bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstraction in perceptual symbol systems
Authors: Barsalou Lawrence W.
Published: September 2003

After reviewing six senses of abstraction, this article focuses on abstractions that take the form of summary representations. Three central properties of these abstractions are established: (i) type–token interpretation; (ii) structured representation; and (iii) dynamic realization. Traditional theories of representation handle interpretation and structure well but are not sufficiently dynamical. Conversely, connectionist theories are exquisitely dynamic but have problems with structure. Perceptual symbol systems offer an approach that implements all three properties naturally. Within this framework, a loose collection of property and relation simulators develops to represent abstractions. Type–token interpretation results from binding a property simulator to a region of a perceived or simulated category member. Structured representation results from binding a configuration of property and relation simulators to multiple regions in an integrated manner. Dynamic realization results from applying different subsets of property and relation simulators to category members on different occasions. From this standpoint, there are no permanent or complete abstractions of a category in memory. Instead, abstraction is the skill to construct temporary online interpretations of a category's members. Although an infinite number of abstractions are possible, attractors develop for habitual approaches to interpretation. This approach provides new ways of thinking about abstraction phenomena in categorization, inference, background knowledge and learning.
Introduction
Authors: Zeki Semir
Published: September 2003

The papers in this issue of Philosophical Transactions have an interesting history. They were prepared within a research programme entitled Cognitique, instituted by the French Ministry of Education and Research within the broader context of a research effort that sought to combine, as far as possible, a study of the humanities and cognitive sciences, including studies that explore brain function through modern imaging techniques. The programme was launched and given a high priority by the then French Minister for Education and Research, Claude Allègre, in a far-sighted move that presages future directions in research into the human brain.
The basis and significance of pre–patterning in mammals
Authors: Gardner Richard L. , Davies Timothy J.
Published: September 2003

The second polar body (Pb) provides an enduring marker of the animal pole of the zygote, thereby revealing that the axis of bilateral symmetry of the early blastocyst is aligned with the zygote's animal–vegetal axis. That this relationship is biologically significant appeared likely when subsequent studies showed that the equator of the blastocyst tended to correspond with the plane of first cleavage. However, this cleavage plane varies both with respect to the position of the second Pb and to the distribution of components of the fertilizing sperm that continue to mark the point where it entered the egg. It also maps too variably on the blastocyst to play a causal role in early patterning. The zygote has been found transiently to exhibit bilateral symmetry before regaining an essentially spherical shape prior to first cleavage. Marking experiments indicate that the plane of bilateral symmetry of the blastocyst is aligned with, and the plane of first cleavage is typically orthogonal to, the zygote's bilateral plane. The bilateral symmetry of the zygote bears no consistent relationship either to the point of sperm entry or to the distribution of the pronuclei, and may therefore be a manifestation of intrinsic organization of the egg. Finally, the two–cell blastomere inheriting the sperm entry point has not been found to differ consistently in fate from the one that does not.
Imprinting errors and developmental asymmetry
Authors: Bestor Timothy H.
Published: September 2003

There are, in the broadest sense, two mechanisms by which gene expression can be extinguished in vertebrates. The first of these is based on mass action effects of positive and negative regulatory factors and is termed activation and repression; the second is independent of positive regulatory factors but is based on the history of the affected gene and is termed silencing. It can be said, again in the broadest sense, that imprinted genes, genes subject to X inactivation, and transposon promoters are subject to silencing, while the promoters of tissue–specific genes in non–expressing tissues are controlled by activation and repression. The escape of imprinted genes from silencing through unknown mechanisms can cause developmental abnormalities and can predispose to the formation of embryonal tumours. One developmental disorder caused by loss of imprinting of genes on chromosome 11p15.5 is Beckwith–Wiedemann syndrome (BWS). This syndrome has long been known to be inexplicably common in monozygotic twins; the twins are nearly always discordant for BWS, and nearly all twins are female. A loss of imprinting model based on stochastic errors in the nucleocytoplasmic trafficking of the DNA methyltransferase DNMT1, or a paternally expressed function that opposes maintenance methylation of maternally repressed growth–enhancing genes, is proposed to explain the perplexing genetics of BWS in monozygotic twins.
The origin of dorsoventral polarity inDrosophila
Authors: Roth Siegfried
Published: September 2003

InDrosophiladorsoventral (DV) polarity arises during oogenesis when the oocyte nucleus moves from a central posterior to an asymmetrical anterior position. Nuclear movement is a symmetry–breaking step and establishes orthogonality between the anteroposterior and the DV axes. The asymmetrically anchored nucleus defines a cortical region within the oocyte which accumulates high levels of gurken messenger RNA (mRNA) and protein. Gurken is an ovarian–specific member of the transforming growth factor–α (TGF–α) family of secreted ligands. SecretedGurkenforms a concentration gradient that results in a dorsal–to–ventral gradient of EGF receptor activation in the follicle cells surrounding the oocyte. This leads to concentration–dependent activation or repression of target genes of the EGF pathway in the follicular epithelium. One outcome of this process is the restriction ofpipeexpression to a ventral domain that comprises 40% of the egg circumference. Pipe presumably modifies extracellular matrix components that are secreted by the follicle cells and are present at the ventral side of embryo after egg deposition. Here, they activate a proteolytic cascade that generates a gradient of the diffusible ligand, Spätzle. Spätzle activates the Toll receptor at the surface of the embryo that stimulates the nuclear uptake of the transcription factor Dorsal. This leads to a nuclear concentration gradient of Dorsal that specifies the cell types along the DV axis of the embryo.
Epigenetic asymmetry in the mammalian zygote and early embryo: relationship to lineage commitment?
Authors: Reik Wolf , Santos Fatima , Mitsuya Kohzoh , Morgan Hugh , Dean Wendy
Published: September 2003

Epigenetic asymmetry between parental genomes and embryonic lineages exists at the earliest stages of mammalian development. The maternal genome in the zygote is highly methylated in both its DNA and its histones and most imprinted genes have maternal germline methylation imprints. The paternal genome is rapidly remodelled with protamine removal, addition of acetylated histones, and rapid demethylation of DNA before replication. A minority of imprinted genes have paternal germline methylation imprints. Methylation and chromatin reprogramming continues during cleavage divisions, but at the blastocyst stage lineage commitment to inner cell mass (ICM) or trophectoderm (TE) fate is accompanied by a dramatic increase in DNA and histone methylation, predominantly in the ICM. This may set up major epigenetic differences between embryonic and extraembryonic tissues, including in X–chromosome inactivation and perhaps imprinting. Maintaining epigenetic asymmetry appears important for development as asymmetry is lost in cloned embryos, most of which have developmental defects, and in particular an imbalance between extraembryonic and embryonic tissue development.
Genesis of embryonic stem cells
Authors: Buehr Mia , Smith Austin
Published: September 2003

Embryonic stem (ES) cells are permanent pluripotent stem cell lines established from pre–implantation mouse embryos. There is currently great interest in the potential therapeutic applications of analogous cells derived from human embryos. The isolation of ES cells is commonly presented as a straightforward transfer of cells in the early embryo into culture. In reality, however, continuous expansion of pluripotent cells does not occur in vivo, and
in vitro
is the exception rather than the norm. Both genetic and epigenetic factors influence the ability to derive ES cells. We have tracked the expression of a key marker and determinant of pluripotency, the transcription factor Oct–4, in primary cultures of mouse epiblasts and used this to assay the effect of experimental manipulations on the maintenance of a pluripotent cell compartment. We find that expression of Oct–4 is often lost prior to overt cytodifferentiation of the epiblast. The rate and extent of Oct–4 extinction varies with genetic background. We report that treatment with the MAP kinase/ERK kinase inhibitor PD98059, which suppresses activation of the mitogen–activated protein kinases Erk1 and Erk2, results in increased persistence of Oct–4–expressing cells. Oct–4 expression is also relatively sustained in cultures of diapause embryos and of isolated inner cell masses. Combination of all three conditions allowed the derivation of germline–competent ES cells from the normally refractory CBA mouse strain. These findings suggest that the genesis of an ES cell is a relatively complex process requiring epigenetic modulation of key gene expression over a brief time–window. Procedures that extend this time–window and/or directly regulate the critical genes should increase the efficiency of ES cell derivation.
Functional intergenic transcription: a case study of the X–inactivation centre
Authors: Lee Jeannie T.
Published: September 2003

Long known to be riddled with repetitive elements and regarded as ‘junk’, intergenic regions in the mammalian genome now appear to be more than incidental spacers between coding sequences. Here, I review the example ofXite, an intergenic region at the X–inactivation centre which was recently shown to regulate the X–chromosome choice decision.Xitecontains a series of DNaseI–hypersensitive sites and harbours two intergenic transcription start sites. These intergenic transcription elements act at the onset of X–chromosome inactivation (XCI) to bias the selection of the active X. It has been proposed thatXiteactsin cis on Tsixby promoting its persistence during XCI.Xitehas also been proposed to be a candidate for the X–controlling element, a naturally occurring modifier of XCI ratios in mice and possibly also in humans. It seems likely that intergenic transcription will turn out to be a widespread phenomenon in mammals and that, more importantly, it will emerge as a significant regulatory mechanism for the expression of coding sequences.
Lineage allocation and asymmetries in the early mouse embryo
Authors: Rossant Janet , Chazaud Claire , Yamanaka Yojiro
Published: September 2003

The mouse blastocyst, at the time of implantation, has three distinct cell lineages: epiblast (EPI), trophoblast and primitive endoderm (PE). Interactions between these three lineages and their directional growth and migration are critical for establishing the initial asymmetries that result in anterior–posterior patterning of the embryo proper. We have re–investigated the timing of specification of the three lineages in relation to the differential allocation of progeny of the first two blastomeres to the embryonic versus abembryonic axis of the blastocyst. We find that the majority of cells of the inner cell mass (ICM) are specified to be EPI or PE by the mid 3.5 day blastocyst and that this is associated with localized expression of GATA–6 in the ICM. We propose a model for molecular specification of the blastocyst lineages in which a combination of cell division order, signal transduction differences between inner and outer cells and segregation of key transcription factors can produce a blastocyst in which all three lineages are normally set up in an ordered, lineage–dependent manner, but which can also reconstruct a blastocyst when division order or cell interactions are disturbed.
Molecular control of the oocyte to embryo transition
Authors: Knowles Barbara B. , Evsikov Alexei V. , de Vries Wilhelmine N. , Peaston Anne E. , Solter Davor
Published: September 2003

The elucidation of the molecular control of the initiation of mammalian embryogenesis is possible now that the transcriptomes of the full–grown oocyte and two–cell stage embryo have been prepared and analysed. Functional annotation of the transcriptomes using gene ontology vocabularies, allows comparison of the oocyte and two–cell stage embryo between themselves, and with all known mouse genes in the Mouse Genome Database. Using this methodology one can outline the general distinguishing features of the oocyte and the two–cell stage embryo. This, when combined with oocyte–specific targeted deletion of genes, allows us to dissect the molecular networks at play as the differentiated oocyte and sperm transit into blastomeres with unlimited developmental potential.
Regulative germ cell specification in axolotl embryos: a primitive trait conserved in the mammalian lineage
Authors: Johnson Andrew D. , Crother Brian , White Mary E. , Patient Roger , Bachvarova Rosemary F. , Drum Matthew , Masi Thomas
Published: September 2003

How germ cells are specified in the embryos of animals has been a mystery for decades. Unlike most developmental processes, which are highly conserved, embryos specify germ cells in very different ways. Curiously, in mouse embryos germ cells are specified by extracellular signals; they are not autonomously specified by maternal germ cell determinants (germ plasm), as are the germ cells in most animal model systems. We have developed the axolotl (Ambystoma mexicanum), a salamander, as an experimental system, because classic experiments have shown that the germ cells in this species are induced by extracellular signals in the absence of germ plasm. Here, we provide evidence that the germ cells in axolotls arise from naive mesoderm in response to simple inducing agents. In addition, by analysing the sequences of axolotl germ–cell–specific genes, we provide evidence that mice and urodele amphibians share a common mechanism of germ cell development that is ancestral to tetrapods. Our results imply that germ plasm, as found in species such as frogs and teleosts, is the result of convergent evolution. We discuss the evolutionary implications of our findings.
Nuclear reprogramming in cell–free extracts
Authors: Collas Philippe
Published: September 2003

Methods for directly turning a somatic cell type into another type (a process referred to as transdifferentiation) would be beneficial for producing replacement cells for therapeutic applications. Adult stem cells have been shown to display a broader differentiation potential than anticipated and may contribute to tissues other than those in which they reside. In addition, novel transdifferentiation strategies are being developed. I report recent results on the functional reprogramming of a somatic cell using a nuclear and cytoplasmic extract derived from another somatic cell type. The reprogramming of 293T fibroblasts in an extract from T cells is evidenced by nuclear uptake and the assembly of transcription factors, induction of activity of a chromatin remodelling complex, changes in chromatin composition and activation of lymphoid cell–specific genes. The reprogrammed cells express T–cell–specific surface molecules and a complex regulatory function. Reprogramming cells in cell–free extracts may create possibilities for producing replacement cells for therapeutic applications. The system may also constitute a powerful tool to examine the mechanisms of nuclear reprogramming, at least as they occurin vitro.
Introduction
Authors: Gardner R. L. , Surani M. A. , Solter D.
Published: September 2003

The elaboration of a physiologically integrated organism from a fertilized egg depends on processes of cellular growth and diversification that require very precise coordination in both space and time. The extent to which the final outcome is presaged in the egg is an issue that has engaged those seeking to explain embryonic development since antiquity. According to the concept of preformation espoused by Charles Bonnet, the new organism was already present in its final form in the egg, so that development simply entailed enlargement without any accompanying increase in complexity (Oppenheimer 1967). This extreme view was shown to be untenable by Caspar Friedrich Wolff, whose relevant studies included careful documentation of the emergence of increasingly complex organization during the course of embryogenesis in the chick. As a result, the opposing concept of epigenesis, namely that order and form emerge de novo during the course of development, rapidly gained dominance (Oppenheimer 1967). However, by the latter half of the nineteenth century, preformation was revived in a subtler guise to explain the development of various marine invertebrates in which both patterns of cleavage and differentiation of the resulting blastomeres were essentially invariant. Here, cellular diversification was attributed to the localization within the cytoplasm of the egg of factors, or ‘determinants’, which dictated the fate of the cells that inherited them. The stereotypical pattern of cleavage exhibited by such organisms was referred to as ‘mosaic’, in contrast to the variable or ‘regulative’ pattern shown by many others. Mosaic soon came to be equated with a determinant–based or neo–preformationist, and regulative with an epigenetic, view of development. We now know that this distinction is not valid because cellular interactions play a vital part in the development even of organisms with invariant lineage like Caenorhabditis elegans, whereas ‘determinants’ such as those for the germline occur in species whose lineage is variable.
Transformation of myeloid progenitors by MLL oncoproteins is dependent on Hoxa7 and Hoxa9
Authors: Ayton Paul M. , Cleary Michael L.
Published: September 2003

Transcriptional deregulation through the production of dominant-acting chimeric transcription factors derived from chromosomal translocations is a common theme in the pathogenesis of acute leukemias; however, the essential target genes for acute leukemogenesis are unknown. We demonstrate here that primary myeloid progenitors immortalized by various MLL oncoproteins exhibit a characteristic Hoxa gene cluster expression profile, which reflects that preferentially expressed in the myeloid clonogenic progenitor fraction of normal bone marrow. Continued maintenance of this MLL-dependent Hoxa gene expression profile is associated with conditional MLL-associated myeloid immortalization. Moreover, Hoxa7 and Hoxa9 were specifically required for efficient in vitro myeloid immortalization by an MLL fusion protein but not other leukemogenic fusion proteins. Finally, in a bone marrow transduction/transplantation model, Hoxa9 is essential for MLL-dependent leukemogenesis in vivo, a primary requirement detected at the earliest stages of disease initiation. Thus, a genetic reliance on Hoxa7 and Hoxa9 in MLL-mediated transformation demonstrates a gain-of-function mechanism for MLL oncoproteins as upstream constitutive activators that promote myeloid transformation via a Hox-dependent mechanism.
Stable inheritance of telomere chromatin structure and function in the absence of telomeric repeats
Authors: Sadaie Mahito , Naito Taku , Ishikawa Fuyuki
Published: September 2003

It is generally believed that telomeric repeats are a necessary and sufficient cis-element for telomere function. Here we show that telomere structure and meiotic function are stably inherited in fission yeast circular chromosomes that have lost all telomeric repeats. We found that the telomeric repeat binding protein, Taz1, and the heterochromatin protein, Swi6, remain associated with subtelomeres in the absence of telomeric repeats. We also found that the fusion point of circular chromosomes that lack telomeric repeats associates with SPB (the yeast counterpart of the centrosome) in the premeiotic horsetail stage, similarly to wild-type telomeres. However, a taz1+ deletion/reintroduction experiment revealed that the maintenance of Taz1 binding and premeiotic function is achieved via different strategies. Taz1 is recruited to subtelomeres by an autonomous element present in subtelomeric DNA, thus in a genetic mechanism. In contrast, the premeiotic subtelomere-SPB association is maintained in an epigenetic manner. These results shed light on the previously unrecognized role played by the subtelomere and underscore the robust nature of the functional telomere complex that is maintained by both genetic and epigenetic mechanisms. Furthermore, we suggest that the establishment and the maintenance of the functional telomere complex are mechanistically distinguishable.
Ubiquitin-dependent degradation of the yeast Matα2 repressor enables a switch in developmental state
Authors: Laney Jeffrey D. , Hochstrasser Mark
Published: September 2003

Developmental transitions in eukaryotic cell lineages revolve around two general processes: the dismantling of the regulatory program specifying an initial differentiated state and its replacement by a new system of regulators. However, relatively little is known about the mechanisms by which a previous regulatory state is inactivated. Protein degradation is implicated in a few examples, but the molecular reasons that a formerly used regulator must be removed are not understood. Many yeast strains undergo a developmental transition in which cells of one mating type differentiate into a distinct cell type by a programmed genetic rearrangement at the MAT locus. We find that Matα2,a MAT-encoded transcriptional repressor that is key to creating several cell types, must be rapidly degraded for cells to switch their mating phenotype properly. Strikingly, ubiquitin-dependent proteolysis of α2 is required for two mechanistically distinct purposes: It allows the timely inactivation of one transcriptional repressor complex, and it prevents the de novo assembly of a different, inappropriate regulatory complex. Analogous epigenetic mechanisms for reprogramming transcription are likely to operate in many developmental pathways.
Virulence-related surface glycoproteins in the yeast pathogen Candida glabrata are encoded in subtelomeric clusters and subject to RAP1- and SIR-dependent transcriptional silencing
Authors: De Las Peñas Alejandro , Pan Shih-Jung , Castaño Irene , Alder Jonathan , Cregg Robert , Cormack Brendan P.
Published: September 2003

Candida glabrata is an important opportunistic pathogen causing both mucosal and bloodstream infections. C. glabrata is able to adhere avidly to mammalian cells, an interaction that depends on the Epa1p lectin. EPA1 is shown here to be a member of a larger family of highly related genes encoded in subtelomeric clusters. Subtelomeric clustering of large families of surface glycoprotein-encoding genes is a hallmark of several pathogens, including Plasmodium, Trypanosoma, and Pneumocystis. In these other pathogens, a single surface glycoprotein is expressed, whereas other genes in the family are transcriptionally silent. Similarly, whereas EPA1 is expressed in vitro, EPA2-5 are transcriptionally repressed. This repression is shown to be due to regional silencing of the subtelomeric loci. In Saccharomyces cerevisiae, subtelomeric silencing is initiated by Rap1p binding to the telomeric repeats and subsequent recruitment of the Sir complex by protein-protein interaction. We demonstrate here that silencing of the subtelomeric EPA loci also depends on functional Sir3p and Rap1p. This identification and analysis of the EPA gene family provides a compelling example in an ascomycete of chromatin-based silencing of natural subtelomeric genes and provides for the first time in a pathogen, molecular insight into the transcriptional silencing of large subtelomeric gene families.
Dkk1 and noggin cooperate in mammalian head induction
Authors: del Barco Barrantes Ivan , Davidson Gary , Gröne Hermann-Josef , Westphal Heiner , Niehrs Christof
Published: September 2003

Growth factor antagonists play important roles in mediating the inductive effects of the Spemann organizer in amphibian embryos and its equivalents in other vertebrates. Dual inhibition of Wnt and BMP signals has been proposed to confer head organizer activity. We tested the requirement of this coinhibition in Xenopus and mice. In Xenopus, simultaneous reduction of the BMP antagonists chordin and noggin, and the Wnt antagonist dickkopf1 (dkk1) leads to anterior truncations. In mice, compound mutants for dkk1 and noggin display severe head defects, with deletion of all head structures anterior to the mid-hindbrain boundary. These defects arise as a result of a failure in anterior specification at the gastrula stage. The results provide genetic evidence for the dual inhibition model and indicate that dkk1 and noggin functionally cooperate in the head organizer.
Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus
Authors: Zhang Ningxin , Harrex Annette L. , Holland Barbara R. , Fenton Lauren E. , Cannon Richard D. , Schmid Jan
Published: September 2003

The ALS (agglutinin-like sequence) gene family encodes proteins that play a role in adherence of the yeast Candida albicans to endothelial and epithelial cells. The proteins are proposed as virulence factors for this important fungal pathogen of humans. We analyzed 66 C. albicans strains, representing a worldwide collection of 266 infection-causing isolates, and discovered 60 alleles of the ALS7 open reading frame (ORF). Differences between alleles were largely caused by rearrangements of repeat elements in the so-called tandem repeat domain (21 different types occurred) and the VASES region (19 different types). C. albicans is diploid, and combinations of ALS7 alleles generated 49 different genotypes. ALS7 expression was detected in samples isolated directly from five oral candidosis patients. ORFs in the opposite direction contained within the ALS7 ORF were also transcribed in all strains tested. Isolates representing a more pathogenic general-purpose genotype (GPG) cluster of strains tended to have more tandem repeats than other strains. Two types of VASES regions were largely exclusive to GPG strains; the remaining types were largely exclusive to noncluster strains. Our results provide evidence that ALS7 is a hypermutable contingency locus and important for the success of C. albicans as an opportunistic pathogen of humans.
Whole-Genome Shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and Its Use for Whole-Genome Shotgun Sequence Assembly
Authors: Zhou Shiguo , Kvikstad Erika , Kile Andrew , Severin Jessica , Forrest Dan , Runnheim Rod , Churas Chris , Hickman Jason W. , Mackenzie Chris , Choudhary Madhusudan , Donohue Timothy , Kaplan Samuel , Schwartz David C.
Published: September 2003

Rhodobacter sphaeroides 2.4.1 is a facultative photoheterotrophic bacterium with tremendous metabolic diversity, which has significantly contributed to our understanding of the molecular genetics of photosynthesis, photoheterotrophy, nitrogen fixation, hydrogen metabolism, carbon dioxide fixation, taxis, and tetrapyrrole biosynthesis. To further understand this remarkable bacterium, and to accelerate an ongoing sequencing project, two whole-genome restriction maps (EcoRI and HindIII) of R. sphaeroides strain 2.4.1 were constructed using shotgun optical mapping. The approach directly mapped genomic DNA by the random mapping of single molecules. The two maps were used to facilitate sequence assembly by providing an optical scaffold for high-resolution alignment and verification of sequence contigs. Our results show that such maps facilitated the closure of sequence gaps by the early detection of nascent sequence contigs during the course of the whole-genome shotgun sequencing process.
Pleiotropy, Homeostasis, and Functional Networks Based on Assays of Cardiovascular Traits in Genetically Randomized Populations
Authors: Nadeau Joseph H. , Burrage Lindsay C. , Restivo Joe , Pao Yoh-Han , Churchill Gary , Hoit Brian D.
Published: September 2003

A major problem in studying biological traits is understanding how genes work together to provide organismal structures and functions. Conventional reductionist paradigms attribute functions to particular proteins, motifs, and amino acids. An equally important but harder problem involves the synthesis of data at fundamental levels of biological systems to understand functionality at higher levels. We used subtle, naturally occurring, multigenic variation of cardiovascular (CV) properties in a panel of genetically randomized strains that are derived from the A/J and C57BL/6J strains of mice to perturb CV functions in nonpathologic ways. In this proof-of-concept study, computational analysis correctly identified the known relations among CV properties and revealed functionality at higher levels of the CV system. The network was then used to account for pleiotropies and homeostatic responses in single gene mutant mice and in mice treated with a pharmacologic agent (anesthesia). The CV network accounted for functional dependencies in complementary ways to the insights obtained from genetic networks and biochemical pathways. These networks are therefore an important approach for defining and characterizing functional relations in complex biological systems in health and disease.
A Sensitive Method for Detecting Variation in Copy Numbers of Duplicated Genes
Authors: Pielberg Gerli , Day Andy E. , Plastow Graham S. , Andersson Leif
Published: September 2003

Gene duplications are common in the vertebrate genome, and duplicated loci often show a variation in copy number that may have important phenotypic effects. Here we describe a powerful method for quantification of duplicated copies based on pyrosequencing. A reliable quantification was obtained by amplification of the duplication break-point and a corresponding nonduplicated sequence in a competitive PCR assay. A comparison with an independent method for quantification based on the Invader technology revealed an excellent correlation between the two methods. The pyrosequencing-based method was evaluated by analyzing variation in copy number at the duplicatedKIT/Dominant whitelocus in pigs. We were able to distinguish haplotypes at this locus by combining the duplication breakpoint test with a diagnostic test for a functionally important splice mutation in the duplicated gene. An extensive allelic variation, including the presence of a new allele carrying a singleKITcopy expected to encode a truncated KIT receptor, was revealed when analyzing white pigs from commercial lines.
Retrotransposons and Their Recognition of pol II Promoters: A Comprehensive Survey of the Transposable Elements From the Complete Genome Sequence of Schizosaccharomyces pombe
Authors: Bowen Nathan J. , Jordan I. King , Epstein Jonathan A. , Wood Valerie , Levin Henry L.
Published: September 2003

The complete DNA sequence of the genome of Schizosaccharomyces pombe provides the opportunity to investigate the entire complement of transposable elements (TEs), their association with specific sequences, their chromosomal distribution, and their evolution. Using homology-based sequence identification, we found that the sequenced strain of S. pombe contained only one family of full-length transposons. This family, Tf2, consisted of 13 full-length copies of a long terminal repeat (LTR) retrotransposon. We found that LTR-LTR recombination of previously existing transposons had resulted in extensive populations of solo LTRs. These included 35 solo LTRs of Tf2, as well as 139 solo LTRs from other Tf families. Phylogenetic analysis of solo Tf LTRs reveals that Tf1 and Tf2 were the most recently active elements within the genome. The solo LTRs also served as footprints for previous insertion events by the Tf retrotransposons. Analysis of 186 genomic insertion events revealed a close association with RNA polymerase II promoters. These insertions clustered in the promoter-proximal regions of genes, upstream of protein coding regions by 100 to 400 nucleotides. The association of Tf insertions with pol II promoters was very similar to the preference previously observed for Tf1 integration. We found that the recently active Tf elements were absent from centromeres and pericentromeric regions of the genome containing tandem tRNA gene clusters. In addition, our analysis revealed that chromosome III has twice the density of insertion events compared to the other two chromosomes. Finally we describe a novel repetitive sequence, wtf, which was also preferentially located on chromosome III, and was often located near solo LTRs of Tf elements.
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Authors: Li Li , Stoeckert Christian J. , Roos David S.
Published: September 2003

The identification of orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics, and the identification of taxonomically restricted sequences. Methods successfully exploited for prokaryotic genome analysis have proved difficult to apply to eukaryotes, however, as larger genomes may contain multiple paralogous genes, and sequence information is often incomplete. OrthoMCL provides a scalable method for constructing orthologous groups across multiple eukaryotic taxa, using a Markov Cluster algorithm to group (putative) orthologs and paralogs. This method performs similarly to the INPARANOID algorithm when applied to two genomes, but can be extended to cluster orthologs from multiple species. OrthoMCL clusters are coherent with groups identified by EGO, but improved recognition of “recent” paralogs permits overlapping EGO groups representing the same gene to be merged. Comparison with previously assigned EC annotations suggests a high degree of reliability, implying utility for automated eukaryotic genome annotation. OrthoMCL has been applied to the proteome data set from seven publicly available genomes (human, fly, worm, yeast,Arabidopsis,the malaria parasitePlasmodium falciparum, andEscherichia coli). A Web interface allows queries based on individual genes or user-defined phylogenetic patterns (http://www.cbil.upenn.edu/gene-family). Analysis of clusters incorporatingP. falciparumgenes identifies numerous enzymes that were incompletely annotated in first-pass annotation of the parasite genome.
Asymmetric Sequence Divergence of Duplicate Genes
Authors: Conant Gavin C. , Wagner Andreas
Published: September 2003

Much like humans, gene duplicates may be created equal, but they do not stay that way for long. For four completely sequenced genomes we show that 20%–30% of duplicate gene pairs show asymmetric evolution in the amino acid sequence of their protein products. That is, one of the duplicates evolves much faster than the other. The greater this asymmetry, the greater the ratio Ka/Ks of amino acid substitutions (Ka) to silent substitutions (Ks) in a gene pair. This indicates that most asymmetric divergence may be caused by relaxed selective constraints on one of the duplicates. However, we also find some candidate duplicates where positive (directional) selection of beneficial mutations (Ka/Ks > 1) may play a role in asymmetric divergence. Our analysis rests on a codon-based model of molecular evolution that allows a test for asymmetric divergence in Ka. The method is also more sensitive in detecting positive selection (Ka/Ks > 1) than models relying only on pairwise gene comparisons.
Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes
Authors: Katz Luba , Burge Christopher B.
Published: September 2003

Redundancy of the genetic code dictates that a given protein can be encoded by a large collection of distinct mRNA species, potentially allowing mRNAs to simultaneously optimize desirable RNA structural features in addition to their protein-coding function. To determine whether natural mRNAs exhibit biases related to local RNA secondary structure, a new randomization procedure was developed, DicodonShuffle, which randomizes mRNA sequences while preserving the same encoded protein sequence, the same codon usage, and the same dinucleotide composition as the native message. Genes from 10 of 14 eubacterial species studied and one eukaryote, the yeast Saccharomyces cerevisiae, exhibited statistically significant biases in favor of local RNA structure as measured by folding free energy. Several significant associations suggest functional roles for mRNA structure, including stronger secondary structure bias in the coding regions of intron-containing yeast genes than in intronless genes, and significantly higher folding potential in polycistronic messages than in monocistronic messages in Escherichia coli. Potential secondary structure generally increased in genes from the 5′ to the 3′ end of E. coli operons, and secondary structure potential was conserved in homologous Salmonella typhi operons. These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control.
Conserved Noncoding Sequences in the Grasses4
Authors: Inada Dan Choffnes , Bashir Ali , Lee Chunghau , Thomas Brian C. , Ko Cynthia , Goff Stephen A. , Freeling Michael
Published: September 2003

As orthologous genes from related species diverge over time, some sequences are conserved in noncoding regions. In mammals, large phylogenetic footprints, or conserved noncoding sequences (CNSs), are known to be common features of genes. Here we present the first large-scale analysis of plant genes for CNSs. We used maize and rice, maximally diverged members of the grass family of monocots. Using a local sequence alignment set to deliver only significant alignments, we found one or more CNSs in the noncoding regions of the majority of genes studied. Grass genes have dramatically fewer and much smaller CNSs than mammalian genes. Twenty-seven percent of grass gene comparisons revealed no CNSs. Genes functioning in upstream regulatory roles, such as transcription factors, are greatly enriched for CNSs relative to genes encoding enzymes or structural proteins. Further, we show that a CNS cluster in an intron of the knotted1 homeobox gene serves as a site of negative regulation. We showthat CNSs in the adh1 gene do not correlate with known cis-acting sites. We discuss the potential meanings of CNSs and their value as analytical tools and evolutionary characters. We advance the idea that many CNSs function to lock-in gene regulatory decisions.
PCAP: A Whole-Genome Assembly Program
Authors: Huang Xiaoqiu , Wang Jianmin , Aluru Srinivas , Yang Shiaw-Pyng , Hillier LaDeana
Published: September 2003

We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple processors are used to perform most time-consuming computations in assembly. A more sensitive method is used to avoid missing overlaps caused by sequencing errors. Repetitive regions of reads are detected on the basis of many overlaps with other reads, instead of many shorter word matches with other reads. Contaminated end regions of reads are identified and removed. Generation of a consensus sequence for a contig is based on an alignment of reads in the contig, in which both base quality values and coverage information are used to determine every consensus base. The PCAP program was tested on a mouse whole-genome data set of 30 million reads and a human Chromosome 20 data set of 1.7 million reads. The program is freely available for academic use.
The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis
Authors: Boeke Jef D.
Published: September 2003

Retrotransposons have proliferated extensively in eukaryotic lineages; the genomes of many animals and plants comprise 50% or more retrotransposon sequences by weight. There are several persuasive arguments that the enzymatic lynchpin of retrotransposon replication, reverse transcriptase (RT), is an ancient enzyme. Moreover, the direct progenitors of retrotransposons are thought to be mobile self-splicing introns that actively propagate themselves via reverse transcription, the group II introns, also known as retrointrons. Retrointrons are represented in modern genomes in very modest numbers, and thus far, only in certain eubacterial and organellar genomes. Archaeal genomes are nearly devoid of RT in any form. In this study, I propose a model to explain this unusual distribution, and rationalize it with the proposed ancient origin of the RT gene. A cap and tail hypothesis is proposed. By this hypothesis, the specialized terminal structures of eukaryotic mRNA provide the ideal molecular environment for the lengthening, evolution, and subsequent massive expansion of highly mobile retrotransposons, leading directly to the retrotransposon-cluttered structure that typifies modern metazoan genomes and the eventual emergence of retroviruses.
Application of DNA Microarrays to Study the Evolutionary Genomics of Yersinia pestis and Yersinia pseudotuberculosis
Authors: Hinchliffe Stewart J. , Isherwood Karen E. , Stabler Richard A. , Prentice Michael B. , Rakin Alexander , Nichols Richard A. , Oyston Petra C.F. , Hinds Jason , Titball Richard W. , Wren Brendan W.
Published: September 2003

Yersinia pestis, the causative agent of plague, diverged from Yersinia pseudotuberculosis, an enteric pathogen, an estimated 1500–20,000 years ago. Genetic characterization of these closely related organisms represents a useful model to study the rapid emergence of bacterial pathogens that threaten mankind. To this end, we undertook genome-wide DNA microarray analysis of 22 strains of Y. pestis and 10 strains of Y. pseudotuberculosis of diverse origin. Eleven Y. pestis DNA loci were deemed absent or highly divergent in all strains of Y. pseudotuberculosis. Four were regions of phage origin, whereas the other seven included genes encoding a vitamin B12 receptor and the insect toxin sepC. Sixteen differences were identified between Y. pestis strains, with biovar Antiqua and Mediaevalis strains showing most divergence from the arrayed CO92 Orientalis strain. Fifty-eight Y. pestis regions were specific to a limited number of Y. pseudotuberculosis strains, including the high pathogenicity island, three putative autotransporters, and several possible insecticidal toxins and hemolysins. The O-antigen gene cluster and one of two possible flagellar operons had high levels of divergence between Y. pseudotuberculosis strains. This study reports chromosomal differences between species, biovars, serotypes, and strains of Y. pestis and Y. pseudotuberculosis that may relate to the evolution of these species in their respective niches.
Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms
Authors: Lu Xin , Niu Tianhua , Liu Jun S.
Published: September 2003

Single nucleotide polymorphisms in the human genome have become an increasingly popular topic in that their analyses promise to be a key step toward personalized medicine. We investigate two related questions, how much the haplotype information contributes to linkage disequilibrium (LD) mapping and whether an in silico haplotype construction preceding the LD analysis can help. For disease gene mapping, using both simulated and real data sets on cystic fibrosis and the Alzheimer disease, we reached the following conclusions: (1) for simple Mendelian diseases, in which case a tractable full statistical model can be developed, the loss of haplotype information for either control or disease data do not have a great impact on LD fine mapping, and haplotype inference should be carried out jointly with LD mapping; (2) for complex diseases, inferring haplotype phases for individuals prior to LD mapping helps achieve a better accuracy. An improved version of the linkage disequilibrium mapping program, BLADE v2, is available at http://www.fas.harvard.edu/junliu/TechRept/03folder/bladev2.tgz.
GANESH: Software for Customized Annotation of Genome Regions
Authors: Huntley Derek , Hummerich Holger , Smedley Damian , Kittivoravitkul Sasivimol , McCarthy Mark , Little Peter , Sergot Marek
Published: September 2003

GANESH is a software package designed to support the genetic analysis of regions of human and other genomes. It provides a set of components that may be assembled to construct a self-updating database of DNA sequence, mapping data, and annotations of possible genome features. Once one or more remote sources of data for the target region have been identified, all sequences for that region are downloaded, assimilated, and subjected to a (configurable) set of standard database-searching and genome-analysis packages. The results are stored in compressed form in a relational database, and are updated automatically on a regular schedule so that they are always immediately available in their most up-to-date versions. A Java front-end, executed as a stand alone application or web applet, provides a graphical interface for navigating the database and for viewing the annotations. There are facilities for importing and exporting data in the format of the Distributed Annotation System (DAS), enabling a GANESH database to be used as a component of a DAS configuration. The system has been used to construct databases for about a dozen regions of human chromosomes and for three regions of mouse chromosomes.
Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster
Authors: Mi Huaiyu , Vandergriff Jody , Campbell Michael , Narechania Apurva , Majoros William , Lewis Suzanna , Thomas Paul D. , Ashburner Michael
Published: September 2003

The functional classification of genes on a genome-wide scale is now in its infancy, and we make a first attempt to assess existing methods and identify sources of error. To this end, we compared two independent efforts for associating proteins with functions, one implemented by FlyBase and the other by PANTHER at Celera Genomics. Both methods make inferences based on sequence similarity and the available experimental evidence. However, they differ considerably in methodology and process. Overall, assuming that the systematic error across the two methods is relatively small, we find the protein-to-function association error rate of both the FlyBase and PANTHER methods to be <2%. The primary source of error for both methods appears to be simple human error. Although homology-based inference can certainly cause errors in annotation, our analysis indicates that the frequency of such errors is relatively small compared with the number of correct inferences. Moreover, these homology errors can be minimized by careful tree-based inference, such as that implemented in PANTHER. Often, functional associations are made by one method and not the other, indicating that one of the greatest challenges lies in improving the completeness of available ontology associations.