bluuebunny/crossref_metadata_2025 huggingface dataset:
The metalloprotease Kuzbanian (ADAM10) mediates the transactivation of EGF receptor by G protein–coupled receptors
Authors: Yan Yibing , Shirakabe Kyoko , Werb Zena
Published: July 2002

Communication between different signaling pathways enables cells to coordinate the responses to diverse environmental signals. Activation of the transmembrane growth factor precursors plays a critical role in this communication and often involves metalloprotease-mediated proteolysis. Stimulation of G protein–coupled receptors (GPCR) transactivates the EGF receptors (EGFRs), which occurs via a metalloprotease-dependent cleavage of heparin-binding EGF (HB-EGF). However, the metalloprotease mediating the transactivation remains elusive. We show that the integral membrane metalloprotease Kuzbanian (KUZ; ADAM10), which controls Notch signaling in Drosophila, stimulates GPCR transactivation of EGFR. Upon stimulation of the bombesin receptors, KUZ increases the docking and activation of adaptors Src homology 2 domain–containing protein and Gab1 on the EGFR, and activation of Ras and Erk. In contrast, transfection of a protease domain–deleted KUZ, or blocking endogenous KUZ by morpholino antisense oligonucleotides, suppresses the transactivation. The effect of KUZ on shedding of HB-EGF and consequent transactivation of the EGFR depends on its metalloprotease activity. GPCR activation enhances the association of KUZ and its substrate HB-EGF with tetraspanin CD9. Thus, KUZ regulates the relay between the GPCR and EGFR signaling pathways.
Requirement for RAR-mediated gene repression in skeletal progenitor differentiation
Authors: Weston Andrea D. , Chandraratna Roshantha A.S. , Torchia Joseph , Underhill T. Michael
Published: July 2002

Chondrogenesis is a multistep process culminating in the establishment of a precisely patterned template for bone formation. Previously, we identified a loss in retinoid receptor–mediated signaling as being necessary and sufficient for expression of the chondroblast phenotype (Weston et al., 2000. J. Cell Biol. 148:679–690). Here we demonstrate a close association between retinoic acid receptor (RAR) activity and the transcriptional activity of Sox9, a transcription factor required for cartilage formation. Specifically, inhibition of RAR-mediated signaling in primary cultures of mouse limb mesenchyme results in increased Sox9 expression and activity. This induction is attenuated by the histone deacetylase inhibitor, trichostatin A, and by coexpression of a dominant negative nuclear receptor corepressor-1, indicating an unexpected requirement for RAR-mediated repression in skeletal progenitor differentiation.

Inhibition of RAR activity results in activation of the p38 mitogen-activated protein kinase (MAPK) and protein kinase A (PKA) pathways, indicating their potential role in the regulation of chondrogenesis by RAR repression. Accordingly, activation of RAR signaling, which attenuates differentiation, can be rescued by activation of p38 MAPK or PKA. In summary, these findings demonstrate a novel role for active RAR-mediated gene repression in chondrogenesis and establish a hierarchical network whereby RAR-mediated signaling functions upstream of the p38 MAPK and PKA signaling pathways to regulate emergence of the chondroblast phenotype.
Modulation of receptor cycling by neuron-enriched endosomal protein of 21 kD
Authors: Steiner Pascal , Sarria J.-C. Floyd , Glauser Liliane , Magnin Sarah , Catsicas Stefan , Hirling Harald
Published: July 2002

Although correct cycling of neuronal membrane proteins is essential for neurite outgrowth and synaptic plasticity, neuron-specific proteins of the implicated endosomes have not been characterized. Here we show that a previously cloned, developmentally regulated, neuronal protein of unknown function binds to syntaxin 13. We propose to name this protein neuron-enriched endosomal protein of 21 kD (NEEP21), because it is colocalized with transferrin receptors, internalized transferrin (Tf), and Rab4. In PC12 cells, NEEP21 overexpression accelerates Tf internalization and recycling, whereas its down-regulation strongly delays Tf recycling. In primary neurons, NEEP21 is localized to the somatodendritic compartment, and, upon N-methyl-d-aspartate (NMDA) stimulation, the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptor subunit GluR2 is internalized into NEEP21-positive endosomes. NEEP21 down-regulation retards recycling of GluR1 to the cell surface after NMDA stimulation of hippocampal neurons. In summary, NEEP21 is a neuronal protein that is localized to the early endosomal pathway and is necessary for correct receptor recycling in neurons.
The cytoplasmic filaments of the nuclear pore complex are dispensable for selective nuclear protein import
Authors: Walther Tobias C. , Pickersgill Helen S. , Cordes Volker C. , Goldberg Martin W. , Allen Terry D. , Mattaj Iain W. , Fornerod Maarten
Published: July 2002

The nuclear pore complex (NPC) mediates bidirectional macromolecular traffic between the nucleus and cytoplasm in eukaryotic cells. Eight filaments project from the NPC into the cytoplasm and are proposed to function in nuclear import. We investigated the localization and function of two nucleoporins on the cytoplasmic face of the NPC, CAN/Nup214 and RanBP2/Nup358. Consistent with previous data, RanBP2 was localized at the cytoplasmic filaments. In contrast, CAN was localized near the cytoplasmic coaxial ring. Unexpectedly, extensive blocking of RanBP2 with gold-conjugated antibodies failed to inhibit nuclear import. Therefore, RanBP2-deficient NPCs were generated by in vitro nuclear assembly in RanBP2-depleted Xenopus egg extracts. NPCs were formed that lacked cytoplasmic filaments, but that retained CAN. These nuclei efficiently imported nuclear localization sequence (NLS) or M9 substrates. NPCs lacking CAN retained RanBP2 and cytoplasmic filaments, and showed a minor NLS import defect. NPCs deficient in both CAN and RanBP2 displayed no cytoplasmic filaments and had a strikingly immature cytoplasmic appearance. However, they showed only a slight reduction in NLS-mediated import, no change in M9-mediated import, and were normal in growth and DNA replication. We conclude that RanBP2 is the major nucleoporin component of the cytoplasmic filaments of the NPC, and that these filaments do not have an essential role in importin α/β– or transportin-dependent import.
L1 endocytosis is controlled by a phosphorylation-dephosphorylation cycle stimulated by outside-in signaling by L1
Authors: Schaefer Andrew W. , Kamei Yoshimasa , Kamiguchi Hiroyuki , Wong Eric V. , Rapoport Iris , Kirchhausen Tomas , Beach Carol M. , Landreth Gary , Lemmon Sandra K. , Lemmon Vance
Published: July 2002

Dynamic regulation of the cell surface expression of adhesion molecules is an important mechanism for controlling neuronal growth cone motility and guidance. Clathrin-mediated vesicular internalization of L1 via the tyrosine-based endocytosis motif YRSL regulates adhesion and signaling by this Ig superfamily molecule. Here, we present evidence that tyrosine-1176 (Y1176) of the YRSL motif is phosphorylated in vivo. The nonreceptor tyrosine kinase (p60src) is implicated in L1-mediated neurite outgrowth, and we find that p60src phosphorylates Y1176 in vitro. Phosphorylation of Y1176 prevents L1 binding to AP-2, an adaptor required for clathrin-mediated internalization of L1. mAb 74-5H7 recognizes the sequence immediately NH2-terminal to the tyrosine-based motif and binds L1 only when Y1176 is dephosphorylated. 74-5H7 identifies a subset of L1 present at points of cell–cell contact and in vesicle-like structures that colocalize with an endocytosis marker. L1–L1 binding or L1 cross-linking induces a rapid increase in 74-5H7 immunoreactivity. Our data suggest a model in which homophilic binding or L1 cross-linking triggers transient dephosphorylation of the YRSL motif that makes L1 available for endocytosis. Thus, the regulation of L1 endocytosis through dephosphorylation of Y1176 is a critical regulatory point of L1-mediated adhesion and signaling.
Antigen-independent Induction of Histamine Synthesis by Immunoglobulin E in Mouse Bone Marrow–derived Mast Cells
Authors: Tanaka Satoshi , Takasu Yuhji , Mikura Sonoko , Satoh Norio , Ichikawa Atsushi
Published: July 2002

Immunoglobulin (Ig)E-mediated activation of mast cells has long been thought to occur only when FcϵRI receptor-bound IgE is cross-linked via multivalent antigens. However, recent studies have raised the possibility that mast cells may be activated by the binding of IgE to the FcϵRI receptor in the absence of antigen. Here we demonstrate that IgE binding without antigen induces the expression of histidine decarboxylase (HDC) in mouse interleukin (IL)-3–dependent bone marrow–derived mast cells (BMMCs). The induction of HDC by the binding of IgE was found to require an influx of extracellular calcium ions, which was attenuated by pretreatment with U73122, a phospholipase C inhibitor. Furthermore, the increase in HDC activity upon sensitization with IgE was completely suppressed by pretreatment of BMMCs with protein kinase C inhibitors, such as H7, staurosporine, and Gö6976. In addition, immediate activation of the tyrosine kinase Lyn was not detectable upon treatment with IgE. These results suggest that the binding of IgE to its receptor in the absence of antigen results in de novo synthesis of HDC in BMMCs through a signaling pathway distinct to that operating during antigen-stimulated FcϵRI activation.
The Immune Regulatory Function of Lymphoproliferative Double Negative T Cells In Vitro and In Vivo
Authors: Ford Megan S. , Young Kevin J. , Zhang Zhuxu , Ohashi Pamela S. , Zhang Li
Published: July 2002

Lymphoproliferative (lpr) mice, which lack functional Fas receptor expression and develop autoimmune lymphoproliferative disease, have an accumulation of T cell receptor-αβ+CD4−CD8− (double negative T cells [DNTC]) in the periphery. The function of the accumulating DNTC is not clear. In this study we demonstrate that B6/lpr DNTC can dose dependently kill syngeneic CD8+ and CD4+ T cells from wild-type B6 mice through Fas/Fas ligand interactions in vitro. We also demonstrate that B6/lpr DNTC that are activated and expand in vivo are able to specifically down-regulate allogeneic immune responses mediated by syngeneic Fas+CD4+ and CD8+ T cells in vivo. B6/lpr DNTC that have been preactivated in vivo by infusion of either class I– (bm1) or class II– (bm12) mismatched allogeneic lymphocytes are able to specifically enhance the survival of bm1 or bm12, but not third-party skin allografts when adoptively transferred into naive B6+/+ mice. These findings clearly demonstrate that B6/lpr DNTC have a potent immune regulatory function in vitro and in vivo. They also provide new insights into the mechanisms involved in the development of autoimmune disease in lpr mice.
Overexpression of Interleukin (IL)-7 Leads to IL-15–independent Generation of Memory Phenotype CD8+ T Cells
Authors: Kieper William C. , Tan Joyce T. , Bondi-Boyd Brea , Gapin Laurent , Sprent Jonathan , Ceredig Rhodri , Surh Charles D.
Published: July 2002

Transgenic (TG) mice expressing a high copy number of interleukin (IL)-7 cDNA under the control of the major histocomaptability complex (MHC) class II promoter display a 10–20-fold increase in total T cell numbers. Here, we show that the increase in T cell numbers in IL-7 TG mice is most apparent at the level of memory phenotype CD44hi CD122hi CD8+ cells. Based on studies with T cell receptor (TCR) TG mice crossed to IL-7 TG mice, increased levels of IL-7 may provide costimulation for TCR recognition of self-MHC ligands and thus cause naive CD8+ cells to proliferate and differentiate into memory phenotype cells. In addition, a marked increase in CD44hi CD122hi CD8+ cells was found in IL-7 TG IL-15− mice. Since these cell are rare in normal IL-15− mice, the dependency of memory phenotype CD8+ cells on IL-15 can be overcome by overexpression of IL-7.
A Critical Role for Natural Killer T Cells in Immunosurveillance of Methylcholanthrene-induced Sarcomas
Authors: Crowe Nadine Y. , Smyth Mark J. , Godfrey Dale I.
Published: July 2002

Natural killer (NK) T cells initiate potent antitumor responses when stimulated by exogenous factors such as interleukin (IL)-12 or α-galactosylceramide (α-GalCer), however, it is not clear whether this reflects a physiological role for these cells in tumor immunity. Through adoptive transfer of NK T cells from wild-type to NK T cell–deficient (T cell receptor [TCR] Jα281−/−) mice, we demonstrate a critical role for NK T cells in immunosurveillance of methylcholanthrene (MCA)-induced fibrosarcomas, in the absence of exogenous stimulatory factors. Using the same approach with gene-targeted and/or antibody-depleted donor or recipient mice, we have shown that this effect depends on CD1d recognition and requires the additional involvement of both NK and CD8+ T cells. Interferon-γ production by both NK T cells and downstream, non-NK T cells, is essential for protection, and perforin production by effector cells, but not NK T cells, is also critical. The protective mechanisms in this more physiologically relevant system are distinct from those associated with α-GalCer–induced, NK T cell–mediated, tumor rejection. This study demonstrates that, in addition to their importance in tumor immunotherapy induced by IL-12 or α-GalCer, NK T cells can play a critical role in tumor immunosurveillance, at least against MCA-induced sarcomas, in the absence of exogenous stimulation.
Contributions of the T Cell Receptor–associated CD3γ–ITAM to Thymocyte Selection
Authors: Haks Mariëlle C. , Pépin Elsa , van den Brakel Jeroen H.N. , Smeele Sigrid A.A. , Belkowski Stanley M. , Kessels Helmut W.H.G. , Krimpenfort Paul , Kruisbeek Ada M.
Published: July 2002

The immunoreceptor tyrosine-based activation motifs (ITAMs) in the CD3 chains associated with the T cell receptor (TCR) are crucial for TCR signaling. To probe the role of the CD3γ–ITAM in T cell development, we created knock-in mice in which the CD3γ chain of the TCR complex is replaced by a mutant signaling-deficient CD3γ chain, lacking the CD3γ–ITAM. This mutation results in considerable impairment in positive selection in the polyclonal TCR repertoire. When CD3γ–ΔITAM mice are crossed to mice expressing transgenic F5 TCRs, their thymocytes are completely unable to perform positive selection in vivo in response to intrathymic ligands. Also, the in vitro positive selection response of double-positive (DP) thymocytes with F5–CD3γ–ΔITAM mutant receptors to their agonist ligand and many of its variants is severely impaired or abrogated. Yet, the binding and dissociation constants of agonist ligands for the F5 receptor are not affected by the CD3γ–ΔITAM mutation. Furthermore, DP thymocytes with mutant receptors can respond to agonist ligand with normal antigen sensitivity and to normal levels, as shown by their ability to induce CD69 up-regulation, TCR down-regulation, negative selection, and ZAP70 and c-Jun NH2-terminal kinase activation. In sharp contrast, induction of extracellular signal-regulated kinase (ERK) activation and linker for activation of T cells (LAT) phosphorylation are severely impaired in these cells. Together, these findings underscore that intrinsic properties of the TCR–CD3 complex regulate selection at the DP checkpoint. More importantly, this analysis provides the first direct genetic evidence for a role of the CD3γ–ITAM in TCR-driven thymocyte selection.
Interleukin 15 Is Required for Proliferative Renewal of Virus-specific Memory CD8 T Cells
Authors: Becker Todd C. , Wherry E. John , Boone David , Murali-Krishna Kaja , Antia Rustom , Ma Averil , Ahmed Rafi
Published: July 2002

The generation and efficient maintenance of antigen-specific memory T cells is essential for long-lasting immunological protection. In this study, we examined the role of interleukin (IL)-15 in the generation and maintenance of virus-specific memory CD8 T cells using mice deficient in either IL-15 or the IL-15 receptor α chain. Both cytokine- and receptor-deficient mice made potent primary CD8 T cell responses to infection with lymphocytic choriomeningitis virus (LCMV), effectively cleared the virus and generated a pool of antigen-specific memory CD8 T cells that were phenotypically and functionally similar to memory CD8 T cells present in IL-15+/+ mice. However, longitudinal analysis revealed a slow attrition of virus-specific memory CD8 T cells in the absence of IL-15 signals.This loss of CD8 T cells was due to a severe defect in the proliferative renewal of antigen-specific memory CD8 T cells in IL-15−/− mice. Taken together, these results show that IL-15 is not essential for the generation of memory CD8 T cells, but is required for homeostatic proliferation to maintain populations of memory cells over long periods of time.
Infectious Tolerance
Authors: Jonuleit Helmut , Schmitt Edgar , Kakirman Hacer , Stassen Michael , Knop Jürgen , Enk Alexander H.
Published: July 2002

Regulatory CD4+CD25+ T cells (Treg) are mandatory for maintaining immunologic self-tolerance. We demonstrate that the cell-cell contact–mediated suppression of conventional CD4+ T cells by human CD25+ Treg cells is fixation resistant, independent from membrane-bound TGF-β but requires activation and protein synthesis of CD25+ Treg cells. Coactivation of CD25+ Treg cells with Treg cell–depleted CD4+ T cells results in anergized CD4+ T cells that in turn inhibit the activation of conventional, freshly isolated CD4+ T helper (Th) cells. This infectious suppressive activity, transferred from CD25+ Treg cells via cell contact, is cell contact–independent and partially mediated by soluble transforming growth factor (TGF)-β. The induction of suppressive properties in conventional CD4+ Th cells represents a mechanism underlying the phenomenon of infectious tolerance. This explains previously published conflicting data on the role of TGF-β in CD25+ Treg cell–induced immunosuppression.
Human CD4+CD25+ Regulatory, Contact-dependent T Cells Induce Interleukin 10–producing, Contact-independent Type 1-like Regulatory T Cells
Authors: Dieckmann Detlef , Bruett Cord Henrik , Ploettner Heidi , Lutz Manfred Bernhard , Schuler Gerold
Published: July 2002

It has been recently demonstrated that regulatory CD4+CD25+ CD45RO+ T cells are present in the peripheral blood of healthy adults and exert regulatory function similar to their rodent counterparts. It remains difficult to understand how the small fraction of these T cells that regulate via direct cell-to-cell contact and not via secretion of immunosuppressive cytokines could mediate strong immune suppression. Here we show that human CD4+CD25+ T cells induce long-lasting anergy and production of interleukin (IL)-10 in CD4+CD25− T cells. These anergized CD4+CD25− T cells then suppress proliferation of syngenic CD4+ T cells via IL-10 but independent of direct cell contact, similar to the so-called type 1 regulatory T (Tr1) cells. This ‘catalytic’ function of CD4+CD25+ T cells to induce Tr1-like cells helps to explain their central role for the maintenance of immune homeostasis.
Magnetic Properties and Magnetoresistance Effect of
YMn6Sn6-x
Cr
x
(x = 0-0.8) Compounds
Authors: Zhang Li-Gang  , Li Yun-Bao  , Zhang Shao-Ying  , Yao Jin-Lei  , Shen Bao-Gen
Published: July 2002

The magnetic properties and magnetoresistance effect of
YMn6Sn6-x
Cr
x
(x = 0-0.8) compounds have been experimentally
studied by magnetic properties and resistivity measurements in the applied
field range 0-5 T. The compound (x = 0.8) displays a ferromagnetic behaviour,
while the compounds (x = 0-0.4) display an antiferromagnetic behaviour in the
whole ordering temperature range. The compounds (x = 0.5, 0.6) experienced a
transition from an antiferromagnetic state to a ferromagnetic state with
increasing temperature. The compound with x = 0.8 is rapidly saturated in the
lower magnetic field with saturation magnetization of 35.92 emu/g. The
compounds (x = 0-0.6) display a field-induced metamagnetic transition, and the
threshold fields decrease with increasing Cr content. The cell-volume V
of compounds (x = 0-0.8) increases, and the ordering temperature decreases
with the increasing Cr content. A large magnetoresistance effect was
observed for the compounds (x = 0.4, 0.5), and the maximum absolute
value at 5 K are 32% and 24% under 5 T for x = 0.4 and x = 0.5, respectively.
MOUSE (Mitochondrial and Other Useful SEquences)
a compilation of population genetic markers
Authors: Burckhardt Florian
Published: July 2002

Summary: Mitochondrial and Other Useful SEquences (MOUSE) is an integrated and comprehensive compilation of mtDNA from hypervariable regions I and II and of the low recombining nuclear loci Xq13.3 from about 11 200 humans and great apes, whose geographic and if applicable, linguistic classification is stored with their aligned sequences and publication details. The goal is to provide population geneticists and genetic epidemiologists with a comprehensive and user friendly repository of sequences and population information that is usually dispersed in a variety of other sources.

Availability: http://www.gen-epi.de/mouse

Contact: florian.burckhardt@gsf.de

Supplementary Information: Documentation and detailed information on population subgroups is available on the homepage: http://www.gen-epi.de/mouse
Determining a unique defining DNA sequence for yeast species using hashing techniques
Authors: Wesselink Jan-Jaap , de la Iglesia Beatriz , James Stephen A. , Dicks Jo L. , Roberts Ian N. , Rayward-Smith Vic J.
Published: July 2002

Motivation: Yeasts are often still identified with physiological growth tests, which are both time consuming and unsuitable for detection of a mixture of organisms. Hence, there is a need for molecular methods to identify yeast species.

Results: A hashing technique has been developed to search for unique DNA sequences in 702 26S rRNA genes. A unique DNA sequence has been found for almost every yeast species described to date. The locations of the unique defining sequences are in accordance with the variability map of large subunit ribosomal RNA and provide detail of the evolution of the D1/D2 region. This approach will be applicable to the rapid identification of unique sequences in other DNA sequence sets.

Availability: Freely available upon request from the authors.

Supplementary information: Results are available at http://www.sys.uea.ac.uk/~jjw/project/paper

Contact: jjw@sys.uea.ac.uk

* To whom correspondence should be addressed.
About the use of protein models
Authors: Peitsch Manuel C.
Published: July 2002

Protein models can be of great assistance in functional genomics, as they provide the structural insights often necessary to understand protein function. Although comparative modelling is far from yielding perfect structures, this is still the most reliable method and the quality of the predictions is now well understood. Models can be classified according to their correctness and accuracy, which will impact their applicability and usefulness in functional genomics and a variety of situations.

Contact: manuel.peitsch@pharma.novartis.com; manuel.peitsch@isb-sib.ch
UNOFFICIAL EXCHANGE RATES IN BANGLADESH: A COINTEGRATION ANALYSIS
Authors: Siddiki Jalal U.
Published: July 2002

This article estimates a structural model for unofficial market foreign exchange (forex) rates (EU) and examines the stability of the forex market in Bangladesh using an autoregressive distributed lag approach to cointegration analysis on quarterly data from 1976Q2–1995Q2. It also compares the in‐sample and out‐of‐sample (from 1995Q3–1999Q2) forecasting performances of the structural model with other timE‐series models. With EU as a dependent variable and official exchange rates (EO), money supply (M), the difference between foreign and domestic interest rates (I), forex reserves relative to imports (Q) and political along with some structural factors (D85) as explanatory variables, a multivariate cointegrated relationship is found in which EO, Q, and I cause an appreciation and M and D85 cause a depreciation in EU. These results imply that the overvaluation of the official exchange rate, increases in money supply, the paucity of official forex reserves, and structural factors are the main causes for the creation of the unofficial market for forex in Bangladesh. Results also reveal that the forex market in Bangladesh is stable during the sample period. The structural model performs well in in‐sample prediction, and the random walk model performs best in out‐of‐sample forecasting.
A Disinflation Trade‐Off: Speed Versus Final Destination
Authors: Carlson John A. , Valev Neven T.
Published: July 2002

When introducing a new monetary regime designed to reduce inflation, does a central bank prefer more or fewer economic agents who form informed forecasts of inflation? The relevance of the question arises because the central bank can make a decision about how much information to disseminate about the nature of the new regime. We find that the central bank will prefer a higher proportion of agents who form rational expectations if it disinflates from a high level of inflation, but not so if it disinflates from a moderate or low inflation level.
Critical evaluation of the role of the Toll‐like receptor 18‐Wheeler in the host defense of Drosophila
Authors: Ligoxygakis Petros , Bulet Philippe , Reichhart Jean‐Marc
Published: July 2002

Essential aspects of innate immune responses to microbial infections appear to be conserved between insects and mammals. In particular, in both groups, transmembrane receptors of the Toll superfamily play a crucial role in activating immune defenses. The Drosophila Toll family member 18‐Wheeler had been proposed to sense Gram‐negative infection and direct selective expression of peptides active against Gram‐negative bacteria. Here we re‐examine the role of 18‐Wheeler and show that in adults it is dispensable for immune responses. In larvae, 18wheeler is required for normal fat body development, and in mutant larvae induction of all antimicrobial peptide genes, and not only of those directed against Gram‐negative bacteria, is compromised. 18‐Wheeler does not qualify as a pattern recognition receptor of Gram‐negative bacteria.
CARD games in apoptosis and immunity
Authors: Bouchier‐Hayes Lisa , Martin Seamus J
Published: July 2002

A bewildering array of proteins containing the caspase recruitment domain (CARD) have now been identified. Previously, CARD–CARD interactions have been shown to be involved in the assembly of protein complexes that promote caspase processing and activation in the context of apoptosis. However, as the family of CARD‐containing proteins has grown, it has become apparent that the majority of these proteins do not recruit caspases or promote caspase activation. Instead, many participate in NF‐κB signalling pathways associated with innate or adaptive immune responses. Here, we suggest a simplified classification of the CARD proteins based upon their domain structures and discuss the divergent roles of these proteins in the context of host defence.
Designed transcription factors as structural, functional and therapeutic probes of chromatin in vivo
Authors: Urnov Fyodor D , Rebar Edward J , Reik Andreas , Pandolfi Pier Paolo
Published: July 2002

Despite its central importance in gene regulation, chromatin in mammalian cells remains relatively poorly understood—a predicament due to the paucity of robust genetic tools in mammals, the complexity of the chromatin remodeling machinery, and the dynamic properties of chromatin in vivo. Here we review recent developments in understanding endogenous mammalian gene regulation via the use of designed transcription factors (TFs). These include mutated forms of naturally occurring TFs that exhibit dominant‐negative activity, and designed proteins with novel, predetermined DNA‐binding specificities. Systematic targeting of designed TFs to particular promoters is helping to illuminate the complex rules that chromatin imposes on TF access and action in vivo. We evaluate the potential applications of these proteins as probes of mammalian chromatin‐based regulatory pathways and their potential for the therapy of human disease, highlighting leukemia in particular.
What Counts as Evidence? Reply
Authors: Seawright Jason
Published: July 2002

The complex question of what counts as appropriate evidence for necessary and/or sufficient causation merits careful, ongoing discussion. I thank Kevin Clarke (2002) and Bear Braumoeller and Gary Goertz (2002) for their thoughtful responses to my (Seawright 2002) article, and I discuss their comments in turn.
Physiological and ecological significance of biological ice nucleators
Authors: Lundheim Rolv
Published: July 2002

When a pure water sample is cooled it can remain in the liquid state at temperatures well below its melting point (0 °C). The initiation of the transition from the liquid state to ice is called nucleation. Substances that facilitate this transition so that it takes place at a relatively high sub–zero temperature are called ice nucleators. Many living organisms produce ice nucleators. In some cases, plausible reasons for their production have been suggested. In bacteria, they could induce frost damage to their hosts, giving the bacteria access to nutrients. In freeze–tolerant animals, it has been suggested that ice nucleators help to control the ice formation so that it is tolerable to the animal. Such ice nucleators can be called adaptive ice nucleators. There are, however, also examples of ice nucleators in living organisms where the adaptive value is difficult to understand. These ice nucleators might be structures with functions other than facilitating ice formation. These structures might be called incidental ice nucleators.
Genomics and plant cells: application of genomics strategies to
Arabidopsis
cell biology
Authors: Bevan Michael
Published: July 2002

In this review I seek to describe how the complete catalogue of plant genes and proteins, revealed by genome sequencing, can provide novel insights into cell biology. Many new analytical methods have been developed to digest the flood of genome sequence data, including analysis of the transcriptome, proteome and metabolites. High-throughput analysis of protein targeting and other methods will ascribe new information to proteins and create important links with other large datasets. To fulfil the potential revealed by this genomic information, many challenges have to be met. Among these are organizational changes needed to create common datasets accessible to all scientists, and bioinformatics solutions to capture and integrate diverse datasets. Once harnessed, these new strategies will irrevocably change the way we conduct plant science.
Cytoskeleton and plant organogenesis
Authors: Kost Benedikt , Bao Yi-Qun , Chua Nam-Hai
Published: July 2002

The functions of microtubules and actin filaments during various processes that are essential for the growth, reproduction and survival of single plant cells have been well characterized. A large number of plant structural cytoskeletal or cytoskeleton–associated proteins, as well as genes encoding such proteins, have been identified. Although many of these genes and proteins have been partially characterized with respect to their functions, a coherent picture of how they interact to execute cytoskeletal functions in plant cells has yet to emerge. Cytoskeleton–controlled cellular processes are expected to play crucial roles during plant cell differentiation and organogenesis, but what exactly these roles are has only been investigated in a limited number of studies in the whole plant context. The intent of this review is to discuss the results of these studies in the light of what is known about the cellular functions of the plant cytoskeleton, and about the proteins and genes that are required for them. Directions are outlined for future work to advance our understanding of how the cytoskeleton contributes to plant organogenesis and development.
Roles for kinesin and myosin during cytokinesis
Authors: Hepler Peter K. , Valster Aline , Molchan Tasha , Vos Jan W.
Published: July 2002

Cytokinesis in higher plants involves the phragmoplast, a complex cytoplasmic structure that consists of microtubules (MTs), microfilaments (MFs) and membrane elements. Both MTs and MFs are essential for cell plate formation, although it is not clear which motor proteins are involved. Some candidate processes for motor proteins include transport of Golgi vesicles to the plane of the cell plate and the spatiotemporal organization of the cytoskeletal elements in order to achieve proper deposition and alignment of the cell plate. We have focused on the kinesin–like calmodulin binding protein (KCBP) and, more broadly, on myosins. Using an antibody that constitutively activates KCBP, we find that this MT motor, which is minus–end directed, contributes to the organization of the spindle and phragmoplast MTs. It does not participate in vesicle transport; rather, because of the orientation of the phragmoplast MTs, it is supposed that plus–end kinesins fill this role. Myosins, on the other hand, based on their inhibition with 2,3–butanedione monoxime and 1–(5–iodonaphthalene–1–sulphonyl)–1H–hexahydro–1,4–diazepine (ML–7), are associated with the process of post–mitotic spindle/phragmoplast alignment and with late lateral expansion of the cell plate. They are also not the principal motors involved in vesicle transport.
Preface
Authors: Bowles Diana J. , Lillford Peter J. , Rees David A. , Shanks Ian A.
Published: July 2002

Many scientists are exploring the survival strategies of organisms that experience cold climates and freezing conditions. Necessarily, research is focused on particular terrains, species, or the molecular adaptations they display that contribute to their survival. Rarely, however, is the current knowledge assembled and compared, so it was the intention of this meeting to begin such a process.
Microtubule capture by the cleavage apparatus is required for proper spindle positioning in yeast
Authors: Kusch Justine , Meyer Anne , Snyder Michael P. , Barral Yves
Published: July 2002

Cell division is the result of two major cytoskeletal events: partition of the chromatids by the mitotic spindle and cleavage of the cell by the cytokinetic apparatus. Spatial coordination of these events ensures that each daughter cell inherits a nucleus. Here we show that, in budding yeast, capture and shrinkage of astral microtubules at the bud neck is required to position the spindle relative to the cleavage apparatus. Capture required the septins and the microtubule-associated protein Kar9. Like Kar9-defective cells, cells lacking the septin ring failed to position their spindle correctly and showed an increased frequency of nuclear missegregation. Microtubule attachment at the bud neck was followed by shrinkage and a pulling action on the spindle. Enhancement of microtubule shrinkage at the bud neck required the Par-1-related, septin-dependent kinases (SDK) Hsl1 and Gin4. Neither the formin Bnr1 nor the actomyosin contractile ring was required for either microtubule capture or microtubule shrinkage. Together, our results indicate that septins and septin-dependent kinases may coordinate microtubule and actin functions in cell division.
The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes
Authors: Lespinet Olivier , Wolf Yuri I. , Koonin Eugene V. , Aravind L.
Published: July 2002

A computational procedure was developed for systematic detection of lineage-specific expansions (LSEs) of protein families in sequenced genomes and applied to obtain a census of LSEs in five eukaryotic species, the yeasts Saccharomyces cerevisiae andSchizosaccharomyces pombe, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the green plant Arabidopsis thaliana. A significant fraction of the proteins encoded in each of these genomes, up to 80% in A. thaliana, belong to LSEs. Many paralogous gene families in each of the analyzed species are almost entirely comprised of LSEs, indicating that their diversification occurred after the divergence of the major lineages of the eukaryotic crown group. The LSEs show readily discernible patterns of protein functions. The functional categories most prone to LSE are structural proteins, enzymes involved in an organism's response to pathogens and environmental stress, and various components of signaling pathways responsible for specificity, including ubiquitin ligase E3 subunits and transcription factors. The functions of several previously uncharacterized, vastly expanded protein families were predicted through in-depth protein sequence analysis, for example, small-molecule kinases and methylases that are expanded independently in the fly and in the nematode. The functions of several other major LSEs remain mysterious; these protein families are attractive targets for experimental discovery of novel, lineage-specific functions in eukaryotes. LSEs seem to be one of the principal means of adaptation and one of the most important sources of organizational and regulatory diversity in crown-group eukaryotes.

[Supplemental material is available online at ftp://ncbi.nlm.nih.gov/pub/aravind/expansions, and http://www.genome.org.]
Glyphosate-Resistant Goosegrass. Identification of a Mutation in the Target Enzyme 5-Enolpyruvylshikimate-3-Phosphate Synthase
Authors: Baerson Scott R. , Rodriguez Damian J. , Tran Minhtien , Feng Yongmei , Biest Nancy A. , Dill Gerald M.
Published: July 2002

The spontaneous occurrence of resistance to the herbicide glyphosate in weed species has been an extremely infrequent event, despite over 20 years of extensive use. Recently, a glyphosate-resistant biotype of goosegrass (Eleusine indica) was identified in Malaysia exhibiting an LD50 value approximately 2- to 4-fold greater than the sensitive biotype collected from the same region. A comparison of the inhibition of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity by glyphosate in extracts prepared from the resistant (R) and sensitive (S) biotypes revealed an approximately 5-fold higher IC50(glyphosate) for the (R) biotype. Sequence comparisons of the predicted EPSPS mature protein coding regions from both biotypes revealed four single-nucleotide differences, two of which result in amino acid changes. One of these changes, a proline to serine substitution at position 106 in the (R) biotype, corresponds to a substitution previously identified in a glyphosate-insensitive EPSPS enzyme from Salmonella typhimurium. Kinetic data generated for the recombinant enzymes suggests that the second substitution identified in the (R) EPSPS does not contribute significantly to its reduced glyphosate sensitivity. Escherichia coli aroA− (EPSPS deficient) strains expressing the mature EPSPS enzyme from the (R) biotype exhibited an approximately 3-fold increase in glyphosate tolerance relative to strains expressing the mature EPSPS from the (S) biotype. These results provide the first evidence for an altered EPSPS enzyme as an underlying component of evolved glyphosate resistance in any plant species.
Variation in Growth Rate between Arabidopsis Ecotypes Is Correlated with Cell Division and A-Type Cyclin-Dependent Kinase Activity
Authors: Beemster Gerrit T.S. , De Vusser Kristof , De Tavernier Evelien , De Bock Kirsten , Inzé Dirk
Published: July 2002

We used a kinematic analysis to investigate the growth processes responsible for variation in primary root growth between 18 ecotypes of Arabidopsis. Root elongation rate differed 4-fold between the slowest (Landsberg erecta, 71 μm h−1) and fastest growing line (Wassilewskija [Ws]; 338 μm h−1). This difference was contributed almost equally by variations in mature cortical cell length (84 μm [Landsbergerecta] to 237 μm [Ws]) and rate of cell production (0.63 cell h−1 [NW108] to 1.83 cell h−1[Ws]). Cell production, in turn, was determined by variation in cell cycle duration (19 h [Tsu] to 48 h [NW108]) and, to a lesser extent, by differences in the number of dividing cells (32 [Weiningen] to 61 [Ws]). We found no correlation between mature cell size and endoreduplication, refuting the hypothesis that the two are linked. However, there was a strong correlation between cell production rates and the activity of the cyclin-dependent kinase (CDKA). The level of the protein could explain 32% of the variation in CDKA. Therefore, it is likely that regulators of CDKA, such as cyclins and inhibitors, are also involved. These data provide a functional link between cell cycle regulation and whole-plant growth rate as affected by genetic differences.
Heterology Expression of the ArabidopsisC-Repeat/Dehydration Response Element Binding Factor 1 Gene Confers Elevated Tolerance to Chilling and Oxidative Stresses in Transgenic Tomato
Authors: Hsieh Tsai-Hung , Lee Jent-Turn , Yang Pei-Tzu , Chiu Li-Hui , Charng Yee-yung , Wang Yu-Chie , Chan Ming-Tsair
Published: July 2002

In an attempt to improve stress tolerance of tomato (Lycopersicon esculentum) plants, an expression vector containing an Arabidopsis C-repeat/dehydration responsive element binding factor 1 (CBF1) cDNA driven by a cauliflower mosaic virus 35S promoter was transferred into tomato plants. Transgenic expression of CBF1 was proved by northern- and western-blot analyses. The degree of chilling tolerance of transgenic T1 and T2 plants was found to be significantly greater than that of wild-type tomato plants as measured by survival rate, chlorophyll fluorescence value, and radical elongation. The transgenic tomato plants exhibited patterns of growth retardation; however, they resumed normal growth after GA3(gibberellic acid) treatment. More importantly, GA3-treated transgenic plants still exhibited a greater degree of chilling tolerance compared with wild-type plants. Subtractive hybridization was performed to isolate the responsive genes of heterologous ArabidopsisCBF1 in transgenic tomato plants.CATALASE1 (CAT1) was obtained and showed activation in transgenic tomato plants. The CAT1 gene and catalase activity were also highly induced in the transgenic tomato plants. The level of H2O2 in the transgenic plants was lower than that in the wild-type plants under either normal or cold conditions. The transgenic plants also exhibited considerable tolerance against oxidative damage induced by methyl viologen. Results from the current study suggest that heterologous CBF1expression in transgenic tomato plants may induce several oxidative-stress responsive genes to protect from chilling stress.
Analysis of the NRT2 Nitrate Transporter Family in Arabidopsis. Structure and Gene Expression
Authors: Orsel Mathilde , Krapp Anne , Daniel-Vedele Françoise
Published: July 2002

Nitrate is an essential element for plant growth, both as a primary nutrient in the nitrogen assimilation pathway and as an important signal for plant development. The uptake of nitrate from the soil and its translocation throughout the plant has been the subject of intensive physiological and molecular studies. Using a reverse genetic approach, the AtNRT2.1 gene has been shown to be involved in the inducible component of the high-affinity nitrate transport system in Arabidopsis. The Arabidopsis Genome Initiative has released nearly the whole genome sequence of Arabidopsis, allowing the identification of a small NRT2 multigene family in this species. Thus, we investigated the phylogenetic relationship between NRT2 proteins belonging to several kingdoms and compared the structure of the different members of the Arabidopsis family. We analyzed, by semiquantitative reverse transcriptase-polymerase chain reaction, the expression pattern of each gene depending on plant organ and development or nutritional status, and compared the relative level of each gene by real-time polymerase chain reaction. We also evaluated the significance of each paralog on the basis of the relative levels of gene expression. The results are discussed in relation with distinct roles for the individual members of the AtNRT2 family.
A modular plate for the optimization of protein crystallization conditions
Authors: Lorber Bernard , Cudney Robert
Published: July 2002

A modular crystallization plate that simplifies the optimization of crystallization conditions after a preliminary screening procedure has been designed and manufactured.
Triangular dendrites of LiAlSiO4–SiO2: evolution between threefold- and sixfold-symmetric morphologies
Authors: Zhao Shanrong , Tan Jin , Wang Jiyang , Hu Xiaobo , Liu Hong
Published: July 2002

A special kind of triangular dendrite of LiAlSiO4–SiO2(or Li1−xAl1−xSi1+xO4, 0 ≤x≤ 1) in matt glaze has been observed by DIC (differential interference contrast) microscopy. This triangular dendrite is β-quartz with a sixfold-symmetric structure. For polyhedral crystals, a crystal with threefold-symmetric structure prefers to develop a hexagonal prismatic habit rather than a trigonal prismatic habit, because a trigonal prism has a higher surface energy than a hexagonal prism. However, for dendritic crystals, a special kind of triangular dendrite, with a pattern formed by the aggregation of many small triangles, can develop. As supercooling decreases, β-quartz can develop a series of morphologies with different surface energies, from snowflake-shaped dendrite to triangular dendrite, and finally to a polyhedral crystal in the form of a hexagonal prism. This series of crystal morphologies shows a morphological evolution from dendrite to polyhedral crystal, and also shows a morphological evolution between sixfold and threefold symmetries.
The effect of sodium peroxide on the corrosion behaviour of some stainless steel alloys in a carbonate melt
Authors: Salih S.A. , Attia A.A. , El‐Masri A.N.
Published: July 2002

The corrosion behaviour of a ferritic (alloy 1) and two austenitic stainless steel alloys (alloys 2 and 3) was studied in a molten Li2CO3‐Na2CO3‐K2CO3 ternary mixture in the presence of Na2O2 additions at temperatures of 475, 500, 525 and 550°C. The techniques of measurements were open circuit potential, galvanostatic anodic polarisation and cyclic voltametry. The addition of Na2O2 increased the concentration of oxide ions in the carbonate melt. There is a tendency for oxidation and passivation of the alloys to commence immediately on their immersion in the melt, and end at the passivity breakdown, where the decomposition of carbonate ions occurs with the formation of CO2 and O2 gases. The oxide scales of a ferritic alloy are less protective than those formed on the austenitic alloys. The oxide scales, in most cases, are multilayered, and the presence of Na2O2 in the carbonate melt gives rise to the formation of a more protective inner layer of oxide scales on the surface of the austenitic alloys.
Factors associated with perceived quality influencing beef consumption behaviour in Ireland
Authors: Mannion Michael A. , Cowan Cathal , Gannon Michael
Published: July 2002

There has been a steady decline in beef consumption in Ireland for over a decade, although 1997 data show that this decline has been reversed. A cognitive representation of perceived meat quality based on prior to purchase considerations, point of purchase considerations and consumption stage considerations was used as a conceptual framework to investigate which quality factors have influenced the decline of beef consumption in Ireland. A representative sample of Irish beef consumers was surveyed in 1997. After measuring the determinants of perceived beef quality, an attribute level factor analysis was used to examine inter‐dependence between the variables. In all, seven factors, accounting for 58 per cent of the variance, were derived. Discriminant analysis found that two of the factors, safety and meat status, differentiated significantly between those who had maintained and those who had reduced beef consumption.