bluuebunny/crossref_metadata_2025 huggingface dataset:
Dendritic cell preactivation impairs MHC class II presentation of vaccines and endogenous viral antigens
Authors: Young Louise J. , Wilson Nicholas S. , Schnorrer Petra , Mount Adele , Lundie Rachel J. , La Gruta Nicole L. , Crabb Brendan S. , Belz Gabrielle T. , Heath William R. , Villadangos Jose A.
Published: November 2007

When dendritic cells (DCs) encounter signals associated with infection or inflammation, they become activated and undergo maturation. Mature DCs are very efficient at presenting antigens captured in association with their activating signal but fail to present subsequently encountered antigens, at leastin vitro. Such impairment of MHC class II (MHC II) antigen presentation has generally been thought to be a consequence of down-regulation of endocytosis, so it might be expected that antigens synthesized by the DCs themselves (for instance, viral antigens) would still be presented by mature DCs. Here, we show that DCs maturedin vivocould still capture and process soluble antigens, but were unable to present peptides derived from these antigens. Furthermore, presentation of viral antigens synthesized by the DCs themselves was also severely impaired. Indeed, i.v. injection of pathogen mimics, which caused systemic DC activationin vivo, impaired the induction of CD4 T cell responses against subsequently encountered protein antigens. This immunosuppressed state could be reversed by adoptive transfer of DCs loaded exogenously with antigens, demonstrating that impairment of CD4 T cell responses was due to lack of antigen presentation rather than to overt suppression of T cell activation. The biochemical mechanism underlying this phenomenon was the down-regulation of MHC II–peptide complex formation that accompanied DC maturation. These observations have important implications for the design of prophylactic and therapeutic DC vaccines and contribute to the understanding of the mechanisms causing immunosuppression during systemic blood infections.
Function and dynamics of PKD2 in Chlamydomonas reinhardtii flagella
Authors: Huang Kaiyao , Diener Dennis R. , Mitchell Aaron , Pazour Gregory J. , Witman George B. , Rosenbaum Joel L.
Published: November 2007

To analyze the function of ciliary polycystic kidney disease 2 (PKD2) and its relationship to intraflagellar transport (IFT), we cloned the gene encoding Chlamydomonas reinhardtii PKD2 (CrPKD2), a protein with the characteristics of PKD2 family members. Three forms of this protein (210, 120, and 90 kD) were detected in whole cells; the two smaller forms are cleavage products of the 210-kD protein and were the predominant forms in flagella. In cells expressing CrPKD2–GFP, about 10% of flagellar CrPKD2–GFP was observed moving in the flagellar membrane. When IFT was blocked, fluorescence recovery after photobleaching of flagellar CrPKD2–GFP was attenuated and CrPKD2 accumulated in the flagella. Flagellar CrPKD2 increased fourfold during gametogenesis, and several CrPKD2 RNA interference strains showed defects in flagella-dependent mating. These results suggest that the CrPKD2 cation channel is involved in coupling flagellar adhesion at the beginning of mating to the increase in flagellar calcium required for subsequent steps in mating.
Proliferation-dependent and cell cycle–regulated transcription of mouse pericentric heterochromatin
Authors: Lu Junjie , Gilbert David M.
Published: November 2007

Pericentric heterochromatin transcription has been implicated in Schizosaccharomyces pombe heterochromatin assembly and maintenance. However, in mammalian systems, evidence for such transcription is inconsistent. We identify two populations of RNA polymerase II–dependent mouse γ satellite repeat sequence–derived transcripts from pericentric heterochromatin that accumulate at different times during the cell cycle. A small RNA species was synthesized exclusively during mitosis and rapidly eliminated during mitotic exit. A more abundant population of large, heterogeneous transcripts was induced late in G1 phase and their synthesis decreased during mid S phase, which is coincident with pericentric heterochromatin replication. In cells that lack the Suv39h1,2 methyltransferases responsible for H3K9 trimethylation, transcription occurs from more sites but is still cell cycle regulated. Transcription is not detected in quiescent cells and induction during G1 phase is sensitive to serum deprivation or the cyclin-dependent kinase inhibitor roscovatine. We demonstrate that mammalian pericentric heterochromatin transcription is linked to cellular proliferation. Our data also provide an explanation for inconsistencies in the detection of such transcripts in different systems.
The Tyrosine Kinase Activity of c-Src Regulates Actin Dynamics and Organization of Podosomes in Osteoclasts
Authors: Destaing Olivier , Sanjay Archana , Itzstein Cecile , Horne William C. , Toomre Derek , De Camilli Pietro , Baron Roland
Published: November 2007

Podosomes are dynamic actin-rich structures composed of a dense F-actin core surrounded by a cloud of more diffuse F-actin. Src performs one or more unique functions in osteoclasts (OCLs), and podosome belts and bone resorption are impaired in the absence of Src. Using Src−/−OCLs, we investigated the specific functions of Src in the organization and dynamics of podosomes. We found that podosome number and the podosome-associated actin cloud were decreased in Src−/−OCLs. Videomicroscopy and fluorescence recovery after photobleaching analysis revealed that the life span of Src−/−podosomes was increased fourfold and that the rate of actin flux in the core was decreased by 40%. Thus, Src regulates the formation, structure, life span, and rate of actin polymerization in podosomes and in the actin cloud. Rescue of Src−/−OCLs with Src mutants showed that both the kinase activity and either the SH2 or the SH3 binding domain are required for Src to restore normal podosome organization and dynamics. Moreover, inhibition of Src family kinase activities in Src−/−OCLs by Src inhibitors or by expressing dominant-negative SrcK295Minduced the formation of abnormal podosomes. Thus, Src is an essential regulator of podosome structure, dynamics and organization.
Formation of a Tap/NXF1 Homotypic Complex Is Mediated through the Amino-Terminal Domain of Tap and Enhances Interaction with Nucleoporins
Authors: Matzat Leah H. , Berberoglu Stephen , Lévesque Lyne
Published: November 2007

Nuclear export of mRNAs is mediated by the Tap/Nxt1 pathway. Tap moves its RNA cargo through the nuclear pore complex by direct interaction with nucleoporin phenylalanine-glycine repeats. This interaction is strengthened by the formation of a Tap/Nxt1 heterodimer. We now present evidence that Tap can form a multimeric complex with itself and with other members of the NXF family. We also show that the homotypic Tap complex can interact with both Nxt1 and nucleoporins in vitro. The region mediating this oligomerization is localized to the first 187 amino acids of Tap, which overlaps with its RNA-binding domain. Removal of this domain greatly reduces the ability of Tap to bind nucleoporins in vitro and in vivo. This is the first report showing that the Tap amino terminus modulates the interaction of Tap with nucleoporins. We speculate that this mechanism has a regulatory role for RNA export independent of RNA binding.
Distinct Roles for Two Gα–Gβ Interfaces in Cell Polarity Control by a Yeast Heterotrimeric G Protein
Authors: Strickfaden Shelly C. , Pryciak Peter M.
Published: November 2007

Saccharomyces cerevisiae mating pheromones trigger dissociation of a heterotrimeric G protein (Gαβγ) into Gα-guanosine triphosphate (GTP) and Gβγ. The Gβγ dimer regulates both mitogen-activated protein (MAP) kinase cascade signaling and cell polarization. Here, by independently activating the MAP kinase pathway, we studied the polarity role of Gβγ in isolation from its signaling role. MAP kinase signaling alone could induce cell asymmetry but not directional growth. Surprisingly, active Gβγ, either alone or with Gα-GTP, could not organize a persistent polarization axis. Instead, following pheromone gradients (chemotropism) or directional growth without pheromone gradients (de novo polarization) required an intact receptor–Gαβγ module and GTP hydrolysis by Gα. Our results indicate that chemoattractant-induced cell polarization requires continuous receptor–Gαβγ communication but not modulation of MAP kinase signaling. To explore regulation of Gβγ by Gα, we mutated Gβ residues in two structurally distinct Gα–Gβ binding interfaces. Polarity control was disrupted only by mutations in the N-terminal interface, and not the Switch interface. Incorporation of these mutations into a Gβ–Gα fusion protein, which enforces subunit proximity, revealed that Switch interface dissociation regulates signaling, whereas the N-terminal interface may govern receptor–Gαβγ coupling. These findings raise the possibility that the Gαβγ heterotrimer can function in a partially dissociated state, tethered by the N-terminal interface.
A Novel Function of Arp2p in Mediating Prk1p-specific Regulation of Actin and Endocytosis in Yeast
Authors: Jin Mingji , Cai Mingjie
Published: November 2007

The yeast protein Pan1p plays essential roles in actin cytoskeleton organization and endocytosis. It couples endocytosis with actin polymerization through its dual function in endocytic complex assembly and activation of the actin polymerization initiation complex Arp2/3p. Phosphorylation of Pan1p and other components of the endocytic complex by the kinase Prk1p leads to disassembly of the coat complex and the termination of vesicle-associated actin polymerization. A homologous kinase, Ark1p, has also been implicated in this regulatory process. In this study, we investigated the distinct roles of Prk1p and Ark1p. We found that the nonkinase domains determined the functional specificity of the two kinases. A short region located adjacent to the kinase domain unique to Prk1p was found to be required for the kinase to interact with Arp2p. Further studies demonstrated that the Prk1p-Arp2p interaction is critical for down-regulation of Pan1p. These findings reveal that, in addition to its role in the nucleation of actin polymerization, Arp2p also mediates what appears to be an auto-regulatory mechanism possibly adapted for efficient coordination of actin assembly and disassembly during endocytosis.
Moment invariants as shape recognition technique for comparing protein binding sites
Authors: Sommer Ingolf , Müller Oliver , Domingues Francisco S. , Sander Oliver , Weickert Joachim , Lengauer Thomas
Published: November 2007

Motivation: An approach for identifying similarities of protein–protein binding sites is presented. The geometric shape of a binding site is described by computing a feature vector based on moment invariants. In order to search for similarities, feature vectors of binding sites are compared. Similar feature vectors indicate binding sites with similar shapes.

Results: The approach is validated on a representative set of protein–protein binding sites, extracted from the SCOPPI database. When querying binding sites from a representative set, we search for known similarities among 2819 binding sites. A median area under the ROC curve of 0.98 is observed. For half of the queries, a similar binding site is identified among the first two of 2819 when sorting all binding sites according the proposed similarity measure. Typical examples identified by this method are analyzed and discussed. The nitrogenase iron protein-like SCOP family is clustered hierarchically according to the proposed similarity measure as a case study.

Availability: Python code is available on request from the authors.

Contact:  sommer@mpi-inf.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.
CONSORF: a consensus prediction system for prokaryotic coding sequences
Authors: Kang Sungsoo , Yang Sung-Jin , Kim Sangsoo , Bhak Jong
Published: November 2007

Summary: CONSORF is a fully automatic high-accuracy identification system that provides consensus prokaryotic CDS information. It first predicts the CDSs supported by consensus alignments. The alignments are derived from multiple genome-to-proteome comparisons with other prokaryotes using the FASTX program. Then, it fills the empty genomic regions with the CDSs supported by consensus ab initio predictions. From those consensus results, CONSORF provides prediction reliability scores, predicted frame-shifts, alternative start sites and best pair-wise match information against other prokaryotes. These results are easily accessed from a website.

Availability: The regularly updated CDS predictions of prokaryotic genomes as well as the source code are freely accessible through http://consorf.kobic.re.kr and http://orfome.org.

Contact:  j@bio.cc, jong@kribb.re.kr or sskimb@ssu.ac.kr

Supplementary information: The detailed methods and evaluation results can be found at http://consorf.kobic.re.kr/supplementary/.
NPIDB: a Database of Nucleic Acids–Protein Interactions
Authors: Spirin Sergei , Titov Mikhail , Karyagina Anna , Alexeevski Andrei
Published: November 2007

Summary: The database NPIDB (Nucleic Acids—Protein Interaction DataBase) contains information derived from structures of DNA–protein and RNA–protein complexes extracted from PDB (1834 complexes in July 2007). It is organized as a collection of files in PDB format and is equipped with a web-interface and a set of tools for extracting biologically meaningful characteristics of complexes. The content of the database is weekly updated.

Availability:  http://monkey.belozersky.msu.ru/NPIDB/

Contact:  sas@belozersky.msu.ru
PfamAlyzer: domain-centric homology search
Authors: Hollich Volker , Sonnhammer Erik L.L.
Published: November 2007

Summary: PfamAlyzer is a Java applet that enables exploration of Pfam domain architectures using a user-friendly graphical interface. It can search the UniProt protein database for a domain pattern. Domain patterns similar to the query are presented graphically by PfamAlyzer either in a ranked list or pinned to the tree of life. Such domain-centric homology search can assist identification of distant homologs with shared domain architecture.

Availability: PfamAlyzer has been integrated with the Pfam database and can be accessed at http://pfam.cgb.ki.se/pfamalyzer.

Contact:  Erik.Sonnhammer@ki.se
Aggregata octopiana (Protista: Apicomplexa): a dangerous pathogen during commercial Octopus vulgaris ongrowing
Authors: Gestal Camino , Guerra Angel , Pascual Santiago
Published: November 2007

Gestal, C., Guerra, A., and Pascual, S. 2007. Aggregata octopiana (Protista: Apicomplexa): a dangerous pathogen during commercial Octopus vulgaris ongrowing. – ICES Journal of Marine Science, 64. The haemolymph parameters for Octopus vulgaris and the condition index at molecular level were analysed using RNA/DNA and RNA/protein ratios on animals reared in floating cage systems and naturally infected by the coccidian Aggregata octopiana. Statistical analysis showed that as A. octopiana infection increased, there was a decrease in most inorganic elements and/or in haemocyte concentrations in cellular and/or plasma fractions. Also, the protein concentrations in the haemolymph plasma fraction dropped significantly as the coccidian infection increased. Results suggest that the severity of the infection by A. octopiana is a limiting factor during commercial ongrowing of the common octopus, at least in floating cage systems. Control measurements are needed in aquaculture to avoid this environmental stressor.
Structure of the retinoblastoma protein bound to adenovirus E1A reveals the molecular basis for viral oncoprotein inactivation of a tumor suppressor
Authors: Liu Xin , Marmorstein Ronen
Published: November 2007

The adenovirus (Ad) E1A (Ad-E1A) oncoprotein mediates cell transformation, in part, by displacing E2F transcription factors from the retinoblastoma protein (pRb) tumor suppressor. In this study we determined the crystal structure of the pRb pocket domain in complex with conserved region 1 (CR1) of Ad5-E1A. The structure and accompanying biochemical studies reveal that E1A-CR1 binds at the interface of the A and B cyclin folds of the pRb pocket domain, and that both E1A-CR1 and the E2F transactivation domain use similar conserved nonpolar residues to engage overlapping sites on pRb, implicating a novel molecular mechanism for pRb inactivation by a viral oncoprotein.
Cullin 5 regulates Dab1 protein levels and neuron positioning during cortical development
Authors: Feng Libing , Allen Nathaniel S. , Simo Sergi , Cooper Jonathan A.
Published: November 2007

Many laminated regions of the mammalian brain develop by the migration of neuronal precursor cells, whose final positions are coordinated by signals from the secreted molecule Reelin. Early events in Reelin signaling have been identified, but the mechanism of signal down-regulation has been unclear. A possible source of negative feedback is the Reelin-induced degradation of the critical intracellular signaling component, Disabled-1 (Dab1). Here we show that degradation of Dab1 depends on Dab1 phosphorylation at specific tyrosine residues and on the E3 ubiquitin ligase component Cullin 5 (Cul5). Cul5 forms complexes with SOCS (suppressors of cytokine signaling) proteins, which bind to phosphorylated Dab1 and target it for degradation in tissue culture cells. Ablation of Cul5 in migrating neurons causes an accumulation of active Dab1 protein and a unique cortical layering defect, characterized by excess migration and buildup of neurons at the top of the cortical plate. The results implicate Cul5 and SOCS proteins in down-regulation of Dab1 in vivo and show that Cul5 plays an essential role in regulating neuron migrations during cortical development, possibly by opposing a promigratory effect of Dab1.
Global analysis of alternative splicing differences between humans and chimpanzees
Authors: Calarco John A. , Xing Yi , Cáceres Mario , Calarco Joseph P. , Xiao Xinshu , Pan Qun , Lee Christopher , Preuss Todd M. , Blencowe Benjamin J.
Published: November 2007

Alternative splicing is a powerful mechanism affording extensive proteomic and regulatory diversity from a limited repertoire of genes. However, the extent to which alternative splicing has contributed to the evolution of primate species-specific characteristics has not been assessed previously. Using comparative genomics and quantitative microarray profiling, we performed the first global analysis of alternative splicing differences between humans and chimpanzees. Surprisingly, 6%–8% of profiled orthologous exons display pronounced splicing level differences in the corresponding tissues from the two species. Little overlap is observed between the genes associated with alternative splicing differences and the genes that display steady-state transcript level differences, indicating that these layers of regulation have evolved rapidly to affect distinct subsets of genes in humans and chimpanzees. The alternative splicing differences we detected are predicted to affect diverse functions including gene expression, signal transduction, cell death, immune defense, and susceptibility to diseases. Differences in expression at the protein level of the major splice variant of GlutathioneS-transferase omega-2 (GSTO2), which functions in the protection against oxidative stress and is associated with human aging-related diseases, suggests that this enzyme is less active in human cells compared with chimpanzee cells. The results of this study thus support an important role for alternative splicing in establishing differences between humans and chimpanzees.
Initial sequence and comparative analysis of the cat genome
Authors: Pontius Joan U. , Mullikin James C. , Smith Douglas R. ,   Agencourt Sequencing Team, Lindblad-Toh Kerstin , Gnerre Sante , Clamp Michele , Chang Jean , Stephens Robert , Neelam Beena , Volfovsky Natalia , Schäffer Alejandro A. , Agarwala Richa , Narfström Kristina , Murphy William J. , Giger Urs , Roca Alfred L. , Antunes Agostinho , Menotti-Raymond Marilyn , Yuhki Naoya , Pecon-Slattery Jill , Johnson Warren E. , Bourque Guillaume , Tesler Glenn ,   NISC Comparative Sequencing Program, O’Brien Stephen J.
Published: November 2007

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing ∼65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence.
Preparation and Use of Microcolumns for Sample Desalting or Nanoscale IMAC
Authors: Steen Hanno , Stensballe Allan , Jensen Ole N.
Published: November 2007

INTRODUCTION

In this method, microcolumns are prepared using any kind of chromatographic resin. The resin is held in place by making a constriction at the end of a GELoader pipette tip. Sample loading, washing, and elution are performed by loading liquid on top of the resin and applying air pressure to generate a low flow through the column. No frits are necessary.
Preparation of Immobilized Enzyme Microcolumns: Figure 1.
Authors: Larsen Martin R.
Published: November 2007

INTRODUCTION

Peptide mapping by MALDI-TOF-MS has emerged as a powerful proteomics tool for identifying and characterizing proteins. One of the key steps in this method involves the proteolytic cleavage of proteins, followed by MS analysis of the generated peptides. A limitation of the method, especially for high-throughput proteomics, is the speed and efficiency of proteolytic cleavage. In this protocol, a method for rapid tryptic digestion using immobilized enzyme microcolumns is described.
Analysis of Phosphopeptides by μLC-ESI-MS/MS
Authors: Corthals Garry L. , Wasinger Valerie C. , Goodlett David R.
Published: November 2007

INTRODUCTION

Whether using a pressure cell or gel-loader tips, IMAC-purified peptides can be injected into a μLC separation system and analyzed by μLC-ESI-MS/MS. Phosphopeptides behave and elute similarly to nonphosphorylated peptides during RP-HPLC, but because of a decrease in hydrophobicity due to the addition of the phosphate moiety, a phosphopeptide will generally elute before the nonphosphopeptide with the identical amino acid sequence. This difference in elution time is most pronounced for short peptides. Thus, when analyzing phosphopeptides from μLC online with ESI-MS/MS, it is prudent to acquire data during the wash step (i.e., prior to gradient elution), as some short phosphopeptides may not even bind to the C18 resin in 100% aqueous solutions. Otherwise, these very hydrophilic peptides will be missed. This protocol provides typical μLC conditions for the separation of IMAC-enriched phosphopeptides when the μLC system is online with the ESI-MS/MS.
Dewaxing and Rehydrating Sections prior to In Situ Hybridization
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard
Published: November 2007

INTRODUCTION

This protocol describes how to remove wax from embryo or tissue sections that have been affixed to glass slides. Traditionally, xylene has been used for this purpose, but less toxic solutions can also be employed. The embryo or tissue sections are then progressively rehydrated for compatibility with subsequent alcohol stains, aqueous stains, immunohistochemistry, or in situ hybridization.
Imaging Real-Time Gene Expression in Mammalian Cells with Single-Transcript Resolution: Figure 1.
Authors: Wells Amber L. , Condeelis John S. , Singer Robert H. , Zenklusen Daniel
Published: November 2007

INTRODUCTION

The MS2 system provides optimal sensitivity for single-molecule detection in cells. It requires two genetically encoded moieties: a reporter mRNA that contains MS2 binding site (MBS) stem loops and a fluorescent MS2 coat protein (MCP-xFP) that binds to the stem loops with high affinity, thus tagging the mRNA within the cell. This protocol describes transfection of COS-7 cells with reporter RNA (e.g., pRSV-Z-24 MBS-β-actin) and MCP-xFP (e.g., pPolII-MCP-GFP-NLS) plasmids using calcium phosphate precipitation. The reporter mRNA plasmid must be co-transfected with the MCP-xFP-NLS plasmid for simultaneous expression in a cell. The unbound MCP-xFP-NLS is sequestered in the nucleus, leaving only the MCP-xFP-NLS that is bound to the reporter mRNA in the cytoplasm. This provides a high signal-to-noise ratio (SNR) that permits detection of single mRNA molecules. The Delta T Imaging System is used for image acquisition of fluorescent particles in the cells.
Imaging Real-Time Gene Expression in Living Systems with Single-Transcript Resolution: Single mRNA Particle Tracking with ImageJ-Based Analysis
Authors: Wells Amber L. , Condeelis John S. , Singer Robert H. , Zenklusen Daniel
Published: November 2007

INTRODUCTION

This protocol describes the use of ImageJ software (freely available from NIH) to analyze particle dynamics in a cell using time-lapse movie frames or image stacks of fluorescent mRNA particles. Maximum intensity projections and kymographs are produced.
Fate-Mapping Technique: Grafting Fluorescent Cells into Gastrula-Stage Mouse Embryos at 7-7.5 Days Post-coitum
Authors: Franklin Vanessa J. , Bildsoe Heidi , Tam Patrick P.L.
Published: November 2007

INTRODUCTION

Analysis of the developmental fate of cell populations in different parts of the embryo enables the construction of fate maps. These reveal the organization of the body plan and can presage the expression of molecular characteristics of cell lineages and the formation of body parts. The efficacy of fate-mapping techniques is critically dependent on their ability to track the cells and all their descendants without compromising the development of the embryo. Cell grafting involves isolating a population of genetically tagged cells from a transgenic embryo and grafting them to a defined site in a nontransgenic host embryo. Tissue colonization is analyzed using a genetic tag (e.g., a fluorescent protein that can be visualized noninvasively) that allows tracking of the transplanted cells and their descendants in the host embryo throughout development in culture. Alternatively, a lacZ transgene can be used to localize graft-derived cells histologically. Differentiation of the graft-derived cells can be studied by examining the expression of molecular markers by in situ hybridization of gene transcripts or immunohistochemical detection of lineage-specific proteins. This protocol describes how to graft cells isolated from a donor embryo into the germ layer of a wild-type host mouse embryo at 7-7.5 days post-coitum (dpc).
Nitrogen‐containing bisphosphonate, YM529/ONO‐5920, inhibits macrophage inflammatory protein 1α expression and secretion in mouse myeloma cells
Authors: Tsubaki Masanobu , Kato Chisato , Nishinobo Minori , Ogaki Mitsuhiko , Satou Takao , Ito Tatsuki , Kusunoki Takashi , Fujiwara Kimiko , Yamazoe Yuzuru , Nishida Shozo
Published: November 2007

Macrophage inflammatory protein 1α (MIP‐1α) is detected at high concentrations in patients with multiple myeloma, and it is thought to play an important role in the etiology of multiple myeloma and osteolysis. Thus, we investigated whether or not YM529/ONO‐5920, a new bisphosphonate, inhibited MIP‐1α mRNA expression in, and MIP‐1α secretion from, mouse myeloma cells. When the cells were stimulated by lipopolysaccharide, increased MIP‐1α mRNA expression and MIP‐1α secretion were observed. YM529/ONO‐5920 inhibited MIP‐1α mRNA expression and MIP‐1α secretion in a concentration‐dependent manner. A transient increase in the phosphorylation of extracellular‐regulated kinase 1/2 (ERK1/2) and Akt was observed after lipopolysaccharide stimulation. After YM529/ONO‐5920 was given, there was no transient increase in the phosphorylation of ERK1/2 or Akt. These results indicated that YM529/ONO‐5920 inhibited the expression and secretion of MIP‐1α through blocking the signaling pathway of the Ras/mitogen‐activated protein kinase kinase/ERK and Ras/phosphatidylinositol‐3 kinase/Akt. Accordingly, YM529/ONO‐5920 appears to have promise for use in effective future therapy for osteolysis and myeloma cell growth that depends on MIP‐1α. (Cancer Sci 2008; 99: 152–158)
Incidence of multiple primary cancers in Nagasaki atomic bomb survivors: Association with radiation exposure
Authors: Nakashima Masahiro , Kondo Hisayoshi , Miura Shiro , Soda Midori , Hayashi Tomayoshi , Matsuo Takeshi , Yamashita Shunichi , Sekine Ichiro
Published: November 2007

To assess the effects of atomic bomb radiation on the incidence of multiple primary cancers (MPC), we analyzed the association between the incidence of second primary cancers in survivors of the atomic bombing of Nagasaki, and exposure distance. The incidence rate (IR) of a second primary cancer was calculated and stratified by the distance from the hypocenter and age at the time of bombing for the years 1968 through 1999. The IR of the first primary cancer was also calculated and compared with the second primary cancer to determine whether atomic bomb radiation was associated with the multiplicity of tumors. There were 511 confirmed cases of MPC in the 7572 cancer‐bearing survivors. The crude IR was 27.6 per 100 000 person‐years. The IR of second primaries decreased significantly with increasing distance from the hypocenter: relative risk, 0.89 per 1.0 km; 95% confidence interval, 0.84–0.94. A significant decrease was also noted for those of older ages at the time of the bombing, based on the attained age of the second primary cancer: relative risk, 0.91 per 1 year; 95% confidence interval, 0.90–0.92. These findings suggest that the radiation has affected the incidence of MPC. Furthermore, when compared with the first primary cancer, a stronger distance effect was suggested on the occurrence of a second primary cancer in the survivors. The present study suggests the significance of atomic bomb radiation on MPC in the survivors. These results on the incidence of MPC in the tumor‐bearing survivors and its correlations with the atomic bombing of 62 years ago are described for the first time in this report. (Cancer Sci 2008; 99: 87–92)
Oral challenges are needed in the diagnosis of β‐lactam hypersensitivity
Authors: Bousquet P. J. , Pipet A. , Bousquet‐Rouanet L. , Demoly P.
Published: November 2007

Backgroundβ‐lactams continue to remain the most commonly involved drug family in allergic drug reactions. They are often essential and there is a cost‐effective and favourable risk‐benefit ratio for the exploration of all suspicions of β‐lactam allergy. A firm diagnosis is always based on skin tests and sometimes on provocation tests. Recommendations have been published by allergy societies and distinguished scientists but they are not always concordant and can lead to some confusion for the practicing allergologist. The situation has even worsened since the world wide withdrawal of these penicillin determinants and since the predominance of amoxicillin and cephalosporin prescriptions in most countries.

Objective – MethodIn a recent article, it was stated that patients with a penicillin allergy history and negative skin tests to major and minor penicillin determinants are at a low risk of relapse (0–5%) when receiving a β‐lactam. In this paper, our Drug Allergy and Hypersensitivity Database, a cohort database, was used to demonstrate that this statement is false. Standardized European Network for Drug Allergy questionnaires, skin test and challenge procedures were followed.

ResultsOne‐thousand two‐hundred and eighteen subjects, 69.8% of female, 51.7% of atopics, were included. 21.1% had a true β‐lactam allergy confirmed by skin tests (178, 69.3%) or by drug provocation (79, 30.7%). 17.4% of the patients with negative skin tests to major and minor penicillin determinants were positive for a β‐lactam.

ConclusionIn the diagnosis of β‐lactams allergy, if all skin tests are negative, skin tests with other determinants and provocation tests under strict surveillance are mandatory.
Leisure time but not occupational physical activity significantly affects cardiovascular risk factors in an adult population
Authors: Sofi F. , Capalbo A. , Marcucci R. , Gori A. M. , Fedi S. , Macchi C. , Casini A. , Surrenti C. , Abbate R. , Gensini G. F.
Published: November 2007

Background  A large number of studies have demonstrated that regular physical activity during leisure time (LTPA) accounts for a significant protection against cardiovascular diseases (CVD). On the other hand, conflicting findings on the beneficial effects of occupational physical activity (OPA) have been reported. The aim of this study is to evaluate the possible influence of different amounts of LTPA and OPA on circulating levels of several parameters associated with an increased risk of CVD.

Materials and methods  We studied 932 individuals (365 M; 567 F, with a mean age of 54 years) living in Florence, Italy, who were enrolled in a population study conducted between 2002 and 2004. Subjects were divided into three classes of LTPA and OPA according to a score derived from a questionnaire that assessed the amount of physical activity performed.

Results  LTPA was inversely related to body mass index (BMI), hip circumference, diastolic blood pressure and triglycerides, as well as directly correlated with high‐density lipoprotein (HDL) cholesterol. Likewise, a higher OPA was found to be associated with higher HDL cholesterol levels. Moreover, a multivariate logistical regression analysis, adjusted for possible confounders, showed that a moderate‐to‐high intensity of LTPA was able to confer a significant protection against having abnormal levels of BMI, waist circumference and triglycerides, main features of the metabolic syndrome, whereas no associations between these parameters and OPA were observed.

Conclusions  A moderate‐to‐high LTPA was found to be significantly associated with a more favourable cardiovascular risk profile in terms of anthropometric, metabolic and lipid parameters among an Italian population. In addition, a relationship between OPA and HDL‐cholesterol was reported.
Immunological decision‐making: how does the immune system decide to mount a helper T‐cell response?
Authors: Kaiko Gerard E. , Horvat Jay C. , Beagley Kenneth W. , Hansbro Philip M.
Published: November 2007

Aberrant T‐cell responses underpin a range of diseases, including asthma and allergy and autoimmune diseases. Pivotal immune elements of these diseases are the development of antigen‐specific effector T‐helper type 2 (Th2) cells, Th1 cells, or the recently defined Th17 cells that are associated with the clinical features and disease progression. In order to identify crucial processes in the pathogenesis of these diseases it is critical to understand how the development of these T cells occurs. The phenotype of a polarized T‐cell that differentiates from a naïve precursor is determined by the complex interaction of antigen‐presenting cells with naïve T cells and involves a multitude of factors, including the dominant cytokine environment, costimulatory molecules, type and load of antigen presented and a plethora of signaling cascades. The decision to take the immune response in a certain direction is not made by one signal alone, instead many different elements act synergistically, antagonistically and through positive feedback loops to activate a Th1, Th2, or Th17 immune response. The elucidation of the mechanisms of selection of T‐cell phenotype will facilitate the development of therapeutic strategies to intervene in the development of deleterious T‐cell responses. This review will focus on the pathways and key factors responsible for the differentiation of the various subsets of effector CD4 T cells. We will primarily discuss what is known of the Th1 and Th2 differentiation pathways, while also reviewing the emerging research on Th17 differentiation.
Predicting weed distribution at the landscape scale: using naturalized Brassica as a model system
Authors: Peltzer D. A , Ferriss S , FitzJohn R. G.
Published: November 2007

Quantifying and predicting the distribution of naturalized plant species is a major concern for weed risk assessment and understanding the potential impacts of gene‐flow between crop species and feral or naturalized populations.

We developed a rapid field assessment to quantify the distribution of naturalized Brassica populations at the landscape scale, using the Canterbury Plains region of New Zealand as a model system. Internationally, brassicas are one of the most widely cultivated crops, and have well‐documented problems of crop escapes, gene‐flow and hybridization with wild relatives. Brassicas are cultivated intensively in the study system for both seed production and forage, are widely naturalized and have raised concerns for gene‐flow from feral populations to cultivated varieties.

Generalized linear models (GLM) were constructed in order to predict the presence–absence of brassicas using survey data of naturalized populations located in 50 3 × 3 km plots. This model was validated subsequently both by ground‐truthing predicted presence–absence in a second field survey, and by comparing cumulative probability distributions from a presence‐only botanical survey.

The best model produced from the field survey predicted naturalized Brassica presence–absence robustly (r2 = 0·52) and was well validated against results from the presence‐only survey carried out in the same year. Results from the second field survey during a different growing season did not match predictions from the original model, suggesting that strong between‐year differences influence large‐scale Brassica distribution. The differences between years were driven by an overall increase in the prevalence of brassicas over the course of the study that was not associated with any predictive variable or climate.

Synthesis and applications. These results have important implications both for developing models of species distribution and for predicting gene‐flow risk at the landscape scale. Despite constructing a model that was subsequently validated from presence‐only data in one year, it did not predict Brassica distribution in a subsequent year; this suggests that between‐year or stochastic factors operate strongly and are a major consideration for risk assessment. Models used to predict species distributions, in general, need to account for these between‐year effects either by incorporating mechanistic processes or long‐term data.
A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi
Authors: Baker Stephen , Holt Kathryn , Whitehead Sally , Goodhead Ian , Perkins Tim , Stocker Bruce , Hardy Jonathan , Dougan Gordon
Published: November 2007

The process by which bacteria regulate flagellar expression is known as phase variation and in Salmonella enterica this process permits the expression of one of two flagellin genes, fliC or fljB, at any one time. Salmonella Typhi (S. Typhi) is normally not capable of phase variation of flagellar antigen expression as isolates only harbour the fliC gene (H:d) and lacks an equivalent fljB locus. However, some S. Typhi isolates, exclusively from Indonesia, harbour an fljB equivalent encoded on linear plasmid, pBSSB1 that drives the expression of a novel flagellin named H:z66. H:z66+S. Typhi isolates were stimulated to change flagellar phase and genetically analysed for the mechanism of variation. The phase change was demonstrated to be unidirectional, reverting to expression from the resident chromosomal fliC gene. DNA sequencing demonstrated that pBSSB1 linear DNA was still detectable but that these derivatives had undergone deletion and were lacking fljAz66 (encoding a flagellar repressor) and fljBz66. The deletion end‐point was found to involve one of the plasmid termini and a palindromic repeat sequence within fljBz66, distinct to that found at the terminus of pBSSB1. These data demonstrate that, like some Streptomyces linear elements, at least one of the terminal inverted repeats of pBSSB1 is non‐essential, but that a palindromic repeat sequence may be necessary for replication.
Apoptosis: a potential triggering mechanism of neurological manifestation in Plasmodium falciparum malaria
Authors: TOURÉ F. S. , OUWE‐MISSI‐OUKEM‐BOYER O. , BISVIGOU U. , MOUSSA O. , ROGIER C. , PINO P. , MAZIER D. , BISSER S.
Published: November 2007

Plasmodium falciparum infection can lead to a life threatening disease and the pathogenetic mechanisms of severe manifestations are not fully understood. Here, we investigated the capacity of P. falciparum‐parasitized red blood cells (PRBC) from 45 children with clinical malaria to induce endothelial cell (EC) apoptosis.

In all subjects, PRBC that cytoadhered to ECs could be found albeit to a variable degree. By contrast, PRBC that induce EC apoptosis were found only in nine (20%) subjects. Interestingly, children with neurological manifestations were significantly more likely to harbour apoptogenic strains. There was no quantitative relationship between the capacity of these isolates to cytoadhere and apoptosis induction. We hypothesize that P. falciparum‐encoded molecules could be responsible for apoptosis induction and therefore suggest new insights in the pathogenesis of P. falciparum malaria. Further investigations are currently in progress to determine whether these results can be confirmed and to identify putative parasite apoptogenic factors.
An objective measure to identify pediatric liver transplant recipients at risk for late allograft rejection related to non‐adherence
Authors: Venkat Veena L. , Nick Todd G. , Wang Yu , Bucuvalas John C.
Published: November 2007

Abstract:  Non‐adherence to a prescribed immunosuppressive regimen increases risk for late allograft rejection (LAR). We implemented a protocol for immunosuppression management which decreased variation in calcineurin inhibitor blood levels in pediatric liver transplant recipients by controlling for confounders such as physician practice variability. We hypothesized that patients with increased variation in tacrolimus blood levels despite implementation of the immunosuppression management protocol were at increased risk for LAR. We conducted a single center retrospective cohort study of 101 pediatric liver transplant recipients who were at least one year post liver transplantation and receiving tacrolimus for immunosuppression. The primary outcome variable was biopsy proven allograft rejection. Primary candidate predictor variables were the standard deviation (SD) of tacrolimus blood levels (a marker of drug level variability), mean tacrolimus blood level, age, and insurance type. SD of tacrolimus blood levels was determined for each patient from a minimum of four outpatient levels during the study period. Unadjusted and adjusted logistic regression models were used to determine the prognostic value of candidate predictors. The median and interquartile range of the SD of tacrolimus blood levels was 1.6 (1.1, 2.1). Eleven episodes of LAR occurred during the study period. Ten of the 11 episodes occurred in patients with tacrolimus blood level SD > 2. Insurance type, mean tacrolimus blood level and SD of tacrolimus blood levels were significantly related to LAR in the unadjusted analyses (p<0.05). A multivariable model including age, insurance type, mean and SD of tacrolimus blood levels was significantly associated with LAR (validated C‐statistic = 0.88, p = 0.012). The adjusted odds of rejection for a one unit increase in the SD of tacrolimus blood level was 3.49 (95% CI 1.31 to 9.29). Effects of age and insurance status on LAR did not provide independent prognostic value after controlling for SD. Variation in tacrolimus blood levels is associated with an increased risk of LAR in pediatric liver transplant recipients. Despite standardized management of tacrolimus levels to control for confounders, some patients were found to have significant variability of tacrolimus blood levels. This may be due to non‐adherence and amenable to targeted psychosocial and behavioral interventions to prevent LAR.
A national conference to determine research priorities in pediatric solid organ transplantation
Authors: Bartosh Sharon M. , Ryckman Frederick C. , Shaddy Robert , Michaels Marian G. , Platt Jeffrey L. , Sweet Stuart C.
Published: November 2007

Abstract:  The need for evidence‐based practice guidelines requires high quality, carefully controlled clinical research trials. This multidisciplinary conference attempted to: identify urgent clinical and research issues, identify obstacles to performing clinical trials, develop concepts for organ‐specific and all‐organ research and generate a report that would serve as a blueprint for future research initiatives. A few themes became evident. First, young children present a unique immunologic environment which may lead to tolerance, therefore, including young children in immunosuppression withdrawal and tolerance trials may increase the potential benefits of these studies. Second, adolescence poses significant barriers to successful transplantation. Non‐adherence may be insufficient to explain poorer outcomes. More studies focused on identification and prevention of non‐adherence, and the potential effects of puberty are required. Third, the relatively naive immune system of the child presents a unique opportunity to study primary infections and alloimmune responses. Finally, relatively small numbers of transplants performed in pediatric centers mandate multicenter collaboration. Investment in registries, tissue and DNA repositories will enhance productivity. The past decade has proven that outcomes after pediatric transplantation can be comparable to adults. The pediatric community now has the opportunity to design and complete studies that enhance outcomes for all transplant recipients.
Standard dosing of tacrolimus leads to overexposure in pediatric renal transplantation recipients
Authors: Kausman Joshua Y. , Patel Bhumik , Marks Stephen D.
Published: November 2007

Abstract:  Tacrolimus dosage in pediatric RTRs is empirically based on weight. There is evidence that adolescents are at greater risk of toxicity than young children on this dosing regimen. We investigated the rate of tacrolimus overexposure within the first three wk post‐transplantation in pediatric RTRs receiving tacrolimus 0.15 mg/kg twice daily. Of 63 RTRs studied, 41 (65.1%) experienced a tacrolimus level above the therapeutic range (supratherapeutic), the majority (48.8%) on days two to four post‐transplant. Patients with supratherapeutic levels were older (14.2 vs. 9.9 yr, p = 0.016), taller (146.7 vs. 126.5 cm, p = 0.029), larger (1.36 vs. 1.01 m2, p = 0.039) and heavier (44.1 vs. 29.3 kg, p = 0.043) and by day 12 were receiving much lower tacrolimus doses than those without supratherapeutic levels (0.425 vs. 0.198 mg/kg/day, p = 0.0002). Supratherapeutic levels were more common among white (British) children than other ethnic groups (74 vs. 45%, p = 0.02). There were no observed differences in rates of patient or graft survival, or acute rejection during the three‐yr study period. Adolescent patients appear to be at greater risk of excessive tacrolimus dosing on a standard regimen. We therefore outline a regimen restricting tacrolimus dosage given to larger/older patients, but emphasize the need for a prospective randomized trial to define optimal dosing.