bluuebunny/crossref_metadata_2025 huggingface dataset:
Essential role of CD91 in re-presentation of gp96-chaperoned peptides
Authors: Binder Robert J. , Srivastava Pramod K.
Published: April 2004

Heat shock proteins (HSPs) such as gp96 are released from cells as a result of necrotic cell death. The ability of endogenous HSP–peptide complexes to elicit antigen-specific T cells requires representation of the chaperoned peptides by antigen-presenting cells. Re-presentation requires the uptake of HSP–peptide complexes through a receptor, suggested to be the low-density lipoprotein receptor-related protein or CD91. We have used short interfering RNA for CD91 to show that, as antigen-presenting cells lose expression of CD91, their re-presenting ability undergoes a corresponding and dramatic decline. Furthermore, as the cells recover from extinction of CD91 expression, they regain the ability to re-present peptides. The ability of cells to bind α2macroglobulin, a previously known CD91 ligand, or HSP gp96, and their ability to process peptides chaperoned by α2macroglobulin, undergo identical variations. These results have been obtained from studiesin vitroand from an assay that measures re-presentationin vivo. In additional studiesin vivo, protective tumor immunity elicited by tumor-derived gp96–peptide complexes is shown to be abrogated by anti-CD91 antisera. These studies show that CD91 is essential for re-presentation of gp96-chaperoned peptides by MHC molecules and have an important bearing on the mechanism of immunogenicity of necrotic cells.
Structural elements responsible for conversion of streptavidin to a pseudoenzyme
Authors: Eisenberg-Domovich Yael , Pazy Yael , Nir Orit , Raboy Bilha , Bayer Edward A. , Wilchek Meir , Livnah Oded
Published: April 2004

Avidin enhances the hydrolysis of biotinylp-nitrophenyl ester (BNP) under mild alkaline conditions, whereas streptavidin prevents hydrolysis of BNP up to pH 12. Recently, we imposed hydrolytic activity on streptavidin by rational mutagenesis, based on the molecular elements responsible for the hydrolysis by avidin. Three mutants were designed, whereby the desired features, the distinctive L124R point mutation (M1), the L3,4 loop replacement (M2), and the combined mutation (M3), were transferred from avidin to streptavidin. The crystal structures of the mutants, in complex with biotinylp-nitroanilide (BNA), the stable amide analogue of BNP, were determined. The results demonstrate that the point mutation alone has little effect on hydrolysis, and BNA exhibits a conformation similar to that of streptavidin. Substitution of a lengthier L3,4 loop (from avidin to streptavidin), resulted in an open conformation, thus exposing the ligand to solvent. Moreover, the amide bond of BNA was flipped relative to that of the streptavidin and M1 complexes, thus deflecting the nitro group toward Lys-121. Consequently, the leaving group potential of the nitrophenyl group of BNP is increased, and M2 hydrolyzes BNP at pH values >8.5. To better emulate the hydrolytic potential of avidin, M3 was required. The combination of loop replacement and point mutation served to further increase the leaving group potential by interaction of the nitro group with Arg-124 and Lys-121. The information derived from this study may provide insight into the design of enzymes and transfer of desired properties among homologous proteins.
CD28 delivers a unique signal leading to the selective recruitment of RelA and p52 NF-κB subunits onIL-8andBcl-xLgene promoters
Authors: Marinari Barbara , Costanzo Antonio , Marzano Valeria , Piccolella Enza , Tuosto Loretta
Published: April 2004

CD28 is one of the most important costimulatory receptors necessary for full T lymphocyte activation. The CD28 receptor can enhance T cell antigen receptor (TCR) signals, as well as deliver independent signals. Indeed, CD28 engagement by B7 can generate TCR-independent signals leading to IκB kinase and NF-κB activation. Here we demonstrate that the TCR-independent CD28 signal leads to the selective transcription of survival (Bcl-xL) and inflammatory (IL-8andB cell activation factor, but not proliferative (IL-2), genes, in a NF-κB-dependent manner. CD28-stimulated T cells actively secrete IL-8, and Bcl-xL up-regulation protects T cells from radiation-induced apoptosis. The transcription of CD28-induced genes is mediated by the specific recruitment of RelA and p52 NF-κB subunits to target promoters. In contrast, p50 and c-Rel, which preferentially bind NF-κB sites on theIL-2gene promoter after anti-CD3 stimulation, are not involved. Thus, we identify CD28 as a key regulator of genes important for both survival and inflammation.
The crystal structure of filamentous hemagglutinin secretion domain and its implications for the two-partner secretion pathway
Authors: Clantin Bernard , Hodak Hélène , Willery Eve , Locht Camille , Jacob-Dubuisson Françoise , Villeret Vincent
Published: April 2004

Filamentous hemagglutinin (FHA), the major 230-kDa adhesin of the whooping cough agent
Bordetella pertussis
, is one of the most efficiently secreted proteins in Gram-negative bacteria. FHA is secreted by means of the two-partner secretion (TPS) pathway. Several important human, animal, and plant pathogens also secrete adhesins and other virulence factors by using this mode of secretion. A TPS system is composed of two separate proteins, with TpsA the secreted protein and TpsB its associated specific outermembrane transporter. All TPS-secreted proteins contain a distinctive N-proximal module essential for secretion, the TPS domain. We report here the 1.7- Å structure of a functionally secreted 30-kDa N-terminal fragment of FHA. It reveals that the TPS domain folds into a β-helix, with three extrahelical motifs, a β-hairpin, a four-stranded β-sheet, and an N-terminal capping, mostly formed by the nonconserved regions of the TPS domain. The structure thus explains why the TPS domain is able to initiate folding of the β-helical motifs that form the central domain of the adhesin, because it is itself a β-helical scaffold. It also contains less conserved extrahelical regions most likely involved in specific properties, such as the recognition of the outer-membrane transporter. This structure is representative of the TPS domains found so far in >100 secreted proteins from pathogenic bacteria. It also provides a mechanistic insight into how protein folding may be linked to secretion in the TPS pathway.
A previously undescribed coronavirus associated with respiratory disease in humans
Authors: Fouchier Ron A. M. , Hartwig Nico G. , Bestebroer Theo M. , Niemeyer Berend , de Jong Jan C. , Simon James H. , Osterhaus Albert D. M. E.
Published: April 2004

The etiology of acute respiratory tract illnesses is sometimes unclear due to limitations of diagnostic tests or the existence of as-yet-unidentified pathogens. Here we describe the identification and characterization of a not previously recognized coronavirus obtained from an 8-mo-old boy suffering from pneumonia. This coronavirus replicated efficiently in tertiary monkey kidney cells and Vero cells, in contrast to human coronaviruses (HCoV) 229E and OC43. The entire cDNA genome sequence of the previously undescribed coronavirus was determined, revealing that it is most closely related to porcine epidemic diarrhea virus and HCoV 229E. The maximum amino acid sequence identity between ORFs of the newly discovered coronavirus and related group 1 coronaviruses ranged from 43% to 67%. Real-time RT-PCR assays were designed to test for the prevalence of the previously undescribed coronavirus in humans. Using these tests, the virus was detected in four of 139 individuals (3%) who were suffering from respiratory illness with unknown etiology. All four patients suffered from fever, runny nose, and dry cough, and all four had underlying or additional morbidity. Our data will enable the development of diagnostic tests to study the prevalence and clinical impact of this virus in humans in more detail. Moreover, it will be important to discriminate this previously undescribed coronavirus from HCoV 229E and OC43 and the severe acute respiratory syndrome coronavirus.
Brain networks underlying human timing behavior are influenced by prior context
Authors: Jantzen Kelly J. , Steinberg Fred L. , Kelso J. A. Scott
Published: April 2004

The continuation paradigm is often used to investigate the behavioral and neural mechanisms of timing. Typically, a movement rate is established by pacing with a metronome. Then, the metronome is turned off and the subject continues at the established rate. Performance during continuation is assumed to be based on internal timing mechanisms. Here, we investigated the degree to which the neural activity underlying time representation depends on the initial pacing context, that is, whether pacing was established by moving in-phase (the usual procedure) or anti-phase (syncopation) with an auditory metronome. Functional MRI was measured from 14 subjects during four conditions: synchronized pacing, synchronized continuation, syncopated pacing, and syncopated continuation. In general, movements were timed consistently for all four conditions. However, a much broader network of activation was engaged during syncopation compared with synchronization, including increased activation in supplementary motor area, left premotor area, right thalamus, bilateral inferior frontal gyrus, and cerebellum. No differences were found when comparing continuation with the preceding pacing phase except for decreased activity in auditory-related regions due to the absence of the metronome. These results demonstrate that the cortical and subcortical areas recruited to support a simple motor timing task depend crucially on the method used to establish the temporal reference. Thus, the neural mechanisms underlying time and timing are highly flexible, reflecting the context in which the timing is established.
Activation of the prefrontal cortex in the human visual aesthetic perception
Authors: Cela-Conde Camilo J. , Marty Gisèle , Maestú Fernando , Ortiz Tomás , Munar Enric , Fernández Alberto , Roca Miquel , Rosselló Jaume , Quesney Felipe
Published: April 2004

Visual aesthetic perception (“aesthetics”) or the capacity to visually perceive a particular attribute added to other features of objects, such as form, color, and movement, was fixed during human evolutionary lineage as a trait not shared with any great ape. Although prefrontal brain expansion is mentioned as responsible for the appearance of such human trait, no current knowledge exists on the role of prefrontal areas in the aesthetic perception. The visual brain consists of “several parallel multistage processing systems, each specialized in a given task such as, color or motion” [Bartels, A. & Zeki, S. (1999)
Proc. R. Soc. London Ser. B
265, 2327–2332]. Here we report the results of an experiment carried out with magnetoencephalography which shows that the prefrontal area is selectively activated in humans during the perception of objects qualified as “beautiful” by the participants. Therefore, aesthetics can be hypothetically considered as an attribute perceived by means of a particular brain processing system, in which the prefrontal cortex seems to play a key role.
Targeting and crossing of the human maternofetal barrier byListeria monocytogenes: Role of internalin interaction with trophoblast E-cadherin
Authors: Lecuit Marc , Nelson D. Michael , Smith Steve D. , Khun Huot , Huerre Michel , Vacher-Lavenu Marie-Cécile , Gordon Jeffrey I. , Cossart Pascale
Published: April 2004

Listeria monocytogenesproduces severe fetoplacental infections in humans. How it targets and crosses the maternofetal barrier is unknown. We used immunohistochemistry to examine the location ofL. monocytogenesin placental and amniotic tissue samples obtained from women with fetoplacental listeriosis. The results raised the possibility thatL. monocytogenescrosses the maternofetal barrier through the villous syncytiotrophoblast, with secondary infection occurring via the amniotic epithelium. Because epidemiological studies indicate that the bacterial surface protein, internalin (InlA), may play a role in human fetoplacental listeriosis, we investigated the cellular patterns of expression of its host receptor, E-cadherin, at the maternofetal interface. E-cadherin was found on the basal and apical plasma membranes of syncytiotrophoblasts and in villous cytotrophoblasts. Established trophoblastic cell lines, primary trophoblast cultures, and placental villous explants were each exposed to isogenic InlA+ or InlA- strains ofL. monocytogenes,and toL. innocuaexpressing or not InlA. Quantitative assays of cellular invasion demonstrated that bacterial entry into syncytiotrophoblasts occurs via the apical membrane in an InlA–E-cadherin dependent manner. In human placental villous explants, bacterial invasion of the syncytiotrophoblast barrier and underlying villous tissue and subsequent replication produces histopathological lesions that mimic those seen in placentas of women with listeriosis. Thus, the InlA–E-cadherin interaction that plays a key role in the crossing of the intestinal barrier in humans is also exploited byL. monocytogenesto target and cross the placental barrier. Such a ligand–receptor interaction allowing a pathogen to specifically cross the placental villous trophoblast barrier has not been reported previously.
Identification of Cryptic MHC I–restricted Epitopes Encoded by HIV-1 Alternative Reading Frames
Authors: Cardinaud Sylvain , Moris Arnaud , Février Michèle , Rohrlich Pierre-Simon , Weiss Laurence , Langlade-Demoyen Pierre , Lemonnier François A. , Schwartz Olivier , Habel André
Published: April 2004

Human immunodeficiency virus (HIV) 1 major histocompatibility complex (MHC) I–restricted epitopes are widely believed to be derived from viral proteins encoded by primary open reading frames. However, the HIV-1 genome contains alternative reading frames (ARFs) potentially encoding small polypeptides. We have identified a panel of epitopes encoded by ARFs within the gag, pol, and env genes. The corresponding epitopic peptides were immunogenic in mice humanized for MHC-I molecules. In addition, cytotoxic T lymphocytes recognizing these epitopes were found in HIV-infected patients. These results reveal the existence of atypical mechanisms of HIV-1 epitope generation. They indicate that the repertoire of epitopes recognized by the cellular anti–HIV-1 immune response is broader than initially thought. This should be taken into account when designing vaccine strategies aimed at activating these responses.
Transgenic Expression of Decoy Receptor 3 Protects Islets from Spontaneous and Chemical-induced Autoimmune Destruction in Nonobese Diabetic Mice
Authors: Sung Hsiang-Hsuan , Juang Jyuhn-Huarng , Lin Yu-Chun , Kuo Chien-Hung , Hung Jung-Tung , Chen An , Chang Der-Ming , Chang Sun-Yran , Hsieh Shie-Liang , Sytwu Huey-Kang
Published: April 2004

Decoy receptor 3 (DCR3) halts both Fas ligand– and LIGHT-induced cell deaths, which are required for pancreatic β cell damage in autoimmune diabetes. To directly investigate the therapeutic potential of DCR3 in preventing this disease, we generated transgenic nonobese diabetic mice, which overexpressed DCR3 in β cells. Transgenic DCR3 protected mice from autoimmune and cyclophosphamide-induced diabetes in a dose-dependent manner and significantly reduced the severity of insulitis. Local expression of the transgene did not alter the diabetogenic properties of systemic lymphocytes or the development of T helper 1 or T regulatory cells. The transgenic islets had a higher transplantation success rate and survived for longer than wild-type islets. We have demonstrated for the first time that the immune-evasion function of DCR3 inhibits autoimmunity and that genetic manipulation of grafts may improve the success and survival of islet transplants.
Differential Trafficking of Transforming Growth Factor-β Receptors and Ligand in Polarized Epithelial Cells
Authors: Murphy S. J. , Doré J. J. E. , Edens M. , Coffey R. J. , Barnard J. A. , Mitchell H. , Wilkes M. , Leof E. B.
Published: April 2004

Epithelial cells in vivo form tight cell-cell associations that spatially separate distinct apical and basolateral domains. These domains provide discrete cellular processes essential for proper tissue and organ development. Using confocal imaging and selective plasma membrane domain activation, the type I and type II transforming growth factor-β (TGFβ) receptors were found to be localized specifically at the basolateral surfaces of polarized Madin-Darby canine kidney (MDCK) cells. Receptors concentrated predominantly at the lateral sites of cell-cell contact, adjacent to the gap junctional complex. Cytoplasmic domain truncations for each receptor resulted in the loss of specific lateral domain targeting and dispersion to both the apical and basal domains. Whereas receptors concentrate basolaterally in regions of direct cell-cell contact in nonpolarized MDCK cell monolayers, receptor staining was absent from areas of noncell contact. In contrast to the defined basolateral polarity observed for the TGFβ receptor complex, TGFβ ligand secretion was found to be from the apical surfaces. Confocal imaging of MDCK cells with an antibody to TGFβ1 confirmed a predominant apical localization, with a stark absence at the basal membrane. These findings indicate that cell adhesion regulates the localization of TGFβ receptors in polarized epithelial cultures and that the response to TGFβ is dependent upon the spatial distribution and secretion of TGFβ receptors and ligand, respectively.
ArrayNorm: comprehensive normalization and analysis of microarray data
Authors: Pieler R. , Sanchez-Cabo F. , Hackl H. , Thallinger G. G. , Trajanoski Z.
Published: April 2004

Summary: ArrayNorm is a user-friendly, versatile and platform-independent Java application for the visualization, normalization and analysis of two-color microarray data. A variety of normalization options were implemented to remove the systematic and random errors in the data, taking into account the experimental design and the particularities of every slide. In addition, ArrayNorm provides a module for statistical identification of genes with significant changes in expression.

Availability: The package is freely available for academic and non-profit institutions from http://genome.tugraz.at
A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor
Authors: Brooks D. J. , Fresco J. R. , Singh M.
Published: April 2004

Motivation: Knowledge of how proteomic amino acid composition has changed over time is important for constructing realistic models of protein evolution and increasing our understanding of molecular evolutionary history. The proteomic amino acid composition of the Last Universal Ancestor (LUA) of life is of particular interest, since that might provide insight into the early evolution of proteins and the nature of the LUA itself.

Results: We introduce a method to estimate ancestral amino acid composition that is based on expectation–maximization. On simulated data, the approach was found to be very effective in estimating ancestral amino acid composition, with accuracy improving as the number of residues in the dataset was increased. The method was then used to infer the amino acid composition of a set of proteins in the LUA. In general, as compared with the modern protein set, LUA proteins were found to be richer in amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those believed to have been unavailable or scarce. Additionally, we found the inferred amino acid composition of this protein set in the LUA to be more similar to the observed composition of the same set in extant thermophilic species than in extant mesophilic species, supporting the idea that the LUA lived in a thermophilic environment.

Availability: The program is available at http://compbio.cs.princeton.edu/ancestralaa
POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins
Authors: Porollo Aleksey A. , Adamczak Rafal , Meller Jaroslaw
Published: April 2004

Summary: The POLYVIEW visualization server can be used to generate protein sequence annotations, including secondary structures, relative solvent accessibilities, functional motifs and polymorphic sites. Two-dimensional graphical representations in a customizable format may be generated for both known protein structures and predictions obtained using protein structure prediction servers. POLYVIEW may be used for automated generation of pictures with structural and functional annotations for publications and proteomic on-line resources.

Availability:  http://polyview.cchmc.org
Pedro: a configurable data entry tool for XML
Authors: Garwood Kevin L. , Taylor Chris F. , Runte Kai J. , Brass Andy , Oliver Stephen G. , Paton Norman W.
Published: April 2004

Summary: Pedro is a Java™ application that dynamically generates data entry forms for data models expressed in XML Schema, producing XML data files that validate against this schema. The software uses an intuitive tree-based navigation system, can supply context-sensitive help to users and features a sophisticated interface for populating data fields with terms from controlled vocabularies. The software also has the ability to import records from tab delimited text files and features various validation routines.

Availability: The application, source code, example models from several domains and tutorials can be downloaded from http://pedro.man.ac.uk/
Combining pattern discovery and discriminant analysis to predict gene co-regulation
Authors: Simonis N. , Wodak S. J. , Cohen G. N. , van Helden J.
Published: April 2004

Motivation: Several pattern discovery methods have been proposed to detect over-represented motifs in upstream sequences of co-regulated genes, and are for example used to predict cis-acting elements from clusters of co-expressed genes. The clusters to be analyzed are often noisy, containing a mixture of co-regulated and non-co-regulated genes. We propose a method to discriminate co-regulated from non-co-regulated genes on the basis of counts of pattern occurrences in their non-coding sequences.

Methods: String-based pattern discovery is combined with discriminant analysis to classify genes on the basis of putative regulatory motifs.

Results: The approach is evaluated by comparing the significance of patterns detected in annotated regulons (positive control), random gene selections (negative control) and high-throughput regulons (noisy data) from the yeast Saccharomyces cerevisiae. The classification is evaluated on the annotated regulons, and the robustness and rejection power is assessed with mixtures of co-regulated and random genes.

Supplementary information:  http://rsat.ulb.ac.be/rsat/
The PDB-Preview database: a repository of in-silico models of ‘on-hold’ PDB entries
Authors: Fischer Daniel , Paś Jakub , Rychlewski Leszek
Published: April 2004

Summary: The PDB-Preview database is a dynamic web repository of in-silico predicted three-dimensional (3D) models of experimentally determined structures that are deposited into the PDB but are not yet publicly released, and are kept ‘on-hold’. The PDB-Preview database is automatically generated on a weekly basis by the bioinfo.pl meta-server, which uses top-of-the-line fold-recognition methods. The PDB-Preview provides biologists with preliminary fold assignments well before the experimentally determined 3D structures are released.

Availability:  http://bioinfo.pl/PDB-Preview/
pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos
Authors: Stathopoulos Angelike , Tam Bergin , Ronshaugen Matthew , Frasch Manfred , Levine Michael
Published: April 2004

The Heartless (Htl) FGF receptor is required for the differentiation of a variety of mesodermal tissues in the Drosophila embryo, yet its ligand is not known. Here we identify two new FGF genes, thisbe (ths) and pyramus (pyr), which probably encode the elusive ligands for this receptor. The two genes exhibit dynamic patterns of expression in epithelial tissues adjacent to Htl-expressing mesoderm derivatives, including the neurogenic ectoderm, stomadeum, and hindgut. Embryos that lack ths+ and pyr+ exhibit defects related to those seen in htl mutants, including delayed mesodermal migration during gastrulation and a loss of cardiac tissues and hindgut musculature. The misexpression of Ths in wild-type and mutant embryos suggests that FGF signaling is required for both cell migration and the transcriptional induction of cardiac gene expression. The characterization of htl and ths regulatory DNAs indicates that high levels of the maternal Dorsal gradient directly activate htl expression, whereas low levels activate ths. It is therefore possible to describe FGF signaling and other aspects of gastrulation as a direct manifestation of discrete threshold readouts of the Dorsal gradient.
Conversion of neurons and glia to external-cell fates in the external sensory organs of Drosophila hamlet mutants by a cousin-cousin cell-type respecification
Authors: Moore Adrian W. , Roegiers Fabrice , Jan Lily Y. , Jan Yuh-Nung
Published: April 2004

The Drosophila external sensory organ forms in a lineage elaborating from a single precursor cell via a stereotypical series of asymmetric divisions. HAMLET transcription factor expression demarcates the lineage branch that generates two internal cell types, the external sensory neuron and thecogen. In HAMLET mutant organs, these internal cells are converted to external cells via an unprecedented cousin-cousin cell-fate respecification event. Conversely, ectopic HAMLET expression in the external cell branch leads to internal cell production. The fate-determining signals NOTCH and PAX2 act at multiple stages of lineage elaboration and HAMLET acts to modulate their activity in a branch-specific manner.
Conversion of myoblasts to physiologically active neuronal phenotype
Authors: Watanabe Yumi , Kameoka Sei , Gopalakrishnan Vidya , Aldape Kenneth D. , Pan Zhizhong Z. , Lang Frederick F. , Majumder Sadhan
Published: April 2004

Repressor element 1 (RE1)-silencing transcription factor (REST)/neuron-restrictive silencer factor (NRSF) can repress several terminal neuronal differentiation genes by binding to a specific DNA sequence (RE1/neuron-restrictive silencer element [NRSE]) present in their regulatory regions. REST-VP16 binds to the same RE1/NRSE, but activates these REST/NRSF target genes. However, it is unclear whether REST-VP16 expression is sufficient to cause formation of functional neurons either from neural stem cells or from heterologous stem cells. Here we show that the expression of REST-VP16 in myoblasts grown under muscle differentiation conditions blocked entry into the muscle differentiation pathway, countered endogenous REST/NRSF-dependent repression, activated the REST/NRSF target genes, and, surprisingly, activated other neuronal differentiation genes and converted the myoblasts to a physiologically active neuronal phenotype. Furthermore, in vitro differentiated neurons produced by REST-VP16-expressing myoblasts, when injected into mouse brain, survived, incorporated into the normal brain, and did not form tumors. This is the first instance in which myoblasts were converted to a neuronal phenotype. Our results suggest that direct activation of REST/NRSF target genes with a single transgene, REST-VP16, is sufficient to activate other terminal neuronal differentiation genes and to override the muscle differentiation pathways, and they suggest that this approach provides an efficient way of triggering neuronal differentiation in myoblasts and possibly other stem cells.
Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers
Authors: Kho Alvin T. , Zhao Qing , Cai Zhaohui , Butte Atul J. , Kim John Y.H. , Pomeroy Scott L. , Rowitch David H. , Kohane Isaac S.
Published: April 2004

Identification of common mechanisms underlying organ development and primary tumor formation should yield new insights into tumor biology and facilitate the generation of relevant cancer models. We have developed a novel method to project the gene expression profiles of medulloblastomas (MBs)—human cerebellar tumors—onto a mouse cerebellar development sequence: postnatal days 1-60 (P1-P60). Genomically, human medulloblastomas were closest to mouse P1-P10 cerebella, and normal human cerebella were closest to mouse P30-P60 cerebella. Furthermore, metastatic MBs were highly associated with mouse P5 cerebella, suggesting that a clinically distinct subset of tumors is identifiable by molecular similarity to a precise developmental stage. Genewise, down- and up-regulated MB genes segregate to late and early stages of development, respectively. Comparable results for human lung cancer vis-a-vis the developing mouse lung suggest the generalizability of this multiscalar developmental perspective on tumor biology. Our findings indicate both a recapitulation of tissue-specific developmental programs in diverse solid tumors and the utility of tumor characterization on the developmental time axis for identifying novel aspects of clinical and biological behavior.
Phosphorylation of eIF4E by Mnk-1 enhances HSV-1 translation and replication in quiescent cells
Authors: Walsh Derek , Mohr Ian
Published: April 2004

Although the activity of the translation initiation factor eIF4F is regulated in part by translational repressors (4E-BPs) that prevent incorporation of eIF4E, the cap-binding protein, into the initiation complex, the contribution of eIF4E phosphorylation to translational control remains controversial. Here, we demonstrate that the herpes simplex virus-1 (HSV-1) ICP0 gene product, a multifunctional transactivator of viral gene expression with ubiquitin E3 ligase activity that is important for vegetative replication and reactivation of latent infections, is required to stimulate phosphorylation of eIF4E as well as 4E-BP1, and promote assembly of eIF4F complexes in infected cells. Furthermore, 4E-BP1 is degraded by the proteasome in an ICP0-dependent manner, establishing that the proteasome can control 4E-BP1 steady-state levels. Preventing eIF4E phosphorylation by inhibiting the eIF4E kinase mnk-1 dramatically reduced viral replication and the translation of viral polypeptides in quiescent cells, providing the first evidence that phosphorylation of eIF4E by mnk-1 is critical for viral protein synthesis and replication. Thus, in marked contrast to many viruses that inactivate eIF4F, HSV-1 stimulates eIF4F complex assembly in quiescent, differentiated cells; moreover, this is important for viral replication, and may be crucial for HSV-1 to initiate its productive growth cycle in resting cells, such as latently infected neurons.
Palmitoylation is required for the production of a soluble multimeric Hedgehog protein complex and long-range signaling in vertebrates
Authors: Chen Miao-Hsueh , Li Ya-Jun , Kawakami Takatoshi , Xu Shan-Mei , Chuang Pao-Tien
Published: April 2004

Hedgehog (Hh) signaling plays a major role in multiple aspects of embryonic development. A key issue in Hh signaling is to elucidate the molecular mechanism by which a Hh protein morphogen gradient is formed despite its membrane association. In this study, we used a combination of genetic, cellular, and biochemical approaches to address the role of lipid modifications in long-range vertebrate Hh signaling. Our molecular analysis of knockout mice deficient in Skn, the murine homolog of the Drosophila ski gene, which catalyzes Hh palmitoylation, and gene-targeted mice producing a nonpalmitoylated form of Shh indicates that Hh palmitoylation is essential for its activity as well as the generation of a protein gradient in the developing embryos. Furthermore, our biochemical data show that Hh lipid modifications are required for producing a soluble multimeric protein complex, which constitutes the major active component for Hh signaling. These results suggest that soluble Hh multimeric complex travels in the morphogenetic field to activate Hh signaling in distant Hh-responsive cells.
Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1
Authors: Doi Kazuyuki , Izawa Takeshi , Fuse Takuichi , Yamanouchi Utako , Kubo Takahiko , Shimatani Zenpei , Yano Masahiro , Yoshimura Atsushi
Published: April 2004

Two evolutionarily distant plant species, rice (Oryza sativa L.), a short-day (SD) plant, and Arabidopsis thaliana, a long-day plant, share a conserved genetic network controlling photoperiodic flowering. The orthologous floral regulators—rice Heading date 1 (Hd1) and Arabidopsis CONSTANS (CO)—integrate circadian clock and external light signals into mRNA expression of the FLOWERING LOCUS T (FT) group floral inducer. Here, we report that the rice Early heading date 1 (Ehd1) gene, which confers SD promotion of flowering in the absence of a functional allele of Hd1, encodes a B-type response regulator that might not have an ortholog in the Arabidopsis genome. Ehd1 mRNA was induced by 1-wk SD treatment, and Ehd1 may promote flowering by inducing FT-like gene expression only under SD conditions. Microarray analysis further revealed a few MADS box genes downstream of Ehd1. Our results indicate that a novel two-component signaling cascade is integrated into the conserved pathway in the photoperiodic control of flowering in rice.
Foxm1b transcription factor is essential for development of hepatocellular carcinomas and is negatively regulated by the p19ARF tumor suppressor
Authors: Kalinichenko Vladimir V. , Major Michael L. , Wang Xinhe , Petrovic Vladimir , Kuechle Joseph , Yoder Helena M. , Dennewitz Margaret B. , Shin Brian , Datta Abhishek , Raychaudhuri Pradip , Costa Robert H.
Published: April 2004

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide. Here, we provide evidence that the Forkhead Box (Fox) m1b (Foxm1b or Foxm1) transcription factor is essential for the development of HCC. Conditionally deleted Foxm1b mouse hepatocytes fail to proliferate and are highly resistant to developing HCC in response to a Diethylnitrosamine (DEN)/Phenobarbital (PB) liver tumor-induction protocol. The mechanism of resistance to HCC development is associated with nuclear accumulation of the cell cycle inhibitor p27Kip1 protein and reduced expression of the Cdk1-activator Cdc25B phosphatase. We showed that the Foxm1b transcription factor is a novel inhibitory target of the p19ARF tumor suppressor. Furthermore, we demonstrated that conditional overexpression of Foxm1b protein in osteosarcoma U2OS cells greatly enhances anchorage-independent growth of cell colonies on soft agar. A p19ARF 26–44 peptide containing nine D-Arg to enhance cellular uptake of the peptide was sufficient to significantly reduce both Foxm1b transcriptional activity and Foxm1b-induced growth of U2OS cell colonies on soft agar. These results suggest that this (D-Arg)9-p19ARF 26–44 peptide is a potential therapeutic inhibitor of Foxm1b function during cellular transformation. Our studies demonstrate that the Foxm1b transcription factor is required for proliferative expansion during tumor progression and constitutes a potential new target for therapy of human HCC tumors.
Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain
Authors: Paul Ralf , Weiser Stefan , Amiot Nicholas C. , Chan Carmen , Schirmer Tilman , Giese Bernd , Jenal Urs
Published: April 2004

Pole development is coordinated with the Caulobacter crescentus cell cycle by two-component signaling proteins. We show that an unusual response regulator, PleD, is required for polar differentiation and is sequestered to the cell pole only when it is activated by phosphorylation. Dynamic localization of PleD to the cell pole provides a mechanism to temporally and spatially control the signaling output of PleD during development. Targeting of PleD to the cell pole is coupled to the activation of a C-terminal guanylate cyclase domain, which catalyzes the synthesis of cyclic di-guanosine monophosphate. We propose that the local action of this novel-type guanylate cyclase might constitute a general regulatory principle in bacterial growth and development.
Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice
Authors: Ma Jianxin , Devos Katrien M. , Bennetzen Jeffrey L.
Published: April 2004

We initially analyzed 11 families of low- and middle-copy-number long terminal repeat (LTR) retrotransposons in rice to determine how their structures have diverged from their predicted ancestral forms. These elements, many highly fragmented, were identified on the basis of sequence homology and structural characteristics. The 11 families, totaling 1000 elements, have copy numbers ranging from 1 to 278. Less than one-quarter of these elements are intact, whereas the remaining are solo LTRs and variously truncated fragments. We also analyzed two highly repetitive families (Osr8 and Osr30) of LTR retrotransposons and observed the same results. Our data indicate that unequal homologous recombination and illegitimate recombination are primarily responsible for LTR-retrotransposon removal. Further analysis suggests that most of the detectable LTR retrotransposons in rice inserted less than 8 million years ago, and have now lost over two-thirds of their encoded sequences. Hence, we predict that the half-life of LTR-retrotransposon sequences in rice is less than 6 million years. Moreover, our data demonstrate that at least 22% (97 Mb) of the current rice genome is comprised of LTR-retrotransposon sequences, and that more than 190 Mb of LTR-retrotransposon sequences have been deleted from the rice genome in the last 8 million years.
Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies
Authors: Zhang Kui , Qin Zhaohui S. , Liu Jun S. , Chen Ting , Waterman Michael S. , Sun Fengzhu
Published: April 2004

Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs) is sufficient to capture most of the haplotype structure of the human genome. In this paper, we develop a method to partition haplotypes into blocks and to identify tag SNPs based on genotype data by combining a dynamic programming algorithm for haplotype block partitioning and tag SNP selection based on haplotype data with a variation of the expectation maximization (EM) algorithm for haplotype inference. We assess the effects of using either haplotype or genotype data in haplotype block identification and tag SNP selection as a function of several factors, including sample size, density or number of SNPs studied, allele frequencies, fraction of missing data, and genotyping error rate, using extensive simulations. We find that a modest number of haplotype or genotype samples will result in consistent block partitions and tag SNP selection. The power of association studies based on tag SNPs using genotype data is similar to that using haplotype data.
Decoding Randomly Ordered DNA Arrays
Authors: Gunderson Kevin L. , Kruglyak Semyon , Graige Michael S. , Garcia Francisco , Kermani Bahram G. , Zhao Chanfeng , Che Diping , Dickinson Todd , Wickham Eliza , Bierle Jim , Doucet Dennis , Milewski Monika , Yang Robert , Siegmund Chris , Haas Juergen , Zhou Lixin , Oliphant Arnold , Fan Jian-Bing , Barnard Steven , Chee Mark S.
Published: April 2004

We have developed a simple and efficient algorithm to identify each member of a large collection of DNA-linked objects through the use of hybridization, and have applied it to the manufacture of randomly assembled arrays of beads in wells. Once the algorithm has been used to determine the identity of each bead, the microarray can be used in a wide variety of applications, including single nucleotide polymorphism genotyping and gene expression profiling. The algorithm requires only a few labels and several sequential hybridizations to identify thousands of different DNA sequences with great accuracy. We have decoded tens of thousands of arrays, each with 1520 sequences represented at ∼30-fold redundancy by up to ∼50,000 beads, with a median error rate of <1 × 10-4 per bead. The approach makes use of error checking codes and provides, for the first time, a direct functional quality control of every element of each array that is manufactured. The algorithm can be applied to any spatially fixed collection of objects or molecules that are associated with specific DNA sequences.
Spectroscopic characterization of heat‐induced nonnative β‐lactoglobulin monomers
Authors: Croguennec Thomas , Mollé Daniel , Mehra Raj , Bouhallab Saïd
Published: April 2004

Previous studies have shown that two altered monomeric species were formed in the early steps of thermal denaturation of bovine β‐lactoglobulin (β‐lg), the well‐known Cys121‐exposed intermediate (Mcys121), and a new, stable monomer with exposed nonnative Cys119 (Mcys119). In this study, circular dichroism and fluorescence spectroscopies were used to characterize the structural features of these molecules. The structural characteristics of MCys121 after heating and cooling cycles are similar to those of native β‐lg. In contrast, Mcys119 monomer exhibits some characteristics of the well‐known molten‐globule state. Combined with other published data, these results indicate that heating induces at least two molten globule‐like states of β‐lg, a highly reactive Mcys121 that returns to native state after cooling, and a less‐reactive Mcys119 that is trapped and stabilized in a molten globule‐like state by nonnative disulfide bond.
Structural stability and heat‐induced conformational change of two complement inhibitors: C4b‐binding protein and factor H
Authors: Kask Lena , Villoutreix Bruno O. , Steen Mårten , Ramesh Bala , Dahlbäck Björn , Blom Anna M.
Published: April 2004

The complement inhibitors C4b‐binding protein (C4BP) and factor H (FH) both consist of complement control protein (CCP) domains. Here we examined the secondary structure of both proteins by circular dichroism and Fourier‐transform infrared technique at temperatures ranging from 30°C–90°C. We found that predominantly β‐sheet structure of both proteins was stable up to 70°C, and that a reversible conformational change toward α‐helix was apparent at temperatures ranging from 70°C to 90°C. The ability of both proteins to inhibit complement was not impaired after incubation at 95°C, exposure to extreme pH conditions, and storage at room temperature for several months. Similar remarkable stability was previously observed for vaccinia virus control protein (VCP), which is also composed of CCP domains; it therefore seems to be a general property of CCP‐containing proteins. A typical CCP domain has a hydrophobic core, which is wrapped in β‐sheets and stabilized by two disulphide bridges. How the CCP domains tolerate harsh conditions is unclear, but it could be due to a combination of high content of prolines, hydrophobic residues, and the presence of two disulphide bridges within each domain. These findings are of interest because CCP‐containing complement inhibitors have been proposed as clinical agents to be used to control unwanted complement activation that contributes to many diseases.
Effect of heat shock on the chilling sensitivity of trichomes and petioles of African violet (Saintpaulia ionantha)
Authors: Saltveit Mikal E. , Hepler Peter K.
Published: April 2004

Chilling at 6°C caused an immediate cessation of protoplasmic streaming in trichomes from African violets (Saintpaulia ionantha), and a slower aggregation of chloroplasts in the cells. Streaming slowly recovered upon warming to 20°C, reaching fairly stable rates after 4, 15, 25 and 35 min for tissue chilled for 2 min and for 2, 14 and 24 h, respectively. The rate of ion leakage from excised petioles into an isotonic 0.2 M mannitol solution increased after 12 h of chilling and reached a maximum after 3 days of chilling. A heat shock at 45°C for 6 min reduced chilling‐induced rates of ion leakage from excised 1‐cm petiole segments by over 50%, namely to levels near that from non‐chilled control tissue. Heat‐shock treatments themselves had no effect on the rate of ion leakage from non‐chilled petiole segments. Protoplasmic streaming was stopped by 1 min of heat shock at 45°C, but slowly recovered to normal levels after about 30 min Chloroplasts aggregation was prevented by a 1 or 2 min 45°C heat‐shock treatment administered 1.5 h before chilling, but heat‐shock treatments up to 6 min only slightly delayed the reduction in protoplasmic streaming caused by chilling. Tradescantia virginiana did not exhibit symptoms associated with chilling injury in sensitive species (i.e. cessation of protoplasmic streaming in stamen hairs and increased ion leakage from leaf tissue).
Lipoxygenase activity and proline accumulation in leaves and roots of olive trees in response to drought stress
Authors: Sofo Adriano , Dichio Bartolomeo , Xiloyannis Cristos , Masia Andrea
Published: April 2004

The olive tree (Olea europaea L.) is commonly grown in the Mediterranean basin and is able to resist severe and prolonged drought. Levels of proline (PRO) and malondialdehyde (MDA), and the lipoxygenase (LOX) activity were determined in 2‐year‐old olive plants (cv. ‘Coratina’) grown in environmental conditions characterized by high temperatures and high photosynthetic photon flux density levels and gradually subjected to a controlled water deficit for 20 days. Before and during the experimental period, leaf and root samples were collected and analysed for PRO and MDA. The levels of PRO increased in parallel with the severity of drought stress in both leaves and roots. Significant increases of LOX activity and MDA content were also observed during the progressive increment of drought stress in both leaf and root tissues. Measurements of transpiration and photosynthetic rate, stomatal conductance and substomatal CO2 concentration were carried out during the experiment. The accumulation of PRO indicates a possible role of PRO in drought tolerance. The increases of MDA content and LOX activity show that the water deficit is associated with lipid peroxidation mechanisms.
Responses induced by high concentration of cadmium in Phragmites australis roots
Authors: Ederli Luisa , Reale Lara , Ferranti Francesco , Pasqualini Stefania
Published: April 2004

Cadmium is an important environmental pollutant with high toxicity to plants. We report the effects of high‐dose Cd (100 µM for 21 days) on the root apparatus of Phragmites australis plants, which are characterized by elevated water detoxification capacity and widely used in phytoremediation programmes. The examination of root sections by light and electron microscopy failed to reveal any significant cadmium‐induced structural or ultra‐structural modifications. However, histochemical localization of Cd disclosed accumulation of the metal in the parenchyma cells below the exodermis. Phytochelatins (PC) are thiol‐rich peptides whose synthesis is induced by a range of metals. Our results indicate that total PC production increases after exposure to Cd, which suggests a pivotal role for phytochelatins in the sequestration of metal. Cd treatment also induced lignin deposition and marked stimulation of root antioxidant systems, suggesting that, because of its ability to adopt different strategies against the harmful effects of cadmium, Phragmites australis is a plant with high detoxification potential.