bluuebunny/crossref_metadata_2025 huggingface dataset:
Rat Optic Nerve Oligodendrocytes Develop in the Absence of Viable Retinal Ganglion Cell Axons
Authors: Ueda H. , Levine J.M. , Miller R.H. , Trapp B.D.
Published: July 2002

Retinal ganglion cell axons and axonal electrical activity have been considered essential for migration, proliferation, and survival of oligodendrocyte lineage cells in the optic nerve. To define axonal requirements during oligodendrogenesis, the developmental appearance of oligodendrocyte progenitors and oligodendrocytes were compared between normal and transected optic nerves. In the absence of viable axons, oligodendrocyte precursors migrated along the length of the nerve and subsequently multiplied and differentiated into myelin basic protein–positive oligodendrocytes at similar densities and with similar temporal and spatial patterns as in control nerves. Since transected optic nerves failed to grow radially, the number of oligodendrocyte lineage cells was reduced compared with control nerves. However, the mitotic indices of progenitors and the percentage of oligodendrocytes undergoing programmed cell death were similar in control and transected optic nerves. Oligodendrocytes lacked their normal longitudinal orientation, developed fewer, shorter processes, and failed to form myelin in the transected nerves. These data indicate that normal densities of oligodendrocytes can develop in the absence of viable retinal ganglion axons, and support the possibility that axons assure their own myelination by regulating the number of myelin internodes formed by individual oligodendrocytes.
The Heat Shock Protein Ssa2p Is Required for Import of Fructose-1,6-Bisphosphatase into Vid Vesicles
Authors: Brown C. Randell , McCann Jameson A. , Chiang Hui-Ling
Published: July 2002

Fructose-1,6-bisphosphatase (FBPase) is targeted to the vacuole for degradation when Saccharomyces cerevisiae are shifted from low to high glucose. Before vacuolar import, however, FBPase is sequestered inside a novel type of vesicle, the vacuole import and degradation (Vid) vesicles. Here, we reconstitute import of FBPase into isolated Vid vesicles. FBPase sequestration into Vid vesicles required ATP and cytosol, but was inhibited if ATP binding proteins were depleted from the cytosol. The heat shock protein Ssa2p was identified as one of the ATP binding proteins involved in FBPase import. A Δssa2 strain exhibited a significant decrease in the rate of FBPase degradation in vivo as compared with Δssa1, Δssa3, or Δssa4 strains. Likewise, in vitro import was impaired for the Δssa2 strain, but not for the other Δssa strains. The cytosol was identified as the site of the Δssa2 defect; Δssa2 cytosol did not stimulate FBPase import into import competent Vid vesicles, but wild-type cytosol supported FBPase import into competent Δssa2 vesicles. The addition of purified recombinant Ssa2p stimulated FBPase import into Δssa2 Vid vesicles, providing Δssa2 cytosol was present. Thus, Ssa2p, as well as other undefined cytosolic proteins are required for the import of FBPase into vesicles.
A new view of the spindle checkpoint
Authors: Hoyt M. Andrew
Published: July 2002

Previous studies of the spindle checkpoint suggested that its ability to prevent entry into anaphase was mediated by the inhibition of the anaphase-promoting complex (APC) ubiquitin ligase by Mad2. Two new studies challenge that view by demonstrating that another checkpoint protein, BubR1, is a far more potent inhibitor of APC function.
Regulation of the Phosphorylation of Human Pharyngeal Cell Proteins by Group A Streptococcal Surface Dehydrogenase: Signal Transduction between Streptococci and Pharyngeal Cells
Authors: Pancholi Vijaykumar , Fischetti Vincent A.
Published: July 2002

Whether cell-to-cell communication results when group A streptococci interact with their target cells is unknown. Here, we report that upon contact with cultured human pharyngeal cells, both whole streptococci and purified streptococcal surface dehydrogenase (SDH) activate pharyngeal cell protein tyrosine kinase as well as protein kinase C, thus regulating the phosphorylation of cellular proteins. SDH, a major surface protein of group A streptococci, has both glyceraldehyde-3-phosphate dehydrogenase and ADP-ribosylating enzyme activities that may relate to early stages of streptococcal infection. Intact streptococci and purified SDH induce a similar protein phosphorylation pattern with the de novo tyrosine phosphorylation of a 17-kD protein found in the membrane/particulate fraction of the pharyngeal cells. However, this phosphorylation required the presence of cytosolic components. NH2-terminal amino acid sequence analysis identified the 17-kD protein as nuclear core histone H3. Both phosphotyrosine and phosphoserine-specific monoclonal antibodies reacted with the 17-kD protein by Western blot, suggesting that the binding of SDH to these pharyngeal cells elicits a novel signaling pathway that ultimately leads to activation of histone H3–specific kinases. Genistein-inhibitable phosphorylation of histone H3 indicates that tyrosine kinase plays a key role in this event. Treatment of pharyngeal cells with protein kinase inhibitors such as genistein and staurosporine significantly inhibited streptococcal invasion of pharyngeal cells. Therefore, these data indicated that streptococci/SDH-mediated phosphorylation plays a critical role in bacterial entry into the host cell. To identify the membrane receptor that elicits these signaling events, we found that SDH bound specifically to 30- and 32-kD membrane proteins in a direct ligand-binding assay. These findings clearly suggest that SDH plays an important role in cellular communication between streptococci and pharyngeal cells that may be important in host cell gene transcription, and hence in the pathogenesis of streptococcal infection.
Identification of a Novel Developmental Stage Marking Lineage Commitment of Progenitor Thymocytes
Authors: Carlyle James R. , Michie Alison M. , Furlonger Caren , Nakano Toru , Lenardo Michael J. , Paige Christopher J. , Zúñiga-Pflücker Juan Carlos
Published: July 2002

Bipotent progenitors for T and natural killer (NK) lymphocytes are thought to exist among early precursor thymocytes. The identification and functional properties of such a progenitor population remain undefined. We report the identification of a novel developmental stage during fetal thymic ontogeny that delineates a population of T/NK-committed progenitors (NK1.1+/CD117+/CD44+/CD25−). Thymocytes at this stage in development are phenotypically and functionally distinguishable from the pool of multipotent lymphoid-restricted (B, T, and NK) precursor thymocytes. Exposure of multipotent precursor thymocytes or fetal liver– derived hematopoietic progenitors to thymic stroma induces differentiation to the bipotent developmental stage. Continued exposure to a thymic microenvironment results in predominant commitment to the T cell lineage, whereas coculture with a bone marrow–derived stromal cell line results in the generation of mature NK cells. Thus, the restriction point to T and NK lymphocyte destinies from a multipotent progenitor stage is marked by a thymus-induced differentiation step.
Somatic Hypermutation Introduces Insertions and Deletions into Immunoglobulin V Genes
Authors: Wilson Patrick C. , Bouteiller Odette de , Liu Yong-Jun , Potter Kathleen , Banchereau Jacques , Capra J. Donald , Pascual Virginia
Published: July 2002

During a germinal center reaction, random mutations are introduced into immunoglobulin V genes to increase the affinity of antibody molecules and to further diversify the B cell repertoire. Antigen-directed selection of B cell clones that generate high affinity surface Ig results in the affinity maturation of the antibody response. The mutations of Ig genes are typically basepair substitutions, although DNA insertions and deletions have been reported to occur at a low frequency. In this study, we describe five insertion and four deletion events in otherwise somatically mutated VH gene cDNA molecules. Two of these insertions and all four deletions were obtained through the sequencing of 395 cDNA clones (∼110,000 nucleotides) from CD38+IgD− germinal center, and CD38−IgD− memory B cell populations from a single human tonsil. No germline genes that could have encoded these six cDNA clones were found after an extensive characterization of the genomic VH4 repertoire of the tonsil donor. These six insertions or deletions and three additional insertion events isolated from other sources occurred as triplets or multiples thereof, leaving the transcripts in frame. Additionally, 8 of 9 of these events occurred in the CDR1 or CDR2, following a pattern consistent with selection, and making it unlikely that these events were artifacts of the experimental system. The lack of similar instances in unmutated IgD+CD38− follicular mantle cDNA clones statistically associates these events to the somatic hypermutation process (P = 0.014). Close scrutiny of the 9 insertion/deletion events reported here, and of 25 additional insertions or deletions collected from the literature, suggest that secondary structural elements in the DNA sequences capable of producing loop intermediates may be a prerequisite in most instances. Furthermore, these events most frequently involve sequence motifs resembling known intrinsic hotspots of somatic hypermutation. These insertion/deletion events are consistent with models of somatic hypermutation involving an unstable polymerase enzyme complex lacking proofreading capabilities, and suggest a downregulation or alteration of DNA repair at the V locus during the hypermutation process.
Selective Recruitment of Immature and Mature Dendritic Cells by Distinct Chemokines Expressed in Different Anatomic Sites
Authors: Dieu Marie-Caroline , Vanbervliet Béatrice , Vicari Alain , Bridon Jean-Michel , Oldham Elisabeth , Aït-Yahia Smina , Brière Francine , Zlotnik Albert , Lebecque Serge , Caux Christophe
Published: July 2002

DCs (dendritic cells) function as sentinels of the immune system. They traffic from the blood to the tissues where, while immature, they capture antigens. They then leave the tissues and move to the draining lymphoid organs where, converted into mature DC, they prime naive T cells. This suggestive link between DC traffic pattern and functions led us to investigate the chemokine responsiveness of DCs during their development and maturation. DCs were differentiated either from CD34+ hematopoietic progenitor cells (HPCs) cultured with granulocyte/macrophage colony–stimulating factor (GM-CSF) plus tumor necrosis factor (TNF)-α or from monocytes cultured with GM-CSF plus interleukin 4. Immature DCs derived from CD34+ HPCs migrate most vigorously in response to macrophage inflammatory protein (MIP)-3α, but also to MIP-1α and RANTES (regulated on activation, normal T cell expressed and secreted). Upon maturation, induced by either TNF-α, lipopolysaccharide, or CD40L, DCs lose their response to these three chemokines when they acquire a sustained responsiveness to a single other chemokine, MIP-3β. CC chemokine receptor (CCR)6 and CCR7 are the only known receptors for MIP-3α and MIP-3β, respectively. The observation that CCR6 mRNA expression decreases progressively as DCs mature, whereas CCR7 mRNA expression is sharply upregulated, provides a likely explanation for the changes in chemokine responsiveness. Similarly, MIP-3β responsiveness and CCR7 expression are induced upon maturation of monocyte- derived DCs. Furthermore, the chemotactic response to MIP-3β is also acquired by CD11c+ DCs isolated from blood after spontaneous maturation. Finally, detection by in situ hybridization of MIP-3α mRNA only within inflamed epithelial crypts of tonsils, and of MIP-3β mRNA specifically in T cell–rich areas, suggests a role for MIP-3α/CCR6 in recruitment of immature DCs at site of injury and for MIP-3β/CCR7 in accumulation of antigen-loaded mature DCs in T cell–rich areas.
Synaptotagmin II Negatively Regulates Ca2+-triggered Exocytosis of Lysosomes in Mast Cells
Authors: Baram Dana , Adachi Roberto , Medalia Ora , Tuvim Michael , Dickey Burton F. , Mekori Yoseph A. , Sagi-Eisenberg Ronit
Published: July 2002

Synaptotagmins (Syts) I and II are believed to act as Ca2+ sensors in the control of neurotransmission. Here we demonstrate that mast cells express Syt II in their lysosomal fraction. We further show that activation of mast cells by either aggregation of FcεRI or by Ca2+ ionophores results in exocytosis of lysosomes, in addition to the well documented exocytosis of their secretory granules. Syt II directly regulates lysosomal exocytosis, whereby overexpression of Syt II inhibited Ca2+-triggered release of the lysosomal processed form of cathepsin D, whereas suppression of Syt II expression markedly potentiated this release. These findings provide evidence for a novel function of Syt II in negatively regulating Ca2+-triggered exocytosis of lysosomes, and suggest that Syt II–regulated secretion from lysosomes may play an important role in mast cell biology.
Evidence for the Chronic in Vivo Production of Human T Cell Leukemia Virus Type I Rof and Tof Proteins from Cytotoxic T Lymphocytes Directed against Viral Peptides
Authors: Pique Claudine , Ureta-Vidal Abel , Gessain Antoine , Chancerel Bruno , Gout Olivier , Tamouza Riad , Agis Frantz , Dokhélar Marie-Christine
Published: July 2002

Human T cell leukemia virus type I (HTLV-I) is a persistent virus that causes adult T cell leukemia and tropical spastic paraparesis/HTLV-I–associated myelopathy. Studies on rabbits have shown that viral proteins encoded by the open reading frames pX-I and pX-II are required for the establishment of the persistent infection. To examine the in vivo production of these proteins in humans, we have investigated whether cytotoxic T lymphocytes isolated from HTLV-I–infected individuals recognized pX-I and pX-II peptides. CD8+ T lymphocytes to pX-I and pX-II peptides were detected in HTLV-I–infected individuals, whatever their clinical status, and even in the absence of any antigenic restimulation. These findings indicate that the HTLV-I pX-I and pX-II proteins are chronically synthesized in vivo, and are targets of the natural immune response to the virus.
Overexpression of Cd40 Ligand in Murine Epidermis Results in Chronic Skin Inflammation and Systemic Autoimmunity
Authors: Mehling Annette , Loser Karin , Varga Georg , Metze Dieter , Luger Thomas A. , Schwarz Thomas , Grabbe Stephan , Beissert Stefan
Published: July 2002

CD40–CD40 ligand (L) interactions play a pivotal role in immune-mediated inflammatory responses via the activation of antigen-presenting cells (APCs). To investigate the effects of continuous activation of resident tissue APCs, in this case the Langerhans cells (LCs) of the skin, CD40L expression was targeted to the basal keratinocytes of the epidermis of mice using the keratin-14 promoter. Approximately 80% of the transgenic (Tg) mice spontaneously developed dermatitis on the ears, face, tail, and/or paws. Compared with littermates, Tgs had a >90% decrease in epidermal LCs yet increased numbers within the dermis suggestive of enhanced emigration of CD40-activated LCs. Tgs also displayed massive regional lymphadenopathy with increased numbers of dendritic cells and B cells. Moreover, a decrease in IgM and an increase in IgG1/IgG2a/IgG2b/IgE serum concentrations was detectable. Screening for autoantibodies revealed the presence of antinuclear antibodies and anti-dsDNA antibodies implicative of systemic autoimmunity. Accordingly, renal Ig deposits, proteinuria, and lung fibrosis were observed. Adoptive transfer of T cells from Tgs to nonTg recipients evoked the development of skin lesions similar to those found in the Tgs. Dermatitis also developed in B cell–deficient CD40L Tg mice. These findings suggest that in situ activation of LCs by CD40L in the skin not only leads to chronic inflammatory dermatitis but also to systemic mixed-connective-tissue-like autoimmune disorders, possibly by breaking immune tolerance against the skin.
Identification of HLA-A2–restricted CD8+ Cytotoxic T Cell Responses in Primary Biliary Cirrhosis
Authors: Kita Hiroto , Lian Zhe-Xiong , Van de Water Judy , He Xiao-Song , Matsumura Shuji , Kaplan Marshall , Luketic Velimir , Coppel Ross L. , Ansari Aftab A. , Gershwin M. Eric
Published: July 2002

Primary biliary cirrhosis (PBC) is characterized by an intense biliary inflammatory CD4+ and CD8+ T cell response. Very limited information on autoantigen-specific cytotoxic T lymphocyte (CTL) responses is available compared with autoreactive CD4+ T cell responses. Using peripheral blood mononuclear cells (PBMCs) from PBC, we identified an HLA-A2–restricted CTL epitope of the E2 component of pyruvate dehydrogenase (PDC-E2), the immunodominant mitochondrial autoantigen. This peptide, amino acids 159–167 of PDC-E2, induces specific MHC class I–restricted CD8+ CTL lines from 10/12 HLA-A2+ PBC patients, but not controls, after in vitro stimulation with antigen-pulsed dendritic cells (DCs). PDC-E2–specific CTLs could also be generated by pulsing DCs with full-length recombinant PDC-E2 protein. Furthermore, using soluble PDC-E2 complexed with either PDC-E2–specific human monoclonal antibody or affinity-purified autoantibodies against PDC-E2, the generation of PDC-E2–specific CTLs, occurred at 100-fold and 10-fold less concentration, respectively, compared with soluble antigen alone. Collectively, these data demonstrate that autoantibody, helper, and CTL epitopes all contain a shared peptide sequence. The finding that autoantigen–immune complexes can not only cross-present but also that presentation of the autoantigen is of a higher relative efficiency, for the first time defines a unique role for autoantibodies in the pathogenesis of an autoimmune disease.
Vav3 Modulates B Cell Receptor Responses by Regulating Phosphoinositide 3-Kinase Activation
Authors: Inabe Kazunori , Ishiai Masamichi , Scharenberg Andrew M. , Freshney Norman , Downward Julian , Kurosaki Tomohiro
Published: July 2002

To elucidate the mechanism(s) by which Vav3, a new member of the Vav family proteins, participates in B cell antigen receptor (BCR) signaling, we have generated a B cell line deficient in Vav3. Here we report that Vav3 influences phosphoinositide 3-kinase (PI3K) function through Rac1 in that phosphatidylinositol-3,4,5-trisphosphate (PIP3) generation was attenuated by loss of Vav3 or by expression of a dominant negative form of Rac1. The functional interaction between PI3K and Rac1 was also demonstrated by increased PI3K activity in the presence of GTP-bound Rac1. In addition, we show that defects of calcium mobilization and c-Jun NH2-terminal kinase (JNK) activation in Vav3-deficient cells are relieved by deletion of a PIP3 hydrolyzing enzyme, SH2 domain-containing inositol polyphosphate 5′-phosphatase (SHIP). Hence, our results suggest a role for Vav3 in regulating the B cell responses by promoting the sustained production of PIP3 and thereby calcium flux.
Functional Expression ofDrosophila paraSodium Channels
Authors: Warmke Jeffrey W. , Reenan Robert A.G. , Wang Peiyi , Qian Su , Arena Joseph P. , Wang Jixin , Wunderler Denise , Liu Ken , Kaczorowski Gregory J. , Ploeg Lex H.T. Van der , Ganetzky Barry , Cohen Charles J.
Published: July 2002

The Drosophila para sodium channel α subunit was expressed in Xenopus oocytes alone and in combination with tipE, a putative Drosophila sodium channel accessory subunit. Coexpression of tipE with para results in elevated levels of sodium currents and accelerated current decay. Para/TipE sodium channels have biophysical and pharmacological properties similar to those of native channels. However, the pharmacology of these channels differs from that of vertebrate sodium channels: (a) toxin II from Anemonia sulcata, which slows inactivation, binds to Para and some mammalian sodium channels with similar affinity (Kd ≅ 10 nM), but this toxin causes a 100-fold greater decrease in the rate of inactivation of Para/TipE than of mammalian channels; (b) Para sodium channels are >10-fold more sensitive to block by tetrodotoxin; and (c) modification by the pyrethroid insecticide permethrin is >100-fold more potent for Para than for rat brain type IIA sodium channels. Our results suggest that the selective toxicity of pyrethroid insecticides is due at least in part to the greater affinity of pyrethroids for insect sodium channels than for mammalian sodium channels.
Scanning the Intracellular S6 Activation Gate in the Shaker K+ Channel
Authors: Hackos David H. , Chang Tsg-Hui , Swartz Kenton J.
Published: July 2002

In Kv channels, an activation gate is thought to be located near the intracellular entrance to the ion conduction pore. Although the COOH terminus of the S6 segment has been implicated in forming the gate structure, the residues positioned at the occluding part of the gate remain undetermined. We use a mutagenic scanning approach in the Shaker Kv channel, mutating each residue in the S6 gate region (T469-Y485) to alanine, tryptophan, and aspartate to identify positions that are insensitive to mutation and to find mutants that disrupt the gate. Most mutants open in a steeply voltage-dependent manner and close effectively at negative voltages, indicating that the gate structure can both support ion flux when open and prevent it when closed. We find several mutant channels where macroscopic ionic currents are either very small or undetectable, and one mutant that displays constitutive currents at negative voltages. Collective examination of the three types of substitutions support the notion that the intracellular portion of S6 forms an activation gate and identifies V478 and F481 as candidates for occlusion of the pore in the closed state.
New practices for electronic publishing 2: New forms of the scientific paper
Authors: Kircz Joost G.
Published: July 2002

We extend the analysis of our previous paper (Learned Publishing 2001: 265–72) to a broader discussion of the major features of electronic publications. We conclude that a distinctly different granularity of information will be required and that this will allow very different levels of authentication and quality control from those currently used for the traditional scientific paper.
A numerical scheme based on mean value solutions for the Helmholtz equation on triangular grids
Authors: Andrade M. , do Val J.
Published: July 2002

A numerical treatment for the Dirichlet boundary value problem on regular triangular grids for homogeneous Helmholtz equations is presented, which also applies to the convection-diffusion problems. The main characteristic of the method is that an accuracy estimate is provided in analytical form with a better evaluation than that obtained with the usual finite difference method. Besides, this classical method can be seen as a truncated series approximation to the proposed method. The method is developed from the analytical solutions for the Dirichlet problem on a ball together with an error evaluation of an integral on the corresponding circle, yielding

O
(

h

4

)

O(h^{4})

accuracy. Some numerical examples are discussed and the results are compared with other methods, with a consistent advantage to the solution obtained here.
High order methods for weakly singular integral equations with nonsmooth input functions
Authors: Monegato G. , Scuderi L.
Published: July 2002

To solve one-dimensional linear weakly singular integral equations on bounded intervals, with input functions which may be smooth or not, we propose to introduce first a simple smoothing change of variable, and then to apply classical numerical methods such as product-integration and collocation based on global polynomial approximations. The advantage of this approach is that the order of the methods can be arbitrarily high and that the associated linear systems one has to solve are very well-conditioned.
The Mordell-Lang conjecture for function fields
Authors: Hrushovski Ehud
Published: July 2002

We give a proof of the geometric Mordell-Lang conjecture, in any characteristic. Our method involves a model-theoretic analysis of the kernel of Manin’s homomorphism and of a certain analog in characteristic

p
p

.
Optimal spliced alignment of homologous cDNA to a genomic DNA
template
Authors: Usuka Jonathan , Zhu Wei , Brendel Volker
Published: July 2002

*To whom correspondence should be addressed.

Motivation: Supplementary cDNA or EST evidence is often decisive for discriminating between alternative gene predictions derived from computational sequence inspection by any of a number of requisite programs. Without additional experimental effort, this approach must rely on the occurrence of cognate ESTs for the gene under consideration in available, generally incomplete, EST collections for the given species. In some cases, particular exon assignments can be supported by sequence matching even if the cDNA or EST is produced from non-cognate genomic DNA, including different loci of a gene family or homologous loci from different species. However, marginally significant sequence matching alone can also be misleading. We sought to develop an algorithm that would simultaneously score for predicted intrinsic splice site strength and sequence matching between the genomic DNA template and a related cDNA or EST. In this case, weakly predicted splice sites may be chosen for the optimal scoring spliced alignment on the basis of surrounding sequence matching. Strongly predicted splice sites will enter the optimal spliced alignment even without strong sequence matching.

Results: We designed a novel algorithm that produces the optimal spliced alignment of a genomic DNA with a cDNA or EST based on scoring for both sequence matching and intrinsic splice site strength. By example, we demonstrate that this combined approach appears to improve gene prediction accuracy compared with current methods that rely only on either search by content and signal or on sequence similarity.

Availability: The algorithm is available as a C subroutine and is implemented in the SplicePredictor and GeneSeqer programs. The source code is available via anonymous ftp from ftp.zmdb.iastate.edu. Both programs are also implemented as a Web service at http://gremlin1.zool.iastate.edu/cgi-bin/sp.cgiand http://gremlin1.zool.iastate.edu/cgi-bin/gs.cgi, respectively.

Contact: vbrendel@iastate.edu
DaliLite workbench for protein structure comparison
Authors: Holm Liisa , Park Jong
Published: July 2002

Summary: DaliLite is a program for pairwise structure comparison and for structure database searching. It is a standalone version of the search engine of the popular Dali server. A web interface is provided to view the results, multiple alignments and 3D superimpositions of structures.

Availability: DaliLite has been ported to the Linux and Irix operating systems and can be compiled in many other UNIX operating systems. It is found at http://www.embl-ebi.ac.uk/dali/DaliLite.

Contact: holm@embl-ebi.ac.uk
A mixture model-based approach to the clustering of microarray
expression data
Authors: McLachlan G. J. , Bean R. W. , Peel D.
Published: July 2002

Motivation: This paper introduces the software EMMIX-GENE that has been developed for the specific purpose of a model-based approach to the clustering of microarray expression data, in particular, of tissue samples on a very large number of genes. The latter is a nonstandard problem in parametric cluster analysis because the dimension of the feature space (the number of genes) is typically much greater than the number of tissues. A feasible approach is provided by first selecting a subset of the genes relevant for the clustering of the tissue samples by fitting mixtures of tdistributions to rank the genes in order of increasing size of the likelihood ratio statistic for the test of one versus two components in the mixture model. The imposition of a threshold on the likelihood ratio statistic used in conjunction with a threshold on the size of a cluster allows the selection of a relevant set of genes. However, even this reduced set of genes will usually be too large for a normal mixture model to be fitted directly to the tissues, and so the use of mixtures of factor analyzers is exploited to reduce effectively the dimension of the feature space of genes.

Results: The usefulness of the EMMIX-GENE approach for the clustering of tissue samples is demonstrated on two well-known data sets on colon and leukaemia tissues. For both data sets, relevant subsets of the genes are able to be selected that reveal interesting clusterings of the tissues that are either consistent with the external classification of the tissues or with background and biological knowledge of these sets.

Availability: EMMIX-GENE is available at http://www.maths.uq.edu.au/~gjm/emmix-gene/

Contact: gjm@maths.uq.edu.au
Presenilin‐dependent γ‐secretase processing of β‐amyloid precursor protein at a site corresponding to the S3 cleavage of Notch
Authors: Sastre Magdalena , Steiner Harald , Fuchs Klaus , Capell Anja , Multhaup Gerd , Condron Margaret M , Teplow David B , Haass Christian
Published: July 2002

The presenilin (PS)‐dependent site 3 (S3) cleavage of Notch liberates its intracellular domain (NICD), which is required for Notch signaling. The similar γ‐secretase cleavage of the β‐amyloid precursor protein (βAPP) results in the secretion of amyloid β‐peptide (Aβ). However, little is known about the corresponding C‐terminal cleavage product (CTFγ). We have now identified CTFγ in brain tissue, in living cells, as well as in an in vitro system. Generation of CTFγ is facilitated by PSs, since a dominant‐negative mutation of PS as well as a PS gene knock out prevents its production. Moreover, γ‐secretase inhibitors, including one that is known to bind to PS, also block CTFγ generation. Sequence analysis revealed that CTFγ is produced by a novel γ‐secretase cut, which occurs at a site corresponding to the S3 cleavage of Notch.
Tobacco mosaic virus: a pioneer to cell–to–cell movement
Authors: Citovsky Vitaly
Published: July 2002

Cell–to–cell movement of tobacco mosaic virus (TMV) is used to illustrate macromolecular traffic through plant intercellular connections, the plasmodesmata. This transport process is mediated by a specialized viral movement protein, P30. In the initially infected cell, P30 is produced by transcription of a subgenomic RNA derived from the invading virus. Presumably, P30 then associates with a certain proportion of the viral RNA molecules, sequestering them from replication and mediating their transport into neighbouring uninfected host cells. This nucleoprotein complex is targeted to plasmodesmata, possibly via interaction with the host cell cytoskeleton. Prior to passage through a plasmodesma, the plasmodesmal channel is dilated by the movement protein. It is proposed that targeting of P30–TMV RNA complexes to plasmodesmata involves binding to a specific cell wall–associated receptor molecule. In addition, a cell wall–associated protein kinase, phosphorylates P30 at its carboxy–terminus and minimizes P30–induced interference with plasmodesmatal permeability during viral infection.
Multiple sclerosis⋮ the disease and its manifestations
Authors: McDonald W. I. , Ron M. A.
Published: July 2002

Multiple sclerosis is an immune–mediated inflammatory demyelinating disease of the central nervous system clinically characterized by relapses and remissions of neurological disturbance. A typical relapse, exemplified by optic neuritis, increases in severity over a week or two and after approximately one month begins to remit. Resolution takes place over the course of two to three months. In the early stages, clinical recovery is virtually complete, though persistent abnormalities of conduction can usually be detected by evoked potential techniques and persistent structural abnormalities can be detected by magnetic resonance imaging (MRI). These techniques, together with cerebrospinal fluid examination for oligoclonal IgG, provide supporting evidence for the diagnosis which, in the absence of a specific test, nevertheless remains primarily clinical. The course of the disease is very variable, but after a number of years neurological deficit begins to accumulate after each relapse. In most patients, the relapsing and remitting phase of the disease is followed by a phase of continuous progression of disability. Cognitive disturbances can be detected in many patients even quite early in the course of the illness. Deficits in attention, memory and executive skills may be prominent and tend to become increasingly prominent as neurological deficit increases, although this is not always the case. There is some correlation between the extent of MRI abnormalities in the cerebral white matter and the severity of cognitive deficit. Depression and anxiety are commonly experienced but are poorly correlated to the lesion load seen on MRI. In contrast, the much rarer psychotic symptoms, euphoria and emotional lability are closely linked to the severity of white matter disease.
Olfactory assessment of predation risk in the aquatic environment
Authors: Wisenden Brain D.
Published: July 2002

The aquatic environment is well suited for the transmission of chemical information. Aquatic animals have evolved highly sensitive receptors for detecting these cues. Here, I review behavioural evidence for the use of chemical cues by aquatic animals for the assessment of predation risk. Chemical cues are released during detection, attack, capture and ingestion of prey. The nature of the cue released depends on the stage of the predation sequence in which cues are released. Predator odours, disturbance pheromones, injury–released chemical cues and dietary cues all convey chemical information to prey. Prey use these cues to minimize their probability of being taken on to the next stage of the sequence. The evolution of specialized epidermal alarm substance cells in fishes in the superorder Ostariophysi represent an amplification of this general phenomenon. These cells carry a significant metabolic cost. The cost is offset by the fitness benefit of the chemical attraction of predators. Attempts of piracy by secondary predators interrupt predation events allowing prey an opportunity for escape. In conclusion, chemical cues are widely used by aquatic prey for risk assessment and this has resulted in the evolution of specialized structures among some taxa.
The evolution of drug–resistant malaria: the role of drug elimination half–life
Authors: Hastings Ian M. , Watkins William M. , White Nicholas J.
Published: July 2002

This paper seeks to define and quantify the influence of drug elimination half–life on the evolution of antimalarial drug resistance. There are assumed to be three general classes of susceptibility of the malaria parasite
Plasmodium falciparum
to a drug:
Res0
, the original, susceptible wildtype;
Res1
, a group of intermediate levels of susceptibility that are more tolerant of the drug but still cleared by treatment; and
Res2
, which is completely resistant to the drug.
Res1
and
Res2
resistance both evolve much faster if the antimalarial drug has a long half–life. We show that previous models have significantly underestimated the rate of evolution of
Res2
resistance by omitting the effects of drug half–life. The methodology has been extended to investigate (i) the effects of using drugs in combination, particularly when the components have differing half–lives, and (ii) the specific example of the development of resistance to the antimalarial pyrimethamine–sulphadoxine. An important detail of the model is the development of drug resistance in two separate phases. In phase A,
Res1
is spreading and replacing the original sensitive forms while
Res2
remains at a low level. Phase B starts once parasites are selected that can escape drug action (
Res1
genotypes with borderline chemosensitivity, and
Res2
): these parasites are rapidly selected, a process that leads to widespread clinical failure. Drug treatment is clinically successful during phase A, and health workers may be unaware of the substantial changes in parasite population genetic structure that predicate the onset of phase B. Surveillance programs are essential, following the introduction of a new drug, to monitor effectively changes in treatment efficacy and thus provide advance warning of drug failure. The model is also applicable to the evolution of antibiotic resistance in bacteria: in particular, the need for these models to incorporate drug pharmacokinetics to avoid potentially large errors in their predictions.
Dmp1 is haplo-insufficient for tumor suppression and modifies the frequencies of Arf and p53 mutations in Myc-induced lymphomas
Authors: Inoue Kazushi , Zindy Frederique , Randle David H. , Rehg Jerold E. , Sherr Charles J.
Published: July 2002

Loss of Dmp1, an Arf transcriptional activator, leads to spontaneous tumorigenesis in mice, causing death from various forms of cancer by two years of age. Retention and expression of the wild-typeDmp1 allele in tumors arising in Dmp1+/−mice demonstrate that Dmp1 can be haplo-insufficient for tumor suppression. The mean latency of Eμ-Myc-induced B-cell lymphomas is halved on a Dmp1−/− orDmp1+/− genetic background. Although p53mutations or Arf deletion normally occur in ∼50% of Eμ-Myc-induced lymphomas, Dmp1 loss obviates selection for such mutations, indicating that Dmp1 is a potent genetic modifier of the Arf–p53 pathway in vivo.
Phenylalanine fluorescence studies of calcium binding to N‐domain fragments ofParameciumcalmodulin mutants show increased calcium affinity correlates with increased disorder
Authors: VanScyoc Wendy S. , Shea Madeline A.
Published: July 2002

Calmodulin (CaM) is a ubiquitous, essential calcium‐binding protein that regulates diverse protein targets in response to physiological calcium fluctuations. Most high‐resolution structures of CaM‐target complexes indicate that the two homologous domains of CaM are equivalent partners in target recognition. However, mutations between calcium‐binding sites I and II in the N‐domain ofParameciumcalmodulin (PCaM) selectively affect calcium‐dependent sodium currents. To understand these domain‐specific effects, N‐domain fragments (PCaM1–75) of six of these mutants were examined to determine whether energetics of calcium binding to sites I and II or conformational properties had been perturbed. These PCaM(1–75)sequences naturally contain 5 Phe residues but no Tyr or Trp; calcium binding was monitored by observing the reduction in intrinsic phenylalanine fluorescence at 280 nm. To assess mutation‐induced conformational changes, thermal denaturation of the apo PCaM(1–75)sequences, and calcium‐dependent changes in Stokes radii were determined. The free energy of calcium binding to each mutant was within 1 kcal/mole of the value for wild type and calcium reduced the Rsof all of them. A striking trend was observed whereby mutants showing an increase in calcium affinity and Rshad a concomitant decrease in thermal stability (by as much as 18°C). Thus, mutations between the binding sites that increased disorder and reduced tertiary constraints in the apo state promoted calcium coordination. This finding underscores the complexity of the linkage between calcium binding and conformational change and the difficulty in predicting mutational effects.
Computation of energy imparted in diagnostic radiology
Authors: Gkanatsios Nikolaos A. , Huda Walter
Published: July 2002

Energy imparted is a measure of the total ionizing energy deposited in the patient during a radiologic examination and may be used to quantify the patient dose in diagnostic radiology. Values of the energy imparted per unit exposure‐area product, absorbed by a semi‐infinite water phantom with a thickness were computed for x‐ray spectra with peak x‐ray tube voltages ranging from 50–140 kV and with added filtration, ranging from 1–6 mm aluminum. For a given phantom thickness and peak x‐ray tube voltage, the energy imparted was found to be directly proportional to the x‐ray beam half‐value layer (HVL) expressed in millimeters of aluminum. Values of were generated for constant waveform x‐ray tube voltages and an anode angle of 12°, and were fitted to the expression Fitted and β parameters are provided that permit the energy imparted to be determined for any combination of tube voltage, half‐value layer, and phantom thickness from the product of the entrance skin exposure (free‐in‐air) and the corresponding x‐ray beam area. The results obtained using our method for calculating energy imparted were compared with values of energy imparted determined using Monte Carlo techniques and anthropomorphic phantoms for a range of diagnostic examinations. At 60, 80, and 120 kV, absolute values of energy imparted obtained using our method differed by 8%, 10%, and 12%, respectively, from the corresponding results of Monte Carlo computations obtained for an anthropomorphic phantom. The method described in this paper permits a simple determination of energy imparted for any type of diagnostic x‐ray examination which may be used to compare the radiologic risks from differing types of x‐ray examinations, optimize imaging techniques with respect to the patient dose, or estimate the patient effective dose equivalent.
Digital radiology using active matrix readout of amorphous selenium: Construction and evaluation of a prototype real‐time detector
Authors: Zhao Wei , Blevis Ira , Germann Stephen , Rowlands J. A. , Waechter David , Huang Zhongshou
Published: July 2002

The goal of the present work is to develop a large area, flat‐panel solid‐state detector for both digital radiography and fluoroscopy. The proposed detector employs a photoconductive layer of amorphous selenium (‐Se) to convert x rays into charge. The charge image formed by the ‐Se layer is electronically read out in situ using a two dimensional array of thin film transistors (TFTs), or active matrix. Since the active matrix readout is capable of producing x‐ray images in real‐time, it can potentially be applied in both radiography and fluoroscopy. In this paper, the imaging performance of this concept is investigated using a prototype x‐ray imaging detector. The designs for the active matrix, the peripheral electronic circuits, and the image acquisition system are described. Measurements of x‐ray imaging properties of the prototype detector, i.e., x‐ray sensitivity, presampling modulation transfer function (MTF), and noise power spectrum (NPS), were performed, and from which the spatial frequency dependent detective quantum efficiency (DQE) of the prototype was derived. The experimental results are in agreement with the results of our theoretical analysis. The factors affecting the imaging performance and methods of improvement in the future are discussed.
Walking a charged pith ball perpendicular to an electric field
Authors: Ouseph P. J. , Davis C. L.
Published: July 2002

The net motion of a charged particle in the electric field between two plates of an almost parallel plate capacitor is in a direction perpendicular to the electric field. An apparatus to demonstrate this effect is discussed and the motion of the charged particle is described by simple theoretical considerations.
Understanding the Laughlin wave function for the fractional quantum Hall effect
Authors: Johnson B. L.
Published: July 2002

We study the behavior of an interacting two-dimensional charged particle system in a transverse magnetic field and give a simple picture of the features that lead to the fractional quantum Hall effect. In particular, we discuss how the interparticle interactions give rise to an energy-level substructure in the lowest Landau level and develop a relatively simple model that gives insight into the analytical form of the Laughlin wave function. We analyze the model by transforming to a reference frame that rotates at half the cyclotron angular frequency. In the rotating frame, the vector potential for the magnetic field is replaced by a quadratic scalar potential. It is then evident that the system of interacting particles is a bound state, even in the absence of a charge-neutralizing background. We solve exactly a many-particle system in the rotating frame using a harmonic model interaction. In addition to being a good example for demonstrating basic methods in quantum mechanics, we show explicitly that the Laughlin function is an eigenstate of this model system.
Millikan Lecture 1998: Building a Science of Teaching Physics
Authors: Redish Edward F.
Published: July 2002

Individual teachers of college level physics sometimes develop deep insights into how their students learn and what elements of classroom instruction are valuable in facilitating the learning process. Yet these insights rarely persist beyond the individual instructor. Educational methods seem to cycle from one fad to another, rarely cumulating increasingly powerful knowledge in the way scientists expect understanding to grow. In this paper I explore the character of our understanding of the physical world and of teaching about it. The critical factor is using “the culture of science”—the set of processes that allow us to build a community consensus knowledge base. Elements of the beginning of a base for our educational knowledge are discussed and examples given from discipline-based physics education research.
The perceptual consequences of within-talker variability in fricative production
Authors: Newman Rochelle S. , Clouse Sheryl A. , Burnham Jessica L.
Published: July 2002

The effect of talker and token variability on speech perception has engendered a great deal of research. However, most of this research has compared listener performance in multiple-talker (or variable) situations to performance in single-talker conditions. It remains unclear to what extent listeners are affected by the degree of variability within a talker, rather than simply the existence of variability (being in a multitalker environment). The present study has two goals: First, the degree of variability among speakers in their /s/ and /∫/ productions was measured. Even among a relatively small pool of talkers, there was a range of speech variability: some talkers had /s/ and /∫/ categories that were quite distinct from one another in terms of frication centroid and skewness, while other speakers had categories that actually overlapped one another. The second goal was to examine whether this degree of variability within a talker influenced perception. Listeners were presented with natural /s/ and /∫/ tokens for identification, under ideal listening conditions, and slower response times were found for speakers whose productions were more variable than for speakers with more internal consistency in their speech. This suggests that the degree of variability, not just the existence of it, may be the more critical factor in perception.
Evaluation of decay times in coupled spaces: Bayesian parameter estimation
Authors: Xiang Ning , Goggans Paul M.
Published: July 2002

Determination of sound decay times in coupled spaces often demands considerable effort. Based on Schroeder’s backward integration of room impulse responses, it is often difficult to distinguish different portions of multirate sound energy decay functions. A model-based parameter estimation method, using Bayesian probabilistic inference, proves to be a powerful tool for evaluating decay times. A decay model due to one of the authors [N. Xiang, J. Acoust. Soc. Am. 98, 2112–2121 (1995)] is extended to multirate decay functions. Following a summary of Bayesian model-based parameter estimation, the present paper discusses estimates in terms of both synthesized and measured decay functions. No careful estimation of initial values is required, in contrast to gradient-based approaches. The resulting robust algorithmic estimation of more than one decay time, from experimentally measured decay functions, is clearly superior to the existing nonlinear regression approach.