryonic development in midbrain and midface.
Human metalloprotease/disintegrin-like (MDC) gene: exon-intron organization and alternative splicing
Authors: Katagiri T. , Harada Y. , Emi M. , Nakamura Y.
Published: May 2008

A recently identified gene encoding a metalloprotease-like, disintegrin-like, cysteine-rich protein (MDC) represents a candidate tumor suppressor gene for human breast cancer based on its location within a minimal region of chromosome 17q21 previously defined by tumor deletion mapping. The work reported here has shown that the MDC gene consists of 28 exons interrupted by relatively short introns, most of them 67 bp to 5 kb in length. We have identified two forms of transcripts generated by alternative splicing. The more abundant form encodes a protein of 769 amino acids; the other, a previously described cDNA, encodes 524 amino acids. Exons 1a, 1b, 1c, 1d, and 2–7 encode a proprotein domain; exons 7–13, a metalloprotease-like domain; exons 14–17, a disintegrin domain; exons 18–22, a cysteine-rich domain, including an epidermal growth factor (EGF)-like repeat domain within exons 21 and 22; exon 23, a transmembrane domain; and exons 24 and 25, a short cytoplasmic domain. These results show that human MDC contains a mosaic of exons capable of encoding several functional domains.
Mapping of the gene for human xanthine dehydrogenase (oxidase) (XDH) to band p23 of chromosome 2
Authors: Minoshima S. , Wang Y. , Ichida K. , Nishino T. , Shimizu N.
Published: May 2008

Fluorescent in situ hybridization in combination with Q-banding revealed that the human xanthine dehydrogenase (XDH) gene is located on band p23 of chromosome 2.
C-band-positive double minutes have kinetochore proteins
Authors: Wettergren Y. , Arnason U. , Haaf T. , Levan A. , Levan G.
Published: May 2008

Double minutes (DMs) have been shown generally to lack centromeres. In the present paper we report on C-band-positive DMs in Colcemid-resistant SEWA cells. These DMs were heavily labeled after in situ hybridization with mouse major satellite DNA and, furthermore, reacted positively with antikinetochore antibodies. Upon antikinetochore antibody labeling, the immunofluorescent signals of some DMs were strong, indicating that they had functional centromeres.
Instant PRINS: a rapid method for chromosome identification by detecting repeated sequences in situ
Authors: Gosden J. , Lawson D.
Published: May 2008

We describe a method for labeling specific chromosomes in situ by oligonucleotide-primed synthesis and incorporation of fluorochrome-labeled dUTP, together with an accelerated protocol for the reaction. The combination of the two developments produces extremely rapid results, in some cases taking less than 5 min for the complete process. The significance of this development for clinical diagnosis is discussed.
Localization of the human melanocortin-5 receptor gene (MC5R) to chromosome band 18p11.2 by fluorescence in situ hybridization
Authors: Chowdhary B.P. , Gustavsson I. , Wikberg J.E.S. , Chhajlani V.
Published: May 2008

The recently cloned novel MC5R gene is suggested to be a mediator of neural functions of the melanocortic peptides, such as melanocyte-stimulating hormone (MSH) and adrenocorticotropic hormone (ACTH). We now report the localization of the human MC5R locus to chromosome 18pll.2.
5S rRNA gene hybridizes to human chromosome 1 at two sites (1q42.11→q42.13 and1q43)
Authors: Kost M.V. , Alimov A.A. , Sarafanov A.G. , Tikchomirova T.P. , Gumeniuk R.R. , Timofeeva M.Ja. , Zelenin A.V.
Published: May 2008

Hybridization of a loach (Misgurnus fossilis) oocyte 5S rRNA gene repeat with human chromosomes was carried out to refine the localization of the 5S RNA gene in the human genome. Preliminary in situ hybridization analysis showed that this repeat hybridized with human chromosome region 1q42→q43, the same location previously reported for the human 5S rRNA gene. High-resolution banding revealed the presence of two sites of hybridization, with a main peak in chromosome region 1q42.1 and a second peak in 1q43. These results are consistent with our data on the existence in the human genome of different 5S rRNA gene clusters specified by BamHl and Hindlll restriction sites in spacer DNA (Timofeeva et al., 1993) and suggest a multicluster organization of the human 5S rRNA genes.
Localization of human ARF2 and NCK genes and 13 other Notl-linking clones to chromosome 3 by fluorescence in situ hybridization
Authors: Vorobieva N. , Protopopov A. , Protopopova M. , Kashuba V. , Allikmets R.L. , Modi W. , Zabarovsky E.R. , Klein G. , Kisselev L. , Graphodatsky A.
Published: May 2008

Two human genes containing Notl sites, ADP-ribosylation factor (ARF2) and melanoma NCK protein, were mapped by fluorescence in situ hybridization to 3p21.2→ p21.1 and 3q21, respectively. Thirteen other NotI linking clones, representing sequence tagged sites, were also mapped to different regions of human chromosome 3. Two of these clones that contain sequences 80% homologous to the rat tropoelastin gene and brain Cl– channel protein CLC-2 gene probably represent new human genes closely related to the known rat genes.
Spontaneous amplification of interstitial telomeric bands in Chinese hamster ovary cells
Authors: Pandita T.K. , DeRubeis D.
Published: May 2008

Chinese hamster cell lines have been widely used to explore the mechanism of gene amplification under stress conditions. Investigations of gene amplification in Chinese hamster cells under nonstress conditions, however, have been limited due to technical reasons. We initiated studies on the amplification mechanism by examining the frequency of interstitial telomeric bands (ITBs) in continuously growing cultures by fluorescence in situ hybridization (FISH), using a (TTAGGG)n probe. We found that one of the chromosomes uniquely exhibit amplification of ITBs in Chinese hamster ovary (CHO) cells but not in drug-resistant mutant CHO cells or in Chinese hamster V79 cells. Amplification of ITBs could not be induced by DNA damaging agents or DNA synthesis inhibitors. To investigate the early events that mediate ITB amplification, we developed clones and determined that the frequency of acquisition of additional ITBs on the marker chromosome was in the range of 10–5 to 10–3 per cell doubling. Using DNA strand-specific FISH, we found that one of the initial events of amplification is isochromosome formation. Our observations support the involvement of sister chromatid fusion in the initiation of spontaneous ITB amplification.
Assignment of five loci from human chromosome 8q onto sheep chromosome 9
Authors: Broad T.E. , Burkin D.J. , Cambridge L.M. , Maher D.W. , Lewis P.E. , Ansari H.A. , Pearce P.D. , Jones C.
Published: May 2008

Using a chromosomally characterized minipanel of sheep × hamster cell hybrids, five new loci, including carbonic anhydrase II (CA2), calbindin 1 (28 kDa) (CALB1), corticotropin releasing hormone (CRH), cytochrome P450 11B subfamily XIB (steroid-11-β-hydroxylase), polypeptide 1 (CYP11B1), and interleukin 7 (IL7), have been assigned to sheep chromosome 9. A homolog of mosome 9 as the sheep equivalent of cattle chromosome 14 and indicates that CALB1, CYP11B1, and IL7, which have not been mapped on the cattle genome, are likely to be present on cattle chromosome 14. It also shows by comparative genome analysis that a large segment of human chromosome 8q is highly conserved in sheep chromosome 9 and cattle chromosome 14. Based on these data, we propose that sheep chromosome 9 be recognised as the equivalent of cattle chromosome 14.
Genetic map of eight microsatellite markers comprising two linkage groups on rat chromosome 6
Authors: Du Y. , Remmers E.F. , Zha H. , Goldmuntz E.A. , Mathern P. , Crofford L.J. , Szpirer J. , Szpirer C. , Wilder R.L.
Published: May 2008

Five genes and three anonymous DNA loci were mapped to rat chromosome 6 by genetic linkage and somatic cell hybrid analyses. The eight loci were all identified by PCR-based microsatellite polymorphism analysis and were characterized in 40 F2 intercross progeny of Fischer (F344/N) and Lewis (LEW/N) inbred rats for segregation analysis. These markers formed two linkage groups spanning, respectively, 58.1 cM and 4.0 cM. The first linkage group is comprised of two anonymous DNA loci and four genes with the following map order and distances: D6Cep8 (previously D3)-17.9 cM-D6Arb309–2.5 cM-Vsnl1 (neural visinin-like protein)-20.4 cM-Prkar2b (type IIβ regulatory subunit of cAMP-dependent protein kinase)-8.8 cM-Fkhl1 (forkhead-like transcription factor BF-1)-8.5 cM-Rnu1c (18-3AU1 RNA). The second linkage group is comprised of one gene, Ckb (creatine kinase, brain) and one anonymous DNA locus, D6Arb54, separated by 4.0 cM. For each marker, two to eight alleles were detected in a panel of 16 inbred rat strains (ACI/N, BN/SsN, BUF/N, DA/Bkl, F344/N, LER/N, LEW/N, LOU/MN, MNR/N, MR/N, SHR/N, SR/Jr, SS/Jr, WBB1/N, WBB2/N, and WKY/N). Comparative mapping information indicated that rat chromosome 6 exhibits syntenic conservation with mouse chromosome 12. Homologs of the rat chromosome 6 loci have been identified on human chromosomes 2, 7, and 14.