bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of vortex-like and non-thermal ion distributions on non-linear dust-acoustic waves
Authors: Mamun A. A. , Cairns R. A. , Shukla P. K.
Published: July 2002

The effects of vortex-like and non-thermal ion distributions are incorporated in the study of nonlinear dust-acoustic waves in an unmagnetized dusty plasma. It is found that owing to the departure from the Boltzmann ion distribution to a vortex-like phase space distribution, the dynamics of small but finite amplitude dust-acoustic waves is governed by a modified Kortweg–de Vries equation. The latter admits a stationary dust-acoustic solitary wave solution, which has larger amplitude, smaller width, and higher propagation velocity than that involving adiabatic ions. On the other hand, consideration of a non-thermal ion distribution provides the possibility of coexistence of large amplitude rarefactive as well as compressive dust-acoustic solitary waves, whereas these structures appear independently when the wave amplitudes become infinitely small. The present investigation should help us to understand the salient features of the non-linear dust-acoustic waves that have been observed in a recent numerical simulation study.
Ignition target design and robustness studies for the National Ignition Facility
Authors: Krauser William J. , Hoffman Nelson M. , Wilson Douglas C. , Wilde Bernhard H. , Varnum William S. , Harris David B. , Swenson Fritz J. , Bradley Paul A. , Haan Steven W. , Pollaine Stephen M. , Wan Alan S. , Moreno Juan C. , Amendt Peter A.
Published: July 2002

Recent results are presented from two-dimensional LASNEX [G. B. Zimmerman and W. L. Kruer, Comments Plasmas Phys. Controlled Thermonucl. Fusion 2, 51 (1975)] calculations of the indirectly driven hohlraum and ignition capsules proposed for the National Ignition Facility (NIF). The calculations concentrate on two capsule designs, the baseline design that has a bromine-doped plastic ablator, and the beryllium design that has a copper-doped beryllium ablator. Both capsules have a cryogenic fuel layer. Primary emphasis in these calculations is placed upon robustness studies detailing various sensitivities. Because of computer modeling limitations these studies fall into two categories: those performed with integrated modeling where the capsule, hohlraum, and laser rays all are modeled simultaneously with the laser power levels as the only energy input; and those performed in a capsule-only mode where an externally imposed radiative flux is applied to the exterior of the capsule, and only the capsule performance is modeled. Integrated modeling calculations address sensitivities to, e.g., the laser pointing; among other things, capsule-only calculations address yield degradation due to the growth of hydrodynamic instabilities seeded by initial surface roughnesses on the capsules. Limitations of the calculational models and directions for future research are discussed. The results of the robustness studies performed to date enhance the authors’ confidence that the NIF can achieve ignition and produce 10–15 MJ of capsule yield with one or more capsule designs.
Second harmonic generation and its interaction with relativistic plasma waves driven by forward Raman instability in underdense plasmas
Authors: Malka V. , Modena A. , Najmudin Z. , Dangor A. E. , Clayton C. E. , Marsh K. A. , Joshi C. , Danson C. , Neely D. , Walsh F. N.
Published: July 2002

High conversion efficiency (0.1%) into second harmonic light generated in the interaction of a short-pulse intense laser with underdense plasma has been observed. In this experiment the plasma is created by optical field ionization of hydrogen or helium gas. Second harmonic spectra observed in the forward direction show Stokes and anti-Stokes satellites. This is due to the interaction of the second harmonic light with large-amplitude relativistic plasma waves. Second harmonic images taken at 30° from the propagation axis show that the radiation is generated over a length of a few times the Rayleigh length and that the origin of the second harmonic light is due to the radial electron density gradients created by the ionization process and the radial ponderomotive force.
Nonlinear propagation of ion-acoustic waves in a hot magnetized plasma with vortexlike electron distribution
Authors: Mamun A. A.
Published: July 2002

Effects of external magnetic field, ion temperature, and vortexlike electron distribution are incorporated in the study of nonlinear ion-acoustic waves in a hot magnetized plasma that consists of a positively charged, hot ion fluid and trapped, as well as, free electrons. It is found that, owing to the departure from the Boltzmann electron distribution to a vortexlike one, the dynamics of small but finite amplitude ion-acoustic waves is governed by a nonlinear equation of K-dV (Korteweg-de Vries) type. The latter admits a stationary ion-acoustic solitary wave solution, which has larger amplitude, smaller width, and higher propagation velocity, than that involving isothermal electrons. The effects of external magnetic field and ion temperature on the properties of these ion-acoustic solitary structures are also discussed.
Effects of dust temperature and fast ions on gravitational instability in a self-gravitating magnetized dusty plasma
Authors: Mamun A. A.
Published: July 2002

A theoretical investigation has been made of effects of dust temperature, fast (nonthermal) ions, and external magnetic field on gravitational instability in a self-gravitating magnetized hot dusty plasma, which consists of extremely massive, negatively charged hot dust fluid, nonthermally distributed ions, and Boltzmann distributed electrons, where the gravitational force is comparable to or greater than the electrostatic force. The effects of dust temperature, fast ions, and external magnetic field have been found to modify the criterion for this gravitational instability. It has been shown that the growth rate of this gravitational instability decreases with dust temperature, fast ions, and external magnetic field, but increases with the number of free electrons, with the ratio of ion temperature to electron temperature, and with the ratio of dust mass to dust charge. The implications of this result in some astrophysical situations are briefly discussed.
Parametric study of kinetic Alfvén solitons in a two electron temperature plasma
Authors: Berthomier Matthieu , Pottelette Raymond , Treumann Rudolf A.
Published: July 2002

The nonlinear regime of the kinetic Alfvén wave is studied in a collisionless low-β plasma that is composed of a cold ion population and of two electron populations. In the one electron population plasma, it is known that solitary kinetic Alfvén waves (SKAW) propagate either at the Alfvén velocity υA or at the ion-acoustic velocity cs. In this latter case, only plasma compressions exist. In the two electron population plasma, rarefactions, as well as compressions, may exist at this velocity. Furthermore, when the electron-acoustic mode exists and when υA>υea (vea is the electron-acoustic velocity), the inertia of the cold electron component allows for the existence of compressive SKAW which propagate with a velocity lying in a limited interval above υea. When υA<vea, these solitons are rarefactive and continuously evolve from classical SKAW moving at υA to electron-acoustic-like SKAW moving at υea. The possibility of applying these results to some astrophysical plasma observations is investigated.
Review of indirect-drive ignition design options for the National Ignition Facility
Authors: Dittrich T. R. , Haan S. W. , Marinak M. M. , Pollaine S. M. , Hinkel D. E. , Munro D. H. , Verdon C. P. , Strobel G. L. , McEachern R. , Cook R. C. , Roberts C. C. , Wilson D. C. , Bradley P. A. , Foreman L. R. , Varnum W. S.
Published: July 2002

Several inertial confinement fusion (ICF) capsule designs have been proposed as possible candidates for achieving ignition by indirect drive on the National Ignition Facility (NIF) laser [Paisner et al., Laser Focus World 30, 75 (1994)]. This article reviews these designs, their predicted performance using one-, two-, and three-dimensional numerical simulations, and their fabricability. Recent design work at a peak x-ray drive temperature of 250 eV with either 900 or 1300 kJ total laser energy confirms earlier capsule performance estimates [Lindl, Phys. Plasmas 2, 3933 (1995)] that were based on hydrodynamic stability arguments. These simulations at 250 eV and others at the nominal 300 eV drive show that capsules having either copper doped beryllium (Be+Cu) or polyimide (C22H10N2O4) ablators have favorable implosion stability and material fabrication properties. Prototypes of capsules using these ablator materials are being constructed using several techniques: brazing together machined hemishells (Be+Cu), sputter deposition (Be+Cu), and monomer deposition followed by thermal processing (polyimide).
Metalorganic vapor phase epitaxial growth of a high quality GaN film using an AlN buffer layer
Authors: Amano H. , Sawaki N. , Akasaki I. , Toyoda Y.
Published: July 2002

Atmospheric pressure metalorganic vapor phase epitaxial growth and characterization of high quality GaN on sapphire (0001) substrates are reported. Using AlN buffer layers, GaN thin films with optically flat surfaces free from cracks are successfully grown. The narrowest x-ray rocking curve from the (0006) plane is 2.70′ and from the (202̄4) plane is 1.86′. Photoluminescence spectra show strong near band edge emission. The growth condition dependence of crystalline quality is also studied.
Generation of subpicosecond solitonlike optical pulses at 0.3 THz repetition rate by induced modulational instability
Authors: Tai K. , Tomita A. , Jewell J. L. , Hasegawa A.
Published: July 2002

We report the generation of 0.5 ps full width at half-maximum optical pulses at >0.3 THz (tunable) repetition rate via an induced modulational instability in a single-mode fiber. A 1.319-μm neodymium:yttrium aluminum garnet laser is chosen as the carrier wave and the initial modulation on this carrier is introduced by mixing it with an external-grating-cavity InGaAsP laser. The use of this all-optical modulating scheme and the nonlinear optical propagation effect in fiber (i.e., modulational instability) allows one to reach into the terahertz regime, which is about two orders of magnitude beyond the fastest data limited by the finite response of electronics.
Structural basis for the conformational adaptability of apolipophorin III, a helix-bundle exchangeable apolipoprotein
Authors: Wang Jianjun , Sykes Brian D. , Ryan Robert O.
Published: July 2002

The high-resolution NMR structure of apolipophorin III from the sphinx moth,
Manduca sexta
, has been determined in the lipid-free state. We show that lipid-free apolipophorin III adopts a unique helix-bundle topology that has several characteristic structural features. These include a marginally stable, up-and-down helix bundle that allows for concerted opening of the bundle about “hinged” loops upon lipid interaction and buried polar/ionizable residues and buried interhelical H-bonds located in the otherwise hydrophobic interior of the bundle that adjust protein stability and facilitate lipid-induced conformational opening. We suggest that these structural features modulate the conformational adaptability of the lipid-free helix bundle upon lipid binding and control return of the open conformation to the original lipid-free helix-bundle state. Taken together, these data provide a structural rationale for the ability of exchangeable apolipoproteins to reversibly interact with circulating lipoprotein particles.
The binding conformation of Taxol in β-tubulin: A model based on electron crystallographic density
Authors: Snyder James P. , Nettles James H. , Cornett Ben , Downing Kenneth H. , Nogales Eva
Published: July 2002

The chemotherapeutic drug Taxol is known to interact within a
specific site on β-tubulin. Although the general location of the site
has been defined by photoaffinity labeling and electron
crystallography, the original data were insufficient to make an
absolute determination of the bound conformation. We have now
correlated the crystallographic density with analysis of Taxol
conformations and have found the unique solution to be a T-shaped Taxol
structure. This T-shaped or butterfly structure is optimized within the
β-tubulin site and exhibits functional similarity to a portion of the
B9-B10 loop in the α-tubulin subunit. The model provides structural
rationalization for a sizeable body of Taxol structure–activity
relationship data, including binding affinity, photoaffinity labeling,
and acquired mutation in human cancer cells.
Point mutations and sequence variability in proteins: Redistributions of preexisting populations
Authors: Sinha Neeti , Nussinov Ruth
Published: July 2002

Here we study the effect of point mutations in proteins on the
redistributions of the conformational substates. We show that
regardless of the location of a mutation in the protein structure and
of its type, the observed movements of the backbone recur largely at
the same positions in the structures. Despite the different
interactions that are disrupted and formed by the residue substitution,
not only are the conformations very similar, but the regions that move
are also the same, regardless of their sequential or spatial distance
from the mutation. This observation leads us to conclude that, apart
from some extreme cases, the details of the interactions are not
critically important in determining the protein conformation or in
specifying which parts of the protein would be more prone to take on
different local conformations in response to changes in the sequence.
This finding further illustrates why proteins manifest a robustness
toward many mutational events. This nonuniform distribution of the
conformer population is consistently observed in a variety of protein
structural types. Topology is critically important in determining
folding pathways, kinetics, building block cutting, and anatomy trees.
Here we show that topology is also very important in determining which
regions of the protein structure will respond to sequence changes,
regardless of the sequential or spatial location of the mutation.
Genetic disruption of
PPAR
δ decreases the tumorigenicity of human colon cancer cells
Authors: Park Ben Ho , Vogelstein Bert , Kinzler Kenneth W.
Published: July 2002

Peroxisome proliferator-activated receptors (PPARs) are nuclear
hormone receptors that have been implicated in a variety of biologic
processes. The PPARδ isotype was recently proposed as a downstream
target of the adenomatous polyposis coli (APC)/β-catenin
pathway in colorectal carcinogenesis. To evaluate its role in
tumorigenesis, a PPARδ null cell line was created by targeted
homologous recombination. When inoculated as xenografts in nude mice,
PPARδ −/− cells exhibited a decreased ability to form tumors
compared with PPARδ +/− and wild-type controls. These data suggest
that suppression of PPARδ expression contributes to the
growth-inhibitory effects of the APC tumor suppressor.
Activation of Trp3 by inositol 1,4,5-trisphosphate receptors through displacement of inhibitory calmodulin from a common binding domain
Authors: Zhang Zongming , Tang Jisen , Tikunova Svetlana , Johnson J. David , Chen Zhangguo , Qin Ning , Dietrich Alexander , Stefani Enrico , Birnbaumer Lutz , Zhu Michael Xi
Published: July 2002

Mammalian homologues of
Drosophila
Trp form plasma
membrane channels that mediate Ca
2+
influx in response to
activation of phospholipase C and internal Ca
2+
store
depletion. Previous studies showed that human Trp3 is activated by
inositol 1,4,5-trisphosphate (IP
3
) receptors
(IP
3
Rs) and identified interacting domains, one on Trp and
two on IP
3
R. We now find that Trp3 binds
Ca
2+
-calmodulin (Ca
2+
/CaM) at a
site that overlaps with the IP
3
R binding domain. Using
patch-clamp recordings from inside-out patches, we further show that
Trp3 has a high intrinsic activity that is suppressed by
Ca
2+
/CaM under resting conditions, and that Trp3 is
activated by the following: a Trp-binding peptide from IP
3
R
that displaces CaM from Trp3, a myosin light chain kinase
Ca
2+
/CaM binding peptide that prevents CaM from binding
to Trp3, and calmidazolium, an inactivator of Ca
2+
/CaM.
We conclude that inhibition of the inhibitory action of CaM is a key
step of Trp3 channel activation by IP
3
Rs.
Drying-induced hydrophobic polymer collapse
Authors: ten Wolde Pieter Rein , Chandler David
Published: July 2002

We have used computer simulation to study the collapse of a hydrophobic chain in water. We find that the mechanism of collapse is much like that of a first-order phase transition. The evaporation of water in the vicinity of the polymer provides the driving force for collapse, and the rate limiting step is the nucleation of a sufficiently large vapor bubble. The study is made possible through the application of transition path sampling and a coarse-grained treatment of liquid water. Relevance of our findings to understanding the folding and assembly of proteins is discussed.
Localization of CD4+T cell epitope hotspots to exposed strands of HIV envelope glycoprotein suggests structural influences on antigen processing
Authors: Surman Sherri , Lockey Timothy D. , Slobod Karen S. , Jones Bart , Riberdy Janice M. , White Stephen W. , Doherty Peter C. , Hurwitz Julia L.
Published: July 2002

The spectrum of immunogenic epitopes presented by the H2-IAbMHC class II molecule to CD4+T cells has been defined for two different (clade B and clade D) HIV envelope (gp140) glycoproteins. Hybridoma T cell lines were generated from mice immunized by a sequential prime and boost regime with DNA, recombinant vaccinia viruses, and protein. The epitopes recognized by reactive T cell hybridomas then were characterized with overlapping peptides synthesized to span the entire gp140 sequence. Evidence of clonality also was assessed with antibodies to T cell receptor Vα and Vβ chains. A total of 80 unique clonotypes were characterized from six individual mice. Immunogenic peptides were identified within only four regions of the HIV envelope. These epitope hotspots comprised relatively short sequences (≈20–80 aa in length) that were generally bordered by regions of heavy glycosylation. Analysis in the context of the gp120 crystal structure showed a pattern of uniform distribution to exposed, nonhelical strands of the protein. A likely explanation is that the physical location of the peptide within the native protein leads to differential antigen processing and consequent epitope selection.
A physiologic signaling role for the γ-secretase-derived intracellular fragment of APP
Authors: Leissring Malcolm A. , Murphy M. Paul , Mead Tonya R. , Akbari Yama , Sugarman Michael C. , Jannatipour Mehrdad , Anliker Brigitte , Müller Ulrike , Saftig Paul , De Strooper Bart , Wolfe Michael S. , Golde Todd E. , LaFerla Frank M.
Published: July 2002

Presenilins mediate an unusual intramembranous proteolytic activity known as γ-secretase, two substrates of which are the Notch receptor (Notch) and the β-amyloid precursor protein (APP). γ-Secretase-mediated cleavage of APP, like that of Notch, yields an intracellular fragment [
A
PP
i
ntra
c
ellular
d
omain (AICD)] that forms a transcriptively active complex. We now demonstrate a functional role for AICD in regulating phosphoinositide-mediated calcium signaling. Genetic ablation of the presenilins or pharmacological inhibition of γ-secretase activity (and thereby AICD production) attenuated calcium signaling in a dose-dependent and reversible manner through a mechanism involving the modulation of endoplasmic reticulum calcium stores. Cells lacking APP (and hence AICD) exhibited similar calcium signaling deficits, and—notably—these disturbances could be reversed by transfection with APP constructs containing an intact AICD, but not by constructs lacking this domain. Our findings indicate that the AICD regulates phosphoinositide-mediated calcium signaling through a γ-secretase-dependent signaling pathway, suggesting that the intramembranous proteolysis of APP may play a signaling role analogous to that of Notch.
Bradykinin antagonist dimer, CU201, inhibits the growth of human lung cancer cell lines by a “biased agonist” mechanism
Authors: Chan Daniel , Gera Lajos , Stewart John , Helfrich Barbara , Verella-Garcia Marileila , Johnson Gary , Baron Anna , Yang Jie , Puck Theodore , Bunn Paul
Published: July 2002

All small cell (SCLCs) and many non-small cell lung cancers (NSCLCs) have neuroendocrine features including production of neuropeptides and cell surface receptors creating autocrine and paracrine growth loops. Neuropeptides bind to a family of 7-transmembrane receptors and activate heterotrimeric G proteins consisting of G
αq
and G
α12,13
. Substance P derivatives (SPDs) induced apoptosis and inhibited growth of lung cancer cells by discoordinately inhibiting G
αq
and stimulating G
α12,13
. However, these SPDs had low potency and short half-lives. In this report we show that a bradykinin antagonist dimer, CU201, inhibited the growth of SCLC and NSCLC cell lines with or without multidrug-resistant proteins and was 10-fold more potent with a longer plasma half-life than SPDs. Bradykinin agonists in either monomeric or dimeric form and monomeric bradykinin antagonist have no effect on lung cancer cell growth. The dimeric linking moiety of the two molecules was created, requiring a sufficient number of carbon chains to provide critical spacing between the two antagonists. CU201 inhibited intracellular Ca
2+
release in response to bradykinin, indicating blockage of the G
αq
signal, and stimulated c-Jun kinases, indicating stimulation of the G
α12,13
pathway. CU201-induced apoptosis was preceded by unique changes in apparent nuclear DNA binding and by c-Jun kinase and caspase-3 activation. At the concentration at which CU201 inhibited the growth of the cancer cells, it had no effect on the growth of normal lung cells
in vitro
. CU201 and similar compounds offer hope of becoming a new form of targeted therapy for tumors with neuroendocrine properties.
Evolutionary conservation of zebrafish linkage group 14 with frequently deleted regions of human chromosome 5 in myeloid malignancies
Authors: Liu Ting Xi , Zhou Yi , Kanki John P. , Deng Min , Rhodes Jennifer , Yang Hong Wei , Sheng Xiao Ming , Zon Leonard I. , Look A. Thomas
Published: July 2002

Recurring interstitial loss of all or part of the long arm of chromosome 5, del(5q), is a hallmark of myelodysplastic syndrome and acute myeloid leukemia. Although the genes affected by these changes have not been identified, two critically deleted regions (CDRs) are well established. We have identified 76 zebrafish cDNAs orthologous to genes located in these 5q CDRs. Radiation hybrid mapping revealed that 33 of the 76 zebrafish orthologs are clustered in a genomic region on linkage group 14 (LG14). Fifteen others are located on LG21, and two on LG10. Although there are large blocks of conserved syntenies, the gene order between human and zebrafish is extensively inverted and transposed. Thus, intrachromosomal rearrangements and inversions appear to have occurred more frequently than translocations during evolution from a common chordate ancestor. Interestingly, of the 33 orthologs located on LG14, three have duplicates on LG21, suggesting that the duplication event occurred early in the evolution of teleosts. Murine orthologs of human 5q CDR genes are distributed among three chromosomes, 18, 11, and 13. The order of genes within the three syntenic mouse chromosomes appears to be more colinear with the human order, suggesting that translocations occurred more frequently than inversions during mammalian evolution. Our comparative map should enhance understanding of the evolution of the del(5q) chromosomal region. Mutant fish harboring deletions affecting the 5q CDR syntenic region may provide useful animal models for investigating the pathogenesis of myelodysplastic syndrome and acute myeloid leukemia.
Evidence for two active branches for electron transfer in photosystem I
Authors: Guergova-Kuras Mariana , Boudreaux Brent , Joliot Anne , Joliot Pierre , Redding Kevin
Published: July 2002

All photosynthetic reaction centers share a common structural theme. Two related, integral membrane polypeptides sequester electron transfer cofactors into two quasi-symmetrical branches, each of which incorporates a quinone. In type II reaction centers [photosystem (PS) II and proteobacterial reaction centers], electron transfer proceeds down only one of the branches, and the mobile quinone on the other branch is used as a terminal acceptor. PS I uses iron-sulfur clusters as terminal acceptors, and the quinone serves only as an intermediary in electron transfer. Much effort has been devoted to understanding the unidirectionality of electron transport in type II reaction centers, and it was widely thought that PS I would share this feature. We have tested this idea by examiningin vivokinetics of electron transfer from the quinone in mutant PS I reaction centers. This transfer is associated with two kinetic components, and we show that mutation of a residue near the quinone in one branch specifically affects the faster component, while the corresponding mutation in the other branch specifically affects the slower component. We conclude that both electron transfer branches in PS I are active.
β-Amyloid peptide blocks the response of α7-containing nicotinic receptors on hippocampal neurons
Authors: Liu Qing-song , Kawai Hideki , Berg Darwin K.
Published: July 2002

Alzheimer's disease produces a devastating decline in mental
function, with profound effects on learning and memory. Early
consequences of the disease include the specific loss of cholinergic
neurons in brain, diminished cholinergic signaling, and the
accumulation of β-amyloid peptide in neuritic plaques. Of the
nicotinic acetylcholine receptors at risk, the most critical may be
those containing the α7 gene product (α7-nAChRs), because they are
widespread, have a high relative permeability to calcium, and regulate
numerous cellular events in the nervous system. With the use of
whole-cell patch–clamp recording we show here that nanomolar
concentrations of β-amyloid peptides specifically and reversibly
block α7-nAChRs on rat hippocampal neurons in culture. The block is
noncompetitive, voltage-independent, and use-independent and is
mediated through the N-terminal extracellular domain of the receptor.
It does not appear to require either calcium influx or G protein
activation. β-Amyloid blockade is likely to be a common feature of
α7-nAChRs because it applies to the receptors at both
somato-dendritic and presynaptic locations on rat hippocampal neurons
and extends to homologous receptors on chick ciliary ganglion neurons
as well. Because α7-nAChRs in the central nervous system are thought
to have numerous functions and recently have been implicated in
learning and memory, impaired receptor function in this case may
contribute to cognitive deficits associated with Alzheimer's disease.
Expression and disruption of the
Arabidopsis TOR
(target of rapamycin) gene
Authors: Menand Benoît , Desnos Thierry , Nussaume Laurent , Berger Frédéric , Bouchez David , Meyer Christian , Robaglia Christophe
Published: July 2002

TOR (target of rapamycin) protein kinases were identified in yeasts, mammals, and
Drosophila
as central controllers of cell growth in response to nutrient and growth factors. Here we show that
Arabidopsis thaliana
possesses a single
TOR
gene encoding a protein able to complex with yeast 12-kDa FK506-binding protein and rapamycin despite the insensitivity of
Arabidopsis
vegetative growth to rapamycin. Analysis of two T-DNA insertion mutants shows that disruption of
AtTOR
leads to the premature arrest of endosperm and embryo development. A T-DNA-mediated translational fusion of
AtTOR
with the
GUS
reporter gene allows us to show that
AtTOR
is expressed in primary meristem, embryo, and endosperm, but not in differentiated cells. The implications of these features for the plant TOR pathway are discussed.
The chaperone GroEL is required for the final assembly of the molybdenum-iron protein of nitrogenase
Authors: Ribbe Markus W. , Burgess Barbara K.
Published: July 2002

It is known that an E146D site-directed variant of the
Azotobacter vinelandii
iron protein (Fe protein) is
specifically defective in its ability to participate in iron-molybdenum
cofactor (FeMoco) insertion. Molybdenum-iron protein (MoFe protein)
from the strain expressing the E146D Fe protein is partially (≈45%)
FeMoco deficient. The “free” FeMoco that is not inserted
accumulates in the cell. We were able to insert this “free”
FeMoco into the partially pure FeMoco-deficient MoFe protein. This
insertion reaction required crude extract of the Δ
nifHDK A.
vinelandii
strain CA12, Fe protein and MgATP. We used this as
an assay to purify a required “insertion” protein. The purified
protein was identified as GroEL, based on the molecular mass of its
subunit (58.8 kDa), crossreaction with commercially available
antibodies raised against
E. coli
GroEL, and its
NH
2
-terminal polypeptide sequence. The
NH
2
-terminal polypeptide sequence showed identity of up to
84% to GroEL from various organisms. Purified GroEL of
A.
vinelandii
alone or in combination with MgATP and Fe protein
did not support the FeMoco insertion into pure FeMoco-deficient MoFe
protein, suggesting that there are still other proteins and/or
factors missing. By using GroEL-containing extracts from a
Δ
nifHDK
strain of
A. vinelandii
CA12
along with FeMoco, Fe protein, and MgATP, we were able to supply all
required proteins and/or factors and obtained a fully active
reconstituted E146D
nifH
MoFe protein. The involvement
of the molecular chaperone GroEL in the insertion of a metal cluster
into an apoprotein may have broad implications for the maturation of
other metalloenzymes.
Protein quantification from complex protein mixtures using a proteomics methodology with single-cell resolution
Authors: Zhang Hong-Tao , Kacharmina Janet E. , Miyashiro Kevin , Greene Mark I. , Eberwine James
Published: July 2002

We have developed an extremely sensitive technique, termed
immuno-detection amplified by T7 RNA polymerase (IDAT) that is capable
of monitoring proteins, lipids, and metabolites and their modifications
at the single-cell level. A double-stranded oligonucleotide containing
the T7 promoter is conjugated to an antibody (Ab), and then T7 RNA
polymerase is used to amplify RNA from the double-stranded
oligonucleotides coupled to the Ab in the Ab-antigen complex. By using
this technique, we are able to detect the p185
her2/neu
receptor from the crude lysate of T6–17 cells at 10
−13
dilution, which is 10
9
-fold more sensitive than the
conventional ELISA method. Single-chain Fv fragments or complementarity
determining region peptides of the Ab also can be substituted for the
Ab in IDAT. In a modified protocol, the oligonucleotide has been
coupled to an Ab against a common epitope to create a universal
detector species. With the linear amplification ability of T7 RNA
polymerase, IDAT represents a significant improvement over immuno-PCR
in terms of sensitivity and has the potential to provide a robotic
platform for proteomics.
Elucidation of the function of lipoprotein-sorting signals that determine membrane localization
Authors: Masuda Kazuhiro , Matsuyama Shin-ichi , Tokuda Hajime
Published: July 2002

Escherichia coli
lipoproteins are anchored to the inner or outer membrane depending on the residue at position 2. Aspartate at this position makes lipoproteins specific to the inner membrane, whereas other residues cause the release of lipoproteins from the inner membrane in a manner dependent on both ATP binding cassette (ABC) transporter LolCDE and molecular chaperone LolA, followed by LolB-dependent localization in the outer membrane. The function of lipoprotein-sorting signals was examined in proteoliposomes reconstituted from LolCDE and lipoproteins. The release of outer membrane-specific lipoproteins was inhibited on reconstitution with other outer membrane-specific, but not inner membrane-specific, lipoproteins. Outer membrane-specific lipoproteins stimulated ATP hydrolysis by LolCDE whereas inner membrane-specific ones did not. LolA was not required for the stimulation of ATP hydrolysis. These results revealed a previously undocumented function of aspartate at position 2, i.e., lipoproteins having this signal avoid being recognized by LolCDE, thereby remaining in the inner membrane.
Effects of estrogen on growth plate senescence and epiphyseal fusion
Authors: Weise Martina , De-Levi Stacy , Barnes Kevin M. , Gafni Rachel I. , Abad Veronica , Baron Jeffrey
Published: July 2002

Estrogen is critical for epiphyseal fusion in both young men and
women. In this study, we explored the cellular mechanisms by which
estrogen causes this phenomenon. Juvenile ovariectomized female rabbits
received either 70 μg/kg estradiol cypionate or vehicle i.m. once a
week. Growth plates from the proximal tibia, distal tibia, and distal
femur were analyzed after 2, 4, 6, or 8 weeks of treatment. In
vehicle-treated animals, there was a gradual senescent decline in
tibial growth rate, rate of chondrocyte proliferation, growth plate
height, number of proliferative chondrocytes, number of hypertrophic
chondrocytes, size of terminal hypertrophic chondrocytes, and column
density. Estrogen treatment accelerated the senescent decline in all of
these parameters. In senescent growth plates, epiphyseal fusion was
observed to be an abrupt event in which all remaining chondrocytes were
rapidly replaced by bone elements. Fusion occurred when the rate of
chondrocyte proliferation approached zero. Estrogen caused this
proliferative exhaustion and fusion to occur earlier. Our data suggest
that (
i
) epiphyseal fusion is triggered when the
proliferative potential of growth plate chondrocytes is exhausted; and
(
ii
) estrogen does not induce growth plate ossification
directly; instead, estrogen accelerates the programmed senescence of
the growth plate, thus causing earlier proliferative exhaustion and
consequently earlier fusion.
Replication-induced transcription of an autorepressed gene: The replication initiator gene of plasmid P1
Authors: Mukhopadhyay Suman , Chattoraj Dhruba K.
Published: July 2002

The replication origin of plasmid P1 contains an array of five repeats (iterons) that bind the plasmid-encoded initiator RepA. Within the array lies the
repA
promoter, which becomes largely repressed on RepA binding (autorepression). One might expect that extra iterons produced on plasmid replication would titrate RepA and release the repression. The promoter, however, is induced poorly by extra iterons. The P1 copy number is reduced by extra iterons in the presence of the autorepressed
repA
gene but not when additional RepA is provided from constitutive sources. It has been proposed that the iteron-bound RepA couples with the promoter-bound RepA and thereby maintains repression. Although not the product of replication, we find that the act of replication itself can renew RepA synthesis. Replication apparently cleans the promoter of bound RepA and provides a window of opportunity for
repA
transcription. We propose that replication-induced transcription is required to ensure initiator availability in a system that is induced poorly when challenged with additional initiator binding sites.
Antiapoptotic role of the p38 mitogen-activated protein kinase–myocyte enhancer factor 2 transcription factor pathway during neuronal differentiation
Authors: Okamoto Shu-ichi , Krainc Dimitri , Sherman Katerina , Lipton Stuart A.
Published: July 2002

Myocyte enhancer factor 2 (MEF2) is in the MADS (MCM1agamous-deficiens-serum response factor) family of transcription factors. Although MEF2 is known as a myogenic factor, the expression pattern of the MEF2 family of genes (MEF2A-D) in developing brain also suggests a role in neurogenesis. Here we show that transfection with MEF2C, the predominant form in mammalian cerebral cortex, induces a mixed neuronal/myogenic phenotype in undifferentiated P19 precursor cells. During retinoic acid-induced neurogenesis of these cells, a dominant negative form of MEF2 enhances apoptosis but does not affect cell division. The mitogen-activated protein kinase p38α activates MEF2C. Dominant negative p38α also enhances apoptotic death of differentiating neurons, but these cells can be rescued from apoptosis by coexpression of constitutively active MEF2C. These findings suggest that the p38α/MEF2 pathway prevents cell death during neuronal differentiation.
Genome-wide scan for body composition in pigs reveals important role of imprinting
Authors: de Koning Dirk-Jan , Rattink Annemieke P. , Harlizius Barbara , van Arendonk Johan A. M. , Brascamp E. W. , Groenen Martien A. M.
Published: July 2002

The role of imprinting in body composition was investigated in an experimental cross between Chinese Meishan pigs and commercial Dutch pigs. A whole-genome scan revealed significant evidence for five quantitative trait loci (QTL) affecting body composition, of which four were imprinted. Imprinting was tested with a statistical model that separated the expression of paternally and maternally inherited alleles. For back fat thickness, a paternally expressed QTL was found onSus scrofachromosome 2 (SSC2), and a Mendelian-expressed QTL was found on SSC7. In the same region of SSC7, a maternally expressed QTL affecting muscle depth was found. Chromosome 6 harbored a maternally expressed QTL on the short arm and a paternally expressed QTL on the long arm, both affecting intramuscular fat content. The individual QTL explained from 2% up to 10% of the phenotypic variance. The known homologies to human and mouse did not reveal positional candidate genes. This study demonstrates that testing for imprinting should become a standard procedure to unravel the genetic control of multifactorial traits.
Functional expression and characterization of a
Drosophila
odorant receptor in a heterologous cell system
Authors: Wetzel Christian H. , Behrendt Hans-Jörg , Gisselmann Günter , Störtkuhl Klemens F. , Hovemann Bernd , Hatt Hanns
Published: July 2002

Odorant receptors (ORs) constitute the molecular basis for the detection of volatile odorous molecules and the perception of smell. Our understanding of chemical senses has been greatly expanded by the discovery of the OR gene families in vertebrates and in the nematode
Caenorhabditis elegans
. Recently, candidate
Drosophila
OR genes have been identified. The putative ORs do not possess any primary sequence identity with known vertebrate or
C. elegans
receptors, but belong to the family of G protein-coupled receptors according to their predicted seven transmembrane topology. To prove olfactory function of these proteins, we expressed a member of the putative
Drosophila
OR gene family, Or43a, in
Xenopus
laevis
oocytes. Using two-electrode voltage-clamp recording we identified four odors (cyclohexanone, cyclohexanol, benzaldehyde, and benzyl alcohol) that activated the receptor at low micromolar concentration and structurally related substances that did not. This report shows the function and specificity of a member of the recently identified family of
Drosophila
ORs expressed in a heterologous system.
Treatment of spinal muscular atrophy by sodium butyrate
Authors: Chang Jan-Gowth , Hsieh-Li Hsiu-Mei , Jong Yuh-Jyh , Wang Nancy M. , Tsai Chang-Hai , Li Hung
Published: July 2002

Spinal muscular atrophy (SMA) is an autosomal recessive disease
characterized by degeneration of the anterior horn cells of the spinal
cord, leading to muscular paralysis with muscular atrophy. No effective
treatment of this disorder is presently available. Studies of the
correlation between disease severity and the amount of survival motor
neuron (SMN) protein have shown an inverse relationship. We report that
sodium butyrate effectively increases the amount of exon 7-containing
SMN protein in SMA lymphoid cell lines by changing the alternative
splicing pattern of exon 7 in the
SMN
2 gene.
In
vivo
, sodium butyrate treatment of SMA-like mice resulted in
increased expression of SMN protein in motor neurons of the spinal cord
and resulted in significant improvement of SMA clinical symptoms. Oral
administration of sodium butyrate to intercrosses of heterozygous
pregnant knockout-transgenic SMA-like mice decreased the birth rate of
severe types of SMA-like mice, and SMA symptoms were ameliorated for
all three types of SMA-like mice. These results suggest that sodium
butyrate may be an effective drug for the treatment of human SMA
patients.
Gene program for cardiac cell survival induced by transient ischemia in conscious pigs
Authors: Depre Christophe , Tomlinson James E. , Kudej Raymond K. , Gaussin Vinciane , Thompson Erika , Kim Song-Jung , Vatner Dorothy E. , Topper James N. , Vatner Stephen F.
Published: July 2002

Therapy for ischemic heart disease has been directed traditionally at limiting cell necrosis. We determined by genome profiling whether ischemic myocardium can trigger a genetic program promoting cardiac cell survival, which would be a novel and potentially equally important mechanism of salvage. Although cardiac genomics is usually performed in rodents, we used a swine model of ischemia/reperfusion followed by ventricular dysfunction (stunning), which more closely resembles clinical conditions. Gene expression profiles were compared by subtractive hybridization between ischemic and normal tissue of the same hearts. About one-third (23/74) of the nuclear-encoded genes that were up-regulated in ischemic myocardium participate in survival mechanisms (inhibition of apoptosis, cytoprotection, cell growth, and stimulation of translation). The specificity of this response was confirmed by Northern blot and quantitative PCR. Unexpectedly, this program also included genes not previously described in cardiomyocytes. Up-regulation of survival genes was more profound in subendocardium over subepicardium, reflecting that this response in stunned myocardium was proportional to the severity of the ischemic insult. Thus, in a swine model that recapitulates human heart disease, nonlethal ischemia activates a genomic program of cell survival that relates to the time course of myocardial stunning and differs transmurally in relation to ischemic stress, which induced the stunning. Understanding the genes up-regulated during myocardial stunning, including those not previously described in the heart, and developing strategies that activate this program may open new avenues for therapy in ischemic heart disease.
Increase of androgen-induced cell death and androgen receptor transactivation by BRCA1 in prostate cancer cells
Authors: Yeh Shuyuan , Hu Yueh-Chiang , Rahman Mujib , Lin Hui-Kuan , Hsu Cheng-Lung , Ting Huei-Ju , Kang Hong-Yo , Chang Chawnshang
Published: July 2002

Although mutations of the breast cancer susceptibility gene 1
(BRCA1) may play important roles in breast and prostate cancers, the
detailed mechanism linking the functions of BRCA1 to these two
hormone-related tumors remains to be elucidated. Here, we report that
BRCA1 interacts with androgen receptor (AR) and enhances AR target
genes, such as p21
(WAF1/CIP1)
, that may result in the
increase of androgen-induced cell death in prostate cancer cells. The
BRCA1-enhanced AR transactivation can be further induced
synergistically with AR coregulators, such as CBP, ARA55, and ARA70.
Together, these data suggest that the BRCA1 may function as an AR
coregulator and play positive roles in androgen-induced cell death in
prostate cancer cells and other androgen/AR target organs.
Deformation and seismicity of Taiwan
Authors: Vita-Finzi Claudio
Published: July 2002

14
C-dated Holocene coastal uplift, conventional and
satellite geodetic measurements, and coseismic and aseismic fault slip
reveal the pattern of distributed deformation at Taiwan resulting from
convergence between the Philippine Sea plate and Eurasia; as in other
subduction orogenic settings, the locus of strain release and
accumulation is strongly influenced by changes in fault geometry across
strike. Uplift evidence from the islands of Lutao and Lanhsu is
consistent with progressive oblique collision between the Luzon arc and
the Chinese continental margin. In the Coastal Range, geodetic and
seismic records show that shortening is taken up serially by
discontinuous slip on imbricate faults. The geodetic data point to net
extension across the Central Range, but deformed Holocene shorelines in
the Hengchun Peninsula at its southern extremity suggest that the
extension is a superficial effect partly caused by blind reverse
faulting. The fastest shortening rates indicated by geodesy are
recorded on the Longitudinal Valley fault and across the Chukou fault
within the fold-and-thrust belt. In the former, the strain is
dissipated mainly as aseismic reverse and strike-slip displacement. In
contrast, the fold-and-thrust belt has witnessed five earthquakes with
magnitudes of 6.5 or above in the 20th century, including the 1999.9.21
Chi-Chi earthquake (magnitude ≈ 7.6) on a branch of the Chukou fault.
The neotectonic and geodetic data for Taiwan as a whole suggest that
the fold-and-thrust belt will continue to host the majority of great
earthquakes on the island.
A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species
Authors: Allander Tobias , Emerson Suzanne U. , Engle Ronald E. , Purcell Robert H. , Bukh Jens
Published: July 2002

Identification of previously unrecognized viral agents in serum or
plasma samples is of great medical interest but remains a major
challenge, primarily because of abundant host DNA. The current methods,
library screening or representational difference analysis (RDA), are
very laborious and require selected sample sets. We have developed a
simple and reproducible method for discovering viruses in single serum
samples that is based on DNase treatment of the serum followed by
restriction enzyme digestion and sequence-independent single primer
amplification (SISPA) of the fragments, and have evaluated its
performance on known viruses. Both DNA viruses and RNA viruses at a
concentration of ≈10
6
genome equivalents per ml were
reproducibly identified in 50 μl of serum. While evaluating the
method, two previously unknown parvoviruses were discovered in the
bovine sera used as diluent. The near complete genome sequence of each
virus was determined; their classification as two species
(provisionally named bovine parvoviruses 2 and 3) was confirmed by
phylogenetic analysis. Both viruses were found to be frequent
contaminants of commercial bovine serum. DNase treatment of serum
samples may prove to be a very useful tool for virus discovery. The
DNase-SISPA method is suitable for screening of a large number of
samples and also enables rapid sequence determination of high-titer
viruses.