bluuebunny/crossref_metadata_2025 huggingface dataset:
Aerosol flow reactor production of fine Y1Ba2Cu3O7 powder: Fabrication of superconducting ceramics
Authors: Kodas T. T. , Engler E. M. , Lee V. Y. , Jacowitz R. , Baum T. H. , Roche K. , Parkin S. S. P. , Young W. S. , Hughes S. , Kleder J. , Auser W.
Published: July 2002

An aerosol flow reactor operating at 900–1000 °C is used to prepare high-purity Y1Ba2Cu3O7 powders with a uniform chemical composition and a submicron to micron average particle size by thermally decomposing aerosol droplets of a solution consisting of the nitrate salts of Y, Ba, and Cu in a 1:2:3 ratio. The powders were at least 99% reacted based on thermogravimetric analysis, and the x-ray diffraction pattern is essentially that of Y1Ba2Cu3O7. Magnetic susceptibility measurements showed the powders to be superconducting with a transition at 90 K even for average reactor residence times as short as 20 s. Sintering cold-pressed pellets between 900 and 1000 °C provides dense, fine grained (average size on the order of 1 μm) superconducting ceramics with sharp 90 K transitions. The grain size and shape of a final sintered part could be varied depending on powder production, processing, and sintering conditions.
Formation of YBa2Cu3O7 superconducting films by ion implantation
Authors: Nastasi M. , Tesmer J. R. , Hollander M. G. , Smith J. F. , Maggiore C. J.
Published: July 2002

We have fabricated superconducting thin films by ion implanting Y into a base material formed by the coevaporation of BaF2 and Cu. The implantations were carried out at 77 K and resulted in the formation of an amorphous Y-Ba-Cu-F surface layer. Oxygen annealing with the addition of water vapor renders the base material insulating with a room-temperature resistance of 105 Ω. An identical annealing treatment on the Y-implanted material produces a superconductor with an onset temperature of 85 K.
Effect of the lifting of Kramer’s degeneracy on excitonic linewidths in quantum well optical modulators
Authors: Hong Songcheol , Singh Jasprit , Sahai Rajeshwar , Lastufka Chewlan
Published: July 2002

In symmetric quantum well structures, the hole subband states maintain the spin degeneracy (Kramer’s degeneracy), but in asymmetric quantum wells and in optical modulators in the presence of electric field, the degeneracy is lifted. This results in splitting of excitonic transitions due to splitting in the exciton binding energy. For small splitting this will result in exciton broadening. Comparisons are presented for this broadening in symmetric and asymmetric quantum well structures as a function of electric field. The light hole exciton is found to broaden at an order of magnitude higher rate than the heavy hole exciton. Field-dependent experimental results for symmetric GaAs/Al0.3Ga0.7As multiquantum well structures are carried out and support the theoretical results.
Epitaxy-substrate discrimination in the photoluminescence characterization of epitaxial Si
Authors: Steele A. G. , Thewalt M. L. W. , Huffman J. E.
Published: July 2002

We show that the difficulty in separating the epilayer and substrate contributions to the photoluminescence of epitaxial Si samples can be solved simply by growing test samples on a substrate which has no photoluminescence in the region of interest for impurity characterization. Lightly In-doped Si is shown to be an ideal substrate material for the characterization of epitaxial layers of ultrahigh-purity Si.
Modulated optical reflectance: A method for characterizing polycrystalline silicon
Authors: Alpern P. , Kakoschke R. , Schöninger M. , Wurm S.
Published: July 2002

We describe modulated optical reflectance experiments with polycrystalline silicon layers treated by rapid optical annealing. The layers were deposited on SiO2 or on crystalline Si. It turns out that the modulated optical reflectance signals are very sensitive to small variations of the grain size in the first case and to epitaxial realignment in the second one.
Interfacial defect creation by interstitial lithium doping of amorphous hydrogenated silicon
Authors: Winer K. , Street R. A.
Published: July 2002

We study interstitial doping in amorphous hydrogenated silicon (a-Si:H) by indiffusion of lithium at 230 °C using secondary ion mass spectrometry, photothermal deflection spectroscopy (PDS), and electron spin resonance. Lithium is distributed nonuniformly in the films with peak concentrations within 300 nm of either interface. Lithium doping introduces up to 1018 paramagnetic defects per cc in a-Si:H (g=2.0061, ΔHp.p. =5.2 G), equal to the concentration of deep defects created as measured by PDS. The nature of these defects is discussed.
Influence of compressive and tensile strain on growth mode during epitaxical growth: A computer simulation study
Authors: Ghaisas S. V. , Madhukar A.
Published: July 2002

The influence of compressive and tensile strain on the growth front morphology during molecular beam epitaxy is examined via computer simulations. It is found that the tendency for occurrence of three (two) dimensional morphology for compressive (tensile) strain indicated in reflection high-energy electron diffraction intensity measurements can be understood in terms of the influence of strain on the surface migration kinetics provided it is assumed that (i) for compressive in-plane strain the intraplanar migration is lowered whereas the interplanar migration is enhanced, and (ii) the opposite holds for tensile in-plane strain.
Toward
Anopheles
transformation:
Minos
element activity in anopheline cells and embryos
Authors: Catteruccia Flaminia , Nolan Tony , Blass Claudia , Müller Hans-Michael , Crisanti Andrea , Kafatos Fotis C. , Loukeris Thanasis G.
Published: July 2002

The ability of the
Minos
transposable element to function as a transformation vector in anopheline mosquitoes was assessed. Two recently established
Anopheles gambiae
cell lines were stably transformed by using marked
Minos
transposons in the presence of a helper plasmid expressing transposase. The markers were either the green fluorescent protein or the hygromycin B phosphotransferase gene driven by the
Drosophila
Hsp70 promoter. Cloning and sequencing of the integration sites demonstrated that insertions in the cell genome occurred through the action of
Minos
transposase. Furthermore, an interplasmid transposition assay established that
Minos
transposase is active in the cytoplasmic environment of
Anopheles stephensi
embryos: interplasmid transposition events isolated from injected preblastoderm embryos were identified as
Minos
transposase-mediated integrations, and no events were recorded in the absence of an active transposase. These results demonstrate that
Minos
vectors are suitable candidates for germ-line transformation of anopheline mosquitoes.
Human cytomegalovirus UL69 protein is required for efficient accumulation of infected cells in the G
1
phase of the cell cycle
Authors: Hayashi Mansuo Lu , Blankenship Catherine , Shenk Thomas
Published: July 2002

Human cytomegalovirus blocks cell-cycle progression in the
G
1
compartment upon infection of primary human fibroblasts.
The virus-coded UL69 protein can institute a G
1
block when
expressed in cells in the absence of virus infection. We have
constructed a cytomegalovirus mutant, TN
sub
UL69, that
lacks the UL69 coding region. This virus grows slowly in fibroblasts,
but produces a wild-type yield after an extended delay. It grows with
normal kinetics in cells coinfected with a recombinant retrovirus,
retroUL69, which expresses UL69 protein, demonstrating that its growth
defect results from the mutation in the
UL69
gene. UL69
protein is packaged within virus particles, and it was possible for us
to produce two types of virus stocks.
TN
sub
UL69
+pUL69
lacks the
UL69
gene but contains UL69 protein in virus particles. It is produced by
growth in fibroblasts that are coinfected with retroUL69.
TN
sub
UL69
−pUL69
lacks the
UL69
gene and protein. It is produced by growth in fibroblasts that do not
contain UL69 protein. The mutant virions lacking both the
UL69
gene and protein fail to induce a cell-cycle block
with normal efficiency, whereas the mutant particles lacking the gene
but containing the protein can institute the block. These results are
consistent with the view that the UL69 protein contributes to the
cytomegalovirus-induced cell-cycle block, and they suggest that UL69
protein delivered to cells within virions can induce the block without
the synthesis of additional UL69 protein encoded by the infecting viral
genome.
Spontaneous retinopathy in HLA-A29 transgenic mice
Authors: Szpak Yann , Vieville Jean-Claude , Tabary Thierry , Naud Marie-Christine , Chopin Martine , Edelson Catherine , Cohen Jacques H. M. , Dausset Jean , de Kozak Yvonne , Pla Marika
Published: July 2002

Humans who have inherited the class I major histocompatibility allele HLA-A29 have a markedly increased relative risk of developing the eye disease termed birdshot chorioretinopathy. This disease affecting adults is characterized by symmetrically scattered, small, cream-colored spots in the fundus associated with retinal vasculopathy and inflammatory signs causing damage to the ocular structures, leading regularly to visual loss. To investigate the role of HLA-A29 in this disease, we introduced the HLA-A29 gene into mice. Aging HLA-A29 transgenic mice spontaneously developed retinopathy, showing a striking resemblance to the HLA-A29-associated chorioretinopathy. These results strongly suggest that HLA-A29 is involved in the pathogenesis of this disease. Elucidation of the role of HLA-A29 should be assisted by this transgenic model.
Cardiovascular abnormalities with normal blood pressure in tissue kallikrein-deficient mice
Authors: Meneton Pierre , Bloch-Faure May , Hagege Albert A. , Ruetten Hartmut , Huang Wei , Bergaya Sonia , Ceiler Debbie , Gehring Doris , Martins Isabelle , Salmon Georges , Boulanger Chantal M. , Nussberger Jürg , Crozatier Bertrand , Gasc Jean-Marie , Heudes Didier , Bruneval Patrick , Doetschman Tom , Ménard Joël , Alhenc-Gelas François
Published: July 2002

Tissue kallikrein is a serine protease thought to be involved in
the generation of bioactive peptide kinins in many organs like the
kidneys, colon, salivary glands, pancreas, and blood vessels. Low renal
synthesis and urinary excretion of tissue kallikrein have been
repeatedly linked to hypertension in animals and humans, but the exact
role of the protease in cardiovascular function has not been
established largely because of the lack of specific inhibitors. This
study demonstrates that mice lacking tissue kallikrein are unable to
generate significant levels of kinins in most tissues and develop
cardiovascular abnormalities early in adulthood despite normal blood
pressure. The heart exhibits septum and posterior wall thinning and a
tendency to dilatation resulting in reduced left ventricular mass.
Cardiac function estimated
in vivo
and
in
vitro
is decreased both under basal conditions and in response
to βadrenergic stimulation. Furthermore, flow-induced
vasodilatation is impaired in isolated perfused carotid arteries, which
express, like the heart, low levels of the protease. These data show
that tissue kallikrein is the main kinin-generating enzyme
in
vivo
and that a functional kallikrein–kinin system is
necessary for normal cardiac and arterial function in the mouse. They
suggest that the kallikrein–kinin system could be involved in the
development or progression of cardiovascular diseases.
Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd
3+
Authors: Tsuchiya Daisuke , Kunishima Naoki , Kamiya Narutoshi , Jingami Hisato , Morikawa Kosuke
Published: July 2002

Crystal structures of the extracellular ligand-binding region of the metabotropic glutamate receptor, complexed with an antagonist, (S)-(α)-methyl-4-carboxyphenylglycine, and with both glutamate and Gd
3+
ion, have been determined by x-ray crystallographic analyses. The structure of the complex with the antagonist is similar to that of the unliganded resting dimer. The antagonist wedges the protomer to maintain an inactive open form. The glutamate/Gd
3+
complex is an exact 2-fold symmetric dimer, where each bi-lobed protomer adopts the closed conformation. The surface of the C-terminal domain contains an acidic patch, whose negative charges are alleviated by the metal cation to stabilize the active dimeric structure. The structural comparison between the active and resting dimers suggests that glutamate binding tends to induce domain closing and a small shift of a helix in the dimer interface. Furthermore, an interprotomer contact including the acidic patch inhibited dimer formation by the two open protomers in the active state. These findings provide a structural basis to describe the link between ligand binding and the dimer interface.
Muscle-specific mutations accumulate with aging in critical human mtDNA control sites for replication
Authors: Wang Yan , Michikawa Yuichi , Mallidis Con , Bai Yan , Woodhouse Linda , Yarasheski Kevin E. , Miller Carol A. , Askanas Valerie , Engel W. King , Bhasin Shalender , Attardi Giuseppe
Published: July 2002

The recently discovered aging-dependent large accumulation of point
mutations in the human fibroblast mtDNA control region raised the
question of their occurrence in postmitotic tissues. In the present
work, analysis of biopsied or autopsied human skeletal muscle revealed
the absence or only minimal presence of those mutations. By contrast,
surprisingly, most of 26 individuals 53 to 92 years old, without a
known history of neuromuscular disease, exhibited at mtDNA replication
control sites in muscle an accumulation of two new point mutations,
i.e., A189G and T408A, which were absent or marginally present in 19
individuals younger than 34 years. These two mutations were not found
in fibroblasts from 22 subjects 64 to 101 years of age (T408A), or were
present only in three subjects in very low amounts (A189G).
Furthermore, in several older individuals exhibiting an accumulation in
muscle of one or both of these mutations, they were nearly absent in
other tissues, whereas the most frequent fibroblast-specific mutation
(T414G) was present in skin, but not in muscle. Among eight additional
individuals exhibiting partial denervation of their biopsied muscle,
four subjects >80 years old had accumulated the two muscle-specific
point mutations, which were, conversely, present at only very low
levels in four subjects ≤40 years old. The striking tissue specificity
of the muscle mtDNA mutations detected here and their mapping at
critical sites for mtDNA replication strongly point to the involvement
of a specific mutagenic machinery and to the functional relevance of
these mutations.
The
Caenorhabditis elegans
mucolipin-like gene
cup-5
is essential for viability and regulates lysosomes in multiple cell types
Authors: Hersh Bradley M. , Hartwieg Erika , Horvitz H. Robert
Published: July 2002

The misregulation of programmed cell death, or apoptosis, contributes to the pathogenesis of many diseases. We used Nomarski microscopy to screen for mutants containing refractile cell corpses in a
C. elegans
strain in which all programmed cell death is blocked and such corpses are absent. We isolated a mutant strain that accumulates refractile bodies resembling irregular cell corpses. We rescued this mutant phenotype with the
C. elegans
mucolipidosis type IV (ML-IV) homolog, the recently identified
cup-5
(
c
oelomocyte-
up
take defective) gene. ML-IV is a human autosomal recessive lysosomal storage disease characterized by psychomotor retardation and ophthalmological abnormalities. Our null mutations in
cup-5
cause maternal-effect lethality. In addition,
cup-5
mutants contain excess lysosomes in many and possibly all cell types and contain lamellar structures similar to those observed in ML-IV cell lines. The human ML-IV gene is capable of rescuing both the maternal-effect lethality and the lysosome-accumulation abnormality of
cup-5
mutants.
cup-5
mutants seem to contain excess apoptotic cells as detected by staining with terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling. We suggest that the increased apoptosis seen in
cup-5
mutants is a secondary consequence of the lysosomal defect, and that abnormalities in apoptosis may be associated with human lysosomal storage disorders.
Effects of the twin-arginine translocase on secretion of virulence factors, stress response, and pathogenesis
Authors: Ochsner Urs A. , Snyder Aleksandra , Vasil Adriana I. , Vasil Michael L.
Published: July 2002

A novel secretion pathway originally found in plants has recently been discovered in bacteria and termed TAT, for “twin-arginine translocation,” with respect to the presence of an Arg-Arg motif in the signal sequence of TAT-secreted products. However, it is unknown whether the TAT system contributes in any way to virulence through the secretion of factors associated with pathogenesis or stress response. We found that the opportunistic pathogen
Pseudomonas aeruginosa
produces several virulence factors that depend on the TAT system for proper export to the periplasm, outer membrane, or extracellular milieu. We identified at least 18 TAT substrates of
P. aeruginosa
and characterized the pleiotropic phenotypes of a
tatC
deletion mutant. The TAT system proved essential for the export of phospholipases, proteins involved in pyoverdine-mediated iron-uptake, anaerobic respiration, osmotic stress defense, motility, and biofilm formation. Because all these traits have been associated with virulence, we studied the role of TAT in a rat lung model. A
tatC
mutant did not cause the typical multifocal pulmonary abscesses and did not evoke a heavy inflammatory host response compared with wild type, indicating that
tatC
mutant cells are attenuated for virulence. Because the TAT apparatus is well conserved among important bacterial pathogens yet absent in mammalian cells, it represents a potential target for novel antimicrobial compounds.
Rapid regulated dense-core vesicle exocytosis requires the CAPS protein
Authors: Rupnik M. , Kreft M. , Sikdar S. K. , Grilc S. , Romih R. , Zupanc̆ic̆ G. , Martin T. F. J. , Zorec R.
Published: July 2002

Although many proteins essential for regulated neurotransmitter and peptide hormone secretion have been identified, little is understood about their precise roles at specific stages of the multistep pathway of exocytosis. To study the function of CAPS (Ca
2+
-dependent activator protein for secretion), a protein required for Ca
2+
-dependent exocytosis of dense-core vesicles, secretory responses in single rat melanotrophs were monitored by patch-clamp membrane capacitance measurements. Flash photolysis of caged Ca
2+
elicited biphasic capacitance increases consisting of rapid and slow components with distinct Ca
2+
dependencies. A threshold of ≈10 μM Ca
2+
was required to trigger the slow component, while the rapid capacitance increase was recorded already at a intracellular Ca
2+
activity < 10 μM. Both kinetic membrane capacitance components were abolished by botulinum neurotoxin B or E treatment, suggesting involvement of SNARE (soluble
N
-ethylmaleimide-sensitive factor attachment protein receptor)-dependent vesicle fusion. The rapid but not the slow component was inhibited by CAPS antibody. These results were further clarified by immunocytochemical studies that revealed that CAPS was present on only a subset of dense-core vesicles. Overall, the results indicate that dense-core vesicle exocytosis in melanotrophs occurs by two parallel pathways. The faster pathway exhibits high sensitivity to Ca
2+
and requires the presence of CAPS, which appears to act at a late stage in the secretory pathway.
Homologous-pairing activity of the human DNA-repair proteins Xrcc3⋅Rad51C
Authors: Kurumizaka Hitoshi , Ikawa Shukuko , Nakada Maki , Eda Keiko , Kagawa Wataru , Takata Minoru , Takeda Shunichi , Yokoyama Shigeyuki , Shibata Takehiko
Published: July 2002

The human Xrcc3 protein is involved in the repair of damaged DNA
through homologous recombination, in which homologous pairing is a key
step. The Rad51 protein is believed to be the only protein factor that
promotes homologous pairing in recombinational DNA repair in mitotic
cells. In the brain, however,
Rad51
expression is
extremely low, whereas
XRCC3
, a human homologue of
Saccharomyces cerevisiae RAD57
that activates the
Rad51-dependent homologous pairing with the yeast Rad55 protein, is
expressed. In this study, a two-hybrid analysis conducted with the use
of a human brain cDNA library revealed that the major Xrcc3-interacting
protein is a Rad51 paralog, Rad51C/Rad51L2. The purified
Xrcc3⋅Rad51C complex, which shows apparent 1:1 stoichiometry, was
found to catalyze the homologous pairing. Although the activity is
reduced, the Rad51C protein alone also catalyzed homologous pairing,
suggesting that Rad51C is a catalytic subunit for homologous pairing.
The DNA-binding activity of Xrcc3⋅Rad51C was drastically decreased
in the absence of Xrcc3, indicating that Xrcc3 is important for the DNA
binding of Xrcc3⋅Rad51C. Electron microscopic observations
revealed that Xrcc3⋅Rad51C and Rad51C formed similar filamentous
structures with circular single-stranded DNA.
The genetics of maternal care: Direct and indirect genetic effects on phenotype in the dung beetleOnthophagus taurus
Authors: Hunt John , Simmons Leigh W.
Published: July 2002

While theoretical models of the evolution of parental care are based on the assumption of underlying genetic variance, surprisingly few quantitative genetic studies of this life-history trait exist. Estimation of the degree of genetic variance in parental care is important because it can be a significant source of maternal effects, which, if genetically based, represent indirect genetic effects. A major prediction of indirect genetic effect theory is that traits without heritable variation can evolve because of the heritable environmental variation that indirect genetic effects provide. In the dung beetle,Onthophagus taurus, females provide care to offspring by provisioning a brood mass. The size of the brood mass has pronounced effects on offspring phenotype. Using a half-sib breeding design we show that the weight of the brood mass females produce exhibits significant levels of additive genetic variance due to sires. However, variance caused by dams is considerably larger, demonstrating that maternal effects are also important. Body size exhibited low additive genetic variance. However, body size exerts a strong maternal influence on the weight of brood masses produced, accounting for 22% of the nongenetic variance in offspring body size. Maternal body size also influenced the number of offspring produced but there was no genetic variance for this trait. Offspring body size and brood mass weight exhibited positive genetic and phenotypic correlations. We conclude that both indirect genetic effects, via maternal care, and nongenetic maternal effects, via female size, play important roles in the evolution of phenotype in this species.
Topological challenges to DNA replication: Conformations at the fork
Authors: Postow Lisa , Crisona Nancy J. , Peter Brian J. , Hardy Christine D. , Cozzarelli Nicholas R.
Published: July 2002

The unwinding of the parental DNA duplex during replication causes a positive linking number difference, or superhelical strain, to build up around the elongating replication fork. The branching at the fork and this strain bring about different conformations from that of (−) supercoiled DNA that is not being replicated. The replicating DNA can form (+) precatenanes, in which the daughter DNAs are intertwined, and (+) supercoils. Topoisomerases have the essential role of relieving the superhelical strain by removing these structures. Stalled replication forks of molecules with a (+) superhelical strain have the additional option of regressing, forming a four-way junction at the replication fork. This four-way junction can be acted on by recombination enzymes to restart replication. Replication and chromosome folding are made easier by topological domain barriers, which sequester the substrates for topoisomerases into defined and concentrated regions. Domain barriers also allow replicated DNA to be (−) supercoiled. We discuss the importance of replicating DNA conformations and the roles of topoisomerases, focusing on recent work from our laboratory.
Analysis of a library of macaque nuclear mitochondrial sequences confirms macaque origin of divergent sequences from old oral polio vaccine samples
Authors: Vartanian Jean-Pierre , Wain-Hobson Simon
Published: July 2002

Nuclear mtDNA sequences (numts) are a widespread family of paralogs evolving as pseudogenes in chromosomal DNA [Zhang, D. E. & Hewitt, G. M. (1996)
TREE
11, 247–251 and Bensasson, D., Zhang, D., Hartl, D. L. & Hewitt, G. M. (2001)
TREE
16, 314–321]. When trying to identify the species origin of an unknown DNA sample by way of an mtDNA locus, PCR may amplify both mtDNA and numts. Indeed, occasionally numts dominate confounding attempts at species identification [Bensasson, D., Zhang, D. X. & Hewitt, G. M. (2000)
Mol. Biol. Evol.
17, 406–415; Wallace, D. C.,
et al.
(1997)
Proc. Natl. Acad. Sci. USA
94, 14900–14905]. Rhesus and cynomolgus macaque mtDNA haplotypes were identified in a study of oral polio vaccine samples dating from the late 1950s [Blancou, P.,
et al.
(2001)
Nature
(
London
) 410, 1045–1046]. They were accompanied by a number of putative numts. To confirm that these putative numts were of macaque origin, a library of numts corresponding to a small segment of 12S rDNA locus has been made by using DNA from a Chinese rhesus macaque. A broad distribution was found with up to 30% sequence variation. Phylogenetic analysis showed that the evolutionary trajectories of numts and
bona fide
mtDNA haplotypes do not overlap with the signal exception of the host species; mtDNA fragments are continually crossing over into the germ line. In the case of divergent mtDNA sequences from old oral polio vaccine samples [Blancou, P.,
et al.
(2001)
Nature
(
London
) 410, 1045–1046], all were closely related to numts in the Chinese macaque library.
Identification of the human cytochrome P450, P450RAI-2, which is predominantly expressed in the adult cerebellum and is responsible for all-trans-retinoic acid metabolism
Authors: White Jay A. , Ramshaw Heather , Taimi Mohammed , Stangle Wayne , Zhang Anqi , Everingham Stephanie , Creighton Shelly , Tam Shui-Pang , Jones Glenville , Petkovich Martin
Published: July 2002

Retinoids, particularly all-trans-retinoic acid (RA), are potent regulators of cell differentiation, cell proliferation, and apoptosis. The role of all-trans-RA during development and in the maintenance of adult tissues has been well established. The control of all-trans-RA levels in cells and tissues is regulated by the balance between its biosynthesis and its catabolism to inactive metabolites. The cytochrome P450 enzyme P450RAI (herein renamed P450RAI-1) is partially responsible for this inactivation of all-trans-RA. In this report, we describe the identification, molecular cloning, and characterization of a second related enzyme, P450RAI-2, which is also involved in the specific inactivation of all-trans-RA. Transiently transfected P450RAI-2 can convert all-trans-RA to more polar metabolites including 4-oxo-, 4-OH-, and 18-OH-all-trans-RA. Competition experiments with other retinoids suggest that all-trans-RA is the preferred substrate. The high level of expression of P450RAI-2, particularly in the cerebellum and pons of human adult brain, suggests a unique role for this enzyme in the protection of specific tissues from exposure to retinoids.
Long-term impacts of the
Exxon Valdez
oil spill on sea otters, assessed through age-dependent mortality patterns
Authors: Monson Daniel H. , Doak Daniel F. , Ballachey Brenda E. , Johnson Ancel , Bodkin James L.
Published: July 2002

We use age distributions of sea otters (
Enhydra lutris
) found dead on beaches of western Prince William Sound, Alaska, between 1976 and 1998 in conjunction with time-varying demographic models to test for lingering effects from the 1989
Exxon Valdez
oil spill. Our results show that sea otters in this area had decreased survival rates in the years following the spill and that the effects of the spill on annual survival increased rather than dissipated for older animals. Otters born after the 1989 spill were affected less than those alive in March 1989, but do show continuing negative effects through 1998. Population-wide effects of the spill appear to have slowly dissipated through time, due largely to the loss of cohorts alive during the spill. Our results demonstrate that the difficult-to-detect long-term impacts of environmental disasters may still be highly significant and can be rigorously analyzed by using a combination of population data, modeling techniques, and statistical analyses.
Documenting a significant relationship between macroevolutionary origination rates and Phanerozoic pCO
2
levels
Authors: Cornette James L. , Lieberman Bruce S. , Goldstein Robert H.
Published: July 2002

We show that the rates of diversification of the marine fauna and the levels of atmospheric CO
2
have been closely correlated for the past 545 million years. These results, using two of the fundamental databases of the Earth's biota and the Earth's atmospheric composition, respectively, are highly statistically significant (
P
< 0.001). The strength of the correlation suggests that one or more environmental variables controlling CO
2
levels have had a profound impact on evolution throughout the history of metazoan life. Comparing our work with highly significant correlations described by D. H. Rothman [Rothman, D. H. (2001)
Proc. Natl. Acad. Sci. USA
98, 4305–4310] between total biological diversity and a measure of stable carbon isotope fractionation, we find that the rates of diversification rather than total diversification correlate with environmental variables, and that the rate of diversification follows the record of CO
2
projected by R. A. Berner and Z. Kothavala [Berner, R. A. & Kothavala, Z. (2001)
Am. J. Sci.
301, 182–204] more closely than that predicted by Rothman.
Historical overview: Searching for replication help in all of the rec places
Authors: Cox Michael M.
Published: July 2002

For several decades, research into the mechanisms of genetic recombination proceeded without a complete understanding of its cellular function or its place in DNA metabolism. Many lines of research recently have coalesced to reveal a thorough integration of most aspects of DNA metabolism, including recombination. In bacteria, the primary function of homologous genetic recombination is the repair of stalled or collapsed replication forks. Recombinational DNA repair of replication forks is a surprisingly common process, even under normal growth conditions. The new results feature multiple pathways for repair and the involvement of many enzymatic systems. The long-recognized integration of replication and recombination in the DNA metabolism of bacteriophage T4 has moved into the spotlight with its clear mechanistic precedents. In eukaryotes, a similar integration of replication and recombination is seen in meiotic recombination as well as in the repair of replication forks and double-strand breaks generated by environmental abuse. Basic mechanisms for replication fork repair can now inform continued research into other aspects of recombination. This overview attempts to trace the history of the search for recombination function in bacteria and their bacteriophages, as well as some of the parallel paths taken in eukaryotic recombination research.
The decomposition of peroxynitrite does not yield nitroxyl anion and singlet oxygen
Authors: Merényi Gábor , Lind Johan , Czapski Gidon , Goldstein Sara
Published: July 2002

In a recent article [Khan, A. U., Kovacic, D., Kolbanovsky, A., Desai, M., Frenkel, K. & Geacintov, N. E. (2000)
Proc. Natl. Acad. Sci. USA
97, 2984–2989], the authors claimed that ONOO
−
, after protonation to ONOOH, decomposes into
1
HNO and
1
O
2
according to a spin-conserved unimolecular mechanism. This claim was based partially on their observation that nitrosylhemoglobin is formed via the reaction of peroxynitrite with methemoglobin at neutral pH. However, thermochemical considerations show that the yields of
1
O
2
and
1
HNO are about 23 orders of magnitude lower than those of
⋅
NO
2
and
⋅
OH, which are formed via the homolysis of ONOOH. We also show that methemoglobin does not form with peroxynitrite any spectrally detectable product, but with contaminations of nitrite and H
2
O
2
present in the peroxynitrite sample. Thus, there is no need to modify the present view of the mechanism of ONOOH decomposition, according to which initial homolysis into a radical pair, [ONO
⋅
⋅
OH]
cage
, is followed by the diffusion of about 30% of the radicals out of the cage, while the rest recombines to nitric acid in the solvent cage.
Somatic mosaicism in Wiskott–Aldrich syndrome suggestsin vivoreversion by a DNA slippage mechanism
Authors: Wada Taizo , Schurman Shepherd H. , Otsu Makoto , Garabedian Elizabeth K. , Ochs Hans D. , Nelson David L. , Candotti Fabio
Published: July 2002

Somatic mosaicism caused byin vivoreversion of inherited mutations has been described in several human genetic disorders. Back mutations resulting in restoration of wild-type sequences and second-site mutations leading to compensatory changes have been shown in mosaic individuals. In most cases, however, the precise genetic mechanisms underlying the reversion events have remained unclear, except for the few instances where crossing over or gene conversion have been demonstrated. Here, we report a patient affected with Wiskott–Aldrich syndrome (WAS) caused by a 6-bp insertion (ACGAGG) in the WAS protein gene, which abrogates protein expression. Somatic mosaicism was documented in this patient whose majority of T lymphocytes expressed nearly normal levels of WAS protein. These lymphocytes were found to lack the deleterious mutation and showed a selective growth advantagein vivo. Analysis of the sequence surrounding the mutation site showed that the 6-bp insertion followed a tandem repeat of the same six nucleotides. These findings strongly suggest that DNA polymerase slippage was the cause of the original germ-line insertion mutation in this family and that the same mechanism was responsible for its deletion in one of the propositus T cell progenitors, thus leading to reversion mosaicism.
A minimalist model protein with multiple folding funnels
Authors: Locker C. Rebecca , Hernandez Rigoberto
Published: July 2002

Kinetic and structural studies of wild-type proteins such as prions and amyloidogenic proteins provide suggestive evidence that proteins may adopt multiple long-lived states in addition to the native state. All of these states differ structurally because they lie far apart in configuration space, but their stability is not necessarily caused by cooperative (nucleation) effects. In this study, a minimalist model protein is designed to exhibit multiple long-lived states to explore the dynamics of the corresponding wild-type proteins. The minimalist protein is modeled as a 27-monomer sequence confined to a cubic lattice with three different monomer types. An order parameter—the winding index—is introduced to characterize the extent of folding. The winding index has several advantages over other commonly used order parameters like the number of native contacts. It can distinguish between enantiomers, its calculation requires less computational time than the number of native contacts, and reduced-dimensional landscapes can be developed when the native state structure is not known
a priori
. The results for the designed model protein prove by existence that the rugged energy landscape picture of protein folding can be generalized to include protein “misfolding” into long-lived states.
Regulation of the transcriptional coactivator PGC-1 via MAPK-sensitive interaction with a repressor
Authors: Knutti Darko , Kressler Dieter , Kralli Anastasia
Published: July 2002

Mechanisms and signals that regulate transcriptional coactivators
are still largely unknown. Here we provide genetic evidence for a
repressor that interacts with and regulates the nuclear receptor
coactivator PGC-1. Association with the repressor requires a PGC-1
protein interface that is similar to the one used by nuclear receptors.
Removal of the repressor enhances PGC-1 coactivation of steroid hormone
responses. We also provide evidence that interaction of the repressor
with PGC-1 is regulated by mitogen-activated protein kinase (MAPK)
signaling. Activation of the MAPK p38 enhances the activity of
wild-type PGC-1 but not of a PGC-1 variant that no longer interacts
with the repressor. Finally, p38 activation enhances steroid hormone
response in a PGC-1-dependent manner. Our data suggest a model where
the repressor and nuclear receptors compete for recruiting PGC-1 to an
inactive and active state, respectively. Extracellular signals such as
nuclear receptor ligands or activators of the MAPK p38 can shift the
equilibrium between the two states.
Direct enumeration ofBorrelia-reactive CD4 T cellsex vivoby using MHC class II tetramers
Authors: Meyer Abbie L. , Trollmo Christina , Crawford Frances , Marrack Philippa , Steere Allen C. , Huber Brigitte T. , Kappler John , Hafler David A.
Published: July 2002

We characterized antigen-specific CD4+T cells in six patients with treatment-resistant Lyme arthritis, using an HLA-DRB1*0401 major histocompatibility complex (MHC) class II tetramer covalently loaded with OspA164–175, an immunodominant epitope ofBorrelia burgdorferi. Direct analysis of OspA-tetramer binding CD4+cells in patients expressing the HLA-DRB1*0401 allele revealed frequencies of between <0.005 and 0.1% in peripheral blood (n= 6), and between <0.005 and 3.1% in synovial fluid (n= 3). OspA-tetramer+CD4+cells were directly cloned at 1 cell per well and expanded by mitogen and IL-2 on allogeneic feeder cells. As measured by [3H]thymidine incorporation, 95% of 168 T cell clones from synovial fluid binding the OspA-tetramer were antigen-reactive. Clones generated from peripheral blood revealed a different pattern of responsiveness when compared with clones generated from synovial fluid, as measured by proliferation, IFN-γ, and IL-13 secretion. These clones, selected on the basis of their peptide binding, also responded to whole protein, but with a different cytokine profile. Our studies demonstrate that MHC class II tetramers can be used in humans to directly identify, isolate, and characterize antigen-reactive T cells from an inflammatory compartment.
Interaction between growth arrest-DNA damage protein 34 and Src kinase Lyn negatively regulates genotoxic apoptosis
Authors: Grishin Anatoly V. , Azhipa Olga , Semenov Igor , Corey Seth J.
Published: July 2002

Genotoxic stresses activate intracellular signaling molecules, which lead to growth arrest, DNA repair, and/or apoptosis. Among these molecules are the growth arrest and DNA damage protein 34 (GADD34) and the Src-related protein tyrosine kinase Lyn. Here, we report that these two proteins physically and functionally interact to regulate DNA damage-induced apoptosis. Multiple isolates of GADD34 and the related murine protein MyD116 were identified as binding partners of Lyn in a yeast two-hybrid screen. The specific interaction was confirmed byin vitroassociation of GADD34 with glutathioneS-transferase fusion proteins containing the Src Homology 3 (SH3) domain of Lyn, as well as coimmunoprecipitation of GADD34 and Lyn from mammalian cells. GADD34 was tyrosine-phosphorylatedin vivoin a Lyn-dependent manner. Lyn efficiently phosphorylated affinity-purified GADD34in vitro. Lyn negatively regulated the proapoptotic function of GADD34 in a kinase-dependent manner. Expression of wild-type, but not kinase-inactive, Lyn weakened promotion of apoptosis by GADD34 following treatment with methyl-methanesulfonate or ionizing radiation in HEK293 and HeLa cells. In contrast, pretreatment of cells with the Src-specific tyrosine kinase inhibitor PP1 strengthened promotion of apoptosis by GADD34. We propose that Lyn regulates the proapoptotic function of GADD34 by binding and phosphorylating it.
Growth inhibition by keratinocyte growth factor receptor of human salivary adenocarcinoma cells through induction of differentiation and apoptosis
Authors: Zhang Yan , Wang Hua , Toratani Shigeaki , Sato J. Denry , Kan Mikio , McKeehan Wallace L. , Okamoto Tetsuji
Published: July 2002

We have reported that normal human salivary gland-derived
epithelial cells exclusively express keratinocyte growth factor
receptor (KGFR). In the process of malignant transformation of human
salivary gland tumors, KGFR gene expression disappeared concomitantly
with the
de novo
expression of the fibroblast growth
factor receptor 1 (FGFR1) and FGFR4 genes. In the present study, we
introduced wild-type KGFR cDNA or chimeric KGFR/FGFR1 cDNA, which
encoded the extracellular domain of KGFR and the intracellular domain
of FGFR1, into the HSY human salivary adenocarcinoma cell line. The
KGFR tyrosine kinase suppressed the activity of FGF receptor substrate
2 (FRS2) and inhibited the growth of HSY by inducing differentiation
and apoptosis
in vitro
and
in
vivo
. Our results provided significant insight into the
mechanism of KGFR tumor suppression and suggest that KGFR gene therapy
might be a viable method of inhibiting human salivary adenocarcinoma
growth.
Mechanism-based discovery of ligands that counteract inhibition of the nicotinic acetylcholine receptor by cocaine and MK-801
Authors: Hess George P. , Ulrich Henning , Breitinger Hans-Georg , Niu Li , Gameiro Armanda M. , Grewer Christof , Srivastava Sanjay , Ippolito Joseph E. , Lee Sean M. , Jayaraman Vasanthi , Coombs Susan E.
Published: July 2002

Nicotinic acetylcholine receptors (AChR) belong to a family
of proteins that form ligand-gated transmembrane ion channels. They are
involved in the fast transmission of signals between cells and the
control of intercellular communication in the nervous system. A variety
of therapeutic agents and abused drugs, including cocaine, inhibit the
AChR and monoamine transporters and interfere with nervous system
function. Here we describe a mechanism-based approach to prevent this
inhibition. We had previously developed presteady-state kinetic
(transient kinetic) techniques, with microsecond-to-millisecond time
resolutions, for investigations of reactions on cell surfaces that
allow one to determine the effects of inhibitors not only on the
channel-opening probability but also on the opening and closing rates
of the AChR channel. The transient kinetic measurements led to two
predictions. (
i
) Ligands that bind to a regulatory site
on the closed-channel conformation of the AChR with higher affinity
than to the site on the open-channel form shift the equilibrium toward
the closed-channel form, thereby inhibiting the receptor.
(
ii
) Ligands that bind to a regulatory site with an
affinity for the open conformation equal to or higher than their
affinity for the closed conformations are expected not to inhibit the
receptor and to displace inhibitors. The identification of such ligands
in a combinatorial library of RNA ligands is reported. The implication
of this approach to other protein-mediated reactions in which an
inhibitor changes the equilibrium between active and inactive
conformations is discussed.
Testing a biosynthetic theory of the genetic code: Fact or artifact?
Authors: Ronneberg Terres A. , Landweber Laura F. , Freeland Stephen J.
Published: July 2002

It has long been conjectured that the canonical genetic code
evolved from a simpler primordial form that encoded fewer amino acids
[e.g., Crick, F. H. C. (1968)
J. Mol. Biol
.
38, 367–379]. The most influential form of this idea, “code
coevolution” [Wong, J. T.-F. (1975)
Proc. Natl. Acad.
Sci. USA
72, 1909–1912], proposes that the genetic code
coevolved with the invention of biosynthetic pathways for new amino
acids. It further proposes that a comparison of modern codon
assignments with the conserved metabolic pathways of amino acid
biosynthesis can inform us about this history of code expansion. Here
we re-examine the biochemical basis of this theory to test the validity
of its statistical support. We show that the theory's definition of
“precursor-product” amino acid pairs is unjustified biochemically
because it requires the energetically unfavorable reversal of steps in
extant metabolic pathways to achieve desired relationships. In
addition, the theory neglects important biochemical constraints when
calculating the probability that chance could assign precursor-product
amino acids to contiguous codons. A conservative correction for these
errors reveals a surprisingly high 23% probability that apparent
patterns within the code are caused purely by chance. Finally, even
this figure rests on post hoc assumptions about primordial codon
assignments, without which the probability rises to 62% that chance
alone could explain the precursor-product pairings found within the
code. Thus we conclude that coevolution theory cannot adequately
explain the structure of the genetic code.
Akt/PKB regulates laminin and collagen IV isotypes of the basement membrane
Authors: Li Xiaofeng , Talts Ulrika , Talts Jan F. , Arman Esther , Ekblom Peter , Lonai Peter
Published: July 2002

Basement membranes are important for epithelial
differentiation, cell survival, and normal and metastatic cell
migration. Much is known about their breakdown and remodeling, yet
their positive regulation is poorly understood. Our previous analysis
of a fibroblast growth factor (FGF) receptor mutation raised the
possibility that protein kinase B (Akt/PKB) activated by FGF is
connected to the expression of certain laminin and type IV collagen
isotypes. Here we test this hypothesis and demonstrate that
constitutively active Akt/PKB, an important downstream element of
phosphoinositide 3′-kinase signaling, induces the synthesis of
laminin-1 and collagen IV isotypes and causes their translocation to
the basement membrane. By using promoter–reporter constructs, we show
that constitutively active phosphoinositide 3′-kinase-p110 or
Akt/PKB activates, whereas dominant negative Akt/PKB inhibits,
transcription of laminin β1 and collagen IV α1 in differentiating
C2 myoblast- and insulin-induced Chinese hamster ovary–T cell
cultures. These results suggest that Akt/PKB activated by receptor
tyrosine kinases is involved in the positive regulation of basement
membrane formation. The possible role of Akt/PKB-induced laminin and
collagen IV synthesis in cell survival and differentiation will be
discussed.
Bazooka is required for localization of determinants and controlling proliferation in the sensory organ precursor cell lineage in
Drosophila
Authors: Roegiers Fabrice , Younger-Shepherd Susan , Jan Lily Yeh , Jan Yuh Nung
Published: July 2002

Asymmetric divisions with two different division orientations
follow different polarity cues for the asymmetric segregation of
determinants in the sensory organ precursor (SOP) lineage. The
first asymmetric division depends on
frizzled
function
and has the mitotic spindle of the pI cell in the epithelium
oriented along the anterior–posterior axis, giving rise to pIIa and
pIIb, which divide in different orientations. Only the pIIb division
resembles neuroblast division in daughter-size asymmetry, spindle
orientation along the apical–basal axis, basal Numb localization, and
requirement for
inscuteable
function. Because the PDZ
domain protein Bazooka is required for spindle orientation and basal
localization of Numb in neuroblasts, we wondered whether Bazooka plays
a similar role in the pIIb in the SOP lineage. Surprisingly, Bazooka
controls asymmetric localization of the Numb-anchoring protein Pon, but
not spindle orientation, in pI and all subsequent divisions. Bazooka
also regulates cell proliferation in the SOP lineage; loss of
bazooka
function results in supernumerary cell divisions
and apoptotic cell death.