bluuebunny/crossref_metadata_2025 huggingface dataset:
First observation of the two-dimensional properties of the electron gas in Ga0.49In0.51P/GaAs heterojunctions grown by low pressure metalorganic chemical vapor deposition
Authors: Razeghi M. , Maurel P. , Omnés F. , Armor S. Ben , Dmowski L. , Portal J. C.
Published: July 2002

We report the first observation of a two-dimensional electron gas from Shubnikov–de Haas and quantum hall effect experiments in GaInP/GaAs heterostructures grown by low pressure metalorganic chemical vapor deposition. Angular-dependent Shubnikov–de Haas measurements confirm two dimensionality of the system. Low-temperature persistent photoconductivity was observed. Critical density at which the second electric subband starts to be populated was determined to be 7.3×1011 cm−2.
New method to determine the carbon concentration in silicon
Authors: Weber J. , Singh M.
Published: July 2002

Silicon samples subjected to a CF4 reactive ion etch exhibit the G-line luminescence known from photoluminescence studies of irradiation damage in Si. We investigate the mechanism of low-energy carbon implantation by CF4 plasma and find a linear dependence of the G-line luminescence intensity on the substitutional carbon concentration in the samples. By a standardized etching and photoluminescence procedure, we expect to determine carbon concentrations two orders of magnitude smaller than the ASTM infrared absorption method.
Compound materials for reversible, phase-change optical data storage
Authors: Chen M. , Rubin K. A. , Barton R. W.
Published: July 2002

Results of rapid (laser induced) and slow (heating stage induced) crystallization studies on Te1−xGex, 0≤x≤0.6, are reported. The time it takes to laser crystallize varies with x by more than four orders of magnitude. Films with stoichiometric compositions, Te and GeTe, can be crystallized using laser pulses of less than 100 ns duration. Unlike Te, which spontaneously crystallizes at room temperature, GeTe has a crystallization temperature of >150 °C. From these results we argue that, in general, compound materials allow realization of fast-switching, reversible, phase-change optical recording media. Furthermore, this fast-switching capability, from the amorphous to the crystalline state and back, can be attained simultaneously with long term data (amorphous phase) stability, provided the melting temperature of the compound is sufficiently high.
Control of orientation of CdTe grown on clean GaAs and the reconstruction of the precursor surfaces
Authors: Srinivasa R. , Panish M. B. , Temkin H.
Published: July 2002

The orientation of CdTe grown epitaxially onto clean (100) GaAs by molecular beam epitaxy can be predetermined by the GaAs precursor surface reconstruction that is present where the CdTe growth is initiated. A Ga-stabilized GaAs starting surface yields CdTe (111) and an As-stabilized GaAs surface yields CdTe (100).
Measurement of hole velocity in n-type InGaAs
Authors: Hill P. , Schlafer J. , Powazinik W. , Urban M. , Eichen E. , Olshansky R.
Published: July 2002

Hole drift velocities in n-type In0.53Ga0.47As have been determined experimentally for the first time. Measured values of the frequency response of transit-time-limited InGaAs p-i-n photodiodes were fit with the theoretical response using hole velocity as the only free parameter. Measurements over field strengths from 54 to 108 kV/cm showed the drift velocity to be relatively constant at (4.8±0.2) 106 cm/s, indicating that velocity saturation has occurred at field levels below 54 kV/cm.
3-ps compressed pulses from a mode-locked Kr+ laser
Authors: Valk B. , Vilhelmsson K. , Salour M. M.
Published: July 2002

We report on 33× compression of 100-ps mode-locked Kr+ laser pulses at 647.1 nm by using a fiber-grating-pair compressor. Pulses with very low wings have been achieved by making use of the nonlinear birefringence effect leading to an intensity-dependent state of polarization. The discrimination of the wings took place in the grating compressor which acted as a polarizer.
Enhanced PtSi formation using a gold layer between Pt and Si
Authors: Song Jerng-Sik , Chang Chin-An
Published: July 2002

When gold is deposited on a clean silicon surface, it reacts with silicon readily even at room temperature. After prolonged time, silicon atoms diffuse out through a gold film and accumulate on the top surface. To study the effects of this phenomenon on the silicide formation kinetics, two kinds of samples were prepared on silicon substrates; one with a gold layer between platinum and silicon layers (Pt/Au/a-Si/Si substrate) and the other without a gold layer (Pt/a-Si/Si substrate). After annealing, the samples were investigated with Rutherford backscattering spectrometry. It was found that the rate of Pt2Si formation was the same for both kinds of samples. However, in the case of PtSi formation, the samples with a Au layer showed a faster reaction rate than those without a Au layer. These observations are explained by considering the dominant diffusing species during the formation of Pt2Si and PtSi.
Plasma enhanced chemical vapor deposition of epitaxial mercury telluride
Authors: Williams L. M. , Lu P.-Y. , Wang C.-H. , Parsey J. M. , Chu S. N. G.
Published: July 2002

Epitaxial layers of mercury telluride were deposited onto cadmium telluride substrates at 85 °C using a glow discharge to enhance the reaction between dimethylmercury and dimethyltelluride. Hall-effect measurements showed the material to be n type with room-temperature and 77 K carrier concentrations of 5.0×1017 and 1.0×1017 cm−3, respectively: room-temperature Hall mobility was 22 000 cm2/V s and 77 K mobility was 52 000 cm2/V s.
Fivefold and threefold symmetries in silver clusters
Authors: Giorgio S. , Urban J.
Published: July 2002

The structures of small silver clusters supported by carbon have been determined in high-resolution electron microscopy. Undistorted crystals displaying fivefold and threefold symmetries were found with sizes ranging from 30 to 100 Å. Such large particles displaying fivefold symmetries are generally believed to be unstable. However, in this case stabilization was achieved by shifting the center of symmetry with respect to the individual faces. The magnitude of the shift increases with the growth of the particles. The center of symmetry for particles with a threefold axis was always found to be unshifted.
X-ray study of the crystalline structure of CdTe layers grown on (001), (111)A, and (111)B CdTe surfaces by metalorganic chemical vapor deposition
Authors: Oron M. , Raizman A. , Shtrikman Hadas , Cinader G.
Published: July 2002

CdTe layers grown by metalorganic chemical vapor deposition on (111)A, (111)B, and (001) CdTe substrates exhibited substantial differences in crystalline microstructure. Double crystal diffractometry was used to resolve and identify the (111) microtwins. (111)B layers were found to be composed of lamella microtwins, while (111)A layers contained double positioning type twins and had a better structural quality. (001) layers exhibited the best crystalline quality and were found to be free of (111) twins.
Plasma-controlled deposition of GaAs and GaAsP by metalorganic chemical vapor deposition
Authors: Huelsman A. D. , Zien L. , Reif R.
Published: July 2002

Alternating layers of GaAs and GaAsxP1−x with varying x were grown at low temperatures using a plasma-enhanced metalorganic chemical vapor deposition process. A remote plasma localized to a region above the substrate was used to selectively dissociate arsine and phosphine and allow GaAs and GaAsxP1−x to be grown at low temperatures where no appreciable deposition takes place without the plasma. This made it possible to use the plasma as a switch to turn deposition on and off. The technique was used to produce very abrupt multiple layers of GaAs and GaAsxP1−x by changing gases when the plasma was off.
Texture formation and enhanced critical currents in YBa2Cu3O7
Authors: Malik M. K. , Nair V. D. , Biswas A. R. , Raghavan R. V. , Chaddah P. , Mishra P. K. , Kumar G. Ravi , Dasannacharya B. A.
Published: July 2002

We report an increase of a factor up to 5 in JC on mixing varying amounts of Ag2O with YBa2Cu3O7. The increase correlates with an increase in texture as seen by x-ray diffraction intensities. Microstructure indicates the formation of platelets with c axis normal to the platelets.
Production of zebrafish germ-line chimeras from embryo cell cultures
Authors: Ma Chunguang , Fan Lianchun , Ganassin Rosemarie , Bols Niels , Collodi Paul
Published: July 2002

Although the zebrafish possesses many characteristics that make it
a valuable model for genetic studies of vertebrate development, one
deficiency of this model system is the absence of methods for
cell-mediated gene transfer and targeted gene inactivation. In mice,
embryonic stem cell cultures are routinely used for gene transfer and
provide the advantage of
in vitro
selection for rare
events such as homologous recombination and targeted mutation.
Transgenic animals possessing a mutated copy of the targeted gene are
generated when the selected cells contribute to the germ line of a
chimeric embryo. Although zebrafish embryo cell cultures that exhibit
characteristics of embryonic stem cells have been described, successful
contribution of the cells to the germ-cell lineage of a host embryo has
not been reported. In this study, we demonstrate that short-term
zebrafish embryo cell cultures maintained in the presence of cells from
a rainbow trout spleen cell line (RTS34st) are able to produce
germ-line chimeras when introduced into a host embryo. Messenger RNA
encoding the primordial germ-cell marker,
vasa
, was
present for more than 30 days in embryo cells cocultured with RTS34st
cells or their conditioned medium and disappeared by 5 days in the
absence of the spleen cells. The RTS34st cells also inhibited
melanocyte and neuronal cell differentiation in the embryo cell
cultures. These results suggest that the RTS34st splenic–stromal cell
line will be a valuable tool in the development of a cell-based gene
transfer approach to targeted gene inactivation in zebrafish.
Stress-induced enhancement of skin immune function: A role for γ interferon
Authors: Dhabhar Firdaus S. , Satoskar Abhay R. , Bluethmann Horst , David John R. , McEwen Bruce S.
Published: July 2002

Contrary to the widespread belief that stress is necessarily immunosuppressive, recent studies have shown that, under certain conditions, stress can induce a significant enhancement of a skin cell-mediated immune response [delayed-type hypersensitivity (DTH) or contact hypersensitivity]. Adrenal stress hormones and a stress-induced trafficking of leukocytes from the blood to the skin have been identified as systemic mediators of this immunoenhancement. Because γ interferon (IFNγ) is an important cytokine mediator of DTH, the studies described here were designed to examine its role as a local mediator of the stress-induced enhancement of skin DTH. The effect of acute stress on skin DTH was examined in wild-type and IFNγ receptor-deficient (IFNγR−/−) mice that had previously been sensitized with 2,4-dinitro-1-fluorobenzene. Acutely stressed wild-type mice showed a significantly larger DTH response than nonstressed mice. In contrast, IFNγR−/− mice failed to show a stress-induced enhancement of skin DTH. Immunoneutralization of IFNγ in wild-type mice significantly reduced the stress-induced enhancement of skin DTH. In addition, an inflammatory response induced by direct IFNγ administration to the skin was significantly enhanced by acute stress. Our results suggest that IFNγ is an important local mediator of a stress-induced enhancement of skin DTH. These studies are clinically relevant because, depending on the nature of the antigen, DTH reactions mediate numerous protective (e.g., resistance to viral, bacterial, parasitic, and fungal infections) or pathological (e.g., autoimmune reactions and contact sensitivity reactions such as that to poison ivy) immune responses.
CD38 expressed on human monocytes: A coaccessory molecule in the superantigen-induced proliferation
Authors: Zilber Marie-Thérèse , Gregory Stéphane , Mallone Roberto , Deaglio Silvia , Malavasi Fabio , Charron Dominique , Gelin Catherine
Published: July 2002

This work analyzes the hypothesis that human CD38 may cooperate with MHC Class II by acting as coreceptor in a superantigen-induced activation. The initial evidence is that CD38 ligation by specific monoclonal antibodies inhibits superantigen-induced T lymphocyte proliferation. Inhibitory effects become apparent after engagement of CD38 expressed by monocytes, whereas ligation of CD38 expressed by T lymphocytes does not apparently affect activation. The inhibition requires a cell-to-cell interaction, followed by the relevant transmembrane signaling that is reproduced by CD38 ligation. Indeed, CD38 ligation on monocytes induces tyrosine phosphorylation of several intracellular proteins including the protooncogene product c-cbl and the fgr and hck tyrosine kinases. The receptorial nature of the CD38-mediated events is confirmed by the observation of an intracellular calcium flux in monocytes secondary to CD38 ligation. These effects are additive with the similar events elicited by MHC Class II ligation, a likely indication that CD38 and MHC Class II share a common activation pathway. This conclusion is strengthened by results of comodulation experiments, indicating that CD38 and MHC Class II display lateral associations on monocytes. These results attribute to CD38 expressed by monocytes a role in the transduction of signal(s) involved in superantigen-induced activation, operating in synergy with MHC Class II.
Poly(ADP-ribose) polymerase-1 is required for efficient HIV-1 integration
Authors: Ha Hyo Chol , Juluri Krishna , Zhou Yan , Leung Steve , Hermankova Monika , Snyder Solomon H.
Published: July 2002

Poly(ADP-ribose) polymerase-1 (PARP-1; EC
2.4.2.30
) is an abundant
nuclear enzyme, activated by DNA strand breaks to attach up to 200
ADP-ribose groups to nuclear proteins. As retroviral infection requires
integrase-catalyzed DNA strand breaks, we examined infection of
pseudotyped HIV type I in fibroblasts from mice with a targeted
deletion of PARP-1. Viral infection is almost totally abolished in
PARP-1 knockout fibroblasts. This protection from infection reflects
prevention of viral integration into the host genome. These findings
suggest a potential for PARP inhibitors in therapy of HIV type I
infection.
L-selectin can facilitate metastasis to lymph nodes in a transgenic mouse model of carcinogenesis
Authors: Qian Fawn , Hanahan Douglas , Weissman Irving L.
Published: July 2002

L-selectin mediates homing of lymphocytes to lymph nodes (LN). Transgenic mice that express rat insulin promoter regulated simian virus 40 Tag (RIP-Tag) develop large, local cancers that metastasize to liver but not LN. To test whether this lack of LN metastases reflects their absence from the circulation, transgenic mice were produced that express Tag (T), L-selectin (L), andEscherichia coliLacZ (Z), in pancreatic β cells. LTZ mice developed insulinomas that specifically had LN metastases; metastasis was blocked by an anti L-selectin mAb. LacZ+tumor cells from these LN homed to secondary LN upon transfer. These results suggest that the highly vascularized islet carcinomas are shedding tumor cells into the bloodstream, which is a necessary but insufficient condition for metastasis to occur; L-selectin can facilitate homing of such tumor cells to LN, resulting in metastasis.
Phase transfer of monosaccharides through noncovalent interactions: Selective extraction of glucose by a lipophilic cage receptor
Authors: Ryan Theo J. , Lecollinet Grégory , Velasco Trinidad , Davis Anthony P.
Published: July 2002

We have previously shown that macrotricyclic host 1a is a powerful receptor for glucopyranosyl units in the nonpolar medium of chloroform. However, the solubility properties of 1a did not permit studies of the extraction of carbohydrates from aqueous solution. This paper describes the synthesis of the new variant 1b, furnished with a highly lipophilic exterior array of 12 benzyloxy substituents. In homogeneous solution, 1b behaves much as 1a, binding
n
-octyl β-
d
-glucoside with
K
a
= 720 M
−1
in CD
3
OH/CDCl
3
(8:92). In two-phase experiments, the improved solubility of 1b allows carbohydrate extraction to be observed. Three hexoses (glucose, galactose, and mannose), two pentoses (ribose and xylose), and the two methyl glucosides are all extracted substantially into chloroform from 1 M aqueous solutions. Among the hexoses, 1b shows notable affinity and selectivity for glucose, extracting detectable amounts even from 0.1 M aqueous solutions.
Circadian 5-HT production regulated by adrenergic signaling
Authors: Sun Xing , Deng Jie , Liu Tiecheng , Borjigin Jimo
Published: July 2002

Using on-line microdialysis, we have characterized
in vivo
dynamics of pineal 5-hydroxytryptamine (5-HT; serotonin) release. Daily pineal 5-HT output is triphasic: (
i
) 5-HT levels are constant and high during the day; (
ii
) early in the night, there is a novel sharp rise in 5-HT synthesis and release, which precedes the nocturnal rise in melatonin synthesis; and (
iii
) late in the night, levels are low. This triphasic 5-HT production persists in constant darkness and is influenced strongly by intrusion of light at night. We demonstrate that both diurnal 5-HT synthesis and 5-HT release are activated by sympathetic innervation from the superior cervical ganglion and show that these processes are controlled by distinct receptors. The increase in 5-HT synthesis is controlled by β-adrenergic receptors, whereas the increase in 5-HT release is mediated by α-adrenergic signaling. On the other hand, the marked decrease in 5-HT content and release late at night is a passive process, influenced by the extent of melatonin synthesis. In the absence of melatonin synthesis, the late-night decline in 5-HT release is prevented, reaching levels roughly twice as high as that of the day value. In summary, our results demonstrate that 5-HT levels display marked circadian rhythms that depend on adrenergic signaling.
Integrated control of appetite and fat metabolism by the leptin-proopiomelanocortin pathway
Authors: Forbes Stacy , Bui Stephanie , Robinson Brian R. , Hochgeschwender Ute , Brennan Miles B.
Published: July 2002

Leptin deficiency results in a complex obesity phenotype comprising
both hyperphagia and lowered metabolism. The hyperphagia results, at
least in part, from the absence of induction by leptin of melanocyte
stimulating hormone (MSH) secretion in the hypothalamus; the MSH
normally then binds to melanocortin-4 receptor expressing neurons and
inhibits food intake. The basis for the reduced metabolic rate has been
unknown. Here we show that leptin administered to leptin-deficient
(
ob/ob
) mice results in a large increase in peripheral
MSH levels; further, peripheral administration of an MSH analogue
results in a reversal of their abnormally low metabolic rate, in an
acceleration of weight loss during a fast, in partial restoration of
thermoregulation in a cold challenge, and in inducing serum free fatty
acid levels. These results support an important peripheral role for MSH
in the integration of metabolism with appetite in response to perceived
fat stores indicated by leptin levels.
Mammalian mad2 and bub1/bubR1 recognize distinct spindle-attachment and kinetochore-tension checkpoints
Authors: Skoufias Dimitrios A. , Andreassen Paul R. , Lacroix Françoise B. , Wilson Leslie , Margolis Robert L.
Published: July 2002

Metaphase checkpoint controls sense abnormalities of chromosome
alignment during mitosis and prevent progression to anaphase until
proper alignment has been attained. A number of proteins, including
mad2, bub1, and bubR1, have been implicated in the metaphase checkpoint
control in mammalian cells. Metaphase checkpoints have been shown, in
various systems, to read loss of either spindle tension or microtubule
attachment at the kinetochore. Characteristically, HeLa cells arrest in
metaphase in response to low levels of microtubule inhibitors that
leave an intact spindle and a metaphase plate. Here we show that the
arrest induced by nanomolar vinblastine correlates with loss of tension
at the kinetochore, and that in response the checkpoint proteins bub1
and bubR1 are recruited to the kinetochore but mad2 is not. mad2
remains competent to respond and is recruited at higher drug doses that
disrupt spindle association with the kinetochores. Further, although
mad2 forms a complex with cdc20, it does not associate with bub1 or
bubR1. We conclude that mammalian bub1/bubR1 and mad2 operate as
elements of distinct pathways sensing tension and attachment,
respectively.
A mutant hunt for defects in membrane protein assembly yields mutations affecting the bacterial signal recognition particle and Sec machinery
Authors: Tian Hongping , Boyd Dana , Beckwith Jon
Published: July 2002

We describe an
Escherichia coli
genetic screen that yields mutations affecting two different cellular processes: disulfide bond formation and membrane protein assembly. The mutants defective in disulfide bond formation include additional classes of
dsbA
and
dsbB
mutations. The membrane protein assembly defective mutants contain a mutation in the
secA
operon and three mutations in the
ffs
gene, which encodes 4.5S RNA. These latter mutations are the only ones to be isolated in a gene encoding a component of the bacterial signal recognition particle by screening
in vivo
for defects in membrane protein insertion. A sensitive method for examining membrane protein localization shows that the
ffs
and
secA
locus mutations affect membrane assembly of the polytopic membrane protein, MalF. The
ffs
mutations also affect the membrane insertion of the FtsQ and the AcrB proteins. Although both the
ffs
and the
secA
locus mutations interfere with membrane protein assembly, only the latter also reduces export of a protein containing a cleavable signal sequence.
Evolutionary relationships among Rel domains indicate functional diversification by recombination
Authors: Graef Isabella A. , Gastier Julie M. , Francke Uta , Crabtree Gerald R.
Published: July 2002

The recent sequencing of several complete genomes has made it
possible to track the evolution of large gene families by their genomic
structure. Following the large-scale association of exons encoding
domains with well defined functions in invertebrates could be useful in
predicting the function of complex multidomain proteins in mammals
produced by accretion of domains. With this objective, we have
determined the genomic structure of the 14 genes in invertebrates and
vertebrates that contain rel domains. The sequence encoding the rel
domain is defined by intronic boundaries and has been recombined with
at least three structurally and functionally distinct genomic sequences
to generate coding sequences for: (
i
) the
rel/Dorsal/NFκB proteins that are retained in the cytoplasm by
IkB-like proteins; (
ii
) the NFATc proteins that sense
calcium signals and undergo cytoplasmic-to-nuclear translocation in
response to dephosphorylation by calcineurin; and (
iii
)
the TonEBP tonicity-responsive proteins. Remarkably, a single exon in
each NFATc family member encodes the entire
Ca
2+
/calcineurin sensing region, including nuclear
import/export, calcineurin-binding, and substrate regions. The
Rel/Dorsal proteins and the TonEBP proteins are present in
Drosophila
but not
Caenorhabditis
elegans
. On the other hand, the calcium-responsive NFATc
proteins are present only in vertebrates, suggesting that the NFATc
family is dedicated to functions specific to vertebrates such as a
recombinational immune response, cardiovascular development, and
vertebrate-specific aspects of the development and function of the
nervous system.
β-Catenin stabilization dysregulates mesenchymal cell proliferation, motility, and invasiveness and causes aggressive fibromatosis and hyperplastic cutaneous wounds
Authors: Cheon Sophia S. , Cheah Alexander Y. L. , Turley Stefanie , Nadesan Puviindran , Poon Raymond , Clevers Hans , Alman Benjamin A.
Published: July 2002

Fibroproliferative processes are a group of disorders in which there is excessive proliferation of spindle (mesenchymal fibroblast-like) cells. They range from hypertrophic scars to neoplasms such as aggressive fibromatosis. Cells from these disorders share cytologic similarity with fibroblasts present during the proliferative phase of wound healing, suggesting that they represent a prolonged wounding response. A critical role for β-catenin in mesenchymal cells in fibroproliferative processes is suggested by its high rate of somatic mutation in aggressive fibromatosis. Using a Tcf-reporter mouse we found that β-catenin protein level and Tcf-transcriptional activity are elevated in fibroblasts during the proliferative phase of healing. We generated a transgenic mouse in which stabilized β-catenin is expressed in mesenchymal cells under control of a tetracycline-regulated promoter. Fibroblasts from the transgenic mice exhibited increased proliferation, motility, and invasiveness when expressing stabilized β-catenin and induced tumors after induction of the transgene when grafted into nude mice. Mice developed aggressive fibromatoses and hyperplastic gastrointestinal polyps after 3 months of transgene induction and healed with hyperplastic cutaneous wounds compared with control mice, which demonstrates an important function for β-catenin in mesenchymal cells and shows a central role for β-catenin in wound healing and fibroproliferative disorders.
On the origin of and phylogenetic relationships among living amphibians
Authors: Zardoya Rafael , Meyer Axel
Published: July 2002

The phylogenetic relationships among the three orders of modern amphibians (Caudata, Gymnophiona, and Anura) have been estimated based on both morphological and molecular evidence. Most morphological and paleontological studies of living and fossil amphibians support the hypothesis that salamanders and frogs are sister lineages (the Batrachia hypothesis) and that caecilians are more distantly related. Previous interpretations of molecular data based on nuclear and mitochondrial rRNA sequences suggested that salamanders and caecilians are sister groups to the exclusion of frogs. In an attempt to resolve this apparent conflict, the complete mitochondrial genomes of a salamander (Mertensiella luschani) and a caecilian (Typhlonectes natans) were determined (16,656 and 17,005 bp, respectively) and compared with previously published sequences from a frog (Xenopuslaevis) and several other groups of vertebrates. Phylogenetic analyses of the mitochondrial data supported with high bootstrap values the monophyly of living amphibians with respect to other living groups of tetrapods, and a sister group relationship of salamanders and frogs. The lack of phylogenetically informative sites in the previous rRNA data sets (because of its shorter size and higher among-site rate variation) likely explains the discrepancy between our results and those based on previous molecular data. Strong support of the Batrachia hypothesis from both molecule- and morphology-based studies provides a robust phylogenetic framework that will be helpful to comparative studies among the three living orders of amphibians and will permit better understanding of the considerably divergent vertebral, brain, and digit developmental patterns found in frogs and salamanders.
Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment
Authors: Szyperski Thomas , Yeh Deok C. , Sukumaran Dinesh K. , Moseley Hunter N. B. , Montelione Gaetano T.
Published: July 2002

A suite of reduced-dimensionality
13
C,
15
N,
1
H-triple-resonance NMR experiments is presented for rapid and complete protein resonance assignment. Even when using short measurement times, these experiments allow one to retain the high spectral resolution required for efficient automated analysis. “Sampling limited” and “sensitivity limited” data collection regimes are defined, respectively, depending on whether the sampling of the indirect dimensions or the sensitivity of a multidimensional NMR experiments
per se
determines the minimally required measurement time. We show that reduced-dimensionality NMR spectroscopy is a powerful approach to avoid the “sampling limited regime”—i.e., a standard set of ten experiments proposed here allows one to effectively adapt minimal measurement times to sensitivity requirements. This is of particular interest in view of the greatly increased sensitivity of NMR spectrometers equipped with cryogenic probes. As a step toward fully automated analysis, the program
autoassign
has been extended to provide sequential backbone and
13
C
β
resonance assignments from these reduced-dimensionality NMR data.
Titration of chaos with added noise
Authors: Poon Chi-Sang , Barahona Mauricio
Published: July 2002

Deterministic chaos has been implicated in numerous natural and man-made complex phenomena ranging from quantum to astronomical scales and in disciplines as diverse as meteorology, physiology, ecology, and economics. However, the lack of a definitive test of chaos vs. random noise in experimental time series has led to considerable controversy in many fields. Here we propose a
numerical titration
procedure as a simple “litmus test” for highly sensitive, specific, and robust detection of chaos in short noisy data without the need for intensive surrogate data testing. We show that the controlled addition of white or colored noise to a signal with a preexisting noise floor results in a titration index that: (
i
) faithfully tracks the onset of deterministic chaos in all standard bifurcation routes to chaos; and (
ii
) gives a relative measure of chaos intensity. Such reliable detection and quantification of chaos under severe conditions of relatively low signal-to-noise ratio is of great interest, as it may open potential practical ways of identifying, forecasting, and controlling complex behaviors in a wide variety of physical, biomedical, and socioeconomic systems.
Redesign of substrate-selectivity determining modules of glutathione transferase A1–1 installs high catalytic efficiency with toxic alkenal products of lipid peroxidation
Authors: Nilsson Lisa O. , Gustafsson Ann , Mannervik Bengt
Published: July 2002

The evolution of proteins for novel functions involves point mutations and recombinations of domains or structural segments. Mimicking this process by rational design
in vitro
is still a major challenge. The present report demonstrates that the active site of the enzyme glutathione transferase (GST) A1–1 can be tailored for high catalytic efficiency with alkenals. The result is a >3,000-fold change in substrate selectivity involving a noteworthy change in preferred catalyzed reaction from aromatic nucleophilic substitution to Michael addition. The hydrophobic substrate binding pocket of GST A1–1 is formed by three structural modules, which were redesigned sequentially with four point mutations and the exchange of a helical segment. The substitutions were made to mimic first-sphere interactions with a substrate in GST A4–4, which naturally has high activity with alkenals. These substrates are toxic lipid peroxidation products of pathophysiological significance, and glutathione conjugation is a route of their inactivation. The final product of the sequential redesign of GST A1–1, mutant GIMFhelix, had a 300-fold increase in catalytic efficiency with nonenal and a >10 times decreased activity with 1-chloro-2,4-dinitrobenzene. In absolute values, GIMFhelix is more efficient than wild-type GST A4–4 with some alkenal substrates, with a
k
cat
/
K
m
value of 1.5 ± 0.1 10
6
M
-1
⋅s
−1
for nonenal. The pKa value of the active-site Tyr-9 of GIMFhelix is 7.3 ± 0.1, approaching the unusually low value of GST A4–4. Thus, rational redesign of the active-site region of an enzyme may be sufficient for the generation of efficient catalysts with altered chemical mechanism and novel selectivity.
Integration of the ubiquitin-proteasome pathway with a cytosolic oligopeptidase activity
Authors: Wang Evelyn W. , Kessler Benedikt M. , Borodovsky Anna , Cravatt Benjamin F. , Bogyo Matthew , Ploegh Hidde L. , Glas Rickard
Published: July 2002

Cytosolic proteolysis is carried out predominantly by the proteasome. We show that a large oligopeptidase, tripeptidylpeptidase II (TPPII), can compensate for compromised proteasome activity. Overexpression of TPPII is sufficient to prevent accumulation of polyubiquitinated proteins and allows survival of EL-4 cells at otherwise lethal concentrations of the covalent proteasome inhibitor NLVS (NIP-leu-leu-leu-vinylsulfone). Elevated TPPII activity also partially restores peptide loading of MHC molecules. Purified proteasomes from adapted cells lack the chymotryptic-like activity, but still degrade longer peptide substrates via residual activity of their Z subunits. However, growth of adapted cells depends on induction of other proteolytic activities. Therefore, cytosolic oligopeptidases such as TPPII normalize rates of intracellular protein breakdown required for normal cellular function and viability.
Cloning and characterization of PIMT, a protein with a methyltransferase domain, which interacts with and enhances nuclear receptor coactivator PRIP function
Authors: Zhu Yijun , Qi Chao , Cao Wen-Qing , Yeldandi Anjana V. , Rao M. Sambasiva , Reddy Janardan K.
Published: July 2002

The nuclear receptor coactivators participate in the transcriptional activation of specific genes by nuclear receptors. In this study, we report the isolation of a nuclear receptor coactivator-interacting protein from a human liver cDNA library by using the coactivator peroxisome proliferator-activated receptor-interacting protein (PRIP) (ASC2/AIB3/RAP250/NRC/TRBP) as bait in a yeast two-hybrid screen. Human PRIP-interacting protein cDNA has an ORF of 2,556 nucleotides, encodes a protein with 852 amino acids, and contains a 9-aa VVDAFCGVG methyltransferase motif I and an invariant G
XX
G
XX
I segment found in K-homology motifs of many RNA-binding proteins. The gene encoding this protein, designated PRIP-interacting protein with methyltransferase domain (PIMT), is localized on chromosome 8q11 and spans more than 40 kb. PIMT mRNA is ubiquitously expressed, with a high level of expression in heart, skeletal muscle, kidney, liver, and placenta. Using the immunofluorescence localization method, we found that PIMT and PRIP proteins appear colocalized in the nucleus. PIMT strongly interacts with PRIP under
in vitro
and
in vivo
conditions, and the PIMT-binding site on PRIP is in the region encompassing amino acids 773–927. PIMT binds
S
-adenosyl-
l
-methionine, the methyl donor for methyltransfer reaction, and it also binds RNA, suggesting that it is a putative RNA methyltransferase. PIMT enhances the transcriptional activity of peroxisome proliferator-activated receptor γ and retinoid-X-receptor α, which is further stimulated by coexpression of PRIP, implying that PIMT is a component of nuclear receptor signal transduction apparatus acting through PRIP. Definitive identification of the specific substrate of PIMT and the role of this RNA-binding protein in transcriptional regulation remain to be determined.
A growth cost of begging in captive canary chicks
Authors: Kilner Rebecca M.
Published: July 2002

Nestling birds solicit food from adults by using begging displays that appear paradoxically costly and wasteful. Theoretical work suggests that the evolution of such exuberant offspring behavior reflects parent–offspring conflict over the supply of parental investment. Originally, extravagant begging was seen as a means of psychological trickery by which offspring could wheedle additional resources from resistant parents. Subsequently, costly begging came to be viewed as the hallmark of resolved parent–offspring conflict, serving either to prevent escalated scramble competition or to enforce honest signaling. However, the theoretical assumption of costly solicitation has been called into question by the low level of energy expenditure measured empirically during begging. This finding has prompted new theoretical work that shows that begging can be cost-free and yet still resolve parent–offspring conflict. Here, I report that begging is more costly than recent work suggests. My experimental evidence from captive canaries demonstrates a marginal cost of begging through impaired growth. Furthermore, I argue that previous studies of energy expenditure during solicitation do not measure the cost of begging, as defined theoretically. More generally, my results may account for the evolution of nestling growth rates, as well as the observation that begging is typically most flamboyant in older offspring.
Design of potent inhibitors of HIV-1 entry from the gp41 N-peptide region
Authors: Eckert Debra M. , Kim Peter S.
Published: July 2002

The HIV-1 gp41 envelope glycoprotein promotes fusion of the
virus and cell membranes through the formation of a trimer-of-hairpins
structure, in which the amino- and carboxyl-terminal regions of the
gp41 ectodomain are brought together. Synthetic peptides derived from
these two regions (called N and C peptides, respectively) inhibit HIV-1
entry. In contrast to C peptides, which inhibit in the nanomolar range,
N peptides are weak inhibitors with IC
50
values in the
micromolar range. To test the hypothesis that the weak inhibition of N
peptides results from their tendency to aggregate, we have constructed
chimeric variants of the N-peptide region of gp41 in which soluble
trimeric coiled coils are fused to portions of the gp41 N peptide.
These molecules, which present the N peptide in a trimeric coiled-coil
conformation, are remarkably more potent inhibitors than the N peptides
themselves and likely target the carboxyl-terminal region of the gp41
ectodomain. The best inhibitors described here inhibit HIV-1 entry at
nanomolar concentrations.
Soluble HLA-G protein secreted by allo-specific CD4+T cells suppresses the allo-proliferative response: A CD4+T cell regulatory mechanism
Authors: Lila Nermine , Rouas-Freiss Nathalie , Dausset Jean , Carpentier Alain , Carosella Edgardo D.
Published: July 2002

We recently reported that the nonclassical HLA class I molecule HLA-G was expressed in the endomyocardial biopsies and sera of 16% of heart transplant patients studied. The aim of the present report is to identify cells that may be responsible for HLA-G protein expression during the allogeneic reaction. Carrying out mixed lymphocyte cultures in which the responder cell population was depleted either in CD4+or CD8+T cells, we found that soluble HLA-G5 protein but not the membrane-bound HLA-G isoform was secreted by allo-specific CD4+T cells from the responder population, which suppressed the allogeneic proliferative T cell response. This inhibition may be reversed by adding the anti-HLA-G 87G antibody to a mixed lymphocyte culture. That may indicate a previously uncharacterized regulatory mechanism of CD4+T cell proliferative response.
Large libraries reveal diverse solutions to an RNA recognition problem
Authors: Barrick Jeffrey E. , Takahashi Terry T. , Ren Jinsong , Xia Tianbing , Roberts Richard W.
Published: July 2002

RNA loops that adopt a characteristic GNRA “tetraloop” fold are common in natural RNAs. Here, we have usedin vitroselection by means of mRNA-peptide fusions to select peptides that bind an example of this RNA loop motif. Starting with the RNA recognition domain from the λ N protein, we have constructed libraries containing 150, 1,600, and 9 trillion different peptide sequences as mRNA-peptide fusions and isolated those capable of high-affinity RNA binding. These selections have resulted in more than 80 different peptides that bind the same RNA loop. The highest affinity peptides exhibit low nanomolar dissociation constants as well as the ability to discriminate RNA hairpins differing by a single loop nucleotide. Thus, our work demonstrates that numerous, chemically distinct solutions exist for a particular RNA recognition problem.
Cell cycle regulation and cell type-specific localization of the FtsZ division initiation protein in Caulobacter.
Authors: Quardokus E , Din N , Brun Y V
Published: July 2002

Many genes involved in cell division and DNA replication and their protein products have been identified in bacteria; however, little is known about the cell cycle regulation of the intracellular concentration of these proteins. It has been shown that the level of the tubulin-like GTPase FtsZ is critical for the initiation of cell division in bacteria. We show that the concentration of FtsZ varies dramatically during the cell cycle of Caulobacter crescentus. Caulobacter produce two different cell types at each cell division: (i) a sessile stalked cell that can initiate DNA replication immediately after cell division and (ii) a motile swarmer cell in which DNA replication is blocked. After cell division, only the stalked cell contains FtsZ. FtsZ is synthesized slightly before the swarmer cells differentiate into stalked cells and the intracellular concentration of FtsZ is maximal at the beginning of cell division. Late in the cell cycle, after the completion of chromosome replication, the level of FtsZ decreases dramatically. This decrease is probably mostly due to the degradation of FtsZ in the swarmer compartment of the predivisional cell. Thus, the variation of FtsZ concentration parallels the pattern of DNA synthesis. Constitutive expression of FtsZ leads to defects in stalk biosynthesis suggesting a role for FtsZ in this developmental process in addition to its role in cell division.
Chemical basis of courtship in a beetle (Neopyrochroa flabellata): cantharidin as precopulatory "enticing" agent.
Authors: Eisner T , Smedley S R , Young D K , Eisner M , Roach B , Meinwald J
Published: July 2002

Male Neopyrochroa flabellata have a natural affinity for cantharidin (Spanish fly). They are attracted to cantharidin baits in the field and feed on the compound if it is offered to them in the laboratory. Males that ingest cantharidin secrete cantharidin from a cephalic gland. Females sample secretion from this gland during courtship and mate preferentially with males that had fed on cantharidin. Cantharidin-unfed males can be rendered acceptable to females if cantharidin is added to their cephalic gland.
Replication infidelity during a single cycle of Ty1 retrotransposition.
Authors: Gabriel A , Willems M , Mules E H , Boeke J D
Published: July 2002

Retroviruses undergo a high frequency of genetic alterations during the process of copying their RNA genomes. However, little is known about the replication fidelity of other elements that transpose via reverse transcription of an RNA intermediate. The complete sequence of 29 independently integrated copies of the yeast retrotransposon Ty1 (173,043 nt) was determined, and the mutation rate during a single cycle of replication was calculated. The observed base substitution rate of 2.5 x 10(-5) bp per replication cycle suggests that this intracellular element can mutate as rapidly as retroviruses. The pattern and distribution of errors in the Ty1 genome is nonrandom and provides clues to potential in vivo molecular mechanisms of reverse transcriptase-mediated error generation, including heterogeneous RNase H cleavage of Ty1 RNA, addition of terminal nontemplated bases, and transient dislocation and realignment of primer-templates. Overall, analysis of errors generated during Ty1 replication underscores the utility of a genetically tractable model system for the study of reverse transcriptase fidelity.
The physical and genomic organization of microsatellites in sugar beet.
Authors: Schmidt T , Heslop-Harrison J S
Published: July 2002

Microsatellites, tandem arrays of short (2-5 bp) nucleotide motifs, are present in high numbers in most eukaryotic genomes. We have characterized the physical distribution of microsatellites on chromosomes of sugar beet (Beta vulgaris L.). Each microsatellite sequence shows a characteristic genomic distribution and motif-dependent dispersion, with site-specific amplification on one to seven pairs of centromeres or intercalary chromosomal regions and weaker, dispersed hybridization along chromosomes. Exclusion of some microsatellites from 18S-5.8S-25S rRNA gene sites, centromeres, and intercalary sites was observed. In-gel and in situ hybridization patterns are correlated, with highly repeated restriction fragments indicating major centromeric sites of microsatellite arrays. The results have implications for genome evolution and the suitability of particular microsatellite markers for genetic mapping and genome analysis.
Direct modulation of calmodulin targets by the neuronal calcium sensor NCS-1.
Authors: Schaad N C , De Castro E , Nef S , Hegi S , Hinrichsen R , Martone M E , Ellisman M H , Sikkink R , Rusnak F , Sygush J , Nef P
Published: July 2002

Ca2+ and its ubiquitous intracellular receptor calmodulin (CaM) are required in the nervous system, among a host of cellular responses, for the modulation of several important enzymes and ion channels involved in synaptic efficacy and neuronal plasticity. Here, we report that CaM can be replaced by the neuronal calcium sensor NCS-1 both in vitro and in vivo. NCS-1 is a calcium binding protein with two Ca(2+)-binding domains that shares only 21% of homology with CaM. We observe that NCS-1 directly activates two Ca2+/CaM-dependent enzymes (3':5'-cyclic nucleotide phosphodiesterase and protein phosphatase calcineurin). Co-activation of nitric oxide synthase by NCS-1 and CaM results in a higher activity than with CaM alone. Moreover, NCS-1 is coexpressed with calcineurin and nitric oxide synthase in several neuron populations. Finally, injections of NCS-1 into calmodulin-defective cam1 Paramecium partially restore wildtype behavioral responses. With this highly purified preparation of NCS-1, we have obtained crystals suitable for crystallographic structure studies. NCS-1, despite its very different structure, distribution, and Ca(2+)-binding affinity as compared with CaM, can substitute for or potentiate CaM functions. Therefore, NCS-1 represents a novel protein capable of mediating multiple Ca(2+)-signaling pathways in the nervous system.
Fate of biological control introductions: monitoring an Australian fungal pathogen of grasshoppers in North America.
Authors: Bidochka M J , Walsh S R , Ramos M E , St Leger R J , Silver J C , Roberts D W
Published: July 2002

In North America there are two generally recognized pathotypes (pathotypes 1 and 2) of the fungus Entomophaga grylli which show host-preferential infection of grasshopper subfamilies. Pathotype 3, discovered in Australia, has a broader grasshopper host range and was considered to be a good biocontrol agent. Between 1989 and 1991 pathotype 3 was introduced at two field sites in North Dakota. Since resting spores are morphologically indistinguishable among pathotypes, we used pathotype-specific DNA probes to confirm pathotype identification in E. grylli-infected grasshoppers collected at the release sites in 1992, 1993, and 1994. In 1992, up to 23% of E. grylli-infected grasshoppers of the subfamilies Melanoplinae, Oedipodinae, and Gomphocerinae were infected by pathotype 3, with no infections > 1 km from the release sites. In 1993, pathotype 3 infections declined to 1.7%. In 1994 grasshopper populations were low and no pathotype 3 infections were found. The frequency of pathotype 3 infection has declined to levels where its long-term survival in North America is questionable. Analyses of biocontrol releases are critical to evaluating the environmental risks associated with these ecological manipulations, and molecular probes are powerful tools for monitoring biocontrol releases.