bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction of a 750-kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the progressive myoclonus epilepsy gene.
Authors: Stone N E , Fan J B , Willour V , Pennacchio L A , Warrington J A , Hu A , de la Chapelle A , Lehesjoki A E , Cox D R , Myers R M
Published: June 2007

The gene responsible for progressive myoclonus epilepsy of the Unverricht-Lundborg type (EPM1) is located on human chromosome 21q22.3 in a region defined by recombination breakpoints and linkage disequilibrium. As part of an effort to clone the EPM1 gene on the basis of its chromosomal location, we have constructed a 753-kb bacterial clone contig that encompasses the region containing the gene. Because DNA markers from the region did not identify intact yeast artificial chromosome (YAC) clones after screening several libraries, we built the contig from cosmid clones and used bacterial artificial chromosome (BAC) and bacteriophage P1 clones to fill gaps. In addition to constructing the clone contig, we determined the locations of the EcoRI, SacII, EagI, and NotI restriction sites in the clones, resulting in a high-resolution restriction map of the region. Most of the contig is represented by a level of redundancy that allows the orders of most restriction sites to be determined, provides multiple data points supporting the clone orders and orientations, and allows a set of clones with a minimum degree of overlap to be chosen for efficient additional analysis. The clone and restriction maps are in excellent agreement with maps generated of the region by other methods. These ordered bacterial clones and the mapping information obtained from them provide valuable reagents for isolating candidate genes for EPM1, as well as for determining the nucleotide sequence of a 750 kb region of the human genome.
Mapping the human Y chromosome by fingerprinting cosmid clones.
Authors: Taylor K , Hornigold N , Conway D , Williams D , Ulinowski Z , Agochiya M , Fattorini P , de Jong P , Little P F , Wolfe J
Published: June 2007

We have used Y-specific cosmid clones in a random fingerprinting approach to build contigs on the human Y chromosome. Clones derived from two libraries have been analyzed. The construction of one library is described here, the second was the Y chromosome-specific library LLOYNCO3 "M" (Lawrence Livermore National Laboratory). To date, we have fingerprinted 4430 cosmids: 377 contigs have been constructed containing from 2 to 39 clones. Along with the singletons, we estimate that we have covered 72.5% of the euchomatic portion of the Y chromosome with fingerprinted clones. Sequence tagged sites are being used to anchor cosmids and contigs onto the YAC framework.
Dominantly and recessively inherited cornea plana congenita map to the same small region of chromosome 12.
Authors: Tahvanainen E , Villanueva A S , Forsius H , Salo P , de la Chapelle A
Published: June 2007

Cornea plana congenita occurs in a mild autosomal dominant (CNA1) and a more severe autosomal recessive (CNA2) form. We recently assigned a CNA2 locus to a region on chromosome 12 by linkage analysis and excluded linkage to that locus in two Finnish CNA1 families. Here we describe a Cuban pedigree in which 14 members are affected with dominantly inherited cornea plana. By linkage analysis this phenotype was mapped to the immediate vicinity of markers D12S82 and D12S351 on 12q, that is, precisely the same small region (3 cM or less) to which CNA2 previously had been assigned. Our results support the existence of at least three genetically distinct forms of cornea plana. It remains to be determined whether recessive and dominant cornea plana are caused by different mutations of a single gene or whether the region in 12q harbors two or more genes whose mutations cause corneal maldevelopment.
A palindromic structure in the pericentromeric region of various human chromosomes.
Authors: Wöhr G , Fink T , Assum G
Published: June 2007

The primate-specific multisequence family chAB4 is represented with approximately 40 copies within the haploid human genome. Former analyis revealed that unusually long repetition units ( > 35 kb) are distributed to at least eight different chromosomal loci. Remarkably varying copy-numbers within the genomes of closely related primate species as well as the existence of human specific subfamilies, which most probably arose by frequent sequence exchanges, demonstrate that chAB4 is an unstable genomic element, at least in an evolutionary sense. To analyze the chAB4 basic unit in more detail we established a cosmid contig and found it to be organized as inverted duplications of approximately 90 kb flanking a noninverted core sequence of approximately 60 kb. FISH as well as the analysis of chromosome-specific hybrid cell lines revealed a chromosomal localization of chAB4 on chromosomes 1, 3, 4, 9, Y, and the pericentromeric region of all acrocentrics. Furthermore, we can detect chAB4 sequences together with alpha satellites, beta satellites, and satellite III sequences within a single chromosome 22-specific YAC clone, indicating that chAB4 is located in close proximity to the centromere, at least on the acrocentrics. Hence, chAB4 represents an unstable genomic structure that is located just in the chromosomal region that is very often involved in translocation processes.
Genetic mapping in Xiphophorus hybrid fish: assignment of 43 AP-PCR/RAPD and isozyme markers to multipoint linkage groups.
Authors: Kazianis S , Morizot D C , McEntire B B , Nairn R S , Borowsky R L
Published: June 2007

The combined use of the arbitrarily primed polymerase chain reaction [AP-PCR, also known as random amplification of polymorphic DNA (RAPD)] and isozyme mapping resulted in the production of 87 potential marker loci, enabling an overall expansion within the genetic map of the fish genus Xiphophorus. Use of DNA sequencing-style acrylamide gels and carefully controlled conditions of amplification and silver staining allowed exceptional resolution and reproducibility of AP-PCR/RAPD generated markers. Linkage analysis of AP-PCR/RAPD and isozyme markers resulted in the addition of 16 new markers to Xiphophorus linkage groups (LGs) I, II, III, V, IX, X, XII, and XIV. Addition of 5 AP-PCR/RAPD markers to linkage group U6 containing the Tailspot pigment pattern locus (P) and designation of eight new unassigned linkage groups with 22 markers was also accomplished. Genetic linkage data allowed inference of the existence of a novel pigment pattern modifier locus. Expansion of the Xiphophorus gene map by linkage analysis of AP-PCR/RAPD markers in conjunction with isozyme polymorphisms should lead to the rapid saturation of genetic linkage groups such as LG V, which will probably be instrumental to cloning the Diff tumor suppressor gene locus.
Toward the construction of integrated physical and genetic maps of the mouse genome using interspersed repetitive sequence PCR (IRS-PCR) genomics.
Authors: Hunter K W , Riba L , Schalkwyk L , Clark M , Resenchuk S , Beeghly A , Su J , Tinkov F , Lee P , Ramu E , Lehrach H , Housman D
Published: June 2007

Using two recently developed techniques, IRS-PCR YAC walking and IRS-PCR genotyping, a framework-integrated physical and genetic map of the mouse genome was constructed. The map consists of 821 contigs, containing 7746 YAC clones originating from three different YAC libraries. Three hundred eighty of the contigs have been anchored to the genetic map. Approximately 16% of the physical length of the mouse genome is estimated to be represented.
A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13.
Authors: Ansari-Lari M A , Muzny D M , Lu J , Lu F , Lilley C E , Spanos S , Malley T , Gibbs R A
Published: June 2007

The genomic sequence of the human CD4 gene and its neighboring region, located at chromosome 12p13, was generated using the large-scale shotgun sequencing strategy. A total of 117 kb of genomic sequence and approximately 11 kb of cDNA sequence were obtained. Six genes, including CD4, triosephosphate isomerase, B3 subunit of G proteins (GNB3), and ubiquitin isopeptidase T (ISOT), with known functions, and two new genes with unknown functions were identified. Using a battery of strategies, the exon/intron boundaries, splice variants, and tissue expression patterns of the genes were determined. Various computer software was utilized for analyses of the DNA and amino acid sequences. The results of the analyses and sequence-based strategies for gene identification are discussed.
An efficient method for isolating putative promoters and 5'-transcribed sequences from large genomic clones.
Authors: Mortlock D P , Nelson M R , Innis J W
Published: June 2007

Efficient strategies to isolate promoters and flanking exons from large genomic clones would facilitate the assembly of transcription units, complement existing techniques to isolate expressed sequences, and provide 5' regulatory elements. We have developed a rapid and simple method to isolate promoters from large mammalian genomic DNA clones by exploiting the abundance of binding sites for the ubiquitous transcription factor Sp1 in gene promoters. Using this method, putative promoter sequences with Sp1-binding sites are enriched approximately 100-fold from fragmented P1 clone DNA. Based on the abundance of Sp1-binding motifs in promoters, we predict that a significant subset of vertebrate promoters could be isolated by this method.
Genetic and physical mapping of the progressive epilepsy with mental retardation (EPMR) locus on chromosome 8p.
Authors: Ranta S , Lehesjoki A E , Hirvasniemi A , Weissenbach J , Ross B , Leal S M , de la Chapelle A , Gilliam T C
Published: June 2007

Progressive epilepsy with mental retardation (EPMR) is an autosomal recessive disorder discovered recently from an isolated region in Finland. The disorder is characterized by normal early development, generalized tonic-clonic seizures with onset at 5-10 years of age, and progressive mental retardation beginning 2-5 years after the onset of seizures. We recently mapped the EPMR locus to a 7-cM region on chromosome 8p between markers AFM185xb2 and D8S262. A recombination detected with a new microsatellite marker AFMa054td9 narrows the region to 4 cM. A yeast artificial chromosome (YAC) contig containing 22 YACs was constructed across the disease gene region. The YAC contig is characterized by a collection of 19 YAC-end sequence-tag sites together with seven microsatellite markers. The entire YAC contig spans a minimum of 3 Mb. Moreover, the distal end of the contig contains a subtelomeric YAC yRM2205 that anchors the contig to the telomere. Construction of a YAC contig across the disease gene region is an essential step toward the isolation of the EPMR gene.
Genomic organization of TEL: the human ETS-variant gene 6.
Authors: Baens M , Peeters P , Guo C , Aerssens J , Marynen P
Published: June 2007

We have constructed a detailed map of the genomic region containing the ETS-variant gene 6 (ETV6), involved in translocations and deletions associated with hematologic malignancies. Thirty-eight cosmids were characterized belonging to two contigs spanning 340 kb, and an EcoRl restriction map was developed. The gap between the two contigs, 2 kb in size, was closed by PCR. The contigs contain the complete coding sequence and the 5' and 3' UTRs of ETV6. Eight exons accounting for the ETV6 cDNA sequence were identified. The helix-loop-helix (HLH) motif is coded by exons 3 and 4, whereas exons 6-8 code for the ETS DNA-binding domain. All introns show consensus 5' donor and 3' acceptor splice sites. Introns 1 and 2 span 100 and 82 kb, respectively, and introns 3-7 range from 15 to 1.3 kb. An alternative exon 1 (exon 1B) is localized in intron 2. The 5' end of the ETV6 gene is associated with a CpG island characterized by the presence of four Notl, four Sacll, and three BssHll recognition sites and several SP1- and AP2-binding motifs. Alternative polyadenylation at the 3' end of the ETV6 gene generates the three transcripts of 6200, 4300, and 2400 nucleotides, respectively. The ETV6 gene spans 240 kb and is flanked at its 5' and 3' end by D12S1697 and D12S98, respectively. The markers D12S1095 and D12S89 are located in the first intron. Two new DNA polymorphisms were identified in the ETV6 gene, which will be useful for the analysis of loss of heterozygosity reported for the ETV6 gene in leukemia.
Identification and characterization of a new gene physically linked to the ATM gene.
Authors: Imai T , Yamauchi M , Seki N , Sugawara T , Saito T , Matsuda Y , Ito H , Nagase T , Nomura N , Hori T
Published: June 2007

Ataxia telangiectasia (AT) is an autosomal recessive disease of unknown etiology associated with cerebellar ataxia, oculocutaneous telangiectasia, immunodeficiency, and hypersensitivity to ionizing radiation. Although AT has been divided into four complementation groups by its radioresistant-DNA synthesis phenotype, the ATM gene has been isolated as the candidate gene responsible for all AT groups. We identified a new gene, designated NPAT, from the major AT locus on human chromosome 11q22-q23. The gene encoded a 1421-amino-acid protein containing nuclear localization signals and phosphorylation target sites by cyclin-dependent protein kinases associated with E2F. The messenger RNA of NPAT was detected in all human tissues examined, and its genomic sequence was strongly conserved through eukaryotes, suggesting that the NPAT gene may be essential for cell maintenance and may be a member of the housekeeping genes. Analysis of the genomic region of NPAT surprisingly revealed that the gene existed only 0.5 kb apart from the 5' end of the ATM transcript with opposite transcriptional direction. It may be possible to propose the idea that the promoter region could be shared by both housekeeping genes and that each gene could influence the expression of the other.
Transcription mapping in a 700-kb region around the DXS52 locus in Xq28: isolation of six novel transcripts and a novel ATPase isoform (hPMCA5).
Authors: Heiss N S , Rogner U C , Kioschis P , Korn B , Poustka A
Published: June 2007

The chromosomal band Xq28 has been a focus of interest in human genetics because > 20 hereditary diseases have been mapped to this region. However, about two-thirds of the disease genes remain uncloned. The region around the polymorphic DXS52 locus (ST14) within Xq28 lies in the candidate regions for several as-yet-uncloned disease genes. So far, only four melanoma antigen genes (MAGE) and the human biglycan (BGN) gene, have been mapped within the 700-kb stretch around DXS52, suggesting that more genes may reside in this region. By combining exon trapping and direct cDNA selection methods, we sought to identify novel transcripts around the DXS52 locus. In addition to recovering the MAGE and BGN genes, we isolated and mapped six putative novel genes (XAP103-XAP108), the caltractin gene, and a gene encoding a novel Ca(2+)-transporting ATPase isoform (hPMCA5). The newly isolated sequences were considered as representing parts of putative genes if they contained at least one unique exon-trap product and/or at least one expressed sequence tag (EST) from sequence data bases and if, in addition, they showed evidence of expressed RT-OCT and/or Northern blot analysis. Our data facilitated the integration of the transcription map with the physical map around the DXS52 locus. Future analysis of the novel genes as candidates for Barth syndrome (BTHS) and chondrodysplasia punctata (CDPX2) is in progress.
Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array.
Authors: Piétu G , Alibert O , Guichard V , Lamy B , Bois F , Leroy E , Mariage-Sampson R , Houlgatte R , Soularue P , Auffray C
Published: June 2007

A set of 1091 human skeletal muscle cDNA clone inserts representing more than 800 human gene transcripts were spotted as PCR products at high density on nylon membranes. Replicas of the filters were hybridized in stringent conditions with 33P-radiolabeled cDNA probes transcribed from skeletal muscle poly(A)+ RNA. Hybridization signals were collected on phosphor screens and processed using a software specifically adapted for this application to identify and quantitate each spot. Parameters likely to influence the hybridization signal intensity were assessed to eliminate artifacts. Each clone was assigned to one of four intensity classes reflecting the steady-state level of transcription of the corresponding gene in skeletal muscle. Differential expression of specific gene transcripts was detected using complex cDNA probes derived from nine different tissues, allowing assessment of their tissue specificity. This made it possible to identify 48 novel gene transcripts (including 7 homologous or related to known sequences) with a muscle-restricted pattern of expression. These results were validated through the analysis of known muscle-specific transcripts and by Northern analysis of a subset of the novel gene transcripts. All these genes have been registered in the Genexpress Index, such that sequence, map, and expression data can be used to decipher their role in the physiology and pathology of human muscles.
Generation of a transcriptional map for a 700-kb region surrounding the polycystic kidney disease type 1 (PKD1) and tuberous sclerosis type 2 (TSC2) disease genes on human chromosome 16p3.3.
Authors: Burn T C , Connors T D , Van Raay T J , Dackowski W R , Millholland J M , Klinger K W , Landes G M
Published: June 2007

A 700-kb region of DNA in human chromosome 16p13.3 has been shown to contain the polycystic kidney disease 1 (PKD1) and the tuberous sclerosis type 2 (TSC2) disease genes. An estimated 20 genes are present in this region of chromosome 16. We have initiated studies to identify transcribed sequences in this region using a bacteriophage P1 contig containing 700 kb of DNA surrounding the PKD1 and TSC2 genes. We have isolated 96 unique exon traps from this interval, with 23 of the trapped exons containing sequences from five genes known to be in the region. Thirty exon traps have been mapped to additional transcription units based on data base homologies, Northern analysis, or their presence in cDNA or reverse transcriptase (RT)-PCR products. We have mapped the human RNPS gene to the cloned interval. We have obtained cDNAs or RT-PCR products from eight novel genes, with sequences from seven of these genes having homology to sequences in the data bases. Two of the newly identified genes represent human homologs for rat and murine genes identified previously. We have isolated three exon traps with homology to sequences in the data bases but have been unable to confirm the presence of these exon traps in expressed sequences. In addition, we have isolated 43 exon traps that do not map to our existing cDNAs or PCR products and have no homology to sequences in the data bases. In this report we present a transcriptional map for the 700 kb of DNA surrounding the PKD1 and TSC2 genes.
Gene transfer into corn earworm (Helicoverpa zea) embryos.
Authors: DeVault J D , Hughes K J , Leopold R A , Johnson O A , Narang S K
Published: June 2007

Transposable elements with short inverted repeats at their termini have been identified in a number of diverse insect species and have proven to be useful gene delivery vectors for the transformation of Drosophila melanogaster. In this report we examine the ability of the D. melanogaster hobo element to transpose in lepidopteran species. A Trichoplusia ni (cabbage looper) and a Helicoverpa zea (corn earworm) embryonic cell line were found to be capable of supporting productive transposition of the hobo element as measured by a plasmid-based excision assay. Furthermore, hobo transposition was detected in H. zea embryos in a manner consistent with that seen for the cell line. In both cases, transposition/excision was found to be independent of vector-encoded transposase functions, indicating that endogenous genes are involved in hobo mobility. Finally, we demonstrate the stable insertion of the bacterial lacZ gene into the H. zea genome. These data demonstrate that hobo elements are capable of transgressing species boundaries and functioning in non-drosophilid cellular environments. More importantly, this represents the first description of a genetic transformation system for a lepidopteran species.
Sequencing the 500-kb GC-rich symbiotic replicon of Rhizobium sp. NGR234 using dye terminators and a thermostable "sequenase": a beginning.
Authors: Freiberg C , Perret X , Broughton W J , Rosenthal A
Published: June 2007

Genomes of the soil-borne nitrogen-fixing symbionts of legumes [Azo(Brady)Rhizobium species] typically have GC contents of 59-65 mol%. As a consequence, compressions (up to 400 per cosmid) are common using automated dye primer shotgun sequencing methods. To overcome this difficulty, we have exclusively applied dye terminators in combination with a thermostable "sequenase" for shotgun sequencing GC-rich cosmids from pNGR234a, the 500-kbp symbiotic replicon of Rhizobium sp. NGR234. A thermostable sequenase incorporates dye terminators into DNA more efficiently than Taq DNA polymerase, thus reducing the concentrations needed (20- to 250-fold). Unincorporated dye terminators can simply be removed by ethanol precipitation. Here, we present data of pXB296, one of 23 overlapping cosmids representing pNGR234a. We demonstrate that the greatly reduced number of compressions results in a much faster assembly of cosmid sequence data by comparing assembly of the shotgun data from pXB296 and the data from another pNGR234a cosmid (pXB110) sequenced using dye primer methods. Within the 34,010-bp sequence from pXB296, 28 coding regions were predicted. All of them showed significant homologies to known proteins, including oligopeptide permeases, an essential cluster for nitrogen fixation, and the C4-dicarboxylate transporter DctA.
The genomic structure of discoidin receptor tyrosine kinase.
Authors: Playford M P , Butler R J , Wang X C , Katso R M , Cooke I E , Ganesan T S
Published: June 2007

The discoidin domain receptor (DDR) is a new class of receptor tyrosine kinase that is distinguished by a unique extracellular domain homologous to the lectin Discoidin I found Dictyostelium discoideum. A cosmid was isolated from a human chromosome 6 cosmid library containing the DDR gene. A complete genomic contig of the DDR gene was constructed from seven subclones of the cosmid. The cosmid fragments were analyzed by PCR, sequencing, and comparison of genomic/cDNA sequence. The DDR gene is composed of 17 exons, ranging in size from 96 to 1014 bp, distributed along approximately 12 kb of genomic DNA. The extracellular domain is encoded by 8 exons of which three code for the discoidin domain. The transmembrane domain is encoded by 1 exon, the juxtamembrane by 3 exons, and the catalytic domain by 5 exons. The generation of the two splice variants of DDR, EDDR1 and EDDR2 are explained by the genomic structure. Exon 11 (111 bp in the juxtamembrane domain) is present in DDR and absent in the splice variant EDDR1. An inverted repeat of 20 bp was identified at the 3' exon-intron junction of exon 11, which results in a lariat loop-like secondary structure. EDDR2 is generated because of a cryptic splice acceptor site that results in an extra 18 bp (6 amino acids) inserted 5' of exon 14 in the catalytic domain. A polymorphic (GT)17 repeat was identified in intron 5 with a heterozygosity of 0.71. The exon-intron structure of the DDR gene will be helpful in further understanding of its function and explains the possible structural basis for the two splice variants.
A linkage map of the ovine X chromosome.
Authors: Galloway S M , Hanrahan V , Dodds K G , Potts M D , Crawford A M , Hill D F
Published: June 2007

A genetic linkage map of the ovine X chromosome containing type I and type II markers has been constructed. The map contains 7 known gene markers and 14 microsatellite markers with a recombination length of 141.9 cM. Segregation of polymorphic markers was observed in a three-generation pedigree containing 480 animals. The maximum number of informative meioses was 912. Additional information was obtained for some markers by following segregation in the AgResearch International Mapping Flock, consisting of nine three-generation full-sib pedigrees. A pseudoautosomal region containing two markers has been identified at one end of the linkage map. Comparisons with mouse and human X chromosomes confirms the observation of Ohno (1973) that the gene content of the mammalian X chromosome is retained. In particular, the conserved grouping of the genes PHKA1, ATP7A, and XIST observed in both the human and the mouse X chromosome appears to be conserved in the sheep X chromosome, and XIST has been mapped to near the center of the chromosome. This study provides the first reported genetic linkage map combining both type I and type II markers for any ruminant X chromosome.
Isolation and mapping of novel mouse brain cDNA clones containing trinucleotide repeats, and demonstration of novel alleles in recombinant inbred strains.
Authors: Chambers D M , Abbott C M
Published: June 2007

Abnormal expansion of trinucleotide repeats (TRs) has now been implicated in the pathogenesis of at least nine human genetic disorders, particularly those in which anticipation and/or fragile sites have been demonstrated. Anticipation, the phenomenon of increasing severity of phenotype in successive generations, has never been seen in species other than man. Nevertheless, animal models for the dynamic mutation of TRs would be extremely valuable. We have screened a mouse brain cDNA library in an attempt to identify clones representing each of the 10 possible classes of trinucleotide repeat. Thirty-seven clones were analyzed in detail. Of the 37 sequences, 18 displayed significant levels of homology with sequences in GenBank, 10 of them with human expressed sequence tags (ESTs). We then analyzed 25 of the clones by PCR of the sequence containing the repeat in a number of different mouse strains and species to assess levels of variability of repeat length. Of the 25 clones analyzed in this way, 64% showed length variation between Mus musculus spp. and Mus spretus, and 32% showed variation between Mus musculus musculus-derived standard laboratory inbred strains. Where variation was detected (17 repeat-containing clones in all), the gene was mapped by linkage analysis. None of the repeats isolated showed any signs of extreme expansion. However, two of the repeats were shown to have undergone size changes during the establishment of a number of recombinant inbred strains, suggesting that these repeats are at least moderately unstable.
14-3-3 epsilon has no homology to LIS1 and lies telomeric to it on chromosome 17p13.3 outside the Miller-Dieker syndrome chromosome region.
Authors: Chong S S , Tanigami A , Roschke A V , Ledbetter D H
Published: June 2007

Previously, we isolated several cDNA clones of the LIS1 gene implicated in Miller-Dieker syndrome. Analysis of the 5' end of one of the clones (8-1), which was originally thought to represent the 5' end of LIS1, indicates a striking similarity to mouse 14-3-3 epsilon. We have isolated a full-length cDNA of human 14-3-3 epsilon, for which sequence analysis reveals a strong nucleotide conservation with mouse 14-3-3 epsilon in both translated and untranslated regions (UTRs). Additionally, the predicted peptides of human, sheep, rat, and mouse 14-3-3 epsilon are identical. Using a 205-bp fragment common to LIS1 (8-1) and 14-3-3 epsilon as probe on adult and fetal multiple-tissue Northern blots, a -2-kb transcript is detected, identical to the pattern observed with a full-length 14-3-3 epsilon cDNA probe. LIS1-specific transcripts of approximately 7.5 and approximately 5 kb are not detected by the 0.2-kb probe, indicating that the similarity between the 5' sequence of LIS1 (8-1) and the 3' UTR of 14-3-3 epsilon is not the result of shared homology between the two genes. Instead, clone 8-1 is a chimera of 14-3-3 epsilon and LIS1 partial cDNAs, and therefore its 5' sequence does not represent the LIS1 5' end. Interestingly, we have mapped the 14-3-3 epsilon gene to the same chromosomal sub-band as LIS1 (17p13.3). However, 14-3-3 epsilon lies telomeric to LIS1 and outside the Miller-Dieker syndrome chromosome region but in a region frequently deleted in several types of cancer, and is a reasonable candidate tumor suppressor gene.
Identification of a novel paternally expressed transcript adjacent to snRPN in the Prader-Willi syndrome critical region.
Authors: Ning Y , Roschke A , Christian S L , Lesser J , Sutcliffe J S , Ledbetter D H
Published: June 2007

Small nuclear ribonucleoprotein-associated polypeptide N (snRPN) and an anonymous transcript, PAR-5, are two of the paternally expressed transcripts mapped to the Prader-Willi syndrome critical region. Using long-range PCR, we have isolated the genomic interval between snRPN and PAR-5, identified a novel transcript in this region, and termed it PAR-SN. Northern analysis demonstrates that PAR-SN is expressed in brain, skeletal muscle, and heart. Like snRPN and PAR-5, PAR-SN is expressed exclusively from the paternal homolog in cultured lymphoblasts. Sequence analysis of the transcript revealed no significant open reading frame but did include a polymorphic dinucleotide repeat (CA)17.
Hybrid selection as a method of increasing mapping power for radiation hybrids.
Authors: Jones H B
Published: June 2007

Radiation hybrids have become a widely used tool for physical mapping. A drawback of the technique is that large numbers of hybrids are required to construct robust, high-resolution maps. The information contained within a panel of radiation hybrids is limited by the frequency of retention of chromosomal fragments from the donor cell line. In almost all experiments to date, the retention frequency has been below the optimal level; therefore, many hybrids are needed to produce high-quality maps. Because of the labor-intensive nature of large-scale mapping projects, it is important to make panels as small as possible. One method that has been adopted is to produce initially a large number of hybrids that are all typed with a few loci. Those hybrids showing satisfactorily high retention are admitted to the final panel and the rest are discarded. In this way, a panel of radiation hybrids with higher than expected retention can be created. Methods for conducting such a selection regime are discussed. To investigate the potential advantages of selecting hybrids based on their retention frequency, simulations were run under a variety of conditions. As expected panels with high retention (40%) provided better mapping resources than panels with lower (20%) retention. Beginning with an initial panel of 200 hybrids, comparisons of a random sample of 100 hybrids and the set of those 100 hybrids showing the highest marker retention demonstrated that selection may not be always the best strategy despite the increase in mean retention it yields. The selection of hybrids containing large numbers of fragments leads to an overestimation of the frequency of radiation-induced breaks. When breaks occur with high frequency (for example, when high radiation doses are used), the selection of hybrids leads to a loss of linkage and hence an inability to order the markers. As such, the merits of screening hybrids depends on both the radiation dose and the desired map resolution.
Generation and analysis of 280,000 human expressed sequence tags.
Authors: Hillier L D , Lennon G , Becker M , Bonaldo M F , Chiapelli B , Chissoe S , Dietrich N , DuBuque T , Favello A , Gish W , Hawkins M , Hultman M , Kucaba T , Lacy M , Le M , Le N , Mardis E , Moore B , Morris M , Parsons J , Prange C , Rifkin L , Rohlfing T , Schellenberg K , Marra M
Published: June 2007

We report the generation of 319,311 single-pass sequencing reactions (known as expressed sequence tags, or ESTs) obtained from the 5' and 3' ends of 194,031 human cDNA clones. Our goal has been to obtain tag sequences from many different genes and to deposit these in the publicly accessible Data Base for Expressed Sequence Tags. Highly efficient automatic screening of the data allows deposition of the annotated sequences without delay. Sequences have been generated from 26 oligo(dT) primed directionally cloned libraries, of which 18 were normalized. The libraries were constructed using mRNA isolated from 17 different tissues representing three developmental states. Comparisons of a subset of our data with nonredundant human mRNA and protein data bases show that the ESTs represent many known sequences and contain many that are novel. Analysis of protein families using Hidden Markov Models confirms this observation and supports the contention that although normalization reduces significantly the relative abundance of redundant cDNA clones, it does not result in the complete removal of members of gene families.
Tracing an ancestral mutation: genealogical and haplotype analysis of the infantile onset spinocerebellar ataxia locus.
Authors: Varilo T , Nikali K , Suomalainen A , Lönnqvist T , Peltonen L
Published: June 2007

Infantile onset spinocerebellar ataxia (IOSCA) is a progressive neurological syndrome exhibiting an autosomal recessive pattern of inheritance. The characteristic features were described in Finland in the beginning of 1990s. Having shown that IOSCA does not segregate with any of the markers linked to other hereditary ataxias and thus represents a genetically distinct disease, we assigned the locus of this new hereditary ataxia to 10q23.3-q24.1. To approximate the age of the Finnish IOSCA mutation and to investigate the possible existence of more than one mutation underlying the disease, the ancestors of 13 IOSCA families were identified by use of church records dating back to the 1500s. The IOSCA pedigrees were frequently merged, providing support for these having one common ancestor. Analysis of the extended IOSCA haplotypes exposed ancient recombination events and revealed one core haplotype of four markers on a region of approximately 2 cM, which was unequivocally present in 92% of disease chromosomes. Both genealogical and haplotype data thus suggest that a single IOSCA ancestral mutation was introduced into the Finnish population most probably approximately 30-40 generations ago before the time when the general east-west migration took place within Finland.
Use of asymmetric PCR to generate long primers and single-stranded DNA for incorporating cross-linking analogs into specific sites in a DNA probe.
Authors: Wooddell C I , Burgess R R
Published: June 2007

Photoactivatable DNA analogs have been incorporated enzymatically into DNA and used to map the locations of polypeptides in protein complexes bound to DNA. We have developed a procedure for generating long primers from short oligodeoxyribonucleotides (oligos) to incorporate DNA cross-linkers at specific sites within either strand of DNA probes of < or = 206 bp. Single-stranded DNA molecules of 52-206 nucleotides in length were generated by asymmetric polymerase chain reactions (aPCR), using an excess of one short sense-strand primer to be extended and a limiting amount of each short antisense primer that is complementary to and defines the 3' end of the long primer to be generated. The noncross-linking strand of the DNA probe was also generated by aPCR from the DNA sequence of interest. The long primers were annealed to the full-length noncross-linking DNA strand to form a partially double-stranded DNA. Cross-linking analogs and radioactive deoxyribonucleotides (dNTPs), followed by normal dNTPs, were enzymatically incorporated onto the long primers to form the double-stranded DNA cross-linking probes. This method is reproducible and avoids many of the difficulties encountered by other published methods.
The human reelin gene: isolation, sequencing, and mapping on chromosome 7.
Authors: DeSilva U , D'Arcangelo G , Braden V V , Chen J , Miao G G , Curran T , Green E D
Published: June 2007

The mouse reelin gene (Reln) encodes a novel protein that, when mutated, results in the characteristic reeler phenotype. A key component of this phenotype is the extensive disruption of the organization of many brain structures. Reelin is believed to be an extracellular protein that controls neural cell positioning during brain development. The reelin gene is conserved in many vertebrate species, including humans. To study the role of the reelin homolog in human brain development, we have isolated and characterized the human gene (RELN). Like its murine counterpart, RELN is large, encoding an mRNA of approximately 12 kb. Overlapping cDNA clones containing the entire open reading frame were isolated and sequenced, revealing that the predicted mouse and human proteins are similar in size (388 kD) and that the amino acid and nucleotide sequences are 94.2% and 87.2% identical, respectively. Northern hybridization analyses revealed that RELN is expressed in fetal and postnatal brain as well as liver. The expression of RELN in postnatal human brain was high in the cerebellum. RELN was mapped to human chromosome 7q22, based on both fluorescence in situ hybridization studies and localization within a well-positioned yeast artificial chromosome (YAC) contig. The YAC contig also contains a number of gentic markers. Together, these studies provide the sequence information and genetic tools for performing more detailed analyses of RELN in an attempt to define its role in human brain development and possibly in human disease.
Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group.
Authors: Ghosh S , Karanjawala Z E , Hauser E R , Ally D , Knapp J I , Rayman J B , Musick A , Tannenbaum J , Te C , Shapiro S , Eldridge W , Musick T , Martin C , Smith J R , Carpten J D , Brownstein M J , Powell J I , Whiten R , Chines P , Nylund S J , Magnuson V L , Boehnke M , Collins F S
Published: June 2007

Large-scale genotyping is required to generate dense identity-by-descent maps to map genes for human complex disease. In some studies the number of genotypes needed can approach or even exceed 1 million. Generally, linkage and linkage disequilibrium analyses depend on clear allele identification and subsequent allele frequency estimation. Accurate grouping or categorization of each allele in the sample (allele calling or binning) is therefore an absolute requirement. Hence, a genotyping system that can reliably achieve this is necessary. In the case of affected sib-pair analysis without parents, the need for accurate allele calling is even more critical. We describe methods that permit precise sizing of alleles across multiple gels using the fluorescence-based, Applied Biosystems (ABI) genotyping technology and discuss ways to reduce genotyping error rates. Using database utilities, we show how to minimize intergel allele size variation, to combine data effectively from different models of ABI sequencing machines, and automatically bin alleles. The final data can then be converted into a format ready for analysis by statistical genetic packages such as MENDEL.
Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination.
Authors: Ansari-Lari M A , Shen Y , Muzny D M , Lee W , Gibbs R A
Published: June 2007

The detailed genomic organization of a gene-dense region at human chromosome 12p13, spanning 223 kb of contiguous sequence, was determined. This region is composed of 20 genes and several other expressed sequences. Experimental tools including RT-PCR and cDNA sequencing, combined with gene prediction programs, were utilized in the analysis of the sequence. Various computer software programs were employed for sequence similarity searches and functional predictions. The high number of genes with diverse functions and complex transcriptional patterns make this region ideal for addressing challenges of gene discovery and genomic characterization amenable to large-scale sequence analysis.
2006 expressed-sequence tags derived from human chromosome 7-enriched cDNA libraries.
Authors: Touchman J W , Bouffard G G , Weintraub L A , Idol J R , Wang L , Robbins C M , Nussbaum J C , Lovett M , Green E D
Published: June 2007

The establishment and mapping of gene-specific DNA sequences greatly complement the ongoing efforts to map and sequence all human chromosomes. To facilitate our studies of human chromosome 7, we have generated and analyzed 2006 expressed-sequence tags (ESTs) derived from a collection of direct selection cDNA libraries that are highly enriched for human chromosome 7 gene sequences. Similarity searches indicate that approximately two-thirds of the ESTs are not represented by sequences in the public databases, including those in dbEST. In addition, a large fraction (68%) of the ESTs do not have redundant or overlapping sequences within our collection. Human DNA-specific sequence-tagged sites (STSs) have been developed from 190 of the ESTs. Remarkably, 180 (96%) of these STSs map to chromosome 7, demonstrating the robustness of chromosome enrichment in constructing the direct selection cDNA libraries. Thus far, 140 of these EST-specific STSs have been assigned unequivocally to YAC contigs that are distributed across the chromosome. Together, these studies provide > 2000 ESTs highly enriched for chromosome 7 gene sequences, 180 new chromosome 7 STSs corresponding to ESTs, and a definitive demonstration of the ability to enrich for chromosome-specific cDNAs by direct selection. Furthermore, the libraries, sequence data, and mapping information will contribute to the construction of a chromosome 7 transcript map.
A role for a chicken homolog of the neural cell adhesion molecule L1 in consolidation of memory for a passive avoidance task in the chick.
Authors: Scholey A B , Mileusnic R , Schachner M , Rose S P
Published: June 2007

Intracranial injection of antibodies directed against the neural cell adhesion molecule L1 resulted in amnesia for passive avoidance training in day-old chicks tested 24 hr subsequently. L1 antibodies were amnesic when administered at one of two time windows: 30 min pretraining and 5.5-8 hr post-training. No amnesia was apparent if injections were made at times before, between, or after these time windows (-2, +1, +3, +4, or +12 hr relative to training). A fragment of the L1 molecule derived from the external fibronectin domains FN1-5 produced amnesia only when injected at the 5.5-hr timepoint, whereas a fragment of the immunoglubin-like domains Ig I-VI produced amnesia only when injected 30 min prior to training. We have shown previously that long-term memory for the passive avoidance task requires two waves of glycoprotein synthesis, the first occurring immediately after training, and the second some 6 hr thereafter. The glycoprotein synthesis inhibitor 2-deoxygalactose results in amnesia if injected at either time, whereas the neural cell adhesion molecule (N-CAM) is specifically involved only in the second wave. The coincidence of the time course of memory disruption resulting from injection of L1 antibodies with that occurring with 2-deoxygalactose supports the hypothesis that establishment of an enduring memory for the experience of passive avoidance training requires two waves of glycoprotein synthesis, each wave being biochemically and functionally discrete. The differential effects of the two L1 fragments suggests that separate mechanisms of synaptic stabilization are involved at the two time points.
Associative learning and stimulus novelty influence the song-induced expression of an immediate early gene in the canary forebrain.
Authors: Jarvis E D , Mello C V , Nottebohm F
Published: June 2007

To identify variables that affect immediate early gene (IEG) expression in the auditory telencephalon of songbirds, we developed a conditioning paradigm that trained adult male canaries to associate song with a mild shock. Learning of the association was measured by a bird's fear and avoidance responses. Birds exposed to paired song and shock were compared to yoked controls exposed to each stimulus alone or to both unpaired. Additional groups examined the effects of attention and stress, and of the novelty of the stimulus situation. In situ hybridization analysis of brain sections revealed an enhancement of ZENK expression in birds learning the association between song and shock above levels induced by song alone or yoked-unpaired song and shock. This effect was specifically seen in the caudomedial auditory telencephalon (NCM-HVCM). A comparison of the several control groups indicated that novelty of the song stimulus or of its pairing with shock were the main variables that predicted ZENK levels in NCM-HVCM. These observations are compatible with ZENK playing a role in the formation of song perceptual memories.
Metabotropic glutamate receptors in spatial and nonspatial learning in rats studied by means of agonist and antagonist application.
Authors: Riedel G , Wetzel W , Reymann K G
Published: June 2007

We examined the effects of both the metabotropic glutamate receptor (mGluR) antagonist MCPG and the agonist tADA in two behavioral paradigms in rats: (1) brightness discrimination and (2) spatial alternation. Compounds were applied intracerebroventricularly at different times, either 30 min prior to training or immediately after training, and rats were tested for retention 24 hr later in the same paradigms. Both MCPG and tADA caused amnesia in the spatial alternation test, when applied pretraining, but no effect was obtained in the brightness discrimination paradigm. Drug-induced amnesia was shown not to be attributable to state-dependent effects of MCPG or tADA. Moreover, the memory inhibiting effect of MCPG was dose dependent, with a low dose (20 mM/5 ml) having no effect on learning and memory and a 10 times higher concentration (200 mM/5 ml) causing complete amnesia. Application of both saline and MCPG immediately post-training prevented memory formation, which may be attributable to an interference by the injection procedure with the process of memory formation. The mGluR agonist tADA, however, facilitated memory formation in the spatial alternation task, when injected immediately after training. Post-training application of the compounds had no effect on retention in the brightness discrimination task. On the basis of these data we conclude that (1) mGluRs are of particular importance for spatial learning and play no role in visual discrimination; (2) both the block and the activation of mGluRs inhibit spatial learning, suggesting that saturated activation prevents further modulation of mGluRs, which may be required during learning or memory formation; and (3) mGluR agonist tADA may be memory facilitating when applied after training, thus enhancing the establishment of the memory trace.
7-Nitro indazole, a selective neuronal nitric oxide synthase inhibitor in vivo, impairs spatial learning in the rat.
Authors: Hölscher C , McGlinchey L , Anwyl R , Rowan M J
Published: June 2007

Nitric oxide (NO) is an intercellular messenger that has been suggested to have a role in learning and memory formation. Previous studies with nonselective NO synthase inhibitors have produced contradictory results in learning experiments. However, these drugs also produced blood pressure changes, as NO is an endothelial-derived relaxing factor. A novel NO synthase inhibitor, 7-nitro indazole (7-NI), as a dose (30 mg/kg i.p.) shown previously to inhibit neuronal NO synthase by 85% without affecting blood pressure, produced amnesic effects both in a water maze and in an 8-arm radial maze. Latency as well as distance was greater in the 7-NI group in the water maze while swim speed was not affected. Latency, working memory (WM), and reference memory (RF) errors were also higher in the 7-NI group in the 8-arm maze. At the end of the second training day, these differences were no longer apparent. However, on the fourth training day, a transfer test in the water maze showed that 7-NI had produced a spatial memory deficit, reducing quadrant bias and the number of annulus crossings. Learning of a visual cue task was not affected. No difference between groups was visible in an open field test. We conclude that neuronal NO synthase activity plays a role in learning and memory formation in the rat.