bluuebunny/crossref_metadata_2025 huggingface dataset:
Human chromosome-specific cDNA libraries: new tools for gene identification and genome annotation.
Authors: Del Mastro R G , Wang L , Simmons A D , Gallardo T D , Clines G A , Ashley J A , Hilliard C J , Wasmuth J J , McPherson J D , Lovett M
Published: June 2007

To date, only a small percentage of human genes have been cloned and mapped. To facilitate more rapid gene mapping and disease gene isolation, chromosome 5-specific cDNA libraries have been constructed from five sources. DNA sequencing and regional mapping of 205 unique cDNAs indicates that 25 are from known chromosome 5 genes and 138 are from new chromosome 5 genes (a frequency of 79.5%). Sequence complexity estimates indicate that each library contains -20% of the approximately 5000 genes that are believed to reside on chromosome 5. This study more than doubles the number of genes mapped to chromosome 5 and describes an important new tool for disease gene isolation.
Directed integration of the physical and genetic linkage maps of swine chromosome 7 reveals that the SLA spans the centromere.
Authors: Smith T P , Rohrer G A , Alexander L J , Troyer D L , Kirby-Dobbels K R , Janzen M A , Cornwell D L , Louis C F , Schook L B , Beattie C W
Published: June 2007

The first integrated physical and genetic linkage map encompassing the entire swine chromosome 7 (SSC7) reveals that the porcine MHC (SLA) spans the centromere. A SLA class II antigen gene lies on the q arm, whereas class I and III genes lie on the p arm, suggesting that the presence of a centromere within the SLA does not preclude a functional complex. The SLA appears smaller than other mammalian MHC, as the genetic distance across two class I, three class II, and three class III SLA gene markers is only 1.1 cM. There are significant variations in recombination rates as a function of position along the chromosome, and the SLA lies in the region with the lowest rate. Furthermore, the directed integration approach used in this study was more efficient than previous efforts that emphasized the screening of large insert libraries for random microsatellites.
An autosomal recessive nonsyndromic form of sensorineural hearing loss maps to 3p-DFNB6.
Authors: Fukushima K , Ramesh A , Srisailapathy C R , Ni L , Wayne S , O'Neill M E , Van Camp G , Coucke P , Jain P , Wilcox E R
Published: June 2007

Autosomal recessive nonsyndromic hearing loss (ARNSHL) is the most common form of congenitally acquired inherited hearing impairment. Although numerous loci are believed to exist, only five have been identified. Using a pooled genomic DNA screening strategy, we have identified a sixth locus, DFNB6, on 3p in the interval bounded by D3S1619 and D3S1766.
PCR-LIS-SSCP (Low ionic strength single-stranded conformation polymorphism)--a simple method for high-resolution allele typing of HLA-DRB1, -DQB1, and -DPB1.
Authors: Maruya E , Saji H , Yokoyama S
Published: June 2007

We have developed a simple and efficient procedure with which to form single-stranded DNA [ssDNA] and then applied HLA-DRB1, -DQB1, and -DPB1 allele typing. This method is referred to as low ionic strength single-stranded conformation polymorphism (LIS-SSCP), and is based on the diversity in the electrophoretic mobility of ssDNA formed by heat denaturation in low ionic strength solutions. This method detected DNA polymorphisms, including point mutations at a variety of positions in the DNA fragments of the HLA-DRB1, -DQB1, and -DPB1 genes. Under our experimental conditions, stable ssDNA could be kept at room temperature > or = 5 hr without having been cooled on ice immediately after heat denaturation. A total of 41 HLA-DRB1, 14 HLA-DQB1, and 17 HLA-DPB1 alleles from 220 healthy people were analyzed using a combination of PCR-LIS-SSCP with group-specific amplification. All of the alleles analyzed were discriminated among the DRB1, DQB1, and DPB1 groups except for DPB1*0402 and 0201. The efficiency of ssDNA formation using the LIS-SSCP procedure was higher than that of the traditional formamide method, and the SSCP profiles were clearer than those of the original SSCP. This procedure is useful for screening new alleles as well as the donor-recipient molecular matching of HLA class II genes. It is simple, rapid, and cost effective, requiring neither radioisotopes nor enzymes to confirm the typing results of other methods.
Use of a fluorescent-PCR reaction to detect genomic sequence copy number and transcriptional abundance.
Authors: Chiang P W , Song W J , Wu K Y , Korenberg J R , Fogel E J , Van Keuren M L , Lashkari D , Kurnit D M
Published: June 2007

We present a fluorescent-PCR-based technique to assay genomic sequence copy number and transcriptional abundance. This technique relies on the ability to follow fluorescent PCR progressively in real time during the exponential phase of the reaction so that quantitative PCR is accomplished. We demonstrated the ability of this technique to quantitate both known deletions and amplifications of loci that have been measured previously by other methods, and to measure transcriptional abundance. Using an efficient variant of the fluorescent-PCR technology, we can monitor transcription semiquantitatively. The ability to detect all amplifications and deletions at any single copy locus by PCR makes this the technique of choice to assay genomic sequence copy number anomalies in birth defects and cancers. The ability to detect variations in transcript abundance enables this technique to fashion a time and tissue analysis of transcription.
An expanded CAG repeat sequence in spinocerebellar ataxia type 7.
Authors: Lindblad K , Savontaus M L , Stevanin G , Holmberg M , Digre K , Zander C , Ehrsson H , David G , Benomar A , Nikoskelainen E , Trottier Y , Holmgren G , Ptacek L J , Anttinen A , Brice A , Schalling M
Published: June 2007

Expanded CAG repeat sequences have been identified in the coding region of genes mutated in several neurodegenerative disorders, including spinocerebellar ataxia type 1 and Machado-Joseph disease. In all disorders described to date the CAG expansion codes for an elongated polyglutamine chain. An increased polyglutamine chain size leads to a more severe disease, thus correlating with the genetic anticipation seen in repeat expansion disorders. Spinocerebellar ataxia type 7 (SCA7) is an autosomal dominant spinocerebellar ataxia with anticipation and a progressive degeneration of the cerebellar cortex. Using repeat expansion detection (RED), a method in which a thermostable ligase is used to detect repeat expansions directly from genomic DNA, we have analyzed 8 SCA7 families for the presence of CAG repeat expansions. RED products of 150-240 bp were found in all affected individuals and found to cosegregate with the disease (P < 0.000001, n = 66), indicating strongly that a CAG expansion is the cause of SCA7. On the basis of a previously established correlation between RED product sizes and actual repeat sizes in Machado-Joseph disease, we were able to estimate the average expansion size in SCA7 to be 64 CAG copies.
Novel susceptibility locus for mouse hepatomas: evidence for a conserved tumor suppressor gene.
Authors: Zenklusen J C , Rodriguez L V , LaCava M , Wang Z , Goldstein L S , Conti C J
Published: June 2007

We have identified previously a putative tumor suppressor gene (TSG) locus at human chromosome (hchr) 7q31 showing that it is altered in a variety of human epithelial tumors. To determine whether this TSG is conserved in mice, we studied loss of heterozygosity (LOH) in chemically induced mouse liver adenomas. The LOH analysis was performed by polymerase chain reaction amplification of 17 (CA)n microsatellite repeats on mouse chromosome (mchr) 6 A2-C3. Ninety-six of 106 cases (90.6%) had LOH at D6Mit50, and 89.5% had LOH at D6Mit179. These two loci are 0.2 cM apart on mchr 6A2. Another high-LOH site was found in the C3 band. The high incidence of LOH in the 7q-homologous segment of mchr 6 indicates that the human TSG is conserved and is involved in the development of hepatomas.
A simple and efficient method for making site-directed mutants, deletions, and fusions of large DNA such as P1 and BAC clones.
Authors: Borén J , Lee I , Callow M J , Rubin E M , Innerarity T L
Published: June 2007

This study addresses two important technical problems: how to perform targeted alterations such as site-directed mutagenesis and deletions in large fragments of DNA and how to construct full-length genes from two partly overlapping bacterial artificial chromosome (BAC) plasmids. Given the size and the lack of convenient unique restriction sites in these large-insert bacterial clones, these are nontrivial tasks. Here we describe a simple and efficient protocol based on RecA-assisted restriction endonuclease (RARE) cleavage, a method that enables sequence-specific cleavage of genomic DNA. The same protocol has been used with minor modifications to introduce site-specific mutations into an apolipoprotein-B 90-kb P1 clone, to generate deletions in a 160-kb BAC, and to generate a 160-kb BAC containing the complete 92-kb gene for low-density lipoprotein-related protein-1 (LRP-1) from two smaller overlapping BACs ("BAC marriage").
Long-range mapping and construction of a YAC contig within the cat eye syndrome critical region.
Authors: McDermid H E , McTaggart K E , Riazi M A , Hudson T J , Budarf M L , Emanuel B S , Bell C J
Published: June 2007

Cat eye syndrome (CES) is typically associated with a supernumerary bisatellited marker chromosome derived from human chromosome 22pter to 22q11.2. The region of 22q duplicated in the typical CES marker chromosome extends between the centromere and locus D22S36. We have constructed a long-range restriction map of this region using pulsed-field gel electrophoresis and probes to 10 loci (11 probes). The map covers -3.6 Mb. We have also used 15 loci to construct a yeast artificial chromosome contig, which encompasses about half of the region critical to the production of the CES phenotype (centromere to D22S57). Thus, the CES critical region has been mapped and a substantial portion of it cloned in preparation for the isolation of genes in this region.
Chromosome-specific panels of tri- and tetranucleotide microsatellite markers for multiplex fluorescent detection and automated genotyping: evaluation of their utility in pathology and forensics.
Authors: Lindqvist A K , Magnusson P K , Balciuniene J , Wadelius C , Lindholm E , Alarcón-Riquelme M E , Gyllensten U B
Published: June 2007

A set of 391 microsatellite markers (Weber set 6), 85% of which consist of tri- and tetranucleotide repeat markers, were used to design chromosome-specific panels that allowed for a high degree of multiplexing with respect to the fragment size range and fluorophore (FAM, HEX, TET). This marker set has an average coverage of 10.5 cM, with the largest gap being 28.1 cM. The markers were divided into 49 panels, with a maximum degree of multiplexing of 15 markers per panel. The utility of the markers for analysis of DNA from blood, hair, and formalin-fixed archival tissue biopsies was evaluated with respect to amplification efficiency, product yield, and degree of preferential amplification of the shorter allele in heterozygotes. The amplification efficiency was inversely related to repeat length and amplicon length. Based on the analysis of DNA from formalin-fixed biopsies, 51 markers suitable for loss of heterozygosity (LOH) studies were identified. The utility of the marker set for genome scanning, LOH, and forensic analyses is discussed.
Cross-screening: a new method to assemble clones rapidly and unambiguously into contigs.
Authors: Locke J , Rairdan G , McDermid H , Nash D , Pilgrim D , Bell J , Roy K , Hodgetts R
Published: June 2007

We have developed a new procedure that relies on an array of cross-hybridization tests to order a set of random clones into a contig. The method, called cross-screening, uses each clone as a target and its end sequences as probes, in a matrix of reciprocal cross-hybridization tests performed on a single blot. The relationships among the clones are determined rapidly from the pairwise tests, allowing clone order to be determined directly. We have applied this technique to DNAs from a set of overlapping lambda clones from Drosophila chromosome 4. The location and orientation of each clone derived from the cross-screening data was that expected from the map assembled from overlapping restriction sites and chromosomal walking. The procedure provided additional information on a previously unknown, internally repeated DNA sequence. To demonstrate the general utility of the procedure, we have applied it to a previously described clone set within a contig in region 22q12 of human chromosome 22. The correct relative position and orientation of these clones were derived from the cross-screening data without knowledge of, or reference to, any nucleotide sequence or restriction site analysis of the DNA concerned. The cross-screening procedure is fast, economical, and robust and allows clone overlaps to be determined efficiently, with minimal interference from repeated DNA sequences. This new procedure is specifically designed for small groups of overlapping clones (tens to hundreds) and should facilitate the ordering of subclone libraries derived from small chromosomes or the large cloned inserts carried in YAC, BAC, and P1 vectors.
Sorsby's fundus dystrophy in the British Isles: demonstration of a striking founder effect by microsatellite-generated haplotypes.
Authors: Wijesuriya S D , Evans K , Jay M R , Davison C , Weber B H , Bird A C , Bhattacharya S S , Gregory C Y
Published: June 2007

Sorsby's fundus dystrophy (SFD) has been mapped to a genetic interval of 8 cM between loci D22S275 and D22S278. A total of 15 families, unrelated on the basis of genealogy and expressing the SFD phenotype were identified from a large data base of genetic eye disease families originating from diverse parts of the British Isles. The identification of the same Ser181Cys mutation cosegregating with disease in each family led us to consider the hypothesis of a founder effect being present. In all families studied, the same relatively infrequent allele (occurring in just 11% of the control group) was associated with disease at marker locus D22S280. A highly significant disease-associated haplotype, spanning across 3 cM of the SFD locus, was conserved in 11 of the 15 families (68% of all affected chromosomes); a further extended haplotype spanning up to 7 cM, was identified in 5 families (27% of SFD-associated chromosomes) and possibly represents the ancestral haplotype. This haplotype analysis has refined the TIMP3 gene localization to a 1- to 3-cM interval between marker loci D22S273 and D22S281 and provides strong evidence for a single mutational event being responsible for the majority of SFD identified in the British Isles.
Positional candidate genes for congenital chloride diarrhea suggested by high-resolution physical mapping in chromosome region 7q31.
Authors: Höglund P , Haila S , Scherer S W , Tsui L C , Green E D , Weissenbach J , Holmberg C , de la Chapelle A , Kere J
Published: June 2007

Congenital chloride diarrhea affects intestinal transportation of electrolytes, resulting in potentially fatal diarrhea. Linkage disequilibrium analyses have suggested the congenital chloride diarrhea gene (CLD) to lie within 0.37 cM from D7S496 in human chromosome 7q31. To clone the CLD gene, we have constructed and refined a physical map based on a 2.7-Mb YAC contig around D7S496 and identified two candidate genes. The physical positions of 4 known genes (DRA, PRKAR2B, LAMB1, DLD), 7 polymorphic repeat markers, and 13 CpG islands were established. DRA (down-regulated in adenoma) is expressed in the gut and encodes a protein with sequence homology to anion transporters, whereas PRKAR2B encodes a regulatory subunit for protein kinase A. Both genes map within 450 kb from D7S496, making them functionally and positionally relevant candidates for CLD.
The human homolog T of the mouse T(Brachyury) gene; gene structure, cDNA sequence, and assignment to chromosome 6q27.
Authors: Edwards Y H , Putt W , Lekoape K M , Stott D , Fox M , Hopkinson D A , Sowden J
Published: June 2007

We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic clones and derived the mRNA sequence and gene structure. There is 91% amino acid identity between human and mouse T proteins overall and complete identity across 77 amino acids of the T-box motif within the DNA-binding domain. Human T expression is very similar to that found for T in other vertebrate species and is confined to cells derived from the notochord. The human T gene maps to chromosome 6q27 and is only the second human member of the T-box gene family to be described.
The characterization and localization of the mouse thymopoietin/lamina-associated polypeptide 2 gene and its alternatively spliced products.
Authors: Berger R , Theodor L , Shoham J , Gokkel E , Brok-Simoni F , Avraham K B , Copeland N G , Jenkins N A , Rechavi G , Simon A J
Published: June 2007

Thymopoietins (Tmpos) are a group of ubiquitously expressed nuclear proteins, with sequence homology to lamina-associated polypeptide 2 (LAP2). Here we report the isolation and characterization of seven mouse Tmpo mRNA transcripts named Tmpo alpha, beta, beta', gamma, epsilon, delta, and zeta. The alpha, beta, and gamma Tmpo cDNA clones are the mouse homologs of the previously characterized human alpha, beta, and gamma TMPOs, respectively, whereas Tmpo epsilon, delta, and zeta are novel cDNAs. Additionally, the mouse Tmpo gene was cloned and characterized. It is a single-copy gene organized in 10 exons spanning approximately 22 kb, which encodes all of the described Tmpo cDNA sequences, located in the central region of mouse chromosome 10. The almost identical genomic organization between the human and mouse genes, and the novel alternatively spliced mouse transcripts, led us to reanalyze the human TMPO gene. The human beta-specific domain was found to be encoded by 3 exons designated 6a, 6b, and 6c and not by a single exon as described previously. These findings suggest that there may be more human transcripts than currently recognized. The possible involvement of the new growing family of Tmpo proteins in nuclear architecture and cell cycle control is discussed.
A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing.
Authors: Sorokin A , Lapidus A , Capuano V , Galleron N , Pujic P , Ehrlich S D
Published: June 2007

An efficient approach for structural studies on bacterial chromosomes is presented. It is based on high-resolution PCR map construction by using a multiplex long accurate PCR (MLA PCR) protocol and a YAC clone carrying the region to be mapped as indicator. The high-resolution PCR map of the bacillus subtilis rrnB-dnaB region is presented as an example. Data are also presented on the use of DNA generated by LA PCR for sequencing; they are relevant to LA PCR induced mutations and justify the application of such mapping for sequencing long stretches of bacterial chromosomes.
The region surrounding the PKD1 gene: a 700-kb P1 contig from a YAC-deficient interval.
Authors: Dackowski W R , Connors T D , Bowe A E , Stanton V , Housman D , Doggett N A , Landes G M , Klinger K W
Published: June 2007

As part of an effort to identify the gene responsible for the predominant form of polycystic kidney disease (PKD1), we used a gridded human P1 library for contig assembly. The interval of interest, a 700-kb segment on chromosome 16p13.3, can be physically delineated by the genetic markers D16S125 and D16S84 and chromosomally characterized as a GC-rich isochore enriched for CpG islands, genes, and Alu-like repeats. Our attempts to recover CEPH YACs that encode this region of chromosome 16 were unsuccessful. However, we screened an arrayed P1 library using 15 distinct probes from the D16S125-D16S84 interval and identified 56 independent P1 clones. Only one probe from the interval was unsuccessful in identifying a P1 clone. Forty-four P1 clones were determined to be unique based on restriction enzyme analysis, and 42 of these were found to originate from chromosome 16p13.3, based on FISH to metaphase chromosomes. The 700-kb interval could be defined by a single sequence-ready contig comprised of 12 P1 clones and 1 cosmid clone. Our studies support the use of multiple libraries to generate the requisite physical reagents for positional cloning and encourage the use of Escherichia coli-based large-insert cloning systems to recover clones from YAC-deficient chromosomal intervals.
One-tube post-PCR fluorescent labeling of DNA fragments.
Authors: Inazuka M , Tahira T , Hayashi K
Published: June 2007

A method for fluorescent postlabeling of PCR products has been developed. The method uses Klenow fragment of DNA polymerase I that exchanges the 3'-terminal residue of PCR-amplified DNA fragment for fluorescent nucleotides. All reactions, including PCR, are performed in one tube simply by successive addition of reagents. The products can be applied directly to fluorescence-based automated DNA sequencers without purification for either length determination in denaturing electrophoresis or mutation detection in SSCP electrophoresis.
Bacterial artificial chromosome cloning and mapping of a 630-kb human extrachromosomal structure.
Authors: Wang M , Shouse S , Lipes B , Kim U J , Shizuya H , Lai E
Published: June 2007

We have cloned and mapped a circular 630-kb human extrachromosomal structure (termed amplisome) using the bacterial artificial chromosome (BAC) cloning system. Twenty-one BACs were isolated from an amplisome-enriched library by colony hybridization. The insert sizes range from 25 to 143 kb, with an average size of 82 kb. The coverage of the amplisome in clones is approximately 2.7-fold. To construct a physical map of the amplisome, we used three different but complementary methods: hybridization, STS content mapping, and fingerprinting. In addition, we compared the advantages and the drawbacks of these techniques in mapping the amplisomal BACs. The 21 BACs were grouped into two contigs and the two small gaps (3.5 and 26.5 kb) were filled by screening of a human genomic BAC library. The organization of the amplisome revealed by the BAC-based physical map is consistent with the long-range restriction map reported previously. Our results demonstrate that a 630-kb region can be rapidly cloned and mapped into contigs by use of the BAC system. Because of the low frequency (<0.1%) of chimerism and rearrangement, these BAC clones are ready for DNA sequencing and functional analysis.
A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.
Authors: Shalon D , Smith S J , Brown P O
Published: June 2007

Detecting and determining the relative abundance of diverse individual sequences in complex DNA samples is a recurring experimental challenge in analyzing genomes. We describe a general experimental approach to this problem, using microscopic arrays of DNA fragments on glass substrates for differential hybridization analysis of fluorescently labeled DNA samples. To test the system, 864 physically mapped lambda clones of yeast genomic DNA, together representing >75% of the yeast genome, were arranged into 1.8-cm x 1.8-cm arrays, each containing a total of 1744 elements. The microarrays were characterized by simultaneous hybridization of two different sets of isolated yeast chromosomes labeled with two different fluorophores. A laser fluorescent scanner was used to detect the hybridization signals from the two fluorophores. The results demonstrate the utility of DNA microarrays in the analysis of complex DNA samples. This system should find numerous applications in genome-wide genetic mapping, physical mapping, and gene expression studies.
Microsatellite hybrid capture technique for simultaneous isolation of various STR markers.
Authors: Prochazka M
Published: June 2007

The microsatellite hybrid capture technique was designed to enrich simultaneously for various microsatellite repeats from a genomic clone. It is illustrated in this report that different repeat motifs, including polymorphic ones, can be efficiently isolated in a single experiment. In principle, this technique can be applied to any type of genomic clones to facilitate the isolation of informative markers for fine mapping of subchromosomal regions of interest, and for linkage and association studies of candidate genes for which no polymorphic markers are available yet.
Perspectives: sequence data base searching in the era of large-scale genomic sequencing.
Authors: Smith R F
Published: June 2007

Large-scale sequencing of human and model organism genomes will have a profound impact on our ability to use sequence data base searching to predict the biochemical functions of sequences of interest. Despite the great value of more sequences in the data bases, a huge increase in data base size will also have adverse effects on data base searches. Upcoming problems will include (1) greatly increased search times, (2) an increase in background noise of high-scoring but biologically irrelevant matches, (3) inaccurate coding region prediction, leading to problems in protein data base searching, and (4) limited first-pass sequence annotation, making it difficult to determine the biological relevance of data base hits. Improved data base annotation tools and construction of smaller data bases of representative and highly-annotated sequences for first-pass analyses will be essential to deal with the impending flood of new genomic sequence.
Identification and localization of the gene for EXTL, a third member of the multiple exostoses gene family.
Authors: Wise C A , Clines G A , Massa H , Trask B J , Lovett M
Published: June 2007

Hereditary multiple exostoses (EXT) is an autosomal dominant disorder characterized by multiple bony outgrowths from the juxtaepiphyseal region of long bones. In a small proportion of cases, these exostoses progress to malignant chondrosarcomas. Genetic linkage of this disorder has been described to three independent loci on chromosomes 8q24.1 (EXT1), 11p11-13 (EXT2), and 19p (EXT-3). The EXT1 and EXT2 genes were isolated recently and show extensive sequence homology to each other. These genes are deleted in exostoses-derived tumors, supporting the hypothesis that they encode tumor suppressors. We have identified a third gene that shows striking sequence similarity to both EXT1 and EXT2 at the nucleotide and amino acid sequence levels, and have derived its entire coding sequence. Although the mRNA transcribed from this gene is similar in size to that from EXT1 and EXT2, its pattern of expression is quite different. We have localized this gene by fluorescence in situ hybridization to metaphase chromosomes and by whole genome radiation hybrid mapping to chromosome 1p36.1 between DIS458 and DIS511, region that frequently shows loss of heterozygosity in a variety of tumor types. This gene, EXTL (for EXT-like), is therefore a new member of the EXT gene family and is a potential candidate for several disease phenotypes.
Phylogenetics of the laboratory rat Rattus norvegicus.
Authors: Canzian F
Published: June 2007

A genealogic tree was constructed for inbred strains of the laboratory rat, including 63 strains and 214 of their substrains. Information on genetic and biochemical marker typings of these lines was collected from the literature and from the World Wide Web. Data on 995 polymorphisms were processed into a phylogenetic distance matrix, and a tree was obtained by the Fitch-Margoliash distance matrix method. The inbred strains of the laboratory rat showed an average polymorphism for pairwise comparison of 53%. Strain BN showed the highest genetic divergence from all the other ones. Comparison with the mouse phylogenetic tree indicated that laboratory rats possess a higher diversity than inbred strains of mice not derived from wild species. These results provide a phylogenetic basis in the choice of rat strains for genetic linkage experiments.
Cognitive decline associated with normal aging in rats: a neuropsychological approach.
Authors: Zyzak D R , Otto T , Eichenbaum H , Gallagher M
Published: June 2007

The effects of aging on cognitive capacities were examined by comparing the performance of young and old rats on tasks characterized as dependent on different brain systems. This neuropsychological approach was employed to determine the extent to which multiple neural systems are compromised in aging and whether deterioration of one system correlates with that of another. The two tasks used in the present study were an odor-guided recognition memory task, for which different aspects of performance have been shown to be dependent on the integrity of the orbital prefrontal and perirhinal-entorhinal cortex, and the Morris water maze, for which performance depends on the medial prefrontal cortex and hippocampus. Rats were trained on the recognition memory task under minimal memory load and then challenged with longer memory delays and higher levels of inter-item interference. Considerable variation was observed in the performance of aged rats on acquisition of the recognition memory task, and unlike young rats, some aged rats could not acquire the task. Nevertheless, those aged rats who did acquire the cDNM task performed as well as young animals when the memory delay was extended and interference was elevated. In addition, consistent with previous findings, the performance of the same aged rats was highly variable in the Morris water maze task. Furthermore, although correlations between scores on the two tasks for individual aged rats were not reliable, only those aged rats that performed outside the performance range of young rats in the water maze were impaired on acquisition of the recognition memory task. This pattern of findings is consistent with age-related dysfunction in multiple subdivisions of the prefrontal cortex as well as the hippocampus and suggests that these brain regions may deteriorate in the same subgroup of aged rats.
Learning "what" and "how" in a human motor task.
Authors: Brooks V , Hilperath F , Brooks M , Ross H G , Freund H J
Published: June 2007

We studied the development of implicit and of verbally declared knowledge for normal human subjects who learned an unfamiliar motor task in one learning session. The exploratory nature of motor learning and a special period for optimizing skill were followed in real time. Subjects understood the goal for task success, but they had to learn a motor strategy of what pattern of serial movements to make and the tactics of how much to scale their amplitudes and timing. We compared the time course for acquiring tactical skill with that for acquiring knowledge of strategy and of tactics, and their necessary cues. Implicit and declarative knowledge were distinguished from one another by correlating subjects' verbal self-reports with movement kinematics and their results. Implicit generation of the correct strategy and of the tactics developed in an exploratory manner from the beginning of the learning session. Implicit strategy learning soon gave way to conscious efforts, but tactical learning remained implicit until its first unambiguous verbal declaration (with one exception). First strategy declarations were voiced before those for tactics, during trial-and-error learning that did not require task success, and referred to reversing the direction of hand movements (one exception). In contrast, first declarations of tactics almost always required actual or imminent success, referred to when direction was to be reversed, and it was achieved near the top of a sigmoid learning curve that rose to tactical skill (with one exception). During the sigmoid rise, movement amplitudes and timing were optimized in a distinct manner, although tactics usually adapted thereafter to movements of more moderate speed that could still be successful.
Higher-order associative processing in Hermissenda suggests multiple sites of neuronal modulation.
Authors: Rogers R F , Matzel L D
Published: June 2007

Two important features of modern accounts of associative learning are (1) the capacity for contextual stimuli to serve as a signal for an unconditioned stimulus (US) and (2) the capacity for a previously conditioned (excitatory) stimulus to "block" learning about a redundant stimulus when both stimuli serve as a signal for the same US. Here, we examined the process of blocking, thought by some to reflect a cognitive aspect of classical conditioning, and its underlying mechanisms in the marine mollusc Hermissenda. In two behavioral experiments, a context defined by chemosensory stimuli was made excitatory by presenting unsignalled USs (rotation) in that context. The excitatory context subsequently blocked overt learning about a discrete conditioned stimulus (CS; light) paired with the US in that context. In a third experiment, the excitability of the B photoreceptors in the Hermissenda eye, which typically increases following light-rotation pairings, was examined in behaviorally blocked animals, as well as in animals that had acquired a normal CS-US association or animals that had been exposed to the CS and US unpaired. Both the behaviorally blocked and the "normal" learning groups exhibited increases in neuronal excitability relative to unpaired animals. However, light-induced multiunit activity in pedal nerves was suppressed following normal conditioning but not in blocked or unpaired control animals, suggesting that the expression of blocking is mediated by neuronal modifications not directly reflected in B-cell excitability, possibly within an extensive network of central light-responsive interneurons.
Effects of a conditional Drosophila PKA mutant on olfactory learning and memory.
Authors: Li W , Tully T , Kalderon D
Published: June 2007

The requirement for cAMP-dependent protein kinase (PKA) in associative learning of Drosophila was assessed in mutant flies hemizygous for a cold-sensitive allele, X4, of the DC0 gene, which encodes the major catalytic subunit of PKA. DC0X4 hemizygotes died as third-instar larvae at 18 degrees C, the restrictive temperature, but were viable when raised at 25 degrees C. Shifting adult DC0X4 hemizygotes from 25 degrees C to 18 degrees C led to a decrease in PKA activity from 24% to 16% of wild-type without impairing viability. At 25 degrees C, DC0X4 hemizygotes exhibited reduced initial learning relative to controls but normal memory decay in a Pavlovian olfactory learning assay. Shifting the temperature from 25 degrees C to 18 degrees C prior to training reduced initial learning to a similar extent in DC0X4 hemizygotes and controls but resulted in a steeper memory decay curve only in DC0X4 hemizygotes. These observations are suggestive of a role for PKA in medium-term memory formation in addition to its previously established role in initial learning.
Examination of the role of cGMP in long-term potentiation in the CA1 region of the hippocampus.
Authors: Selig D K , Segal M R , Liao D , Malenka R C , Malinow R , Nicoll R A , Lisman J E
Published: June 2007

The mechanisms underlying the generation of NMDA receptor-dependent LTP in the CA1 region of the hippocampus continue to receive a great deal of attention because of the postulated importance of LTP as a synaptic mechanism for learning and memory. It is well accepted that the initial induction of LTP occurs in the postsynaptic cell, but the site of expression remains controversial. One prominent hypothesis is that LTP involves the release of one or more retrograde messengers that act on the presynaptic terminal to enhance transmitter release. Recently, evidence has been presented that retrograde messengers function to activate presynaptic guanylyl cyclase and that the resulting rise in presynaptic cGMP levels, when accompanied by presynaptic activity, is responsible for generating an early component of LTP. We have tested this hypothesis by examining whether synaptic strength is increased by coupling tetanic stimulation with application of a membrane-permeable analog of cGMP. The experiments were done in the presence of an NMDA receptor antagonist to block postsynaptic induction mechanisms. Under a variety of experimental conditions, this manipulation failed to generate LTP, suggesting that an increase in cGMP levels accompanied by presynaptic activity is not sufficient to generate LTP in the CA1 region of the hippocampus.
Training in the Morris water maze occludes the synergism between ACPD and arachidonic acid on glutamate release in synaptosomes prepared from rat hippocampus.
Authors: McGahon B , Holscher C , McGlinchey L , Rowan M J , Lynch M A
Published: June 2007

We report here that release of glutamate, inositol phospholipid metabolism, and protein kinase C (PKC) activity are increased in synaptosomes prepared from hippocampi of rats that had been trained in a spatial learning task. In hippocampi obtained from animals that were untrained, activation of the metabotropic glutamate receptor by the specific agonist trans-1-amino-cyclopentyl-1,3-dicarboxylate (ACPD) increased release of glutamate but only in the presence of a low concentration of arachidonic acid. A similar interaction between arachidonic acid and ACPD was observed on inositol phospholipid turnover and on PKC activity. However, the synergistic effect of arachidonic acid and ACPD on glutamate release was occluded in hippocampal synaptosomes prepared from trained rats. Occlusion of the effect on inositol phospholipid turnover and PKC activation was also observed. These data suggest that the molecular changes that underlie spatial learning may include activation of metabotropic glutamate receptors in the presence of arachidonic acid and that the interaction between arachidonic acid and ACPD triggers the presynaptic changes that accompany learning.
Multiple forms of facilitation produced by aversive tentacular stimuli in cerebral ganglion sensory neurons of Aplysia.
Authors: Fitzgerald K K , Carew T J
Published: June 2007

Aversive tentacular stimuli can produce both nonassociative and associative modification of head-waving behavior of Aplysia. Sensory neurons (the J/K cluster SNs) in the cerebral ganglion of Aplysia constitute an afferent pathway for aversive stimuli of the anterior tentacles. We used intracellular recording to examine plasticity in these neurons, particularly side-specific or site-specific alterations, which may be involved in mediating aspects of the learning induced by tentacle shock. The results of these experiments indicate that the J/K SNs exhibit several forms of plasticity: (1) Post-tetanic potentiation (PTP); (2) heterosynaptic facilitation; (3) activity-dependent synaptic facilitation; and (4) side-specific spike broadening. Furthermore, by activating SNs directly to produce PTP and producing heterosynaptic facilitation with tentacular stimuli that were either inside or outside the receptive field of individual SNs, it was possible to dissect and analyze the differential contribution of intrinsic SN activity and heterosynaptic modulation to activity-dependent facilitation induced by behaviorally relevant stimuli. Collectively, these data raise the possibility that plasticity in primary afferent SNs may be involved in US processing during learning induced by tentacle stimulation.
The Drosophila mutation turnip has pleiotropic behavioral effects and does not specifically affect learning.
Authors: Mihalek R M , Jones C J , Tully T
Published: June 2007

The Drosophila mutant turnip (tur) was isolated on the basis of its poor performance in an olfactory learning task, and also has a reduction in protein kinase C (PKC) activity. PKC has been found in the nervous systems of a wide range of organisms and appears to have an important role in learning and memory-related processes. Unfortunately, previous reports documenting the learning defect of tur lacked the controls required to assess the origins of the poor performance of the mutant. We have analyzed the effects of the tur mutation on both associative and nonassociative learning as well as on PKC activity. Additionally, the effects of the mutation on the task-relevant sensorimotor abilities of the flies were assessed. Although we were able to replicate previous behavioral and biochemical results obtained with tur, we discovered that the tur mutation also affected response to electric shock and caused a drastic reduction in the locomotor ability of the flies. Because locomotion is an essential component of the learning assays, this result makes it impossible to conclude that tur specifically affects learning and demonstrates the crucial importance of sensorimotor controls in conditioning experiments.
A neural model of cerebellar learning for arm movement control: cortico-spino-cerebellar dynamics.
Authors: Contreras-Vidal J L , Grossberg S , Bullock D
Published: June 2007

A neural network model of opponent cerebellar learning for arm movement control is proposed. The model illustrates how a central pattern generator in cortex and basal ganglia, a neuromuscular force controller in spinal cord, and an adaptive cerebellum cooperate to reduce motor variability during multijoint arm movements using mono- and bi-articular muscles. Cerebellar learning modifies velocity commands to produce phasic antagonist bursts at interpositus nucleus cells whose feed-forward action overcomes inherent limitations of spinal feedback control of tracking. Excitation of alpha motoneuron pools, combined with inhibition of their Renshaw cells by the cerebellum, facilitate movement initiation and optimal execution. Transcerebellar pathways are opened by learning through long-term depression (LTD) of parallel fiber-Purkinje cell synapses in response to conjunctive stimulation of parallel fibers and climbing fiber discharges that signal muscle stretch errors. The cerebellar circuitry also learns to control opponent muscles pairs, allowing cocontraction and reciprocal inhibition of muscles. Learning is stable, exhibits load compensation properties, and generalizes better across movement speeds if motoneuron pools obey the size principle. The intermittency of climbing fiber discharges maintains stable learning. Long-term potentiation (LTP) in response to uncorrelated parallel fiber signals enables previously weakened synapses to recover. Loss of climbing fibers, in the presence of LTP, can erode normal opponent signal processing. Simulated lesions of the cerebellar network reproduce symptoms of cerebellar disease, including sluggish movement onsets, poor execution of multijoint plans, and abnormally prolonged endpoint oscillations.
Acquisition of a new-latency conditioned nictitating membrane response--major, but not complete, dependence on the ipsilateral cerebellum.
Authors: Yeo C H , Lobo D H , Baum A
Published: June 2007

Classical conditioning of the nictitating membrane response (NMR) of rabbits is simple associative learning of a motor response. In several two-stage experiments, reversible inactivations of the deep cerebellar nuclei in stage 1 appeared to prevent acquisition of NMR conditioning in naive rabbits--no conditioned responses (CRs) were evident after inactivations were lifted in stage 2. Results of a three-stage experiment were different. When subjects were first trained with a light conditional stimulus (CS) in stage 1, reversible cerebellar inactivations during conditioning to a different, tone CS during stage 2 did not appear to prevent new learning because CRs to the tone CS were evident when the inactivation was lifted. Results from the two-stage experiments support the suggestion that the cerebellum is essential for the acquisition of NMR conditioning, but results from the three-stage experiment do not. Here, we use a three-stage design with different interstimulus intervals (ISIs) in stages 1 and 2. Because CRs develop with latencies-to-peak dependent on the ISI, learning during stage 1 can be dissociated from that accruing in stage 2. Complete inactivation of the ipsilateral cerebellar nuclei with muscimol substantially but not completely prevented learning with the second ISI during stage 2 because small CR peaks around the stage 2 ISI could be detected in some subjects after the inactivation had been lifted in stage 3. We suggest that the weak levels of conditioning possible during unilateral inactivation depend on the contralateral cerebellum or on extracerebellar circuitry and that these may be capable of supporting transfer of conditioning in a previous three-stage experiment. But, we confirm that normal NMR conditioning is critically dependent on the ipsilateral cerebellum.
Environmental signals modulate olfactory acuity, discrimination, and memory in Caenorhabditis elegans.
Authors: Colbert H A , Bargmann C I
Published: June 2007

Caenorhabditis elegans uses a variety of attractive olfactory cues to detect food. We show here that the responses to olfactory cues are regulated in a dynamic way by behavioral context and the animal's previous experience. Prolonged exposure to an odorant leads to a decreased response to that odorant, a form of behavioral plasticity called olfactory adaptation. We show that starvation can increase the extent of olfactory adaptation to the odorant benzaldehyde; this effect of starvation persists for several hours after the animals have been returned to food. The effect of starvation is antagonized by exogenous serotonin, which induces many of the same behavioral responses in C. elegans as are induced by food. Starvation also inhibits recovery from adaptation to a different odorant, 2-methylpyrazine, thus enhancing olfactory memory. In addition to its effects on adaptation, starvation modulates olfactory discrimination in C. elegans; starved animals discriminate more classes of odorants than fed animals. Increased olfactory discrimination is also seen in the adaptation-defective mutant adp-1 (ky20). These various forms of behavioral plasticity enhance the ability of starved animals to respond to novel, potentially informative odorants.
Behavioral modulation induced by food odor aversive conditioning and its influence on the olfactory responses of an oscillatory brain network in the slug Limax marginatus.
Authors: Kimura T , Toda S , Sekiguchi T , Kirino Y
Published: June 2007

We compared behaviorally and physiologically the olfactory responses of slugs (Limax marginatus) that had been subjected to aversive, appetitive, or unpaired training with food odors (carrot or cucumber). In the aversive training, the slugs were exposed to the food odor as a conditioned stimulus (CS), and then quinidine sulfate solution as an unconditioned stimulus (UCS) was immediately applied to the lip of the slugs. This training caused a decrease in preference level for the CS. The unpaired training, in which the CS and the UCS were presented to the slugs with a 5-min interval, induced no change in the preference level for the CS. In the appetitive training, the slugs were allowed to eat the CS odor source without UCS application. When we used nonstarved slugs, it was found that the preference level for the CS increased upon the appetitive training. These results indicate that each training changed the preference for the odors in a characteristic manner. In the physiological experiments, we used brain-inferior tentacular nose preparations isolated from slugs and investigated the olfactory responses of the oscillations in the local field potential (LFP) of the procerebral (PC) lobe. We found that odor presentation induced various types of changes in the LFP oscillation frequency, although the rate of occurrence of the frequency modulation differed between odors used in the aversive and the unpaired training (aversive-conditioned and unpaired odors). The aversive-conditioned odors induced a decrease in the oscillatory frequency. Unpaired odors did not change it. Moreover, odors used in the appetitive training (appetitive-conditioned odors) induced an increase in the frequency. Thus, it was considered that those modulations of PC lobe oscillatory activity were independent of odor and reflected learned preference for odors.