bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetostatic atmospheres possessing identical invariants of ideal magnetohydrodynamics
Authors: Manchester Ward , Low B. C.
Published: July 2002

A physical analysis is presented of two distinct families of two-dimensional (2D) analytical solutions for isothermal periodic magnetostatic atmospheres in uniform gravity, one arrived at by Dungey and the other arrived at by Low and Manchester. It is demonstrated that particular members of the two families of 2D equilibria may be generated from the same planar state by plasma displacements which move the system through continuous sequences of equilibria while ensuring flux freezing. The two families of solutions both possess undulating magnetic field lines but geometrically different flux surfaces. The Dungey solutions can be created from a planar state by an undulating deformation whose spatial variation is along the field lines. By contrast, the 2D plane of variation of the Low-Manchester solutions lies at an angle to the field lines of the planar state. As a result, a mixed mode of undulating, interchange and shearing displacements must be made to the planar state to produce the more complex 2D state. Finally, the physical properties of these topologically equivalent states, including the magnetic and electrical helicities and the hydromagnetic potential energy, as introduced by Mouschovias, are discussed in terms of the variational principles of Kruskal and Kulsrud.
Numerical study of a plasma opening switch conduction phase
Authors: Zabaydullin Oleg Z.
Published: July 2002

Dynamics of a Plasma Opening Switch (POS) during a conduction phase is numerically studied within the frame of a two-dimensional two-fluid system of magnetohydrodynamic (MHD) equations. The initial conditions for simulations are chosen to ensure the fast magnetic field propagation to a load plasma edge near the cathode. Simulations demonstrate that the POS dynamics depends on two plasma parameters: number of ions near the cathode and electron Hall parameter. It is shown that with respect to these parameters one of the three following regimes of POS operation can occur: dominant Hall effect, dominant MHD effects, and intermediate regime with equal influence of Hall and MHD effects. Two sets of simulations are carried out to derive the numerical scalings for conduction current and for conduction time of each of these regimes. The numerical scalings correlate with scalings proposed for the HAWK generator.
Effect of edge biasing on electrostatic fluctuations and particle transport in a nonfusion magnetoplasma
Authors: Riccardi C. , Bevilacqua C. , Chiodini G. , Fontanesi M.
Published: July 2002

This paper concerns experiments about the role of a radial electric field on the plasma turbulence in a toroidal magnetoplasma, and the possibility of anomalous transport reduction through the application of external biasing potentials to the plasma edge. The experiments show, for positive applied bias potential, a progressive reduction of radial anomalous particle flux, as well as electrostatic fluctuations. Some results on statistical and spectral properties of plasma and density fluctuations are reported.
Interference peaks in double-crystal x-ray rocking curves of laser structures
Authors: Chu X. , Tanner B. K.
Published: July 2002

Interference peaks in double-crystal x-ray rocking curves have been observed in GaAlAs laser structures. The interference has been shown to arise from phase coherence of the x-ray waves across a thin heteroepitaxial layer sandwiched between two layers of equal composition. It is shown that the interference fringes can be used to measure active layer thicknesses to ±200 Å. This is despite the fact that the active layer peak cannot be resolved in the rocking curve.
Observation of Néel structure walls on the surface of 1.4-μm-thick magnetic films using spin-polarized scanning electron microscopy
Authors: Koike K. , Matsuyama H. , Hayakawa K. , Mitsuoka K. , Narishige S. , Sugita Y. , Shiiki K. , Saka C.
Published: July 2002

Néel-type surface magnetic wall structure is observed on thick samples such as 1.4-μm-thick Permalloy polycrystal film and 1-μm-thick Co-based amorphous films. The structure is observed by using spin-polarized scanning electron microscopy. These observations are consistent with Hubert’s two-dimensional domain wall model for thick films [Z. Angew. Phys. 32, 58 (1971)].
Subsurface molecule formation in hydrogen-implanted graphite
Authors: Möller W. , Scherzer B. M. U.
Published: July 2002

A saturated bilayer of hydrogen isotopes has been formed in graphite by implanting protons and deuterons at different energies. Residual gas analysis during thermal desorption strongly suggests that hydrogen atoms recombine locally in the bulk of the damaged material and diffuse to the surface in molecular form. This model of local recombination and molecular diffusion is consistent with the predictions of the local saturation model. It also explains recent data of the low-energy chemical erosion during hydrogen bombardment at room temperature.
Simultaneous, multiple wavelength lasing of (Er, Nd):Y3Al5O12
Authors: Shi W. Q. , Kurtz R. , Machan J. , Bass M. , Birnbaum M. , Kokta M.
Published: July 2002

Simultaneous lasing of both Er3+ and Nd3+ ions in yttrium aluminum garnet is reported. The crystal was doped with 15% Er3+ and 1% Nd3+ ions. The Er3+ ions lased at 2.94 μm and the Nd3+ ions in a broadband from 1.01 to 1.15 μm with a strong peak at 1.064 μm. Significant ion-ion interaction is suggested by the drastically altered fluorescent lifetimes and unusual lasing properties.
In silico
chromosome staining: Reconstruction of Giemsa bands from the whole human genome sequence
Authors: Niimura Yoshihito , Gojobori Takashi
Published: July 2002

Giemsa staining has been used for identifying individual human chromosomes. Giemsa-dark and -light bands generally are thought to correspond to GC-poor and GC-rich regions; however, several experiments showed that the correspondence is quite poor. To elucidate the precise relationship between GC content and Giemsa banding patterns, we developed an “
in silico
chromosome staining” method for reconstructing Giemsa bands computationally from the whole human genome sequence. Here we show that 850-level Giemsa bands are best correlated with the difference in GC content between a local window of 2.5 megabases and a regional window of 9.3 megabases along a chromosome. The correlations are of strong statistical significance for almost all 43 chromosomal arms. Our results clearly show that Giemsa-dark bands are
locally
GC-poor regions compared with the flanking regions. These findings are consistent with the model that matrix-associated regions, which are known to be AT-rich, are present more densely in Giemsa-dark bands than in -light bands.
The intramembrane cleavage site of the amyloid precursor protein depends on the length of its transmembrane domain
Authors: Lichtenthaler Stefan F. , Beher Dirk , Grimm Heike S. , Wang Rong , Shearman Mark S. , Masters Colin L. , Beyreuther Konrad
Published: July 2002

Proteolytic processing of the amyloid precursor protein by β-secretase generates C99, which subsequently is cleaved by γ-secretase, yielding the amyloid β peptide (Aβ). This γ-cleavage occurs within the transmembrane domain (TMD) of C99 and is similar to the intramembrane cleavage of Notch. However, Notch and C99 differ in their site of intramembrane cleavage. The main γ-cleavage of C99 occurs in the middle of the TMD, whereas the cleavage of Notch occurs close to the C-terminal end of the TMD, making it unclear whether both are cleaved by the same protease. To investigate whether γ-cleavage always occurs in the middle of the TMD of C99 or may also occur at the end of the TMD, we generated C99-mutants with an altered length of the TMD and analyzed their γ-cleavage in COS7 cells. The C terminus of Aβ and thus the site of γ-cleavage were determined by using monoclonal antibodies and mass spectrometry. Compared with C99-wild type (wt), most mutants with an altered length of the TMD changed the cleavage site of γ-secretase, whereas control mutants with mutations outside the TMD did not. Thus, the length of the whole TMD is a major determinant for the cleavage site of γ-secretase. Moreover, the C99-mutants were not only cleaved at one site but at two sites within their TMD. One cleavage site was located around the middle of the TMD, regardless of its actual length. An additional cleavage occurred within the N-terminal half of their TMD and thus at the opposite side of the Notch cleavage site.
The Pythagorean Theorem: II. The infinite discrete case
Authors: Kadison Richard V.
Published: July 2002

The study of the Pythagorean Theorem and variants of it as the basic result of noncommutative, metric, Euclidean Geometry is continued. The emphasis in the present article is the case of infinite discrete dimensionality.
Crystal structure of the OpcA integral membrane adhesin from
Neisseria
meningitidis
Authors: Prince Stephen M. , Achtman Mark , Derrick Jeremy P.
Published: July 2002

OpcA is an integral outer membrane protein from
Neisseria meningitidis
, the causative agent of meningococcal meningitis and septicemia. It mediates the adhesion of
N. meningitidis
to epithelial and endothelial cells by binding to vitronectin and proteoglycan cell-surface receptors. Here, we report the determination of the crystal structure of OpcA to 2.0 Å resolution. OpcA adopts a 10-stranded β-barrel structure with extensive loop regions that protrude above the predicted surface of the membrane. The second external loop adopts an unusual conformation, traversing the axis of the β-barrel and apparently blocking formation of a pore through the membrane. Loops 2, 3, 4, and 5 associate to form one side of a crevice in the external surface of the structure, the other side being formed by loop 1. The crevice is lined by positively charged residues and would form an ideal binding site for proteoglycan polysaccharide. The structure, therefore, suggests a model for how adhesion of this important human pathogen to proteoglycan is mediated at the molecular level.
How native-state topology affects the folding of dihydrofolate reductase and interleukin-1β
Authors: Clementi Cecilia , Jennings Patricia A. , Onuchic José N.
Published: July 2002

The overall structure of the transition-state and intermediate ensembles observed experimentally for dihydrofolate reductase and interleukin-1β can be obtained by using simplified models that have almost no energetic frustration. The predictive power of these models suggests that, even for these very large proteins with completely different folding mechanisms and functions, real protein sequences are sufficiently well designed, and much of the structural heterogeneity observed in the intermediates and the transition-state ensembles is determined by topological effects.
Arabidopsis
nph1 and npl1: Blue light receptors that mediate both phototropism and chloroplast relocation
Authors: Sakai Tatsuya , Kagawa Takatoshi , Kasahara Masahiro , Swartz Trevor E. , Christie John M. , Briggs Winslow R. , Wada Masamitsu , Okada Kiyotaka
Published: July 2002

UV-A/blue light acts to regulate a number of physiological
processes in higher plants. These include light-driven chloroplast
movement and phototropism. The
NPH1
gene of
Arabidopsis
encodes an autophosphorylating protein
kinase that functions as a photoreceptor for phototropism in response
to low-intensity blue light. However,
nph1
mutants have
been reported to exhibit normal phototropic curvature under
high-intensity blue light, indicating the presence of an additional
phototropic receptor. A likely candidate is the nph1 homologue, npl1,
which has recently been shown to mediate the avoidance response of
chloroplasts to high-intensity blue light in
Arabidopsis.
Here we demonstrate that npl1, like nph1,
noncovalently binds the chromophore flavin mononucleotide (FMN) within
two specialized PAS domains, termed LOV domains. Furthermore, when
expressed in insect cells, npl1, like nph1, undergoes light-dependent
autophosphorylation, indicating that npl1 also functions as a light
receptor kinase. Consistent with this conclusion, we show that a
nph1npl1
double mutant exhibits an impaired phototropic
response under both low- and high-intensity blue light. Hence, npl1
functions as a second phototropic receptor under high fluence rate
conditions and is, in part, functionally redundant to nph1. We also
demonstrate that both chloroplast accumulation in response to
low-intensity light and chloroplast avoidance movement in response to
high-intensity light are lacking in the
nph1npl1
double
mutant. Our findings therefore indicate that nph1 and npl1 show
partially overlapping functions in two different responses,
phototropism and chloroplast relocation, in a fluence rate-dependent
manner.
Elucidating the mechanism of familial amyloidosis– Finnish type: NMR studies of human gelsolin domain 2
Authors: Kazmirski Steven L. , Howard Mark J. , Isaacson Rivka L. , Fersht Alan R.
Published: July 2002

Familial amyloidosis–Finnish type (FAF) results from a single
mutation at residue 187 (D187N or D187Y) within domain 2 of the
actin-regulating protein gelsolin. The mutation somehow allows a masked
cleavage site to be exposed, leading to the first step in the formation
of an amyloidogenic fragment. We have performed NMR experiments
investigating structural and dynamic changes between wild-type (WT) and
D187N gelsolin domain 2 (D2). On mutation, no significant structural or
dynamic changes occur at or near the cleavage site. Areas in
conformational exchange are observed between β-strand 4 and α-helix
1 and within the loop region following β-strand 5. Chemical shift
differences are noted along the face of α-helix 1 that packs onto the
β-sheet, suggesting an altered conformation. Conformational changes
within these areas can have an effect on actin binding and may explain
why D187N gelsolin is inactive. {
1
H-
15
N}
nuclear Overhauser effect and chemical shift data suggest that the
C-terminal tail of D187N gelsolin D2 is less structured than WT by up
to six residues. In the crystal structure of equine gelsolin, the
C-terminal tail of D2 lies across a large cleft between domains 1 and 2
where the masked cleavage site sits. We propose that the D187N mutation
destabilizes the C-terminal tail of D2 resulting in a more exposed
cleavage site leading to the first proteolysis step in the formation of
the amyloidogenic fragment.
Folding simulations of a three-stranded antiparallel β-sheet peptide
Authors: Ferrara Philippe , Caflisch Amedeo
Published: July 2002

Protein folding is a grand challenge of the postgenomic era. In
this paper, 58 folding events sampled during 47 molecular dynamics
trajectories for a total simulation time of more than 4 μs provide an
atomic detail picture of the folding of a 20-residue synthetic peptide
with a stable three-stranded antiparallel β-sheet fold. The
simulations successfully reproduce the NMR solution conformation,
irrespective of the starting structure. The sampling of the
conformational space is sufficient to determine the free energy surface
and localize the minima and transition states. The statistically
predominant folding pathway involves the formation of contacts between
strands 2 and 3, starting with the side chains close to the turn,
followed by association of the N-terminal strand onto the preformed
2–3 β-hairpin. The folding mechanism presented here, formation of a
β-hairpin followed by consolidation, is in agreement with a
computational study of the free energy surface of another synthetic
three-stranded antiparallel β-sheet by Bursulaya and Brooks [(1999)
J. Am. Chem. Soc.
121, 9947–9951]. Hence, it
might hold in general for antiparallel β-sheets with short turns.
Inactivation of the endoplasmic reticulum protein translocation factor, Sec61p, or its homolog, Ssh1p, does not affect peroxisome biogenesis
Authors: South Sarah T. , Baumgart Eveline , Gould Stephen J.
Published: July 2002

Peroxisomes are single membrane-bound organelles present in virtually all eukaryotes. These organelles participate in several important metabolic processes, and defects in peroxisome function and biogenesis are a significant contributor to human disease. Several models propose that peroxisomes arise from the endoplasmic reticulum (ER) in a process that involves the translocation of “group I” peroxisomal membrane proteins into the ER, the exit of these group I peroxisomal membrane proteins from the ER by vesicle budding, and the formation of nascent peroxisomes from vesicles containing the group I peroxisomal membrane proteins. A central prediction of these models is that the formation of nascent peroxisomes requires protein translocation into the ER. Sec61p is an essential component of the ER translocon, and we show here that loss of Sec61p activity has no effect on peroxisome biogenesis. In addition, loss of the
SEC61
-related gene,
SSH1
, also has no effect on peroxisome biogenesis. Although some proteins may enter the ER independently of Sec61p or Ssh1p, none are known, leading us to propose that peroxisome biogenesis may not require protein import into the ER, and by extension, transfer of proteins from the ER to the peroxisome.
Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from
Thermochromatium tepidum
: Thermostability and electron transfer
Authors: Nogi Terukazu , Fathir Insan , Kobayashi Masayuki , Nozawa Tsunenori , Miki Kunio
Published: July 2002

The reaction center (RC) of photosynthetic bacteria is a membrane
protein complex that promotes a light-induced charge separation during
the primary process of photosynthesis. In the photosynthetic electron
transfer chain, the soluble electron carrier proteins transport
electrons to the RC and reduce the photo-oxidized special-pair of
bacteriochlorophyll. The high-potential iron-sulfur protein (HiPIP) is
known to serve as an electron donor to the RC in some species, where
the
c
-type cytochrome subunit, the peripheral subunit of
the RC, directly accepts electrons from the HiPIP. Here we report the
crystal structures of the RC and the HiPIP from
Thermochromatium
(
Tch.
)
tepidum
, at 2.2-Å and 1.5-Å resolution, respectively.
Tch. tepidum
can grow at the highest temperature of all
known purple bacteria, and the
Tch. tepidum
RC shows
some degree of stability to high temperature. Comparison with the RCs
of mesophiles, such as
Blastochloris viridis
, has shown
that the
Tch. tepidum
RC possesses more Arg residues at
the membrane surface, which might contribute to the stability of this
membrane protein. The RC and the HiPIP both possess hydrophobic patches
on their respective surfaces, and the HiPIP is expected to interact
with the cytochrome subunit by hydrophobic interactions near the
heme-1, the most distal heme to the special-pair.
Medicago truncatula
plants overexpressing the early nodulin gene
enod40
exhibit accelerated mycorrhizal colonization and enhanced formation of arbuscules
Authors: Staehelin Christian , Charon Celine , Boller Thomas , Crespi Martin , Kondorosi Ádám
Published: July 2002

The mutualistic symbiosis between flowering plants and arbuscular
mycorrhizal fungi is extremely abundant in terrestrial
ecosystems. In this symbiosis, obligately biotrophic fungi
colonize the root of the host plants, which can benefit from these
fungi by enhanced access to mineral nutrients in the soil, especially
phosphorus. One of the main goals of research on this symbiosis is to
find plant genes that control fungal development in the host plant. In
this work, we show that mycorrhizal colonization is regulated by
enod40
, an early nodulin gene known to be involved in
the nodule symbiosis of legumes with nitrogen-fixing bacteria.
Medicago truncatula
plants overexpressing
enod40
exhibited stimulated mycorrhizal colonization in
comparison with control plants. Overexpression of
enod40
promoted fungal growth in the root cortex and increased the frequency
of arbuscule formation. Transgenic lines with suppressed levels of
enod40
transcripts, likely via a cosuppression
phenomenon induced by the transgene, exhibited reduced mycorrhizal
colonization. Hence,
enod40
might be a plant
regulatory gene involved in the control of the mycorrhizal
symbiosis.
Diazepam binding inhibitor is a potent cholecystokinin-releasing peptide in the intestine.
Authors: Herzig K H , Schön I , Tatemoto K , Ohe Y , Li Y , Fölsch U R , Owyang C
Published: July 2002

Pancreatic proteases in the duodenum inhibit the release of cholecystokinin (CCK) and thus exert feedback control of pancreatic exocrine secretion. Exclusion of proteases from the duodenum either by the diversion of bile-pancreatic juice or by the addition of protease inhibitors stimulates exocrine pancreatic secretion. The mechanism by which pancreatic proteases in the duodenum regulate CCK secretion is unknown. In this study, we isolated a trypsin-sensitive peptide that is secreted intraduodenally, releases CCK, and stimulates pancreatic enzyme secretion in rats. This peptide was found to be identical to the porcine diazepam binding inhibitor by peptide sequencing and mass spectrometry analysis. Intraduodenal infusion of 200 ng of synthetic porcine diazepam binding inhibitor1-86 in rats significantly stimulated pancreatic amylase output. Infusion of the CCK antagonist MK-329 completely blocked the diazepam binding inhibitor-stimulated amylase secretion. Similarly, diazepam binding inhibitor33-52 [corrected] also stimulated CCK release and pancreatic secretion in a dose-dependent manner although it was 100 times less potent than the whole peptide. Using a perfusion system containing isolated mucosal cells from the proximal intestine of rats, porcine diazepam binding inhibitor 10(-12) M) dose dependently stimulated CCK secretion. In separate studies, it was demonstrated that luminal secretion of the diazepam binding inhibitor immunoreactivity (7.5 X 10(11) M) could be detected in rat's intestinal washing following the diversion of bile-pancreatic juice. The secretion of this peptide was inhibited by atropine. In conclusion, we have isolated and characterized a CCK-releasing peptide that has a sequence identical to the porcine diazepam binding inhibitor from pig intestinal mucosa and that stimulates CCK release when administered intraduodenally in rat. This peptide may mediate feedback regulation of pancreatic enzyme secretion.
Influence of general anesthetics on a specific neural pathway in Drosophila melanogaster.
Authors: Lin M , Nash H A
Published: July 2002

The neural pathway that governs an escape response of Drosophila to sudden changes in light intensity can be artificially induced by electrical stimulation of the brain and monitored by electrical recording from the effector muscles. We have refined previous work in this system to permit reliable ascertainment of two kinds of response: (i) a short-latency response that follows from direct excitation of a giant fiber neuron in the interior of the fly brain and (ii) a long-latency response in which electrical stimulation triggers neurons in the optic ganglia that ultimately impinge on the giant fiber neuron. The general anesthetic halothane is reported here to have very different potencies in inhibiting these two responses. The long-latency response is obliterated at concentrations similar to those that cause gross behavioral effects in adult flies, whereas the short-latency response is only partially inhibited at doses that are 10-fold higher. Three other volatile anesthetic agents show a similar pattern. Thus, as in higher organisms, the Drosophila nervous system is differentiated into components of high and low sensitivity to general anesthetics. Moreover, this work shows that one of the sensitive components of the nervous system lies in the optic lobe and is readily assayed by its effect on downstream systems; it should provide a focus for exploring the effects of genetic alteration of anesthetic sensitivity.
The photoisomerization of retinal in bacteriorhodopsin: Experimental evidence for a three-state model
Authors: Hasson K. C. , Gai Feng , Anfinrud Philip A.
Published: July 2002

The primary events in the all-
trans
to
13-
cis
photoisomerization of retinal in
bacteriorhodopsin have been investigated with
femtosecond time-resolved absorbance spectroscopy. Spectra measured
over a broad range extending from 7000 to 22,400 cm
−1
reveal features whose dynamics are inconsistent with a model proposed
earlier to account for the highly efficient photoisomerization process.
Emerging from this work is a new three-state model. Photoexcitation of
retinal with visible light accesses a shallow well on the excited state
potential energy surface. This well is bounded by a small barrier,
arising from an avoided crossing that separates the Franck–Condon
region from the nearby reactive region of the photoisomerization
coordinate. At ambient temperatures, the reactive region is accessed
with a time constant of ≈500 fs, whereupon the retinal rapidly twists
and encounters a second avoided crossing region. The protein mediates
the passage into the second avoided crossing region and thereby exerts
control over the quantum yield for forming 13-
cis
retinal. The driving force for photoisomerization resides in the
retinal, not in the surrounding protein. This view contrasts with an
earlier model where photoexcitation was thought to access directly a
reactive region of the excited-state potential and thereby drive the
retinal to a twisted conformation within 100–200 fs.
Substantial narrowing of the Niemann–Pick C candidate interval by yeast artificial chromosome complementation
Authors: Gu Jessie Z. , Carstea Eugene D. , Cummings Christiano , Morris Jill A. , Loftus Stacie K. , Zhang Dana , Coleman Katherine G. , Cooney Adele M. , Comly Marcy E. , Fandino Laura , Roff Calvin , Tagle Danilo A. , Pavan William J. , Pentchev Peter G. , Rosenfeld Melissa A.
Published: July 2002

Niemann–Pick disease type C (NP-C) is an autosomal recessive
lipidosis linked to chromosome 18q11–12, characterized by lysosomal
accumulation of unesterified cholesterol and delayed induction of
cholesterol-mediated homeostatic responses. This cellular phenotype is
identifiable cytologically by filipin staining and biochemically by
measurement of low-density lipoprotein-derived cholesterol
esterification. The mutant Chinese hamster ovary cell line (CT60),
which displays the NP-C cellular phenotype, was used as the recipient
for a complementation assay after somatic cell fusions with normal and
NP-C murine cells suggested that this Chinese hamster ovary cell line
carries an alteration(s) in the hamster homolog(s) of NP-C. To narrow
rapidly the candidate interval for NP-C, three overlapping yeast
artificial chromosomes (YACs) spanning the 1 centimorgan human NP-C
interval were introduced stably into CT60 cells and analyzed for
correction of the cellular phenotype. Only YAC 911D5 complemented the
NP-C phenotype, as evidenced by cytological and biochemical analyses,
whereas no complementation was obtained from the other two YACs within
the interval or from a YAC derived from chromosome 7. Fluorescent
in situ
hybridization indicated that YAC 911D5 was
integrated at a single site per CT60 genome. These data substantially
narrow the NP-C critical interval and should greatly simplify the
identification of the gene responsible in mouse and man. This is the
first demonstration of YAC complementation as a valuable adjunct
strategy for positional cloning of a human gene.
A long marine history of carbon cycle modulation by orbital-climatic changes
Authors: Herbert Timothy D.
Published: July 2002

Pacing of the marine carbon cycle by orbital forcing during the
Pliocene and Pleistocene Ice Ages [past 2.5 million years (Myr)] is
well known. As older deep-sea sediment records are being studied at
greater temporal resolution, it is becoming clear that similar
fluctuations in the marine carbon system have occurred throughout the
late Mesozoic and Tertiary, despite the absence of large continental
ice sheets over much of this time. Variations in both the organic and
the calcium carbonate components of the marine carbon system seem to
have varied cyclically in response to climate forcing, and carbon and
carbonate time series appear to accurately characterize the frequency
spectrum of ancient climatic change. For the past 35 Myr, much of the
variance in carbonate content carries the “polar” signal of
obliquity [41,000 years (41 kyr)] forcing. Over the past 125 Myr,
there is evidence from marine sediments of the continued role of
precessional (≈21 kyr) climatic cycles. Repeat patterns of
sedimentation at about 100, 400, and 2,400 kyr, the modulation periods
of precession, persistently enter into marine carbon cycle records as
well. These patterns suggest a nonlinear response of climate and/or
the sedimentation of organic carbon and carbonates to precessional
orbital perturbations. Nonlinear responses of the carbon system may
help to amplify relatively weak orbital insolation anomalies into more
significant climatic perturbations through positive feedback effects.
Nonlinearities in the carbon cycle may have transformed
orbital-climatic cycles into long-wavelength features on time scales
comparable to the residence times of carbon and nutrient elements in
the ocean.
Cisplatin increases meiotic crossing-over in mice
Authors: Hanneman William H. , Legare Marie E. , Sweeney Shannon , Schimenti John C.
Published: July 2002

Genetic mapping of traits and mutations in mammals is dependent upon linkage analysis. The resolution achieved by this method is related to the number of offspring that can be scored and position of crossovers near a gene. Higher precision mapping is obtained by expanding the collection of progeny from an appropriate cross, which in turn increases the number of potentially informative recombinants. A more efficient approach would be to increase the frequency of recombination, rather than the number of progeny. The anticancer drug cisplatin, which causes DNA strand breakage and is highly recombinogenic in some model organisms, was tested for its ability to induce germ-line recombination in mice. Males were exposed to cisplatin and mated at various times thereafter to monitor the number of crossovers inherited by offspring. We observed a striking increase on all three chromosomes examined and established a regimen that nearly doubled crossover frequency. The timing of the response indicated that the crossovers were induced at the early pachytene stage of meiosis I. The ability to increase recombination should facilitate genetic mapping and positional cloning in mice.
Respiratory chain is required to maintain oxidized states of the DsbA-DsbB disulfide bond formation system in aerobically growing
Escherichia coli
cells
Authors: Kobayashi Taeko , Kishigami Satoshi , Sone Michio , Inokuchi Hachiro , Mogi Tatsushi , Ito Koreaki
Published: July 2002

DsbA, the disulfide bond catalyst of
Escherichia coli
, is a periplasmic protein having a thioredoxin-like Cys-30-Xaa-Xaa-Cys-33 motif. The Cys-30–Cys-33 disulfide is donated to a pair of cysteines on the target proteins. Although DsbA, having high oxidizing potential, is prone to reduction, it is maintained essentially all oxidized
in vivo
. DsbB, an integral membrane protein having two pairs of essential cysteines, reoxidizes DsbA that has been reduced upon functioning. It is not known, however, what might provide the overall oxidizing power to the DsbA–DsbB disulfide bond formation system. We now report that
E. coli
mutants defective in the
hemA
gene or in the
ubiA-menA
genes markedly accumulate the reduced form of DsbA during growth under the conditions of protoheme deprivation as well as ubiquinone/menaquinone deprivation. Disulfide bond formation of β-lactamase was impaired under these conditions. Intracellular state of DsbB was found to be affected by deprivation of quinones, such that it accumulates first as a reduced form and then as a form of a disulfide-linked complex with DsbA. This is followed by reduction of the bulk of DsbA molecules. These results suggest that the respiratory electron transfer chain participates in the oxidation of DsbA, by acting primarily on DsbB. It is remarkable that a cellular catalyst of protein folding is connected to the respiratory chain.
Transgenic rats reveal functional conservation of regulatory controls between the
Fugu
isotocin and rat oxytocin genes
Authors: Venkatesh Byrappa , Si-Hoe San Ling , Murphy David , Brenner Sydney
Published: July 2002

We have asked whether comparative genome analysis and rat transgenesis can be used to identify functional regulatory domains in the gene locus encoding the hypothalamic neuropeptides oxytocin (OT) and vasopressin. Isotocin (IT) and vasotocin (VT) are the teleost homologues of these genes. A contiguous stretch of 46 kb spanning the
Fugu
IT-VT locus has been sequenced, and nine putative genes were found. Unlike the OT and vasopressin genes, which are closely linked in the mammalian genome in a tail-to-tail orientation,
Fugu
IT and VT genes are linked head to tail and are separated by five genes. When a cosmid containing the
Fugu
IT-VT locus was introduced into the rat genome, we found that the
Fugu
IT gene was specifically expressed in rat hypothalamic oxytocinergic neurons and mimicked the response of the endogenous OT gene to an osmotic stimulus. These data show that cis-acting elements and trans-acting factors mediating the cell-specific and physiological regulation of the OT and IT genes are conserved between mammals and fish. The combination of
Fugu
genome analysis and transgenesis in a mammal is a powerful tool for identifying and analyzing conserved vertebrate regulatory elements.
Effects of
in vivo
adventitial expression of recombinant endothelial nitric oxide synthase gene in cerebral arteries
Authors: Chen Alex F. Y. , Jiang Shi-Wen , Crotty Thomas B. , Tsutsui Masato , Smith Leslie A. , O’Brien Timothy , Katusic Zvonimir S.
Published: July 2002

Nitric oxide (NO), synthesized from
l
-arginine by NO synthases (NOS), plays an essential role in the regulation of cerebrovascular tone. Adenoviral vectors have been widely used to transfer recombinant genes to different vascular beds. To determine whether the recombinant endothelial NOS (eNOS) gene can be delivered
in vivo
to the adventitia of cerebral arteries and functionally expressed, a replication-incompetent adenoviral vector encoding eNOS gene (AdCMVNOS) or β-galactosidase reporter gene (AdCMVLacZ) was injected into canine cerebrospinal fluid (CSF) via the cisterna magna (final viral titer in CSF, 10
9
pfu/ml). Adventitial transgene expression was demonstrated 24 h later by β-galactosidase histochemistry and quantification, eNOS immunohistochemistry, and Western blot analysis of recombinant eNOS. Electron microscopy immunogold labeling indicated that recombinant eNOS protein was expressed in adventitial fibroblasts. In AdCMVNOS-transduced arteries, basal cGMP production and bradykinin-induced relaxations were significantly augmented when compared with AdCMVLacZ-transduced vessels (
P
< 0.05). The increased receptor-mediated relaxations and cGMP production were inhibited by eNOS inhibitors. In addition, the increase in cGMP production was reversed in the absence of calcium, suggesting that the increased NO production did not result from inducible NOS expression. The present study demonstrates the successful
in vivo
transfer and functional expression of recombinant eNOS gene in large cerebral arteries. It also suggests that perivascular eNOS gene delivery via the CSF is a feasible approach that does not require interruption of cerebral blood flow.
Overexpression of a glutamate receptor (GluR2) ligand binding domain in
Escherichia coli
: Application of a novel protein folding screen
Authors: Chen Guo-Qiang , Gouaux Eric
Published: July 2002

Expression of the S1S2 ligand binding domain [Kuusinen, A., Arvola, M. & Keinänen, K. (1995)
EMBO J.
14, 6327–6332] of the rat α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid-selective glutamate receptor GluR2 in
Escherichia coli
under control of a T7 promoter leads to production of >100 mg/liter of histidine-tagged S1S2 protein (HS1S2) in the form of inclusion bodies. Using a novel fractional factorial folding screen and a rational, step-by-step approach, multiple conditions were determined for the folding of the HS1S2 α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid binding domain. Characterization of the HS1S2 ligand binding domain showed that it is water-soluble, monomeric, has significant secondary structure, and is sensitive to trypsinolysis at sites close to the beginning of the putative transmembrane regions. Application of a fractional factorial folding screen to other proteins may provide a useful means to evaluate
E. coli
as an economical and convenient expression host.
Decreased ability of HIV-1 Tat protein-treated accessory cells to organize cellular clusters is associated with partial activation of T cells
Authors: Wu Mei X. , Schlossman Stuart F.
Published: July 2002

It has been shown in several animal models that HIV infection of accessory cells (ACs) plays an important role in development of AIDS. Here, we report that ACs treated with HIV-1 Tat protein (Tat-ACs) have a decreased ability to organize cellular aggregates as compared with untreated ACs, resulting in incomplete activation of T cells in responses to anti-CD3 mAb or staphylococcal enterotoxin B stimulation. The T cells failed to up-regulate adhesion molecules CD11a and CD2 on the cell surface and had reduced proliferative responses, as determined by [3H]thymidine incorporation, but they obtained lymphoblast-like morphology and expressed early activation antigens on the cell surface such as Fas and CD69 and interleukin 2 receptor, at comparable levels as those T cells undergoing a maximal proliferation. These results suggest that the Tat-AC-induced defect occurs in the late, but not in the early, phases of T cell activation. Normal expression of cell surface Fas antigen accompanied by defects in late activation thus may result in the susceptibility of these T cells to apoptosis. Our studies suggest that dysfunction, hyperactivation, and susceptibility to apoptosis, as observed with T cells isolated from HIV-infected individuals, may be, at least in part, a consequence of abnormal functions of ACs.
A role for the epithelial-cell-specific tyrosine kinase Sik during keratinocyte differentiation
Authors: Vasioukhin Valeri , Tyner Angela L.
Published: July 2002

Sik, the mouse homologue of the breast tumor kinase Brk, is expressed in differentiating cells of the gastrointestinal tract and skin. We examined expression and activity of Sik in primary mouse keratinocytes and a mouse embryonic keratinocyte cell line (EMK). Calcium-induced differentiation of these cells has been shown to be accompanied by the activation of tyrosine kinases and rapid phosphorylation of a 65-kDa GTPase-activating protein (GAP)-associated protein (GAP-A.p65). We demonstrate that Sik is activated within 2 min after calcium addition in primary keratinocytes and EMK cells. In EMK cells, Sik binds GAP-A.p65, and this interaction is mediated by the Sik Src homology 2 domain. Although Sik directly complexes with GAP-A.p65, overexpression of wild-type or kinase defective Sik in EMK cells does not lead to detectable changes in GAP-A.p65 phosphorylation. These data suggest that Sik is not responsible for phosphorylation of GAP-A.p65. GAP-A.p65 may act as an adapter protein, bringing Sik into proximity of an unidentified substrate. Overexpression of Sik in EMK cells results in increased expression of filaggrin during differentiation, supporting a role for Sik in differentiation.
Chemotaxis in a lymphocyte cell line transfected with C-C chemokine receptor 2B: Evidence that directed migration is mediated by βγ dimers released by activation of Gαi-coupled receptors
Authors: Arai Hidenori , Tsou Chia-Lin , Charo Israel F.
Published: July 2002

Chemotaxis is mediated by activation of seven-transmembrane domain, G protein-coupled receptors, but the signal transduction pathways leading to chemotaxis are poorly understood. To identify G proteins that signal the directed migration of cells, we stably transfected a lymphocyte cell line (300-19) with G protein-coupled receptors that couple exclusively to Gαq(the m3 muscarinic receptor), Gαi(the κ-opioid receptor), and Gαs(the β-adrenergic receptor), as well as the human thrombin receptor (PAR-1) and the C-C chemokine receptor 2B. Cells expressing receptors that coupled to Gαi, but not to Gαqor Gαs, migrated in response to a concentration gradient of the appropriate agonist. Overexpression of Gαtransducin, which binds to and inactivates free Gβγdimers, completely blocked chemotaxis although having little or no effect on intracellular calcium mobilization or other measures of cell signaling. The identification of Gβγdimers as a crucial intermediate in the chemotaxis signaling pathway provides further evidence that chemotaxis of mammalian cells has important similarities to polarized responses in yeast. We conclude that chemotaxis is dependent on activation of Gαiand the release of Gβγdimers, and that Gαi-coupled receptors not traditionally associated with chemotaxis can mediate directed migration when they are expressed in hematopoietic cells.
Application of a time-dependent coalescence process for inferring the history of population size changes from DNA sequence data
Authors: Polanski Andrzej , Kimmel Marek , Chakraborty Ranajit
Published: July 2002

Distribution of pairwise differences of nucleotides from data on a sample of DNA sequences from a given segment of the genome has been used in the past to draw inferences about the past history of population size changes. However, all earlier methods assume a given model of population size changes (such as sudden expansion), parameters of which (e.g., time and amplitude of expansion) are fitted to the observed distributions of nucleotide differences among pairwise comparisons of all DNA sequences in the sample. Our theory indicates that for any time-dependent population size,
N
(τ) (in which time τ is counted backward from present), a time-dependent coalescence process yields the distribution,
p
(τ), of the time of coalescence between two DNA sequences randomly drawn from the population. Prediction of
p
(τ) and
N
(τ) requires the use of a reverse Laplace transform known to be unstable. Nevertheless, simulated data obtained from three models of monotone population change (stepwise, exponential, and logistic) indicate that the pattern of a past population size change leaves its signature on the pattern of DNA polymorphism. Application of the theory to the published mtDNA sequences indicates that the current mtDNA sequence variation is not inconsistent with a logistic growth of the human population.
Expression of myogenin during embryogenesis is controlled by Six/
sine oculis
homeoproteins through a conserved MEF3 binding site
Authors: Spitz François , Demignon Josiane , Porteu Arlette , Kahn Axel , Concordet Jean-Paul , Daegelen Dominique , Maire Pascal
Published: July 2002

Myogenin, one of the MyoD family of proteins, is expressed early during somitogenesis and is required for myoblast fusion
in vivo
. Previous studies in transgenic mice have shown that a 184-bp myogenin promoter fragment is sufficient to correctly drive expression of a β-galactosidase transgene during embryogenesis. We show here that mutation of one of the DNA motifs present in this region, the MEF3 motif, abolished correct expression of this β-galactosidase transgene. We have found that the proteins that bind to the MEF3 site are homeoproteins of the Six/
sine oculis
family. Antibodies directed specifically against Six1 or Six4 proteins reveal that each of these proteins is present in the embryo when myogenin is activated and constitutes a muscle-specific MEF3-binding activity in adult muscle nuclear extracts. Both of these proteins accumulate in the nucleus of C2C12 myogenic cells, and transient transfection experiments confirm that Six1 and Six4 are able to transactivate a reporter gene containing MEF3 sites. Altogether these results establish Six homeoproteins as a family of transcription factors controlling muscle formation through activation of one of its key regulators, myogenin.
Altered peptide ligands act as partial agonists by inhibiting phospholipase C activity induced by myasthenogenic T cell epitopes
Authors: Faber-Elmann Anat , Paas-Rozner Miri , Sela Michael , Mozes Edna
Published: July 2002

Myasthenia gravis (MG) is a T cell-regulated, antibody-mediated autoimmune disease. Two peptides representing sequences of the human acetylcholine receptor α-subunit, p195–212 and p259–271, previously were shown to stimulate the proliferation of peripheral blood lymphocytes of patients with MG and were found to be immunodominant T cell epitopes in SJL and BALB/c mice, respectively. Single amino acid-substituted analogs of p195–212 and p259–271, as well as a dual analog composed of the tandemly arranged two single analogs, were shown to inhibit,in vitroandin vivo, MG-associated autoimmune responses. Stimulation of T cells through the antigen-specific T cell receptor activates tyrosine kinases and phospholipase C (PLC). Therefore, in attempts to understand the mechanism of action of the analogs, we first examined whether the myasthenogenic peptides trigger tyrosine phosphorylation and activation of phospholipase C. For that purpose, we measured generation of inositol phosphates and tyrosine phosphorylation of PLC after stimulation of the p195–212- and p259–271-specific T cell lines with these myasthenogenic peptides. Both myasthenogenic peptides stimulated generation of inositol phosphates as well as tyrosine phosphorylation of PLC. However, the single and dual analogs, although inducing tyrosine phosphorylation of PLC, could not induce PLC activity. Furthermore, the single and dual analogs inhibited the induced PLC activity whereas they could not inhibit tyrosine phosphorylation of PLC that was caused by the myasthenogenic peptides. Thus, the altered peptides and the dual analog act as partial agonists. The down-regulation of PLC activity by the analogs may account for their capacity to inhibitin vitroMG-associated T cell responses.
Signaling pathways underlying eosinophil cell motility revealed by using caged peptides
Authors: Walker Jeffery W. , Gilbert Susan H. , Drummond Robert M. , Yamada Misato , Sreekumar R. , Carraway Robert E. , Ikebe Mitsuo , Fay Fredric S.
Published: July 2002

Insights into structure-function relations of many proteins opens the possibility of engineering peptides to selectively interfere with a protein’s activity. To facilitate the use of peptides as probes of cellular processes, we have developed caged peptides whose influence on specific proteins can be suddenly and uniformly changed by near-UV light. Two peptides are described which, on photolysis of a caging moiety, block the action of calcium-calmodulin or myosin light chain kinase (MLCK). The efficacy of theses peptides is demonstrated
in vitro
and
in vivo
by determining their effect before and after photolysis on activities of isolated enzymes and cellular functions known to depend on calcium-calmodulin and MLCK. These caged peptides each were injected into motile, polarized eosinophils, and when exposed to light promptly blocked cell locomotion in a similar manner. The results indicate that the action of calcium-calmodulin and MLCK, and by inference myosin II, are required for the ameboid locomotion of these cells. This methodology provides a powerful means for assessing the role of these and other proteins in a wide range of spatio-temporally complex functions in intact living cells.