bluuebunny/crossref_metadata_2025 huggingface dataset:
Total Path Length for Random Recursive Trees
Authors: DOBROW ROBERT P. , FILL JAMES ALLEN
Published: July 2002

Total path length, or search cost, for a rooted tree is defined as the sum of all
root-to-node distances. Let Tn be the total path
length for a random recursive tree of order n. Mahmoud [10] showed that
Wn := (Tn −
E[Tn])/n converges almost surely
and in L2 to a nondegenerate limiting random variable W.
Here we give recurrence relations for the moments of Wn and of
W and show that Wn converges to W in
Lp for each 0 < p < ∞. We confirm the
conjecture that the distribution of W is not normal. We also show that the
distribution of W is characterized among all distributions having zero mean and finite
variance by the distributional identity

formula here

where [Escr ](x) := − x ln x −
(1 minus; x) ln(1 − x) is the binary entropy function, U
is a uniform (0, 1) random variable, W* and W have the same
distribution, and U, W and W* are mutually independent.
Finally, we derive an approximation for the distribution of W using a Pearson
curve density estimator.
Recent advances in the management of lung disease of prematurity
Authors: Darling Dawn L , Finer Neil N
Published: July 2002

Despite many advances in the management of lung disorders of premature infants, respiratory distress syndrome (RDS) remains the major cause of morbidity and mortality in the preterm infant. Approximately 30% of infants born at less than 34 weeks gestation will develop RDS, secondary to deficiency in surfactant production by alveolar type II pneumocytes. Without surfactant, work of breathing is increased and gas exchange impaired by diffuse atelectasis, reduced pulmonary compliance and ventilation perfusion mismatch.
Expression patterns of histone deacetylases in bovine oocytes and early embryos, and the effect of their inhibition on embryo development
Authors: Segev Hanna , Memili Erdogan , First Neal L.
Published: July 2002

Gene expression at the onset of bovine embryogenesis is developmentally

regulated and histone deacetylases (HDACs) have been shown to play a key

role in the control of gene expression during this period of development

in other species. We determined expression pattern(s) of powerful

repressors, namely histone deacetylase-1, -2 and -3, that may in part

regulate gene expression during bovine oogenesis and early embryogenesis

at the mRNA and protein levels. Detected fragments of the hdac genes were

sequenced and comparison of the sequences showed very high homologies

between DNA and amino acid sequences of bovine HDACs and those of human

and mouse. RPD3, a yeast global regulator of transcription, was also

detected in bovine oocytes and embryos. Results suggest that HDACs may

be operative in regulation of zygotic/embryonic gene expression in

cattle.
The influence of demethylating agents on preimplantation development of mice
Authors: Patkin E.L. , Kustova M.E. , Perticone P.
Published: July 2002

The effects of two demethylating drugs with a different mechanism of action (5-azacytidine (Aza) and L-ethionine (Eth)) on mouse preimplantation development were investigated. Preimplantation embryos were cultured for 24 h in the presence of the drug and for an additional 24 or 48 h (depending on the cleavage stage) in medium supplemented with bromodeoxyuridine to reveal sister chromatid exchanges (SCEs) and the number of cell cycles performed before harvesting. Striking differences between the two drugs were observed in their influence on proliferation of blastomeres, primary differentiation and sister chromatid differentiation (SCD), and in the pattern of DNA methylation and the frequency of SCEs per cell. At a final concentration of 1 μM Aza had no effects, whereas higher concentrations stopped development of all stages except the zygote. In contrast Eth treatments (5 mM) resulted in a severe reduction of the mean cell number per embryo in comparison with controls. Moreover both the absence of blastocyst formation and no effects on mitotic activity were detected. The most prominent effect of Eth was detected at the zygote and 4-cell stages. An unexpected decrease in SCE frequency in Eth-treated morulae and 4-cell embryos has been observed. Data are explained taking into account the different mechanisms of action of the agents.
Between finite state and Prolog: constraint-based
automata for efficient recognition of phrases
Authors: SCHULZ KLAUS U. , ŁAJEWSKI TOMEK MIKO
Published: July 2002

In computational linguistics, efficient recognition of
phrases is an important prerequisite for many ambitious goals,
such as automated extraction of terminology,
part of speech disambiguation, and automated translation. If one wants
to recognize
a certain well-defined set of phrases, the question of which type of computational
device to use for this task arises. For sets of phrases that are not
too complex, as well
as for many subtasks of the recognition process, finite state methods
are appropriate
and favourable because of their efficiency Gross and Perrin 1989; Silberztein
1993;
Tapanainen 1995. However, if very large sets of possibly complex phrases
are
considered where correct resolution of grammatical structure requires morphological
analysis (e.g. verb argument structure, extraposition of relative
clauses, etc.), then the
design and implementation of an appropriate finite state automaton might
turn out
to be infeasible in practice due to the immense number of morphological
variants
to be captured.
INTRUSIVE THOUGHTS, RESPONSIBILITY ATTITUDES, THOUGHT-ACTION FUSION, AND CHRONIC THOUGHT SUPPRESSION IN RELATION TO OBSESSIVE-COMPULSIVE SYMPTOMS
Authors: Smári Jakob , Hólmsteinsson Hólmsteinn Eidur
Published: July 2002

Relationships between obsessive-compulsive symptoms and several cognitive constructs that are theoretically
related to such symptoms were investigated among university students. A total of 211 subjects filled in a measure of
the frequency of intrusive thoughts based on Clark and de Silva (1985), Salkovskis' Responsibility Attitudes Scale
(RAS) (Salkovskis et al., 2000), the Thought-Action Fusion Scale (TAF) (Shafran, Thordarson, & Rachman, 1996),
Wegner and Zanakos' (1994) White Bear Suppression Inventory (WBSI), and the Maudsley Obsessive-Compulsive
Inventory (MOCI) (Hodgson & Rachman, 1977). The main hypothesis addressed was that in accordance with
Salkovskis' model (1996) responsibility and thought suppression serve as mediators between intrusive thoughts and
obsessive-compulsive symptoms as measured with the MOCI. The results were consistent with the model.
PROMOTING PERFORMANCE FLUENCY IN A PERSON WITH PROFOUND INTELLECTUAL DISABILITY AND BLINDNESS
Authors: Lancioni Giulio E. , O'Reilly Mark F. , Campodonico Francesca , Mantini Margherita
Published: July 2002

A combination of synchronous reinforcement and verbal prompts (automatically delivered through portable
technology) was used to promote performance fluency in a person with profound intellectual disability and blindness.
Performance fluency was measured on indoor walking and task engagement. Data indicated that the combination of
reinforcement (favourite songs) and prompts was quite effective; it increased the distance covered per minute and the
number of objects disassembled per minute. Implications of the findings are discussed.
Social and perceptual processes in the installation The Trade
Authors: KELLER DAMIÁN , CAPASSO ADRIANA
Published: July 2002

Through a discussion of the installation piece, The Trade / Oro por
Baratijas, we address the theoretical issues behind the development of
ecologically based compositional work. We discuss whether ecologically based
music can be studied using linguistic tools. The concepts of potentiality
and actuality are situated within the perspective of individual–environment
interactions. A process that describes the relationship between an
individual and his specific social context is proposed: the personal
environment. Consistency is discussed in relation to environmental sound
listening processes and ecological modelling work. The first part of the
paper concludes by suggesting that form-creation is dynamically determined
by a process of mutual adaptation between listener and environment. The
second part focuses on compositional methods and contextual elements as
they are used in The Trade. This work has been developed through a
multilevel approach where visual and sonic materials stem from social and
historical issues. The organisational processes of the sound piece are based
on the micro-temporal and spectral properties suggested by the visual
elements in the installation. The meso-temporal dynamic is organised
through ecologically constrained events. The macro-structural shape and the
sources used in the piece make reference to a specific historical context,
i.e. the conquest of the American continent by the European armies during
the first half of the sixteenth century.
Composition and diffusion: space in sound in space
Authors: TRUAX BARRY
Published: July 2002

Composition and diffusion can be understood as two complementary and
related processes: bringing sounds together, and spreading them
out again in an organised fashion. In the Western tradition, these two
processes are frequently carried out by different people at different times,
each drawing on specialised knowledge. The electroacoustic tradition, even
if much briefer, offers the possibility of the composer designing and
implementing both aspects of the music, and interrelating them in highly
specific ways. Computer control offers the greatest precision in dealing
with the complexities of these processes, even though, at present, separate
programs are usually required.
Psychologically Distressed Refugee Children in the United Kingdom
Authors: Hodes Matthew
Published: July 2002

There are at least 50000 refugee children and adolescents in the UK,
mostly living in London. These young people and their families will have
been exposed to high levels of violence, disruption of social life and losses,
all of which will increase their risk for psychiatric disorders. Up to 40% may
have psychiatric disorders, mostly depression, posttraumatic stress
disorder and other anxiety related difficulties. Multi-agency support to
refugee youngsters and families is important. Some refugee children and
adolescents will require help from specialist mental health services that will
need to be flexible in view of the refugees' cultural diversity, mobility and
the need for the full range of treatments. Special efforts are required to
reach this vulnerable group, and links with social services and schools in
particular should be considered.
Inhibition of Wnt activity induces heart formation from posterior mesoderm
Authors: Marvin Martha J. , Di Rocco Giuliana , Gardiner Aaron , Bush Sara M. , Lassar Andrew B.
Published: July 2002

In the chick, heart mesoderm is induced by signals from the anterior endoderm. Although BMP-2 is expressed in the anterior endoderm, BMP activity is necessary but not sufficient for heart formation. Previous work from our lab has suggested that one or more additional factors from anterior endoderm are required. Crescent is a Frizzled-related protein that inhibits Wnt-8c and is expressed in anterior endoderm during gastrulation. At the same stages, expression of Wnt-3a and Wnt-8c is restricted to the primitive streak and posterior lateral plate, and is absent from the anterior region where crescent is expressed. Posterior lateral plate mesoderm normally forms blood, but coculture of this tissue with anterior endoderm or infection with RCAS–crescent induces formation of beating heart muscle and represses formation of blood. Dkk-1, a Wnt inhibitor of a different protein family, similarly induces heart-specific gene expression in posterior lateral plate mesoderm. Furthermore, we have found that ectopic Wnt signals can repress heart formation from anterior mesoderm in vitro and in vivo and that forced expression of either Wnt-3a or Wnt-8c can promote development of primitive erythrocytes from the precardiac region. We conclude that inhibition of Wnt signaling promotes heart formation in the anterior lateral mesoderm, whereas active Wnt signaling in the posterior lateral mesoderm promotes blood development. We propose a model in which two orthogonal gradients, one of Wnt activity along the anterior-posterior axis and the other of BMP signals along the dorsal-ventral axis, intersect in the heart-forming region to induce cardiogenesis in a region of high BMP and low Wnt activity.
The RssB response regulator directly targets ςS for degradation by ClpXP
Authors: Zhou YanNing , Gottesman Susan , Hoskins Joel R. , Maurizi Michael R. , Wickner Sue
Published: July 2002

The ςS subunit of Escherichia coli RNA polymerase regulates the expression of stationary phase and stress response genes. Control over ςS activity is exercised in part by regulated degradation of ςS. In vivo, degradation requires the ClpXP protease together with RssB, a protein homologous to response regulator proteins. Using purified components, we reconstructed the degradation of ςS in vitro and demonstrate a direct role for RssB in delivering ςS to ClpXP. RssB greatly stimulates ςS degradation by ClpXP. Acetyl phosphate, which phosphorylates RssB, is required. RssB participates in multiple rounds of ςS degradation, demonstrating its catalytic role. RssB promotes ςSdegradation specifically; it does not affect degradation of other ClpXP substrates or other proteins not normally degraded by ClpXP. ςS and RssB form a stable complex in the presence of acetyl phosphate, and together they form a ternary complex with ClpX that is stabilized by ATP[γ-S]. Alone, neither ςS nor RssB binds ClpX with high affinity. When ClpP is present, a larger ςS–RssB–ClpXP complex forms. The complex degrades ςS and releases RssB from ClpXP in an ATP-dependent reaction. Our results illuminate an important mechanism for regulated protein turnover in which a unique targeting protein, whose own activity is regulated through specific signaling pathways, catalyzes the delivery of a specific substrate to a specific protease.
Drosophila Brain Tumor is a translational repressor
Authors: Sonoda Junichiro , Wharton Robin P.
Published: July 2002

The Drosophila brain tumor (brat) gene encodes a member of the conserved NHL family of proteins, which appear to regulate differentiation and growth in a variety of organisms. One of the founding family members, Caenorhabditis elegans LIN-41, is thought to control posttranscriptional gene expression. However, the mechanism by which LIN-41, or any other NHL protein, acts has not been clear. Using a yeast “four-hybrid” interaction assay, we show that Brain Tumor is recruited to hunchback (hb) mRNA through interactions with Nanos and Pumilio, which bind to the RNA to repress its translation. Interaction with the Nanos/Pumilio/RNA complex is mediated by the Brat NHL domain; single amino acid substitutions in this domain compromise quaternary complex assembly in vitro andhb regulation in vivo. Thus, recruitment of Brat is necessary for translational repression and the normal development of posterior embryonic pattern. In addition to regulating abdominal segmentation, previous genetic analysis has shown that Brat, Nanos, and Pumilio govern a variety of developmental processes. We examined the role of Brat in two of these processes—regulation of maternal Cyclin BmRNA in the embryo and regulation of imaginal disc development. The results of these experiments suggest that NHL domain proteins are recruited to various mRNAs by combinatorial protein–protein interactions.
A mutation in a mitochondrial transmembrane protein is responsible for the pleiotropic hematological and skeletal phenotype of flexed-tail (f/f) mice
Authors: Fleming Mark D. , Campagna Dean R. , Haslett Judith N. , Trenor Cameron C. , Andrews Nancy C.
Published: July 2002

We have studied the flexed-tail (f) mouse to gain insight into mammalian mitochondrial iron metabolism. Flexed-tailanimals have axial skeletal abnormalities and a transient embryonic and neonatal anemia characterized by pathologic intramitochondrial iron deposits in erythrocytes. Mitochondrial iron accumulation is the hallmark of sideroblastic anemias, which typically result from defects in heme biosynthesis or other pathways that lead to abnormal erythroid mitochondrial iron utilization. To clone thef gene, we used positional cloning techniques, and identified a frameshift mutation in a mitochondrial transmembrane protein. The mutated gene, Sfxn1, is the prototype of a novel family of evolutionarily conserved proteins present in eukaryotes.
Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis
Authors: Holm Magnus , Ma Li-Geng , Qu Li-Jia , Deng Xing-Wang
Published: July 2002

Arabidopsis COP1 acts to repress photomorphogenesis in the absence of light. It was shown that in the dark, COP1 directly interacts with the bZIP transcription factor HY5, a positive regulator of photomorphogenesis, and promotes its proteasome-mediated degradation. Here we identify a novel bZIP protein HYH, as a new target of COP1. We identify a physical and genetic interaction between HYH and COP1 and show that this interaction results in dark-specific degradation of HYH. Genetic analysis indicates that HYH is predominantly involved in blue-light regulation of development and gene expression, and that the function of HYH in part overlaps with that of HY5. The accumulation of HYH protein, not the mRNA, is dependent on the presence of HY5. Our data suggest that HYH and HY5 can, respectively, act as heterodimers and homodimers, thus mediating light-regulated expression of overlapping as well as distinct target genes. We propose that COP1 mediates light control of gene expression through targeted degradation of multiple photomorphogenesis-promoting transcription factors in the nucleus.
The Human Adult Skeletal Muscle Transcriptional Profile Reconstructed by a Novel Computational Approach
Authors: Bortoluzzi Stefania , d'Alessi Fabio , Romualdi Chiara , Danieli Gian Antonio
Published: July 2002

By applying a novel software tool, information on 4080 UniGene clusters was retrieved from three adult human skeletal muscle cDNA libraries, which were selected for being neither normalized nor subtracted. Reconstruction of a transcriptional profile of the corresponding tissue was attempted by a computational approach, classifying each transcript according to its level of expression. About 25% of the transcripts accounted for about 80% of the detected transcriptional activity, whereas most genes showed a low level of expression. This in silico transcriptional profile was then compared with data obtained by a SAGE study. A fairly good agreement between the two methods was observed. About 400 genes, highly expressed in skeletal muscle or putatively skeletal muscle-specific, may represent the minimal set of genes needed to determine the tissue specificity. These genes could be used as a convenient reference to monitor major changes in the transcriptional profile of adult human skeletal muscle in response to different physiological or pathological conditions, thus providing a framework for designing DNA microarrays and initiating biological studies.
Structure of Chromosomal Duplicons and their Role in Mediating Human Genomic Disorders
Authors: Ji Yonggang , Eichler Evan E. , Schwartz Stuart , Nicholls Robert D.
Published: July 2002

Chromosome-specific low-copy repeats, or duplicons, occur in multiple regions of the human genome. Homologous recombination between different duplicon copies leads to chromosomal rearrangements, such as deletions, duplications, inversions, and inverted duplications, depending on the orientation of the recombining duplicons. When such rearrangements cause dosage imbalance of a developmentally important gene(s), genetic diseases now termed genomic disorders result, at a frequency of 0.7–1/1000 births. Duplicons can have simple or very complex structures, with variation in copy number from 2 to >10 repeats, and each varying in size from a few kilobases in length to hundreds of kilobases. Analysis of the different duplicons involved in human genomic disorders identifies features that may predispose to recombination, including large size and high sequence identity between the recombining copies, putative recombination promoting features, and the presence of multiple genes/pseudogenes that may include genes expressed in germ cells. Most of the chromosome rearrangements involve duplicons near pericentromeric regions, which may relate to the propensity of such regions to accumulate duplicons. Detailed analyses of the structure, polymorphic variation, and mechanisms of recombination in genomic disorders, as well as the evolutionary origin of various duplicons will further our understanding of the structure, function, and fluidity of the human genome.
Construction of a BAC Contig Map of Chromosome 16q by Two-Dimensional Overgo Hybridization
Authors: Han Cliff S. , Sutherland Robert D. , Jewett Phillip B. , Campbell Mary L. , Meincke Linda J. , Tesmer Judy G. , Mundt Mark O. , Fawcett John J. , Kim Ung-Jin , Deaven Larry L. , Doggett Norman A.
Published: July 2002

We have used sequence-based markers from an integrated YAC STS-content/somatic cell hybrid breakpoint physical map and radiation hybrid maps of human chromosome 16 to construct a new sequence-ready BAC map of the long arm of this chromosome. The integrated physical map was generated previously in our laboratory and contains 1150 STSs, providing a marker on average every 78 kb on the euchromatic arms of chromosome 16. The other two maps used for this effort were the radiation hybrid maps of chromosome 16 from Whitehead Institute and Stanford University. To create large sequenceable targets of this chromosome, we used a systematic approach to screen high-density BAC filters with probes generated from overlapping oligonucleotides (overgos). We first identified all available sequences in the three maps. These include sequences from genes, ESTs, STSs, and cosmid end sequences. We then used BLASTto identify 36-bp unique fragments of DNA for overgo probes. A total of 906 overgos were selected from the long arm of chromosome 16. Hybridizations occurred in three stages: (1) superpool hybridizations against the 12× coverage human BAC library (RPCI-11); (2) two-dimensional hybridizations against rearrayed positive BACs identified in the superpool hybridizations; and (3) pooled tertiary hybridizations for those overgos that had ambiguous positives remaining after the two-dimensional hybridization. For the superpool hybridizations, up to 236 overgos have been pooled in a single hybridization against the 12× BAC library. A total of 5187 positive BACs from chromosome 16q were identified as a result of five superpool hybridizations. These positive clones were rearrayed on membranes and hybridized with 161 two-dimensional subpools of overgos to determine which BAC clones were positive for individual overgos. An additional 46 tertiary hybridizations were required to resolve ambiguous overgo–BAC relationships. Thus, after a total of 212 hybridizations, we have constructed an initial probe-content BAC map of chromosome 16q consisting of 828 overgo markers and 3363 BACs providing >85% coverage of the long arm of this chromosome. The map has been confirmed by the fingerprinting data and BAC end PCR screening.
Expression-based Genetic/Physical Maps of Single-Nucleotide Polymorphisms Identified by the Cancer Genome Anatomy Project
Authors: Clifford Robert , Edmonson Michael , Hu Ying , Nguyen Cu , Scherpbier Titia , Buetow Kenneth H.
Published: July 2002

SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional cloning. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. In addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site (http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use.

[The sequence data described in this paper have been submitted to the db SNP data library under accession nos. SS8196–SS18418.]
Additional Complexity on Human Chromosome 15q: Identification of a Set of Newly Recognized Duplicons (LCR15) on 15q11–q13, 15q24, and 15q26
Authors: Pujana Miguel Angel , Nadal Marga , Gratacòs Mònica , Peral Belén , Csiszar Katalin , González-Sarmiento Rogelio , Sumoy Lauro , Estivill Xavier
Published: July 2002

Several cytogenetic alterations affect the distal part of the long arm of human chromosome 15, including recurrent rearrangements between 12p13 and 15q25, which cause congenital fibrosarcoma (CFS). We present here the construction of a BAC/PAC contig map that spans 2 Mb from the neurotrophin-3 receptor (NTRK3) gene region on 15q25.3 to the proximal end of the Bloom's syndrome region on 15q26.1, and the identification of a set of new chromosome 15 duplicons. The contig reveals the existence of several regions of sequence similarity with other chromosomes (6q, 7p, and 12p) and with other 15q cytogenetic bands (15q11–q13 and 15q24). One region of similarity maps on 15q11–q13, close to the Prader-Willi/Angelman syndromes (PWS/AS) imprinting center. The 12p similar sequence maps on 12p13, at a distance to the ets variant 6 (ETV6) gene that is equivalent on 15q26.1 to the distance to the NTRK3 gene. These two genes are the targets of the CFS recurrent translocations, suggesting that misalignments between these two chromosomes regions could facilitate recombination. The most striking similarity identified is based on a low copy repeat sequence, mainly present on human chromosome 15 (LCR15), which could be considered a newly recognized duplicon. At least 10 copies of this duplicon are present on chromosome 15, mainly on 15q24 and 15q26. One copy is located close to a HERC2sequence on the distal end of the PWS/AS region, three around the lysyl oxidase-like (LOXL1) gene on 15q24, and three on 15q26, one of which close to the IQ motif containing GTPase-activating protein 1 (IQGAP1) gene on 15q26.1. These LCR15 span between 13 and 22 kb and contain high identities with the golgin-like protein (GLP) and the SH3 domain-containing protein (SH3P18) gene sequences and have the characteristics of duplicons. Because duplicons flank chromosome regions that are rearranged in human genomic disorders, the LCR15 described here could represent new elements of rearrangements affecting different regions of human chromosome 15q.

[The sequence data described in this paper have been submitted to EMBL GenBank with the accession nos.AJ272070, AJ276448, AJ276449, AJ286892-AJ286929, AJ400620, AJ400621,AJ400817-AJ400820, AJ277869AJ277874.]
A Bacterial Artificial Chromosome Library for Sequencing the Complete Human Genome
Authors: Osoegawa Kazutoyo , Mammoser Aaron G. , Wu Chenyan , Frengen Eirik , Zeng Changjiang , Catanese Joseph J. , de Jong Pieter J.
Published: July 2002

A 30-fold redundant human bacterial artificial chromosome (BAC) library with a large average insert size (178 kb) has been constructed to provide the intermediate substrate for the international genome sequencing effort. The DNA was obtained from a single anonymous volunteer, whose identity was protected through a double-blind donor selection protocol. DNA fragments were generated by partial digestion with EcoRI (library segments 1–4: 24-fold) and MboI (segment 5: sixfold) and cloned into the pBACe3.6 and pTARBAC1 vectors, respectively. The quality of the library was assessed by extensive analysis of 169 clones for rearrangements and artifacts. Eighteen BACs (11%) revealed minor insert rearrangements, and none was chimeric. This BAC library, designated as “RPCI-11,” has been used widely as the central resource for insert-end sequencing, clone fingerprinting, high-throughput sequence analysis and as a source of mapped clones for diagnostic and functional studies.

The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AQ936150–AQ936491.]
The 1.4-Mb CMT1A Duplication/HNPP Deletion Genomic Region Reveals Unique Genome Architectural Features and Provides Insights into the Recent Evolution of New Genes
Authors: Inoue Ken , Dewar Ken , Katsanis Nicholas , Reiter Lawrence T. , Lander Eric S. , Devon Keri L. , Wyman Dudley W. , Lupski James R. , Birren Bruce
Published: July 2002

Duplication and deletion of the 1.4-Mb region in 17p12 that is delimited by two 24-kb low copy number repeats (CMT1A–REPs) represent frequent genomic rearrangements resulting in two common inherited peripheral neuropathies, Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsy (HNPP). CMT1A and HNPP exemplify a paradigm for genomic disorders wherein unique genome architectural features result in susceptibility to DNA rearrangements that cause disease. A gene within the 1.4-Mb region,PMP22, is responsible for these disorders through a gene-dosage effect in the heterozygous duplication or deletion. However, the genomic structure of the 1.4-Mb region, including other genes contained within the rearranged genomic segment, remains essentially uncharacterized. To delineate genomic structural features, investigate higher-order genomic architecture, and identify genes in this region, we constructed PAC and BAC contigs and determined the complete nucleotide sequence. This CMT1A/HNPP genomic segment contains 1,421,129 bp of DNA. A low copy number repeat (LCR) was identified, with one copy inside and two copies outside of the 1.4-Mb region. Comparison between physical and genetic maps revealed a striking difference in recombination rates between the sexes with a lower recombination frequency in males (0.67 cM/Mb) versus females (5.5 cM/Mb). Hypothetically, this low recombination frequency in males may enable a chromosomal misalignment at proximal and distal CMT1A–REPs and promote unequal crossing over, which occurs 10 times more frequently in male meiosis. In addition to three previously described genes, five new genes (TEKT3, HS3ST3B1, NPD008/CGI-148, CDRT1, andCDRT15) and 13 predicted genes were identified. Most of these predicted genes are expressed only in embryonic stages. Analyses of the genomic region adjacent to proximal CMT1A–REP indicated an evolutionary mechanism for the formation of proximal CMT1A–REP and the creation of novel genes by DNA rearrangement during primate speciation.
A Predictive Model for Regulatory Sequences Directing Liver-Specific Transcription
Authors: Krivan William , Wasserman Wyeth W.
Published: July 2002

The identification and interpretation of the regulatory signals within the human genome remain among the greatest goals and most difficult challenges in genome analysis. The ability to predict the temporal and spatial control of transcription is likely to require a combination of methods to address the contribution of sequence-specific signals, protein–protein interactions and chromatin structure. We present here a new procedure to identify clusters of transcription factor binding sites characteristic of sequence modules experimentally verified to direct transcription selectively to liver cells. This algorithm is sufficiently specific to identify known regulatory sequences in genes selectively expressed in liver, promising acceleration of experimental promoter analysis. In combination with phylogenetic footprinting, this improvement in the specificity of predictions is sufficient to motivate a scan of the human genome. Potential regulatory modules were identified in orthologous human and rodent genomic sequences containing both known and uncharacterized genes.

[Supplementary data and the submission of sequences for analysis are available athttp://www.cgb.ki.se/krivan/liver/liver.html.]
Divergence of Function in Sequence-Related Groups of Escherichia coli Proteins
Authors: Nahum Laila Alves , Riley Monica
Published: July 2002

The most prominent mechanism of molecular evolution is believed to have been duplication and divergence of genes. Proteins that belong to sequence-related groups in any one organism are candidates to have emerged from such a process and to share a common ancestor. Groups of proteins in Escherichia coli having sequence similarity are mostly composed of proteins with closely related function, but some groups comprise proteins with unrelated functions. In order to understand how function can change while sequences remain similar, we have examined some of these groups in detail. The enzymes analyzed in this work include representatives of amidotransferases, phosphotransferases, decarboxylases, and others. Most sequence-related groups contain enzymes that are in the same classes of Enzyme Commission (EC) numbers. We have concentrated on groups that are heterogeneous in that respect, and also on groups containing more than one enzyme of any pathway. We find that although the EC number may differ, the reaction chemistry of these sequence-related proteins is the same or very similar. Some of these families illustrate how diversification has taken place in evolution, using common features of either reaction chemistry or ligand specificity, or both, to create catalysts for different kinds of biochemical reactions. This information has relevance to the area of functional genomics in which the activities of gene products of unknown reading frames are attributed by analogy to the functions of sequence-related proteins of known function.
Identification of Alternate Polyadenylation Sites and Analysis of their Tissue Distribution Using EST Data
Authors: Beaudoing Emmanuel , Gautheret Daniel
Published: July 2002

Alternate polyadenylation affects a large fraction of higher eucaryote mRNAs, producing mature transcripts with 3′ ends of variable length. This variation is poorly represented in the current transcript catalogs derived from whole genome sequences, mostly because such posttranscriptional events are not detectable directly at the DNA level. Alternate polydenylation of an mRNA is better understood by comparision to EST databases. Comparing ESTs to mRNAs, however, is a difficult task subjected to the pitfalls of internal priming, presence of intron sequences, repeated elements, chimerical ESTs or matches with EST from paralogous genes. We present here a computer program that addresses these problems and displays ESTs matches to a query mRNA sequence to predict alternate polyadenylation and to suggest library-specific forms. The output highlights effective polyadenylation signals, possible sources of artifacts such as A-rich stretches in the mRNA sequences, and allows for a direct visualization of EST libraries using color codes. Statistical biases in the distribution of alternative mRNA forms among EST libraries were systematically sought. About 1450 human and 200 mouse mRNAs displayed such biases, suggesting in each case a tissue- or disease-specific regulation of polyadenylation.
Computation-Based Discovery of Related Transcriptional Regulatory Modules and Motifs Using an Experimentally Validated Combinatorial Model
Authors: Halfon Marc S. , Grad Yonatan , Church George M. , Michelson Alan M.
Published: July 2002

Gene expression is regulated by transcription factors that interact with cis-regulatory elements. Predicting these elements from sequence data has proven difficult. We describe here a successful computational search for elements that direct expression in a particular temporal-spatial pattern in the Drosophila embryo, based on a single well characterized enhancer model. The fly genome was searched to identify sequence elements containing the same combination of transcription factors as those found in the model. Experimental evaluation of the search results demonstrates that our method can correctly predict regulatory elements and highlights the importance of functional testing as a means of identifying false-positive results. We also show that the search results enable the identification of additional relevant sequence motifs whose functions can be empirically validated. This approach, combined with gene expression and phylogenetic sequence data, allows for genome-wide identification of related regulatory elements, an important step toward understanding the genetic regulatory networks involved in development.

[Sequence data reported in this paper have been deposited in GenBank with accession nos. AF513981 (EveMHE) and AF513982 (Hbr DME). Supplementary material is available online at http://www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: R. Blackman]
Transcriptional Regulation of the Stem Cell Leukemia Gene (SCL) — Comparative Analysis of Five Vertebrate SCL Loci
Authors: Göttgens Berthold , Barton Linda M. , Chapman Michael A. , Sinclair Angus M. , Knudsen Bjarne , Grafham Darren , Gilbert James G.R. , Rogers Jane , Bentley David R. , Green Anthony R.
Published: July 2002

The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hematopoiesis and vasculogenesis and a pattern of expression that is highly conserved between mammals and zebrafish. Here we report the isolation and characterization of the zebrafish SCL locus together with the identification of three neighboring genes, IER5,MAP17, and MUPP1. This region spans 68 kb and comprises the longest zebrafish genomic sequence currently available for comparison with mammalian, chicken, and pufferfish sequences. Our data show conserved synteny between zebrafish and mammalian SCL and MAP17 loci, thus suggesting the likely genomic domain necessary for the conserved pattern ofSCL expression. Long-range comparative sequence analysis/phylogenetic footprinting was used to identify noncoding conserved sequences representing candidate transcriptional regulatory elements. The SCL promoter/enhancer, exon 1, and the poly(A) region were highly conserved, but no homology to other known mouseSCL enhancers was detected in the zebrafish sequence. A combined homology/structure analysis of the poly(A) region predicted consistent structural features, suggesting a conserved functional role in mRNA regulation. Analysis of the SCL promoter/enhancer revealed five motifs, which were conserved from zebrafish to mammals, and each of which is essential for the appropriate pattern or level ofSCL transcription.

[The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: N. Tanese.]
Caenorhabditis elegans Has Scores of hedgehogRelated Genes: Sequence and Expression Analysis
Authors: Aspöck Gudrun , Kagoshima Hiroshi , Niklaus Gisela , Bürglin Thomas R.
Published: July 2002

Previously, we have described novel families of genes, warthog(wrt) and groundhog (grd), inCaenorhabditis elegans. They are related to Hedgehog (Hh) through the carboxy-terminal autoprocessing domain (called Hog or Hint). A comprehensive survey revealed 10 genes with Hog/Hint modules in C. elegans. Five of these are associated with a Wart domain in wrt genes, and three with multiple copies of the Ground domain in grd genes. Both the Wart domain and the Ground domain occur also in genes encoding no Hog domain. Further, we define a new group of genes related to the grd genes, calledground-like (grl). Overall, C. elegans has more than 50 genes belonging to these gene families. Phylogenetic and sequence analysis shows that the wrt, grd, and grlgenes are derived from each other. Further examination reveals a sequence motif with similarity to the core of the amino-terminal-signaling domain of Hh proteins. Our data suggest that the wrt, grd, grl, and hh genes are derived from a single ancestral gene. wrt, grd, and grl genes are also present in other nematodes, but so far not in any other phyla. Conversely, hh is not found presently in C. elegansnor other nematodes. Thus, the nematode genes could be the homologs of Hh molecules in other phyla. The membrane molecule Patched has been shown previously to be a receptor of Hh. Many Patched-related proteins are present in C. elegans, which may be targets of thehh-related genes. No Hedgehog-interacting protein (Hip) was found. We analyzed the expression patterns of eight wrt and eight grd genes. The results show that some closely related genes are expressed in the same tissues, but, overall, the expression patterns are diverse, comprising hypodermis, seam cells, the excretory cell, sheath and socket cells, and different types of neurons.

[Hog domain-containing genes are available as an online supplement table at www.genome.org. The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AF139522, AF139520, AF139521]
Generation and Analysis of 25 Mb of Genomic DNA from the Pufferfish Fugu rubripes by Sequence Scanning
Authors: Elgar Greg , Clark Melody S. , Meek Stephen , Smith Sarah , Warner Sarah , Edwards Yvonne J.K. , Bouchireb Nassima , Cottage Amanda , Yeo Giles S.H. , Umrania Yagnesh , Williams Gary , Brenner Sydney
Published: July 2002

We have generated and analyzed >50,000 shotgun clones from 1059Fugu cosmid clones. All sequences have been minimally edited and searched against protein and DNA databases. These data are all displayed on a searchable, publicly available web site athttp://fugu.hgmp.mrc.ac.uk/. With an average of 50 reads per cosmid, this is virtually nonredundant sequence skimming, covering 30%–50% of each clone. This essentially random data set covers nearly 25 Mb (>6%) of the Fugu genome and forms the basis of a series of whole genome analyses which address questions regarding gene density and distribution in the Fugu genome and the similarity between Fugu and mammalian genes. The Fugu genome, with eight times less DNA but a similar gene repertoire, is ideally suited to this type of study because most cosmids contain more than one identifiable gene. General features of the genome are also discussed. We have made some estimation of the syntenic relationship between mammals and Fugu and looked at the efficacy of ORF prediction from short, unedited Fugu genomic sequences. Comparative DNA sequence analyses are an essential tool in the functional interpretation of complex vertebrate genomes. This project highlights the utility of using the Fugu genome in this kind of study.
A Prokaryotic Gene Cluster Involved in Synthesis of Lysine through the Amino Adipate Pathway: A Key to the Evolution of Amino Acid Biosynthesis
Authors: Nishida Hiromi , Nishiyama Makoto , Kobashi Nobuyuki , Kosuge Takehide , Hoshino Takayuki , Yamane Hisakazu
Published: July 2002

In previous studies we determined the nucleotide sequence of the gene cluster containinglys20, hacA(lys4A),hacB(lys4B),orfE, orfF,rimK, argC, andargBofThermus thermophilus, an extremely thermophilic bacterium. In this study, we characterized the role of each gene in the cluster by gene disruption and examined auxotrophy in the disruptants. All disruptants except for theorfEdisruption showed a lysine auxotrophic phenotype. This was surprising because this cluster consists of genes coding for unrelated proteins based on their names, which had been tentatively designated by homology analysis. Although the newly found pathway contains α-aminoadipic acid as a lysine biosynthetic intermediate, this pathway is not the same as the eukaryotic one. When each of the gene products was phylogenetically analyzed, we found that genes evolutionarily-related to the lysine biosynthetic genes inT. thermophiluswere all present in a hyperthermophilic and anaerobic archaeon,Pyrococcus horikoshii, and formed a gene cluster in a manner similar to that inT. thermophilus. Furthermore, this gene cluster was analogous in part to the present leucine and arginine biosyntheses pathways. This lysine biosynthesis cluster is assumed to be one of the origins of lysine biosynthesis and could therefore become a key to the evolution of amino acid biosynthesis.
Perfect Conserved Linkage Across the Entire Mouse Chromosome 10 Region Homologous to Human Chromosome 21
Authors: Wiltshire Tim , Pletcher Mathew , Cole Susan E. , Villanueva Melissa , Birren Bruce , Lehoczky Jessica , Dewar Ken , Reeves Roger H.
Published: July 2002

The distal end of human Chromosome (HSA) 21 from PDXK to the telomere shows perfect conserved linkage with mouse Chromosome (MMU) 10. This region is bounded on the proximal side by a segment of homology to HSA22q11.2, and on the distal side by a region of homology with HSA19p13.1. A high-resolution PAC-based physical map is described that spans 2.8 Mb, including the entire 2.1 Mb from Pdxk toPrmt2 corresponding to HSA21. Thirty-four expressed sequences are mapped, three of which were not mapped previously in any species and nine more that are mapped in mouse for the first time. These genes confirm and extend the conserved linkage between MMU10 and HSA21. The ordered PACs and dense STS map provide a clone resource for biological experiments, for rapid and accurate mapping, and for genomic sequencing. The new genes identified here may be involved in Down syndrome (DS) or in several genetic diseases that map to this conserved region of HSA21.
The Genexpress IMAGE Knowledge Base of the Human Muscle Transcriptome: A Resource of Structural, Functional, and Positional Candidate Genes for Muscle Physiology and Pathologies
Authors: Piétu Geneviève , Eveno Eric , Soury-Segurens Béatrice , Fayein Nicole-Adeline , Mariage-Samson Régine , Matingou Christiane , Leroy Elisabeth , Dechesne Claude , Krieger Sabine , Ansorge Wilhelm , Reguigne-Arnould Isabelle , Cox David , Dehejia Anindya , Polymeropoulos Mihael H. , Devignes Marie-Dominique , Auffray Charles
Published: July 2002

Sequence, gene mapping, and expression data corresponding to 910 genes transcribed in human skeletal muscle have been integrated to form the muscle module of the Genexpress IMAGE Knowledge Base. Based on cDNA array hybridization, a set of 14 transcripts preferentially or specifically expressed in muscle have been selected and characterized in more detail: Their pattern of expression was confirmed by Northern blot analysis; their structure was further characterized by full-insert cDNA sequencing and cDNA extension; the map location of the corresponding genes was refined by radiation hybrid mapping. Five of the 14 selected genes appear as interesting positional and functional candidate genes to study in relation with muscle physiology and/or specific orphan muscular pathologies. One example is discussed in more detail. The expression profiling data and the associated Genexpress Index2 entries for the 910 genes and the detailed characterization of the 14 selected transcripts are available from a dedicated Web server athttp://idefix.upr420.vjf.cnrs.fr/IMAGE/Page_unique/welcome_muscles.html. The database has been organized to provide the users with a working space where they can find curated, annotated, integrated data for their genes of interest. Different navigation routes to exploit the resource are discussed.

[Tables A and B are available as supplementary information at www.genome.org and also athttp://idefix.upr420.vjf.cnrs.fr/IMAGE/Page_unique/welcome_muscles.html.]