bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large Functional Range of Steady-State Levels of Nuclear and Mitochondrial Transcripts Coding for the Subunits of the Human Mitochondrial OXPHOS System
Authors: Duborjal Hervé , Beugnot Réjane , de Camaret Bénédicte Mousson , Issartel Jean-Paul 
Published: December 2002

We have measured, by reverse transcription and real-time quantitative PCR, the steady-state levels of the mitochondrial and nuclear transcripts encoding several subunits of the human oxidative phosphorylation (OXPHOS) system, in different normal tissues (muscle, liver, trachea, and kidney) and in cultured cells (normal fibroblasts, 143B osteosarcoma cells, 143B206 ρ0 cells). Five mitochondrial transcripts and nine nuclear transcripts were assessed. The measured amounts of these OXPHOS transcripts in muscle samples corroborated data obtained by others using the serial analysis of gene expression (SAGE) method to appraise gene expression in the same type of tissue. Steady-state levels for all the transcripts were found to range over more than two orders of magnitude. Most of the time, the mitochondrial H-strand transcripts were present at higher levels than the nuclear transcripts. The mitochondrial L-strand transcript ND6 was usually present at a low level. Cultured 143B cells contained significantly reduced amounts of mitochondrial transcripts in comparison with the tissue samples. In 143B206 ρ0 cells, fully depleted of mitochondrial DNA, the levels of nuclear OXPHOS transcripts were not modified in comparison with the parental cells. This observation indicated that nuclear transcription is not coordinated with mitochondrial transcription. We also observed that in the different tissues and cells, there is a transcriptional coregulation of all the investigated nuclear genes. Nuclear OXPHOS gene expression seems to be finely regulated.[The following individual kindly provided reagents, samples, or unpublished information as indicated in the paper: G. Attardi.]
A Nonsense Mutation in the FMO3 Gene Underlies Fishy Off-Flavor in Cow's Milk
Authors: Lundén Anne , Marklund Stefan , Gustafsson Victoria , Andersson Leif 
Published: December 2002

Fish-odor syndrome or Trimethylaminuria (OMIM #602079) in humans is an inborn error of metabolism associated with a characteristic fishy body odor due to elevated levels of trimethylamine (TMA) in body fluids. It is caused by loss-of-function mutations in FMO3encoding flavin-containing mono-oxygenase 3. A fishy off-flavor is occasionally observed in cow's milk and it has been established recently that this phenotype is due to elevated TMA levels. Here, we report that fishy off-flavor in cow's milk is caused by a nonsense mutation (R238X) in the bovine FMO3 ortholog. RT–PCR analysis indicated that the mutant transcript is present in a very low amount. The mutation was found to be surprisingly common (q = 0.155) in one breed of cattle.[The sequence data described in this paper have been submitted to GenBank with accession nos.AF488417–AF488422. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: K. Sandberg and I. Hansson.]
Evidence for a Fast, Intrachromosomal Conversion Mechanism From Mapping of Nucleotide Variants Within a Homogeneous α-Satellite DNA Array
Authors: Schindelhauer Dirk , Schwarz Tobias 
Published: December 2002

Assuming that patterns of sequence variants within highly homogeneous centromeric tandem repeat arrays can tell us which molecular turnover mechanisms are presently at work, we analyzed the α-satellite tandem repeat array DXZ1 of one human X chromosome. Here we present accurate snapshots from this dark matter of the genome. We demonstrate stable and representative cloning of the array in a P1 artificial chromosome (PAC) library, use samples of higher-order repeats subcloned from five unmapped PACs (120–160 kb) to identify common variants, and show that such variants are presently in a fixed transition state. To characterize patterns of variant spread throughout homogeneous array segments, we use a novel partial restriction and pulsed-field gel electrophoresis mapping approach. We find an older large-scale (35–50 kb) duplication event supporting the evolutionarily important unequal crossing-over hypothesis, but generally find independent variant occurrence and a paucity of potential de novo mutations within segments of highest homogeneity (99.1%–99.3%). Within such segments, a highly nonrandom variant clustering within adjacent higher-order repeats was found in the absence of haplotypic repeats. Such variant clusters are hardly explained by interchromosomal, fixation-driving mechanisms and likely reflect a fast, localized, intrachromosomal sequence conversion mechanism.[Supplemental material is available online atwww.genome.org and www.pedgen.med.uni-muenchen.de. The sequence data from this study have been submitted to DDBJ, EMBL, and GenBank under accession nos. AJ509815–AJ509823, AJ509829–AJ509852,AJ509874–AJ510031. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: P. Warburton, and C. Roos.]
Diversity in Nucleotide Binding Site–Leucine-Rich Repeat Genes in Cereals
Authors: Bai Jianfa , Pennill Lourdes A. , Ning Jianchang , Lee Se Weon , Ramalingam Jegadeesan , Webb Craig A. , Zhao Bingyu , Sun Qing , Nelson James C. , Leach Jan E. , Hulbert Scot H. 
Published: December 2002

The diversity of the largest group of plant disease resistance genes, the nucleotide binding site–leucine-rich repeat (NBS–LRR) genes, was examined in cereals following polymerase chain reaction (PCR) cloning and database mining. NBS–LRR genes in rice are a large and diverse class with more than 600 genes, at least three to four times the complement of Arabidopsis. Most occur in small families containing one or a few cross-hybridizing members. Unlike inArabidopsis and other dicots, the class of NBS–LRR genes coding for a Toll and mammalian interleukin-1 receptor (TIR) domain were not amplified during the evolution of the cereals. Genes coding for TIR domains are present in the rice genome, but have diverged from the NBS–LRR genes. Most cereal genes are similar in structure to the members of the non-TIR class of dicots, although many do not code for a coiled-coil domain in their amino termini. One unique class of cereal genes, with ∼50 members, codes for proteins similar to the N-termini and NBS domains of resistance genes but does not code for LRR domains. The resistance gene repertoire of grasses has changed from that of dicots in their independent evolution since the two groups diverged. It is not clear whether this reflects a difference in downstream defense signaling pathways.[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos.AF516886–AF516895.]
Haplotype and Linkage Disequilibrium Architecture for Human Cancer-Associated Genes
Authors: Bonnen Penelope E. , Wang Peggy J. , Kimmel Marek , Chakraborty Ranajit , Nelson David L. 
Published: December 2002

To facilitate association-based linkage studies we have studied the linkage disequilibrium (LD) and haplotype architecture around five genes of interest for cancer risk: ATM, BRCA1,BRCA2, RAD51, and TP53. Single nucleotide polymorphisms (SNPs) were identified and used to construct haplotypes that span 93–200 kb per locus with an average SNP density of 12 kb. These markers were genotyped in four ethnically defined populations that contained 48 each of African Americans, Asian Americans, Hispanic Americans, and European Americans. Haplotypes were inferred using an expectation maximization (EM) algorithm, and the data were analyzed using D‘, R2, Fisher’s exactP-values, and the four-gamete test for recombination. LD levels varied widely between loci from continuously high LD across 200 kb to a virtual absence of LD across a similar length of genome. LD structure also varied at each gene and between populations studied. This variation indicates that the success of linkage-based studies will require a precise description of LD at each locus and in each population to be studied. One striking consistency between genes was that at each locus a modest number of haplotypes present in each population accounted for a high fraction of the total number of chromosomes. We conclude that each locus has its own genomic profile with regard to LD, and despite this there is the widespread trend of relatively low haplotype diversity. As a result, a low marker density should be adequate to identify haplotypes that represent the common variation at a locus, thereby decreasing costs and increasing efficacy of association studies.[Supplemental material is available online at http://www.genome.org.]
A Novel Method for SNP Detection Using a New Duplex-Specific Nuclease From Crab Hepatopancreas
Authors: Shagin Dmitry A. , Rebrikov Denis V. , Kozhemyako Valery B. , Altshuler Ilia M. , Shcheglov Alex S. , Zhulidov Pavel A. , Bogdanova Ekaterina A. , Staroverov Dmitry B. , Rasskazov Valery A. , Lukyanov Sergey 
Published: December 2002

We have characterized a novel nuclease from the Kamchatka crab, designated duplex-specific nuclease (DSN). DSN displays a strong preference for cleaving double-stranded DNA and DNA in DNA-RNA hybrid duplexes, compared to single-stranded DNA. Moreover, the cleavage rate of short, perfectly matched DNA duplexes by this enzyme is essentially higher than that for nonperfectly matched duplexes of the same length. Thus, DSN differentiates between one-nucleotide variations in DNA. We developed a novel assay for single nucleotide polymorphism (SNP) detection based on this unique property, termed “duplex-specific nuclease preference” (DSNP). In this innovative assay, the DNA region containing the SNP site is amplified and the PCR product mixed with signal probes (FRET-labeled short sequence-specific oligonucleotides) and DSN. During incubation, only perfectly matched duplexes between the DNA template and signal probe are cleaved by DSN to generate sequence-specific fluorescence. The use of FRET-labeled signal probes coupled with the specificity of DSN presents a simple and efficient method for detecting SNPs. We have employed the DSNP assay for the typing of SNPs in methyltetrahydrofolate reductase, prothrombin and p53 genes on homozygous and heterozygous genomic DNA.[Supplemental material is available online atwww.genome.org. The sequence data from this study have been submitted to GenBank/EMBL/Date Bank under accession nos. AF520591. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: N.K. Yankovsky, A.V. Polyakov, and G.N. Rudenskaya.]
Interrogating a High-Density SNP Map for Signatures of Natural Selection
Authors: Akey Joshua M. , Zhang Ge , Zhang Kun , Jin Li , Shriver Mark D. 
Published: December 2002

Identifying genomic regions that have been targets of natural selection remains one of the most important and challenging areas of research in genetics. To this end, we report an analysis of 26,530 single nucleotide polymorphisms (SNPs) with allele frequencies that were determined in three populations. Specifically, we calculated a measure of genetic differentiation, FST, for each locus and examined its distribution at the level of the genome, the chromosome, and individual genes. Through a variety of analyses, we have found statistically significant evidence supporting the hypothesis that selection has influenced extant patterns of human genetic variation. Importantly, by contrasting the FST of individual SNPs to the empirical genome-wide distribution of FST, our results are not confounded by tenuous assumptions of population demographic history. Furthermore, we have identified 174 candidate genes with distribution of genetic variation that indicates that they have been targets of selection. Our work provides a first generation natural selection map of the human genome and provides compelling evidence that selection has shaped extant patterns of human genomic variation.[Supplemental material is available online atwww.genome.org.]
Assembly, Verification, and Initial Annotation of the NIA Mouse 7.4K cDNA Clone Set
Authors: VanBuren Vincent , Piao Yulan , Dudekula Dawood B. , Qian Yong , Carter Mark G. , Martin Patrick R. , Stagg Carole A. , Bassey Uwem C. , Aiba Kazuhiro , Hamatani Toshio , Kargul George J. , Luo Amber G. , Kelso Janet , Hide Winston , Ko Minoru S.H. 
Published: December 2002

A set of 7407 cDNA clones (NIA mouse 7.4K) was assembled from >20 cDNA libraries constructed mainly from early mouse embryos, including several stem cell libraries. The clone set was assembled from embryonic and newborn organ libraries consisting of ∼120,000 cDNA clones, which were initially re-arrayed into a set of ∼11,000 unique cDNA clones. A set of tubes was constructed from the racks in this set to prevent contamination and potential mishandling errors in all further re-arrays. Sequences from this set (11K) were analyzed further for quality and clone identity, and high-quality clones with verified identity were re-arrayed into the final set (7.4K). The set is freely available, and a corresponding database was built to provide comprehensive annotation for those clones with known identity or homology, and has been made available through an extensive Web site that includes many link-outs to external databases and analysis servers.[The sequence data from this study have been submitted to GenBank under accession nos. BQ550036–BQ563104.]
Gene Expression Profiling of Embryo-Derived Stem Cells Reveals Candidate Genes Associated With Pluripotency and Lineage Specificity
Authors: Tanaka Tetsuya S. , Kunath Tilo , Kimber Wendy L. , Jaradat Saied A. , Stagg Carole A. , Usuda Masayuki , Yokota Takashi , Niwa Hitoshi , Rossant Janet , Ko Minoru S.H. 
Published: December 2002

Large-scale gene expression profiling was performed on embryo-derived stem cell lines to identify molecular signatures of pluripotency and lineage specificity. Analysis of pluripotent embryonic stem (ES) cells, extraembryonic-restricted trophoblast stem (TS) cells, and terminally-differentiated mouse embryo fibroblast (MEF) cells identified expression profiles unique to each cell type, as well as genes common only to ES and TS cells. Whereas most of the MEF-specific genes had been characterized previously, the majority (67%) of the ES-specific genes were novel and did not include known differentiated cell markers. Comparison with microarray data from embryonic material demonstrated that ES-specific genes were underrepresented in all stages sampled, whereas TS-specific genes included known placental markers. Investigation of four novel TS-specific genes showed trophoblast-restricted expression in cell lines and in vivo, whereas one uncharacterized ES-specific gene, Esg-1, was found to be exclusively associated with pluripotency. We suggest that pluripotency requires a set of genes not expressed in other cell types, whereas lineage-restricted stem cells, like TS cells, express genes predictive of their differentiated lineage.[Supplemental material is available online at www.genome.org andhttp://lgsun.grc.nia.nih.gov/microarray/data.html]
Rapid Mapping of Zebrafish Mutations With SNPs and Oligonucleotide Microarrays
Authors: Stickney Heather L. , Schmutz Jeremy , Woods Ian G. , Holtzer Caleb C. , Dickson Mark C. , Kelly Peter D. , Myers Richard M. , Talbot William S. 
Published: December 2002

Large-scale genetic screens in zebrafish have identified thousands of mutations in hundreds of essential genes. The genetic mapping of these mutations is necessary to link DNA sequences to the gene functions defined by mutant phenotypes. Here, we report two advances that will accelerate the mapping of zebrafish mutations: (1) The construction of a first generation single nucleotide polymorphism (SNP) map of the zebrafish genome comprising 2035 SNPs and 178 small insertions/deletions, and (2) the development of a method for mapping mutations in which hundreds of SNPs can be scored in parallel with an oligonucleotide microarray. We have demonstrated the utility of the microarray technique in crosses with haploid and diploid embryos by mapping two known mutations to their previously identified locations. We have also used this approach to localize four previously unmapped mutations. We expect that mapping with SNPs and oligonucleotide microarrays will accelerate the molecular analysis of zebrafish mutations.[Supplemental material is available online atwww.genome.org. The sequence data described in this paper have been submitted to dbSNP under accession nos. 5103507–5105537. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J. Postlethwait, C.-B. Chien, C. Kimmel, L. Maves, and M. Westerfield.]
Regulation of Root Hair Initiation and Expansin Gene Expression in Arabidopsis[W]
Authors: Cho Hyung-Taeg , Cosgrove Daniel J. 
Published: December 2002

AbstractThe expression of two Arabidopsis expansin genes (AtEXP7 and AtEXP18) is tightly linked to root hair initiation; thus, the regulation of these genes was studied to elucidate how developmental, hormonal, and environmental factors orchestrate root hair formation. Exogenous ethylene and auxin, as well as separation of the root from the medium, stimulated root hair formation and the expression of these expansin genes. The effects of exogenous auxin and root separation on root hair formation required the ethylene signaling pathway. By contrast, blocking the endogenous ethylene pathway, either by genetic mutations or by a chemical inhibitor, did not affect normal root hair formation and expansin gene expression. These results indicate that the normal developmental pathway for root hair formation (i.e., not induced by external stimuli) is independent of the ethylene pathway. Promoter analyses of the expansin genes show that the same promoter elements that determine cell specificity also determine inducibility by ethylene, auxin, and root separation. Our study suggests that two distinctive signaling pathways, one developmental and the other environmental/hormonal, converge to modulate the initiation of the root hair and the expression of its specific expansin gene set.
Generating and Exploiting Polarity in Bacteria
Authors: Shapiro Lucy , McAdams Harley H. , Losick Richard 
Published: December 2002

Bacteria are often highly polarized, exhibiting specialized structures at or near the ends of the cell. Among such structures are actin-organizing centers, which mediate the movement of certain pathogenic bacteria within the cytoplasm of an animal host cell; organized arrays of membrane receptors, which govern chemosensory behavior in swimming bacteria; and asymmetrically positioned septa, which generate specialized progeny in differentiating bacteria. This polarization is orchestrated by complex and dynamic changes in the subcellular localization of signal transduction and cytoskeleton proteins as well as of specific regions of the chromosome. Recent work has provided information on how dynamic subcellular localization occurs and how it is exploited by the bacterial cell.
The main task of a bacterial cell is to survive and duplicate itself. The bacterium must replicate its genetic material and divide at the correct site in the cell and at the correct time in the cell cycle with high precision. Each kind of bacterium also executes its own strategy to find nutrients in its habitat and to cope with conditions of stress from its environment. This involves moving toward food, adapting to environmental extremes, and, in many cases, entering and exploiting a eukaryotic host. These activities often involve processes that take place at or near the poles of the cell. Here we explore some of the schemes bacteria use to orchestrate dynamic changes at their poles and how these polar events execute cellular functions.

In spite of their small size, bacteria have a remarkably complex internal organization and external architecture. Bacterial cells are inherently asymmetric, some more obviously so than others. The most easily recognized asymmetries involve surface structures, e.g., flagella, pili, and stalks that are preferentially assembled at one pole by many bacteria. “New” poles generated at the cell division plane differ from old poles from the previous round of cell division. Even in
Escherichia coli
, which is generally thought to be symmetrical, old poles are more static than new poles with respect to cell wall assembly (
1
), and they differ in the deposition of phospholipid domains (
2
). There are many instances of differential polar functions; among these is the preferential use of old poles when attaching to host cells as in the interaction of
Bradyrhizobium
with plant root hairs (
3
) or the polar pili-mediated attachment of the
Pseudomonas aeruginosa
pathogen to tracheal epithelia (
4
). An unusual polar organelle that mediates directed motility on solid surfaces is found in the nonpathogenic bacterium
Myxococcus xanthus
. The gliding motility of this bacterium is propelled by a nozzle-like structure that squirts a polysaccharide-containing slime from the pole of the cell (
5
). Interestingly,
M. xanthus
, which has nozzles at both poles, can reverse direction by closing one nozzle and opening the other in response to end-to-end interactions between cells.
Calcium Binding Is Required for Calmodulin Function in
Aspergillus nidulans
Authors: Joseph James D. , Means Anthony R. 
Published: December 2002

ABSTRACT

To explore the structural basis for the essential role of calmodulin (CaM) in
Aspergillus nidulans,
we have compared the biochemical and in vivo properties of
A. nidulans
CaM (AnCaM) with those of heterologous CaMs. Neither
Saccharomyces cerevisiae
CaM (ScCaM) nor a Ca
2+
binding mutant of
A. nidulans
CaM (1234) interacts appreciably with
A. nidulans
CaM binding proteins by an overlay assay or activates two essential CaMKs, CMKA and CMKB. In contrast, although vertebrate CaM (VCaM) binds a spectrum of proteins similar to that for AnCaM, it is unable to fully activate CMKA and CMKB, displaying a higher
K
CaM
and reduced
V
max
for both enzymes. In correlation with the biochemical analysis, neither ScCaM nor 1234 can support
A. nidulans
growth in the absence of the endogenous protein, whereas VCaM only partially complements the absence of wild-type CaM. Analysis of VCaM and AnCaM chimeras demonstrates that amino acid variations in both N- and C-terminal domains contribute to the inability of VCaM to activate CMKB, but differences in the N terminus are largely responsible for the reduced activity towards CMKA. In vivo, the chimeric molecules support growth equivalently, but only to levels intermediate between those of VCaM and AnCaM, suggesting that the reduced ability to activate the CaMKs is not solely responsible for the inability of VCaM to complement the absence of the wild-type protein. Thus, not only is Ca
2+
binding required for CaM function in
A. nidulans,
but the essential in vivo functions of
A. nidulans
CaM are uniquely sensitive to the subtle amino acid variations present in vertebrate CaM.