bluuebunny/crossref_metadata_2025 huggingface dataset:
A transgenic mouse model to analyze CD8+effector T cell differentiationin vivo
Authors: Manjunath N. , Shankar P. , Stockton B. , Dubey P. D. , Lieberman J. , von Andrian U. H.
Published: July 2002

Antigen-specific effector T cells are prerequisite to immune protection, but because of the lack of effector cell-specific markers, their generation and differentiation has been difficult to study. We report that effector cells are highly enriched in a T cell subset that can be specifically identified in transgenic (T-GFP) mice expressing green fluorescent protein (GFP) under control of the murine CD4 promoter and proximal enhancer. Consistent with previous studies of these transcriptional control elements, GFP was strongly and specifically expressed in nearly all resting and short-term activated CD4+and CD8+T cells. However, when T-GFP mice were challenged with vaccinia virus, allogeneic tumor cells, or staphylococcal enterotoxin A, the cytotoxic and IFN-γ-producing T cells lost GFP expression. Upon T cell receptor (TCR) ligation by αCD3, sorted GFP+cells fluxed calcium and proliferated vigorously. In contrast, GFP−effector cells showed a diminished calcium flux and did not proliferate. Instead, they underwent apoptosis unless supplied with exogenous IL-2. By reverse transcription–PCR analysis, the GFP−cells up-regulated the pro-apoptotic molecule, Fas-L, and down-regulated gene expression of the proximal TCR signaling molecule, CD3ζ, and c-jun, a component of the AP-1 transcription factor. Thus, differential regulation of TCR signaling may explain the divergent responses of naïve and effector T cells to antigen stimulation.
Transforming growth factor β targeted inactivation of cyclin E:cyclin-dependent kinase 2 (Cdk2) complexes by inhibition of Cdk2 activating kinase activity
Authors: Nagahara Hikaru , Ezhevsky Sergei A. , Vocero-Akbani Adamina M. , Kaldis Philipp , Solomon Mark J. , Dowdy Steven F.
Published: July 2002

Transforming growth factor β (TGF-β)-mediated G
1
arrest previously has been shown to specifically target inactivation of cyclin D:cyclin-dependent kinase (Cdk) 4/6 complexes. We report here that TGF-β-treated human HepG2 hepatocellular carcinoma cells arrest in G
1
, but retain continued cyclin D:Cdk4/6 activity and active, hypophosphorylated retinoblastoma tumor suppressor protein. Consistent with this observation, TGF-β-treated cells failed to induce p15
INK4b
, down-regulate CDC25A, or increase levels of p21
CIP1
, p27
KIP1
, and p57
KIP2
. However, TGF-β treatment resulted in the specific inactivation of cyclin E:Cdk2 complexes caused by absence of the activating Thr
160
phosphorylation on Cdk2. Whole-cell lysates from TGF-β-treated cells showed inhibition of Cdk2 Thr
160
Cdk activating kinase (CAK) activity; however, cyclin H:Cdk7 activity, a previously assumed mammalian CAK, was not altered.
Saccharomyces cerevisiae
contains a genetically and biochemically proven CAK gene,
CAK1
, that encodes a monomeric 44-kDa Cak1p protein unrelated to Cdk7. Anti-Cak1p antibodies cross-reacted with a 45-kDa human protein with CAK activity that was specifically down-regulated in response to TGF-β treatment. Taken together, these observations demonstrate that TGF-β signaling mediates a G
1
arrest in HepG2 cells by targeting Cdk2 CAK and suggests the presence of at least two mammalian CAKs: one specific for Cdk2 and one for Cdk4/6.
The MITE familyHeartbreaker(Hbr): Molecular markers in maize
Authors: Casa Alexandra M. , Brouwer Cory , Nagel Alexander , Wang Lianjiang , Zhang Qiang , Kresovich Stephen , Wessler Susan R.
Published: July 2002

Transposable elements are ubiquitous in plant genomes, where they frequently comprise the majority of genomic DNA. The maize genome, which is believed to be structurally representative of large plant genomes, contains single genes or small gene islands interspersed with much longer blocks of retrotransposons. Given this organization, it would be desirable to identify molecular markers preferentially located in genic regions. In this report, the features of a newly described family of miniature inverted repeat transposable elements (MITEs) (calledHeartbreaker), including high copy number and polymorphism, stability, and preference for genic regions, have been exploited in the development of a class of molecular markers for maize. To this end, a modification of the AFLP procedure called transposon display was used to generate and display hundreds of genomic fragments anchored inHbrelements. An average of 52 markers were amplified for each primer combination tested. In all, 213 polymorphic fragments were reliably scored and mapped in 100 recombinant inbred lines derived from a cross between the maize inbreds B73 × Mo17. In this mapping population,Hbrmarkers are distributed evenly across the 10 maize chromosomes. This procedure should be of general use in the development of markers for other MITE families in maize and in other plant and animal species where MITEs have been identified.
Optimal prediction and the Mori–Zwanzig representation of irreversible processes
Authors: Chorin Alexandre J. , Hald Ole H. , Kupferman Raz
Published: July 2002

Optimal prediction methods compensate for a lack of resolution in the numerical solution of complex problems through the use of prior statistical information. We point out a relation between optimal prediction and the statistical mechanics of irreversible processes, and use a version of the Mori–Zwanzig formalism to produce a higher-order optimal prediction method.
Regulatory evolution and the origin of the bilaterians
Authors: Peterson Kevin J. , Davidson Eric H.
Published: July 2002

The adult body plan of bilaterians is achieved by imposing regional
specifications on pluripotential cells. The establishment of spatial
domains is governed in part by regulating expression of transcription
factors. The key to understanding bilaterian evolution is contingent on
our understanding of how the regulation of these transcription factors
influenced bilaterian stem-group evolution.
ECONOMIC SOCIOLOGY IN FRANCE
Authors: Heilbron Johan
Published: July 2002

With the work of Durkheimian scholars like François Simiand, Maurice Halbwachs and Marcel Mauss, economic sociology became an original and particularly creative research tradition in France. When the Durkheimian approach to the economy was gradually replaced by the sociology of work, it survived outside of sociology proper, especially among economic historians, heterodox economists and anthropologists. At the end of the twentieth century economic sociology re-emerged as a major research field. The revival was part of a multidisciplinary movement for a critical rethinking of the economy (represented notably by the so-called Regulation School, the economics of conventions, and the Mauss movement). Within this context three research tendencies have acquired a specific significance: the work of Pierre Bourdieu and his collaborators, various ethnographic and anthropological approaches, and research on alternative economic arrangements distinct from market exchange as well as from the public sector.
FROM NEEDS TO THE MARKET: The changing inequality of household income in the Czech transition
Authors: Večerník Jiří
Published: July 2002

Statistical income surveys are used to document systemic changes in distribution and redistribution of household income and its determinants over the period 1988 to 1996. First, the growing difficulties facing income surveys under the democratic regime are considered. Second, the substantive meaning of various income indicators and their relation to the social and economic situation is discussed. Third, growing disparities in income after 1989 and the shift away from demographic factors (numbers of active earners and children, age) to socioeconomic factors (education, branch, occupation) are displayed. The fourth part documents the increased redistribution of income achieved through taxes and social benefits. The fifth part compares the Czech case with Western countries in order to evaluate the extent to which income distribution has adjusted to the market economy. The conclusion offers a summary of main findings and discusses some additional resources of family welfare during the transition period.
European patterns of labour market entry: A dichotomy of occupationalized vs. non-occupationalized systems?
Authors: Gangl Markus
Published: July 2002

Many recent comparative studies of school-to-work transitions have revolved around the notion of an institutional dichotomy of transition arrangements that distinguishes the occupational labour markets of countries exhibiting extensive systems of vocational training and apprenticeships from the organizational markets found in countries with less integrated education and employment systems. This study scrutinizes this idea by assessing the extent to which patterns of labour market entry in twelve European Union countries empirically conform to the expected dichotomy. Based on cluster and discriminant analyses, three rather than two typical patterns emerge from the analyses: first, the continental European countries running extensive vocational training systems; second, those Northern European countries lacking such systems, and finally, a homogeneous set of Southern European countries. While the first contrast is apparently broadly consistent with current institutionalist arguments about the impact of linkages between training systems and labour markets, the explanation for the deviation of the Southern European case is wanting. The results suggest both the need to incorporate additional institutional aspects into current transition research, but also stress the limitations of typological approaches in explaining cross-national differences in transition processes more generally.
Old-age pensions: Individual or collective responsibility?: An investigation of public opinion across European welfare states
Authors: Gelissen John
Published: July 2002

The question of who should be responsible for the provision of retirement income is becoming increasingly important, given the general trend of ageing populations in many European countries. In this article, we study the determinants of popular preferences concerning individual or collective responsibilities in the context of old-age pensions. Using data from the Eurobarometer survey series, we investigate whether - and to what extent - people's views about who should be responsible for the provision of pensions are related to market selectivist and collectivist features of the particular welfare state regimes in Europe. Moreover, the impact of structural characteristics of pension systems and social characteristics of individuals on public preferences is investigated. The cross-national patterns of popular views on responsibilities for the provision of pensions suggest a link to the specifics of welfare state regimes, but not as decisively as one would expect. Structural characteristics of pension systems also appear to be important determinants of public opinion. However, effects of contextual variables are only found when measurements of public opinion are used, which refer to specific institutional arrangements for pension provision. Finally, the results show important divisions among social categories.
Aminopeptidase I Is Targeted to the Vacuole by a Nonclassical Vesicular Mechanism
Authors: Scott Sidney V. , Baba Misuzu , Ohsumi Yoshinori , Klionsky Daniel J.
Published: July 2002

The yeast vacuolar protein aminopeptidase I (API) is synthesized as a cytosolic precursor that is transported to the vacuole by a nonclassical targeting mechanism. Recent genetic studies indicate that the biosynthetic pathway that transports API uses many of the same molecular components as the degradative autophagy pathway. This overlap coupled with both in vitro and in vivo analysis of API import suggested that, like autophagy, API transport is vesicular. Subcellular fractionation experiments demonstrate that API precursor (prAPI) initially enters a nonvacuolar cytosolic compartment. In addition, subvacuolar vesicles containing prAPI were purified from a mutant strain defective in breakdown of autophagosomes, further indicating that prAPI enters the vacuole inside a vesicle. The purified subvacuolar vesicles do not appear to contain vacuolar marker proteins. Immunogold EM confirms that prAPI is localized in cytosolic and in subvacuolar vesicles in a mutant strain defective in autophagic body degradation. These data suggest that cytosolic vesicles containing prAPI fuse with the vacuole to release a membrane-bounded intermediate compartment that is subsequently broken down, allowing API maturation.
Rho- and Rac-dependent Assembly of Focal Adhesion Complexes and Actin Filaments in Permeabilized Fibroblasts: An Essential Role for Ezrin/Radixin/Moesin Proteins
Authors: Mackay Deborah J.G. , Esch Fred , Furthmayr Heinz , Hall Alan
Published: July 2002

The small GTPases Rho and Rac regulate actin filament assembly and the formation of integrin adhesion complexes to produce stress fibers and lamellipodia, respectively, in mammalian cells. Although numerous candidate effectors that might mediate these responses have been identified using the yeast two-hybrid and affinity purification techniques, their cellular roles remain unclear. We now describe a biological assay that allows components of the Rho and Rac signaling pathways to be identified. Permeabilization of serum-starved Swiss 3T3 cells with digitonin in the presence of guanosine 5′-O-(3-thiotriphosphate) (GTPγS) induces both actin filament and focal adhesion complex assembly through activation of endogenous Rho and Rac. These responses are lost when GTPγS is added 6 min after permeabilization, but can be reconstituted using concentrated cytosolic extracts. We have achieved a 10,000-fold purification of the activity present in pig brain cytosol and protein sequence analysis shows it to contain moesin. Using recombinant proteins, we show that moesin and its close relatives ezrin and radixin can reconstitute stress fiber assembly, cortical actin polymerization and focal complex formation in response to activation of Rho and Rac.
Translation of the Chloroplast psbA mRNA Requires the Nuclear-encoded Poly(A)-binding Protein, RB47
Authors: Yohn Christopher B. , Cohen Amybeth , Rosch Cristen , Kuchka Michael R. , Mayfield Stephen P.
Published: July 2002

A set of nuclear mutants of C. reinhardtii were identified that specifically lack translation of the chloroplast-encoded psbA mRNA, which encodes the photosystem II reaction center polypeptide D1. Two of these mutants are deficient in the 47-kD member (RB47) of the psbA RNA-binding complex, which has previously been identified both genetically and biochemically as a putative translational activator of the chloroplast psbA mRNA. RB47 is a member of the poly(A)-binding protein family, and binds with high affinity and specificity to the 5′ untranslated region of the psbA mRNA. The results presented here confirm RB47's role as a message-specific translational activator in the chloroplast, and bring together genetic and biochemical data to form a cohesive model for light- activated translational regulation in the chloroplast.
ZAP-70 Tyrosine Kinase Is Required for LFA-1–dependent T Cell Migration
Authors: Soede Ron D.M. , Wijnands Yvonne M. , Van Kouteren-Cobzaru Ioana , Roos Ed
Published: July 2002

The ZAP-70 tyrosine kinase is essential for T cell activation by the T cell receptor. We show that ZAP-70 is also required for migration of T cells that is dependent on the integrin LFA-1. Invasion of TAM2D2 T cell hybridoma cells into fibroblast monolayers, which is LFA-1–dependent, was blocked by overexpression of dominant-negative ZAP-70 and by piceatannol but not by herbimycin A. The Syk inhibitor piceatannol blocks the Syk homologue ZAP-70, which is expressed by TAM2D2 cells, with the same dose dependence as the inhibition of invasion. Dominant-negative ZAP-70 completely inhibited the extensive metastasis formation of TAM2D2 cells to multiple organs upon i.v. injection into mice. Migration of TAM2D2 cells through filters coated with the LFA-1 ligand ICAM-1, induced by 1 ng/ml of the chemokine SDF-1, was blocked by anti–LFA-1 mAb and also abrogated by dominant-negative ZAP-70 and piceatannol. In contrast, migration induced by 100 ng/ml SDF-1 was independent of both LFA-1 and ZAP-70. LFA-1 cross-linking induced tyrosine phosphorylation, which was blocked by dominant-negative ZAP-70 and piceatannol. We conclude that LFA-1 engagement triggers ZAP-70 activity that is essential for LFA-1–dependent migration.
A Monoclonal Antibody to the COOH-terminal Acidic Portion of Ran Inhibits Both the Recycling of Ran and Nuclear Protein Import in Living Cells
Authors: Hieda Miki , Tachibana Taro , Yokoya Fumihiko , Kose Shingo , Imamoto Naoko , Yoneda Yoshihiro
Published: July 2002

A small GTPase Ran is a key regulator for active nuclear transport. In immunoblotting analysis, a monoclonal antibody against recombinant human Ran, designated ARAN1, was found to recognize an epitope in the COOH-terminal domain of Ran. In a solution binding assay, ARAN1 recognized Ran when complexed with importin β, transportin, and CAS, but not the Ran-GTP or the Ran-GDP alone, indicating that the COOH-terminal domain of Ran is exposed via its interaction with importin β–related proteins. In addition, ARAN1 suppressed the binding of RanBP1 to the Ran–importin β complex. When injected into the nucleus of BHK cells, ARAN1 was rapidly exported to the cytoplasm, indicating that the Ran–importin β–related protein complex is exported as a complex from the nucleus to the cytoplasm in living cells. Moreover, ARAN1, when injected into the cultured cells induces the accumulation of endogenous Ran in the cytoplasm and prevents the nuclear import of SV-40 T-antigen nuclear localization signal substrates. From these findings, we propose that the binding of RanBP1 to the Ran–importin β complex is required for the dissociation of the complex in the cytoplasm and that the released Ran is recycled to the nucleus, which is essential for the nuclear protein transport.
Centriolar Satellites
Authors: Kubo Akiharu , Sasaki Hiroyuki , Yuba-Kubo Akiko , Tsukita Shoichiro , Shiina Nobuyuki
Published: July 2002

We identified Xenopus pericentriolar material-1 (PCM-1), which had been reported to constitute pericentriolar material, cloned its cDNA, and generated a specific pAb against this molecule. Immunolabeling revealed that PCM-1 was not a pericentriolar material protein, but a specific component of centriolar satellites, morphologically characterized as electron-dense granules, ∼70–100 nm in diameter, scattered around centrosomes. Using a GFP fusion protein with PCM-1, we found that PCM-1–containing centriolar satellites moved along microtubules toward their minus ends, i.e., toward centrosomes, in live cells, as well as in vitro reconstituted asters. These findings defined centriolar satellites at the molecular level, and explained their pericentriolar localization. Next, to understand the relationship between centriolar satellites and centriolar replication, we examined the expression and subcellular localization of PCM-1 in ciliated epithelial cells during ciliogenesis. When ciliogenesis was induced in mouse nasal respiratory epithelial cells, PCM-1 immunofluorescence was markedly elevated at the apical cytoplasm. At the electron microscopic level, anti–PCM-1 pAb exclusively labeled fibrous granules, but not deuterosomes, both of which have been suggested to play central roles in centriolar replication in ciliogenesis. These findings suggested that centriolar satellites and fibrous granules are identical novel nonmembranous organelles containing PCM-1, which may play some important role(s) in centriolar replication.
Ankyrin-B Is Required for Intracellular Sorting of Structurally Diverse Ca2+ Homeostasis Proteins
Authors: Tuvia Shmuel , Buhusi Mona , Davis Lydia , Reedy Mary , Bennett Vann
Published: July 2002

This report describes a congenital myopathy and major loss of thymic lymphocytes in ankyrin-B (−/−) mice as well as dramatic alterations in intracellular localization of key components of the Ca2+ homeostasis machinery in ankyrin-B (−/−) striated muscle and thymus. The sacoplasmic reticulum (SR) and SR/T-tubule junctions are apparently preserved in a normal distribution in ankyrin-B (−/−) skeletal muscle based on electron microscopy and the presence of a normal pattern of triadin and dihydropyridine receptor. Therefore, the abnormal localization of SR/ER Ca ATPase (SERCA) and ryanodine receptors represents a defect in intracellular sorting of these proteins in skeletal muscle. Extrapolation of these observations suggests defective targeting as the basis for abnormal localization of ryanodine receptors, IP3 receptors and SERCA in heart, and of IP3 receptors in the thymus of ankyrin-B (−/−) mice. Mis-sorting of SERCA 2 and ryanodine receptor 2 in ankyrin-B (−/−) cardiomyocytes is rescued by expression of 220-kD ankyrin-B, demonstrating that lack of the 220-kD ankyrin-B polypeptide is the primary defect in these cells. Ankyrin-B is associated with intracellular vesicles, but is not colocalized with the bulk of SERCA 1 or ryanodine receptor type 1 in skeletal muscle. These data provide the first evidence of a physiological requirement for ankyrin-B in intracellular targeting of the calcium homeostasis machinery of striated muscle and immune system, and moreover, support a catalytic role that does not involve permanent stoichiometric complexes between ankyrin-B and targeted proteins. Ankyrin-B is a member of a family of adapter proteins implicated in restriction of diverse proteins to specialized plasma membrane domains. Similar mechanisms involving ankyrins may be essential for segregation of functionally defined proteins within specialized regions of the plasma membrane and within the Ca2+ homeostasis compartment of the ER.
IκBα Overexpression Delays Tumor Formation in v-rel Transgenic Mice
Authors: Carrasco Daniel , Perez Paloma , Lewin Anne , Bravo Rodrigo
Published: July 2002

We have previously shown that transgenic mice expressing the oncoprotein v-Rel under the control of a T cell–specific promoter develop T cell lymphomas. Tumor formation was correlated with the presence of p50/v-Rel and v-Rel/v-Rel nuclear κB-binding activity. Since experimental evidence has led to the suggestion of a potential tumor suppressor activity for IκBα, we have studied the role of IκBα in the transforming activity of v-Rel by overexpressing IκBα in v-rel transgenic mice. Overexpression of IκBα in v-rel transgenic mice resulted in an extended survival, and the development of cutaneous T cell lymphomas of CD8+CD4− phenotype. These phenotypic alterations were associated with a dramatic reduction of p50/v-Rel, but not v-Rel/v-Rel nuclear DNA binding activity and an increased expression of the intercellular adhesion molecule 1. Our results indicate that v-Rel homodimers are active in transformation and that the capacity of v-Rel–containing complexes to escape the inhibitory effect of IκBα may be a key element in its transforming capability.
Early Murine Cytomegalovirus (MCMV) Infection Induces Liver Natural Killer (NK) Cell Inflammation and Protection Through Macrophage Inflammatory Protein 1α (MIP-1α)–dependent Pathways
Authors: Salazar-Mather Thais P. , Orange Jordan S. , Biron Christine A.
Published: July 2002

Natural killer (NK) cells mediate defense against early murine cytomegalovirus (MCMV) infections in liver. The chemokine, macrophage inflammatory protein 1α (MIP-1α), can promote inflammatory responses. Our studies evaluated contributions of NK cells to early MCMV-induced liver inflammation and MIP-1α requirements for inflammation and delivery of antiviral defenses. NK cells were shown to be responsible for focal inflammation, and to be induced to migrate at high levels, in MCMV-infected livers. MIP-1α gene expression was elevated at coinciding times, and mice deficient in MIP-1α function were dramatically inhibited in both inflammatory and protective liver responses. The results precisely define MIP-1α–dependent steps required to achieve NK cell inflammation during, and mechanisms promoting defense against, viral infections in tissues.
Human Immunodeficiency Virus Type 1 Vpr Is a Positive Regulator of  Viral Transcription and Infectivity in Primary Human Macrophages
Authors: Subbramanian Ramu A. , Kessous-Elbaz Allegria , Lodge Robert , Forget Janique , Yao Xiao-Jian , Bergeron Dominique , Cohen Eric A.
Published: July 2002

It is currently well established that HIV-1 Vpr augments viral replication in primary human macrophages. In its virion-associated form, Vpr has been suggested to aid efficient translocation of the proviral DNA into the cell nucleus. Although Vpr growth-arrests dividing T cells, the relevance of this biological activity in nondividing macrophages is unclear. Here we use Vpr-mutants to demonstrate that the molecular determinants involved in G2-arresting T cells are also involved in increasing viral transcription in macrophages, even though these cells are refractive to the diploid DNA status typical of G2 phase. Our results suggest that the two phenotypes, namely the nuclear localization and the G2-arrest activity of the protein, segregate functionally among the late and early functions of Vpr. The nuclear localization property of Vpr correlates with its ability to effectively target the proviral DNA to the cell nucleus early in the infection, whereas the G2-arrest phenotype correlates with its ability to activate viral transcription after establishment of an infection. These two functions may render Vpr's role essential and not accessory under infection conditions that closely mimic the in vivo situation, that is, primary cells being infected at low viral inputs.
The Fluctuating Phenotype of the Lymphohematopoietic Stem Cell with Cell Cycle Transit
Authors: Habibian Houri K. , Peters Stefan O. , Hsieh C.C. , Wuu Joanne , Vergilis Kristin , Grimaldi Christina I. , Reilly Judith , Carlson Jane E. , Frimberger Angela E. , Stewart F.M. , Quesenberry Peter J.
Published: July 2002

The most primitive engrafting hematopoietic stem cell has been assumed to have a fixed phenotype, with changes in engraftment and renewal potential occurring in a stepwise irreversible fashion linked with differentiation. Recent work shows that in vitro cytokine stimulation of murine marrow cells induces cell cycle transit of primitive stem cells, taking 40 h for progression from G0 to mitosis and 12 h for subsequent doublings. At 48 h of culture, progenitors are expanded, but stem cell engraftment is markedly diminished. We have investigated whether this effect on engraftment was an irreversible step or a reversible plastic feature correlated with cell cycle progression. Long-term engraftment (2 and 6 mo) of male BALB/c marrow cells exposed in vitro to interleukin (IL)-3, IL-6, IL-11, and steel factor was assessed at 2–4-h intervals of culture over 24–48 h using irradiated female hosts; the engraftment phenotype showed marked fluctuations over 2–4-h intervals, with engraftment nadirs occurring in late S and early G2. These data show that early stem cell regulation is cell cycle based, and have critical implications for strategies for stem cell expansion and engraftment or gene therapy, since position in cell cycle will determine whether effective engraftment occurs in either setting.
Differential Effect of B Lymphocyte–induced Maturation Protein (Blimp-1) Expression on Cell Fate during B Cell Development
Authors: Messika Eric J. , Lu Peter S. , Sung Yen-Jen , Yao Tony , Chi Jen-Tsan , Chien Yueh-hsiu , Davis Mark M.
Published: July 2002

The B lymphocyte–induced maturation protein (Blimp-1) upregulates the expression of syndecan-1 and J chain and represses that of c-myc. We have transfected Blimp-1 into two sublines of the BCL1 B cell lymphoma that represent distinct stages of B cell development in secondary lymphoid tissues. After interleukin (IL)-2 and IL-5 stimulation, the BCL1 3B3 cells differentiate into centrocyte-like cells, whereas the BCL1 5B1b cells blast and appear to be blocked at the centroblast stage. This blasting effect and the increase in IgM secretion that follows it can be blocked by a dominant negative form of Blimp-1. At the same time, the ectopic expression of Blimp-1 in these partially activated cells induces an apoptotic response that also can be suppressed by the same dominant negative protein. A similar effect was noticed when Blimp-1 was expressed in the mature L10A and the immature WEHI-231 lines, indicating this may be a general effect at earlier stages of the B cell development, and distinct from the ability of Blimp-1 to induce maturation in late stages of differentiation. Truncation mutants indicate that the induction of the apoptotic response relies mainly on 69 amino acids within Blimp-1's proline-rich domain. We propose that Blimp-1 expression defines a checkpoint beyond which fully activated B cells proceed to the plasma cell stage, whereas immature and partially activated cells are eliminated at this point.
A Processed Pseudogene Codes for a New Antigen Recognized by a Cd8+ T Cell Clone on Melanoma
Authors: Moreau-Aubry Agnès , Le Guiner Soizic , Labarrière Nathalie , Gesnel Marie-Claude , Jotereau Francine , Breathnach Richard
Published: July 2002

The M88.7 T cell clone recognizes an antigen presented by HLA B*1302 on the melanoma cell line M88. A cDNA encoding this antigen (NA88-A) was isolated using a library transfection approach. Analysis of the genomic gene's sequence identified it is a processed pseudogene, derived from a retrotranscript of mRNA coding for homeoprotein HPX42B. The NA88-A gene exhibits several premature stop codons, deletions, and insertions relative to the HPX42B gene. In NA88-A RNA, a short open reading frame codes for the peptide MTQGQHFLQKV from which antigenic peptides are derived; a stop codon follows the peptide's COOH-terminal Val codon. Part of the HPX42B mRNA's 3′ untranslated region codes for a peptide of similar sequence (MTQGQHFSQKV). If produced, this peptide can be recognized by M88.7 T cells. However, in HPX42B mRNA, the peptide's COOH-terminal Val codon is followed by a Trp codon. As a result, expression of HPX42B mRNA does not lead to antigen production. A model is proposed for events that participated in creation of a gene coding for a melanoma antigen from a pseudogene.
Inhibition of Hepatitis B Virus Replication during Schistosoma mansoni Infection in Transgenic Mice
Authors: McClary Heike , Koch Rick , Chisari Francis V. , Guidotti Luca G.
Published: July 2002

Although coinfection of hepatitis B virus (HBV) and Schistosoma mansoni is a frequent event in humans, little is known about the interactions between these two pathogens. S. mansoni infection induces T helper cell type 2 (Th2)–type cytokines in the liver of humans and mice. The intrahepatic induction of nitric oxide (NO) and Th1-type cytokines, such as interferon (IFN)-γ and IFN-α/β, inhibits HBV replication noncytopathically in the liver of transgenic mice. To examine whether S. mansoni infection and the accompanying induction of Th2-type cytokines could interfere with HBV replication in the liver, HBV transgenic mice were infected with S. mansoni. By 5 wk after infection, HBV replication disappeared concomitant with the intrahepatic induction of NO and Th1-type cytokines, and in the absence of Th2-type cytokines. By 6–8 wk after infection, HBV replication remained undetectable and this was associated with further induction of NO and Th1-type cytokines together with the appearance of Th2-type cytokines. The S. mansoni–dependent antiviral effect was partially blocked by genetically deleting IFN-γ, although it was unaffected by deletion of IFN-α/β. These results indicate that IFN-γ (probably via NO) mediates most of this antiviral activity and that Th2-type cytokines do not counteract the antiviral effect of IFN-γ. Similar events may suppress HBV replication during human S. mansoni infection.
Functional Coupling of Ca2+ Channels to Ryanodine Receptors at Presynaptic Terminals
Authors: Narita K. , Akita T. , Hachisuka J. , Huang S.-M. , Ochi K. , Kuba K.
Published: July 2002

Ca2+-induced Ca2+ release (CICR) enhances a variety of cellular Ca2+ signaling and functions. How CICR affects impulse-evoked transmitter release is unknown. At frog motor nerve terminals, repetitive Ca2+ entries slowly prime and subsequently activate the mechanism of CICR via ryanodine receptors and asynchronous exocytosis of transmitters. Further Ca2+ entry inactivates the CICR mechanism and the absence of Ca2+ entry for >1 min results in its slow depriming. We now report here that the activation of this unique CICR markedly enhances impulse-evoked exocytosis of transmitter. The conditioning nerve stimulation (10–20 Hz, 2–10 min) that primes the CICR mechanism produced the marked enhancement of the amplitude and quantal content of end-plate potentials (EPPs) that decayed double exponentially with time constants of 1.85 and 10 min. The enhancement was blocked by inhibitors of ryanodine receptors and was accompanied by a slight prolongation of the peak times of EPP and the end-plate currents estimated from deconvolution of EPP. The conditioning nerve stimulation also enhanced single impulse- and tetanus-induced rises in intracellular Ca2+ in the terminals with little change in time course. There was no change in the rate of growth of the amplitudes of EPPs in a short train after the conditioning stimulation. On the other hand, the augmentation and potentiation of EPP were enhanced, and then decreased in parallel with changes in intraterminal Ca2+ during repetition of tetani. The results suggest that ryanodine receptors exist close to voltage-gated Ca2+ channels in the presynaptic terminals and amplify the impulse-evoked exocytosis and its plasticity via CICR after Ca2+-dependent priming.
A classification of all 𝐷 such that {𝐼𝑛𝑡}(𝐷) is a Prüfer domain
Authors: Loper K.
Published: July 2002

Let

D
D

be an integral domain with quotient field

K
K

. The ring of integer-valued polynomials

I
n
t

(
D
)

\mathrm {Int}(D)

over

D
D

is defined by
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="normal upper I normal n normal t left-parenthesis upper D right-parenthesis equals left-brace f left-parenthesis x right-parenthesis element-of upper K left-bracket x right-bracket bar f left-parenthesis upper D right-parenthesis subset-of-or-equal-to upper D right-brace">

I
n
t

(
D
)
=
{
f
(
x
)
∈
K
[
x
]
∣
f
(
D
)
⊆
D
}

\mathrm {Int}(D) = \{f(x) \in K[x] \mid f(D) \subseteq D\}

. It is known that if

I
n
t

(
D
)

\mathrm {Int}(D)

is a Prüfer domain, then

D
D

is an almost Dedekind domain with all residue fields finite. This condition is necessary and sufficient if

D
D

is Noetherian, but has been shown to not be sufficient if

D
D

is not Noetherian. Several authors have come close to a complete characterization by imposing bounds on orders of residue fields of

D
D

and on normalized values of particular elements of

D
D

. In this note we give a double-boundedness condition which provides a complete charaterization of all integral domains

D
D

such that

I
n
t

(
D
)

\mathrm {Int}(D)

is a Prüfer domain.
On the computation of all extensions of a 𝑝-adic field of a given degree
Authors: Pauli Sebastian , Roblot Xavier-François
Published: July 2002

Let

k

\mathbf {k}

be a

p
p

-adic field. It is well-known that

k

\mathbf {k}

has only finitely many extensions of a given finite degree. Krasner has given formulae for the number of extensions of a given degree and discriminant. Following his work, we present an algorithm for the computation of generating polynomials for all extensions

K

/

k

\mathbf {K}/\mathbf {k}

of a given degree and discriminant.
B-splines and optimal stability
Authors: Peña J.
Published: July 2002

It is proved that, among all nonnegative bases of its space, the B-spline basis is optimally stable for evaluating spline functions.
Approximation properties of multivariate wavelets
Authors: Jia Rong-Qing
Published: July 2002

Wavelets are generated from refinable functions by using multiresolution analysis. In this paper we investigate the approximation properties of multivariate refinable functions. We give a characterization for the approximation order provided by a refinable function in terms of the order of the sum rules satisfied by the refinement mask. We connect the approximation properties of a refinable function with the spectral properties of the corresponding subdivision and transition operators. Finally, we demonstrate that a refinable function in

W

1

k
−
1

(

R

s

)

W_{1}^{k-1}(\mathbb {R}^{s})

provides approximation order

k
k

.
Power series with restricted coefficients and a root on a given ray
Authors: Beaucoup Franck , Borwein Peter , Boyd David , Pinner Christopher
Published: July 2002

We consider bounds on the smallest possible root with a specified argument

ϕ
\phi

of a power series

f
(
z
)
=
1
+

∑

n
=
1

∞

a

i

z

i

f(z)=1+{ \sum _{n=1}^{\infty }} a_{i}z^{i}

with coefficients

a

i

a_{i}

in the interval

[
−
g
,
g
]

[-g,g]

. We describe the form that the extremal power series must take and hence give an algorithm for computing the optimal root when

ϕ

/

2
π

\phi /2\pi

is rational. When

g
≥
2

2

+
3

g\geq 2\sqrt {2}+3

we show that the smallest disc containing two roots has radius

(

g

+
1

)

−
1

(\sqrt {g}+1)^{-1}

coinciding with the smallest double real root possible for such a series. It is clear from our computations that the behaviour is more complicated for smaller

g
g

. We give a similar procedure for computing the smallest circle with a real root and a pair of conjugate roots of a given argument. We conclude by briefly discussing variants of the beta-numbers (where the defining integer sequence is generated by taking the nearest integer rather than the integer part). We show that the conjugates,

λ
\lambda

, of these pseudo-beta-numbers either lie inside the unit circle or their reciprocals must be roots of

[
−
1

/

2
,
1

/

2
)

[-1/2,1/2)

power series; in particular we obtain the sharp inequality

|

λ

|

≤
3

/

2

|\lambda |\leq 3/2

.
On the generic degrees of cyclotomic algebras
Authors: Malle Gunter
Published: July 2002

We determine the generic degrees of cyclotomic Hecke algebras attached to exceptional finite complex reflection groups. The results are used to introduce the notion of spetsial reflection group, which in a certain sense is a generalization of the finite Weyl group. In particular, to spetsialWWthere is attached a set of unipotent degrees which in the case of a Weyl group is just the set of degrees of unipotent characters of finite reductive groups with Weyl groupWW, and in general enjoys many of their combinatorial properties.
Cohomology of classifying spaces and hermitian representations
Authors: Lusztig George
Published: July 2002

It is shown that a large part of the cohomology of the classifying space of a Lie group satisfying certain hypotheses can be obtained by a difference construction from hermitian representations of that Lie group. This result is relevant to the study of Novikov’s higher signatures.
Mocca: semi-automatic method for domain hunting
Authors: Notredame Cédric
Published: July 2002

Motivation: Multiple OCCurrences Analysis (Mocca) is a new method for repeat extraction. It is based on the T-Coffee package (Notredame et al. , JMB , 302, 205–217, 2000). Given a sequence or a set of sequences, and a library of local alignments, Mocca extracts every segment of sequence homologous to a pre-specified master. The implementation is meant for domain hunting and makes it fast and easy to test for new boundaries or extend known repeats in an interactive manner. Mocca is designed to deal with highly divergent protein repeats (less than 30% amino acid identity) of more than 30 amino acids.

Availability: Mocca is available on request (cedric.notredame@europe.com). The software is free of charge and comes with complete documentation.
PhyloBLAST: facilitating phylogenetic analysis of BLAST results
Authors: Brinkman Fiona S. L. , Wan Ivan , Hancock Robert E. W. , Rose Ann M. , Jones Steven J.
Published: July 2002

Summary: PhyloBLAST is an internet-accessed application based on CGI/Perl programming that compares a users protein sequence to a SwissProt/TREMBL database using BLAST2 and then allows phylogenetic analyses to be performed on selected sequences from the BLAST output. Flexible features such as ability to input your own multiple sequence alignment and use PHYLIP program options provide additional web-based phylogenetic analysis functionality beyond the analysis of a BLAST result.

Availability: This program is available from http://www.pathogenomics.bc.ca/phyloBLAST/ and the source code is freely available from the authors.

Contact: info@pathogenomics.bc.ca

* To whom correspondence should be addressed.
The utility of different representations of protein sequence
for predicting functional class
Authors: King Ross D. , Karwath Andreas , Clare Amanda , Dehaspe Luc
Published: July 2002

Motivation: Data Mining Prediction (DMP) is a novel approach to predicting protein functional class from sequence. DMP works even in the absence of a homologous protein of known function. We investigate the utility of different ways of representing protein sequence in DMP (residue frequencies, phylogeny, predicted structure) using the Escherichia coli genome as a model.

Results: Using the different representations DMP learnt prediction rules that were more accurate than default at every level of function using every type of representation. The most effective way to represent sequence was using phylogeny (75% accuracy and 13% coverage of unassigned ORFs at the most general level of function: 69% accuracy and 7% coverage at the most detailed). We tested different methods for combining predictions from the different types of representation. These improved both the accuracy and coverage of predictions, e.g. 40% of all unassigned ORFs could be predicted at an estimated accuracy of 60% and 5% of unassigned ORFs could be predicted at an estimated accuracy of 86%.

Availability: The rules and data are freely available. Warmr is free to academics.

Contact: rdk@aber.ac.uk

Supplementary information: http://www.aber.ac.uk/~dcswww/Research/bio/ProteinFunction

* To whom correspondence should be addressed.
MAC5: Bayesian inference of phylogenetic trees from DNA

sequences incorporating gaps
Authors: McGuire Gráinne , Denham Michael C. , Balding David J.
Published: July 2002

Summary: MAC5 implements MCMC sampling of the posterior distribution of tree topologies from DNA sequences containing gaps by using a five state model of evolution (the four nucleotides and the gap character).

Availability: MAC5 is available from http://www.reading.ac.uk/statistics/genetics/ under the software link.

Contact: gmcguire@hgmp.mrc.ac.uk
Prevention of severe ovarian hyperstimulation syndrome in IVF with or without ICSI and embryo transfer: a modified `coasting' strategy based on ultrasound for identification of high-risk patients
Authors: Al-Shawaf T. , Zosmer A. , Hussain S. , Tozer A. , Panay N. , Wilson C. , Lower A.M. , Grudzinskas J.G.
Published: July 2002

Ovarian hyperstimulation syndrome (OHSS) can be a severe and potentially life-threatening complication of ovarian stimulation for IVF. Coasting or withholding gonadotrophin stimulation relies on frequent estimation of serum oestradiol to identify patients at risk. A modified coasting protocol was developed in which identification of patients at risk of severe OHSS was based on ultrasound monitoring. Serum oestradiol concentrations were measured only in patients with >20 follicles on ultrasound (high risk). If serum oestradiol concentrations were <3000 pmol/l, the gonadotrophin dose was maintained; if concentrations were ≥3000 pmol/l but <13200 pmol/l and ≥25% of the follicles had a diameter of ≥13 mm, the gonadotrophin dose was halved; and if serum oestradiol concentrations were ≥13 200 pmol/l and ≥25% of the follicles had a diameter of ≥15 mm, patients were coasted. In the latter group, human chorionic gonadotrophin (HCG) 10000 IU was administered when at least three follicles had a diameter of ≥18 mm and serum oestradiol concentrations were <10000 pmol/l. Over a 10 month period, serum oestradiol concentrations were measured in 123 out of 580 cycles (24%) and in 50 cycles, gonadotrophins were withheld. Overall, moderate OHSS occurred in three patients (0.7%) and severe OHSS in one patient (0.2%). The pregnancy rates in the cycles where the gonadotrophin dose was reduced or withheld were 39.6 and 40% per cycle respectively; corresponding implantation rates were 30.7 and 25.6%. It is concluded that the modified coasting strategy is associated with a low risk of moderate and severe OHSS to a minimum without compromising pregnancy rates. Identification of patients at risk by ultrasound reduces the number of serum oestradiol measurements and thus inconvenience to patients as well as costs and workload.
Monitor unit settings for intensity modulated beams delivered using a step‐and‐shoot approach
Authors: Sharpe M. B. , Miller B. M. , Yan D. , Wong J. W.
Published: July 2002

Two linear accelerators have been commissioned for delivering IMRT treatments using a step‐and‐shoot approach. To assess beam startup stability for 6 and 18 MV x‐ray beams, dose delivered per monitor unit (MU), beam flatness, and beam symmetry were measured as a function of the total number of MU delivered at a clinical dose rate of 400 MU per minute. Relative to a 100 MU exposure, the dose delivered per MU by both linear accelerators was found to be within ±2% for exposures larger than 4 MU. Beam flatness and symmetry also met accepted quality assurance standards for a minimum exposure of 4 MU. We have found that the performance of the two machines under study is well suited to the delivery of step‐and‐shoot IMRT. A system of dose calculation has also been commissioned for applying head scatter corrections to fields as small as 1×1 cm2. The accuracy and precision of the relative output calculations in water was validated for small fields and fields offset from the axis of collimator rotation. For both 6 and 18 MV x‐ray beams, the dose per MU calculated in a water phantom agrees with measured data to within 1% on average, with a maximum deviation of 2.5%. The largest output factor discrepancies were seen when the actual radiation field size deviated from the set field size. The measured output in water can vary by as much 16% for 1×1 cm2 fields, when the measured field size deviates from the set field size by 2 mm. For a 1 mm deviation, this discrepancy was reduced to 8%. Steps should be taken to ensure collimator precision is tightly controlled when using such small fields. If this is not possible, very small fields should not contribute to a significant portion of the treatment, or uncertainties in the collimator position may effect the accuracy of the dose delivered.
Elasticity reconstruction from experimental MR displacement data: initial experience with an overlapping subzone finite element inversion process
Authors: Van Houten E. E. W. , Weaver J. B. , Miga M. I. , Kennedy F. E. , Paulsen K. D.
Published: July 2002

The determination of the elastic property distribution in heterogeneous gel samples with a finite element based reconstruction scheme is considered. The algorithm operates on small overlapping subzones of the total field to allow for a high degree of spatial discretization while maintaining computational tractability. By including a Maxwellian‐type viscoelastic property in the model physics and optimizing the spatial distribution of this property in the same manner as elasticity, a Young's modulus image is obtained which reasonably reflects the true distribution within the gel. However, the image lacks the clarity and accuracy expected based on simulation experience. Preliminary investigations suggest that transient effects in the data are the cause of a significant mismatch between the inversion model, which assumes steady‐state conditions, and the actual displacements as measured by a phase contrast MR technique.