bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosomal Deletion Formation System Based on Tn5 Double Transposition: Use For Making Minimal Genomes and Essential Gene Analysis
Authors: Goryshin Igor Y. , Naumann Todd A. , Apodaca Jennifer , Reznikoff William S. 
Published: April 2003

In this communication, we describe the use of specialized transposons (Tn5 derivatives) to create deletions in theEscherichia coli K-12 chromosome. These transposons are essentially rearranged composite transposons that have been assembled to promote the use of the internal transposon ends, resulting in intramolecular transposition events. Two similar transposons were developed. The first deletion transposon was utilized to create a consecutive set of deletions in the E. coli chromosome. The deletion procedure has been repeated 20 serial times to reduce the genome an average of 200 kb (averaging 10 kb per deletion). The second deletion transposon contains a conditional origin of replication that allows deleted chromosomal DNA to be captured as a complementary plasmid. By plating cells on media that do not support plasmid replication, the deleted chromosomal material is lost and if it is essential, the cells do not survive. This methodology was used to analyze 15 chromosomal regions and more than 100 open reading frames (ORFs). This provides a robust technology for identifying essential and dispensable genes.[Supplemental material is available online at www.genome.org and is supplied as an extended table enumerating genes lost in two multiple round deletion strains (Δ20-1 and Δ20-4). These data are summarized in Table 1.]
Identification of Novel Imprinted Genes in a Genome-Wide Screen for Maternal Methylation
Authors: Smith Rachel J. , Dean Wendy , Konfortova Galia , Kelsey Gavin 
Published: April 2003

A characteristic of imprinted genes is that the maternal and paternal alleles show differences in methylation. To perform a genome-wide screen for novel imprinted loci, we applied methylation-sensitive representational difference analysis (Me-RDA) to parthenogenetic mouse embryos, to identify differentially methylated regions (DMRs) methylated specifically on the maternal allele. We isolated a total of 26 distinct clones from known and novel DMRs and identified three novel imprinted genes. Nap1l5 is located on proximal chromosome 6 and encodes a protein with homology with nucleosome assembly proteins (NAPs); it has tissue-specific imprinting with expression from the paternal allele. We identified two DMRs on chromosome 15, a chromosome that was not thought to contain imprinted loci, and demonstrated that each is associated with a paternally expressed transcript. Peg13 gives rise to a noncoding RNA that is highly expressed in the brain and imprinted in all tissues examined. A DMR was also identified at the chromosome 15 Slc38a4 gene, which encodes a system A amino acid transporter; we show thatSlc38a4 is imprinted in a tissue-specific manner. Interestingly, two of the three novel genes identified in this screen are located within the introns of other genes; their identification indicates that such “microimprinted” domains may be more common than previously thought.[The sequence data from this study have been submitted to GenBank under accession nos. AY151252 andAY151253. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: C. Beechey, J. Peters and D. Bodle.]
Comparative Evolutionary Genomics Unveils the Molecular Mechanism of Reassignment of the CTG Codon inCandidaspp.
Authors: Massey Steven E. , Moura Gabriela , Beltrão Pedro , Almeida Ricardo , Garey James R. , Tuite Mick F. , Santos Manuel A.S. 
Published: April 2003

Using the (near) complete genome sequences of the yeastsCandida albicans, Saccharomyces cerevisiae, andSchizosaccharomyces pombe, we address the evolution of a unique genetic code change, which involves decoding of the standard leucine-CTG codon as serine inCandidaspp. By using two complementary comparative genomics approaches, we have been able to shed new light on both the origin of the novelCandidaspp. Ser-tRNACAG, which has mediated CTG reassignment, and on the evolution of the CTG codon in the genomes ofC. albicans,S. cerevisiae, andS. pombe. Sequence analyses of newly identified tRNAs from theC. albicansgenome demonstrate that the Ser-tRNACAGis derived from a serine and not a leucine tRNA in the ancestor yeast species and that this codon reassignment occurred ∼170 million years ago, but the origin of the Ser-tRNACAGis more ancient, implying that the ancestral Leu-tRNA that decoded the CTG codon was lost after the appearance of the Ser-tRNACAG. Ambiguous CTG decoding by the Ser-tRNACAGcombined with biased AT pressure forced the evolution of CTG into TTR codons and have been major forces driving evolution of the CTN codon family inC. albicans. Remarkably, most of the CTG codons present in extantC. albicansgenes are encoded by serine and not leucine codons in homologousS. cerevisiaeandS. pombegenes, indicating that a significant number of serine TCN and AGY codons evolved into CTG codons either directly by simultaneous double mutations or indirectly through an intermediary codon. In either case, CTG reassignment had a major impact on the evolution of the coding component of theCandidaspp. genome.[Supplemental material is available online athttp://www.genome.organd athttp://www.bio.ua.pt/genomica/Lab/Genomedata.html. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: N. Federspiel.]
Data-Mining Approaches Reveal Hidden Families of Proteases in the Genome of Malaria Parasite
Authors: Wu Yimin , Wang Xiangyun , Liu Xia , Wang Yufeng 
Published: April 2003

The search for novel antimalarial drug targets is urgent due to the growing resistance of Plasmodium falciparum parasites to available drugs. Proteases are attractive antimalarial targets because of their indispensable roles in parasite infection and development, especially in the processes of host erythrocyte rupture/invasion and hemoglobin degradation. However, to date, only a small number of proteases have been identified and characterized in Plasmodiumspecies. Using an extensive sequence similarity search, we have identified 92 putative proteases in the P. falciparum genome. A set of putative proteases including calpain, metacaspase, and signal peptidase I have been implicated to be central mediators for essential parasitic activity and distantly related to the vertebrate host. Moreover, of the 92, at least 88 have been demonstrated to code for gene products at the transcriptional levels, based upon the microarray and RT-PCR results, and the publicly available microarray and proteomics data. The present study represents an initial effort to identify a set of expressed, active, and essential proteases as targets for inhibitor-based drug design.[Supplemental material is available online at www.genome.org.]
Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements
Authors: Nunes Luiz R. , Rosato Yoko B. , Muto Nair H. , Yanai Giane M. , da Silva Vivian S. , Leite Daniela B. , Gonçalves Edmilson R. , de Souza Alessandra A. , Coletta-Filho Helvécio D. , Machado Marcos A. , Lopes Silvio A. , de Oliveira Regina Costa 
Published: April 2003

Genetically distinct strains of the plant bacterium Xylella fastidiosa (Xf) are responsible for a variety of plant diseases, accounting for severe economic damage throughout the world. Using as a reference the genome of Xf 9a5c strain, associated with citrus variegated chlorosis (CVC), we developed a microarray-based comparison involving 12 Xf isolates, providing a thorough assessment of the variation in genomic composition across the group. Our results demonstrate that Xf displays one of the largest flexible gene pools characterized to date, with several horizontally acquired elements, such as prophages, plasmids, and genomic islands (GIs), which contribute up to 18% of the final genome. Transcriptome analysis of bacteria grown under different conditions shows that most of these elements are transcriptionally active, and their expression can be influenced in a coordinated manner by environmental stimuli. Finally, evaluation of the genetic composition of these laterally transferred elements identified differences that may help to explain the adaptability of Xf strains to infect such a wide range of plant species.[Supplemental material is available online at www.genome.org.]
Species-Specific Class I Gene Expansions Formed the Telomeric 1 Mb of the Mouse Major Histocompatibility Complex
Authors: Takada Toyoyuki , Kumánovics Attila , Amadou Claire , Yoshino Masayasu , Jones Elsy P. , Athanasiou Maria , Evans Glen A. , Lindahl Kirsten Fischer 
Published: April 2003

We have determined the complete sequence of 951,695 bp from the class I region ofH2,the mouse major histocompatibility complex (Mhc) from strain 129/Sv (haplotypebc). The sequence contains 26 genes. The sequence spans from the last 50 kb of theH2-Tregion, including 2 class I genes and 3 class I pesudogenes, and includes theH2-Mregion up toGabbr1.A 500-kb stretch of theH2-Mregion contains 9 class I genes and 4 pseudogenes, which fall into two subfamilies,M1andM10, distinct from other mouse class I genes. ThisM1/M10class I gene-cluster is separated from the centromericH2-Tand the telomericH2-M4, -5 and-6class I genes by “nonclass I genes”. Comparison with the corresponding 853-kb region of the humanMhc,which includes theHLA-Aregion, shows a mosaic of conserved regions of orthologous nonclass I genes separated by regions of species-specific expansion of paralogousMhcclass I genes. The analysis of this mosaic structure illuminates the dynamic evolution of theMhcclass I region among mammals and provides evidence for the framework hypothesis.[Supplemental material is available online atwww.genome.org. The sequence data from this study have been submitted to GenBank under accession nos.AC005413,AC005665,AF532111–AF532117. A preliminary draft sequence was earlier submitted asAC002615and replaced this year by NT002615.]
On the Links–Gould Invariant of Links
Authors: DE WIT DAVID , LINKS JON R , KAUFFMAN LOUIS H. 
Published: April 2003

[Formula: see text]We introduce and study in detail an invariant of (1, 1) tangles. This invariant, derived from a family of four dimensional representations of the quantum superalgebra Uq[gl(2|1)], will be referred to as the Links–Gould invariant. We find that our invariant is distinct from the Jones, HOMFLY and Kauffman polynomials (detecting chirality of some links where these invariants fail), and that it does not distinguish mutants or inverses. The method of evaluation is based on an abstract tensor state model for the invariant that is quite useful for computation as well as theoretical exploration.
WOVEN BRAIDS AND THEIR CLOSURES
Authors: KNEISSLER JAN A. 
Published: April 2003

A special class of braids, called woven, is introduced and it is shown that every conjugation class of the braid group contains woven braids. In consequence tame links can be presented as plats and closures of woven braids. Restricting on knots we get the 'woven version' of the well-known theorem of Markov, giving moves that are capable of producing all woven braids with equivalent closures. As corollary we obtain that a link in which each component is dyed with at least two different colors can be projected on a plane without crossing strands of the same color. The lowest order part of the HOMFLY polynomial of a closed woven braid can be read off directly; a complete characterization of all occuring terms is given. Finally, a table of all minimal woven braids for the 84 prime knots with at most nine crossings is appended. The average word length and the average number of entries per knot type tune out to be suprising small.
THE SIMPLEST HYPERBOLIC KNOTS
Authors: CALLAHAN PATRICK J. , DEAN JOHN C. , WEEKS JEFFREY R. 
Published: April 2003

While the crossing number is the standard notion of complexity for knots, the number of ideal tetrahedra required to construct the complement provides a natural alternative. We determine which hyperbolic manifolds with 6 or fewer ideal tetrahedra are knot complements, and explicitly describe the corresponding knots in the 3-sphere. Thus, these 72 knots are the simplest knots according to this notion of complexity. Many of these knots have the structure of twisted torus knots. The initial observation that led to the project was the abundance of knot complements with small Seifert-fibered Dehn fillings among the census manifolds. Since many of these knots have rather large crossing number they do not appear in the knot tables. Our methods, while ad hoc, yield some detailed information about the knot complements as well as the manifolds that arise from exceptional surgeries on these knots.
THE BRAID INDEX AND THE GROWTH OF VASSILIEV INVARIANTS
Authors: Stoimenow A. 
Published: April 2003

We use the new approach of braiding sequences to prove exponential upper bounds for the number of Vassiliev invariants on knots with bounded braid index, bounded bridge number and arborescent knots. We prove, that any Vassiliev invariant of degree k is determined by its values on knots with braid index at most k + 1.
GUESTHOOD AS ETHICAL DECOLONISING RESEARCH METHOD
Authors: Harvey Graham 
Published: April 2003

AbstractDebates about research methods have often been concerned with the situation of the researcher in relation to those they research among, about or "on." Reiterating the dualisms embedded in Western culture, many of these have privileged allegedly objective distance between researcher and researched, and worried about researchers "going native." This paper argues that researchers are always more than these dualities suggest, and that an acceptance and outworking of an alternative relational position would greatly enhance research and its outcomes. That alternative position is explored in dialogue with the protocols by which Maori convert strangers into guests, while allowing the possibility that strangers might be enemies. Similar protocols and relationships are available among other indigenous people, and more widely. Ethical and decolonising research might find rich resources for resolving some typically Western problems in the enhancement of dialogues and relationships that, reflection suggests, underpin the research experiences of many people (researchers and researched included). The paper argues that benefits will accrue not only to academic communities but also to those with whom they engage.
BUDDHISM, RELIGION, AND THE CONCEPT OF "GOD"
Authors: Pyysiäinen Ilkka 
Published: April 2003

AbstractIt is here argued that, although the Buddha and the buddhas are not regarded as gods by Buddhists, they clearly fulfill the criteria of "counter-intuitive agents" as they have been presented by Pascal Boyer. To the extent that religion can be understood as human thought, action, and experience that involve counter-intuitive representations, Buddhism does not have to be the problematic touchstone for a global concept of religion.
ARYENS ET SÉMITES: QUEL AVENIR? ARCHÉOLOGIES, LANGUES ET VISIONS DU MONDE
Authors: Van Berg Paul-Louis 
Published: April 2003

AbstractFriedrich Max Mueller thought that the "absurdity" of Aryan myths could be explained by a "disease of language," that is a shift implying that metaphor was taken for reality. Thus, cosmic and meteorological phenomena came to be considered as human beings living human adventures. He found the etiology of this disease in language, and specially in the polysemy and ambiguity of Vedic Sanskrit which he opposed to the limpidity of Hebrew. While the difference between the two languages does exist, the explanation has long been acknowledged to be false. Actually, the opposition becomes understandable if we consider that Indo-Europeans and Semites belong to much wider cultural basins. Indeed, characteristics attributed by Max Mueller to the Aryans also belong to the Altaic cultures, while those assigned to the Semites are shared not only by Hebrews, but also by many other Semitic and by non-Semitic cultures of the Near East. Hence, we can define two large cultural sets north and south of the Black Sea and the Caucasus. In the northern one, Indo-European and Altaic cultures share many traits: organization of space and time, society and knowledge, unreliability of the visible world, conception of the human body, rejection of figuration, for instance. In the southern one, we find radically different conceptions shared by the indigenous Near Eastern cultures. Considering that linguistic communication and ways of thinking are only aspects of these two cultural sets, elaborated separately since the Neolithic and adapted to different conditions of life, we may expect mythologies to reflect these differences and understand that the opposition of Vedic Sanskrit and Hebrew is only a small facet of a global phenomenon.
DID THE HINDUS LACK A SENSE OF HISTORY?
Authors: Sharma Arvind 
Published: April 2003

AbstractThe view that the Hindus do not possess a sense of history has become so commonplace as to virtually achieve the status of an axiom in the study of Indic religion and culture. It is the argument of this paper that this view may stand in need of revision in the light of the epigraphic, literary, and even artisitic evidence presented therein, specially when it is assessed in the context of the various foreign invasions to which India has been subject.
Human neutrophils utilize a Rac/Cdc42-dependent MAPK pathway to direct intracellular granule mobilization toward ingested microbial pathogens
Authors: Zhong Bin , Jiang Kun , Gilvary Danielle L. , Epling-Burnette Pearlie K. , Ritchey Connie , Liu Jinhong , Jackson Rosalind J. , Hong-Geller Elizabeth , Wei Sheng 
Published: April 2003

AbstractElevated levels of mitogen-activated protein kinase/extracellular regulatory kinase (MAPK/ERK) activity are frequently found in some cancer cells. In efforts to reduce tumor growth, attempts have been made to develop cancer therapeutic agents targeting the MAPK. Here, by use of biologic, biochemical, and gene manipulation methods in human polymorphonuclear neutrophils (PMNs), we have identified a key pathway important in normal cell function involving MAPK/ERK in PMNs for growth inhibition of Candida albicans. Contact withC albicans triggered MAPK/ERK activation in PMNs within 5 minutes, and blocking of MAPK/ERK activation, either by the pharmacologic reagent PD098059 or by dominant-negative MAPK kinase (MEK) expression via vaccinia viral delivery, suppressed antimicrobial activity. Rac and Cdc42, but not Ras or Rho, were responsible for this MAPK/ERK activation. Expression of dominant-negative Rac (N17Rac) or Cdc42 (N17Cdc42) eliminated not only C albicans– mediated ERK phosphorylation but also phagocytosis and granule migration toward the ingested microbes, whereas dominant-negative Ras (N17Ras) and Rho (N19Rho) did not. PAK1 (p21-activated kinase 1) activation is induced by C albicans, suggesting that PAK1 may also be involved in the Rac1 activation of MAPK/ERK. We conclude from these data that Rac/Cdc42-dependent activation of MAPK/ERK is a critical event in the immediate phagocytic response of PMNs to microbial challenge. Therefore, use of MAPK pharmacologic inhibitors for the treatment of cancer may result in the interruption of normal neutrophil function. A balance between therapeutic outcome and undesirable side effects must be attained to achieve successful and safe anticancer therapy.
Novel epinephrine and cyclic AMP-mediated activation of BCAM/Lu-dependent sickle (SS) RBC adhesion
Authors: Hines Patrick C. , Zen Qin , Burney Sharran N. , Shea Deborah A. , Ataga Kenneth I. , Orringer Eugene P. , Telen Marilyn J. , Parise Leslie V. 
Published: April 2003

AbstractThe vasoocclusive crisis is the major clinical feature of sickle cell anemia, which is believed to be initiated or sustained by sickle (SS) red blood cell (RBC) adhesion to the vascular wall. SS RBCs, but not unaffected (AA) RBCs, adhere avidly to multiple components of the vascular wall, including laminin. Here we report a novel role for epinephrine and cyclic adenosine monophosphate (cAMP) in the regulation of human SS RBC adhesiveness via the laminin receptor, basal cell adhesion molecule/Lutheran (BCAM/Lu). Our data demonstrate that peripheral SS RBCs contain greater than 4-fold more cAMP than AA RBCs under basal conditions. Forskolin or the stress mediator epinephrine further elevates cAMP in SS RBCs and increases adhesion of SS RBCs to laminin in a protein kinase A (PKA)–dependent manner, with the low-density population being the most responsive. Epinephrine-stimulated adhesion to laminin, mediated primarily via the β2-adrenergic receptor, occurred in SS RBC samples from 46% of patients and was blocked by recombinant, soluble BCAM/Lu, implicating this receptor as a target of cAMP signaling. Thus, these studies demonstrate a novel, rapid regulation of SS RBC adhesion by a cAMP-dependent pathway and suggest that components of this pathway, particularly PKA, the β2-adrenergic receptor, and BCAM/Lu, should be further explored as potential therapeutic targets to inhibit SS RBC adhesion.
Regulation of neutrophil and eosinophil secondary granule gene expression by transcription factors C/EBPε and PU.1
Authors: Gombart Adrian F. , Kwok Scott H. , Anderson Karen L. , Yamaguchi Yuji , Torbett Bruce E. , Koeffler H. Phillip 
Published: April 2003

AbstractIn the bone marrow of C/EBPε−/− mice, expression of neutrophil secondary and tertiary granule mRNAs is absent for lactoferrin (LF), neutrophil gelatinase (NG), murine cathelinlike protein (MCLP), and the cathelin B9; it is severely reduced for neutrophil collagenase (NC) and neutrophil gelatinase-associated lipocalin (NGAL). In addition, the expression of eosinophil granule genes, major basic protein (MBP), and eosinophil peroxidase (EPX) is absent. These mice express C/EBPα, C/EBPβ, and C/EBPδ in the bone marrow at levels similar to those of their wild-type counterparts, suggesting a lack of functional redundancy among the family in vivo. Stable inducible expression of C/EBPε and C/EBPα in the murine fibroblast cell line NIH 3T3 activated expression of mRNAs for B9, MCLP, NC, and NGAL but not for LF. In transient transfections of C/EBPε and C/EBPα, B9 was strongly induced with weaker induction of the other genes. C/EBPβ and C/EBPδ proteins weakly induced B9 expression, but C/EBPδ induced NC expression more efficiently than the other C/EBPs. The expression of MBP was inefficiently induced by C/EBPε alone and weakly induced with C/EBPε and GATA-1, but the addition of PU.1 resulted in a striking cooperative induction of MBP in NIH 3T3 cells. Mutation of a predicted PU.1 site in the human MBP promoter-luciferase reporter construct abrogated the response to PU.1. Gel-shift analysis demonstrated binding of PU.1 to this site. MBP and EPX mRNAs were absent in a PU.1-null myeloid cell line established from the embryonic liver of PU.1−/− mice. Restitution of PU.1 protein expression restored MBP and EPX protein expression. This study demonstrates that C/EBPε is essential and sufficient for the expression of a particular subset of neutrophil secondary granule genes. Furthermore, it indicates the importance of PU.1 in the cooperative activation of eosinophil granule genes.