bluuebunny/crossref_metadata_2025 huggingface dataset:
Equilibrium of a magnet floating above a superconducting disk
Authors: Williams Richard , Matey J. R.
Published: July 2002

A superconducting body will repel a nearby magnet. The repulsion is due to the perfect diamagnetism resulting from the Meissner effect. A small magnet will float above a superconducting disk at an equilibrium position over the disk center, stable against lateral displacements. It is not intuitively obvious why the potential energy of the magnet over a flat disk should have a minimum at the center, rather than a maximum. We have measured the properties of the attractive potential well of a YBa2Cu3O7 disk by two experiments. In the first, we use a low-frequency magnetic field, 0–100 Hz, to excite oscillations of a small, freely levitating bar magnet about its equilibrium position. We find sharp resonances, corresponding to longitudinal, transverse, and torsional modes of oscillation. The frequencies of these resonances define the properties near the bottom of the potential well. In the second experiment, we attach the magnet to a vertical glass fiber of known stiffness. The magnet is suspended horizontally a small known distance, z, above the superconducting disk. By moving the magnet from the center of the disk to the edge and measuring the bending of the support fiber as a function of position we determine the shape of the potential curve for large displacements and the total energy needed to escape from the well.
Submillimeter high brightness pulsed x-ray source
Authors: Lau J. H. W. , Kekez M. M. , Lougheed G. D. , Gupta R. P.
Published: July 2002

By inducing an electrical discharge in an annular gas plenum connected to a vacuum diode by a narrow annular slit, we demonstrate that microgram preionized plasma liners can be formed and imploded by a dc charged Blumlein pulser to efficiently convert electrical energy into soft x rays. The submillimeter x-ray source can in principle be scaled to the high repetition rate needed for x-ray lithography. In a proof of principle experiment, we have observed using krypton up to 0.5, 20, and 100 J of x-ray output above 1.5 keV, 500 eV, and 150 eV photon energies, respectively.
Infrared detection of gaseous species during the filament-assisted growth of diamond
Authors: Celii F. G. , Pehrsson P. E. , Wang H.-t. , Butler J. E.
Published: July 2002

Infrared diode laser absorption spectroscopy is employed as an in situ method to examine gas phase species present during filament-assisted deposition of diamond films. From a reactant mixture of 0.5% methane in hydrogen, methyl radical (CH3 ), acetylene (C2H2), and ethylene (C2H4 ) are detected above the growing surface, while ethane (C2H6 ), various C3 hydrocarbons, and methylene (CH2) radicals are below our sensitivity levels. The growth of polycrystalline diamond films on Si wafers and polycrystalline Ni is confirmed with x-ray and Raman scattering, scanning electron microscopy, and Auger electron spectroscopy.
Structural determinants of oxidative folding in proteins
Authors: Welker Ervin , Narayan Mahesh , Wedemeyer William J. , Scheraga Harold A.
Published: July 2002

A method for determining the kinetic fate of structured disulfide
species (i.e., whether they are preferentially oxidized or reshuffle
back to an unstructured disulfide species) is introduced. The method
relies on the sensitivity of unstructured disulfide species to low
concentrations of reducing agents. Because a structured des species
that preferentially reshuffles generally first rearranges to an
unstructured species, a small concentration of reduced DTT (e.g., 260
μM) suffices to distinguish on-pathway intermediates from dead-end
species. We apply this method to the oxidative folding of bovine
pancreatic ribonuclease A (RNase A) and show that des[40–95] and
des[65–72] are productive intermediates, whereas des[26–84]
and des[58–110] are metastable dead-end species that preferentially
reshuffle. The key factor in determining the kinetic fate of these des
species is the relative accessibility of both their thiol groups and
disulfide bonds. Productive intermediates tend to be
disulfide-secure
, meaning that their structural
fluctuations preferentially expose their thiol groups, while keeping
their disulfide bonds buried. By contrast, dead-end species tend to be
disulfide-insecure
, in that their structural
fluctuations expose their disulfide bonds in concert with their thiol
groups. This distinction leads to four generic types of oxidative
folding pathways. We combine these results with those of earlier
studies to suggest a general three-stage model of oxidative folding of
RNase A and other single-domain proteins with multiple disulfide bonds.
The carboxyl tail forms a discrete functional domain that blocks closure of the yeast K
+
channel
Authors: Loukin Stephen H. , Lin Junyu , Athar Umair , Palmer Christopher , Saimi Yoshiro
Published: July 2002

Non-targeted mutagenesis studies of the yeast K
+
channel, TOK1, have led to identification of functional domains common to other cation channels as well as those so far not found in other channels. Among the latter is the ability of the carboxyl tail to prevent channel closure. Here, we show that the tail can fulfill this function in
trans
. Coexpression of the carboxyl tail with the tail-deleted channel core restores normal channel behavior
.
A Ser/Thr-rich region at its amino end and an acidic stretch at its carboxyl end delineate the minimal region required for tail function. This region of 160 aa apparently forms a discrete functional domain. Interaction of this domain with the channel core is strong, being recalcitrant to removal from excised membrane patches by both high salt and reducing agents. Although the use of a cytoplasmic domain to regulate channel is common among animal channels, by using it as a “foot-in-the-door” to maintain open state appears unique to TOK1, the first fungal K
+
channel studied in depth.
Electron tunneling in protein crystals
Authors: Tezcan F. Akif , Crane Brian R. , Winkler Jay R. , Gray Harry B.
Published: July 2002

The current understanding of electron tunneling
through
proteins has come from work on systems where
donors and acceptors are held at fixed distances and orientations. The
factors that control electron flow
between
proteins are
less well understood, owing to uncertainties in the relative
orientations and structures of the reactants during the very short time
that tunneling occurs. As we report here, the way around such
structural ambiguity is to examine oxidation–reduction reactions in
protein crystals. Accordingly, we have measured and analyzed the
kinetics of electron transfer between native and Zn-substituted tuna
cytochrome
c
(cyt
c
) molecules in
crystals of known structure. Electron transfer rates [(320
s
−1
for *Zn-cyt
c
→ Fe(III)-cyt
c
; 2000 s
−1
for Fe(II)-cyt
c
→ Zn-cyt
c
+
)] over a Zn–Fe distance of
24.1 Å closely match those for intraprotein electron tunneling over
similar donor–acceptor separations. Our results indicate that van der
Waals interactions and water-mediated hydrogen bonds are effective
coupling elements for tunneling across a protein–protein interface.
Pectin engineering: Modification of potato pectin by
in vivo
expression of an endo-1,4-β-
d
-galactanase
Authors: Oxenbøll Sørensen Susanne , Pauly Markus , Bush Max , Skjøt Michael , McCann Maureen C. , Borkhardt Bernhard , Ulvskov Peter
Published: July 2002

Potato tuber pectin is rich in galactan (oligomer of β-1,4-linked galactosyl residues). We have expressed a fungal endo-galactanase cDNA in potato under control of the granule bound starch synthase promoter to obtain expression of the enzyme in tubers during growth. The transgenic plants displayed no altered phenotype compared with the wild type. Fungal endo-galactanase activity was quantified in the transgenic tubers, and its expression was verified by Western blot analysis. The effect of the endo-galactanase activity on potato tuber pectin was studied by Fourier transform infrared microspectroscopy, immuno-gold labeling, and sugar analysis. All analyses revealed alterations in pectin composition. Monosaccharide composition of total cell walls and isolated rhamnogalacturonan I fragments showed a reduction in galactosyl content to 30% in the transformants compared with the wild type. Increased solubility of pectin from transgenic cell walls by endo-polygalacturonase/pectin methylesterase digestion points to other changes in wall architecture.
PAS kinase: An evolutionarily conserved PAS domain-regulated serine/threonine kinase
Authors: Rutter Jared , Michnoff Carolyn H. , Harper Shannon M. , Gardner Kevin H. , McKnight Steven L.
Published: July 2002

PAS domains regulate the function of many intracellular signaling pathways in response to both extrinsic and intrinsic stimuli. PAS domain-regulated histidine kinases are common in prokaryotes and control a wide range of fundamental physiological processes. Similarly regulated kinases are rare in eukaryotes and are to date completely absent in mammals. PAS kinase (PASK) is an evolutionarily conserved gene product present in yeast, flies, and mammals. The amino acid sequence of PASK specifies two PAS domains followed by a canonical serine/threonine kinase domain, indicating that it might represent the first mammalian PAS-regulated protein kinase. We present evidence that the activity of PASK is regulated by two mechanisms. Autophosphorylation at two threonine residues located within the activation loop significantly increases catalytic activity. We further demonstrate that the N-terminal PAS domain is a cis regulator of PASK catalytic activity. When the PAS domain-containing region is removed, enzyme activity is significantly increased, and supplementation of the purified PAS-A domain in trans selectively inhibits PASK catalytic activity. These studies define a eukaryotic signaling pathway suitable for studies of PAS domains in a purified
in vitro
setting.
Dimerization and N-terminal domain proximity underlie the function of the molecular chaperone heat shock protein 90
Authors: Chadli Ahmed , Bouhouche Ilham , Sullivan William , Stensgard Bridget , McMahon Nancy , Catelli Maria G. , Toft David O.
Published: July 2002

Heat shock protein (hsp)90 functions in a complex chaperoning
pathway where its activity is modulated by ATP and by interaction with
several co-chaperones. One co-chaperone, p23, binds selectively to the
ATP-bound state of hsp90. However, the isolated ATP-binding domain of
hsp90 does not bind p23. In an effort to identify the p23-binding
domain, we have constructed a series of hsp90 deletion mutants fused
with glutathione-
S
-transferase (GST). Full-length
GST-hsp90 is able to bind p23, and also, to chaperone assembly of
progesterone receptor complexes. Truncations from the C terminus of
GST-hsp90 reveal a C-terminal boundary for the p23-binding domain at
approximately residue 490. This fragment contains, in order, the
ATP-binding domain, a highly charged region, and 203 residues beyond
the charged region. p23 binding is unaffected by deletion of the
charged region, indicating that two noncontiguous regions of hsp90 are
involved in p23 binding. These regions are only effective when hsp90 is
in a dimeric state as shown by loss of p23 binding upon removal of GST
or as shown by use of FK506-binding protein12-hsp90 constructs that
form dimers and bind p23 only in the presence of a bivalent drug. Thus,
p23 binding requires an hsp90 dimer with close proximity between
N-terminal regions of hsp90 and a conformation specified by ATP.
Evolutionary route to diploidy and sex
Authors: Tüzel Erkan , Sevim Volkan , Erzan Ayşe
Published: July 2002

By using a bit-string model of evolution, we find a successful route to diploidy and sex in simple organisms. Allowing the sexually reproducing diploid individuals to also perform mitosis, as they do in a haploid-diploid cycle, leads to the complete takeover of the population by sexual diploids. This mechanism is so robust that even the accidental conversion and pairing of only two diploids give rise to a sexual population.
Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy
Authors: Ladoux Benoit , Quivy Jean-Pierre , Doyle Patrick , Roure Olivia du , Almouzni Geneviève , Viovy Jean-Louis
Published: July 2002

Fluorescence videomicroscopy and scanning force microscopy were
used to follow, in real time, chromatin assembly on individual DNA
molecules immersed in cell-free systems competent for physiological
chromatin assembly. Within a few seconds, molecules are already
compacted into a form exhibiting strong similarities to native
chromatin fibers. In these extracts, the compaction rate is more than
100 times faster than expected from standard biochemical assays. Our
data provide definite information on the forces involved (a few
piconewtons) and on the reaction path. DNA compaction as a function of
time revealed unique features of the assembly reaction in these
extracts. They imply a sequential process with at least three steps,
involving DNA wrapping as the final event. An absolute and quantitative
measure of the kinetic parameters of the early steps in chromatin
assembly under physiological conditions could thus be obtained.
Constitutive receptor activation by Crouzon syndrome mutations in fibroblast growth factor receptor (FGFR)2 and FGFR2/Neu chimeras.
Authors: Galvin B D , Hart K C , Meyer A N , Webster M K , Donoghue D J
Published: July 2002

Crouzon syndrome is an autosomal dominant condition primarily characterized by craniosynostosis. This syndrome has been associated with a variety of amino acid point mutations in the extracellular domain of fibroblast growth factor receptor 2 (FGFR2). FGFR2/Neu chimeras were generated by substituting the extracellular domain of Neu with that of FGFR2 containing the following Crouzon mutations: Tyr-340-->His; Cys-342-->Tyr; Cys-342-->Arg; Cys-342-->Ser; Ser-354-->Cys: and delta17 (deletion of amino acids 345-361). Each of the mutant chimeric FGFR2/Neu constructs stimulated focus formation in NIH 3T3 cells, indicating that Crouzon mutations can stimulate signal transduction through a heterologous receptor tyrosine kinase. In vitro kinase assay results indicate that FGFR2 receptors containing Crouzon mutations have increased tyrosine kinase activity and, when analyzed under nonreducing conditions, exhibited disulfide-bonded dimers. Thus the human developmental abnormality Crouzon syndrome arises from constitutive activation of FGFR2 due to aberrant intermolecular disulfide-bonding. These results together with our earlier observation that achondroplasia results from constitutive activation of the related receptor FGFR3, leads to the prediction that other malformation syndromes attributed to FGFRs, such as Pfeiffer syndrome and Thanatophoric dysplasia, also arise from constitutive receptor activation.
A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in
Xenopus
Authors: Tycowski Kazimierz T. , Smith Christine M. , Shu Mei-Di , Steitz Joan A.
Published: July 2002

Vertebrate cells contain a large number of small nucleolar RNA
(snoRNA) species, the vast majority of which bind fibrillarin. Most of
the fibrillarin-associated snoRNAs can form 10- to 21-nt duplexes with
rRNA and are thought to guide 2′-
O
-methylation of
selected nucleotides in rRNA. These include mammalian UHG (U22 host
gene)-encoded U25–U31 snoRNAs. We have characterized two novel human
snoRNA species, U62 and U63, which similarly exhibit 15- (with one
interruption) and 12-nt complementarities and are therefore predicted
to direct 2′-
O
-methylation of A590 in 18S and A4531 in
28S rRNA, respectively. To establish the function of antisense snoRNAs
in vertebrates, we exploited the
Xenopus
oocyte system.
Cloning of the
Xenopus
U25–U31 snoRNA genes indicated
that they are encoded within multiple homologs of mammalian UHG.
Depletion of U25 from the
Xenopus
oocyte abolished
2′-
O
-methylation of G1448 in 18S rRNA; methylation could
be restored by injecting either the
Xenopus
or human U25
transcript into U25-depleted oocytes. Comparison of
Xenopus
and human U25 sequences revealed that only boxes
C, D, and D′, as well as the 18S rRNA complement, were invariant,
suggesting that they may be the only elements required for U25 snoRNA
stability and function.
Apoptosis of hemopoietic cells by the human granulocyte-macrophage colony-stimulating factor mutant E21R.
Authors: Iversen P O , To L B , Lopez A F
Published: July 2002

Human granulocyte-macrophage colony-stimulating factor (GM-CSF) binds to a high-affinity heterodimeric receptor composed of a specific alpha chain and a common beta chain (beta(c)), which is shared with the receptors for interleukins 3 and 5. Hemopoietic cell survival requires GM-CSF binding this high-affinity receptor. We have recently developed the GM-CSF mutant E21R, which selectively binds to the alpha chain and behaves as a competitive GM-CSF antagonist. We have now examined the role of E21R on the survival of hemopoietic cells and found that E21R causes apoptosis (programmed cell death) of normal and malignant cells directly in the absence of GM-CSF. The direct apoptotic effect of E21R occurred in a dose- and time-dependent manner. Apoptosis by E21R was dependent on cells expressing the high-affinity GM-CSF receptor and could be blocked by GM-CSF. Significantly, apoptosis of the cells occurred even in the presence of the survival factors granulocyte CSF and stem cell factor but was prevented by engagement of beta(c) with interleukin 3. The initiation of apoptosis required phosphorylation, transcriptional activity, and protein synthesis. These findings support a model whereby binding of E21R to the alpha chain leads to apoptosis, while beta(c) plays an important role in cell survival. This model may be applicable to other multimeric cytokine receptors and offers a novel approach for the treatment of human leukemia.
Expression of p24, a novel p21
Waf1/Cip1/Sdi1
-related protein, correlates with measurement of the finite proliferative potential of rodent embryo fibroblasts
Authors: Mazars G. Raoul , Jat Parmjit S.
Published: July 2002

Normal mammalian fibroblasts undergo a limited number of divisions
when cultured
in vitro
before entering a state of
replicative senescence. The molecular basis for the determination of
the finite mitotic potential is not known. Nevertheless, simian virus
40 T antigen, among other oncogenes, is able to prevent senescence in
rodent embryo fibroblasts. T antigen immortalized cells are dependent
upon this protein for maintaining growth once their normal mitotic life
span has elapsed. Even though the mechanism that measures the finite
mitotic potential of rodent fibroblasts is not known, it has been shown
that it continues to function normally in the presence of this
immortalizing gene. Accumulation of cyclin-dependent kinase inhibitors
such as p21
Waf1/Cip1/Sdi1
could potentially be a component
of the mechanism that determines the finite life span. Here we show
that accumulation of p21
Waf1/Cip1/Sdi1
does not correlate
with this biological counting mechanism, but we have identified p24, a
p21
Waf1/Cip1/Sdi1
-related protein, whose accumulation does
correlate with the measurement of the finite proliferative potential of
rodent embryo fibroblasts and suggest that sequestration might be a
mechanism by which its activity is regulated.
Kostant polynomials and the cohomology ring for
G
/
B
Authors: Billey Sara C.
Published: July 2002

The Schubert calculus for
G
/
B
can be completely determined by a certain matrix related to the Kostant
polynomials introduced in section 5 of Bernstein, Gelfand, and Gelfand
[Bernstein, I., Gelfand, I. & Gelfand, S. (1973)
Russ. Math.
Surv.
28, 1–26]. The polynomials are defined by vanishing
properties on the orbit of a regular point under the action of the Weyl
group. For each element
w
in the Weyl group the
polynomials also have nonzero values on the orbit points corresponding
to elements which are larger in the Bruhat order than
w
.
The main theorem given here is an explicit formula for these values.
The matrix of orbit values can be used to determine the cup product for
the cohomology ring for
G
/
B
, using
only linear algebra or as described by Lascoux and Schützenberger
[Lascoux, A. & Schützenberger, M.-P. (1982)
C. R. Seances
Acad. Sci. Ser. A
294, 447–450]. Complete proofs of all the
theorems will appear in a forthcoming paper.
Reducing the flexibility of retinal restores a wild-type-like photocycle in bacteriorhodopsin mutants defective in protein–retinal coupling
Authors: Delaney John K. , Yahalom G. , Sheves M. , Subramaniam Sriram
Published: July 2002

The thermal re-isomerization of retinal from the 13-
cis
to the all-
trans
state is a key step in the final stages of the photocycle of the light-driven proton pump, bacteriorhodopsin. This step is greatly slowed upon replacement of Leu-93, a residue in van der Waals contact with retinal. The most likely role of this key interaction is that it restricts the flexibility of retinal. To test this hypothesis, we have exchanged native retinal in Leu-93 mutants with bridged retinal analogs that render retinal less flexible by restricting free rotation around either the C10—C11 (9,11-bridged retinal) or C12—C13 (11,13-bridged retinal) single bonds. The effect of the analogs on the photocycle was then determined spectroscopically by taking advantage of the previous finding that the decay of the O intermediate in the Leu-93 mutants provides a convenient marker for retinal re-isomerization. Time-resolved spectroscopic studies showed that both retinal analogs resulted in a dramatic acceleration of the photocycling time by increasing the rate of decay of the O intermediate. In particular, exchange of native retinal in the Leu-93 → Ala mutant with the 9,11-bridged retinal resulted in an acceleration of the decay of the O intermediate to a rate similar to that seen in wild-type bacteriorhodopsin. We conclude that the protein-induced restriction of conformational flexibility in retinal is a key structural requirement for efficient protein–retinal coupling in the bacteriorhodopsin photocycle.
High genetic instability of heterochromatin after transposition of the LINE-like
I
factor in
Drosophila melanogaster
Authors: Dimitri Patrizio , Arcà Bruno , Berghella Libera , Mei Elisabetta
Published: July 2002

In the present work, we have asked whether a group of 13 essential genes mapping to the heterochromatin of
Drosophila melanogaster
chromosome
2
are mutable following transposition of the
I
factor during I-R hybrid dysgenesis. We found that the frequency of lethal events mapping to chromosome
2
heterochromatin is surprisingly high, despite the low density of genetic functions identified in this region compared with euchromatin. Cytogenetic and molecular analyses indicated that the recovered mutations correspond either to insertions or to rearrangements. Moreover, chromosomes bearing specific heterochromatic lethal mutations were generated by recombination in the heterochromatin. Together, these data indicate that
I
factors transpose with high frequency into pericentric regions of chromosome
2
and may play a role in the evolution of constitutive heterochromatin.
Nitric oxide in the contractile action of bradykinin, oxytocin, and prostaglandin F
2
α in the estrogenized rat uterus
Authors: Chaud M. , Franchi A. M. , Rettori V. , McCann S. M. , Gimeno M. F.
Published: July 2002

Experiments were performed on uteri from estrogen-primed female rats. Bradykinin (BK) (10
−8
M) significantly augmented biosynthesis of prostaglandin F
2
α (PGF
2
α) and prostaglandin E
2
(PGE
2
), and this synthesis was completely blocked by
N
G
-monomethyl
l
-arginine (NMMA) (300 μM), a competitive inhibitor of nitric oxide synthase (NOS). Blockade of prostaglandin synthesis by indomethacin caused rapid dissipation of isometric developed tension (IDT) induced by BK. Blockade of NOS with NMMA had similar but less marked effects. Combining the two inhibitors produced an even more rapid decay in IDT, suggesting that BK-induced NO release maintains IDT by release of prostanoids. The decline of frequency of contraction (FC) was not significantly altered by either indomethacin or NMMA but was markedly accelerated by combination of the inhibitors, which suggests that PGs maintain FC and therefore FC decline is accelerated only when PG production is blocked completely by combination of the two inhibitors of PG synthesis. The increase in IDT induced by oxytocin was unaltered by indomethacin, NMMA or their combination indicating that neither NO nor PGs are involved in the contractions induced by oxytocin. However, the decline in FC with time was significantly reduced by the inhibitor of NOS, NMMA, suggesting that FC decay following oxytocin is caused by NO released by the contractile process. In the case of PGF
2
α, NMMA resulted in increased initial IDT and FC. The decline in FC was rapid and dramatically inhibited by NMMA. Receptor-mediated contraction by BK, oxytocin, and PGF
2
α is modulated by NO that maintains IDT by releasing PGs but reduces IDT and FC via cyclic GMP.
Zeste-mediated activation by an enhancer is independent of cooperative DNA binding
in vivo
Authors: Laney Jeffrey D. , Biggin Mark D.
Published: July 2002

It is not clear how transcription factors bound at distal enhancer and proximal promoter sequences cooperate to stimulate transcription
in vivo
. To distinguish between different models for the action of enhancer elements, we have directly measured DNA binding of the
Drosophila
activator zeste by
in vivo
UV crosslinking. Experiments in
Drosophila
embryos show that binding of zeste protein to either the proximal promoter of the
Ultrabithorax
(
Ubx
) gene or to a
Ubx
enhancer element does not require the presence of the other element. However, significant transcription is observed only when both elements are present and bound by zeste. The results indicate that stimulation by an enhancer can occur by a mechanism other than increasing the occupancy of an activator to binding sites near the start site of transcription.
Assembly, subunit composition, and footprint of human DNA repair excision nuclease
Authors: Wakasugi Mitsuo , Sancar Aziz
Published: July 2002

The assembly and composition of human excision nuclease were investigated by electrophoretic mobility shift assay and DNase I footprinting. Individual repair factors or any combination of up to four repair factors failed to form DNA–protein complexes of high specificity and stability. A stable complex of high specificity can be detected only when XPA/RPA, transcription factor IIH, XPC⋅HHR23B, and XPG and ATP are present in the reaction mixture. The XPF⋅ERCC1 heterodimer changes the electrophoretic mobility of the DNA–protein complex formed with the other five repair factors, but it does not confer additional specificity. By using proteins with peptide tags or antibodies to the repair factors in electrophoretic mobility shift assays, it was found that XPA, replication protein A, transcription factor IIH, XPG, and XPF⋅excision repair cross-complementing 1 but not XPC⋅HHR23B were present in the penultimate and ultimate dual incision complexes. Thus, it appears that XPC⋅HHR23B is a molecular matchmaker that participates in the assembly of the excision nuclease but is not present in the ultimate dual incision complex. The excision nuclease makes an assymmetric DNase I footprint of ≈30 bp around the damage and increases the DNase I sensitivity of the DNA on both sides of the footprint.
Aspirin suppresses the mutator phenotype associated with hereditary nonpolyposis colorectal cancer by genetic selection
Authors: Rüschoff Josef , Wallinger Sabine , Dietmaier Wolfgang , Bocker Tina , Brockhoff Gero , Hofstädter Ferdinand , Fishel Richard
Published: July 2002

Nonsteroidal anti-inflammatory drugs (NSAIDs) are well-known cancer preventives, which have been largely attributed to their antiproliferative and apoptosis-inducing activities. In this study, we show that microsatellite instability (MSI) in colorectal cancer cells deficient for a subset of the human mismatch repair (MMR) genes (
hMLH1
,
hMSH2
, and
hMSH6
), is markedly reduced during exposure to aspirin or sulindac [or Clinoril, which is chemically related to indomethacin (Indocin)]. This effect was reversible, time and concentration dependent, and appeared independent of proliferation rate and cyclooxygenase function. In contrast, the MSI phenotype of a
hPMS2
-deficient endometrial cancer cell line was unaffected by aspirin/sulindac. We show that the MSI reduction in the susceptible MMR-deficient cells was confined to nonapoptotic cells, whereas apoptotic cells remained unstable and were eliminated from the growing population. These results suggest that aspirin/sulindac induces a genetic selection for microsatellite stability in a subset of MMR-deficient cells and may provide an effective prophylactic therapy for hereditary nonpolyposis colorectal cancer kindreds where alteration of the
hMSH2
and
hMLH1
genes are associated with the majority of cancer susceptibility cases.
On representations of finite type
Authors: Kadison Richard V.
Published: July 2002

Representations of the (infinite) canonical anticommutation relations and the associated operator algebra, the fermion algebra, are studied. A “coupling constant” (in (0,1]) is defined for primary states of “finite type” of that algebra. Primary, faithful states of finite type with arbitrary coupling are constructed and classified. Their physical significance for quantum thermodynamical systems at high temperatures is discussed. The scope of this study is broadened to include a large class of operator algebras sharing some of the structural properties of the fermion algebra.
Interference with gene regulation in living sea urchin embryos: Transcription factor Knock Out (TKO), a genetically controlled vector for blockade of specific transcription factors
Authors: Bogarad Leonard D. , Arnone Maria I. , Chang Chieh , Davidson Eric H.
Published: July 2002

“TKO” is an expression vector that knocks out the activity of a transcription factor
in vivo
under genetic control. We describe a successful test of this concept that used a sea urchin transcription factor of known function, P3A2, as the target. The TKO cassette employs modular cis-regulatory elements to express an encoded single-chain antibody that prevents the P3A2 protein from binding DNA
in vivo
. In normal development, one of the functions of the P3A2 transcription factor is to repress directly the expression of the
CyIIIa
cytoskeletal actin gene outside the aboral ectoderm of the embryo. Ectopic expression in oral ectoderm occurs if P3A2 sites are deleted from
CyIIIa
expression constructs, and we show here that introduction of an α
P3A2
⋅
TKO
expression cassette causes exactly the same ectopic oral expression of a coinjected wild-type
CyIIIa
construct. Furthermore, the
αP3A2
⋅
TKO
cassette derepresses the endogenous
CyIIIa
gene in the oral ectoderm and in the endoderm.
αP3A2
⋅
TKO
thus abrogates the function of the endogenous SpP3A2 transcription factor with respect to spatial repression of the
CyIIIa
gene. Widespread expression of
αP3A2
⋅
TKO
in the endoderm has the additional lethal effect of disrupting morphogenesis of the archenteron, revealing a previously unsuspected function of SpP3A2 in endoderm development. In principle, TKO technology could be utilized for spatially and temporally controlled blockade of any transcription factor in any biological system amenable to gene transfer.
Rotational symmetry of the C ring and a mechanism for the flagellar rotary motor
Authors: Thomas Dennis R. , Morgan David Gene , DeRosier David J.
Published: July 2002

FliG, FliM, and FliN, key proteins for torque generation, are
located in two rings. The first protein is in the M ring and the last
two are in the C ring. The rotational symmetries of the C and M rings
have been determined to be about 34 (this paper) and 26 (previous
work), respectively. The mechanism proposed here depends on the
symmetry mismatch between the rings: the C ring extends 34 levers, of
which 26 can bind to the 26 equivalent sites on the M ring. The
remaining 8 levers bind to proton–pore complexes (studs) to form 8
torque generators. Movement results from the swapping of stud-bound
levers with M ring-bound levers. The model predicts that both the M and
C rings rotate in the same direction but at different speeds.
Development of B cells expressing surface immunoglobulin molecules that lack V(D)J-encoded determinants in the avian embryo bursa of Fabricius
Authors: Sayegh Camil E. , Demaries Sandra L. , Iacampo Sandra , Ratcliffe Michael J. H.
Published: July 2002

Immunoglobulin gene rearrangement in avian B cell precursors generates surface Ig receptors of limited diversity. It has been proposed that specificities encoded by these receptors play a critical role in B lineage development by recognizing endogenous ligands within the bursa of Fabricius. To address this issue directly we have introduced a truncated surface IgM, lacking variable region domains, into developing B precursors by retroviral gene transferin vivo. Cells expressing this truncated receptor lack endogenous surface IgM, and the low level of endogenous Ig rearrangements that have occurred within this population of cells has not been selected for having a productive reading frame. Such cells proliferate rapidly within bursal epithelial buds of normal morphology. In addition, despite reduced levels of endogenous light chain rearrangement, those light chain rearrangements that have occurred have undergone variable region diversification by gene conversion. Therefore, although surface expression of an Ig receptor is required for bursal colonization and the induction of gene conversion, the specificity encoded by the prediversified receptor is irrelevant and, consequently, there is no obligate ligand for V(D)J-encoded determinants of prediversified avian cell surface IgM receptor.
BCR-ABL and v-SRC tyrosine kinase oncoproteins support normal erythroid development in erythropoietin receptor-deficient progenitor cells
Authors: Ghaffari Saghi , Wu Hong , Gerlach Melissa , Han Ying , Lodish Harvey F. , Daley George Q.
Published: July 2002

Erythropoietin (Epo)-independent differentiation of erythroid progenitors is a major characteristic of myeloproliferative disorders, including chronic myeloid leukemia. Epo receptor (EpoR) signaling is crucial for normal erythroid development, as evidenced by the properties of Epo
−/−
and EpoR
−/−
mice, which contain a normal number of fetal liver erythroid progenitors but die
in utero
from a severe anemia attributable to the absence of red cell maturation. Here we show that two constitutively active cytoplasmic protein tyrosine kinases, P210
BCR-ABL
and v-SRC, can functionally replace the EpoR and support full proliferation, differentiation, and maturation of fetal liver erythroid progenitors from EpoR
−/−
mice. These protein tyrosine kinases can also partially complement the myeloid growth factors IL-3, IL-6, and Steel factor, which are normally required in addition to Epo for erythroid development. Additionally, BCR-ABL mutants that lack residues necessary for transformation of fibroblasts or bone marrow cells can fully support normal erythroid development. These results demonstrate that activated tyrosine kinase oncoproteins implicated in tumorigenesis and human leukemia can functionally complement for cytokine receptor signaling pathways to support normal erythropoiesis in EpoR-deficient cells. Moreover, terminal differentiation of erythroid cells requires generic signals provided by activated protein tyrosine kinases and does not require a specific signal unique to a cytokine receptor.
Real or virtual large-scale structure?
Authors: Evrard August E.
Published: July 2002

Modeling the development of structure in
the universe on galactic and larger scales is the challenge that drives
the field of computational cosmology. Here, photorealism is used as a
simple, yet expert, means of assessing the degree to which virtual
worlds succeed in replicating our own.
Two mechanisms for transducer adaptation in vertebrate hair cells
Authors: Holt Jeffrey R. , Corey David P.
Published: July 2002

Deflection of the hair bundle atop a sensory hair cell modulates
the open probability of mechanosensitive ion channels. In response to
sustained deflections, hair cells adapt. Two fundamentally distinct
models have been proposed to explain transducer adaptation. Both models
support the notion that channel open probability is modulated by
calcium that enters via the transduction channels. Both also suggest
that the primary effect of adaptation is to shift the
deflection-response [I(X)] relationship in the direction of the
applied stimulus, thus maintaining hair bundle sensitivity. The models
differ in several respects. They operate on different time scales: the
faster on the order of a few milliseconds or less and the slower on the
order of 10 ms or more. The model proposed to explain fast adaptation
suggests that calcium enters and binds at or near the transduction
channels to stabilize a closed conformation. The model proposed to
explain the slower adaptation suggests that adaptation is mediated by
an active, force-generating process that regulates the effective
stimulus applied to the transduction channels. Here we discuss the
evidence in support of each model and consider the possibility that
both may function to varying degrees in hair cells of different species
and sensory organs.
Developing Conceptual Literacy in Lifelong Learning Research: A case of responsibility?
Authors: Hughes Christina
Published: July 2002

Abstract The article argues that the nature of lifelong learning research is marked by border crossings that require researchers to be conceptually literate. Two aspects of conceptual literacy are discussed. The first relates to the need to recognise the domain‐specific meanings of concepts. The second relates to the need to recognise how meanings are drawn from, often suppressed, counter‐concepts. The article draws on the fields of adult education, employment and family as key domains of lifelong learning research and explores these issues of literacy through a case study of feminist conceptualisations of responsibility.
Learning from Management Consultants: The Lesson for Management Researchers
Authors: MacDonald Stuart , Simpson Mike
Published: July 2002

The forces pushing management researchers inexorably closer to the managers they study are strong, strengthening and generally welcomed. This paper sees disadvantages in such proximity and common interest. Much of the work of management researchers is not rigorous, not sensible, and not useful, even to the managers it is supposed to serve. While it is probably impractical to suggest that management researchers keep their distance from managers, they may have something of value to learn from management consultants. Consultants are able to work closely with their clients without being overwhelmed by them. This is not to suggest that the efforts of consultants are scholarly, but then they do not pretend to be.
Lack of Allelic Exclusion in B Cell Chronic Lymphocytic Leukemia
Authors: Rassenti Laura Z. , Kipps Thomas J.
Published: July 2002

We determined the immunoglobulin (Ig) VH subgroup expressed by the leukemia cells of 108 patients with B cell chronic lymphocytic leukemia (CLL). Surprisingly, we found that six samples (5%) each expressed Ig of more than one VH subgroup. Southern blot analysis demonstrated that these samples each had rearrangements involving both Ig heavy chain alleles. Nucleic acid sequence analyses of the Ig cDNA revealed each to express two functional Ig VH genes: VH3-33 and VH4-39; VH3-7 and VH4-39; VH3-23 and VH4-61; VH2-70 and VH3-30.3; or VH3-30 and VH4-b (DP67). One sample expressed three Ig VH genes: VH2-70, VH3-7, and VH4-59. Despite having more than one Ig heavy chain transcript, each sample was found to express only one functional Ig light chain. From the primary sequence, we deduced that the Ig of some of these CLL samples should react with Lc1, a monoclonal antibody (mAb) reactive with a supratypic cross-reactive idiotype present on Ig encoded by a subgroup of Ig VH4 genes (namely, VH4-39, VH4-b [DP-67], VH4-59, or VH4-61), and B6, an mAb that reacts with Ig encoded by certain Ig VH3 genes (namely, VH3-23, VH3-30, or VH3-30.3), and/or modified staphylococcal protein A (SpA), a 45-kilodalton bacterial “superantigen” that reacts with most Ig of the VH3 subgroup. Flow cytometric analyses revealed that such samples did in fact react with Lc1 and B6 and/or SpA, but not with control mAbs of irrelevant specificity. This study demonstrates that a subset of CLL patients have leukemic B cells that express more than one functional Ig heavy chain.
Prolongation of Actions of Ca2+ Early in Phototransduction by 9-Demethylretinal
Authors: Matthews Hugh R. , Cornwall M.C. , Crouch R.K.
Published: July 2002

During adaptation Ca2+ acts on a step early in phototransduction, which is normally available for only a brief period after excitation. To investigate the identity of this step, we studied the effect of the light-induced decline in intracellular Ca2+ concentration on the response to a bright flash in normal rods, and in rods bleached and regenerated with 11-cis 9-demethylretinal, which forms a photopigment with a prolonged photoactivated lifetime. Changes in cytoplasmic Ca2+ were opposed by rapid superfusion of the outer segment with a 0Na+/0Ca2+ solution designed to minimize Ca2+ fluxes across the surface membrane. After regeneration of a bleached rod with 9-demethlyretinal, the response in Ringer's to a 440-nm bright flash was prolonged in comparison with the unbleached control, and the response remained in saturation for 10–15s. If the dynamic fall in Ca2+i induced by the flash was delayed by stepping the outer segment to 0Na+/0Ca2+ solution just before the flash and returning it to Ringer's shortly before recovery, then the response saturation was prolonged further, increasing linearly by 0.41 ± 0.01 of the time spent in this solution. In contrast, even long exposures to 0Na+/0Ca2+ solution of rods containing native photopigment evoked only a modest response prolongation on the return to Ringer's. Furthermore, if the rod was preexposed to steady subsaturating light, thereby reducing the cytoplasmic calcium concentration, then the prolongation of the bright flash response evoked by 0Na+/0Ca2+ solution was reduced in a graded manner with increasing background intensity. These results indicate that altering the chromophore of rhodopsin prolongs the time course of the Ca2+-dependent step early in the transduction cascade so that it dominates response recovery, and suggest that it is associated with photopigment quenching by phosphorylation.
On integral bases in relative quadratic extensions
Authors: Daberkow M. , Pohst M.
Published: July 2002

Let

F

\mathcal F

be an algebraic number field and

E

\mathcal E

a quadratic extension with

E

=

F

(

μ

)

\mathcal E=\mathcal F(\sqrt {\mu })

. We describe a minimal set of elements for generating the integral elements

o

E

o_{\mathcal E}

of

E

\mathcal E

as an

o

F

o_{\mathcal F}

module. A consequence of this theoretical result is an algorithm for constructing such a set. The construction yields a simple procedure for computing an integral basis of

E

\mathcal E

as well. In the last section, we present examples of relative integral bases which were computed with the new algorithm and also give some running times.
An asymptotic expansion for the incomplete beta function
Authors: Doman B.
Published: July 2002

A new asymptotic expansion is derived for the incomplete beta function

I
(
a
,
b
,
x
)

I(a,b,x)

, which is suitable for large

a
a

, small

b
b

and

x
>
0.5

x > 0.5

. This expansion is of the form
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper I left-parenthesis a comma b comma x right-parenthesis tilde upper Q left-parenthesis b comma minus gamma log x right-parenthesis plus StartFraction normal upper Gamma left-parenthesis a plus b right-parenthesis Over normal upper Gamma left-parenthesis a right-parenthesis normal upper Gamma left-parenthesis b right-parenthesis EndFraction x Superscript gamma Baseline sigma-summation Underscript n equals 0 Overscript normal infinity Endscripts upper T Subscript n Baseline left-parenthesis b comma x right-parenthesis slash gamma Superscript n plus 1 Baseline comma">

I
(
a
,
b
,
x
)

∼

Q
(
b
,
−
γ
log
⁡
x
)
+

Γ
(
a
+
b
)

Γ
(
a
)
Γ
(
b
)

x

γ

∑

n
=
0

∞

T

n

(
b
,
x
)

/

γ

n
+
1

,

\begin{equation*}I(a,b,x) \quad \sim \quad Q(b, -\gamma \log x) + {\frac {\Gamma (a + b)}{\Gamma (a) \Gamma (b)}} x^{\gamma } \sum ^{\infty }_{n=0}T_{n}(b,x)/ \gamma ^{n+1} , \end{equation*}

where

Q
Q

is the incomplete Gamma function ratio and

γ
=
a
+
(
b
−
1
)

/

2

\gamma = a + (b - 1)/2

. This form has some advantages over previous asymptotic expansions in this region in which

T

n

T_{n}

depends on

a
a

as well as on

b
b

and

x
x

.
On a variational approximation method for a class of elliptic eigenvalue problems in composite structures
Authors: Vanmaele M. , Keer R.
Published: July 2002

We consider a second-order elliptic eigenvalue problem on a convex polygonal domain, divided in

M
M

nonoverlapping subdomains. The conormal derivative of the unknown function is continuous on the interfaces, while the function itself is discontinuous. We present a general finite element method to obtain a numerical solution of the eigenvalue problem, starting from a nonstandard formally equivalent variational formulation in an abstract setting in product Hilbert spaces. We use standard Lagrange finite element spaces on the subdomains. Moreover, the bilinear forms are approximated by suitable numerical quadrature formulas. We obtain error estimates for both the eigenfunctions and the eigenvalues, allowing for the case of multiple exact eigenvalues, by a pure variational method.
Rational eigenvectors in spaces of ternary forms
Authors: Lehman Larry
Published: July 2002

We describe the explicit computation of linear combinations of ternary quadratic forms which are eigenvectors, with rational eigenvalues, under all Hecke operators. We use this process to construct, for each elliptic curve

E
E

of rank zero and conductor

N
>
2000

N > 2000

for which

N
N

or

N

/

4

N/4

is squarefree, a weight 3/2 cusp form which is (potentially) a preimage of the weight two newform

ϕ

E

\phi _{E}

under the Shimura correspondence.
Computing irreducible representations of supersolvable groups over small finite fields
Authors: Omrani A. , Shokrollahi A.
Published: July 2002

We present an algorithm to compute a full set of irreducible representations of a supersolvable group

G
G

over a finite field

K
K

,

char
⁡
K
∤

|

G

|

\operatorname {char} K\nmid |G|

, which is not assumed to be a splitting field of

G
G

. The main subroutines of our algorithm are a modification of the algorithm of Baum and Clausen (Math. Comp. 63 (1994), 351–359) to obtain information on algebraically conjugate representations, and an effective version of Speiser’s generalization of Hilbert’s Theorem 90 stating that

H

1

(
Gal
⁡
(
L

/

K
)
,
GL
⁡
(
n
,
L
)
)

H^{1}(\operatorname {Gal}(L/K), \operatorname {GL}(n,L))

vanishes for all

n
≥
1

n\ge 1

.