bluuebunny/crossref_metadata_2025 huggingface dataset:
Physics issues in the design of high-beta, low-aspect-ratio stellarator experiments
Authors: Neilson G. H. , Reiman A. H. , Zarnstorff M. C. , Brooks A. , Fu G.-Y. , Goldston R. J. , Ku L.-P. , Lin Z. , Majeski R. , Monticello D. A. , Mynick H. , Pomphrey N. , Redi M. H. , Reiersen W. T. , Schmidt J. A. , Hirshman S. P. , Lyon J. F. , Berry L. A. , Nelson B. E. , Sanchez R. , Spong D. A. , Boozer A. H. , Miner W. H. , Valanju P. M. , Cooper W. A. , Drevlak M. , Merkel P. , Nuehrenberg C.
Published: July 2002

High-beta, low-aspect-ratio (“compact”) stellarators are promising solutions to the problem of developing a magnetic plasma configuration for magnetic fusion power plants that can be sustained in steady state without disrupting. These concepts combine features of stellarators and advanced tokamaks and have aspect ratios similar to those of tokamaks (2–4). They are based on computed plasma configurations that are shaped in three dimensions to provide desired stability and transport properties. Experiments are planned as part of a program to develop this concept. A β=4% quasi-axisymmetric plasma configuration has been evaluated for the National Compact Stellarator Experiment (NCSX). It has a substantial bootstrap current and is shaped to stabilize ballooning, external kink, vertical, and neoclassical tearing modes without feedback or close-fitting conductors. Quasi-omnigeneous plasma configurations stable to ballooning modes at β=4% have been evaluated for the Quasi-Omnigeneous Stellarator (QOS) experiment. These equilibria have relatively low bootstrap currents and are insensitive to changes in beta. Coil configurations have been calculated that reconstruct these plasma configurations, preserving their important physics properties. Theory- and experiment-based confinement analyses are used to evaluate the technical capabilities needed to reach target plasma conditions. The physics basis for these complementary experiments is described.
Magnetic flux tubes inside the sun
Authors: Fisher G. H. , Fan Y. , Longcope D. W. , Linton M. G. , Abbett W. P.
Published: July 2002

Bipolar magnetic active regions are the largest concentrations of magnetic flux on the Sun. In this paper, the properties of active regions are investigated in terms of the dynamics of magnetic flux tubes which emerge from the base of the solar convection zone, where the solar cycle dynamo is believed to operate, to the photosphere. Flux tube dynamics are computed with the “thin flux tube” approximation, and by using magnetohydrodynamics simulation. Simulations of active region emergence and evolution, when compared with the known observed properties of active regions, have yielded the following results: (1) The magnetic field at the base of the convection zone is confined to an approximately toroidal geometry with a field strength in the range 3–10×104 G. The latitude distribution of the toroidal field at the base of the convection zone is more or less mirrored by the observed active latitudes; there is not a large poleward drift of active regions as they emerge. The time scale for emergence of an active region from the base of the convection zone to the surface is typically 2–4 months. (2) The tilt of active regions is due primarily to the Coriolis force acting to twist the diverging flows of the rising flux loops. The dispersion in tilts is caused primarily by the buffeting of flux tubes by convective motions as they rise through the interior. (3) Coriolis forces also bend active region flux tube shapes toward the following (i.e., antirotational) direction, resulting in a steeper leg on the following side as compared to the leading side of an active region. When the active region emerges through the photosphere, this results in a more rapid separation of the leading spots away from the magnetic neutral line as compared to the following spots. This bending motion also results in the neutral line being closer to the following magnetic polarity. (4) The properties of the strongly sheared, flare productive δ-spot active regions can be accounted for by the dynamics of highly twisted Ω loops that succumb to the helical kink instability as they emerge through the solar interior.
Quasi-single helicity states in the reversed field pinch: Beyond the standard paradigm
Authors: Martin P. , Buffa A. , Cappello S. , D’Angelo F. , Escande D. F. , Franz P. , Marrelli L. , Martines E. , Ortolani S. , Spizzo G. , Bilato R. , Bolzonella T. , Costa S. , Murari A. , Paccagnella R. , Pasqualotto R. , Terranova D. , Zanca P.
Published: July 2002

This paper reports experimental results showing that coherent helical structures are formed in the reversed field pinch (RFP) self-organizing plasma core as a result of transitions to states where the n-spectrum of the m=1 modes is dominated by a single (1,nmax) geometrical helicity. These states are dubbed quasi-single helicity (QSH) states. Their magnetic and thermal properties measured in the reverse field experiment (RFX) [G. Rostagni, Fusion Eng. Des. 25, 301 (1995)] device are described. The present theoretical understanding of QSH states is discussed and some recent theoretical results are presented. The role of aspect ratio is discussed. These results represent a significant step to open a path beyond the standard paradigm that a bath of magnetohydrodynamic (MHD) modes is intrinsic to the RFP.
Ion acoustic shock formation in a converging magnetic field geometry
Authors: Luo Q.-Z. , D’Angelo N. , Merlino R. L.
Published: July 2002

The effect of the magnetic field configuration on the formation of ion acoustic shocks has been investigated experimentally and through numerical solutions of the fluid equations. The tendency for compressive pulses to steepen into shocks is enhanced if the pulses travel into a configuration of converging magnetic field geometry.
Plasma enhanced chemical vapor deposition of titanium diboride films
Authors: Williams L. M.
Published: July 2002

Thin films of titanium borides were deposited at temperatures from 480 to 650 °C using a glow discharge and feed gases of TiCl4, BCl3, and H2. High quality films have been obtained that are smooth, shiny, and crack-free; they have as-deposited resistivities as low as 200 μΩ cm. Films deposited with these moderate conditions have comparable properties to films deposited at high temperatures. These films have potential use as diffusion barriers or in other applications requiring a conducting refractory material.
Characterization of amorphous carbon-hydrogen films by solid-state nuclear magnetic resonance
Authors: Kaplan S. , Jansen F. , Machonkin M.
Published: July 2002

The structure and properties of thin amorphous carbon films are critically dependent upon the preparation conditions. Hydrogenated amorphous carbon films, prepared by both ion beam sputtering and glow discharge techniques, have been investigated by solid-state 13C magic angle spinning nuclear magnetic resonance measurements of the sp2 and sp3 bonding sites. Film hardness and density correlate with the incorporated hydrogen, whereas the optical band gap is controlled by the fraction of tetrahedral (sp3) versus graphitic (sp2) bonding. It is shown that structural trade-offs prevent the formation of so-called amorphous diamond, i.e., a material with simultaneous extreme hardness and wide optical band gap.
Drive-level capacitance profiling: Its application to determining gap state densities in hydrogenated amorphous silicon films
Authors: Michelson C. E. , Gelatos A. V. , Cohen J. D.
Published: July 2002

We have developed a new method of capacitance profiling which is greatly superior to standard profiling techniques for materials like amorphous silicon that contain high densities of deep gap states. This technique, which makes use of the variation of the junction capacitance with the alternating voltage amplitude, is largely immune to the effects of surface states and is readily interpreted in terms of a simple integral over the density of states, g(E). This method is applicable to both doped and semi-insulating undoped samples.
Surface relaxation and pore sizes in rocks—a nuclear magnetic resonance analysis
Authors: Lipsicas Max , Banavar Jayanth R. , Willemsen Jorge
Published: July 2002

The pulsed gradient nuclear magnetic resonance technique has been applied to the measurement of pore sizes in rocks. The measurements also yield an estimate of the strength of the magnetization relaxation at the pore-rock interface.
Low threshold laser operation at room temperature in GaAs/(Al,Ga)As structures grown directly on (100)Si
Authors: Fischer R. , Kopp W. , Morkoç H. , Pion M. , Specht A. , Burkhart G. , Appelman H. , McGougan D. , Rice R.
Published: July 2002

We report the room-temperature pulsed operation of GaAs/(Al,Ga)As double heterojunction laser structures grown directly on (100)Si. Current thresholds of as low as 170 mA in 10-μm-wide stripe lasers have been achieved at 280 K. Power output as high as 44 mW per facet was also obtained. Assuming no current spreading, the corresponding current threshold density is 6.9 kA/cm2. Slope efficiencies and T0 values of 0.18 W/A and 165 K, respectively, have also been obtained. These results are directly attributable to the reduction of dislocations by choosing growth conditions and step density on the surface.
Nonlinear guided waves coupled nonlinearly in a planar GaAs/GaAlAs multiple quantum well structure
Authors: Cada M. , Gauthier R. C. , Paton B. E. , Chrostowski J.
Published: July 2002

A nonlinear guided-wave concept and nonlinear coupled-wave equations are used to study numerically the coupling characteristics of two planar waveguides in a GaAs/GaAlAs multiple quantum well structure with self-defocusing nonlinearities. Both the mode-intensity-dependent critical power and the coupling length are calculated for the first time using the nonlinear field distributions. An optically controlled modulation/switching behavior is predicted.
Low-threshold high-efficiency AlGaAs-GaAs double-heterostructure injection lasers grown on Si substrates by metalorganic chemical vapor deposition
Authors: Dupuis R. D. , van der Ziel J. P. , Logan R. A. , Brown J. M. , Pinzone C. J.
Published: July 2002

We have fabricated low-threshold, high-quantum-efficiency, room-temperature AlGaAs-GaAs double-heterojunction injection lasers from epitaxial structures grown by metalorganic chemical vapor deposition directly on Si substrates. These devices have broad-area (125 μm×250 μm) pulsed threshold current densities as low as Jth =3.5 kA/cm2 at ∼23 °C. Ridge-waveguide stripe-geometry lasers (5 μm×250 μm) have pulsed threshold currents as low as 130 mA at ∼23 °C. These stripe-geometry lasers have total external differential quantum efficiencies as high as ηext ∼70%, a value equal to the ηext measured for similar double-heterostructure lasers grown on GaAs substrates. These are the lowest threshold currents and highest external quantum efficiencies yet reported for lasers grown on Si substrates.
Laser writing of copper lines from metalorganic films
Authors: Gupta A. , Jagannathan R.
Published: July 2002

Direct writing of high-purity copper lines has been achieved by photothermal decomposition of copper formate films under ambient conditions using a focused argon ion laser (514 nm) beam on a scanning quartz or silicon substrate. The fast decomposition kinetics of the precursor allows use of writing speeds as high as 1 cm/s for deposition of micron-thick copper films. There is negligible oxidation of the copper after decomposition in the presence of air due to the rapid heating and cooling of the deposit during laser writing.
Self-assembly of nanoscopic coordination cages of
D

3h

symmetry
Authors: Kuehl Christopher J. , Kryschenko Yury K. , Radhakrishnan Ukkirampandian , Seidel S. Russell , Huang Songping D. , Stang Peter J.
Published: July 2002

A family of nanoscale-sized supramolecular cage compounds with a trigonal prismatic framework was prepared by means of spontaneous self-assembly from the combination of a predesigned molecular “clip” with tritopic pyridyl subunits. As confirmed by x-ray crystallography, the smallest structure of the reported series is ≈1 × 2 nm and possesses a nitrate anion incarcerated inside its molecular cavity. The largest structure has dimensions of ≈ 1 × 4 nm.
Cultured rat hippocampal neural progenitors generate spontaneously active neural networks
Authors: Mistry Sanjay K. , Keefer Edward W. , Cunningham Bruce A. , Edelman Gerald M. , Crossin Kathryn L.
Published: July 2002

We previously demonstrated that the neural cell adhesion molecule (N-CAM) inhibited the proliferation of cultured rat hippocampal progenitor cells and increased the number of neurons generated. We demonstrate here that the continued presence of fibroblast growth factor 2 along with N-CAM or brain-derived neurotrophic factor over 12 days of culture greatly increased the number of both progenitors and neurons. These progenitor-derived neurons expressed neurotransmitters, neurotransmitter receptors, and synaptic proteins
in vitro
consistent with those expressed in the mature hippocampus. Progenitor cells cultured on microelectrode plates formed elaborate neural networks that exhibited spontaneously generated action potentials after 21 days. This activity was observed only in cultures grown in the presence of fibroblast growth factor 2 and either N-CAM or brain-derived neurotrophic factor. Analysis of neuronal activity after various pharmacological treatments indicated that the networks formed functional GABAergic and glutamatergic synapses. We conclude that mitogenic growth factors can synergize with N-CAM or neurotrophins to generate spontaneously active neural networks from neural progenitors.
A spectroscopic method for observing the domain movement of the Rieske iron–sulfur protein
Authors: Brugna Myriam , Rodgers Simon , Schricker Anna , Montoya Guillermo , Kazmeier Michael , Nitschke Wolfgang , Sinning Irmgard
Published: July 2002

The
g-
tensor orientation of the chemically reduced Rieske cluster in cytochrome
bc
1
complex from
Rhodovulum sulfidophilum
with respect to the membrane was determined in the presence and absence of inhibitors and in the presence of oxidized and reduced quinone in the quinol-oxidizing-site (Q
o
-site) by EPR on two-dimensionally ordered samples. Almost identical orientations were observed when oxidized or reduced quinone, stigmatellin, or 5-(
n
-undecyl)-6-hydroxy-4,7-dioxobenzothiazole was present. Occupancy of the Q
o
-site by myxothiazole induced appearance of a minority population with a substantially differing conformation and presence of
E
-β-methoxyacrylate-stilbene significantly reduced the contribution of the major conformation observed in the other cases. Furthermore, when the oxidized iron–sulfur cluster was reduced at cryogenic temperatures by the products of radiolysis, the orientation of its magnetic axes was found to differ significantly from that of the chemically reduced center. The “irradiation-induced” conformation converts to that of the chemically reduced center after thawing of the sample. These results confirm the effects of Q
o
-site inhibitors on the equilibrium conformation of the Rieske iron–sulfur protein and provide evidence for a reversible redox-influenced interconversion between conformational states. Moreover, the data obtained with the iron—sulfur protein demonstrate that the conformation of “EPR-inaccessible” reduction states of redox centers can be studied by inducing changes of redox state at cryogenic temperatures. This technique appears applicable to a wide range of comparable electron transfer systems performing redox-induced conformational changes.
Electrospray ionization mass spectrometry analysis of changes in phospholipids in RBL-2H3 mastocytoma cells during degranulation
Authors: Ivanova Pavlina T. , Cerda Blas A. , Horn David M. , Cohen Jared S. , McLafferty Fred W. , Brown H. Alex
Published: July 2002

Biological membranes contain an extraordinary diversity of lipids. Phospholipids function as major structural elements of cellular membranes, and analysis of changes in the highly heterogeneous mixtures of lipids found in eukaryotic cells is central to understanding the complex functions in which lipids participate. Phospholipase-catalyzed hydrolysis of phospholipids often follows cell surface receptor activation. Recently, we demonstrated that granule fusion is initiated by addition of exogenous, nonmammalian phospholipases to permeabilized mast cells. To pursue this finding, we use positive and negative mode Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) to measure changes in the glycerophospholipid composition of total lipid extracts of intact and permeabilized RBL-2H3 (mucosal mast cell line) cells. The low energy of the electrospray ionization results in efficient production of molecular ions of phospholipids uncomplicated by further fragmentation, and changes were observed that eluded conventional detection methods. From these analyses we have spectrally resolved more than 130 glycerophospholipids and determined changes initiated by introduction of exogenous phospholipase C, phospholipase D, or phospholipase A
2
. These exogenous phospholipases have a preference for phosphatidylcholine with long polyunsaturated alkyl chains as substrates and, when added to permeabilized mast cells, produce multiple species of mono- and polyunsaturated diacylglycerols, phosphatidic acids, and lysophosphatidylcholines, respectively. The patterns of changes of these lipids provide an extraordinarily rich source of data for evaluating the effects of specific lipid species generated during cellular processes, such as exocytosis.
Related homing endonucleases I-
Bmo
I and I-
Tev
I use different strategies to cleave homologous recognition sites
Authors: Edgell David R. , Shub David A.
Published: July 2002

A typical homing endonuclease initiates mobility of its group I intron by recognizing DNA both upstream and downstream of the intron insertion site of intronless alleles, preventing the endonuclease from binding and cleaving its own intron-containing allele. Here, we describe a GIY-YIG family homing endonuclease, I-
Bmo
I, that possesses an unusual recognition sequence, encompassing 1 base pair upstream but 38 base pairs downstream of the intron insertion site. I-
Bmo
I binds intron-containing and intronless substrates with equal affinity but can nevertheless discriminate between the two for cleavage. I-
Bmo
I is encoded by a group I intron that interrupts the thymidylate synthase (TS) gene (
thy
A) of
Bacillus mojavensis
s87-18. This intron resembles one inserted 21 nucleotides further downstream in a homologous TS gene (
td
) of
Escherichia coli
phage T4. I-
Tev
I, the T4
td
intron-encoded GIY-YIG endonuclease, is very similar to I-
Bmo
I, but each endonuclease gene is inserted within a different position of its respective intron. Remarkably, I-
Tev
I and I-
Bmo
I bind a homologous stretch of TS-encoding DNA and cleave their intronless substrates in very similar positions. Our results suggest that each endonuclease has independently evolved the ability to distinguish intron-containing from intronless alleles while maintaining the same conserved recognition sequence centered on DNA-encoding active site residues of TS.
Phospholamban domain IB forms an interaction site with the loop between transmembrane helices M6 and M7 of sarco(endo)plasmic reticulum Ca
2+
ATPases
Authors: Asahi Michio , Green N. Michael , Kurzydlowski Kazimierz , Tada Michihiko , MacLennan David H.
Published: July 2002

Transmembrane helix M6 of the sarco(endo)plasmic reticulum Ca
2+
ATPase (SERCA) has been shown to form a site of interaction with phospholamban (PLN). Site-directed mutagenesis was carried out in the cytoplasmic loop (L67) between M6 and M7 in SERCA1a to detect other SERCA-PLN binding sites. Mutants N810A, D813A, and R822A had diminished ability to interact functionally with PLN, but only D813A and R822A had reduced physical interaction with PLN. PLN mutants R25A, Q26A, N27A, L28A, Q29A, and N30A had enhanced physical interaction with wild-type (wt) SERCA1a, but physical interaction of these PLN mutants with SERCA1a mutants D813A and R822A was reduced about 2.5 fold (range 1.44–2.82). Exceptions were the interactions of PLN N27A and N30A with SERCA1a D813A, which were reduced by 7.3- and 5.8-fold, respectively. A superinhibitory PLN deletion mutant, PLNΔ21–29, had strong physical interactions with SERCA1a and with SERCA1a mutant D813A. Physical interactions with SERCA1a and mutant D813A were sharply diminished, however, for the PLN deletion mutant, PLNΔ21–30, lacking PLN N30. Physical interactions between SERCA1a and a PLN-cytochrome
b
5
chimera containing PLN residues 1–29 were much stronger than those between a PLN-cytochrome
b
5
chimera containing PLN residues 1–21 and lacking N27. These results suggest that a SERCA1-PLN interaction site occurs between L67 of SERCA1a and domain IB of PLN, which involves SERCA1a D813 and PLN N27 and N30.
PS1 N- and C-terminal fragments form a complex that functions in APP processing and Notch signaling
Authors: Levitan Diane , Lee Julie , Song Lixin , Manning Ron , Wong Gwen , Parker Eric , Zhang Lili
Published: July 2002

Presenilin proteins play critical roles in the proteolytic processing of both Notch and amyloid precursor protein (APP). Presenilin itself undergoes endoproteolytic processing to generate an N-terminal and C-terminal fragment. As demonstrated previously, overexpression of presenilin 1 (PS1) holoprotein does not change the levels of the N-terminal and C-terminal fragments (NTF and CTF). When we coexpress the PS1 NTF and CTF, marked increases in the cellular levels of these fragments are seen. By coexpressing the PS1 NTF and CTF, we demonstrate conclusively that a noncovalent complex of the NTF and CTF is the active species of presenilin. However, although the PS1 NTF/CTF complex is necessary for γ-secretase activity, it is not sufficient. Independent overexpression of the PS1 NTF and CTF was also used to show that the Asp-257 and Asp-385 mutations in PS1 decrease Aβ production by a direct effect on γ-secretase activity and not by the inhibition of PS1 endoproteolysis.
Development of a two-part transcription probe to determine the completeness of temporal and spatial compartmentalization of gene expression during bacterial development
Authors: Li Zusheng , Piggot Patrick J.
Published: July 2002

We have developed a two-part test, using the
Bacillus subtilis sacB
/SacY transcription antitermination system, to evaluate the completeness of temporal and spatial compartmentalization of gene expression during bacterial cell development. Transcription of
sacY
(1–55) (encoding a constitutively active form of the antiterminator, SacY) is directed by one promoter, whereas transcription of
sacB
′-′
lacZ
(the target of SacY action) is directed by the same or another promoter. To obtain β-galactosidase activity, SacY(1–55) needs to be present when
sacB
′-′
lacZ
is being transcribed. We tested the system by analyzing the spatial compartmentalization of the activities of RNA polymerase σ factors, which are tightly regulated during sporulation of
B. subtilis
: σ
F
and then σ
G
in the prespore, σ
E
and then σ
K
in the mother cell. We have confirmed that the activities of σ
F
and σ
E
are spatially compartmentalized. We have demonstrated that there is also sharp temporal compartmentalization, with little or no overlap in the activities of σ
F
and σ
G
or of σ
E
and σ
K
. In contrast, we found no compartmentalization of the activity of the main vegetative factor, σ
A
, which continued to be active alongside all of the sporulation-specific σ factors. We also found no temporal compartmentalization of expression of loci that are activated during the development of competent cells of
B. subtilis
, a developmental program distinct from spore formation. A possible mechanism to explain the temporal compartmentalization of σ
F
and σ
G
activities is that the anti-sigma factor SpoIIAB transfers from σ
G
to σ
F
.
Dissection of nodulation signaling using pea mutants defective for calcium spiking induced by Nod factors and chitin oligomers
Authors: Walker Simon A. , Viprey Virginie , Downie J. Allan
Published: July 2002

Changes in intracellular calcium in pea root hairs responding to
Rhizobium leguminosarum
bv.
viciae
nodulation (Nod) factors were analyzed by using a microinjected
calcium-sensitive fluorescent dye (dextran-linked Oregon Green). Within
1–2 min after Nod-factor addition, there was usually an increase in
fluorescence, followed about 10 min later by spikes in fluorescence
occurring at a rate of about one spike per minute. These spikes,
corresponding to an increase in calcium of ≈200 nM, were localized
around the nuclear region, and they were similar in terms of lag and
period to those induced by Nod factors in alfalfa. Calcium responses
were analyzed in nonnodulating pea mutants, representing seven loci
that affect early stages of the symbiosis. Mutations affecting three
loci (
sym8, sym10,
and
sym19
) abolished
Nod-factor-induced calcium spiking, whereas a normal response was seen
in peas carrying alleles of
sym2
A
,
sym7
,
sym9,
and
sym30
.
Chitin oligomers of four or five
N
-acetylglucosamine
residues could also induce calcium spiking, although the response was
qualitatively different from that induced by Nod factors; a rapid
increase in intracellular calcium was not observed, the period between
spikes was lower, and the response was not as sustained. The
chitin-oligomer-induced calcium spiking did not occur in nodulation
mutants (
sym8, sym10,
and
sym19
) that
were defective for Nod-factor-induced spiking, suggesting that this
response is related to nodulation signaling. From our data and previous
observations on the lack of mycorrhizal infection in some of the
sym
mutants, we propose a model for the potential order
of pea nodulation genes in nodulation and mycorrhizal signaling.
Bathorhodopsin structure in the room-temperature rhodopsin photosequence: picosecond time-resolved coherent anti-Stokes Raman scattering.
Authors: Popp A , Ujj L , Atkinson G H
Published: July 2002

Structural changes in the retinal chromophore during the formation of the bathorhodopsin intermediate (bathoRT) in the room-temperature rhodopsin (RhRT) photosequence (i.e., vision) are examined using picosecond time-resolved coherent anti-Stokes Raman scattering. Specifically, the retinal structure assignable to bathoRT following 8-ps excitation of RhRT is measured via vibrational Raman spectroscopy at a 200-ps time delay where the only intermediate present is bathoRT. Significant differences are observed between the C=C stretching frequencies of the retinal chromophore at low temperature where bathorhodopsin is stabilized and at room temperature where bathorhodopsin is a transient species in the RhRT photosequence. These vibrational data are discussed in terms of the formation of bathoRT, an important step in the energy storage/transduction mechanism of RhRT.
Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications.
Authors: Nadir E , Margalit H , Gallily T , Ben-Sasson S A
Published: July 2002

Microsatellites are tandem repeat sequences abundant in the genomes of higher eukaryotes and hitherto considered as "junk DNA." Analysis of a human genome representative data base (2.84 Mb) reveals a distinct juxtaposition of A-rich microsatellites and retroposons and suggests their coevolution. The analysis implies that most microsatellites were generated by a 3'-extension of retrotranscripts, similar to mRNA polyadenylylation, and that they serve in turn as "retroposition navigators," directing the retroposons via homology-driven integration into defined sites. Thus, they became instrumental in the preservation and extension of primordial genomic patterns. A role is assigned to these reiterating A-rich loci in the higher-order organization of the chromatin. The disease-associated triplet repeats are mostly found in coding regions and do not show an association with retroposons, constituting a unique set within the family of microsatellite sequences.
A model of self-thinning through local competition.
Authors: Adler F R
Published: July 2002

Explanations of self-thinning in plant populations have focused on plant shape and packing. A dynamic model based on the structure of local interactions successfully reproduces the pattern and can be approximated to identify key parameters and relationships. The approach generates testable new explanations for differences between species and populations, unifies self-thinning with other patterns in plant population dynamics, and indicates why organisms other than plants can follow the law.
Electric-field-induced Schiff-base deprotonation in D85N mutant bacteriorhodopsin.
Authors: Kolodner P , Lukashev E P , Ching Y C , Rousseau D L
Published: July 2002

The application of an external electric field to dry films of Asp-85-->Asn mutant bacteriorhodopsin causes deprotonation of the Schiff base, resulting in a shift of the optical absorption maximum from 600 nm to 400 nm. This is in marked contrast to the case of wild-type bacteriorhodopsin films, in which electric fields produce a red-shifted product whose optical properties are similar to those of the acid-blue form of the protein. This difference is due to the much weaker binding of the Schiff-base proton in the mutant protein, as indicated by its low pK of approximately 9, as compared with the value pK approximately 13 in the wild type. Other bacteriorhodopsins with lowered Schiff-base pK values should also exhibit a field-induced shift in the protonation equilibrium of the Schiff base. We propose mechanisms to account for these observations.
Localization of 17beta-hydroxysteroid dehydrogenase and characterization of testosterone in the brain of the male frog.
Authors: Mensah-Nyagan A M , Feuilloley M , Do-Rego J L , Marcual A , Lange C , Tonon M C , Pelletier G , Vaudry H
Published: July 2002

Several enzymes involved in the formation of steroids of the pregnene and pregnane series have been identified in the brain, but the biosynthesis of testosterone has never been reported in the central nervous system. In the present study, we have investigated the distribution and bioactivity of 17beta-hydroxysteroid dehydrogenase (17beta-HSD) (EC 1.1.1.62; a key enzyme that is required for the formation of testosterone and estradiol) in the brain of the male frog Rana ridibunda. By using an antiserum against human type I placental 17beta-HSD, immunoreactivity was localized in a discrete group of ependymal glial cells bordering the telencephalic ventricles. HPLC analysis of telencephalon and hypothalamus extracts combined with testosterone radioimmunoassay revealed the existence of two peaks coeluting with testosterone and 5alpha-dihydrotestosterone. After HPLC purification, testosterone was identified by gas chromatography/mass spectrometry. Incubation of telencephalon slices with [3H]pregnenolone resulted in the formation of metabolites which coeluted with progesterone, 17alpha-hydroxyprogesterone, dehydroepiandrosterone, androstenedione, testosterone, and 5alpha-dihydrotestosterone. The newly synthesized steroid comigrating with testosterone was selectively immunodetected by using testosterone antibodies. These data indicate that 17beta-HSD is expressed in a subpopulation of gliocytes in the frog telencephalon and that telencephalic cells are capable of synthesizing various androgens, including dehydroepiandrosterone, androstenedione, testosterone, and 5alpha-dihydrotestosterone.
Calmodulin controls adaptation of mechanoelectrical transduction by hair cells of the bullfrog's sacculus.
Authors: Walker R G , Hudspeth A J
Published: July 2002

Deflection of the mechanically sensitive hair bundle atop a hair cell opens transduction channels, some of which subsequently reclose during a Ca2+-dependent adaptation process. Myosin I in the hair bundle is thought to mediate this adaptation; in the bullfrog's hair cell, the relevant isozyme may be the 119-kDa amphibian myosin I beta. Because this molecule resembles other forms of myosin I, we hypothesized that calmodulin, a cytoplasmic receptor for Ca2+, regulates the ATPase activity of myosin. We identified an approximately 120-kDa calmodulin-binding protein that shares with hair-bundle myosin I the properties of being photolabeled by vanadate-trapped uridine nucleotides and immunoreactive with a monoclonal antibody raised against mammalian myosin I beta. To investigate the possibility that calmodulin mediates Ca2+-dependent adaptation, we inhibited calmodulin action and measured the results with two distinct assays. Calmodulin antagonists increased photolabeling of hair-bundle myosin I by nucleotides. In addition, when introduced into hair cells through recording electrodes, calmodulin antagonists abolished adaptation to sustained mechanical stimuli. Our evidence indicates that calmodulin binds to and controls the activity of hair-bundle myosin I, the putative adaptation motor.
The organization of seismicity on fault networks.
Authors: Knopoff L
Published: July 2002

Although models of homogeneous faults develop seismicity that has a Gutenberg-Richter distribution, this is only a transient state that is followed by events that are strongly influenced by the nature of the boundaries. Models with geometrical inhomogeneities of fracture thresholds can limit the sizes of earthquakes but now favor the characteristic earthquake model for large earthquakes. The character of the seismicity is extremely sensitive to distributions of inhomogeneities, suggesting that statistical rules for large earthquakes in one region may not be applicable to large earthquakes in another region. Model simulations on simple networks of faults with inhomogeneities of threshold develop episodes of lacunarity on all members of the network. There is no validity to the popular assumption that the average rate of slip on individual faults is a constant. Intermediate term precursory activity such as local quiescence and increases in intermediate-magnitude activity at long range are simulated well by the assumption that strong weakening of faults by injection of fluids and weakening of asperities on inhomogeneous models of fault networks is the dominant process; the heat flow paradox, the orientation of the stress field, and the low average stress drop in some earthquakes are understood in terms of the asperity model of inhomogeneous faulting.
A molecular biology-based approach to resolve the subunit orientation of lipoprotein lipase
Authors: Wong Howard , Yang Dawn , Hill John S. , Davis Richard C. , Nikazy Judith , Schotz Michael C.
Published: July 2002

The subunit orientation of a dimeric enzyme influences the mechanism of action and function. To determine the subunit arrangement of lipoprotein lipase (LPL), a molecular biology-based approach was initiated. An eight amino acid linker region was engineered between two LPL monomers and expressed in COS-7 cells. The resultant tandem-repeat molecule (LPL
TR
) was lipolytically active and had kinetic parameters, salt inhibition, cofactor-dependent activity, heparin-binding characteristics, and a functional unit size very similar to the expressed native human enzyme. By these criteria, LPL
TR
was the functional equivalent of native LPL. Considering the length of the linker peptide (no more than 24 Å), monomers in the tethered molecule were restricted to a head-to-tail subunit arrangement. Since LPL
TR
demonstrated native enzyme-like properties while constrained to this subunit arrangement, these results provide the first compelling evidence that native LPL monomers are arranged in a head-to-tail subunit orientation within the active dimer. Thus, LPL function in physiology, lipolysis, and binding to cell-surface components must now be addressed with this subunit orientation in mind. The utility of the tandem-repeat approach to resolve the subunit arrangement of an obligate dimer has been demonstrated with LPL and could be generalized for use with other oligomeric enzymes.
Polycystin:In vitrosynthesis,in vivotissue expression, and subcellular localization identifies a large membrane-associated protein
Authors: Ibraghimov-Beskrovnaya Oxana , Dackowski William R. , Foggensteiner Lukas , Coleman Nick , Thiru Sathia , Petry Linda R. , Burn Timothy C. , Connors Timothy D. , Van Raay Terence , Bradley John , Qian Feng , Onuchic Luiz F. , Watnick Terry J. , Piontek Klaus , Hakim Raymond M. , Landes Gregory M. , Germino Gregory G. , Sandford Richard , Klinger Katherine W.
Published: July 2002

The primary structure of polycystin predicts a large integral membrane protein with multiple cell recognition motifs, but its function remains unknown. Insight into polycystin’s normal function and its role in the development of autosomal dominant polycystic kidney disease (PKD1) requires the assembly of an extensive collection of molecular reagents to examine its expression and create model systems for functional studies. Development of these crucial reagents has been complicated due to the presence of transcriptionally active homologous loci. We have assembled the authentic full-length PKD1 cDNA and demonstrated expression of polycystinin vitro. Polyclonal antibodies directed against distinct extra- and intracellular domains specifically immunoprecipitatedin vitrotranslated polycystin. The panel of antibodies was used to determine localization of polycystin in renal epithelial and endothelial cell lines and tissues of fetal, adult, and cystic origins. In normal adult kidney and maturing fetal nephrons, polycystin expression was confined to epithelial cells of the distal nephron and vascular endothelial cells. Expression in the proximal nephron was only observed after injury-induced cell proliferation. Polycystin expression was confined to ductal epithelium in liver, pancreas, and breast, and restricted to astrocytes in normal brain. We report clear evidence for the membrane localization of polycystin by both tissue sections and by confocal microscopy in cultured renal and endothelial cells. Interestingly, when cultured cells made cell–cell contact, polycystin was localized to the lateral membranes of cells in contact. These data suggest that polycystin is likely to have a widespread role in epithelial cell differentiation and maturation and in cell–cell interactions.
Neurturin shares receptors and signal transduction pathways with glial cell line-derived neurotrophic factor in sympathetic neurons
Authors: Creedon Douglas J. , Tansey Malú G. , Baloh Robert H. , Osborne Patricia A. , Lampe Patricia A. , Fahrner Timothy J. , Heuckeroth Robert O. , Milbrandt Jeffrey , Johnson Eugene M.
Published: July 2002

Neurturin (NTN) is a neurotrophic factor that shares homology with glial cell line-derived neurotrophic factor (GDNF). Recently, a receptor complex has been identified for GDNF that includes the Ret tyrosine kinase receptor and a glycosylphosphatidylinositol-linked protein termed “GDNFRα.” However, differences in the phenotype of Ret and GDNF knockout animals suggest that Ret has at least one additional ligand. In this report, we demonstrate that NTN induces Ret phosphorylation in primary cultures of rat superior cervical ganglion (SCG) neurons. NTN also caused Ret phosphorylation in fibroblasts that were transfected stably with Ret and GDNFRα but not in cells expressing Ret alone. A glycosylphosphatidylinositol-linked protein also was important for NTN and GDNF signaling in SCG neurons; phosphatidylinositol-specific phospholipase C treatment of SCG cultures reduced the ability of NTN to phosphorylate Ret and the ability of NTN or GDNF to activate the mitogen-activated protein kinase pathway. NTN and GDNF also caused sustained activation of Ret and the mitogen-activated protein kinase pathway in SCG neurons. Finally, both NTN and GDNF activated the phosphatidylinositol 3-kinase pathway in SCG neurons, which may be important for the ability of NTN and GDNF to promote neuronal survival. These data indicate that NTN is a physiologically relevant ligand for the Ret receptor and suggest that NTN may have a critical role in the development of many neuronal populations.
Leishmania tarentolae
contains distinct cytosolic and mitochondrial glutaminyl–tRNA synthetase activities
Authors: Nabholz Christoph E. , Hauser Remy , Schneider André
Published: July 2002

The intracellular distribution of glutaminyl–tRNA synthetases and their role in mitochondrial tRNA import were evaluated in the ancient eukaryote
Leishmania tarentolae
. The following results were obtained: (
i
) Glutaminyl–tRNA synthetase was detected in leishmanial mitochondria. This was unexpected because it has been postulated that, in organelles, Gln-tRNA
Gln
is not formed by direct acylation of tRNA
Gln
but by enzymatic transamidation of misacylated Glu-tRNA
Gln
. (
ii
) Whereas the cytosolic extract is able to charge cytosolic and mitochondrial tRNAs
Gln
, the mitochondrial matrix extract does not aminoacylate the cytosol-specific tRNA
Gln
. This indicates that mitochondrial and cytosolic glutaminyl–tRNA synthetases are distinct. (
iii
) Seven of the 11 nucleotides that differ between the cytosolic and the mitochondrial tRNA
Gln
are sufficient to convert the cytosol-specific tRNA
Gln
into an optimal substrate for the mitochondrial enzyme. These nucleotides are arranged in three groups consisting of the nucleotides flanking the anticodon stem, the 5′ nucleotide of the anticodon, and four nucleotides within the acceptor stem. And (
iv
), it was shown that the identity elements for recognition by the mitochondrial glutaminyl–tRNA synthetase do not overlap with a previously identified sequence segment required for mitochondrial import of the tRNA
Gln
.
Evolution of trans-splicing plant mitochondrial introns in pre-Permian times
Authors: Malek Olaf , Brennicke Axel , Knoop Volker
Published: July 2002

Trans-splicing in angiosperm plant mitochondria connects exons from independent RNA molecules by means of group II intron fragments. Homologues of trans-splicing introns in the angiosperm mitochondrialnad2andnad5genes are now identified as uninterrupted group II introns in the fernsAsplenium nidusandMarsilea drummondii.These fern introns are correctly spliced from the pre-mRNA at the sites predicted from their well-conserved secondary structures. The flanking exon sequences of thenad2andnad5genes in the ferns require RNA editing, including the removal of in-frame stop codons by U-to-C changes for correct expression of the genetic information. We conclude that cis-splicing introns like the ones now identified in ferns are the ancestors of trans-splicing introns in angiosperm mitochondria. Intron disruption is apparently due to a size increase of the structurally variable group II intron domain IV followed by DNA recombination in the plant mitochondrial genome.
Multiple imprinted sense and antisense transcripts, differential methylation and tandem repeats in a putative imprinting control region upstream of mouse
Igf2
Authors: Moore T. , Constancia M. , Zubair M. , Bailleul B. , Feil R. , Sasaki H. , Reik W.
Published: July 2002

The mouse insulin-like growth factor 2 (
Igf2
) locus is a complex genomic region that produces multiple transcripts from alternative promoters. Expression at this locus is regulated by parental imprinting. However, despite the existence of putative imprinting control elements in the
Igf2
upstream region, imprinted transcriptional repression is abolished by null mutations at the linked
H19
locus. To clarify the extent to which the
Igf2
upstream region contains autonomous imprinting control elements we have performed functional and comparative analyses of the region in the mouse and human. Here we report the existence of multiple, overlapping imprinted (maternally repressed) sense and antisense transcripts that are associated with a tandem repeat in the mouse
Igf2
upstream region. Regions flanking the repeat exhibit tissue-specific parental allelic methylation patterns, suggesting the existence of tissue-specific control elements in the upstream region. Studies in
H19
null mice indicate that both parental allelic methylation and monoallelic expression of the upstream transcripts depends on an intact
H19
gene acting in cis. The homologous region in human
IGF2
is structurally conserved, with the significant exception that it does not contain a tandem repeat. Our results support the proposal that tandem repeats act to target methylation to imprinted genetic loci.
Abnormal T cell selection on nod thymic epithelium is sufficient to induce autoimmune manifestations in C57BL/6 athymic nude mice
Authors: Thomas-Vaslin Véronique , Damotte Diane , Coltey Monique , Le Douarin Nicole M. , Coutinho Antonio , Salaün Josselyne
Published: July 2002

To investigate the role of primary T cell repertoire selection in the immunopathogenesis of autoimmune diseases, pure thymic epithelium (TE) from nonobese diabetic (NOD) embryos was grafted into non autoimmune prone newborn C57BL/6 athymic mice. The results show that NOD TE selects host T cell repertoires that establish autoimmunity in otherwise nondiabetic animals. Thus, such chimeras regularly show CD4 and CD8 T cell-mediated insulitis and sialitis, in contrast with syngeneic or allogeneic chimeras produced with TE from nonautoimmune strains. This is the first demonstration that autoimmunity to pancreatic β cells and salivary glands can be established by the sole alteration of the thymic environment involved in T cell selection, regardless of the nature and presentation of both major histocompatibility complex and tissue-specific antigens on the target organ. These data indicate that T cell repertoire selection by the NOD thymic epithelium is sufficient to induce specific autoimmune characteristics in the context of an otherwise normal host.
Two binding modes reveal flexibility in kinase/response regulator interactions in the bacterial chemotaxis pathway
Authors: McEvoy Megan M. , Hausrath Andrew C. , Randolph Gannon B. , Remington S. James , Dahlquist Frederick W.
Published: July 2002

The crystal structure at 2.0-Å resolution of the complex of the
Escherichia coli
chemotaxis response regulator CheY and the phosphoacceptor-binding domain (P2) of the kinase CheA is presented. The binding interface involves the fourth and fifth helices and fifth β-strand of CheY and both helices of P2. Surprisingly, the two heterodimers in the asymmetric unit have two different binding modes involving the same interface, suggesting some flexibility in the binding regions. Significant conformational changes have occurred in CheY compared with previously determined unbound structures. The active site of CheY is exposed by the binding of the kinase domain, possibly to enhance phosphotransfer from CheA to CheY. The conformational changes upon complex formation as well as the observation that there are two different binding modes suggest that the plasticity of CheY is an essential feature of response regulator function.
Both DNA strands of antibody genes are hypermutation targets
Authors: Milstein Cesar , Neuberger Michael S. , Staden Rodger
Published: July 2002

During the maturation of the immune response, antibody genes are subjected to localized hypermutation. Mutations are not evenly distributed along the V gene; intrinsic hot spots exist that are correlated with primary sequence motifs. Although the mechanism of hypermutation remains unknown, it has been proposed to exhibit DNA strand polarity because purine residues on the coding strand are more frequently targeted for mutation than pyrimidines. However, this polarity may not be an intrinsic property of the hypermutation mechanism but a consequence of evolutionary-selected peculiarities of V gene sequences. Furthermore, the possibility that both strands are hypermutation targets has received little attention. To discriminate between these possibilities, we have analyzed the average frequency of mutations of each of the three bases of all nucleotide triplets by using large databases taken from both V and non-V mutation targets. We also have reassessed the sequence motifs associated with hot spots. We find that even in non-Ig sequences, A mutates more than T, consistent with a strand-dependent component to targeting. However, the mutation biases of triplets and of their inverted complements are correlated, demonstrating that there is a sequence-specific but strand-independent component to mutational targeting. Thus, there are two aspects of the hypermutation process that are sensitive to local DNA sequences, one that is DNA strand-dependent and the other that is not.