bluuebunny/crossref_metadata_2025 huggingface dataset:
Specific Heterodimer Formation Is a Prerequisite for Uroplakins to Exit from the Endoplasmic Reticulum
Authors: Tu Liyu , Sun Tung-Tien , Kreibich Gert
Published: December 2002

Much of the lower urinary tract, including the bladder, is lined by a stratified urothelium forming a highly differentiated, superficial umbrella cell layer. The apical plasma membrane as well as abundant cytoplasmic fusiform vesicles of the umbrella cells is covered by two-dimensional crystals that are formed by four membrane proteins named uroplakins (UPs) Ia, Ib, II, and III. UPs are synthesized on membrane-bound polysomes, and after several co- and posttranslational modifications they assemble into planar crystals in a post-Golgi vesicular compartment. Distension of the bladder may cause fusiform vesicles to fuse with the apical plasma membrane. We have investigated the early stages of uroplakin assembly by expressing the four uroplakins in 293T cells. Transfection experiments showed that, when expressed individually, only UPIb can exit from the endoplasmic reticulum (ER) and move to the plasma membrane, whereas UPII and UPIII reach the plasma membrane only when they form heterodimeric complexes with UPIa and UPIb, respectively. Heterodimer formation in the ER was confirmed by pulse-chase experiment followed by coimmunoprecipitation. Our results indicate that the initial building blocks for the assembly of crystalline uroplakin plaques are heterodimeric uroplakin complexes that form in the ER.
Domain Regulation of Imprinting Cluster in Kip2/Lit1 Subdomain on Mouse Chromosome 7F4/F5: Large-Scale DNA Methylation Analysis Reveals That DMR-Lit1 Is a Putative Imprinting Control Region
Authors: Yatsuki Hitomi , Joh Keiichiro , Higashimoto Ken , Soejima Hidenobu , Arai Yuji , Wang Youdong , Hatada Izuho , Obata Yayoi , Morisaki Hiroko , Zhang Zhongming , Nakagawachi Tetsuji , Satoh Yuji , Mukai Tsunehiro
Published: December 2002

Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57kip2)/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed large-scale DNA methylation analysis to identify thecis-element crucial for the regulation of the Kip2/Lit1 subdomain. Ten CpG islands (CGIs) were found, and these were located at the promoter sites, upstream of genes, and within intergenic regions. Bisulphite sequencing revealed that CGIs 4, 5, 8, and 10 were differentially methylated regions (DMRs). CGIs 4, 5, and 10 were methylated paternally in somatic tissues but not in germ cells. CGI8 was methylated in oocyte and maternally in somatic tissues during development. Parental-specific DNase I hypersensitive sites (HSSs) were found near CGI8. These data indicate that CGI8, called DMR-Lit1, is not only the region for gametic methylation but might also be the imprinting control region (ICR) of the subdomain.
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.]
A Unified Framework for Mapping Quantitative Trait Loci in Bivalent Tetraploids Using Single-dose Restriction Fragments: A Case Study from Alfalfa
Authors: Ma Chang-Xing , Casella George , Shen Zuo-Jun , Osborn Thomas C. , Wu Rongling
Published: December 2002

The development of statistical methodologies for quantitative trait locus (QTL) mapping in polyploids is complicated by complex polysomic inheritance. In this article, we propose a statistical method for mapping QTL in tetraploids undergoing bivalent formation at meiosis by using single-dose restriction fragments. Our method is based on a unified framework, one that uses chromosome bivalent pairing configuration and gametic recombination to discern different mechanisms of gamete formation. Our bivalent polyploid model can not only provide a simultaneous estimation of the linkage and chromosome pairing configuration—a cytological parameter of evolutionary and systematic interest—but also enhances the precision of estimating QTL effects and position by correctly characterizing gene segregation during polyploid meiosis. By using our method and a linkage map constructed in a previous study, we successfully identify several QTL affecting winter hardiness in bivalent tetraploid alfalfa. Moreover, our results reveal significant preferential chromosome pairing at meiosis in an F1 hybrid population, which indicates the importance of reassessing the traditional view of random chromosome segregation in alfalfa.
Extreme Pathway Lengths and Reaction Participation in Genome-Scale Metabolic Networks
Authors: Papin Jason A. , Price Nathan D. , Palsson Bernhard Ø.
Published: December 2002

Extreme pathways are a unique and minimal set of vectors that completely characterize the steady-state capabilities of genome-scale metabolic networks. A framework is provided to mathematically characterize extreme pathway length and to study how individual reactions participate in the extreme pathway structure of a network. The length of an extreme pathway is the number of reactions that comprise it. Reaction participation is the percentage of extreme pathways that utilize a given reaction. These properties were computed for the production of individual amino acids and protein production inHelicobacter pylori and individual amino acid production inHaemophilus influenzae. Reaction participation classifies the reactions into groups that are always, sometimes, or never utilized for the production of a target product. The utilized reactions can be further grouped into correlated subsets of reactions, some of which are non-obvious, and which may, in turn, suggest regulatory structure. The length of the extreme pathways did not correlate with product yield or chemical complexity. The distributions of extreme pathway lengths inH. pylori were also very different from those in H. influenzae, showing a distinct systemic difference between the two organisms, despite overall similar metabolic networks. Reaction participation and extreme pathway lengths thus serve to elucidate systemic biological features.
A Scalable High-Throughput Chemical Synthesizer
Authors: Livesay Eric A. , Liu Ying-Horng , Luebke Kevin J. , Irick Joel , Belosludtsev Yuri , Rayner Simon , Balog Robert , Johnston Stephen Albert
Published: December 2002

A machine that employs a novel reagent delivery technique for biomolecular synthesis has been developed. This machine separates the addressing of individual synthesis sites from the actual process of reagent delivery by using masks placed over the sites. Because of this separation, this machine is both cost-effective and scalable, and thus the time required to synthesize 384 or 1536 unique biomolecules is very nearly the same. Importantly, the mask design allows scaling of the number of synthesis sites without the addition of new valving. Physical and biological comparisons between DNA made on a commercially available synthesizer and this unit show that it produces DNA of similar quality.
A Strategy to Retrieve the Whole Set of Protein Modules in Microbial Proteomes
Authors: Le Bouder-Langevin Stéphanie , Capron-Montaland Isabelle , De Rosa Renaud , Labedan Bernard
Published: December 2002

Protein homology is often limited to long structural segments that we have previously called modules. We describe here a suite of programs used to catalog the whole set of modules present in microbial proteomes. First, the Darwin AllAll program detects homologous segments using thresholds for evolutionary distance and alignment length, and another program classifies these modules. After assembling these homologous modules in families, we further group families which are related by a chain of neighboring unrelated homologous modules. With the automatic analysis of these groups of families sharing homologous modules in independent multimodular proteins, one can split into their component parts many fused modules and/or deduce by logic more distant modules. All detected and inferred modules are reassembled in refined families. These two last steps are made by a unique program. Eventually, the soundness of the data obtained by this experimental approach is checked using independent tests. To illustrate this modular approach, we compared four proteobacterial proteomes (Campylobacter jejuni, Escherichia coli,Haemophilus influenzae, and Helicobacter pylori). It appears that this method might retrieve from present-day proteins many of the modules which can help to trace back ancient events of gene duplication and/or fusion.
The Human Hox-bearing Chromosome Regions Did Arise by Block or Chromosome (or Even Genome) Duplications
Authors: Larhammar Dan , Lundin Lars-Gustav , Hallböök Finn
Published: December 2002

Many chromosome regions in the human genome exist in four similar copies, suggesting that the entire genome was duplicated twice in early vertebrate evolution, a concept called the 2R hypothesis. Forty-two gene families on the four Hox-bearing chromosomes were recently analyzed by others, and 32 of these were reported to have evolutionary histories incompatible with duplications concomitant with the Hox clusters, thereby contradicting the 2R hypothesis. However, we show here that nine of the families have probably been translocated to the Hox-bearing chromosomes more recently, and that three of these belong to other chromosome quartets where they actually support the 2R hypothesis. We consider 13 families too complex to shed light on the chromosome duplication hypothesis. Among the remaining 20 families, 14 display phylogenies that support or are at least consistent with the Hox-cluster duplications. Only six families seem to have other phylogenies, but these trees are highly uncertain due to shortage of sequence information. We conclude that all relevant and analyzable families support or are consistent with block/chromosome duplications and that none clearly contradicts the 2R hypothesis.
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.]
Highly Efficient Modification of Bacterial Artificial Chromosomes (BACs) Using Novel Shuttle Vectors Containing the R6Kγ Origin of Replication
Authors: Gong Shiaoching , Yang Xiangdong William , Li Chenjian , Heintz Nathaniel
Published: December 2002

Bacterial artificial chromosome (BAC) mediated transgenesis has proven to be a highly reliable way to obtain accurate transgene expression for in vivo studies of gene expression and function. A rate-limiting step in use of this technology to characterize large numbers of genes has been the process with which BACs can be modified by homologous recombination in Escherichia coli. We report here a highly efficient method for modifying BACs by using a novel set of shuttle vectors that contain the R6Kγ origin for DNA replication, the E. coli RecA gene for recombination, and the SacBgene for negative selection. These new vectors greatly increased the ease with which one can clone the shuttle vectors, as well as screen for co-integrated and resolved clones. Furthermore, we simplify the shuttle vector cloning to one step by incorporation of a “built-in” resolution cassette for rapid removal of the unwanted vector sequences. This new system has been used to modify a dozen BACs. It is well suited for efficient production of modified BACs for use in a variety of in vivo studies.
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.]
Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies
Authors: Hill David P. , Blake Judith A. , Richardson Joel E. , Ringwald Martin
Published: December 2002

Structured vocabulary development enhances the management of information in biological databases. As information grows, handling the complexity of vocabularies becomes difficult. Defined methods are needed to manipulate, expand and integrate complex vocabularies. The Gene Ontology (GO) project provides the scientific community with a set of structured vocabularies to describe domains of molecular biology. The vocabularies are used for annotation of gene products and for computational annotation of sequence data sets. The vocabularies focus on three concepts universal to living systems, biological process, molecular function and cellular component. As the vocabularies expand to incorporate terms needed by diverse annotation communities, species-specific terms become problematic. In particular, the use of species-specific anatomical concepts remains unresolved. We present a method for expansion of GO into areas outside of the three original universal concept domains. We combine concepts from two orthogonal vocabularies to generate a larger, more specific vocabulary. The example of mammalian heart development is presented because it addresses two issues that challenge GO; inclusion of organism-specific anatomical terms, and proliferation of terms and relationships. The combination of concepts from orthogonal vocabularies provides a robust representation of relevant terms and an opportunity for evaluation of hypothetical concepts.
Distribution and Characterization of Regulatory Elements in the Human Genome
Authors: Majewski Jacek , Ott Jurg
Published: December 2002

The regulation of transcription and subsequent gene splicing are crucial to correct gene expression. Although a number of regulatory sequences involved in both processes are known, it is not clear how general their functions are in the genomic context, nor how the regulatory regions are distributed throughout the genome. Here we study the distribution of known mutagenic elements within human introns and exons to deduce the properties of regions essential for splicing and transcription. We show that intronic splicing regulators are generally found close to the splice sites, but may be found as far as 200 nucleotides away from the splice junctions. Similarly, sequences important for splicing may be located as far as 125 nucleotides away from the junctions, within exons. We characterize several types of simple repetitive sequences and low-complexity regions that are overrepresented close to both intron ends and are likely to play important roles in the splicing process. We show that the first introns within most genes play a particularly important regulatory role that is most likely, however, to be involved in transcription control. We also study the distribution of two known regulatory motifs, the GGG trinucleotide and the CpG dinucleotide, and deduce their respective importance to splicing and transcription regulation.
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.]
Generalized Gap Model for Bacterial Artificial Chromosome Clone Fingerprint Mapping and Shotgun Sequencing
Authors: Wendl Michael C. , Waterston Robert H.
Published: December 2002

We develop an extension to the Lander-Waterman theory for characterizing gaps in bacterial artificial chromosome fingerprint mapping and shotgun sequencing projects. It supports a larger set of descriptive statistics and is applicable to a wider range of project parameters. We show that previous assertions regarding inconsistency of the Lander-Waterman theory at higher coverages are incorrect and that another well-known but ostensibly different model is in fact the same. The apparent paradox of infinite island lengths is resolved. Several applications are shown, including evolution of the probability density function, calculation of closure probabilities, and development of a probabilistic method for computing stopping points in bacterial artificial chromosome shotgun sequencing.
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]
Selecting for Functional Alternative Splices in ESTs
Authors: Kan Zhengyan , States David , Gish Warren
Published: December 2002

The expressed sequence tag (EST) collection in dbEST provides an extensive resource for detecting alternative splicing on a genomic scale. Using genomically aligned ESTs, a computational tool (TAP) was used to identify alternative splice patterns for 6400 known human genes from the RefSeq database. With sufficient EST coverage, one or more alternatively spliced forms could be detected for nearly all genes examined. To identify high (>95%) confidence observations of alternative splicing, splice variants were clustered on the basis of having mutually exclusive structures, and sample statistics were then applied. Through this selection, alternative splices expected at a frequency of >5% within their respective clusters were seen for only 17%–28% of genes. Although intron retention events (potentially unspliced messages) had been seen for 36% of the genes overall, the same statistical selection yielded reliable cases of intron retention for <5% of genes. For high-confidence alternative splices in the human ESTs, we also noted significantly higher rates both of cross-species conservation in mouse ESTs and of validation in the GenBank mRNA collection. We suggest quantitative analytical approaches such as these can aid in selecting useful targets for further experimental characterization and in so doing may help elucidate the mechanisms and biological implications of alternative splicing.
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

The 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.
Unsteady Heat Transfer Analysis of an Impinging Jet
Authors: Chung Yongmann M. , Luo Kai H.
Published: December 2002

Unsteady heat transfer caused by a confined impinging jet is studied using direct numerical simulation (DNS). The time-dependent compressible Navier-Stokes equations are solved using high-order numerical schemes together with high-fidelity numerical boundary conditions. A sixth-order compact finite difference scheme is employed for spatial discretization while a third-order explicit Runge-Kutta method is adopted for temporal integration. Extensive spatial and temporal resolution tests have been performed to ensure accurate numerical solutions. The simulations cover several Reynolds numbers and two nozzle-to-plate distances. The instantaneous flow fields and heat transfer distributions are found to be highly unsteady and oscillatory in nature, even at relatively low Reynolds numbers. The fluctuation of the stagnation or impingement Nusselt number, for example, can be as high as 20 percent of the time-mean value. The correlation between the vortex structures and the unsteady heat transfer is carefully examined. It is shown that the fluctuations in the stagnation heat transfer are mainly caused by impingement of the primary vortices originating from the jet nozzle exit. The quasi-periodic nature of the generation of the primary vortices due to the Kelvin-Helmholtz instability is behind the nearly periodic fluctuation in impingement heat transfer, although more chaotic and non-linear fluctuations are observed with increasing Reynolds numbers. The Nusselt number distribution away from the impingement point, on the other hand, is influenced by the secondary vortices which arise due to the interaction between the primary vortices and the wall jets. The unsteady vortex separation from the wall in the higher Reynolds number cases leads to a local minimum and a secondary maximum in the Nusselt number distribution. These are due to the changes in the thermal layer thickness accompanying the unsteady flow structures.
Numerical Solution for Transient Conjugate Two-Phase Heat Transfer With Heat Generation in the Pipe Wall
Authors: Fairuzov Yuri V. , Arvizu Hector
Published: December 2002

A method developed earlier for modeling conjugate two-phase heat transfer in flashing flows was used to obtain a numerical solution for transient boiling flow in heated pipes or channels. Two criteria of applicability of the solution obtained were proposed and numerically tested using a more rigorous model, which accounts for the effects of heat conduction with heat generation in the wall and forced convective boiling. The solution obtained provides a simple and reliable alternative to more rigorous methods for modeling transient two-phase flow in heated channels when the material of the wall bounding the flow has a high thermal conductivity and the wall superheat is small.
Heat Transfer From an Isothermal Vertical Surface With Adjacent Heated Horizontal Louvers: Numerical Analysis
Authors: Collins M. , Harrison S. J. , Naylor D. , Oosthuizen P. H.
Published: December 2002

The present study examines the influence of heated, horizontal, and rotatable louvers on the convective and radiative heat transfer from a heated or cooled vertical isothermal surface. The system represents an irradiated Venetian blind adjacent to the indoor surface of a window. Detailed heat transfer results were obtained using a steady, laminar, two-dimensional, conjugate conduction/convection/radiation finite element model for two window temperatures (warm and cool compared to ambient) and irradiation levels, two louver to surface spacings, and three louver angles. The effect of the heated louvers on the heat transfer rate from the surface has been demonstrated.
Heat Transfer From an Isothermal Vertical Surface With Adjacent Heated Horizontal Louvers: Validation
Authors: Collins M. , Harrison S. J. , Naylor D. , Oosthuizen P. H.
Published: December 2002

The present study examines the influence of heated, horizontal, and rotateable louvers on the convective heat transfer from a heated or cooled vertical isothermal surface. The system represents an irradiated Venetian blind adjacent to the indoor surface of a window. Detailed temperature field and local surface flux data were obtained using a Mach-Zehnder Interferometer for two window temperatures (warm and cool compared to ambient) and irradiation levels, two louver to plate spacings, and three louver angles. The results have been compared to a steady, laminar, two-dimensional, conjugate conduction/convection/radiation finite element model of this problem. The effect of the heated louvers on the heat transfer rate from the plate surface has been demonstrated and the results of the numerical study have been validated.
Heat Transfer Coefficients During Condensation of the Zeotropic Refrigerant Mixture HCFC-22/HCFC-142b
Authors: Smit F. J. , Thome J. R. , Meyer J. P.
Published: December 2002

Heat transfer coefficients during condensation of zeotropic refrigerant mixtures were obtained at mass fractions of 90 percent/10 percent, 80 percent/20 percent, 70 percent/30 percent, 60 percent/40 percent, and 50 percent/50 percent for HCFC-22/HCFC-142b and for pure HCFC-22 in a horizontal smooth tube at a high saturation pressure of 2.43 MPa. The measurements were taken in a series of eight 8.11 mm inner diameter smooth tubes with lengths of 1 603 mm. At low mass fluxes, from 40 kg/m2s to 350 kg/m2s where the flow regime is predominately stratified wavy, the refrigerant mass fraction influenced the heat transfer coefficient by up to a factor of two, decreasing as the mass fraction of HCFC-142b is increased. At high mass fluxes of 350 kg/m2s and more, the flow regime was predominately annular and the heat transfer coefficients were not strongly influenced by the refrigerant mass fraction, decreasing only by 7 percent as the refrigerant mass fraction changed from 100 percent HCFC-22 to 50 percent/50 percent HCFC-22/HCFC-142b. The results also indicated that of three methods tested to predict heat transfer coefficients, the flow pattern correlation of Dobson and Chato (1998) gave the best results for pure HCFC-22 and for the mixtures utilizing the Silver-Bell-Ghaly method (1964).
Modeling the Cooling Process Path of a Dehumidifying Coil Under Frosting Conditions
Authors: Mago P. J. , Sherif Dr. S. A.
Published: December 2002

Whenever humid air comes in contact with a cooling coil whose temperature is below both the dew-point of water vapor in air and the freezing point, frost will form. The nature of the frost forming on the coil will depend to a large measure on the psychrometric conditions prevailing inside the freezer and whether the air around the coil is subsaturated or supersaturated. Psychrometric theory and the apparatus-dew-point calculating procedure assume that the cooling process path as the air passes through the coil is a straight-line on the psychrometric chart. The actual path is however a result of a much more complex series of processes and is therefore a curve. While researchers have calculated the actual process path on a dehumidifying coil, none has attempted to do the same for a frosted, multi-row coil. It is believed that determining the actual conditions leaving a given row in a multi-row freezer coil is a crucial step in identifying the coil location in the vicinity of which the transformation from the subsaturated zone to the supersaturated zone occurs. This will prove a key step in identifying a demarcation line between the unfavorable snow-like frost and the more traditional (and more favorable) frost formation patterns. Thus, the objective of this paper is to calculate the air path on an actual industrial-size finned-tube, multi-row coil utilizing experimentally derived data and correlate the shape of the path with the prevailing psychrometric conditions in the freezer in the hope of identifying the demarcation line in question.
Thermal Optimization of a Circular-Sectored Finned Tube Using a Porous Medium Approach
Authors: Kim Sung Jin , Yoo Jae Wook , Jang Seok Pil
Published: December 2002

The present work investigates the heat transfer characteristics of a laminar fully developed forced convection in a circular-sectored finned tube with axially uniform heat flux and peripherally uniform wall temperature. The tubes with circular-sectored fins are modeled as a fluid-saturated porous medium. Using the Brinkman-extended Darcy model for fluid flow and the two-equation model for heat transfer, the analytical solutions for both velocity and temperature distributions are obtained and compared with the exact solution for fluid flow and the numerical solutions for conjugate heat transfer in order to validate the porous medium approach. The agreement between the solutions based on the porous medium approach and the conventional method is close within 5.3 percent. Based on the analytical solutions, parameters of engineering importance are identified to be the angle of the circular sector α and the effective conductivity ratio C, and their effects on fluid flow and heat transfer are studied. Also, the total thermal resistance is derived from the analytical solutions and minimized in order to optimize the thermal performance of a tube with circular-sectored fins.
The Optimal Shape of the Interface Between Two Conductive Bodies With Minimal Thermal Resistance
Authors: Vargas and J. V. C. , Bejan A.
Published: December 2002

This paper considers the fundamental problem of optimizing the geometry of the interface between two conductive bodies, with the objective of minimizing the thermal resistance. The interface geometry is free to change. For simplicity, the geometry is assumed to be two-dimensional with equidistant tooth-shaped features. The tooth shape varies from triangles, to trapezoids and rectangles. The aspect ratio (height/width) of the tooth also varies. The third degree of freedom of the interface architecture is the volume fraction of the higher-conductivity tooth material that is present in the interface region. It is shown that the interface geometry can be optimized with respect to tooth shape. The global thermal resistance minimized with respect to tooth shape varies monotonically with the tooth aspect ratio and volume fraction. The optimized geometry and performance are reported graphically as functions of the physical properties and geometric parameters of the interface region.
Convective Heat Transfer in Vertical Asymmetrically Heated Narrow Channels
Authors: Chin Yun , Lakshminarasimhan Muthu S. , Lu Qing , Hollingsworth D. Keith , Witte Larry C.
Published: December 2002

A calibrated thermochromic liquid crystal technique was used to acquire wall temperature data for laminar and turbulent forced convection in an asymmetrically heated channel. The experiments were carried out in upward flow in rectangular channels with channels spacings of 2.0, 1.0, and 0.5 mm and aspect ratios of 1:10, 1:20, and 1:40. One side was uniformly heated, and the remaining sides were approximately adiabatic. The entire surface temperature field of the heated wall was acquired in one color image, and the temperature was determined by hue-based image processing. In the laminar regime, buoyancy effects elevated the local Nusselt number to values significantly above those expected for purely forced convection in both the developing region and in the fully developed region. In the turbulent regime, the fully developed Nusselt number agreed well with previous observations, but the facility produced an unexplained linear trend in a portion of the developing region of the channel. While the channel aspect ratio affected the fully developed Nusselt number, no evidence was found that small channel spacing in itself produces Nusselt numbers that are at variance with accepted values.
Apparent Radiative Properties and Radiation Scattering by a Semitransparent Hemispherical Shell
Authors: Fan Tai-Hsi , Fedorov Andrei G.
Published: December 2002

Knowledge of the apparent radiative properties of a semitransparent hemispherical shell placed on an opaque surface is of fundamental interest and is also important to a number of applications in materials processing and manufacturing, ranging from metallurgical slag foaming to batch foams in glass melting to hollow bead fabrication. This paper extends our recent work [7]using the analytical and numerical ray tracing techniques to study radiative transfer in the system described. Specifically, the local volumetric heating rate and the scattering phase function of a thin hemispherical shell exposed to incident collimated radiation are calculated both analytically and numerically, and the results are discussed in detail. To further elucidate the results, the comparison is made of the total apparent transmittance of the hemispherical shell to a plane parallel layer of semitransparent material.