bluuebunny/crossref_metadata_2025 huggingface dataset:
AMIGO, a transmembrane protein implicated in axon tract development, defines a novel protein family with leucine-rich repeats
Authors: Kuja-Panula Juha , Kiiltomäki Marjaana , Yamashiro Takashi , Rouhiainen Ari , Rauvala Heikki
Published: March 2003

Ordered differential display identified a novel sequence induced in neurons by the neurite-promoting protein amphoterin. We named this gene amphoterin-induced gene and ORF (AMIGO), and also cloned two other novel genes homologous to AMIGO (AMIGO2 and AMIGO3). Together, these three AMIGOs form a novel family of genes coding for type I transmembrane proteins which contain a signal sequence for secretion and a transmembrane domain. The deduced extracellular parts of the AMIGOs contain six leucine-rich repeats (LRRs) flanked by cysteine-rich LRR NH2- and COOH-terminal domains and by one immunoglobulin domain close to the transmembrane region. A substrate-bound form of the recombinant AMIGO ectodomain promoted prominent neurite extension in hippocampal neurons, and in solution, the same AMIGO ectodomain inhibited fasciculation of neurites. A homophilic and heterophilic binding mechanism is shown between the members of the AMIGO family. Our results suggest that the members of the AMIGO protein family are novel cell adhesion molecules among which AMIGO is specifically expressed on fiber tracts of neuronal tissues and participates in their formation.
PAR-dependent and geometry-dependent mechanisms of spindle positioning
Authors: Tsou Meng-Fu Bryan , Ku Wei , Hayashi Adam , Rose Lesilee S.
Published: March 2003

During intrinsically asymmetric division, the spindle is oriented onto a polarized axis specified by a group of conserved PAR proteins. Extrinsic geometric asymmetry generated by cell shape also affects spindle orientation in some systems, but how intrinsic and extrinsic mechanisms coexist without interfering with each other is unknown. In some asymmetrically dividing cells of the wild-type Caenorhabditis elegans embryo, nuclear rotation directed toward the anterior cortex orients the forming spindle. We find that in such cells, a PAR-dependent mechanism dominates and causes rotation onto the polarized axis, regardless of cell shape. However, when geometric asymmetry is removed, free nuclear rotation in the center of the cell is observed, indicating that the anterior-directed nature of rotation in unaltered embryos is an effect of cell shape. This free rotation is inconsistent with the prevailing model for nuclear rotation, the specialized cortical site model. In contrast, in par-3 mutant embryos, a geometry-dependent mechanism becomes active and causes directed nuclear rotation. These results lead to the model that in wild-type embryos both PAR-3 and PAR-2 are essential for nuclear rotation in asymmetrically dividing cells, but that PAR-3 inhibits geometry-dependent rotation in nonpolarized cells, thus preventing cell shape from interfering with spindle orientation.
Budding yeast PAK kinases regulate mitotic exit by two different mechanisms
Authors: Chiroli Elena , Fraschini Roberta , Beretta Alessia , Tonelli Mariagrazia , Lucchini Giovanna , Piatti Simonetta
Published: March 2003

We report the characterization of the dominant-negative CLA4t allele of the budding yeast CLA4 gene, encoding a member of the p21-activated kinase (PAK) family of protein kinases, which, together with its homologue STE20, plays an essential role in promoting budding and cytokinesis. Overproduction of the Cla4t protein likely inhibits both endogenous Cla4 and Ste20 and causes a delay in the onset of anaphase that correlates with inactivation of Cdc20/anaphase-promoting complex (APC)–dependent proteolysis of both the cyclinB Clb2 and securin. Although the precise mechanism of APC inhibition by Cla4t remains to be elucidated, our results suggest that Cla4 and Ste20 may regulate the first wave of cyclinB proteolysis mediated by Cdc20/APC, which has been shown to be crucial for activation of the mitotic exit network (MEN). We show that the Cdk1-inhibitory kinase Swe1 is required for the Cla4t-dependent delay in cell cycle progression, suggesting that it might be required to prevent full Cdc20/APC and MEN activation. In addition, inhibition of PAK kinases by Cla4t prevents mitotic exit also by a Swe1-independent mechanism impinging directly on the MEN activator Tem1.
Identification of an organelle-specific myosin V receptor
Authors: Ishikawa Kuniko , Catlett Natalie L. , Novak Jennifer L. , Tang Fusheng , Nau Johnathan J. , Weisman Lois S.
Published: March 2003

Class V myosins are widely distributed among diverse organisms and move cargo along actin filaments. Some myosin Vs move multiple types of cargo, where the timing of movement and the destinations of selected cargoes are unique. Here, we report the discovery of an organelle-specific myosin V receptor. Vac17p, a novel protein, is a component of the vacuole-specific receptor for Myo2p, a Saccharomyces cerevisiae myosin V. Vac17p interacts with the Myo2p cargo-binding domain, but not with vacuole inheritance-defective myo2 mutants that have single amino acid changes within this region. Moreover, a region of the Myo2p tail required specifically for secretory vesicle transport is neither required for vacuole inheritance nor for Vac17p–Myo2p interactions. Vac17p is localized on the vacuole membrane, and vacuole-associated Myo2p increases in proportion with an increase in Vac17p. Furthermore, Vac17p is not required for movement of other cargo moved by Myo2p. These findings demonstrate that Vac17p is a component of a vacuole-specific receptor for Myo2p. Organelle-specific receptors such as Vac17p provide a mechanism whereby a single type of myosin V can move diverse cargoes to distinct destinations at different times.
Granzyme B activates procaspase-3 which signals a mitochondrial amplification loop for maximal apoptosis
Authors: Metkar Sunil S. , Wang Baikun , Ebbs Michelle L. , Kim Jin H. , Lee Yong J. , Raja Srikumar M. , Froelich Christopher J.
Published: March 2003

Granzyme B (GrB), acting similar to an apical caspase, efficiently activates a proteolytic cascade after intracellular delivery by perforin. Studies here were designed to learn whether the physiologic effector, GrB–serglycin, initiates apoptosis primarily through caspase-3 or through BH3-only proteins with subsequent mitochondrial permeabilization and apoptosis. Using four separate cell lines that were either genetically lacking the zymogen or rendered deficient in active caspase-3, we measured apoptotic indices within whole cells (active caspase-3, mitochondrial depolarization [ΔΨm] and TUNEL). Adhering to these conditions, the following were observed in targets after GrB delivery: (a) procaspase-3–deficient cells fail to display a reduced ΔΨm and DNA fragmentation; (b) Bax/Bak is required for optimal ΔΨm reduction, caspase-3 activation, and DNA fragmentation, whereas BID cleavage is undetected by immunoblot; (c) Bcl-2 inhibits GrB-mediated apoptosis (reduced ΔΨm and TUNEL reactivity) by blocking oligomerization of caspase-3; and (d) in procaspase-3–deficient cells a mitochondrial-independent pathway was identified which involved procaspase-7 activation, PARP cleavage, and nuclear condensation. The data therefore support the existence of a fully implemented apoptotic pathway initiated by GrB, propagated by caspase-3, and perpetuated by a mitochondrial amplification loop but also emphasize the presence of an ancillary caspase-dependent, mitochondria-independent pathway.
PKA phosphorylation activates the calcium release channel (ryanodine receptor) in skeletal muscle
Authors: Reiken Steven , Lacampagne Alain , Zhou Hua , Kherani Aftab , Lehnart Stephan E. , Ward Chris , Huang Fannie , Gaburjakova Marta , Gaburjakova Jana , Rosemblit Nora , Warren Michelle S. , He Kun-lun , Yi Geng-hua , Wang Jie , Burkhoff Daniel , Vassort Guy , Marks Andrew R.
Published: March 2003

The type 1 ryanodine receptor (RyR1) on the sarcoplasmic reticulum (SR) is the major calcium (Ca2+) release channel required for skeletal muscle excitation–contraction (EC) coupling. RyR1 function is modulated by proteins that bind to its large cytoplasmic scaffold domain, including the FK506 binding protein (FKBP12) and PKA. PKA is activated during sympathetic nervous system (SNS) stimulation. We show that PKA phosphorylation of RyR1 at Ser2843 activates the channel by releasing FKBP12. When FKB12 is bound to RyR1, it inhibits the channel by stabilizing its closed state. RyR1 in skeletal muscle from animals with heart failure (HF), a chronic hyperadrenergic state, were PKA hyperphosphorylated, depleted of FKBP12, and exhibited increased activity, suggesting that the channels are “leaky.” RyR1 PKA hyperphosphorylation correlated with impaired SR Ca2+ release and early fatigue in HF skeletal muscle. These findings identify a novel mechanism that regulates RyR1 function via PKA phosphorylation in response to SNS stimulation. PKA hyperphosphorylation of RyR1 may contribute to impaired skeletal muscle function in HF, suggesting that a generalized EC coupling myopathy may play a role in HF.
Differential kinetochore protein requirements for establishment versus propagation of centromere activity in Saccharomyces cerevisiae
Authors: Mythreye Karthikeyan , Bloom Kerry S.
Published: March 2003

Dicentric chromosomes undergo a breakage–fusion–bridge cycle as a consequence of having two centromeres on the same chromatid attach to opposite spindle poles in mitosis. Suppression of dicentric chromosome breakage reflects loss of kinetochore function at the kinetochore–microtubule or the kinetochore–DNA interface. Using a conditionally functional dicentric chromosome in vivo, we demonstrate that kinetochore mutants exhibit quantitative differences in their degree of chromosome breakage. Mutations in chl4/mcm17/ctf17 segregate dicentric chromosomes through successive cell divisions without breakage, indicating that only one of the two centromeres is functional. Centromere DNA introduced into the cell is unable to promote kinetochore assembly in the absence of CHL4. In contrast, established centromeres retain their segregation capacity for greater than 25 generations after depletion of Chl4p. The persistent mitotic stability of established centromeres reveals the presence of an epigenetic component in kinetochore segregation. Furthermore, this study identifies Chl4p in the initiation and specification of a heritable chromatin state.
Axonal transport of membranous and nonmembranous cargoes
Authors: Brown Anthony
Published: March 2003

Membranous and nonmembranous cargoes are transported along axons in the fast and slow components of axonal transport, respectively. Recent observations on the movement of cytoskeletal polymers in axons suggest that slow axonal transport is generated by fast motors and that the slow rate is due to rapid movements interrupted by prolonged pauses. This supports a unified perspective for fast and slow axonal transport based on rapid movements of diverse cargo structures that differ in the proportion of the time that they spend moving. A Flash feature accompanies this Mini-Review.
Skeletal muscle repair by adult human mesenchymal stem cells from synovial membrane
Authors: De Bari Cosimo , Dell'Accio Francesco , Vandenabeele Frank , Vermeesch Joris R. , Raymackers Jean-Marc , Luyten Frank P.
Published: March 2003

We have demonstrated previously that adult human synovial membrane-derived mesenchymal stem cells (hSM-MSCs) have myogenic potential in vitro (De Bari, C., F. Dell'Accio, P. Tylzanowski, and F.P. Luyten. 2001. Arthritis Rheum. 44:1928–1942). In the present study, we have characterized their myogenic differentiation in a nude mouse model of skeletal muscle regeneration and provide proof of principle of their potential use for muscle repair in the mdx mouse model of Duchenne muscular dystrophy. When implanted into regenerating nude mouse muscle, hSM-MSCs contributed to myofibers and to long term persisting functional satellite cells. No nuclear fusion hybrids were observed between donor human cells and host mouse muscle cells. Myogenic differentiation proceeded through a molecular cascade resembling embryonic muscle development. Differentiation was sensitive to environmental cues, since hSM-MSCs injected into the bloodstream engrafted in several tissues, but acquired the muscle phenotype only within skeletal muscle. When administered into dystrophic muscles of immunosuppressed mdx mice, hSM-MSCs restored sarcolemmal expression of dystrophin, reduced central nucleation, and rescued the expression of mouse mechano growth factor.
RETRACTED: The RasGAP-associated endoribonuclease G3BP assembles stress granules
Authors: Tourrière Hélène , Chebli Karim , Zekri Latifa , Courselaud Brice , Blanchard Jean Marie , Bertrand Edouard , Tazi Jamal
Published: March 2003

Stress granules (SGs) are formed in the cytoplasm in response to various toxic agents, and are believed to play a critical role in the regulation of mRNA metabolism during stress. In SGs, mRNAs are stored in an abortive translation initiation complex that can be routed to either translation initiation or degradation. Here, we show that G3BP, a phosphorylation-dependent endoribonuclease that interacts with RasGAP, is recruited to SGs in cells exposed to arsenite. G3BP may thus determine the fate of mRNAs during cellular stress. Remarkably, SG assembly can be either dominantly induced by G3BP overexpression, or on the contrary, inhibited by expressing a central domain of G3BP. This region binds RasGAP and contains serine 149, whose dephosphorylation is induced by arsenite treatment. Critically, a phosphomimetic mutant (S149E) fails to oligomerize and to assemble SGs, whereas a nonphosphorylatable G3BP mutant (S149A) does both. These results suggest that G3BP is an effector of SG assembly, and that Ras signaling contributes to this process by regulating G3BP dephosphorylation.
Polarized growth and organelle segregation in yeast
Authors: Bretscher Anthony
Published: March 2003

In yeast, growth and organelle segregation requires formin-dependent assembly of polarized actin cables. These tracks are used by myosin Vs to deliver secretory vesicles for cell growth, organelles for their segregation, and mRNA for fate determination. Several specific receptors have been identified that interact with the cargo-binding tails of the myosin Vs. A recent study implicates specific degradation in the bud of the vacuolar receptor, Vac17, as a mechanism for cell cycle–regulated segregation of this organelle.
Further proof of the plasticity of adult stem cells and their role in tissue repair
Authors: Prockop Darwin J.
Published: March 2003

In this issue, De Bari et al. (2003) present elegant data to counter the recent claims that adult stem cells have a limited plasticity. Further, they provide evidence that adult stem cells can seek out damaged tissues and repair them.
Detection of a Functional Hybrid Receptor γc/GM-CSFRβ in Human Hematopoietic CD34+ Cells
Authors: Giron-Michel J. , Fogli M. , Gaggero A. , Ferrini S. , Caignard A. , Brouty-Boyé D. , Baouz S. , Le Bousse-Kerdilès M.-C. , Péault B. , van Dijk M. , Bulfone-Paus S. , Durali D. , Chouaib S. , Azzarone B.
Published: March 2003

A functional hybrid receptor associating the common γ chain (γc) with the granulocyte/macrophage colony-stimulating factor receptor β (GM-CSFRβ) chain is found in mobilized human peripheral blood (MPB) CD34+ hematopoietic progenitors, SCF/Flt3-L primed cord blood (CB) precursors (CBPr CD34+/CD56−), and CD34+ myeloid cell lines, but not in normal natural killer (NK) cells, the cytolytic NK-L cell line or nonhematopoietic cells. We demonstrated, using CD34+ TF1β cells, which express an interleukin (IL)-15Rα/β/γc receptor, that within the hybrid receptor, the GM-CSFRβ chain inhibits the IL-15–triggered γc/JAK3-specific signaling controlling TF1β cell proliferation. However, the γc chain is part of a functional GM-CSFR, activating GM-CSF–dependent STAT5 nuclear translocation and the proliferation of TF1β cells. The hybrid receptor is functional in normal hematopoietic progenitors in which both subunits control STAT5 activation. Finally, the parental TF1 cell line, which lacks the IL-15Rβ chain, nevertheless expresses both a functional hybrid receptor that controls JAK3 phosphorylation and a novel IL-15α/γc/TRAF2 complex that triggers nuclear factor κB activation. The lineage-dependent distribution and function of these receptors suggest that they are involved in hematopoiesis because they modify transduction pathways that play a major role in the differentiation of hematopoietic progenitors.
Regulation and Function of the Interleukin 13 Receptor α 2 During a T Helper Cell Type 2–dominant Immune Response
Authors: Chiaramonte Monica G. , Mentink-Kane Margaret , Jacobson Bruce A. , Cheever Allen W. , Whitters Matthew J. , Goad Mary E.P. , Wong Anthony , Collins Mary , Donaldson Debra D. , Grusby Michael J. , Wynn Thomas A.
Published: March 2003

Highly polarized type 2 cytokine responses can be harmful and even lethal to the host if they are too vigorous or persist too long. Therefore, it is important to elucidate the mechanisms that down-regulate these reactions. Interleukin (IL)-13 has emerged as a central mediator of T helper cell (Th)2-dominant immune responses, exhibiting a diverse array of functional activities including regulation of airway hyperreactivity, resistance to nematode parasites, and tissue remodeling and fibrosis. Here, we show that IL-13 receptor (R)α2 is a critical down-regulatory factor of IL-13–mediated tissue fibrosis induced by the parasitic helminth Schistosoma mansoni. IL-13Rα2 expression was induced after the onset of the fibrotic response, IL-10, IL-13, and Stat6 dependent, and inhibited by the Th1-inducing adjuvant IL-12. Strikingly, schistosome-infected C57BL/6 and BALB/c IL-13Rα2–deficient mice showed a marked exacerbation in hepatic fibrosis, despite displaying no change in granuloma size, tissue eosinophilia, or mastocytosis. Fibrosis increased despite the fact that IL-13 levels decreased significantly in the liver and serum. Importantly, pathology was prevented when IL-13Rα2–deficient mice were treated with a soluble IL-13Rα2-Fc construct, formally demonstrating that their exacerbated fibrotic response was due to heightened IL-13 activity. Together, these studies illustrate the central role played by the IL-13Rα2 in the down-regulation of a chronic and pathogenic Th2-mediated immune response.
Enhanced Interleukin (IL)-13 Responses in Mice Lacking IL-13 Receptor α 2
Authors: Wood Nancy , Whitters Matthew J. , Jacobson Bruce A. , Witek JoAnn , Sypek Joseph P. , Kasaian Marion , Eppihimer Michael J. , Unger Michelle , Tanaka Takashi , Goldman Samuel J. , Collins Mary , Donaldson Debra D. , Grusby Michael J.
Published: March 2003

Interleukin (IL)-13 has recently been shown to play important and unique roles in asthma, parasite immunity, and tumor recurrence. At least two distinct receptor components, IL-4 receptor (R)α and IL-13Rα1, mediate the diverse actions of IL-13. We have recently described an additional high affinity receptor for IL-13, IL-13Rα2, whose function in IL-13 signaling is unknown. To better appreciate the functional importance of IL-13Rα2, mice deficient in IL-13Rα2 were generated by gene targeting. Serum immunoglobulin E levels were increased in IL-13Rα2−/− mice despite the fact that serum IL-13 was absent and immune interferon γ production increased compared with wild-type mice. IL-13Rα2–deficient mice display increased bone marrow macrophage progenitor frequency and decreased tissue macrophage nitric oxide and IL-12 production in response to lipopolysaccharide. These results are consistent with a phenotype of enhanced IL-13 responsiveness and demonstrate a role for endogenous IL-13 and IL-13Rα2 in regulating immune responses in wild-type mice.
Role of Adhesin Release for Mucosal Colonization by a Bacterial Pathogen
Authors: Coutte Loïc , Alonso Sylvie , Reveneau Nathalie , Willery Eve , Quatannens Brigitte , Locht Camille , Jacob-Dubuisson Françoise
Published: March 2003

Pathogen attachment is a crucial early step in mucosal infections. This step is mediated by important virulence factors called adhesins. To exert these functions, adhesins are typically surface-exposed, although, surprisingly, some are also released into the extracellular milieu, the relevance of which has previously not been studied. To address the role of adhesin release in pathogenesis, we used Bordetella pertussis as a model, since its major adhesin, filamentous hemagglutinin (FHA), partitions between the bacterial surface and the extracellular milieu. FHA release depends on its maturation by the specific B. pertussis protease SphB1. We constructed SphB1-deficient mutants and found that they were strongly affected in their ability to colonize the mouse respiratory tract, although they adhered even better to host cells in vitro than their wild-type parent strain. The defect in colonization could be overcome by prior nasal instillation of purified FHA or by coinfection with FHA-releasing B. pertussis strains, but not with SphB1-producing FHA-deficient strains, ruling out a nonspecific effect of SphB1. These results indicate that the release of FHA is important for colonization, as it may facilitate the dispersal of bacteria from microcolonies and the binding to new sites in the respiratory tract.
Biallelic Germline Transcription at the κ Immunoglobulin Locus
Authors: Singh Nandita , Bergman Yehudit , Cedar Howard , Chess Andrew
Published: March 2003

Rearrangement of antigen receptor genes generates a vast array of antigen receptors on lymphocytes. The establishment of allelic exclusion in immunoglobulin genes requires differential treatment of the two sequence identical alleles. In the case of the κ immunoglobulin locus, changes in chromatin structure, methylation, and replication timing of the two alleles are all potentially involved in regulating rearrangement. Additionally, germline transcription of the κ locus which precedes rearrangement has been proposed to reflect an opening of the chromatin structure rendering it available for rearrangement. As the initial restriction of rearrangement to one allele is critical to the establishment of allelic exclusion, a key question is whether or not germline transcription at the κ locus is monoallelic or biallelic. We have used a sensitive reverse transcription-polymerase chain reaction (RT-PCR) assay and an RNA–fluorescence in situ hybridization (FISH) to show that germline transcription of the κ locus is biallelic in wild-type immature B cells and in recombination activating gene (RAG)−/−, μ+ B cells. Therefore, germline transcription is unlikely to dictate which allele will be rearranged first and rather reflects a general opening on both alleles that must be accompanied by a mechanism allowing one of the two alleles to be rearranged first.
Treatment of Relapsing Paralysis in Experimental Encephalomyelitis by Targeting Th1 Cells through Atorvastatin
Authors: Aktas Orhan , Waiczies Sonia , Smorodchenko Alina , Dörr Jan , Seeger Bibiane , Prozorovski Timour , Sallach Stephanie , Endres Matthias , Brocke Stefan , Nitsch Robert , Zipp Frauke
Published: March 2003

Statins, known as inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, exhibit numerous functions related to inflammation, such as MHC class II down-regulation, interference with T cell adhesion, and induction of apoptosis. Here we demonstrate that both subcutaneous and oral administration of atorvastatin inhibit the development of actively induced chronic experimental autoimmune encephalomyelitis in SJL/J mice and significantly reduce the inflammatory infiltration into the central nervous system (CNS). When treatment was started after disease onset, atorvastatin reduced the incidence of relapses and protected from the development of further disability. Both the reduced autoreactive T cell response measured by proliferation toward the encephalitogenic peptide PLP139–151 and the cytokine profile indicate a potent blockade of T helper cell type 1 immune response. In in vitro assays atorvastatin not only inhibited antigen-specific responses, but also decreased T cell proliferation mediated by direct TCR engagement independently of MHC class II and LFA-1. Inhibition of proliferation was not due to apoptosis induction, but linked to a negative regulation on cell cycle progression. However, early T cell activation was unaffected, as reflected by unaltered calcium fluxes. Thus, our results provide evidence for a beneficial role of statins in the treatment of autoimmune attack on the CNS.
Fibrin-mediated Protection Against Infection-stimulated Immunopathology
Authors: Johnson Lawrence L. , Berggren Kiera N. , Szaba Frank M. , Chen Wangxue , Smiley Stephen T.
Published: March 2003

Fibrin, a product of the blood coagulation cascade, accompanies many type 1 immune responses, including delayed-type hypersensitivity, autoimmunity, and graft rejection. In those settings, fibrin is thought to exacerbate inflammation and disease. Here, we evaluate roles for coagulation during infection with Toxoplasma gondii, a pathogen whose control requires robust type 1 immunity. We establish that fibrin prevents infection-stimulated blood loss, thereby performing a protective function that is essential for survival. Remarkably, fibrin does not simply protect against vascular damage caused directly by the infectious agent, but rather, protects against hemorrhage evoked by interferon-γ, a critical mediator of type 1 immunity. This finding, to our knowledge, is the first to document a beneficial role for coagulation during type 1 immunity, and suggests that fibrin deposition protects host tissue from collateral damage caused by the immune system as it combats infection.
Interferon and Granulopoiesis Signatures in Systemic Lupus Erythematosus Blood
Authors: Bennett Lynda , Palucka A. Karolina , Arce Edsel , Cantrell Victoria , Borvak Josef , Banchereau Jacques , Pascual Virginia
Published: March 2003

Systemic lupus erythematosus (SLE) is a prototype systemic autoimmune disease characterized by flares of high morbidity. Using oligonucleotide microarrays, we now show that active SLE can be distinguished by a remarkably homogeneous gene expression pattern with overexpression of granulopoiesis-related and interferon (IFN)-induced genes. Using the most stringent statistical analysis (Bonferroni correction), 15 genes were found highly up-regulated in SLE patients, 14 of which are targets of IFN and one, defensin DEFA-3, a major product of immature granulocytes. A more liberal correction (Benjamini and Hochberg correction) yielded 18 additional genes, 12 of which are IFN-regulated and 4 granulocyte-specific. Indeed immature neutrophils were identified in a large fraction of SLE patients white blood cells. High dose glucocorticoids, a standard treatment of disease flares, shuts down the interferon signature, further supporting the role of this cytokine in SLE. The expression of 10 genes correlated with disease activity according to the SLEDAI. The most striking correlation (P < 0.001, r = 0.55) was found with the formyl peptide receptor-like 1 protein that mediates chemotactic activities of defensins. Therefore, while the IFN signature confirms the central role of this cytokine in SLE, microarray analysis of blood cells reveals that immature granulocytes may be involved in SLE pathogenesis.
Preferential Accumulation of Antigen-specific Effector CD4 T Cells at an Antigen Injection Site Involves CD62E-dependent Migration but Not Local Proliferation
Authors: Reinhardt R. Lee , Bullard Daniel C. , Weaver Casey T. , Jenkins Marc K.
Published: March 2003

The migration of antigen-specific T cells to nonlymphoid tissues is thought to be important for the elimination of foreign antigens from the body. However, recent results showing the migration of activated T cells into many nonlymphoid tissues raised the possibility that antigen-specific T cells do not migrate preferentially to nonlymphoid tissues containing antigen. We addressed this question by tracking antigen-specific CD4 T cells in the whole body after a localized subcutaneous antigen injection. Antigen-specific CD4 T cells proliferated in the skin-draining lymph nodes and the cells that underwent the most cell divisions acquired the ability to bind to CD62P. As time passed, CD62P-binding antigen-specific CD4 T cells with interferon γ production potential accumulated preferentially at the site of antigen injection but only in recipients that expressed CD62E. Surprisingly, these T cells did not proliferate in the injection site despite showing evidence of more cell divisions than the T cells in the draining lymph nodes. The results suggest that the most divided effector CD4 T cells from the lymph nodes enter the site of antigen deposition via recognition of CD62E on blood vessels and are retained there in a nonproliferative state via recognition of peptide–major histocompatibility complex II molecules.
Vaccination against Neisseria meningitidis Using Three Variants of the Lipoprotein GNA1870
Authors: Masignani Vega , Comanducci Maurizio , Giuliani Marzia Monica , Bambini Stefania , Adu-Bobie Jeannette , Aricò Beatrice , Brunelli Brunella , Pieri Alessandro , Santini Laura , Savino Silvana , Serruto Davide , Litt David , Kroll Simon , Welsch Jo Anne , Granoff Dan M. , Rappuoli Rino , Pizza Mariagrazia
Published: March 2003

Sepsis and meningitis caused by serogroup B meningococcus are devastating diseases of infants and young adults, which cannot yet be prevented by vaccination. By genome mining, we discovered GNA1870, a new surface-exposed lipoprotein of Neisseria meningitidis that induces high levels of bactericidal antibodies. The antigen is expressed by all strains of N. meningitidis tested. Sequencing of the gene in 71 strains representative of the genetic and geographic diversity of the N. meningitidis population, showed that the protein can be divided into three variants. Conservation within each variant ranges between 91.6 to 100%, while between the variants the conservation can be as low as 62.8%. The level of expression varies between strains, which can be classified as high, intermediate, and low expressors. Antibodies against a recombinant form of the protein elicit complement-mediated killing of the strains that carry the same variant and induce passive protection in the infant rat model. Bactericidal titers are highest against those strains expressing high yields of the protein; however, even the very low expressors are efficiently killed. The novel antigen is a top candidate for the development of a new vaccine against meningococcus.
Type-I Interferon Receptor Deficiency Reduces Lupus-like Disease in NZB Mice
Authors: Santiago-Raber Marie-Laure , Baccala Roberto , Haraldsson Katarina M. , Choubey Divaker , Stewart Timothy A. , Kono Dwight H. , Theofilopoulos Argyrios N.
Published: March 2003

Indirect evidence suggests that type-I interferons (IFN-α/β) play a significant role in the pathogenesis of lupus. To directly examine the contribution of these pleiotropic molecules, we created congenic NZB mice lacking the α-chain of IFN-α/βR, the common receptor for the multiple IFN-α/β species. Compared with littermate controls, homozygous IFN-α/βR-deleted NZB mice had significantly reduced anti-erythrocyte autoantibodies, erythroblastosis, hemolytic anemia, anti-DNA autoantibodies, kidney disease, and mortality. These reductions were intermediate in the heterozygous-deleted mice. The disease-ameliorating effects were accompanied by reductions in splenomegaly and in several immune cell subsets, including B-1 cells, the major producers of anti-erythrocyte autoantibodies. Decreases of B and T cell proliferation in vitro and in vivo, and of dendritic cell maturation and T cell stimulatory activity in vitro were also detected. Absence of signaling through the IFN-α/βR, however, did not affect increased basal levels of the IFN-responsive p202 phosphoprotein, encoded by a polymorphic variant of the Ifi202 gene associated with the Nba2 predisposing locus in NZB mice. The data indicate that type-I IFNs are important mediators in the pathogenesis of murine lupus, and that reducing their activity in the human counterpart may be beneficial.
DomCut: prediction of inter-domain linker regions in amino acid sequences
Authors: Suyama Mikita , Ohara Osamu
Published: March 2003

Summary: DomCut is a program to predict inter-domain linker regions solely by amino acid sequence information. The prediction is made by using linker index deduced from a data set of domain/linker segments. The linker preference profile, which is the averaged linker index along a sequence, can be visualized in the graphical interface.

Availability: The web server, together with supplementary information, is available at http://www.kazusa.or.jp/tech/suyama/domcut. The distribution version of DomCut is also available upon request from the authors.

Contact: suyama@embl-heidelberg.de

* To whom correspondence should be addressed.

† Present address: Biocomputing, EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany.
The fuzzy polynucleotide space: basic properties
Authors: Torres Angela , Nieto Juan J.
Published: March 2003

Motivation: Any triplet codon may be regarded as a 12-dimensional fuzzy code. Sufficient information about a particular sequence may not be available in certain situations. The investigator will be confronted with imprecise sequences, yet want to make comparisons of sequences. Fuzzy polynucleotides can be compared by using geometrical interpretation of fuzzy sets as points in a hypercube.

Results: We introduce the space of fuzzy polynucleotides and a means of measuring dissimilitudes between them. We establish mathematical principles to measure dissimilarities between fuzzy polynucleotides and present several examples in this metric space.

We calculate the frequencies of the nucleotides at the three base sites of a codon in the coding sequences of Escherichia coli K-12 and Mycobacterium tuberculosis H37Rv, and consider them as points in that fuzzy space. We compute the distance between the genomes of E.coli and M.tuberculosis.

Availability: Available on request from the authors.

Contact: amnieto@usc.es

* To whom correspondence should be addressed.
TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees
Authors: Woolley Steve , Johnson Justin , Smith Matthew J. , Crandall Keith A. , McClellan David A.
Published: March 2003

Summary: The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during cladogenesis, and performs goodness-of-fit and categorical statistical tests.

Availability: The TreeSAAP package (executables for Windows PC or Macintosh OSX, Java source code, documentation, and instruction manual) is available at http://genome.cs.byu.edu/treesaap.htm. UNIX version is available upon request.

Contact: David_McClellan@byu.edu

* To whom correspondence should be addressed.
TRAIT (TRAnscript Integrated Table): a knowledgebase of
human skeletal muscle transcripts
Authors: Toppo Stefano , Cannata Nicola , Fontana Paolo , Romualdi Chiara , Laveder Paolo , Bertocco Emanuela , Lanfranchi Gerolamo , Valle Giorgio
Published: March 2003

Summary: TRAIT is a knowledgebase integrating information on transcripts with related data from genome, proteins, ortholog genes and diseases. It was initially built as a system to manage an EST-based gene discovery project on human skeletal muscle, which yielded over 4500 independent sequence clusters. Transcripts are annotated using automatic as well as manual procedures, linking known transcripts to public databases and unknown transcripts to tables of predicted features. Data are stored in a MySQL database. Complex queries are automatically built by means of a user-friendly web interface that allows the concurrent selection of many fields such as ontology, expression level, map position and protein domains. The results are parsed by the system and returned in a ranked order, in respect to the number of satisfied criteria.

Availability: http://muscle.cribi.unipd.it and http://muscle.cribi.unipd.it/features/querystrait.html

Contact: stefano@cribi.unipd.it; giorgio.valle@unipd.it

* To whom correspondence should be addressed.
MatArray: a Matlab toolbox for microarray data
Authors: Venet David
Published: March 2003

Summary: The microarray technology allows the high-throughput quantification of the mRNA level of thousands of genes under dozens of conditions, generating a wealth of data which must be analyzed using some form of computational means. A popular framework for such analysis is Matlab, a powerful computing language for which many functions have been written. However, although complex topics like neural networks or principal component analysis are freely available in Matlab, functions to perform more basic tasks like data normalization or hierarchical clustering in an efficient manner are not. The MatArray toolbox aims at filling this gap by offering efficient implementations of the most needed functions for microarray analysis. The functions in the toolbox are command-line only, since it is geared toward seasoned Matlab users.

Availability: http://www.ulb.ac.be/medecine/iribhm/microarray/toolbox

Contact: davenet@ulb.ac.be
MENDB: a database of polymorphic loci from natural populations
Authors: Livingstone K. , Rieseberg L.
Published: March 2003

Summary: MENDB is an online database for genetic markers determined to be polymorphic in natural populations. The database contains primer sequences and conditions for PCR, taxonomic information, and links to GenBank records, as well as basic statistics on the level of polymorphism for the surveyed populations/individuals.

Availability: http://snook.bio.indiana.edu/

Contact: klivings@bio.indiana.edu

* To whom correspondence should be addressed.
Recruitment of terminal protein to the ends ofStreptomyceslinear plasmids and chromosomes by a novel telomere-binding protein essential for linear DNA replication
Authors: Bao Kai , Cohen Stanley N.
Published: March 2003

Bidirectional replication ofStreptomyceslinear plasmids and chromosomes from a central origin produces unpaired 3′-leading-strand overhangs at the telomeres of replication intermediates. Filling in of these overhangs leaves a terminal protein attached covalently to the 5′ DNA ends of mature replicons. We report here the essential role of a novel 80-kD DNA-binding protein (telomere-associated protein, Tap) in this process. Biochemical studies, yeast two-hybrid analysis, and immunoprecipitation/immunodepletion experiments indicate that Tap binds tightly to specific sequences in 3′ overhangs and also interacts with Tpg, bringing Tpg to telomere termini. Using DNA microarrays to analyze the chromosomes oftapmutant bacteria, we demonstrate that survivors of Tap ablation undergo telomere deletion, chromosome circularization, and amplification of subtelomeric DNA. Microarray-based chromosome mapping at single-ORF resolution revealed common endpoints for independent deletions, identified amplified chromosomal ORFs adjacent to these endpoints, and quantified the copy number of these ORFs. Sequence analysis confirmed chromosome circularization and revealed the insertion of adventitious DNA between joined chromosome ends. Our results show that Tap is required for linear DNA replication inStreptomycesand suggest that it functions to recruit and position Tpg at the telomeres of replication intermediates. They also identify hotspots for the telomeric deletions and subtelomeric DNA amplifications that accompany chromosome circularization.
Human and mouseTPITgene mutations cause early onset pituitary ACTH deficiency
Authors: Pulichino Anne-Marie , Vallette-Kasic Sophie , Couture Catherine , Gauthier Yves , Brue Thierry , David Michel , Malpuech Georges , Deal Cheri , Van Vliet Guy , De Vroede Monique , Riepe Felix G. , Partsch Carl-Joachim , Sippell Wolfgang G. , Berberoglu Merih , Atasay Begüm , Drouin Jacques
Published: March 2003

Tpit is a highly cell-restricted transcription factor that is required for expression of the pro-opiomelanocortin (POMC) gene and for terminal differentiation of the pituitary corticotroph lineage. Its exclusive expression in pituitary POMC-expressing cells has suggested that its mutation may cause isolated deficiency of pituitary adrenocorticotropin (ACTH). We now show that Tpit-deficient mice constitute a model of isolated ACTH deficiency (IAD) that is very similar to human IAD patients carryingTPITgene mutations. Through genetic analysis of a panel of IAD patients, we show thatTPITgene mutations are associated at high frequency with early onset IAD, but not with juvenile forms of this deficiency. We identified seven differentTPITmutations, including nonsense, missense, point deletion, and a genomic deletion. This work defines congenital early onset IAD as a relatively homogeneous clinical entity caused by recessive transmission of loss-of-function mutations in theTPITgene.
Deconvolution of instrumental aberrations for synchrotron powder X-ray diffractometry
Authors: Ida T. , Hibino H. , Toraya H.
Published: March 2003

A method to remove the effects of instrumental aberrations from the whole powder diffraction pattern measured with a high-resolution synchrotron powder diffractometer is presented. Two types of asymmetry in the peak profiles caused by (i) the axial-divergence aberration of the diffractometer (diffractometer aberration) and (ii) the aberration of the monochromator and focusing optics on the beamline (beamline aberration) are both taken into account. The method is based on the whole-pattern deconvolution by Fourier technique combined with the abscissa-scale transformation appropriate for each instrumental aberration. The experimental powder diffraction data of LaB6(NIST SRM660) measured on beamline BL-4B2at the Photon Factory in Tsukuba have been analysed by the method. The formula of the scale transformation for the diffractometer aberration hasa prioribeen derived from the instrumental function with geometric parameters of the optics. The strongly deformed experimental peak profiles at low diffraction angles have been transformed to sharp peak profiles with less asymmetry by the deconvolution of the diffractometer aberration. The peak profiles obtained by the deconvolution of the diffractometer aberration were modelled by an asymmetric model profile function synthesized by the convolution of the extended pseudo-Voigt function and an asymmetric component function with an empirical asymmetry parameter, which were linearly dependent on the diffraction angle. Fairly symmetric peak profiles have been obtained by further deconvolution of the empirically determined asymmetric component of the beamline aberration.
Large-angle convergent-beam setup for femtosecond X-ray crystallography
Authors: Boschetto Davide , Rischel Christian , Uschmann I. , Perez J. , Fourmaux S. , Hulin D. , Förster E. , Rousse Antoine
Published: March 2003

It is demonstrated how femtosecond plasma X-ray sources can be used to record X-ray diffraction images with many simultaneous reflections. A convergent-beam geometry was implemented and tested with a crystal of a small molecule [Fe-py3(tren)] as well as with a crystal of the protein lysozyme. The results pave the way for femtosecond X-ray crystallography.
Analytical use of the stereographic Wulff net for single-crystal orientation for 1-, 2- and 3-rotated cuts
Authors: Michalski E. , Majchrowski A.
Published: March 2003

A useful set of expressions that allow the analytical use of the stereographic Wulff net,e.g.for orientation in the Laue method, for 1-, 2- and 3-rotated cuts of single crystals fastened on a two-axis goniometric holder are derived. Application of the derived expressions in everyday crystallographic practice is illustrated by examples. The results of lattice-parameter measurements, the choice of planes suitable for diffractometric orientation, and the values of their Bragg angles, useful for orientation in the Laue and diffractometric methods, are described for Ca4GdO(BO3)3:Nd and CsLiB6O10single crystals.
Phase transformation kinetic study and microstructure characterization of ball-milledm-ZrO2–10 mol%a-TiO2by Rietveld method
Authors: Dutta H. , Manik S. K. , Pradhan S. K.
Published: March 2003

High-energy ball milling of a monoclinic ZrO2–10 mol% anatase TiO2mixture results in the formation of a nanocrystalline cubic ZrO2polymorphic phase with equimolar fraction of the starting materials. The cubic phase is presumed to have formed from them-ZrO2solid solution based on the (001) plane of them-ZrO2phase. In the course of milling, the most dense (111) plane of the cubic lattice became parallel to the most dense (\bar{1}11) plane of the monoclinic lattice due to an orientation effect. Annealing of a 12 h milled sample at 773, 873 and 973 K for 1 h results in almost complete transformation of them-ZrO2to thec-ZrO2phase. At 1273 K annealing temperature (1 h), the nanocrystalline sample decomposed into individual starting phases. This suggests that the cubic phase is a metastable one and its stability depends on particle size as well as the working temperature. Formation of the cubic phase at such a low temperature using anatase TiO2as a phase stabilizer has not been reported previously. The microstructures of the unmilled, all the ball-milled and the annealed samples have been characterized by employing Rietveld's X-ray powder structure refinement methodology. The particle size, root mean square (r.m.s.) lattice strain, lattice parameters, molar fraction,etc., of individual phases have been estimated from Rietveld analysis and are utilized to interpret the results.
Energetic materials: variable-temperature crystal structure of β-NTO
Authors: Bolotina Nadezhda B. , Zhurova Elizabeth , Pinkerton A. Alan
Published: March 2003

The crystal structure of the metastable β form of 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (β-NTO, monoclinic,P21/c) has been investigated at five temperatures in the range 100–298 K using single-crystal X-ray diffraction techniques. The second-rank thermal expansion tensor has been determined to describe thermal behavior of the crystal. The most significant thermal expansion is in a plane, which is almost perpendicular to the planes of all the NTO molecules. Perpendicular to the plane of maximal thermal expansion, a modest thermal contraction takes place. Both thermal expansion and contraction of the crystal lattice indicate anharmonicity of the atomic thermal motion. The experimental thermal variation of the unit-cell parameters is in qualitative agreement with that previously obtained from molecular dynamics calculations. Rigid-body analysis of the molecular thermal motion was performed using the libration and translation second-rank tensors. Although the translation part of the thermal motion is not strongly anisotropic, the largest displacements of the NTO molecules are oriented in the plane of maximal thermal expansion of the crystal and have significant anharmonic components. The libration motion is more anisotropic, and the largest libration as well as the largest translation principal axes are directed along the C5—N5 bond in each NTO molecule.
Instrument line-profile synthesis in high-resolution synchrotron powder diffraction
Authors: Masson O. , Dooryhée E. , Fitch A. N.
Published: March 2003

An accurate method for synthesizing the instrumental line profile of high-resolution synchrotron powder diffraction instruments is presented. It is shown that the instrumental profile can be modelled by the convolution of four physical aberration functions: the equatorial intensity distribution, the monochromator and analyser transfer functions, and the axial divergence aberration function. Moreover, each equatorial aberration is related to an angle-independent function by a scale transform factor. The principles of the instrument line-profile calculation are general. They are applied in the case of the angle-dispersive powder X-ray diffraction beamline BM16 at the ESRF. The effects of each optical element on the overall instrument profile are discussed and the importance of the quality of the different optical elements of the instrument is emphasized. Finally, it is shown that the high resolution combined with the precise modelling of the instrument profile shape give access to a particle size as large as 3 µm.