bluuebunny/crossref_metadata_2025 huggingface dataset:
Medieval Socialist Artefacts: Architecture and Discourses of National Identity in Provincial Poland, 1945–1960
Authors: Faraldo José M.
Published: July 2002

Many things allow us to recognize that the Poles have a greater and fuller affinity with the Poznań Land than the Germans, even today. It is interesting, for example, with what confidence Polish architects, in contrast to their German counterparts, incorporate historical and regional characteristics in their designs.

Moritz Jaffé

The Archive of the Town Curator of Monuments in the Polish city Poznań contains material about streets, monuments, Old Town Square, the cathedral, and other valuable constructions there. A folder labeled Nowy Ratusz (New Town Hall) attracted my attention, because I knew nothing about such a building. The folder contained photographs of a largeneo-Gothicbuilding. It looked like a typical Prussian public building, similar to hundreds of other postal, school, and government offices throughout the Prussian/German state. But what of this building? Had it been another casualty of the Second World War? The postwar images showed, that although seriously damaged, the building still stood in the ruins of the Old Town Square.
“Polish-Speaking Germans?” Language and National Identity Among the Masurians
Authors: Blanke Richard
Published: July 2002

Before 1945, Masuria was part of Germany and known primarily as the scene of the 1914 Battle of Tannenberg and as an attractive summer vacationland of numerous lakes, extensive forests, and villages of characteristic wooden houses. Since 1945, Masuria has belonged to Poland, where it is known as the scene of the 1410 Battle of Tannenberg/Grunwald, and as an attractive summer vacationland. To students of nationalism and national identity, however, Masuria is interesting primarily because its predominately Polish-speaking population seems to present the clearest and best-documented example anywhere in Europe of national identity developing counter to native language. Although most Masurians spoke Polish and lived adjacent to Poland, they gave every indication over quite a long period of time of voluntary and virtually unanimous identification with the Prusso-German state and nation. They did so at a time when most of the rest of eastern Europe was increasingly subject to the influence of ethnolinguistic nationalism and the rest of the German–Polish borderlands were witness to one of Europe's classic ethnic-national rivalries. (see Maps 1 and 2)
Where Else Would you Look? Constructivism and the Historiography of Economics
Authors: Emmett Ross B.
Published: July 2002

Eleven years ago, at my first HES conference, I attended a session on the historiography of economics. In my naiveté and brashness (not a good combination!) as a grad student, I asked why so much of the conversation about how to do historical work in economics was dominated by reference to methodological categories provided by philosophers of science like Lakatos, Popper, and Kuhn. I enjoyed my own investigations in the philosophy of economics, and was starting to write about Frank Knight, who was certainly not naive philosophically, but I wanted a different reference point as ahistorianof economics. I remember one member of the panel looking at me somewhat puzzled and asking, “Where else would you look?”

Today, we gather to reflect, once again, on the historiography of economics. This time, we are asked to reflect on a new reference point for our work: the sociology of scientific knowledge or science studies. Jan Golinski has provided us with an excellent survey of work in this field, and a synopsis of its relevance over the past fifteen years or so to the history of the natural sciences. His book is not a rallying cry for constructivism, but rather a careful analysis of the benefits and costs to historians of science if they choose to adopt constructivist techniques.
Adenomatous Polyposis Coli Tumor Suppressor Protein Has Signaling Activity in Xenopus laevis Embryos Resulting in the Induction of an Ectopic Dorsoanterior Axis
Authors: Vleminckx Kris , Wong Ellen , Guger Kathy , Rubinfeld Bonnee , Polakis Paul , Gumbiner Barry M.
Published: July 2002

Mutations in the adenomatous polyposis coli (APC) tumor suppressor gene are linked to both familial and sporadic human colon cancer. So far, a clear biological function for the APC gene product has not been determined. We assayed the activity of APC in the early Xenopus embryo, which has been established as a good model for the analysis of the signaling activity of the APC-associated protein β-catenin. When expressed in the future ventral side of a four-cell embryo, full-length APC induced a secondary dorsoanterior axis and the induction of the homeobox gene Siamois. This is similar to the phenotype previously observed for ectopic β-catenin expression. In fact, axis induction by APC required the availability of cytosolic β-catenin. These results indicate that APC has signaling activity in the early Xenopus embryo. Signaling activity resides in the central domain of the protein, a part of the molecule that is missing in most of the truncating APC mutations in colon cancer. Signaling by APC in Xenopus embryos is not accompanied by detectable changes in expression levels of β-catenin, indicating that it has direct positive signaling activity in addition to its role in β-catenin turnover. From these results we propose a model in which APC acts as part of the Wnt/β-catenin signaling pathway, either upstream of, or in conjunction with, β-catenin.
Inhibition of Endosome Function in CHO Cells Bearing a Temperature-sensitive Defect in the Coatomer (COPI) Component ε-COP
Authors: Daro Elizabeth , Sheff David , Gomez Marie , Kreis Thomas , Mellman Ira
Published: July 2002

Recent evidence has suggested that subunits of the coatomer protein (COPI) complexes are functionally associated with endosomes in mammalian cells. We now provide genetic evidence that COPI plays a role in endocytosis in intact cells. The ldlF mutant CHO cell line bears a temperature-sensitive defect in the COPI subunit ε-COP. In addition to exhibiting conditional defects in the secretory pathway, we find that the cells are also defective at mediating endosome-associated functions. As found for cells microinjected with anti-COPI antibodies, ldlF cells at the restrictive temperature could not be infected by vesicular stomatitis (VSV) or Semliki Forest virus (SFV) that require delivery to acidic endosomes to penetrate into the cytosol. Although there was no temperature-sensitive defect in the internalization of receptor-bound transferrin (Tfn), Tfn recycling and accumulation of HRP were markedly inhibited at the restrictive temperature. Sorting of receptor-bound markers such as EGF to lysosomes was also reduced, although delivery of fluid-phase markers was only partially inhibited. In addition, lysosomes redistributed from their typical perinuclear location to the tips of the ldlF cells. Mutant phenotypes began to emerge within 2 h of temperature shift, the time required for the loss of detectable ε-COP, suggesting that the endocytic defects were not secondary to a block in the secretory pathway. Importantly, the mutant phenotypes were also corrected by transfection of wild-type ε-COP cDNA demonstrating that they directly or indirectly reflected the ε-COP defect. Taken together, the results suggest that ε-COP acts early in the endocytic pathway, most likely inhibiting the normal sorting and recycling functions of early endosomes.
A Novel 95-kD Protein Is Located in a Linker between Cytoplasmic Microtubules and Basal Bodies in a Green Flagellate and Forms Striated Filaments In Vitro
Authors: Geimer Stefan , Clees Judith , Melkonian Michael , Lechtreck Karl-Ferdinand
Published: July 2002

The flagellar basal apparatus comprises the basal bodies and the attached fibrous structures, which together form the organizing center for the cytoskeleton in many flagellated cells. Basal apparatus were isolated from the naked green flagellate Spermatozopsis similis and shown to be composed of several dozens of different polypeptides including a protein band of 95 kD. Screening of a cDNA library of S. similis with a polyclonal antibody raised against the 95-kD band resulted in a full-length clone coding for a novel protein of 834 amino acids (90.3 kD). Sequence analysis identified nonhelical NH2- and COOH-terminal domains flanking a central domain of ∼650 residues, which was predicted to form a series of coiled-coils interrupted by short spacer segments. Immunogold labeling using a polyclonal antibody raised against the bacterially expressed 95-kD protein exclusively decorated the striated, wedge-shaped fibers, termed sinister fibers (sf-fibers), attached to the basal bodies of S. similis. Striated fibers with a periodicity of 98 nm were assembled in vitro from the purified protein expressed from the cloned cDNA indicating that the 95-kD protein could be a major component of the sf-fibers. This structure interconnects specific triplets of the basal bodies with the microtubular bundles that emerge from the basal apparatus. The sf-fibers and similar structures, e.g., basal feet or satellites, described in various eukaryotes including vertebrates, may be representative for cytoskeletal elements involved in positioning of basal bodies/centrioles with respect to cytoskeletal microtubules and vice versa.
Asymmetric Requirements for a Rab Gtpase and Snare Proteins in Fusion of Copii Vesicles with Acceptor Membranes
Authors: Cao Xiaochun , Barlowe Charles
Published: July 2002

Soluble NSF attachment protein receptor (SNARE) proteins are essential for membrane fusion in transport between the yeast ER and Golgi compartments. Subcellular fractionation experiments demonstrate that the ER/Golgi SNAREs Bos1p, Sec22p, Bet1p, Sed5p, and the Rab protein, Ypt1p, are distributed similarly but localize primarily with Golgi membranes. All of these SNARE proteins are efficiently packaged into COPII vesicles and suggest a dynamic cycling of SNARE machinery between ER and Golgi compartments. Ypt1p is not efficiently packaged into vesicles under these conditions. To determine in which membranes protein function is required, temperature-sensitive alleles of BOS1, BET1, SED5, SLY1, and YPT1 that prevent ER/Golgi transport in vitro at restrictive temperatures were used to selectively inactivate these gene products on vesicles or on Golgi membranes. Vesicles bearing mutations in Bet1p or Bos1p inhibit fusion with wild-type acceptor membranes, but acceptor membranes containing these mutations are fully functional. In contrast, vesicles bearing mutations in Sed5p, Sly1p, or Ypt1p are functional, whereas acceptor membranes containing these mutations block fusion. Thus, this set of SNARE proteins is symmetrically distributed between vesicle and acceptor compartments, but they function asymmetrically such that Bet1p and Bos1p are required on vesicles and Sed5p activity is required on acceptor membranes. We propose the asymmetry in SNARE protein function is maintained by an asymmetric distribution and requirement for the Ypt1p GTPase in this fusion event. When a transmembrane-anchored form of Ypt1p is used to restrict this GTPase to the acceptor compartment, vesicles depleted of Ypt1p remain competent for fusion.
Yeast Nucleoporins Involved in Passive Nuclear Envelope Permeability
Authors: Shulga Nataliya , Mosammaparast Nima , Wozniak Richard , Goldfarb David S.
Published: July 2002

The vertebrate nuclear pore complex (NPC) harbors an ∼10-nm diameter diffusion channel that is large enough to admit 50-kD polypeptides. We have analyzed the permeability properties of the Saccharomyces cerevisiae nuclear envelope (NE) using import (NLS) and export (NES) signal-containing green fluorescent protein (GFP) reporters. Compared with wild-type, passive export rates of a classical karyopherin/importin (Kap) Kap60p/Kap95p-targeted NLS-GFP reporter (cNLS-GFP) were significantly faster in nup188-Δ and nup170-Δ cells. Similar results were obtained using two other NLS-GFP reporters, containing either the Kap104p-targeted Nab2p NLS (rgNLS) or the Kap121p-targeted Pho4p NLS (pNLS). Elevated levels of Hsp70 stimulated cNLS-GFP import, but had no effect on the import of rgNLS-GFP. Thus, the role of Hsp70 in NLS-directed import may be NLS- or targeting pathway-specific. Equilibrium sieving limits for the diffusion channel were assessed in vivo using NES-GFP reporters of 36–126 kD and were found to be greater than wild-type in nup188-Δ and nup170-Δ cells. We propose that Nup170p and Nup188p are involved in establishing the functional resting diameter of the NPC's central transport channel.
Acaps Are Arf6 Gtpase-Activating Proteins That Function in the Cell Periphery
Authors: Jackson Trevor R. , Brown Fraser D. , Nie Zhongzhen , Miura Koichi , Foroni Letizia , Sun Jianlan , Hsu Victor W. , Donaldson Julie G. , Randazzo Paul A.
Published: July 2002

The GTP-binding protein ADP-ribosylation factor 6 (Arf6) regulates endosomal membrane trafficking and the actin cytoskeleton in the cell periphery. GTPase-activating proteins (GAPs) are critical regulators of Arf function, controlling the return of Arf to the inactive GDP-bound state. Here, we report the identification and characterization of two Arf6 GAPs, ACAP1 and ACAP2. Together with two previously described Arf GAPs, ASAP1 and PAP, they can be grouped into a protein family defined by several common structural motifs including coiled coil, pleckstrin homology, Arf GAP, and three complete ankyrin-repeat domains. All contain phosphoinositide-dependent GAP activity. ACAP1 and ACAP2 are widely expressed and occur together in the various cultured cell lines we examined. Similar to ASAP1, ACAP1 and ACAP2 were recruited to and, when overexpressed, inhibited the formation of platelet-derived growth factor (PDGF)–induced dorsal membrane ruffles in NIH 3T3 fibroblasts. However, in contrast with ASAP1, ACAP1 and ACAP2 functioned as Arf6 GAPs. In vitro, ACAP1 and ACAP2 preferred Arf6 as a substrate, rather than Arf1 and Arf5, more so than did ASAP1. In HeLa cells, overexpression of either ACAP blocked the formation of Arf6-dependent protrusions. In addition, ACAP1 and ACAP2 were recruited to peripheral, tubular membranes, where activation of Arf6 occurs to allow membrane recycling back to the plasma membrane. ASAP1 did not inhibit Arf6-dependent protrusions and was not recruited by Arf6 to tubular membranes. The additional effects of ASAP1 on PDGF-induced ruffling in fibroblasts suggest that multiple Arf GAPs function coordinately in the cell periphery.
Visualization of a Cytoskeleton-like Ftsz Network in Chloroplasts
Authors: Kiessling Justine , Kruse Sven , Rensing Stefan A. , Harter Klaus , Decker Eva L. , Reski Ralf
Published: July 2002

It has been a long-standing dogma in life sciences that only eukaryotic organisms possess a cytoskeleton. Recently, this belief was questioned by the finding that the bacterial cell division protein FtsZ resembles tubulin in sequence and structure and, thus, may be the progenitor of this major eukaryotic cytoskeletal element. Here, we report two nuclear-encoded plant ftsZ genes which are highly conserved in coding sequence and intron structure. Both their encoded proteins are imported into plastids and there, like in bacteria, they act on the division process in a dose-dependent manner. Whereas in bacteria FtsZ only transiently polymerizes to a ring-like structure, in chloroplasts we identified persistent, highly organized filamentous scaffolds that are most likely involved in the maintenance of plastid integrity and in plastid division. As these networks resemble the eukaryotic cytoskeleton in form and function, we suggest the term “plastoskeleton” for this newly described subcellular structure.
The conserved Pkh–Ypk kinase cascade is required for endocytosis in yeast
Authors: deHart Amy K.A. , Schnell Joshua D. , Allen Damian A. , Hicke Linda
Published: July 2002

Internalization of activated signaling receptors by endocytosis is one way cells downregulate extracellular signals. Like many signaling receptors, the yeast α-factor pheromone receptor is downregulated by hyperphosphorylation, ubiquitination, and subsequent internalization and degradation in the lysosome-like vacuole. In a screen to detect proteins involved in ubiquitin-dependent receptor internalization, we identified the sphingoid base–regulated serine–threonine kinase Ypk1. Ypk1 is a homologue of the mammalian serum– and glucocorticoid-induced kinase, SGK, which can substitute for Ypk1 function in yeast. The kinase activity of Ypk1 is required for receptor endocytosis because mutations in two residues important for its catalytic activity cause a severe defect in α-factor internalization. Ypk1 is required for both receptor-mediated and fluid-phase endocytosis, and is not necessary for receptor phosphorylation or ubiquitination. Ypk1 itself is phosphorylated by Pkh kinases, homologues of mammalian PDK1. The threonine in Ypk1 that is phosphorylated by Pkh1 is required for efficient endocytosis, and pkh mutant cells are defective in α-factor internalization and fluid-phase endocytosis. These observations demonstrate that Ypk1 acts downstream of the Pkh kinases to control endocytosis by phosphorylating components of the endocytic machinery.
Constructing a Golgi complex
Authors: Pfeffer Suzanne R.
Published: July 2002

In this issue, Short et al. report the discovery of a protein named Golgin-45 that is located on the surface of the middle (or medial) cisternae of the Golgi complex. Depletion of this protein disrupts the Golgi complex and leads to the return of a resident, lumenal, medial Golgi enzyme to the endoplasmic reticulum. These findings suggest that Golgin-45 serves as a linchpin for the maintenance of Golgi complex structure, and offer hints as to the mechanisms by which the polarized Golgi complex is constructed.
Changes in Locus-specific V(D)J Recombinase Activity Induced by Immunoglobulin Gene Products during B Cell Development
Authors: Constantinescu Andrei , Schlissel Mark S.
Published: July 2002

The process of V(D)J recombination is crucial for regulating the development of B cells and for determining their eventual antigen specificity. Here we assess the developmental regulation of the V(D)J recombinase directly, by monitoring the double-stranded DNA breaks produced in the process of V(D)J recombination. This analysis provides a measure of recombinase activity at immunoglobulin heavy and light chain loci across defined developmental stages spanning the process of B cell development. We find that expression of a complete immunoglobulin heavy chain protein is accompanied by a drastic change in the targeting of V(D)J recombinase activity, from being predominantly active at the heavy chain locus in pro-B cells to being exclusively restricted to the light chain loci in pre-B cells. This switch in locus-specific recombinase activity results in allelic exclusion at the immunoglobulin heavy chain locus. Allelic exclusion is maintained by a different mechanism at the light chain locus. We find that immature, but not mature, B cells that already express a functional light chain protein can undergo continued light chain gene rearrangement, by replacement of the original rearrangement on the same allele. Finally, we find that the developmentally regulated targeting of V(D)J recombination is unaffected by enforced rapid transit through the cell cycle induced by an Eμ-myc transgene.
Itk Negatively Regulates Induction of  T Cell Proliferation by CD28 Costimulation
Authors: Liao X. Charlene , Fournier Sylvie , Killeen Nigel , Weiss Arthur , Allison James P. , Littman Dan R.
Published: July 2002

CD28 is a cell surface molecule that mediates a costimulatory signal crucial for T cell proliferation and lymphokine production. The signal transduction mechanisms of CD28 are not well understood. Itk, a nonreceptor protein tyrosine kinase specifically expressed in T cells and mast cells, has been implicated in the CD28 signaling pathway because of reports that it becomes phosphorylated on tyrosines and associates with CD28 upon cross-linking of the cell surface molecule. To determine whether Itk plays a functional role in CD28 signaling, we compared T cells from Itk-deficient mice and control mice for their responses to CD28 costimulation. T cells defective in Itk were found to be fully competent to respond to costimulation. Whereas the CD3-mediated proliferative response was severely compromised in the absence of Itk, the calcineurin-independent CD28-mediated response was significantly elevated when compared with cells from control animals. The augmented proliferation was not due to increased production of interleukin-2. The results suggest that Itk has distinct roles in the CD3 versus the CD28 signaling pathways. By negatively regulating the amplitude of signaling upon CD28 costimulation, Itk may provide a means for modulating the outcome of T cell activation during development and during antigen-driven immune responses.
A Balance between Positive and Negative Signals in Cytotoxic Lymphocytes Regulates the Polarization of Lipid Rafts during the Development of Cell-Mediated Killing
Authors: Lou Zhenkun , Jevremovic Dragan , Billadeau Daniel D. , Leibson Paul J.
Published: July 2002

Plasma membrane microdomains containing sphingolipids and cholesterol (lipid rafts) are enriched in signaling molecules. The cross-linking of certain types of cell surface receptors initiates the redistribution of these lipid rafts, resulting in the formation of signaling complexes. However, little is known about the regulation of the initial raft redistribution and whether negative regulatory signaling pathways target this phase of cellular activation. We used natural killer (NK) cells as a model to investigate the regulation of raft redistribution, as both positive and negative signals have been implicated in the development of their cellular function. Here we show that after NK cells form conjugates with sensitive tumor cells, rafts become polarized to the site of target recognition. This redistribution of lipid rafts requires the activation of both Src and Syk family protein tyrosine kinases. In contrast, engagement of major histocompatibility complex (MHC)-recognizing killer cell inhibitory receptors (KIRs) on NK cells by resistant, MHC-bearing tumor targets blocks raft redistribution. This inhibition is dependent on the catalytic activity of KIR-associated SHP-1, a Src homology 2 (SH2) domain containing tyrosine phosphatase. These results suggest that the influence of integrated positive and negative signals on raft redistribution critically influences the development of cell-mediated cytotoxicity.
Interleukin 4–Producing Cd4 T Cells Arise from Different Precursors Depending on the Conditions of Antigen Exposure in Vivo
Authors: Foucras Gilles , Gapin Laurent , Coureau Christiane , Kanellopoulos Jean M. , Guéry Jean-Charles
Published: July 2002

The precursor origin of T helper (Th) cell subsets in vivo has been difficult to study and remains poorly investigated. We have previously shown that chronic administration of soluble protein antigen induces selective development of antigen-specific CD4 Th2 cells in genetically predisposed mouse strains. To analyze the origin of effector T cells in this model, we designed a competitive polymerase chain reaction–based approach to track public BV-J rearrangement expressed by CD4 T cells specific for hen egg white lysozyme (HEL) in BALB/c mice. We show that public T cell clones are predominantly associated with type 1 or 2 effector Th cells recovered after primary immunization in complete or incomplete Freund's adjuvant, respectively. Conversely, continuous administration of soluble antigen, which induces strong memory Th2 response, is associated with a dose-dependent reduction of public clone size by a mechanism resembling clonal anergy. Thus, soluble HEL–induced Th2 cells do not express the public complementarity determining region 3 motifs characteristic of immunogenic challenge in the presence of adjuvant. These results demonstrate that there are multiple pathways of induction of Th2 responses depending on the condition of antigen exposure in vivo, i.e., clonal immune deviation versus recruitment of a different pool of precursor cells.
Permeability of Wild-Type and Mutant Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channels to Polyatomic Anions
Authors: Linsdell Paul , Tabcharani Joseph A. , Rommens Johanna M. , Hou Yue-Xian , Chang Xiu-Bao , Tsui Lap-Chee , Riordan John R. , Hanrahan John W.
Published: July 2002

Permeability of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel to polyatomic anions of known dimensions was studied in stably transfected Chinese hamster ovary cells by using the patch clamp technique. Biionic reversal potentials measured with external polyatomic anions gave the permeability ratio (PX/PCl) sequence NO3− > Cl− > HCO3− > formate > acetate. The same selectivity sequence but somewhat higher permeability ratios were obtained when anions were tested from the cytoplasmic side. Pyruvate, propanoate, methane sulfonate, ethane sulfonate, and gluconate were not measurably permeant (PX/PCl < 0.06) from either side of the membrane. The relationship between permeability ratios from the outside and ionic diameters suggests a minimum functional pore diameter of ∼5.3 Å. Permeability ratios also followed a lyotropic sequence, suggesting that permeability is dependent on ionic hydration energies. Site-directed mutagenesis of two adjacent threonines in TM6 to smaller, less polar alanines led to a significant (24%) increase in single channel conductance and elevated permeability to several large anions, suggesting that these residues do not strongly bind permeating anions, but may contribute to the narrowest part of the pore.
Interactions among Toxins That Inhibit N-type and P-type Calcium Channels
Authors: McDonough Stefan I. , Boland Linda M. , Mintz Isabelle M. , Bean Bruce P.
Published: July 2002

A number of peptide toxins from venoms of spiders and cone snails are high affinity ligands for voltage-gated calcium channels and are useful tools for studying calcium channel function and structure. Using whole-cell recordings from rat sympathetic ganglion and cerebellar Purkinje neurons, we studied toxins that target neuronal N-type (CaV2.2) and P-type (CaV2.1) calcium channels. We asked whether different toxins targeting the same channels bind to the same or different sites on the channel. Five toxins (ω-conotoxin-GVIA, ω-conotoxin MVIIC, ω-agatoxin-IIIA, ω-grammotoxin-SIA, and ω-agatoxin-IVA) were applied in pairwise combinations to either N- or P-type channels. Differences in the characteristics of inhibition, including voltage dependence, reversal kinetics, and fractional inhibition of current, were used to detect additive or mutually occlusive effects of toxins. Results suggest at least two distinct toxin binding sites on the N-type channel and three on the P-type channel. On N-type channels, results are consistent with blockade of the channel pore by ω-CgTx-GVIA, ω-Aga-IIIA, and ω-CTx-MVIIC, whereas grammotoxin likely binds to a separate region coupled to channel gating. ω-Aga-IIIA produces partial channel block by decreasing single-channel conductance. On P-type channels, ω-CTx-MVIIC and ω-Aga-IIIA both likely bind near the mouth of the pore. ω-Aga-IVA and grammotoxin each bind to distinct regions associated with channel gating that do not overlap with the binding region of pore blockers. For both N- and P-type channels, ω-CTx-MVIIC binding produces complete channel block, but is prevented by previous partial channel block by ω-Aga-IIIA, suggesting that ω-CTx-MVIIC binds closer to the external mouth of the pore than does ω-Aga-IIIA.
Folding and coloring problems in mathematics and physics
Authors: Di Francesco P.
Published: July 2002

We review various folding problems arising in the physics of membranes and polymers. These are (1) the phantom folding of tethered membranes, i.e. the two-dimensional lattice folding; (2) the phantom folding of fluid membranes, i.e. the folding of tessellations of arbitrary genus; (3) the self-avoiding folding of polymers, i.e. the meander problem. All three problems are found to be related to coloring problems and possess one kind of underlying integrable structure, in different guises. Many mathematical results follow from taking advantage of this fact.
Reorientation of Mispositioned Spindles in Short Astral Microtubule Mutantspc72Δ Is Dependent on Spindle Pole Body Outer Plaque and Kar3 Motor Protein
Authors: Hoepfner Dominic , Schaerer Florian , Brachat Arndt , Wach Achim , Philippsen Peter
Published: July 2002

Nuclear migration and positioning in Saccharomyces cerevisiae depend on long astral microtubules emanating from the spindle pole bodies (SPBs). Herein, we show by in vivo fluorescence microscopy that cells lacking Spc72, the SPB receptor of the cytoplasmic γ-tubulin complex, can only generate very short (<1 μm) and unstable astral microtubules. Consequently, nuclear migration to the bud neck and orientation of the anaphase spindle along the mother-bud axis are absent in these cells. However,SPC72 deletion is not lethal because elongated but misaligned spindles can frequently reorient in mother cells, permitting delayed but otherwise correct nuclear segregation. High-resolution time-lapse sequences revealed that this spindle reorientation was most likely accomplished by cortex interactions of the very short astral microtubules. In addition, a set of double mutants suggested that reorientation was dependent on the SPB outer plaque and the astral microtubule motor function of Kar3 but not Kip2/Kip3/Dhc1, or the cortex components Kar9/Num1. Our observations suggest that Spc72 is required for astral microtubule formation at the SPB half-bridge and for stabilization of astral microtubules at the SPB outer plaque. In addition, our data exclude involvement of Spc72 in spindle formation and elongation functions.
Regulated Disruption of Inositol 1,4,5-Trisphosphate Signaling inCaenorhabditis elegansReveals New Functions in Feeding and Embryogenesis
Authors: Walker Denise S. , Gower Nicholas J.D. , Ly Sung , Bradley Gemma L. , Baylis Howard A.
Published: July 2002

Inositol 1,4,5-trisphosphate (IP3) is an important second messenger in animal cells and is central to a wide range of cellular responses. The major intracellular activity of IP3is to regulate release of Ca2+from intracellular stores through IP3receptors (IP3Rs). We describe a system for the transient disruption of IP3signaling in the model organismCaenorhabditis elegans. The IP3binding domain of the C. elegans IP3R, ITR-1, was expressed from heat shock-induced promoters in live animals. This results in a dominant-negative effect caused by the overexpressed IP3binding domain acting as an IP3“sponge.” Disruption of IP3signaling resulted in disrupted defecation, a phenotype predicted by previous genetic studies. This approach also identified two new IP3-mediated processes. First, the up-regulation of pharyngeal pumping in response to food is dependent on IP3signaling. RNA-mediated interference studies and analysis of itr-1mutants show that this process is also IP3R dependent. Second, the tissue-specific expression of the dominant-negative construct enabled us to circumvent the sterility associated with loss of IP3signaling through the IP3R and thus determine that IP3-mediated signaling is required for multiple steps in embryogenesis, including cytokinesis and gastrulation.
Paxillin-dependent Paxillin Kinase Linker and p21-Activated Kinase Localization to Focal Adhesions Involves a Multistep Activation Pathway
Authors: Brown Michael C. , West Kip A. , Turner Christopher E.
Published: July 2002

The precise temporal-spatial regulation of the p21-activated serine-threonine kinase PAK at the plasma membrane is required for proper cytoskeletal reorganization and cell motility. However, the mechanism by which PAK localizes to focal adhesions has not yet been elucidated. Indirect binding of PAK to the focal adhesion protein paxillin via the Arf-GAP protein paxillin kinase linker (PKL) and PIX/Cool suggested a mechanism. In this report, we demonstrate an essential role for a paxillin–PKL interaction in the recruitment of activated PAK to focal adhesions. Similar to PAK, expression of activated Cdc42 and Rac1, but not RhoA, stimulated the translocation of PKL from a generally diffuse localization to focal adhesions. Expression of the PAK regulatory domain (PAK1–329) or the autoinhibitory domain (AID 83–149) induced PKL, PIX, and PAK localization to focal adhesions, indicating a role for PAK scaffold activation. We show PIX, but not NCK, binding to PAK is necessary for efficient focal adhesion localization of PAK and PKL, consistent with a PAK–PIX–PKL linkage. Although PAK activation is required, it is not sufficient for localization. The PKL amino terminus, containing the PIX-binding site, but lacking paxillin-binding subdomain 2 (PBS2), was unable to localize to focal adhesions and also abrogated PAK localization. An identical result was obtained after PKLΔPBS2 expression. Finally, neither PAK nor PKL was capable of localizing to focal adhesions in cells overexpressing paxillinΔLD4, confirming a requirement for this motif in recruitment of the PAK–PIX–PKL complex to focal adhesions. These results suggest a GTP-Cdc42/GTP-Rac triggered multistep activation cascade leading to the stimulation of the adaptor function of PAK, which through interaction with PIX provokes a functional PKL PBS2–paxillin LD4 association and consequent recruitment to focal adhesions. This mechanism is probably critical for the correct subcellular positioning of PAK, thereby influencing the ability of PAK to coordinate cytoskeletal reorganization associated with changes in cell shape and motility.
Support vector machines with selective kernel scaling for
protein classification and identification of key amino acid
positions
Authors: Zavaljevski Nela , Stevens Fred J. , Reifman Jaques
Published: July 2002

Motivation: Data that characterize primary and tertiary structures of proteins are now accumulating at a rapid and accelerating rate and require automated computational tools to extract critical information relating amino acid changes with the spectrum of functionally attributes exhibited by a protein. We propose that immunoglobulin-type beta-domains, which are found in approximate 400 functionally distinct forms in humans alone, provide the immense genetic variation within limited conformational changes that might facilitate the development of new computational tools. As an initial step, we describe here an approach based on Support Vector Machine (SVM) technology to identify amino acid variations that contribute to the functional attribute of pathological self-assembly by some human antibody light chains produced during plasma cell diseases.

Results: We demonstrate that SVMs with selective kernel scaling are an effective tool in discriminating between benign and pathologic human immunoglobulin light chains. Initial results compare favorably against manual classification performed by experts and indicate the capability of SVMs to capture the underlying structure of the data. The data set consists of 70 proteins of human antibody κ1 light chains, each represented by aligned sequences of 120 amino acids. We perform feature selection based on a first-order adaptive scaling algorithm, which confirms the importance of changes in certain amino acid positions and identifies other positions that are key in the characterization of protein function.

Contact: nelaz@ra.anl.govfstevens@anl.govjaques.reifman@amedd.army.mil

* To whom correspondence should be addressed.
Fate of mat1 DNA strands during mating‐type switching in fission yeast
Authors: Arcangioli Benoit
Published: July 2002

The mating‐type switching of the fission yeast, Schizosaccharomyces pombe, is highly regulated. Two consecutive asymmetric divisions are required to produce one mating‐type switched cell among the four progeny. Using DNA density‐gradient centrifugation we demonstrate that one‐fourth of the mat1 DNA is not replicated by the conventional semi‐conservative mode, but instead both DNA strands are synthesized de novo. Our data are consistent with a gene conversion event, initiated by a site‐ and strand‐specific DNA break (SSB). We further demonstrate that the virgin switched mat1‐containing chromatid no longer contained the nick, while it is reintroduced during the lagging strand synthesis of the mat1 locus on the sister chromatid. This finding establishes at the molecular level a firm experimental link between the phenotype and genotype in the process of asymmetric mating‐type switching during mitotic divisions.
Control of a robot dinosaur
Authors: Papantoniou V. , Avlakiotis P. , McN. Alexander R.
Published: July 2002

The Palaiomation Consortium, supported by the European Commission, is building a robotIguanodon atherfieldensisfor museum display that is much more sophisticated than existing animatronic exhibits. The current half–size (2.5 m) prototype is fully autonomous, carrying its own computer and batteries. It walks around the room, choosing its own path and avoiding obstacles. A bigger version with a larger repertoire of behaviours is planned.

Many design problems have had to be overcome. A real dinosaur would have had hundreds of muscles, and we have had to devise means of achieving life–like movement with a much smaller number of motors; we have limited ourselves to 20, to keep the control problems manageable. Realistic stance requires a narrower trackway and a higher centre of mass than in previous (often spider–like) legged robots, making it more difficult to maintain stability. Other important differences from previous walking robots are that the forelegs have to be shorter than the hind, and the machinery has had to be designed to fit inside a realistically shaped body shell. Battery life is about one hour, but to achieve this we have had to design the robot to have very low power consumption. Currently, this limits it to unrealistically slow movement.

The control system includes a high–level instructions processor, a gait generator, a motion–coordination generator, and a kinematic model.
Sensory system evolution at the origin of craniates
Authors: Butler Ann B.
Published: July 2002

The multiple events at the transition from non–craniate invertebrate ancestors to craniates included the gain and/or elaboration of migratory neural crest and neurogenic placodes. These tissues give rise to the peripherally located, bipolar neurons of all non–visual sensory systems. The brain was also elaborated at or about this same time. Were the peripheral and central events simultaneous or sequential? A serial transformation hypothesis postulates that paired eyes and an enlarged brain evolved before the elaboration of migratory neural crest–placodal sensory systems. Circumstantial evidence for this scenario is derived from the independent occurrence of the combination of large, paired eyes plus a large, elaborated brain in at least three taxa (cephalochordates, arthropods and craniates) and partly from the exclusivity of the diencephalon for visual system–related distal sensory components versus the restricted distribution of migratory neural crest–placodal sensory systems to the remaining parts of the neuraxis. This scenario accounts for the similarity of all central sensory system pathways due to the primary establishment of descending visual pathways via the diencephalon and midbrain tectum to brainstem motor regions and the subsequent exploitation of the same central beachhead by the migratory neural crest–placodal systems as a template for their organization.
Involvement of the direct and indirect pathways of allorecognition in tolerance induction
Authors: Womer Karl L. , Sayegh Mohamed H. , Auchincloss Hugh
Published: July 2002

It is generally accepted that there are two pathways of allorecognition, direct and indirect, that together contribute to allograft rejection. Although it has been suggested that the direct pathway predominates during early acute rejection and that the indirect pathway provides a continuous supply of alloantigen responsible for chronic rejection, the true relative contribution of each pathway to the overall rejection process is still not entirely known. It is clear, however, that any strategies designed to achieve the ultimate goal in transplantation, the induction of tolerance, will need to take into account both pathways. This review seeks to explore the involvement of the direct and indirect pathways of allorecognition on a mechanistic level as it relates to the induction of tolerance. A brief historical perspective is included for each pathway as well as a comprehensive review of the mechanisms felt to be active during tolerance induction.
Transcriptional cosuppression of yeast Ty1 retrotransposons
Authors: Jiang Yi Wei
Published: July 2002

Cosuppression, the silencing of dispersed homologous genes triggered by high copy number, may have evolved in eukaryotic organisms to control molecular parasites such as viruses and transposons.Ty1 retrotransposons are dispersed gene repeats inSaccharomyces cerevisiae, where no cosuppression has been previously observed. Ty1 elements are seemingly expressed undeterred to a level as high as 10% of total mRNA. UsingTy1–URA3 reporters and negative selection with 5-fluoroorotic acid, it is shown that Ty1 genes can undergo transcriptional cosuppression that is independent of DNA methylation and polycomb-mediated repression. Expression of Ty1-related genes was shown to be in one of two states, the coexpressed state with allTy1-related genes transcribed or the cosuppressed state with all Ty1-related genes shut off, without uncoordinated or mosaic expression in any individual cell. Rapid switches between the two states were observed. A high copy number of Ty1 elements was shown to be required for the initiation of Ty1homology-dependent gene silencing, implying that Ty1 gene expression is under negative feedback control. Ty1transcriptional repressors facilitated the onset of Ty1cosuppression, and the native Ty1 promoters were required forTy1 cosuppression, indicating that Ty1 cosuppression occurs at the transcriptional level.
Monte Carlo calculations of AAPM Task Group Report No. 43 dosimetry parameters for the source
Authors: Rivard Mark J.
Published: July 2002

Brachytherapy dosimetry parameters for sources have been determined in accordance with the AAPM Task Group No. 43 (TG‐43) dosimetry protocol. These data were calculated using the*F8 tally from the MCNP4B2 Monte Carlo radiation transport code with the DLC‐189 cross‐section libraries. Due to motion of the resin beads and gold‐copper markers within the capsule, parameters such as the geometry function, radial dose function, dose rate constant, and anisotropy function were examined with the beads and markers having either “realistic” or “ideal” positions; the realistic position was a weighted combination of “vertical” and “diagonal” capsule orientations. The dose rate constants for the realistic and ideal geometries, and were 1.066 and 1.067 cGy h−1 U−1, respectively, which were within uncertainties of measured values by Wallace and Fan [Med. Phys. 26, 1925–1931 (1999)] and Li et al. [Med. Phys. 27, 1275–1280 (2000)], 1.06 and 1.067 cGy h−1 U−1, respectively. The calculated reference dose rate at and for the realistic source geometry was 0.7% less than for the ideal source geometry. The anisotropy constants, for the realistic and ideal geometries were 0.948 and 0.965, respectively. matched that (0.941) measured by Wallace and Fan, and was significantly different from that (0.948) calculated by Wierzbicki et al. [Med. Phys. 25, 2197–2199 (1998)] for an ideal source.
An optical edge detector for the accurate delineation of the light field in radiotherapy machines
Authors: Woo Milton K. , McParland Craig S.
Published: July 2002

A hand‐held detector was developed which allows for the unambiguous and consistent determination of the edge of the light (optical) field on treatment machines conveniently and practically. The design incorporates an electronic circuit using three miniature photodiodes. The complete module is housed conveniently in a hand‐held box measuring 6 cm×10 cm×1.5 cm. The device eliminates any observer subjectivity on the position of the edge of the light field and hence facilitates greatly any commissioning and quality assurance procedures requiring light‐radiation field coincidence. Other applications are possible, including alignment of the light field on patients.
Investigation into the physical characteristics of active matrix flat panel imagers for radiotherapy
Authors: Lachaine M. , Fourkal E. , Fallone B. G.
Published: July 2002

The effect of physical characteristics on active matrix flat panel imagers (AMFPIs) at megavoltage energies is studied. The detective quantum efficiency (DQE) of both direct and indirect AMFPIs is modeled using a modified cascade analysis combined with Monte Carlo simulations. It is found that for a given thickness of the sensitive layer less than about 1 mm, there should be no significant difference between the detection techniques, but for larger mass thicknesses mm) there should be an advantage to using direct detection if such thick layers can be manufactured. The effect of the front plate on both direct and indirect techniques is also explored in terms of both the DQE and scatter rejection. It is found that for small sensitive layer thicknesses mm) a front plate thickness of about 1 mm Cu is optimal, whereas for larger mass thicknesses about 0.4 mm Cu should lead to better image quality.
A quality and efficiency analysis of the IMFAST™ segmentation algorithm in head and neck “step & shoot” IMRT treatments
Authors: Potter Larry D. , Chang Sha X. , Cullip Timothy J. , Siochi Alfredo C.
Published: July 2002

The performance of segmentation algorithms used in IMFAST for “step & shoot” IMRT treatment delivery is evaluated for three head and neck clinical treatments of different optimization objectives. The segmentation uses the intensity maps generated by the in‐house TPS PLANUNC using the index‐dose minimization algorithm. The dose optimization objectives include PTV dose uniformity and dose volume histogram‐specified critical structure sparing. The optimized continuous intensity maps were truncated into five and ten intensity levels and exported to IMFAST for MLC segments optimization. The MLC segments were imported back to PLUNC for dose optimization quality calculation. The five basic segmentation algorithms included in IMFAST were evaluated alone and in combination with either tongue and groove/match line correction or fluence correction or both. Two criteria were used in the evaluation: treatment efficiency represented by the total number of MLC segments and optimization quality represented by a clinically relevant optimization quality factor. We found that the treatment efficiency depends first on the number of intensity levels used in the intensity map and second the segmentation technique used. The standard optimal segmentation with fluence correction is a consistent good performer for all treatment plans studied. All segmentation techniques evaluated produced treatments with similar dose optimization quality values, especially when ten‐level intensity maps are used.
Characteristics of metal‐plate/film detectors at therapy energies. II. Detective quantum efficiency
Authors: Falco T. , Fallone B. G.
Published: July 2002

Noise power spectrum (NPS) and detective quantum efficiency (DQE) for metal‐plate/film portal detectors are reported for the Co‐60 and Linac 10 MV spectra. The detectors consist of a double‐emulsion portal film secured between plates of aluminum, copper, brass, or lead. The NPS was found to be independent of the detector sensitivity demonstrating that the film grain noise dominates over the quantum noise. Although the detector signal increases with density of the backplates, the resultant electron‐backscatter increases detector blur, thus decreasing the DQE. The lowest DQEs are therefore produced with the lead backplates, irrespective of the front plates. For a given backplate and for front‐plate thicknesses less than the maximum electron range, the DQE increases with density of the front plate.