bluuebunny/crossref_metadata_2025 huggingface dataset:
The LTR enhancer of ERV-9 human endogenous retrovirus is active in oocytes and progenitor cells in transgenic zebrafish and humans
Authors: Pi Wenhu , Yang Zhongan , Wang Jian , Ruan Ling , Yu Xiuping , Ling Jianhua , Krantz Sanford , Isales Carlos , Conway Simon J. , Lin Shuo , Tuan Dorothy
Published: January 2004

The solitary LTRs of ERV-9 human endogenous retrovirus are middle repetitive DNAs associated with 3,000–4,000 human gene loci including the β-globin gene locus where the ERV-9 LTR is juxtaposed to the locus control region (β-LCR) far upstream of the globin genes. The ERV-9 LTRs are conserved during primate evolution, but their function in the primate genomes is unknown. Here, we show that in transgenic zebrafish harboring the β-globin ERV-9 LTR coupled to the GFP gene, the LTR enhancer was active and initiated synthesis of GFP mRNA in oocytes but not in spermatozoa, and GFP expression in the embryos was maternally inherited. The LTR enhancer was active also in stem/progenitor cell regions of adult tissues of transgenic zebrafish. In human tissues, ERV-9 LTR enhancer was active also in oocytes and stem/progenitor cells but not in spermatozoa and a number of differentiated, adult somatic cells. Transcriptional analyses of the human β-globin gene locus showed that the β-globin ERV-9 LTR enhancer initiated RNA synthesis from the LTR in the direction of the downstream β locus control region and globin genes in ovary and erythroid progenitor cells. The findings suggest that, during oogenesis, ERV-9 LTR enhancers in the human genome could activate the cis-linked gene loci to synthesize maternal mRNAs required for early embryogenesis. Alternatively, the ERV-9 LTR enhancers, in initiating RNA syntheses into the downstream genomic DNAs, could transcriptionally potentiate and preset chromatin structure of the cis-linked gene loci in oocytes and adult stem/progenitor cells.
Closterovirus bipolar virion: Evidence for initiation of assembly by minor coat protein and its restriction to the genomic RNA 5′ region
Authors: Satyanarayana Tatineni , Gowda Siddarame , Ayllón María A. , Dawson William O.
Published: January 2004

The long flexuous virions of the Closteroviridae have a unique bipolar architecture incorporating two coat proteins, with most of the helical nucleocapsid encapsidated by the major coat protein (CP) and a small portion of one end encapsidated by the minor coat protein (CPm). It is not known whether CPm encapsidates the genomic RNA and, if so, which end and what effects transition between the two coat proteins. Two other virus-encoded proteins, an HSP70 homolog (HSP70h) and an ≈61-kDa protein, are required to augment virion assembly. In this work, we examine the
in vivo
encapsidation of Citrus tristeza virus by its CPm in the absence of CP. In the absence of other assembly-related proteins, CPm protected a family of 5′ coterminal RNAs, apparently because of pausing at different locations along the genomic RNA. Most of the nucleocapsids formed by CPm were short, but a few were full-length and infectious. Mutations within the 5′ nontranslated region demonstrated that the CPm origin of assembly overlaps the previously described conserved stem-and-loop structures that function as a cis-acting element required for RNA synthesis. Thus, in the absence of CP, the CPm encapsidation is initiated from the 5′ end of the genomic RNA. Coexpression of HSP70h and the p61 protein with CPm in protoplasts restricted encapsidation to the 5′ ≈630 nucleotides, which is close to the normal boundary of the bipolar virion, whereas the presence of either HSP70h or the p61 protein alone did not limit encapsidation by CPm.
Glucocorticoid effects on object recognition memory require training-associated emotional arousal
Authors: Okuda Shoki , Roozendaal Benno , McGaugh James L.
Published: January 2004

Considerable evidence implicates glucocorticoid hormones in the regulation of memory consolidation and memory retrieval. The present experiments investigated whether the influence of these hormones on memory depends on the level of emotional arousal induced by the training experience. We investigated this issue in male Sprague–Dawley rats by examining the effects of immediate posttraining systemic injections of the glucocorticoid corticosterone on object recognition memory under two conditions that differed in their training-associated emotional arousal. In rats that were not previously habituated to the experimental context, corticosterone (0.3, 1.0, or 3.0 mg/kg, s.c.) administered immediately after a 3-min training trial enhanced 24-hr retention performance in an inverted-U shaped dose–response relationship. In contrast, corticosterone did not affect 24-hr retention of rats that received extensive prior habituation to the experimental context and, thus, had decreased novelty-induced emotional arousal during training. Additionally, immediate posttraining administration of corticosterone to nonhabituated rats, in doses that enhanced 24-hr retention, impaired object recognition performance at a 1-hr retention interval whereas corticosterone administered after training to well-habituated rats did not impair 1-hr retention. Thus, the present findings suggest that training-induced emotional arousal may be essential for glucocorticoid effects on object recognition memory.
Erythropoietin both protects from and reverses experimental diabetic neuropathy
Authors: Bianchi Roberto , Buyukakilli Belgin , Brines Michael , Savino Costanza , Cavaletti Guido , Oggioni Norberto , Lauria Giuseppe , Borgna Monica , Lombardi Raffaella , Cimen Burak , Comelekoglu Ulku , Kanik Arzu , Tataroglu Cengiz , Cerami Anthony , Ghezzi Pietro
Published: January 2004

Erythropoietin (EPO) possesses generalized neuroprotective and neurotrophic actions. We tested the efficacy of recombinant human EPO (rhEPO) in preventing and reversing nerve dysfunction in streptozotocin (STZ)-induced diabetes in rats. Two days after STZ [60 mg/kg of body weight (b.w.), i.p.], diabetic animals were administered rhEPO (40 μg/kg of b.w.) three times weekly for 5 weeks either immediately (preventive) before or after a 5-week delay (therapeutic) after induction of hyperglycemia or at a lower dose (8 μg/kg of b.w. once per week) for 8 weeks (prolonged). Tail-nerve conduction velocities (NCV) was assessed at 5 and 11 weeks for the preventive and therapeutic schedule, respectively. Compared to nondiabetic rats, NCV was 20% lower after 5 weeks in the STZ group, and this decrease was attenuated 50% by rhEPO. Furthermore, the reduction of Na
+
,K
+
-ATPase activity of diabetic nerves (by 55%) was limited to 24% in the rhEPO-treated group. In the therapeutic schedule, NCV was reduced by 50% after 11 weeks but by only 23% in the rhEPO-treated group. rhEPO treatment attenuated the decrease in compound muscle action potential in diabetic rats. In addition, rhEPO treatment was associated with a preservation of footpad cutaneous innervation, as assessed by protein gene product 9.5 immunostaining. Diabetic rats developed alterations in mechanical and thermal nociception, which were partially reversed by rhEPO given either in a preventative or therapeutic manner. These observations suggest that administration of rhEPO or its analogues may be useful in the treatment of diabetic neuropathy.
MLL 5 protein forms intranuclear foci, and overexpression inhibits cell cycle progression
Authors: Deng Lih-Wen , Chiu Isaac , Strominger Jack L.
Published: January 2004

MLL5
is a mammalian
trithorax
group (
trx
-
G
) gene identified within chromosome band 7q22, a frequently deleted element found in cytogenetic aberrations of acute myeloid malignancies. MLL5 cDNA was linked with the FLAG and V5 tags at the N and C terminus, respectively, and transfected into 293T cells. Immunofluoresence staining of the expressed tagged MLL5 protein showed localization to the nucleus and exclusion from nucleoli, and no surface staining was detected. Both ectopically introduced and endogenous MLL5 protein displayed a speckled nuclear distribution. By using a series of MLL5-truncated mutants fused with enhanced GFP, a domain (residues 945–1,156) required for foci accumulation was identified, and regions containing functional nuclear localization signals were mapped. Ectopic overexpression of GFP-MLL5 induced cell cycle arrest in G
1
phase. This inhibition of cell cycle progression was indicated by delayed progression into nocodazole-induced mitotic arrest and was confirmed by a lack of BrdUrd incorporation. These findings suggest that MLL5 forms intranuclear protein complexes that may play an important role in chromatin remodeling and cellular growth suppression.
Pattern of diversity in the genomic region near the maize domestication gene
tb1
Authors: Clark Richard M. , Linton Eric , Messing Joachim , Doebley John F.
Published: January 2004

Domesticated maize and its wild ancestor (teosinte) differ strikingly in morphology and afford an opportunity to examine the connection between strong selection and diversity in a major crop species. The
tb1
gene largely controls the increase in apical dominance in maize relative to teosinte, and a region of the
tb1
locus 5′ to the transcript sequence was a target of selection during maize domestication. To better characterize the impact of selection at a major “domestication” locus, we have sequenced the upstream
tb1
genomic region and systematically sampled nucleotide diversity for sites located as far as 163 kb upstream to
tb1
. Our analyses define a selective sweep of ≈60–90 kb 5′ to the
tb1
transcribed sequence. The selected region harbors a mixture of unique sequences and large repetitive elements, but it contains no predicted genes. Diversity at the nearest 5′ gene to
tb1
is typical of that for neutral maize loci, indicating that selection at
tb1
has had a minimal impact on the surrounding chromosomal region. Our data also show low intergenic linkage disequilibrium in the region and suggest that selection has had a minor role in shaping the pattern of linkage disequilibrium that is observed. Finally, our data raise the possibility that maize-like
tb1
haplotypes are present in extant teosinte populations, and our findings also suggest a model of
tb1
gene regulation that differs from traditional views of how plant gene expression is controlled.
On the fundamental group of type II
1
factors
Authors: Popa Sorin
Published: January 2004

We present here a shorter version of the proof of our earlier work, showing that the von Neumann factor associated with the group

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has trivial fundamental group.
Adult male rat hippocampus synthesizes estradiol from pregnenolone by cytochromes P45017α and P450 aromatase localized in neurons
Authors: Hojo Yasushi , Hattori Taka-aki , Enami Taihei , Furukawa Aizo , Suzuki Kumiko , Ishii Hiro-taka , Mukai Hideo , Morrison John H. , Janssen William G. M. , Kominami Shiro , Harada Nobuhiro , Kimoto Tetsuya , Kawato Suguru
Published: January 2004

In adult mammalian brain, occurrence of the synthesis of estradiol from endogenous cholesterol has been doubted because of the inability to detect dehydroepiandrosterone synthase, P45017α. In adult male rat hippocampal formation, significant localization was demonstrated for both cytochromes P45017α and P450 aromatase, in pyramidal neurons in the CA1–CA3 regions, as well as in the granule cells in the dentate gyrus, by means of immunohistochemical staining of slices. Only a weak immunoreaction of these P450s was observed in astrocytes and oligodendrocytes. ImmunoGold electron microscopy revealed that P45017α and P450 aromatase were localized in pre- and postsynaptic compartments as well as in the endoplasmic reticulum in principal neurons. The expression of these cytochromes was further verified by using Western blot analysis and RT-PCR. Stimulation of hippocampal neurons withN-methyl-d-aspartate induced a significant net production of estradiol. Analysis of radioactive metabolites demonstrated the conversion from [3H]pregnenolone to [3H]estradiol through dehydroepiandrosterone and testosterone. This activity was abolished by the application of specific inhibitors of cytochrome P450s. Interestingly, estradiol was not significantly converted to other steroid metabolites. Taken together with our previous finding of a P450scc-containing neuronal system for pregnenolone synthesis, these results imply that 17β-estradiol is synthesized by P45017α and P450 aromatase localized in hippocampal neurons from endogenous cholesterol. This synthesis may be regulated by a glutamate-mediated synaptic communication that evokes Ca2+signals.
Ordered proteolysis in anaphase inactivates Plk1 to contribute to proper mitotic exit in human cells
Authors: Lindon Catherine , Pines Jonathon
Published: January 2004

We have found that key mitotic regulators show distinct patterns of degradation during exit from mitosis in human cells. Using a live-cell assay for proteolysis, we show that two of these regulators, polo-like kinase 1 (Plk1) and Aurora A, are degraded at different times after the anaphase-promoting complex/cyclosome (APC/C) switches from binding Cdc20 to Cdh1. Therefore, events in addition to the switch from Cdc20 to Cdh1 control the proteolysis of APC/CCdh1 substrates in vivo. We have identified a putative destruction box in Plk1 that is required for degradation of Plk1 in anaphase, and have examined the effect of nondegradable Plk1 on mitotic exit. Our results show that Plk1 proteolysis contributes to the inactivation of Plk1 in anaphase, and that this is required for the proper control of mitotic exit and cytokinesis. Our experiments reveal a role for APC/C-mediated proteolysis in exit from mitosis in human cells.
A divergent canonical WNT-signaling pathway regulates microtubule dynamics
Authors: Ciani Lorenza , Krylova Olga , Smalley Matthew J. , Dale Trevor C. , Salinas Patricia C.
Published: January 2004

Dishevelled (DVL) is associated with axonal microtubules and regulates microtubule stability through the inhibition of the serine/threonine kinase, glycogen synthase kinase 3β (GSK-3β). In the canonical WNT pathway, the negative regulator Axin forms a complex with β-catenin and GSK-3β, resulting in β-catenin degradation. Inhibition of GSK-3β by DVL increases β-catenin stability and TCF transcriptional activation. Here, we show that Axin associates with microtubules and unexpectedly stabilizes microtubules through DVL. In turn, DVL stabilizes microtubules by inhibiting GSK-3β through a transcription- and β-catenin–independent pathway. More importantly, axonal microtubules are stabilized after DVL localizes to axons. Increased microtubule stability is correlated with a decrease in GSK-3β–mediated phosphorylation of MAP-1B. We propose a model in which Axin, through DVL, stabilizes microtubules by inhibiting a pool of GSK-3β, resulting in local changes in the phosphorylation of cellular targets. Our data indicate a bifurcation in the so-called canonical WNT-signaling pathway to regulate microtubule stability.
Sinuous is a Drosophila claudin required for septate junction organization and epithelial tube size control
Authors: Wu Victoria M. , Schulte Joost , Hirschi Alexander , Tepass Ulrich , Beitel Greg J.
Published: January 2004

Epithelial tubes of the correct size and shape are vital for the function of the lungs, kidneys, and vascular system, yet little is known about epithelial tube size regulation. Mutations in the Drosophila gene sinuous have previously been shown to cause tracheal tubes to be elongated and have diameter increases. Our genetic analysis using a sinuous null mutation suggests that sinuous functions in the same pathway as the septate junction genes neurexin and scribble, but that nervana 2, convoluted, varicose, and cystic have functions not shared by sinuous. Our molecular analyses reveal that sinuous encodes a claudin that localizes to septate junctions and is required for septate junction organization and paracellular barrier function. These results provide important evidence that the paracellular barriers formed by arthropod septate junctions and vertebrate tight junctions have a common molecular basis despite their otherwise different molecular compositions, morphologies, and subcellular localizations.
A conserved protein interaction network involving the yeast MAP kinases Fus3 and Kss1
Authors: Kusari Anasua B. , Molina Douglas M. , Sabbagh Walid , Lau Chang S. , Bardwell Lee
Published: January 2004

The Saccharomyces cerevisiae mitogen-activated protein kinases (MAPKs) Fus3 and Kss1 bind to multiple regulators and substrates. We show that mutations in a conserved docking site in these MAPKs (the CD/7m region) disrupt binding to an important subset of their binding partners, including the Ste7 MAPK kinase, the Ste5 adaptor/scaffold protein, and the Dig1 and Dig2 transcriptional repressors. Supporting the possibility that Ste5 and Ste7 bind to the same region of the MAPKs, they partially competed for Fus3 binding. In vivo, some of the MAPK mutants displayed reduced Ste7-dependent phosphorylation, and all of them exhibited multiple defects in mating and pheromone response. The Kss1 mutants were also defective in Kss1-imposed repression of Ste12. We conclude that MAPKs contain a structurally and functionally conserved docking site that mediates an overall positively acting network of interactions with cognate docking sites on their regulators and substrates. Key features of this interaction network appear to have been conserved from yeast to humans.
Cell-to-cell transport of proteins and fluorescent tracers via plasmodesmata during plant development
Authors: Zambryski Patricia
Published: January 2004

Plant cells communicate with each other via channels called plasmodesmata (PD). PD are not passive channels, but critical players in gene regulation, controlling intercellular transport of macromolecules between particular cells during development.
HIV-1 Cell to Cell Transfer across an Env-induced, Actin-dependent Synapse
Authors: Jolly Clare , Kashefi Kirk , Hollinshead Michael , Sattentau Quentin J.
Published: January 2004

Direct cell–cell transfer is an efficient mechanism of viral dissemination within an infected host, and human immunodeficiency virus 1 (HIV-1) can exploit this mode of spread. Receptor recognition by HIV-1 occurs via interactions between the viral surface envelope glycoprotein (Env), gp120, and CD4 and a chemokine receptor, CCR5 or CXCR4. Here, we demonstrate that the binding of CXCR4-using HIV-1–infected effector T cells to primary CD4+/CXCR4+ target T cells results in rapid recruitment to the interface of CD4, CXCR4, talin, and lymphocyte function–associated antigen 1 on the target cell, and of Env and Gag on the effector cell. Recruitment of these membrane molecules into polarized clusters was dependent on Env engagement of CD4 and CXCR4 and required remodelling of the actin cytoskeleton. Transfer of Gag from effector to target cell was observed by 1 h after conjugate formation, was independent of cell–cell fusion, and was probably mediated by directed virion fusion with the target cell. We propose that receptor engagement by Env directs the rapid, actin-dependent recruitment of HIV receptors and adhesion molecules to the interface, resulting in a stable adhesive junction across which HIV infects the target cell.
The Activation Status of Neuroantigen-specific T Cells in the Target Organ Determines the Clinical Outcome of Autoimmune Encephalomyelitis
Authors: Kawakami Naoto , Lassmann Silke , Li Zhaoxia , Odoardi Francesca , Ritter Thomas , Ziemssen Tjalf , Klinkert Wolfgang E.F. , Ellwart Joachim W. , Bradl Monika , Krivacic Kimberly , Lassmann Hans , Ransohoff Richard M. , Volk Hans-Dieter , Wekerle Hartmut , Linington Christopher , Flügel Alexander
Published: January 2004

The clinical picture of experimental autoimmune encephalomyelitis (EAE) is critically dependent on the nature of the target autoantigen and the genetic background of the experimental animals. Potentially lethal EAE is mediated by myelin basic protein (MBP)–specific T cells in Lewis rats, whereas transfer of S100β- or myelin oligodendrocyte glycoprotein (MOG)–specific T cells causes intense inflammatory response in the central nervous system (CNS) with minimal disease. However, in Dark Agouti rats, the pathogenicity of MOG-specific T cells resembles the one of MBP-specific T cells in the Lewis rat. Using retrovirally transduced green fluorescent T cells, we now report that differential disease activity reflects different levels of autoreactive effector T cell activation in their target tissue. Irrespective of their pathogenicity, the migratory activity, gene expression patterns, and immigration of green fluorescent protein+ T cells into the CNS were similar. However, exclusively highly pathogenic T cells were significantly reactivated within the CNS. Without local effector T cell activation, production of monocyte chemoattractants was insufficient to initiate and propagate a full inflammatory response. Low-level reactivation of weakly pathogenic T cells was not due to anergy because these cells could be activated by specific antigen in situ as well as after isolation ex vivo.
Salmonella typhimurium Persists within Macrophages in the Mesenteric Lymph Nodes of Chronically Infected Nramp1+/+ Mice and Can Be Reactivated by IFNγ Neutralization
Authors: Monack Denise M. , Bouley Donna M. , Falkow Stanley
Published: January 2004

Host-adapted strains of Salmonella are capable of establishing a persistent infection in their host often in the absence of clinical disease. The mouse model of Salmonella infection has primarily been used as a model for the acute systemic disease. Therefore, the sites of long-term S. typhimurium persistence in the mouse are not known nor are the mechanisms of persistent infection clearly understood. Here, we show that S. typhimurium can persist for as long as 1 yr in the mesenteric lymph nodes (MLNs) of 129sv Nramp1+/+ (Slc11a1+/+) mice despite the presence of high levels of anti–S. typhimurium antibody. Tissues from 129sv mice colonized for 60 d contain numerous inflammatory foci and lesions with features resembling S. typhi granulomas. Tissues from mice infected for 365 d have very few organized inflammatory lesions, but the bacteria continue to persist within macrophages in the MLN and the animals generally remain disease-free. Finally, chronically infected mice treated with an interferon-γ neutralizing antibody exhibited symptoms of acute systemic infection, with evidence of high levels of bacterial replication in most tissues and high levels of fecal shedding. Thus, interferon-γ, which may affect the level of macrophage activation, plays an essential role in the control of the persistent S. typhimurium infection in mice.
Dual, HLA-B27 Subtype-dependent Conformation of a Self-peptide
Authors: Hülsmeyer Martin , Fiorillo Maria Teresa , Bettosini Francesca , Sorrentino Rosa , Saenger Wolfram , Ziegler Andreas , Uchanska-Ziegler Barbara
Published: January 2004

The products of the human leukocyte antigen subtypes HLA-B*2705 and HLA-B*2709 differ only in residue 116 (Asp vs. His) within the peptide binding groove but are differentially associated with the autoimmune disease ankylosing spondylitis (AS); HLA-B*2705 occurs in AS-patients, whereas HLA-B*2709 does not. The subtypes also generate differential T cell repertoires as exemplified by distinct T cell responses against the self-peptide pVIPR (RRKWRRWHL). The crystal structures described here show that pVIPR binds in an unprecedented dual conformation only to HLA-B*2705 molecules. In one binding mode, peptide pArg5 forms a salt bridge to Asp116, connected with drastically different interactions between peptide and heavy chain, contrasting with the second, conventional conformation, which is exclusively found in the case of B*2709. These subtype-dependent differences in pVIPR binding link the emergence of dissimilar T cell repertoires in individuals with HLA-B*2705 or HLA-B*2709 to the buried Asp116/His116 polymorphism and provide novel insights into peptide presentation by major histocompatibility antigens.
Limited conformational space for early-stage protein folding simulation
Authors: Bryliński M. , Jurkowski W. , Konieczny L. , Roterman I.
Published: January 2004

Motivation: The problem of early-stage protein folding is critical for protein structure prediction. The model presented introduces a common definition of protein structures which may be treated as the possible in silico early-stage form of the polypeptide chain. Limitation of the conformational space to the ellipse path on the Ramachandran map was tested as a possible sub-space to represent the early-stage structure for simulation of protein folding. The proposed conformational sub-space was developed on the basis of the backbone conformation, with side-chain interactions excluded.

Results: The ellipse-path-limited conformation of BPTI was created using the criterion of shortest distance between Phi, Psi angles in native form of protein and the Phi, Psi angles belonging to the ellipse. No knots were observed in the structure created according to ellipse-path conformational sub-space. The energy minimization procedure applied to ellipse-path derived conformation directed structural changes toward the native form of the protein with SS-bonds system introduced to the procedure.

Availability: Program ‘Ellipse’ to create the ellipse-path derived structure available on request: myroterm@cyf-kr.edu.pl
Minimal cut sets in biochemical reaction networks
Authors: Klamt Steffen , Gilles Ernst Dieter
Published: January 2004

Motivation: Structural studies of metabolic networks yield deeper insight into topology, functionality and capabilities of the metabolisms of different organisms. Here, we address the analysis of potential failure modes in metabolic networks whose occurrence will render the network structurally incapable of performing certain functions. Such studies will help to identify crucial parts in the network structure and to find suitable targets for repressing undesired metabolic functions.

Results: We introduce the concept of minimal cut sets for biochemical networks. A minimal cut set (MCS) is a minimal (irreducible) set of reactions in the network whose inactivation will definitely lead to a failure in certain network functions. We present an algorithm which enables the computation of the MCSs in a given network related to user-defined objective reactions. This algorithm operates on elementary modes. A number of potential applications are outlined, including network verifications, phenotype predictions, assessing structural robustness and fragility, metabolic flux analysis and target identification in drug discovery. Applications are illustrated by the MCSs in the central metabolism of Escherichia coli for growth on different substrates.

Availability: Computation and analysis of MCSs is an additional feature of the FluxAnalyzer (freely available for academic users upon request, special contracts for industrial companies; see web page below).

Supplementary information:  http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer
Graph-based clustering for finding distant relationships in a large set of protein sequences
Authors: Kawaji Hideya , Takenaka Yoichi , Matsuda Hideo
Published: January 2004

Motivation: Clustering of protein sequences is widely used for the functional characterization of proteins. However, it is still not easy to cluster distantly-related proteins, which have only regional similarity among their sequences. It is therefore necessary to develop an algorithm for clustering such distantly-related proteins.

Results: We have developed a time and space efficient clustering algorithm. It uses a graph representation where its vertices and edges denote proteins and their sequence similarities above a certain cutoff score, respectively. It repeatedly partitions the graph by removing edges that have small weights, which correspond to low sequence similarities. To find the appropriate partitions, we introduce a score combining the normalized cut and a locally minimal cut capacities. Our method is applied to the entire 40 703 human proteins in SWISS-PROT and TrEMBL. The resulting clusters shows a 76% recall (20 529 proteins) of the 26 917 classified by InterPro. It also finds relationships not found by other clustering methods.

Availability: The complete result of our algorithm for all the human proteins in SWISS-PROT and TrEMBL, and other supplementary information are available at http://motif.ics.es.osaka-u.ac.jp/Ncut-KL/
PGTdb: a database providing growth temperatures of prokaryotes
Authors: Huang Shir-Ly , Wu Li-Cheng , Liang Han-Kuen , Pan Kuan-Ting , Horng Jorng-Tzong , Ko Ming-Tat
Published: January 2004

Summary: Included in Prokaryotic Growth Temperature database (PGTdb) are a total of 1334 temperature data from 1072 prokaryotic organisms, Bacteria and Archaea. PGTdb integrates microbial growth temperature data from literature survey with their nucleotide/protein sequence and protein structure data from related databases. A direct correlation is observed between the average growth temperature of an organism and the melting temperature of proteins from the organism. Therefore, this database is useful not only for microbiologists to obtain cultivation condition, but also for biochemists and structure biologists to study the correlation between protein sequences/structures and their thermostability. In addition, the taxonomy and ribosomal RNA sequence(s) of an organism are linked through NCBI Taxonomy and the Ribosomal RNA Operon Copy Number Database umdb, respectively. PGTdb is the only integrated database on the Internet to provide the growth temperature data of the prokaryotes and the combined information of their nucleotide/protein sequences, protein structures, taxonomy and phylogeny.

Availability:  http://pgtdb.csie.ncu.edu.tw
FGDP: functional genomics data pipeline for automated, multiple microarray data analyses
Authors: Grant Jeffrey D. , Somers Luke A. , Zhang Yue , Manion Frank J. , Bidaut Ghislain , Ochs Michael F.
Published: January 2004

Summary: Gene expression microarrays and oligonucleotide GeneChips™ have provided biologists with a means of measuring, in a single experiment, the expression levels of entire genomes under a variety of conditions. As with any nascent field, there is no single accepted method for analyzing the new data types, with new methods appearing monthly. Investigators using the new technology must constantly seek access to the latest tools and explore their data in multiple ways. The functional genomics data pipeline provides an integrated, extendable analysis environment permitting multiple, simultaneous analyses to be automatically performed and provides a web server and interface for presenting results.

Availability: Source code and executables are available under the GNU public license at http://bioinformatics.fccc.edu/
YETI: Yeast Exploration Tool Integrator
Authors: Orton R. J. , Sellers W. I. , Gerloff D. L.
Published: January 2004

Summary: Yeast Exploration Tool Integrator (YETI) is a novel bioinformatics tool for the integrated visualization and analysis of functional genomic data sets from the budding yeast Saccharomyces cerevisiae.

Availability: YETI is freely available for use over the WWW, or download under license, at http://www.bru.ed.ac.uk/~orton/yeti.html
A strategy for assembling the maize (Zea mays L.) genome
Authors: Emrich Scott J. , Aluru Srinivas , Fu Yan , Wen Tsui-Jung , Narayanan Mahesh , Guo Ling , Ashlock Daniel A. , Schnable Patrick S.
Published: January 2004

Summary: Because the bulk of the maize (Zea mays L.) genome consists of repetitive sequences, sequencing efforts are being targeted to its ‘gene-rich’ fraction. Traditional assembly programs are inadequate for this approach because they are optimized for a uniform sampling of the genome and inherently lack the ability to differentiate highly similar paralogs.

Results: We report the development of bioinformatics tools for the accurate assembly of the maize genome. This software, which is based on innovative parallel algorithms to ensure scalability, assembled 730 974 genomic survey sequences fragments in 4 h using 64 Pentium III 1.26 GHz processors of a commodity cluster. Algorithmic innovations are used to reduce the number of pairwise alignments significantly without sacrificing quality. Clone pair information was used to estimate the error rate for improved differentiation of polymorphisms versus sequencing errors. The assembly was also used to evaluate the effectiveness of various filtering strategies and thereby provide information that can be used to focus subsequent sequencing efforts.
Multi-species comparative mapping in silico using the COMPASS strategy
Authors: Liu Lei , Gong George , Liu Yong , Natarajan Shreedhar , Larkin Denis M. , Everts-van der Wind Annelie , Rebeiz Mark , Beever Jonathan E.
Published: January 2004

Motivation: The completion of human and mouse genome sequences provides a valuable resource for decoding other mammalian genomes. The comparative mapping by annotation and sequence similarity (COMPASS) strategy takes advantage of the resource and has been used in several genome-mapping projects. It uses existing comparative genome maps based on conserved regions to predict map locations of a sequence. An automated multiple-species COMPASS tool can facilitate in the genome sequencing effort and comparative genomics study of other mammalian species.

Results: The prerequisite of COMPASS is a comparative map table between the reference genome and the predicting genome. We have built and collected comparative maps among five species including human, cattle, pig, mouse and rat. Cattle–human and pig–human comparative maps were built based on the positions of orthologous markers and the conserved synteny groups between human and cattle and human and pig genomes, respectively. Mouse–human and rat–human comparative maps were based on the conserved sequence segments between the two genomes. With a match to human genome sequences, the approximate location of a query sequence can be predicted in cattle, pig, mouse and rat genomes based on the position of the match relatively to the orthologous markers or the conserved segments.

Availability: The COMPASS-tool and databases are available at http://titan.biotec.uiuc.edu/COMPASS/
A comparative phylogenetic approach for dating whole genome duplication events
Authors: Chapman Brad A. , Bowers John E. , Schulze Stefan R. , Paterson Andrew H.
Published: January 2004

Motivation: Whole genome duplications have played a major role in determining the structure of eukaryotic genomes. Current evidence revealing large blocks of duplicated chromatin yields new insights into the evolutionary history of species, but also presents a major challenge for researchers attempting to utilize comparative genomics techniques. Understanding the timing of duplication events relative to divergence among taxa is critical to accurate and comprehensive cross-species comparisons.

Results: We describe a large-scale approach to estimate the timing of duplication events in a phylogenetic context. The methodology has been previously utilized for analysis of Arabidopsis and Saccharomyces duplication events. This new implementation provides a more flexible and reusable framework for these analyses. Scripts written in the Python programming language drive a number of freely available bioinformatics programs, creating a no-cost tool for researchers. The usefulness of the approach is demonstrated through genome-scale analysis of Arabidopsis and Oryza (rice) duplications.

Availability: Software and documentation are freely available from http://plantgenome.agtec.uga.edu/bioinformatics/dating/
Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA
Authors: Cavaluzzi Michael J , Borer Philip N
Published: January 2004

Ultraviolet absorption provides the nearly universal basis for determining concentrations of nucleic acids. Values for the UV extinction coefficients of DNA and RNA rely on the mononucleotide values determined 30–50 years ago. We show that nearly all of the previously published extinction coefficients for the nucleoside-5′-monophosphates are too large, and in error by as much as 7%. Concentrations based on complete hydrolysis and the older set of values are too low by ∼4% for typical RNA and 2–3% for typical DNA samples. We also analyzed data in the literature for the extinction coefficients of unpaired DNA oligomers. Robust prediction of concentrations can be made using 38 µg/A260 unit for single-stranded DNA (ssDNA) having non-repetitive sequences and 40–80% GC. This is superior to currently used predictions that account for nearest-neighbor frequency or base composition. The latter result in concentrations that are 10–30% too low for typical ssDNA used as primers for PCR and other similar techniques. Methods are described here to accurately measure concentrations of nucleotides by nuclear magnetic resonance. NMR can be used to accurately determine concentrations (and extinction coefficients) of biomolecules within 1%.
Lack of circulating Candida mannoprotein antigen in patients with focal hepatosplenic candidiasis
Authors: Girmenia Corrado , Martino Pietro , De Bernardis Flavia , Boccanera Maria , Cassone Antonio
Published: January 2004

The significance of Candida mannoprotein serum detection in 15 patients with haematological malignancies and proven (six cases) or probable (nine cases) hepatosplenic candidiasis was retrospectively evaluated. Circulating mannoprotein antigen was detected in three of six and in one of two serum samples from two patients with probable infection. The antigen was not detected in 38 serum samples of 13 (87 %) patients. Thus, in contrast to other deep-seated Candida infections, mannoprotein is infrequently detectable during focal hepatosplenic candidiasis and does not appear to be of diagnostic value.
Frameshift mutations in frxA occur frequently and do not provide a reliable marker for metronidazole resistance in UK isolates of Helicobacter pylori
Authors: Chisholm Stephanie A. , Owen Robert J.
Published: January 2004

Mutations in the NAD(P)H flavin oxidoreductase gene (frxA) are thought to contribute to the development of metronidazole resistance inHelicobacter pylori. To test this further, 44frxAsequences in 18 patient isolate sets ofH. pyloriwere examined including a unique collection comprising separated Mtz-sensitive (MtzS) and Mtz-resistant (MtzR) subpopulations pre-treatment and matched MtzRstrains post-treatment. Sequences offrxAcontained frameshift mutations that led to premature protein truncation in at least one strain from most (17/18) patient sets. These mutations were present in all strains, irrespective of Mtz resistotype in 13/18 patients. Frameshift due to a single adenine deletion at nucleotide 53 was the most common mutation and was present in isolates from 11/18 patients. A novel real-time (LightCycler) PCR-based probe hybridization melting-point assay applied to a further 119 isolates confirmed that the frameshift-53 mutation occurred frequently, in 20 % of isolates, and could be present in MtzSas well as MtzRstrains (42 % vs 58 %). This study demonstrates that frameshift mutations occur in MtzSstrains as well as in MtzRstrains, and are thus unlikely to cause Mtz resistance.
Genotypic analysis of multidrug-resistant Mycobacterium tuberculosis isolates from Monterrey, Mexico
Authors: Ramaswamy Srinivas V. , Dou Shu-Jun , Rendon Adrian , Yang Zhenhua , Cave M. Donald , Graviss Edward A.
Published: January 2004

Thirty-seven multidrug-resistant and 13 pan-susceptible isolates of Mycobacterium tuberculosis were analysed for the diversity of genotypes associated with known drug-resistance mechanisms. The isolates were obtained from patients attending a university tuberculosis clinic in Monterrey, Mexico. A total of 25 IS6110-RFLP patterns were obtained from the multidrug-resistant tuberculosis (MDR-TB) isolates. Approximately 65 % of the MDR-TB isolates were attributed to secondary resistance. Different drug-susceptibility patterns were seen with the clustered isolates. The percentage of isolates resistant to isoniazid (INH), rifampicin (RIF), ethambutol (EMB) and streptomycin (STR) was 100, 97.3, 48.7 and 67.6, respectively. The most common resistance-associated polymorphisms for the four drugs were as follows: INH, Ser315Thr (67.6 %) in katG; RIF, Ser450Leu (41.7 %) in rpoB; EMB, Met306Ile/Val/Leu (66.7 %) in embB; and STR, Lys43Arg (24 %) in rpsL. Drug-resistance-associated mutations were similar to changes occurring in isolates from other areas of the world, but unique, previously unreported, mutations in katG (n = 5), rpoB (n = 1) and rrs (n = 3) were also identified.
Lactoferricin influences early events of Listeria monocytogenes infection in THP-1 human macrophages
Authors: Longhi Catia , Conte Maria P. , Penta Michela , Cossu Alessia , Antonini Giovanni , Superti Fabiana , Seganti Lucilla
Published: January 2004

Bovine lactoferrin (BLf) and its derivative peptide lactoferricin B (LfcinB) are known for their antimicrobial activity towards several pathogens, includingListeria monocytogenes, a food-borne Gram-positive invasive bacterium that infects a wide variety of host cells, including professional phagocytes. To add further information on the antibacterial effects of these compounds, the influence of BLf, LfcinB and the antimicrobial centre of LfcinB, the hexapeptide LfcinB4–9, on the invasive behaviour ofL. monocytogeneswas analysed in IFN-γ-activated human macrophagic cells (THP-1). Significant inhibition of bacterial entry in THP-1 cells was observed at LfcinB concentrations that were unable to produce any bacteriostatic or bactericidal effect, compared with BLf and LfcinB4–9peptide. This inhibition occurred when LfcinB was incubated during the bacterial infection step and was not due only to competition for common glycosaminoglycan receptors. Assays performed through a temperature shift from 4 to 37 °C showed that inhibition of invasion took place at an early post-adsorption step, although an effect on a different step of intracellular infection could not be ruled out.
Clostridium difficile colonization in healthy adults: transient colonization and correlation with enterococcal colonization
Authors: Ozaki Eijiro , Kato Haru , Kita Hiroyuki , Karasawa Tadahiro , Maegawa Tsuneo , Koino Youko , Matsumoto Kazumasa , Takada Toshihiko , Nomoto Koji , Tanaka Ryuichiro , Nakamura Shinichi
Published: January 2004

The aim of the present study was to investigate the colonization status of Clostridium difficile in healthy individuals. In total, 139 healthy adults from two study groups were examined at intervals of 3 months. Among the 18 positive subjects, the number of subjects from whom C. difficile was isolated once, twice, three times or four times was 10 (55.6 %), three (16.7 %), two (11.1 %) and three (16.7 %), respectively. In the student group, different subjects were colonized by different PCR ribotype/PFGE types. However, the same PCR ribotype/PFGE types of C. difficile were isolated from different subjects in the employee group, indicating that cross-transmission may have occurred in this group. Continuous colonization by the same PCR ribotype/PFGE type was only observed in three subjects. C. difficile-positive subjects were significantly more densely colonized by enterococci (P < 0.05) than C. difficile-negative subjects: subjects that were found to be C. difficile-positive three or four times appeared to have higher concentrations of enterococci. The present results demonstrate that, although colonization by a C. difficile strain is transient in many cases, there are healthy individuals that are colonized persistently by C. difficile. They also suggest that dense colonization of the intestine by enterococci may be associated with C. difficile colonization.
Protective effect of ethyl-3-(3-dimethyl aminopropyl)urea dihydrochloride (EDU) against LPS-induced death in mice
Authors: Matsumoto Tetsuya , Nieuwenhuis Edward E.S. , Cisneros Ronald L. , Ruiz-Perez Begoña , Yamaguchi Keizo , Blumberg Richard S. , Onderdonk Andrew B.
Published: January 2004

Evaluation of anti-adhesive gels and bioresorbable films in animal models of intra-abdominal infection has shown that a product of the cross-linking reaction between hyaluronic acid (HA) and CM-cellulose, 1-ethyl-3-(3-dimethyl aminopropyl)urea dihydrochloride (EDU), has immunomodulatory properties. The effects of EDU were evaluated by using an endotoxin-induced shock mouse model. Pre-treatment of mice with EDU (50 mg kg−1) in DMSO resulted in a significant reduction in mortality following injection of LPS, compared to vehicle (DMSO) pre-treatment alone. Serum levels of TNF-α, IL1β and IFN-γ in EDU-treated mice were significantly lower than those in vehicle-treated mice. Nitric oxide (NO) concentrations in the sera of mice after inoculation with LPS were significantly lower in the EDU-treated group than in the vehicle-treated group at various time-points. In contrast, EDU pre-treatment was associated with an enhanced IL10 response after LPS injection, compared to vehicle pre-treatment alone. In vitro studies revealed that IL10 production by RAW 264.7 macrophages, elicited by LPS, was increased significantly when EDU was added to the culture medium. These results suggest that the protective effect of EDU during LPS-induced shock in mice is the result of inhibition of proinflammatory cytokines and NO production and an enhanced IL10 response.
Automation of a fluorescence-based multiplex PCR for the laboratory confirmation of common bacterial pathogens
Authors: Smith Karen , Diggle Mathew A. , Clarke Stuart C.
Published: January 2004

A fluorescence-based multiplex PCR was automated for the simultaneous detection of Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae in clinical samples from patients with suspected meningitis. Sensitivity of one to two genome copies per 100 μl sample and specificity of 100 % for each organism were shown. Automation of DNA extraction, liquid handling, PCR and analysis are achieved on a single platform, which enables a high throughput and rapid turnaround of clinical samples that, in turn, leads to faster diagnosis. This is ultimately beneficial to the treatment of the patient and for public health management.
Parvovirus B19 infection in medical students during a hospital outbreak
Authors: Noyola Daniel E. , Padilla-Ruiz M. Lourdes , Obregón-Ramos M. Guadalupe , Zayas Patricia , Pérez-Romano Beatriz
Published: January 2004

From March to May 2002, a parvovirus B19 (B19) outbreak was identified at a general hospital that serves as a teaching facility for the Universidad Autónoma de San Luis Potosí, Mexico. Medical students attending the hospital presented with symptoms suggestive of B19 infection. Previous studies have suggested that apparent hospital-related B19 outbreaks may be a reflection of B19 infection in the community. A study was undertaken to assess whether exposure to the hospital was a risk factor for B19 infection and to determine to what extent medical students were infected during this outbreak. The incidence of B19 infection in medical students attending the teaching hospital during the outbreak (n = 211) was determined and compared to students not attending the hospital (n = 96). To assess if a community-wide outbreak had occurred, 80 blood donors were also evaluated for the presence of B19 antibodies. Acute B19 infection was identified in 40 of 119 (33.6 %) susceptible students attending the hospital and in 20 of 47 (42.6 %) susceptible students not attending the hospital. The frequency of acute infection among susceptible blood donors was lower (9.5 %) than in students, but higher than the rate expected during non-epidemic periods. Most infections (68.3 %) were asymptomatic. Symptoms reported by infected subjects were not specific for B19 infection. Only 11.7 % of subjects with acute infection fulfilled the clinical surveillance definition used to detect cases during the outbreak. In conclusion, hospital exposure was not associated to increased risk of B19 infection among medical students. Medical students may be at increased risk for acquiring and transmitting B19 infection during outbreaks.