bluuebunny/crossref_metadata_2025 huggingface dataset:
Chiral wave propagation manifold of the photonic quantum-ring laser
Authors: Park B. H. , Bae J. , Kim M. J. , Kwon O’Dae
Published: July 2002

A torus knot model is presented to analyze the chiral wave propagation of photonic quantum-ring lasers in a three-dimensional Rayleigh–Fabry–Perot toroidal cavity. The Rayleigh–Fabry–Perot cavity gives rise to peculiar multichromatic spectra with nonequal intermode spacings. In particular, the knot model analysis suggests a strange three-dimensional effective index ellipsoid for the cavity with a large birefringence of neff3D(z)−neff2D(x,y)≈0.4–0.5.
Large-scale ordered macroporous SiO2 thin films by a template-directed method
Authors: Ye Yong-Hong , Badilescu Simona , Truong Vo-Van
Published: July 2002

Ordered three-dimensional macroporous SiO2 films were fabricated by colloidal crystal templating. Scanning electron microscope measurements showed that the size of the air sphere replicates that of the initial polystyrene spheres, and that the porous sample exhibits long-range order. Optical measurements show that the macroporous sample exhibits the behavior of a photonic band gap, indicating crystalline order in the sample. Fourier-transform infrared measurements revealed that a strong network of Si–O–Si bonds have been formed throughout the voids of the template before the solidification of the gel. It is proposed that this network hinders the large volume shrinkage during the subsequent heat treatment, and thus high-quality large-scale ordered macroporous films can be obtained.
Determination of the thickness of Al2O3 barriers in magnetic tunnel junctions
Authors: Buchanan J. D. R. , Hase T. P. A. , Tanner B. K. , Hughes N. D. , Hicken R. J.
Published: July 2002

The barrier thickness in magnetic spin-dependent tunnel junctions with Al2O3 barriers has been measured using grazing incidence x-ray reflectivity and by fitting the tunneling current to the Simmons model. We have studied the effect of glow discharge oxidation time on the barrier structure, revealing a substantial increase in Al2O3 thickness with oxidation. The greater thickness of barrier measured using grazing incidence x-ray reflectivity compared with that obtained by fitting current density–voltage to the Simmons electron tunneling model suggests that electron tunneling is localized to specific regions across the barrier, where the thickness is reduced by fluctuations due to nonconformal roughness.
How to describe protein motion without amino acid sequence and atomic coordinates
Authors: Ming Dengming , Kong Yifei , Lambert Maxime A. , Huang Zhong , Ma Jianpeng
Published: July 2002

This paper reports a computational method, the quantized elastic deformational model, that can reliably describe the conformational flexibility of a protein in the absence of the amino acid sequence and atomic coordinates. The essence of this method lies in the fact that, in modeling the functionally important conformational changes such as domain movements, it is possible to abandon the traditional concepts of protein structure (bonds, angles, dihedrals, etc.) and treat the protein as an elastic object. The shape and mass distribution of the object are described by the electron density maps, at various resolutions, from methods such as x-ray diffraction or cryo-electron microscopy. The amplitudes and directionality of the elastic deformational modes of a protein, whose patterns match the biologically relevant conformational changes, can then be derived solely based on the electron density map. The method yields an accurate description of protein dynamics over a wide range of resolutions even as low as 15–20 Å at which there is nearly no visually distinguishable internal structures. Therefore, this method dramatically enhances the capability of studying protein motions in structural biology. It is also expected to have ample applications in related fields such as bioinformatics, structural genomics, and proteomics, in which one's ability to extract functional information from the not-so-well-defined structural models is vitally important.
Hsp90 enables Ctf13p/Skp1p to nucleate the budding yeast kinetochore
Authors: Stemmann Olaf , Neidig Anke , Köcher Thomas , Wilm Matthias , Lechner Johannes
Published: July 2002

Binding of CBF3, a protein complex consisting of Ndc10p, Cep3p, Ctf13p, and Skp1p, to the centromere DNA nucleates kinetochore formation in budding yeast. Here, we investigate how the Ctf13p/Skp1p complex becomes competent to form the CBF3-centromere DNA complex. As revealed by mass spectrometry, Ctf13p and Skp1p carry two and four phosphate groups, respectively. Complete dephosphorylation of Ctf13p and Skp1p does not interfere with the formation of CBF3-centromere DNA complexes
in vitro
. Furthermore, deletion of corresponding phosphorylation sites results in viable cells. Thus, in contrast to the current view, phosphorylation of Ctf13p and Skp1p is not essential for the formation of CBF3-centromere DNA complexes. Instead, the formation of active Ctf13p/Skp1p requires Hsp90. Several lines of evidence support this conclusion: activation of heterologous Ctf13p/Skp1p by reticulocyte lysate is inhibited by geldanamycin and Hsp90 depletion. skp1 mutants exhibit growth defects on media containing geldanamycin. A skp1 mutation together with Hsp90 mutations exhibits synthetic lethality. An Hsp90 mutant contains decreased levels of active Ctf13p/Skp1p.
Isoform-specific interaction of HP1 with human TAF
II
130
Authors: Vassallo Milo F. , Tanese Naoko
Published: July 2002

The general transcription factor TFIID facilitates recruitment of the transcription machinery to gene promoters and regulates initiation of transcription by RNA polymerase II. hTAF
II
130, a component of TFIID, interacts with and serves as a coactivator for multiple transcriptional regulatory proteins, including Sp1 and CREB. A yeast two-hybrid screen has identified an interaction between hTAF
II
130 and heterochromatin protein 1 (HP1), a chromatin-associated protein whose function has been implicated in gene silencing. We find that hTAF
II
130 associates with HP1 in an isoform-specific manner: HP1α and HP1γ bind to hTAF
II
130, but not HP1β. In addition, we show that endogenous hTAF
II
130 and components of TFIID in HeLa nuclear extracts associate with glutathione
S
-transferase-HP1α and -HP1γ. hTAF
II
130 possesses a pentapeptide HP1-binding motif, and mutation of the hTAF
II
130 HP1 box compromises the interaction of hTAF
II
130 with HP1. We demonstrate that Gal4-HP1 proteins interfere with hTAF
II
130-mediated activation of transcription. Our results suggest that HP1α and HP1γ associate with hTAF
II
130 to mediate repression of transcription, supporting a new model of transcriptional repression involving a specific interaction between a component of TFIID and chromatin.
Antigen challenge leads toin vivoactivation and elimination of highly polarized TH1 memory T cells
Authors: Hayashi Nobuki , Liu Dacai , Min Booki , Ben-Sasson Shlomo Z. , Paul William E.
Published: July 2002

TH1 memory T cells derived from T cell receptor transgenic mice, in which the T cell antigen receptor is specific for a cytochrome C peptide in association with I-Ek, were transferred into normal B10.A mice and allowed to adopt a resting phenotype. When challenged, 30–60 days after transfer, with i.v. cytochrome C, the transgenic cells rapidly became activated, expressed mRNA for IFNγ, and began to divide. However, after 48 h, the frequency of the cells fell progressively, reaching levels only slightly above the limit of detection by day 8 and thereafter remain depressed for up to 90 days. The remaining cells were anergic as shown by limitation in proliferation and IFNγ production in response toin vitroantigen stimulation. Even if challenged with antigen emulsified in complete Freund's adjuvant, the overall pattern was similar, except that in the draining lymph nodes, the surviving antigen-specific cells were not anergic, although spleen cells were still strikingly anergic. Thus, antigenic challenge of mice possessing resting memory TH1 CD4 T cells leads to the unanticipated loss of most of the specific cells and an apparent depletion rather than enhancement of immunologic memory.
Interaction of Gα
12
with Gα
13
and Gα
q
signaling pathways
Authors: Gu Jennifer L. , Müller Stefan , Mancino Valeria , Offermanns Stefan , Simon Melvin I.
Published: July 2002

The G
12
subfamily of heterotrimeric G-proteins consists of two members, G
12
and G
13
. Gene-targeting studies have revealed a role for G
13
in blood vessel development. Mice lacking the α subunit of G
13
die around embryonic day 10 as the result of an angiogenic defect. On the other hand, the physiological role of G
12
is still unclear. To address this issue, we generated Gα
12
-deficient mice. In contrast to the Gα
13
-deficient mice, Gα
12
-deficient mice are viable, fertile, and do not show apparent abnormalities. However, Gα
12
does not seem to be entirely redundant, because in the offspring generated from Gα
12
± Gα
13
± intercrosses, at least one intact Gα
12
allele is required for the survival of animals with only one Gα
13
allele. In addition, Gα
12
and Gα
13
showed a difference in mediating cell migratory response to lysophosphatidic acid in embryonic fibroblast cells. Furthermore, mice lacking both Gα
12
and Gα
q
die
in utero
at about embryonic day 13. These data indicate that the Gα
12
-mediated signaling pathway functionally interacts not only with the Gα
13
- but also with the Gα
q/11
-mediated signaling systems.
Distinct domains of splicing factor Prp8 mediate different aspects of spliceosome activation
Authors: Kuhn Andreas N. , Reichl Elizabeth M. , Brow David A.
Published: July 2002

Prp8 is the largest and most highly conserved protein in the spliceosome yet its mechanism of function is poorly understood. Our previous studies implicate Prp8 in control of spliceosome activation for the first catalytic step of splicing, because substitutions in five distinct regions (a–e) of Prp8 suppress a cold-sensitive block to activation caused by a mutation in U4 RNA. Catalytic activation of the spliceosome is thought to require unwinding of the U1 RNA/5′ splice site and U4/U6 RNA helices by the Prp28 and Prp44/Brr2 DExD/H-box helicases, respectively. Here we show that mutations in regions a, d, and e of Prp8 exhibit allele-specific genetic interactions with mutations in Prp28, Prp44/Brr2, and U6 RNA, respectively. These results indicate that Prp8 coordinates multiple processes in spliceosome activation and enable an initial correlation of Prp8 structure and function. Furthermore, additional genetic interactions with U4-cs1 support a two-state model for this RNA conformational switch and implicate another splicing factor, Prp31, in Prp8-mediated spliceosome activation.
Cyclic electron transfer in plant leaf
Authors: Joliot Pierre , Joliot Anne
Published: July 2002

The turnover of linear and cyclic electron flows has been determined in fragments of dark-adapted spinach leaf by measuring the kinetics of fluorescence yield and of the transmembrane electrical potential changes under saturating illumination. When Photosystem (PS) II is inhibited, a cyclic electron flow around PSI operates transiently at a rate close to the maximum turnover of photosynthesis. When PSII is active, the cyclic flow operates with a similar rate during the first seconds of illumination. The high efficiency of the cyclic pathway implies that the cyclic and the linear transfer chains are structurally isolated one from the other. We propose that the cyclic pathway operates within a supercomplex including one PSI, one cytochrome bf complex, one plastocyanin, and one ferredoxin. The cyclic process induces the synthesis of ATP needed for the activation of the Benson–Calvin cycle. A fraction of PSI (∼50%), not included in the supercomplexes, participates in the linear pathway. The illumination would induce a dissociation of the supercomplexes that progressively increases the fraction of PSI involved in the linear pathway.
Three-dimensional, Bayesian image reconstruction from sparse and noisy data sets: Near-infrared fluorescence tomography
Authors: Eppstein Margaret J. , Hawrysz Daniel J. , Godavarty Anuradha , Sevick-Muraca Eva M.
Published: July 2002

A method for inverting measurements made on the surfaces of tissues for recovery of interior optical property maps is demonstrated for sparse near-infrared (NIR) fluorescence measurement sets on large tissue-simulating volumes with highly variable signal-to-noise ratio. A Bayesian minimum-variance reconstruction algorithm compensates for the spatial variability in signal-to-noise ratio that must be expected to occur in actual NIR contrast-enhanced diagnostic medical imaging. Image reconstruction is demonstrated by using frequency-domain photon migration measurements on 256-cm
3
tissue-mimicking phantoms containing none, one, or two 1-cm
3
heterogeneities with 50- to 100-fold greater concentration of Indocyanine Green dye over background levels. The spatial parameter estimate of absorption owing to the dye was reconstructed from only 160 to 296 surface measurements of emission light at 830 nm in response to incident 785-nm excitation light modulated at 100 MHz. Measurement error of acquired fluence at fluorescent emission wavelengths is shown to be highly variable. Convergence and quality of image reconstructions are improved by Bayesian conditioning incorporating (
i
) experimentally determined measurement error variance, (
ii
) recursively updated estimates of parameter uncertainty, and (
iii
) dynamic zonation. The results demonstrate that, to employ NIR fluorescence-enhanced optical imaging for large volumes, reconstruction approaches must account for the large range of signal-to-noise ratio associated with the measurements.
Ebselen: A substrate for human thioredoxin reductase strongly stimulating its hydroperoxide reductase activity and a superfast thioredoxin oxidant
Authors: Zhao Rong , Masayasu Hiroyuki , Holmgren Arne
Published: July 2002

Ebselen [2-phenyl-1,2-benzisoselenazol-3(2
H
)-one], a seleno-organic compound with glutathione peroxidase-like activity is used in clinical trials against stroke. Human and bovine TrxR catalyzed the reduction of ebselen to ebselen selenol by NADPH with an apparent
K
M
-value of 2.5 μM and a
k
cat
of 588 min
−1
. The addition of thioredoxin (Trx) stimulated the TrxR-catalyzed reduction of ebselen several-fold. This result was caused by a very fast oxidation of reduced Trx by ebselen with a rate constant in excess of 2 × 10
7
M
−1
s
−1
. This rate is orders of magnitude faster than the reaction of dithiol Trx with insulin disulfides. Ebselen competed with disulfide substrates for reduction by Trx and, therefore, acted as an inhibitor of protein disulfide reduction by the Trx system. The inherent H
2
O
2
reductase activity of mammalian TrxR dependent on its active-site selenocysteine residue was stimulated 10-fold by 2 μM ebselen and 25-fold in the additional presence of 5 μM Trx. Furthermore, the apparent
K
M
-value of TrxR for H
2
O
2
was lowered 25-fold to about 100 μM. Our results demonstrate that ebselen is a TrxR peroxidase which, in the presence of Trx, acted as a mimic of a peroxiredoxin. The activity with TrxR and oxidation of reduced Trx offer mechanistic explanations for the
in vivo
effects of ebselen as an antioxidant and anti-inflammatory agent. Our results demonstrate that the mechanism of action of ebselen may be predominantly via the Trx system rather than via glutathione.
Disease surveillance in recombining pathogens: Multilocus genotypes identify sources of humanCoccidioidesinfections
Authors: Fisher Matthew C. , Rannala Bruce , Chaturvedi Vishnu , Taylor John W.
Published: July 2002

Molecular surveillance of pathogenic microbes works by genotyping isolates with DNA fingerprinting techniques and then using these genotypes to assign individuals to populations. Clonality is assumed in many fingerprinting studies, although this assumption has been shown to be false for many organisms. To accommodate recombining organisms into surveillance programs, methods using population allele frequencies in combination with individual multilocus genotypes are necessary. Here, we develop a statistical method appropriate for haploid recombining microbes that allows individuals to be assigned to populations. We illustrate the usefulness of this technique by inferring the source populations forCoccidioidesisolates recovered from patients treated outside the endemic area ofCoccidioidessp., the etiological agents of human coccidioidomycosis, but with a travel history including visits to one or more endemic areas.
Transformation of follicular lymphoma to diffuse large-cell lymphoma: Alternative patterns with increased or decreased expression of
c
-
myc
and its regulated genes
Authors: Lossos Izidore S. , Alizadeh Ash A. , Diehn Maximilian , Warnke Roger , Thorstenson Yvonne , Oefner Peter J. , Brown Patrick O. , Botstein David , Levy Ronald
Published: July 2002

The natural history of follicular lymphoma (FL) is frequently characterized by transformation to a more aggressive diffuse large B cell lymphoma (DLBCL). We compared the gene-expression profiles between transformed DLBCL and their antecedent FL. No genes were observed to increase or decrease their expression in all of the cases of histological transformation. However, two different gene-expression profiles associated with the transformation process were defined, one in which
c-myc
and genes regulated by
c-myc
showed increased expression and one in which these same genes showed decreased expression. Further, there was a striking difference in gene-expression profiles between transformed DLBCL and
de novo
DLBCL, because the gene-expression profile of transformed DLBCL was more similar to their antecedent FL than to
de novo
DLBCL. This study demonstrates that transformation from FL to DLBCL can occur by alternative pathways and that transformed DLBCL and
de novo
DLBCL have very different gene-expression profiles that may underlie the different clinical behaviors of these two types of morphologically similar lymphomas.
Cortical hyperpolarization-activated depolarizing current takes part in the generation of focal paroxysmal activities
Authors: Timofeev Igor , Bazhenov Maxim , Sejnowski Terrence , Steriade Mircea
Published: July 2002

During paroxysmal neocortical oscillations, sudden depolarization leading to the next cycle occurs when the majority of cortical neurons are hyperpolarized. Both the Ca
2+
-dependent K
+
currents (
I
K(Ca)
) and disfacilitation play critical roles in the generation of hyperpolarizing potentials.
In vivo
experiments and computational models are used here to investigate whether the hyperpolarization-activated depolarizing current (
I
h
) in cortical neurons also contributes to the generation of paroxysmal onsets. Hyperpolarizing current pulses revealed a depolarizing sag in ≈20% of cortical neurons. Intracellular recordings from glial cells indirectly indicated an increase in extracellular potassium concentration ([K
+
]
o
) during paroxysmal activities, leading to a positive shift in the reversal potential of K
+
-mediated currents, including
I
h
. In the paroxysmal neocortex, ≈20% of neurons show repolarizing potentials originating from hyperpolarizations associated with depth-electroencephalogram positive waves of spike-wave complexes. The onset of these repolarizing potentials corresponds to maximal [K
+
]
o
as estimated from dual simultaneous impalements from neurons and glial cells. Computational models showed how, after the increased [K
+
]
o
, the interplay between
I
h
,
I
K(Ca)
, and a persistent Na
+
current,
I
Na(P)
, could organize paroxysmal oscillations at a frequency of 2–3 Hz.
Binding sites of different geometries for the
16
-
3
phage repressor
Authors: Papp Péter P. , Nagy Tibor , Ferenczi Szilamér , Élõ Péter , Csiszovszki Zsolt , Buzás Zsuzsanna , Patthy András , Orosz László
Published: July 2002

Prokaryotic repressor–operator systems provide exemplars for the sequence-specific interactions between DNA and protein. The crucial atomic contacts of the two macromolecules are attained in a compact, geometrically defined structure of the DNA–protein complex. The pitch of the DNA interface seems an especially sensitive part of this architecture because changes in its length introduce new spacing and rotational relations in one step. We discovered a natural system that may serve as a model for investigating this problem: the repressor of the
16
-
3
phage of
Rhizobium meliloti
(helix-turn-helix class protein) possesses inherent ability to accommodate to various DNA twistings. It binds the cognate operators, which are 5′-ACAA-4 bp-TTGT-3′ (O
L
) and 5′-ACAA-6 bp-TTGT-3′ (O
R
) and thus differ 2 bp in length, and consequently the two half-sites will be rotated with respect to each other by 72° in the idealized B-DNA (64° by dinucleotide steps calculations). Furthermore, a synthetic intermediate (DNA sequence) 5′-ACAA-5 bp-TTGT-3′ (O
5
) also binds specifically the repressor. The natural operators and bound repressors can form higher order DNA–protein complexes and perform efficient repression, whereas the synthetic operator-repressor complex cannot do either. The natural operators are bent when complexed with the repressor, whereas the O
5
operator does not show bending in electrophoretic mobility assay. Possible structures of the complexes are discussed.
Quantitative evolutionary design of nutrient processing: Glucose
Authors: Steyermark Anthony C. , Lam Mandy M. , Diamond Jared
Published: July 2002

Quantitative evolutionary design involves the numerical relationships, evolved through natural selection, of biological capacities to each other and to natural loads. Here we study the relation of nutrient-processing capacities of the intestine and of organs beyond it (such as liver and kidneys) to each other and to natural loads of nutrients normally consumed. To control experimentally the rate of nutrient delivery to organs beyond the intestine, we administered nutrients directly into the veins of rats by the method of total parenteral nutrition (TPN). Control rats consuming the TPN solution by mouth ingested glucose at 42 mmol/day and processed it completely, as gauged by negligible appearance of glucose in urine and feces. Experimental rats receiving TPN were able to process infused glucose completely at rates up to 92 mmol/day. At higher infusion rates, they were unable to process further glucose, as gauged by rises in serum and urinary glucose levels and serum osmolality. At the highest infusion rates, they exhibited diuresis, dehydration, and both decreased weight gain and survival. These symptoms closely resemble the human diabetic condition known as nonketotic hypertonicity. Thus, a rat's body has a safety factor of 2.2 (=92/42) for glucose processing: it can process glucose at a rate 2.2 times its voluntary intake. This safety factor represents apparent excess capacity that may have evolved to process other nutrients converted into glucose, to minimize the risk of loads swamping capacities, to handle suddenly increased nutrient requirements, or to effect rapid mobilization of glucose.
Apparent role of traveling metabolic waves in oxidant release by living neutrophils
Authors: Kindzelskii Andrei L. , Petty Howard R.
Published: July 2002

Cell metabolism self-organizes into two types of dissipative structures: chemical oscillations and traveling metabolic waves. In the present study we test the hypothesis that traveling NAD(P)H waves within neutrophils are associated spatially and temporally with the release of reactive oxygen metabolites (ROMs). Using high-speed optical microscopy and taking advantage of the autofluorescence of NAD(P)H, we have observed the propagation of NAD(P)H waves within cells. When NAD(P)H waves reach the lamellipodium of morphologically polarized neutrophils, a diffusing plume of superoxide is released as evidenced by the conversion of hydroethidine in the extracellular environment to ethidium bromide. Parallel results were obtained by using high-speed emission microspectrophotometry. These experiments indicate that the spatial and temporal properties of NAD(P)H waves are transformed into ROM pulses in the extracellular environment. Propagating NAD(P)H waves allow neutrophils to specifically deliver substrate to the lamellipodium at high concentrations, thus facilitating the local and periodic release of ROMs in the direction of cell movement and/or a target.
Conformational change of the actomyosin complex drives the multiple stepping movement
Authors: Terada Tomoki P. , Sasai Masaki , Yomo Tetsuya
Published: July 2002

Actin-myosin (actomyosin) generates mechanical force by consuming ATP molecules. We apply the energy landscape perspective to address a controversial issue as to whether the myosin head moves with multiple steps after a single ATP hydrolysis or only a single mechanical event of the lever-arm swinging follows a single ATP hydrolysis. Here we propose a theoretical model in which the refolding of the partially unfolded actomyosin complex and the movement of the myosin head along the actin filament are coupled. A single ATP hydrolysis is followed by the formation of a high free-energy partially unfolded actomyosin complex, which then gradually refolds with a concomitant multiple stepping movement on the way to the lowest free-energy rigor state. The model quantitatively explains the single-molecular observation of the multiple stepping movement and is consistent with structural observations of the disorder in the actomyosin-binding process. The model also explains the observed variety in dwell time before each step, which is not accounted for by previous models, such as the lever-arm or ratchet models.
Increased cell proliferation, but not reduced cell death, induces lymphocytosis in bovine leukemia virus-infected sheep
Authors: Debacq Christophe , Asquith Becca , Kerkhofs Pierre , Portetelle Daniel , Burny Arsène , Kettmann Richard , Willems Luc
Published: July 2002

Lymphocyte homeostasis is the result of a critical balance between cell proliferation and death. Disruption of this subtle equilibrium can lead to the onset of leukemia, an increase in the number of lymphocytes being potentially due to both of these parameters. The relative importance of cell proliferation vs. apoptosis during pathogenesis induced by the primate T cell lymphotropic viruses and bovine leukemia virus (BLV) has been difficult to assess because of conflicting data from a range of
in vitro
and
ex vivo
experimental systems. Here, we aim to resolve this issue by measuring the rates of cell proliferation and death in the BLV-ovine system, an animal model of human T lymphotropic virus (HTLV-1). We use a method based on the i.v. injection of 5-bromodeoxyuridine into BLV-infected sheep. We show that B lymphocytes in BLV
+
asymptomatic sheep proliferate significantly faster than in uninfected controls (average proliferation rate: 0.020 per day vs. 0.011 per day). In contrast, the rates of cell death were not significantly different between aleukemic BLV-infected and control sheep (average death rate 0.089 per day vs. 0.094 per day, respectively). We conclude that the increase in the number of B cells during BLV-induced lymphocytosis results from higher proliferation rates but is not due to a significant decrease in apoptosis, in contrast to data from
in vitro
(
ex vivo
) experiments. The imbalance created by the net increase in proliferation in the absence of compensating cell death reveals a complex mechanism of feedback regulation controlling homeostasis in the blood compartment.
Alternative splicing of RGS8 gene determines inhibitory function of receptor type-specific Gq signaling
Authors: Saitoh Osamu , Murata Yoshimichi , Odagiri Megumi , Itoh Masayuki , Itoh Hiroshi , Misaka Takumi , Kubo Yoshihiro
Published: July 2002

The regulators of G protein signaling (RGS) proteins modulate heterotrimeric G protein signaling. RGS8 is a brain-specific RGS protein of 180 aa. Here we identified a short isoform of RGS8, RGS8S, that arises by alternative splicing. RGS8S cDNA encodes a N terminus of 7 aa instead of amino acids 1–9 of RGS8 and 10–180 of RGS8. The subcellular distribution of RGS8 and RGS8S did not differ significantly in transfected cells. RGS8S accelerated, not as efficiently as RGS8, the turning on and off of Gi/o-mediated modulation of G protein-gated inwardly rectifying K
+
channels in
Xenopus
oocytes. We next examined the effects of RGS8 and RGS8S on Gq-mediated signaling. RGS8 decreased the amplitude of the response upon activation of m1 muscarinic or substance P receptors, but did not remarkably inhibit signaling from m3 muscarinic receptors. In contrast, RGS8S showed much less inhibition of the response of either of these Gq-coupled receptors. By quantitative analysis of the inhibitory effect and the protein expression level, we confirmed that the difference of inhibitory effect is caused by both the qualitative difference between RGS8 and RGS8S and the quantitative difference of the protein expression level. We also confirmed that the receptor-type specificity of inhibition is not caused by the difference of the expression level of the receptors. In summary, we showed that 9 aa in the N terminus of RGS8 contribute to the function to inhibit Gq-coupled signaling in a receptor type-specific manner and that the regulatory function of RGS8S is especially diminished on Gq-coupled responses.
Modeling of automatic capture and focusing of visual attention
Authors: Kohonen Teuvo
Published: July 2002

An explanation, based on simple analysis of the spatiotemporal variations of the visual environment, is given to the automatic capture and focusing of visual attention. It is assumed that the transmittance for the sensory signals is modulated by separate control circuits that sample input from the same area of the visual field but at a lower resolution. When these circuits detect significant spatial and/or temporal variations, they “open gates” for the more accurate information arising from the same area. If the variations are related to the spatial resolution, which varies within wide limits over the retina, the visual field is “opened” up to a radius where it captures the most salient structures of the image. If the temporal variations of the signals are further emphasized, the high spatial frequencies begin to dominate. If then the gaze is moved by a small amount, the transmittance of the foveal signal paths is activated strongest.
Haploinsufficiency of Flap endonuclease (
Fen1
) leads to rapid tumor progression
Authors: Kucherlapati Melanie , Yang Kan , Kuraguchi Mari , Zhao Jie , Lia Maria , Heyer Joerg , Kane Michael F. , Fan Kunhua , Russell Robert , Brown Anthony M. C. , Kneitz Burkhard , Edelmann Winfried , Kolodner Richard D. , Lipkin Martin , Kucherlapati Raju
Published: July 2002

F
lap
e
ndo
n
uclease (Fen1) is required for DNA replication and repair, and defects in the gene encoding Fen1 cause increased accumulation of mutations and genome rearrangements. Because mutations in some genes involved in these processes cause cancer predisposition, we investigated the possibility that Fen1 may function in tumorigenesis of the gastrointestinal tract. Using gene knockout approaches, we introduced a null mutation into murine
Fen1
. Mice homozygous for the
Fen1
mutation were not obtained, suggesting absence of
Fen1
expression leads to embryonic lethality. Most
Fen1
heterozygous animals appear normal. However, when combined with a mutation in the adenomatous polyposis coli (
Apc
) gene, double heterozygous animals have increased numbers of adenocarcinomas and decreased survival. The tumors from these mice show microsatellite instability. Because one copy of the
Fen1
gene remained intact in tumors,
Fen1
haploinsufficiency appears to lead to rapid progression of cancer.
The number of K
+
channels in the plasma membrane of guard cell protoplasts changes in parallel with the surface area
Authors: Homann Ulrike , Thiel Gerhard
Published: July 2002

The activity of the two dominant K
+
channels in the plasma membrane of
Vicia faba
guard cell protoplasts was examined during pressure-driven swelling. For this purpose, the K
+
currents and the membrane capacitance (C
m
) of guard cell protoplasts were recorded in parallel. A rise in C
m
, reflecting an increase of the membrane surface area, was coupled to a proportional rise in conductance of both the K
+
inward and K
+
outward rectifier. The activation kinetics of the K
+
channels were not affected during this process. The quantitative and temporal coupling of C
m
and K
+
conductance can hence be interpreted as the result of the addition of active inward and outward rectifier K
+
channels to the plasma membrane during an increase in surface area.
Representing knowledge: instances of management information
Authors: Hughes John A. , Rouncefield Mark , Tolmie Peter
Published: July 2002

Against the backdrop of discussions about the ‘Information Society’, the ‘Informational Economy’ and the role of IT in realizing organizational change we examine how representations of ‘organizational knowledge’ are constructed and used in work settings. We do this through the explication of ethnographic materials that detail the realization and use of Management Information (MI) in a major UK retail bank undergoing massive organizational change. We focus in particular on explicating how existing metric information was drawn upon to construct a representation of the work of the bank for those involved in managing that work. Systems designers have been increasingly interested in offering ways of conceptualizing the problem of ‘knowledge’ with a view to embedding these properties in systems. In the quest to develop representations of procedural knowledge to support work we argue that it is first necessary to understand how representations are actually created and used in work to support existing work practices.
Indigenization of psychology in the Philippines
Authors: Church A. Timothy , Katigbak Marcia S.
Published: July 2002

The status of efforts to indigenize psychology in the Philippines is reviewed. We address progress in four aspects of indigenization: theoretical/conceptual, methodological, topical, and institutional. Much, but not all, of this progress is the result of efforts associated with the indigenous Sikolohiyang Pilipino (Filipino psychology) movement, which emphasizes (a) the development of a Filipino psychology that reflects the unique experiences and orientations of Filipinos, (b) Filipino identity and national consciousness, (c) explicit socio‐political considerations, (d) application of psychology to societal problems, (e) the study of less elite Filipinos, (f) interdisciplinary efforts, and (g) the use of indigenous languages in the development and dissemination of indigenous psychology. We note considerable progress, but also controversy, in the selection and interpretation of indigenous concepts and less progress in the formulation of indigenous theories. Existing theories are narrow in scope, only partially specified, and have uncertain heuristic value in generating verifiable predictions. Filipino psychologists have also adapted or further specified Western theoretical frameworks to make them more sensitive to Philippine contextual factors. Many indigenous measures have been developed, but more information is needed on their psychometric properties. Several indigenous research methods have been described and these methods typically emphasize the importance of the researcher‐participant relationship. There remain questions about the objectivity and cultural uniqueness of these methods, however, many of which involve (a) unstructured conversations and discussions in lieu of structured interviews, (b) varying degrees of participant observation, or (c) qualitative phenomenological methods. Extensive topical indigenization is evident in studies that focus on everyday Filipinos and Philippine societal concerns. Institutional indigenization is reflected in courses, theses and dissertations, journals, books, conferences, and professional organizations with an indigenous focus. Potential limitations or risks to the indigenous movement include insularity and the limited research culture. Implications of the Philippine case for indigenization efforts in other cultures are discussed.
Progress in Heterodox Economics
Authors: Backhouse Roger E.
Published: July 2002

There is great variety within contemporary economics. As Coats (2000) points out, not only are there several schools of thought that would conventionally be labeled “heterodox,” there are numerous economists whose work is in a significant sense unorthodox or unconventional. How, then, can a dividing line be drawn between dissent within orthodoxy and dissent from orthodoxy? The suggestion I make here is that a heterodox school of thought has to satisfy three criteria.
Comment: It's the Homogeneity, Stupid!
Authors: Goodwin Craufurd D.
Published: July 2002

This topic is more in contemporary economics than in the history of economics, but in this case an historical perspective does help us to understand the present day. Roger Backhouse and Sheila Dow have approached the progress of heterodox economics mainly through the philosophy and methodology of the discipline. I take a more sociological approach. I see the issue as external to the discipline at least as much as internal.
The performance of migrants in occupational labour markets
Authors: Kreyenfeld Michaela , Konietzka Dirk
Published: July 2002

Since the breakdown of communism, Germany has experienced a major influx of Aussiedler who are basically migrants originating from Eastern European countries. In this article, we use data from the German Socio-Economic Panel of the year 1998 to analyse the labour market performance of this group of migrants. Our key hypothesis guiding the empirical investigations is that in occupational labour markets, such as the German one, migrants are faced with specific problems when transferring their educational and vocational skills acquired in other countries. Only if they gain access to their trained occupations are they able to perform well in the labour market. Otherwise, occupational closure hinders them from receiving returns to their educational and vocational qualifications.
Role of KIFC3 motor protein in Golgi positioning and integration
Authors: Xu Ying , Takeda Sen , Nakata Takao , Noda Yasuko , Tanaka Yosuke , Hirokawa Nobutaka
Published: July 2002

KIFC3, a microtubule (MT) minus end–directed kinesin superfamily protein, is expressed abundantly and is associated with the Golgi apparatus in adrenocortical cells. We report here that disruption of the kifC3 gene induced fragmentation of the Golgi apparatus when cholesterol was depleted. Analysis of the reassembly process of the Golgi apparatus revealed bidirectional movement of the Golgi fragments in both wild-type and kifC3−/− cells. However, we observed a markedly reduced inwardly directed motility of the Golgi fragments in cholesterol-depleted kifC3−/− cells compared with either cholesterol-depleted wild-type cells or cholesterol-replenished kifC3−/− cells. These results suggest that (a) under the cholesterol-depleted condition, reduced inwardly directed motility of the Golgi apparatus results in the observed Golgi scattering phenotype in kifC3−/− cells, and (b) cholesterol is necessary for the Golgi fragments to attain sufficient inwardly directed motility by MT minus end–directed motors other than KIFC3, such as dynein, in kifC3−/− cells. Furthermore, we showed that Golgi scattering was much more drastic in kifC3−/− cells than in wild-type cells to the exogenous dynamitin expression even in the presence of cholesterol. These results collectively demonstrate that KIFC3 plays a complementary role in Golgi positioning and integration with cytoplasmic dynein.
Sequential SNARE disassembly and GATE-16–GOS-28 complex assembly mediated by distinct NSF activities drives Golgi membrane fusion
Authors: Müller Joyce M.M. , Shorter James , Newman Richard , Deinhardt Katrin , Sagiv Yuval , Elazar Zvulun , Warren Graham , Shima David T.
Published: July 2002

Characterization of mammalian NSF (G274E) and Drosophila NSF (comatose) mutants revealed an evolutionarily conserved NSF activity distinct from ATPase-dependent SNARE disassembly that was essential for Golgi membrane fusion. Analysis of mammalian NSF function during cell-free assembly of Golgi cisternae from mitotic Golgi fragments revealed that NSF disassembles Golgi SNAREs during mitotic Golgi fragmentation. A subsequent ATPase-independent NSF activity restricted to the reassembly phase is essential for membrane fusion. NSF/α-SNAP catalyze the binding of GATE-16 to GOS-28, a Golgi v-SNARE, in a manner that requires ATP but not ATP hydrolysis. GATE-16 is essential for NSF-driven Golgi reassembly and precludes GOS-28 from binding to its cognate t-SNARE, syntaxin-5. We suggest that this occurs at the inception of Golgi reassembly to protect the v-SNARE and regulate SNARE function.
Lysophospholipids in the limelight
Authors: Moolenaar Wouter H.
Published: July 2002

Lysophosphatidic acid (LPA) is a serum phospholipid that evokes growth factor–like responses in many cell types through the activation of its G protein–coupled receptors. Although much is known about LPA signaling, it has remained unclear where and how bioactive LPA is produced. Umezu-Goto et al. (2002)(this issue, page 227) have purified a serum lysophospholipase D that generates LPA from lysophosphatidylcholine and found it to be identical to autotaxin, a cell motility–stimulating ectophosphodiesterase implicated in tumor progression. This result is surprising, as there was previously no indication that autotaxin could act as a phospholipase.
The Death Domain Kinase RIP Protects Thymocytes from Tumor Necrosis Factor Receptor Type 2–induced Cell Death
Authors: Cusson Nicole , Oikemus Sarah , Kilpatrick Elizabeth D. , Cunningham Leslie , Kelliher Michelle
Published: July 2002

Fas and the tumor necrosis factor receptor (TNFR)1 regulate the programmed cell death of lymphocytes. The death domain kinase, receptor interacting protein (rip), is recruited to the TNFR1 upon receptor activation. In vitro, rip−/− fibroblasts are sensitive to TNF-induced cell death due to an impaired nuclear factor κB response. Because rip−/− mice die at birth, we were unable to examine the effects of a targeted rip mutation on lymphocyte survival. To address the contribution of RIP to immune homeostasis, we examined lethally irradiated mice reconstituted with rip−/− hematopoietic precursors. We observed a decrease in rip−/− thymocytes and T cells in both wild-type C57BL/6 and recombination activating gene 1−/− irradiated hosts. In contrast, the B cell and myeloid lineages are unaffected by the absence of rip. Thus, the death domain kinase rip is required for T cell development. Unlike Fas-associated death domain, rip does not regulate T cell proliferation, as rip−/− T cells respond to polyclonal activators. However, rip-deficient mice contain few viable CD4+ and CD8+ thymocytes, and rip−/− thymocytes are sensitive to TNF-induced cell death. Surprisingly, the rip-associated thymocyte apoptosis was not rescued by the absence of TNFR1, but appears to be rescued by an absence of TNFR2. Taken together, this study implicates RIP and TNFR2 in thymocyte survival.
Proteolytic Processing of Stat6 Signaling in Mast Cells as a Negative Regulatory Mechanism
Authors: Suzuki Kotaro , Nakajima Hiroshi , Kagami Shin-ichiro , Suto Akira , Ikeda Kei , Hirose Koichi , Hiwasa Takaki , Takeda Kiyoshi , Saito Yasushi , Akira Shizuo , Iwamoto Itsuo
Published: July 2002

Accumulating evidence has shown the importance of Stat6-mediated signaling in allergic diseases. In this study, we show a novel regulatory mechanism of Stat6-mediated signaling in mast cells. When Stat6 is activated by interleukin (IL)-4 and translocated to the nucleus, Stat6 is cleaved by a nucleus-associated protease in mast cells. The cleaved 65-kD Stat6 lacks the COOH-terminal transactivation domain and functions as a dominant-negative molecule to Stat6-mediated transcription. The retrovirus-mediated expression of cleavage-resistant Stat6 mutants prolongs the nuclear accumulation of Stat6 upon IL-4 stimulation and enhances IL-4–induced gene expression and growth inhibition in mast cells. These results indicate that the proteolytic processing of Stat6 functions as a lineage-specific negative regulator of Stat6-dependent signaling in mast cells, and thus suggest that it may account for the limited role of Stat6 in IL-4 signaling in mast cells.
Suppression of Lymphoma and Epithelial Malignancies Effected by Interferon γ
Authors: Street Shayna E.A. , Trapani Joseph A. , MacGregor Duncan , Smyth Mark J.
Published: July 2002

The immunosurveillance of transformed cells by the immune system remains one of the most controversial and poorly understood areas of immunity. Gene-targeted mice have greatly aided our understanding of the key effector molecules in tumor immunity. Herein, we describe spontaneous tumor development in gene-targeted mice lacking interferon (IFN)-γ and/or perforin (pfp), or the immunoregulatory cytokines, interleukin (IL)-12, IL-18, and tumor necrosis factor (TNF). Both IFN-γ and pfp were critical for suppression of lymphomagenesis, however the level of protection afforded by IFN-γ was strain specific. Lymphomas arising in IFN-γ-deficient mice were very nonimmunogenic compared with those derived from pfp-deficient mice, suggesting a comparatively weaker immunoselection pressure by IFN-γ. Single loss of IL-12, IL-18, or TNF was not sufficient for spontaneous tumor development. A significant incidence of late onset adenocarcinoma observed in both IFN-γ– and pfp-deficient mice indicated that some epithelial tissues were also subject to immunosurveillance.
Potential Role of Phosphatidylinositol 3 Kinase, rather than DNA-dependent Protein Kinase, in CpG DNA–induced Immune Activation
Authors: Ishii Ken J. , Takeshita Fumihiko , Gursel Ihsan , Gursel Mayda , Conover Jacqueline , Nussenzweig Andre , Klinman Dennis M.
Published: July 2002

Unmethylated CpG motifs present in bacterial DNA stimulate a strong innate immune response. There is evidence that DNA-dependent protein kinase (DNA-PK) mediates CpG signaling. Specifically, wortmannin (an inhibitor of phosphatidylinositol 3 kinase [PI3]-kinases including DNA-PK) interferes with CpG-dependent cell activation, and DNA-PK knockout (KO) mice fail to respond to CpG stimulation. Current studies establish that wortmannin actually inhibits the uptake and colocalization of CpG DNA with toll-like receptor (TLR)-9 in endocytic vesicles, thereby preventing CpG-induced activation of the NF-κB signaling cascade. We find that DNA-PK is not involved in this process, since three strains of DNA-PK KO mice responded normally to CpG DNA. These results support a model in which CpG signaling is mediated through TLR-9 but not DNA-PK, and suggest that wortmannin-sensitive member(s) of the PI3-kinase family play a critical role in shuttling CpG DNA to TLR-9.
Control of P2X2 Channel Permeability by the Cytosolic Domain
Authors: Eickhorst Angela N. , Berson Amy , Cockayne Debra , Lester Henry A. , Khakh Baljit S.
Published: July 2002

ATP-gated P2X channels are the simplest of the three families of transmitter-gated ion channels. Some P2X channels display a time- and activation-dependent change in permeability as they undergo the transition from the relatively Na+-selective I1 state to the I2 state, which is also permeable to organic cations. We report that the previously reported permeability change of rat P2X2 (rP2X2) channels does not occur at mouse P2X2 (mP2X2) channels expressed in oocytes. Domain swaps, species chimeras, and point mutations were employed to determine that two specific amino acid residues in the cytosolic tail domain govern this difference in behavior between the two orthologous channels. The change in pore diameter was characterized using reversal potential measurements and excluded field theory for several organic ions; both rP2X2 and mP2X2 channels have a pore diameter of ∼11 Å in the I1 state, but the transition to the I2 state increases the rP2X2 diameter by at least 3 Å. The I1 to I2 transition occurs with a rate constant of ∼0.5 s−1. The data focus attention on specific residues of P2X2 channel cytoplasmic domains as determinants of permeation in a state-specific manner.