bluuebunny/crossref_metadata_2025 huggingface dataset:
Analytic modeling of axisymmetric disruption halo currents
Authors: Humphreys D. A. , Kellman A. G.
Published: July 2002

Currents which can flow in plasma facing components during disruptions pose a challenge to the design of next generation tokamaks. Induced toroidal eddy currents and both induced and conducted poloidal “halo” currents can produce design-limiting electromagnetic loads. While induction of toroidal and poloidal currents in passive structures is a well-understood phenomenon, the driving terms and scalings for poloidal currents flowing on open field lines during disruptions are less well established. A model of halo current evolution is presented in which the current is induced in the halo by decay of the plasma current and change in enclosed toroidal flux while being convected into the halo from the core by plasma motion. Fundamental physical processes and scalings are described in a simplified analytic version of the model. The peak axisymmetric halo current is found to depend on halo and core plasma characteristics during the current quench, including machine and plasma dimensions, resistivities, safety factor, and vertical stability growth rate. Two extreme regimes in poloidal halo current amplitude are identified depending on the minimum halo safety factor reached during the disruption. A “type I” disruption is characterized by a minimum safety factor that remains relatively high (typically 2–3, comparable to the predisruption safety factor), and a relatively low poloidal halo current. A “type II” disruption is characterized by a minimum safety factor comparable to unity and a relatively high poloidal halo current. Model predictions for these two regimes are found to agree well with halo current measurements from vertical displacement event disruptions in DIII-D [T. S. Taylor, K. H. Burrell, D. R. Baker, G. L. Jackson, R. J. La Haye, M. A. Mahdavi, R. Prater, T. C. Simonen, and A. D. Turnbull, “Results from the DIII-D Scientific Research Program,” in Proceedings of the 17th IAEA Fusion Energy Conference, Yokohama, 1998, to be published in a Special Edition of Nuclear Fusion (1999)].
Scaling of heat transport with collisionality
Authors: Petty C. C. , Luce T. C.
Published: July 2002

The scaling of heat transport with collisionality (ν) in the banana regime has been measured in both L-mode (low confinement) and H-mode (high confinement) plasmas on the DIII-D tokamak [Fusion Technol. 8, 441 (1985)] with the other dimensionless parameters held fixed. Understanding the collisionality scaling of heat transport helps to distinguish between the different proposed mechanisms of turbulent transport and allows the origin of power degradation and density scaling of confinement to be determined. For L-mode plasmas on DIII-D, the scaling of the effective (or one-fluid) thermal diffusivity with collisionality is close to zero at all radii, χeff∝χBν−0.08±0.10, which is the expected scaling for the collisionless ion temperature gradient (ITG) and collisionless trapped electron modes. The ion and electron thermal diffusivities have the same collisionality scaling to within the experimental error. For H-mode plasmas, a stronger collisionality dependence of heat transport is observed, χeff∝χBν0.49±0.08 for a factor-of-8 scan in ν, which falls between the expected scalings of the collisionless ITG and collisionless trapped electron modes and that of the (edge) resistive ballooning mode. A portion of this H-mode collisionality scaling can be attributed to the ν dependence of neoclassical heat transport, especially in low collisionality regions of the plasma.
Gyrokinetic theory of slab electron temperature gradient mode in negative shear tokamaks
Authors: Idomura Y. , Wakatani M. , Tokuda S.
Published: July 2002

With a gyrokinetic integral eigenvalue code, it is shown that both the slab ion temperature gradient (ITG) mode and the slab electron temperature gradient (ETG) mode have three types of branches in the negative shear configuration: a single mode-rational surface mode, a double mode-rational surface mode, and a nonresonant mode. For typical fusion plasma parameters satisfying λDe2≫ρte2, a Weber-type differential eigenmode equation of the ETG mode becomes essentially different from that of the ITG mode, because of the Debye shielding effect, where λDe is the Debye length and ρte is the electron Larmor radius. A scale length of the ETG modes is characterized by λDe, and different types of analytic solutions are obtained for the ETG modes. From a comparison of the transport coefficient based on the mixing length theory, it is shown that in the negative shear configuration, the slab ETG mode gives an order of magnitude larger transport coefficient compared with an estimate for the conventional normal-sheared slab ETG mode.
Growth of high quality epitaxial PbSe onto Si using a (Ca,Ba)F2 buffer layer
Authors: Zogg H. , Hüppi M.
Published: July 2002

Epitaxial layers of PbSe have been grown onto Si(111) by vacuum deposition techniques using a (Ca,Ba)F2 buffer film. For lattice match, the buffer layer is graded with CaF2 at the Si interface and BaF2 at the PbSe interface. Like bulk BaF2, this buffer layer forms a suitable support for the growth of high quality PbSe. The layers grown exhibit smooth surfaces and mobilities as high as those of bulk PbSe, i.e., ∼3×104 cm2 V−1 s−1 at 77 K and >1.2×105 cm2 V−1 s−1 below 20 K. These results are very promising for the fabrication of heteroepitaxial monolithic integrated circuits, with, for example, photovoltaic (Pb,Sn) (S,Se,Te) narrow gap semiconductor infrared detectors on silicon.
Scanning tunneling potentiometry
Authors: Muralt P. , Pohl D. W.
Published: July 2002

In certain problems of electrical transport through condensed matter, it is important to know the potential distribution with microscopic resolution, e.g., at interfaces (Schottky barriers) or pn junctions. Scanning tunneling potentiometry, a new application of scanning tunneling microscopy, is capable of providing this information. The tunnel current is used for simultaneously sensing probe-to-sample distance and local potential. The method was tested with a gold-island metal-insulator-metal structure.
Quadratic electro-optic effect due to the quantum-confined Stark effect in quantum wells
Authors: Weiner Joseph S. , Miller David A. B. , Chemla Daniel S.
Published: July 2002

We have performed a semi-empirical calculation of the refractive index changes induced by a perpendicular electric field in quantum wells. This calculation is based on experimental electroabsorption data, together with absorption sum rules that have recently been developed. We find good agreement with published experimental results. Our results are important to the development of electro-optic and high-speed electroabsorption quantum well devices.
Rapid direct writing of high-aspect-ratio trenches in silicon
Authors: Treyz G. V. , Beach R. , Osgood R. M.
Published: July 2002

Deep trenches have been etched in crystalline silicon with polarization-controlled, variable curvature walls. Scan speeds of up to 10 mm/s have been demonstrated. A qualitative understanding of the etching process has been developed which is based on a local, melt-enhanced etch rate.
Current-density profiles for a Ga+ ion microprobe and their lithographic implications
Authors: Kubena R. L. , Ward J. W.
Published: July 2002

A 50-keV focused Ga+ beam was used to expose dots in a negative-acting bilevel resist structure in an exposure range between 1 μs/pixel and 4 s/pixel. The radii of the resist dots were used to determine the current-density profiles of the Ga+ ion microprobe down to six orders of magnitude below the peak versus system magnification and ion source current. The effect of the beam profile on the limiting pitch for densely packed resist dot arrays was modeled and compared to experimental results.
InP/InGaAsP/InGaAs avalanche photodiodes with 70 GHz gain-bandwidth product
Authors: Campbell J. C. , Tsang W. T. , Qua G. J. , Bowers J. E.
Published: July 2002

A wide bandwidth (8 GHz) and a high gain-bandwidth product (70 GHz) have been achieved with InP/InGaAsP/InGaAs avalanche photodiodes (APD’s) grown by chemical beam epitaxy. These APD’s also exhibit low dark current (<150 nA at 90% breakdown), good external quantum efficiency (>90% at λ=1.3 μm), and high avalanche gain (M0≂40).
Radii broadening due to molecular collision in focused ion beams
Authors: Komuro Masanori
Published: July 2002

Point exposures of poly(methyl methacrylate) resist are carried out with focused ion beams of Si++ and Au++ from a liquid AuSi ion source in order to obtain a current density distribution in the probe. All the distributions are composed of a main Gaussian distribution and a long tail dependent on r−3.3 (r means radial distance). The magnitude of this tail increases with the increase in ambient pressure of the ion-drifting space. When the probe is steered at the corner of deflection field, two types of clear ghost patterns appear: (1) circular patterns and (2) lines trailing from the main spot toward the deflection center. It is revealed that they are produced by exposures to ions or energetic neutrals generated with charge transfer collision of the primary ions with residual gas molecules. It is shown that the long tail in the current density distribution is also due to scattering with the residual gas molecules.
Long-wavelength photoluminescence of InAs1−xSbx (0<x<1) grown by molecular beam epitaxy on (100) InAs
Authors: Yen M. Y. , People R. , Wecht K. W. , Cho A. Y.
Published: July 2002

InAs1−xSbx films have been successfully prepared by molecular beam epitaxy on (100) InAs substrates. Long-wavelength photoluminescence has been investigated over the complete compositional range. Luminescence peak wavelengths as long as 8 μm have been obtained for the first time among III-V compound semiconductor materials in spite of the existence of a large lattice mismatch. These results are indicative of high-quality material.
Hpt, a bacterial homolog of the microsomal glucose- 6-phosphate translocase, mediates rapid intracellular proliferation inListeria
Authors: Chico-Calero Isabel , Suárez Mónica , González-Zorn Bruno , Scortti Mariela , Slaghuis Jörg , Goebel Werner ,   The European Listeria Genome Consortium§, Vázquez-Boland José A.
Published: July 2002

Efficient replicationin vivois essential for a microparasite to colonize its host and the understanding of the molecular mechanisms by which microbial pathogens grow within host tissues can lead to the discovery of novel therapies to treat infection. Here we present evidence that the foodborne bacterial pathogenListeria monocytogenes, a facultative intracellular parasite, exploits hexose phosphates (HP) from the host cell as a source of carbon and energy to fuel fast intracellular growth. HP uptake is mediated by Hpt, a bacterial homolog of the mammalian translocase that transports glucose-6-phosphate from the cytosol into the endoplasmic reticulum in the final step of gluconeogenesis and glycogenolysis. Expression of the Hpt permease is tightly controlled by the central virulence regulator PrfA, which upon entry into host cells induces a set of virulence factors required for listerial intracellular parasitism. Loss of Hpt resulted in impaired listerial intracytosolic proliferation and attenuated virulence in mice. Hpt is the first virulence factor to be identified as specifically involved in the replication phase of a facultative intracellular pathogen. It is also a clear example of how adaptation to intracellular parasitism by microbial pathogens involves mimicry of physiological mechanisms of their eukaryotic host cells.
Anatomy of a proficient enzyme: The structure of orotidine 5′-monophosphate decarboxylase in the presence and absence of a potential transition state analog
Authors: Miller Brian G. , Hassell Anne M. , Wolfenden Richard , Milburn Michael V. , Short Steven A.
Published: July 2002

Orotidine 5′-phosphate decarboxylase produces the largest rate enhancement that has been reported for any enzyme. The crystal structure of the recombinant
Saccharomyces cerevisiae
enzyme has been determined in the absence and presence of the proposed transition state analog 6-hydroxyuridine 5′-phosphate, at a resolution of 2.1 Å and 2.4 Å, respectively. Orotidine 5′-phosphate decarboxylase folds as a TIM-barrel with the ligand binding site near the open end of the barrel. The binding of 6-hydroxyuridine 5′-phosphate is accompanied by protein loop movements that envelop the ligand almost completely, forming numerous favorable interactions with the phosphoryl group, the ribofuranosyl group, and the pyrimidine ring. Lysine-93 appears to be anchored in such a way as to optimize electrostatic interactions with developing negative charge at C-6 of the pyrimidine ring, and to donate the proton that replaces the carboxylate group at C-6 of the product. In addition, H-bonds from the active site to O-2 and O-4 help to delocalize negative charge in the transition state. Interactions between the enzyme and the phosphoribosyl group anchor the pyrimidine within the active site, helping to explain the phosphoribosyl group's remarkably large contribution to catalysis despite its distance from the site of decarboxylation.
Candidate tumor suppressor RIZ is frequently involved in colorectal carcinogenesis
Authors: Chadwick Robert B. , Jiang Guang-Liang , Bennington Garth A. , Yuan Bo , Johnson Cheryl K. , Stevens Michael W. , Niemann Theodore H. , Peltomaki Paivi , Huang Shi , de la Chapelle Albert
Published: July 2002

The distal portion of chromosome 1p is one of the most commonly
affected regions in human cancer. In this study of hereditary and
sporadic colorectal cancer, a region of frequent deletion was
identified at 32.2 centimorgans from 1ptel. Deletion breakpoints
clustered in the vicinity of or inside the gene
RIZ
,
which encodes a retinoblastoma protein-interacting zinc finger protein.
Sequence analysis revealed frequent frameshift mutations of the
RIZ
gene. The mutations consisted of 1- or 2-bp
deletions of a coding (A)
8
or (A)
9
tract and
were confined to microsatellite-unstable colorectal tumors, being
present in 9 of 24 (37.5%) primary tumors and in 6 of 11 (54.5%) cell
lines; in 2 cell lines the mutation was homozygous/hemizygous. The
mutations apparently were selected clonally in tumorigenesis, because
similar poly(A) tracts in other genes were not affected. Two
alternative products of the gene exist, RIZ1, which contains a PR
(
P
RDI-BF1-
R
IZ1) domain implicated in tumor
suppressor function, and RIZ2, which is lacking this motif.
Furthermore, the C-terminal region, which contains the poly(A) tracts,
includes a PR-binding motif, possibly mediating interactions with other
proteins or with RIZ itself (oligomerization). Four of eleven
microsatellite-unstable colorectal cancer cell lines, three of which
had frameshifts, showed reduced or absent mRNA expression of RIZ1. In a
cell line that is homozygous/hemizygous for the typical frameshift
mutation, immunoblotting showed truncated RIZ protein, whereas
adenovirus-mediated RIZ1 expression caused G
2
/M arrest
and apoptosis. We propose that RIZ is a target of the observed
1p alterations, with impairment of the PR domain-mediated function
through either frameshift mutation or genomic deletion.
A large-scale overexpression screen in
Saccharomyces cerevisiae
identifies previously uncharacterized cell cycle genes
Authors: Stevenson Lauren F. , Kennedy Brian K. , Harlow Ed
Published: July 2002

We have undertaken an extensive screen to identify
Saccharomyces cerevisiae
genes whose products are
involved in cell cycle progression. We report the identification of 113
genes, including 19 hypothetical ORFs, which confer arrest or delay in
specific compartments of the cell cycle when overexpressed. The
collection of genes identified by this screen overlaps with those
identified in loss-of-function
cdc
screens but also
includes genes whose products have not previously been implicated in
cell cycle control. Through analysis of strains lacking these
hypothetical ORFs, we have identified a variety of new
CDC
and checkpoint genes.
Identification and characterization of a human DNA glycosylase for repair of modified bases in oxidatively damaged DNA
Authors: Hazra Tapas K. , Izumi Tadahide , Boldogh Istvan , Imhoff Barry , Kow Yoke W. , Jaruga Pawel , Dizdaroglu Miral , Mitra Sankar
Published: July 2002

8-oxoguanine (8-oxoG), ring-opened purines (formamidopyrimidines or Fapys), and other oxidized DNA base lesions generated by reactive oxygen species are often mutagenic and toxic, and have been implicated in the etiology of many diseases, including cancer, and in aging. Repair of these lesions in all organisms occurs primarily via the DNA base excision repair pathway, initiated with their excision by DNA glycosylase/AP lyases, which are of two classes. One class utilizes an internal Lys residue as the active site nucleophile, and includes
Escherichia coli
Nth and both known mammalian DNA glycosylase/AP lyases, namely, OGG1 and NTH1.
E. coli
MutM and its paralog Nei, which comprise the second class, use N-terminal Pro as the active site. Here, we report the presence of two human orthologs of
E. coli mutM nei
genes in the human genome database, and characterize one of their products. Based on the substrate preference, we have named it NEH1 (Nei homolog). The 44-kDa, wild-type recombinant NEH1, purified to homogeneity from
E. coli
, excises Fapys from damaged DNA, and oxidized pyrimidines and 8-oxoG from oligodeoxynucleotides. Inactivation of the enzyme because of either deletion of N-terminal Pro or Histag fusion at the N terminus supports the role of N-terminal Pro as its active site. The tissue-specific levels of NEH1 and OGG1 mRNAs are distinct, and S phase-specific increase in NEH1 at both RNA and protein levels suggests that NEH1 is involved in replication-associated repair of oxidized bases.
The accessory subunit of DNA polymerase γ is essential for mitochondrial DNA maintenance and development in
Drosophila
melanogaster
Authors: Iyengar Balaji , Luo Ningguang , Farr Carol L. , Kaguni Laurie S. , Campos Ana Regina
Published: July 2002

DNA polymerase γ, Pol γ, is the key replicative enzyme in animal mitochondria. The
Drosophila
enzyme is a heterodimer comprising catalytic and accessory subunits of 125 kDa and 35 kDa, respectively. Both subunits have been cloned and characterized in a variety of model systems, and genetic mutants of the catalytic subunit were first identified in
Drosophila
, as chemically induced mutations that disrupt larval behavior (
tamas
)
.
Mutations in the gene encoding the accessory subunit have not yet been described in any organism. Here, we report the consequences of null mutations upon mitochondrial DNA (mtDNA) replication and morphology
,
cell proliferation, and organismal viability. Mutations in the accessory subunit cause lethality during early pupation, concomitant with loss of mtDNA and mitochondrial mass, and reduced cell proliferation in the central nervous system. Surprisingly, the function of the central nervous system and muscle, as assessed in a locomotion assay, are only marginally affected. This finding is in contrast to our previous findings that disruption in the function of the catalytic subunit causes severe reduction in larval locomotion. We discuss our results in the context of current hypotheses for the function of the accessory subunit in mtDNA replication.
Evaluating the binding selectivity of transthyretin amyloid fibril inhibitors in blood plasma
Authors: Purkey Hans E. , Dorrell Michael I. , Kelly Jeffery W.
Published: July 2002

Transthyretin (TTR) tetramer dissociation and misfolding facilitate
assembly into amyloid fibrils that putatively cause senile systemic
amyloidosis and familial amyloid polyneuropathy. We have previously
discovered more than 50 small molecules that bind to and stabilize
tetrameric TTR, inhibiting amyloid fibril formation
in
vitro
. A method is presented here to evaluate the binding
selectivity of these inhibitors to TTR in human plasma, a complex
biological fluid composed of more than 60 proteins and numerous small
molecules. Our immunoprecipitation approach isolates TTR and bound
small molecules from a biological fluid such as plasma, and quantifies
the amount of small molecules bound to the protein by HPLC analysis.
This approach demonstrates that only a small subset of the inhibitors
that saturate the TTR binding sites
in vitro
do so in
plasma. These selective inhibitors can now be tested in animal models
of TTR amyloid disease to probe the validity of the amyloid hypothesis.
This method could be easily extended to evaluate small molecule binding
selectivity to any protein in a given biological fluid without the
necessity of determining or guessing which other protein components may
be competitors. This is a central issue to understanding the
distribution, metabolism, activity, and toxicity of potential drugs.
Precision and functional specificity in mRNA decay
Authors: Wang Yulei , Liu Chih Long , Storey John D. , Tibshirani Robert J. , Herschlag Daniel , Brown Patrick O.
Published: July 2002

Posttranscriptional processing of mRNA is an integral component of the gene expression program. By using DNA microarrays, we precisely measured the decay of each yeast mRNA, after thermal inactivation of a temperature-sensitive RNA polymerase II. The half-lives varied widely, ranging from ∼3 min to more than 90 min. We found no simple correlation between mRNA half-lives and ORF size, codon bias, ribosome density, or abundance. However, the decay rates of mRNAs encoding groups of proteins that act together in stoichiometric complexes were generally closely matched, and other evidence pointed to a more general relationship between physiological function and mRNA turnover rates. The results provide strong evidence that precise control of the decay of each mRNA is a fundamental feature of the gene expression program in yeast.
Domain organization and flavin adenine dinucleotide-binding determinants in the aerotaxis signal transducer Aer of
Escherichia
coli
Authors: Bibikov Sergei I. , Barnes Lindsey A. , Gitin Yakov , Parkinson John S.
Published: July 2002

Aerotactic responses in
Escherichia coli
are mediated by the membrane transducer Aer, a recently identified member of the superfamily of PAS domain proteins, which includes sensors of light, oxygen, and redox state. Initial studies of Aer suggested that it might use a flavin adenine dinucleotide (FAD) prosthetic group to monitor cellular redox changes. To test this idea, we purified lauryl maltoside-solubilized Aer protein by His-tag affinity chromatography and showed by high performance liquid chromatography, mass spectrometry, and absorbance spectroscopy that it bound FAD noncovalently. Polypeptide fragments spanning the N-terminal 290 residues of Aer, which contains the PAS motif, were able to bind FAD. Fusion of this portion of Aer to the flagellar signaling domain of Tsr, the serine chemoreceptor, yielded a functional aerotaxis transducer, demonstrating that the FAD-binding portion of Aer is sufficient for aerosensing. Aerotaxis-defective missense mutants identified two regions, in addition to the PAS domain, that play roles in FAD binding. Those regions flank a central hydrophobic segment needed to anchor Aer to the cytoplasmic membrane. They might contact the FAD ligand directly or stabilize the FAD-binding pocket. However, their lack of sequence conservation in Aer homologs of other bacteria suggests that they play less direct roles in FAD binding. One or both regions probably also play important roles in transmitting stimulus-induced conformational changes to the C-terminal flagellar signaling domain to trigger aerotactic behavioral responses.
The chaperone/usher pathways of
Pseudomonas aeruginosa
: Identification of fimbrial gene clusters (
cup
) and their involvement in biofilm formation
Authors: Vallet Isabelle , Olson John W. , Lory Stephen , Lazdunski Andrée , Filloux Alain
Published: July 2002

Pseudomonas aeruginosa
, an important opportunistic
human pathogen, persists in certain tissues in the form of specialized
bacterial communities, referred to as biofilm. The biofilm is formed
through series of interactions between cells and adherence to surfaces,
resulting in an organized structure. By screening a library of
Tn
5
insertions in a nonpiliated
P.
aeruginosa
strain, we identified genes involved in early stages
of biofilm formation. One class of mutations identified in this study
mapped in a cluster of genes specifying the components of a
chaperone/usher pathway that is involved in assembly of fimbrial
subunits in other microorganisms. These genes, not previously described
in
P. aeruginosa
, were named
cupA1–A5
.
Additional chaperone/usher systems (CupB and CupC) have been
also identified in the genome of
P. aeruginosa
PAO1;
however, they do not appear to play a role in adhesion under the
conditions where the CupA system is expressed and functions in surface
adherence. The identification of these putative adhesins on the cell
surface of
P. aeruginosa
suggests that this organism
possess a wide range of factors that function in biofilm formation.
These structures appear to be differentially regulated and may function
at distinct stages of biofilm formation, or in specific environments
colonized by this organism.
In vitro
and
in vivo
evidence for orphan nuclear receptor RORα function in bone metabolism
Authors: Meyer Thomas , Kneissel Michaela , Mariani Jean , Fournier Brigitte
Published: July 2002

Bone is a major target site for steroid hormone action. Steroid hormones like cortisol, vitamin D, and estradiol are responsible for principal events associated with bone formation and resorption. Over the past decade, new members of the nuclear hormone gene family have been identified that lack known ligands. These orphan receptors can be used to uncover signaling molecules that regulate yet unidentified physiological networks. In the present study the function of retinoic acid receptor-related orphan receptor (ROR) α in bone metabolism has been examined. We showed that RORα and RORγ, but not RORβ, are expressed in mesenchymal stem cells derived from bone marrow. Interestingly, for RORα we observed an increased messenger signal expression between control cells and cells undergoing osteogenic differentiation. Furthermore, the direct activation of mouse bone sialoprotein by RORα, typically 7-fold, has been shown. In contrast, transient overexpression of RORα overrides the activation of the osteocalcin promoter by 1α,25-dihydroxyvitamin D
3
. In addition, we have investigated bone mass parameters and bone geometry in the mouse mutant
staggerer
(
sg/sg
), a mouse strain that carries a deletion within the RORα gene. Homozygote mutants have thin long bones compared with the heterozygote animals and wild-type littermates. More interestingly, the bones of the
sg/sg
animals are osteopenic as indicated by the comparison of bone mineral contents of
sg/sg
animals to the heterozygote and wild-type animals. We conclude that these
in vitro
and
in vivo
results suggest a function for RORα in bone biology. RORα most likely acts by direct modulation of a bone matrix component.
Strength and tempo of directional selection in the wild
Authors: Hoekstra H. E. , Hoekstra J. M. , Berrigan D. , Vignieri S. N. , Hoang A. , Hill C. E. , Beerli P. , Kingsolver J. G.
Published: July 2002

Directional selection is a major force driving adaptation and evolutionary change. However, the distribution, strength, and tempo of phenotypic selection acting on quantitative traits in natural populations remain unclear across different study systems. We reviewed the literature (1984–1997) that reported the strength of directional selection as indexed by standardized linear selection gradients (β). We asked how strong are viability and sexual selection, and whether strength of selection is correlated with the time scale over which it was measured. Estimates of the magnitude of directional selection (|β|) were exponentially distributed, with few estimates greater than 0.50 and most estimates less than 0.15. Sexual selection (measured by mating success) appeared stronger than viability selection (measured by survival). Viability selection that was measured over short periods (days) was typically stronger than selection measured over longer periods (months and years), but the strength of sexual selection did not vary with duration of selection episodes; as a result, sexual selection was stronger than viability selection over longer time scales (months and years), but not over short time scales (days).
Endothelial cell-specific knockout of connexin 43 causes hypotension and bradycardia in mice
Authors: Liao Y. , Day K. H. , Damon D. N. , Duling B. R.
Published: July 2002

Connexin 43 (Cx43) is a protein expressed in a variety of mammalian
tissues. However, the lack of specific blockers and the absence of
known genetic mutants have hampered the investigation of the function
of this protein. Cx43-null mice die shortly after birth, thus
preventing functional studies
in vivo
. Here, we report
the generation and characterization of a vascular endothelial
cell-specific deletion of the
Cx43
gene (VEC Cx43 KO) in
mice by using the loxP/Cre system. Using homologous recombination, a
mouse line was created carrying loxP sites flanking exon 2 of the
Cx43
gene (“floxed” mice). To produce cell
specific deletion of the
Cx43
gene, these mice were
crossed with animals from a line carrying the Tie 2-Cre transgene. The
homozygous VEC Cx43 KO mice survived to maturity. However, they were
hypotensive and bradycardic when compared with heterozygous VEC Cx43 KO
mice, or to the floxed
Cx43
gene mice. The hypotension
was associated with marked elevation of plasma nitric oxide (NO) levels
as well as elevated plasma angiotensin (Ang) I and II. We hypothesize
that endothelial cell Cx43 plays a key role in the formation and/or
action of NO, and that the elevation of Ang II is a secondary event.
The specific cellular basis for the hypotension remains to be
established, but our findings support the idea that endothelial Cx43
gap junctions are involved in maintaining normal vascular function;
moreover, these animals provide the opportunity to determine more
clearly the role of endothelial Cx43 in vascular development and
homeostasis.
Partitioning of Thy-1, GM1, and cross-linked phospholipid analogs into lipid rafts reconstituted in supported model membrane monolayers
Authors: Dietrich Christian , Volovyk Zoya N. , Levi Moshe , Thompson Nancy L. , Jacobson Ken
Published: July 2002

As shown earlier, raft-like domains resembling those thought to be present in natural cell membranes can be formed in supported planar lipid monolayers. These liquid-ordered domains coexist with a liquid-disordered phase and form in monolayers prepared both from synthetic lipid mixtures and lipid extracts of the brush border membrane of mouse kidney cells. The domains are detergent-resistant and are highly enriched in the glycosphingolipid GM1. In this work, the properties of these raft-like domains are further explored and compared with properties thought to be central to raft function in plasma membranes. First, it is shown that domain formation and disruption critically depends on the cholesterol density and can be controlled reversibly by treating the monolayers with the cholesterol-sequestering reagent methyl-β-cyclodextrin. Second, the glycosylphosphatidylinositol-anchored cell-surface protein Thy-1 significantly partitions into the raft-like domains. The extent of this partitioning is reduced when the monolayers contain GM1, indicating that different molecules can compete for domain occupation. Third, the partitioning of a saturated phospholipid analog into the raft phase is dramatically increased (15% to 65%) after cross-linking with antibodies, whereas the distribution of a doubly unsaturated phospholipid analog is not significantly affected by cross-linking (≈10%). This result demonstrates that cross-linking, a process known to be important for certain cell-signaling processes, can selectively translocate molecules to liquid-ordered domains.
Extrasolar planets
Authors: Lissauer Jack J. , Marcy Geoffrey W. , Ida Shigeru
Published: July 2002

The first known extrasolar planet in orbit around a Sun-like star
was discovered in 1995. This object, as well as over two dozen
subsequently detected extrasolar planets, were all identified by
observing periodic variations of the Doppler shift of light emitted by
the stars to which they are bound. All of these extrasolar planets are
more massive than Saturn is, and most are more massive than Jupiter.
All orbit closer to their stars than do the giant planets in our Solar
System, and most of those that do not orbit closer to their star than
Mercury is to the Sun travel on highly elliptical paths. Prevailing
theories of star and planet formation, which are based on observations
of the Solar System and of young stars and their environments, predict
that planets should form in orbit about most single stars. However,
these models require some modifications to explain the properties of
the observed extrasolar planetary systems.
Dual roles of the 11S regulatory subcomplex in condensin functions
Authors: Kimura Keiji , Hirano Tatsuya
Published: July 2002

Condensin is a multisubunit protein complex that reconfigures DNA
structure in an ATP-dependent manner
in vitro
and plays
a central role in mitotic chromosome condensation in
Xenopus
egg cell-free extracts. The
Xenopus
13S condensin complex (13SC) is composed of two
subcomplexes: an 8S core subcomplex (8SC) consisting of two structural
maintenance of chromosomes (SMC) subunits (XCAP-C and -E) and an 11S
regulatory subcomplex (11SR) containing three non-SMC subunits
(XCAP-D2, -G, and -H). We report here the biochemical and functional
dissection of this chromosome condensation machinery. Although both 8SC
and 13SC can bind to DNA
in vitro
and contain the SMC
ATPase subunits, only 13SC is active as a DNA-stimulated ATPase and
supports ATP-dependent supercoiling activity. In the cell-free
extracts, 13SC is the active form that binds to chromosomes and induces
their condensation. Neither 11SR nor 8SC alone is able to bind to
chromatin. Our results suggest that the non-SMC subunits have dual
roles in the regulation of condensin functions: one is to activate SMC
ATPases and the other is to allow the holocomplex to associate with
chromatin in a mitosis-specific manner.
Mono(ADP-ribosyl)ation of 2′-deoxyguanosine residue in DNA by an apoptosis-inducing protein, pierisin-1, from cabbage butterfly
Authors: Takamura-Enya Takeji , Watanabe Masahiko , Totsuka Yukari , Kanazawa Takashi , Matsushima-Hibiya Yuko , Koyama Kotaro , Sugimura Takashi , Wakabayashi Keiji
Published: July 2002

Pierisin-1 is a potent apoptosis-inducing protein derived from the cabbage butterfly,
Pieris rapae
. It has been shown that pierisin-1 has an A⋅B structure–function organization like cholera or diphtheria toxin, where the “A” domain (N-terminal) exhibits ADP-ribosyltransferase activity. The present studies were designed to identify the target molecule for ADP-ribosylation by pierisin-1 in the presence of β-[
adenylate
-
32
P]NAD, and we found DNA as the acceptor, but not protein as is the case with other bacteria-derived ADP-ribosylating toxins. ADP-ribosylation of tRNAs from yeast was also catalyzed by pierisin-1, but the efficiency was around
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of that for calf thymus DNA. Pierisin-1 efficiently catalyzed the ADP-ribosylation of double-stranded DNA containing dG⋅dC, but not dA⋅dT pairs. The ADP-ribose moiety of NAD was transferred to the amino group at
N
2
of 2′-deoxyguanosine to yield
N
2
-(α-ADP-ribos-1-yl)-2′-deoxyguanosine and its β form, which were determined by several spectral analyses including
1
H- and
13
C-NMR and mass spectrometry. The chemical structures were also ascertained by the independent synthesis of
N
2
-(D-ribos-1-yl)-2′-deoxyguanosine, which is the characteristic moiety of ADP-ribosylated dG. Using the
32
P-postlabeling method, ADP-ribosylated dG could be detected in DNA from pierisin-1-treated HeLa cells, in which apoptosis was easily induced. Thus, the targets for ADP-ribosylation by pierisin-1 were concluded to be 2′-deoxyguanosine residues in DNA. This finding may open a new field regarding the biological significance of ADP-ribosylation.
Endogenous regulators of G protein signaling proteins regulate presynaptic inhibition at rat hippocampal synapses
Authors: Chen Huanmian , Lambert Nevin A.
Published: July 2002

Presynaptic inhibition mediated by G protein-coupled receptors
(GPCRs) can develop and decay in a few seconds. This time course is too
rapid to be accounted for by the intrinsic GTPase activity of Gα
subunits alone. Here, we test the hypothesis that
endogenous regulators of G protein signaling (RGS proteins)
are required for rapid, brief presynaptic inhibition.
Endogenous G protein α subunits were uncoupled from GPCRs
by treating cultures with pertussis toxin (PTX). Adenoviral expression
of mutant PTX-insensitive (PTX-i) Gα
i1–3
or
Gα
o
subunits rescued adenosine-induced presynaptic
inhibition in cultured hippocampal neurons. Expression of double mutant
Gα
i1
or Gα
o
subunits that were both
PTX-insensitive and unable to bind RGS proteins (PTX/RGS-i) also
rescued presynaptic inhibition. Presynaptic inhibition mediated by
PTX/RGS-i subunits decayed much more slowly after agonist removal
than that mediated by PTX-i subunits or native G proteins. The onset of
presynaptic inhibition mediated by PTX/RGS-i Gα
o
was
also slower than that mediated by PTX-i Gα
o
. In contrast,
the onset of presynaptic inhibition mediated by PTX/RGS-i
Gα
i1
was similar to that mediated by PTX-i
Gα
i1
. These results suggest that endogenous
RGS proteins regulate the time course of G protein signaling in
mammalian central nervous system presynaptic terminals.
Single 8-oxo-guanine and 8-oxo-adenine lesions induce marked changes in the backbone structure of a 25-base DNA strand
Authors: Malins Donald C. , Polissar Nayak L. , Ostrander Gary K. , Vinson Mark A.
Published: July 2002

Structural changes in a 25-base DNA strand, induced by single
8-oxo-guanine or 8-oxo-adenine substitutions, were shown by using
Fourier transform-infrared spectroscopy with multivariate statistics.
Pronounced differences were demonstrated between the parent and
derivatives with respect to base interactions and changes in the
phospho-deoxyribose backbone. The greatest degree of change in the
backbone likely occurred immediately adjacent to the 8-oxo group,
potentially altering the stereochemistry at a distance. The 8-oxo
lesions, formed from reactive oxygen species (e.g., hydroxyl radicals),
may appreciably alter the conformational properties of strands at the
replication fork, thus affecting the selectivity of polymerases, the
proofreading capability of repair enzymes, and the fidelity of the
transcriptional machinery.
Differentially expressed late constituents of the epidermal cornified envelope
Authors: Marshall D. , Hardman M. J. , Nield K. M. , Byrne C.
Published: July 2002

Barrier activity of skin and internal barrier-forming epithelial linings are conferred by a lipid-corneocyte structure (stratum corneum in skin).The integrity of the corneocytes depends on the outer cornified envelope and is essential for maintenance of barrier function. During epidermal development and differentiation, proteins are sequentially incorporated into the envelope via action of epidermal transglutaminases in a well documented process. However, recent knockouts of major cornified envelope constituents have failed to disrupt barrier function significantly, suggesting that additional unidentified components are involved. We report a new gene cluster in the epidermal differentiation complex at human 1q21 encoding a family of 18 proteins that are substrates for epidermal transglutaminases. These proteins incorporate into the cornified envelope late in development and late in the process of envelope maturation during epidermal differentiation. The genes cluster within the epidermal differentiation complex according to expression pattern, i.e., epidermally expressed proteins cluster together while proteins from internal barrier-forming epithelia also cluster. We propose that these proteins modulate barrier activity over the surface of the animal, in a manner analogous to that proposed for the well characterized cornified envelope precursors, the small proline-rich proteins. To emphasize the incorporation of these proteins late in envelope assembly, we call the human proteins late envelope proteins.
The crystal structure and mechanism of orotidine 5′-monophosphate decarboxylase
Authors: Appleby Todd C. , Kinsland Cynthia , Begley Tadhg P. , Ealick Steven E.
Published: July 2002

The crystal structure of
Bacillus subtilis
orotidine 5′-monophosphate (OMP) decarboxylase with bound uridine 5′-monophosphate has been determined by multiple wavelength anomalous diffraction phasing techniques and refined to an
R
-factor of 19.3% at 2.4 Å resolution. OMP decarboxylase is a dimer of two identical subunits. Each monomer consists of a triosephosphate isomerase barrel and contains an active site that is located across one end of the barrel and near the dimer interface. For each active site, most of the residues are contributed by one monomer with a few residues contributed from the adjacent monomer. The most highly conserved residues are located in the active site and suggest a novel catalytic mechanism for decarboxylation that is different from any previously proposed OMP decarboxylase mechanism. The uridine 5′-monophosphate molecule is bound to the active site such that the phosphate group is most exposed and the C5-C6 edge of the pyrimidine base is most buried. In the proposed catalytic mechanism, the ground state of the substrate is destabilized by electrostatic repulsion between the carboxylate of the substrate and the carboxylate of Asp60. This repulsion is reduced in the transition state by shifting negative charge from the carboxylate to C6 of the pyrimidine, which is close to the protonated amine of Lys62. We propose that the decarboxylation of OMP proceeds by an electrophilic substitution mechanism in which decarboxylation and carbon-carbon bond protonation by Lys62 occur in a concerted reaction.
Targeting of human DNA polymerase ι to the replication machinery via interaction with PCNA
Authors: Haracska Lajos , Johnson Robert E. , Unk Ildiko , Phillips Barbara B. , Hurwitz Jerard , Prakash Louise , Prakash Satya
Published: July 2002

Human DNA polymerase ι (hPolι) promotes translesion synthesis
by inserting nucleotides opposite highly distorting or noninstructional
DNA lesions. Here, we provide evidence for the physical
interaction of hPolι with proliferating cell nuclear antigen (PCNA),
and show that PCNA, together with replication factor C (RFC) and
replication protein A (RPA), stimulates the DNA synthetic activity of
hPolι. In the presence of these protein factors, on undamaged DNA,
the efficiency
(
V
max
/
K
m
) of
correct nucleotide incorporation by hPolι is increased
≈80–150-fold, and this increase in efficiency results from a
reduction in the apparent
K
m
for the
nucleotide. PCNA, RFC, and RPA also stimulate nucleotide incorporation
opposite the 3′-T of the (6) thymine–thymine (T-T) photoproduct and
opposite an abasic site. The interaction of hPolι with PCNA implies
that the targeting of this polymerase to the replication machinery
stalled at a lesion site is achieved via this association.
An unexpected role for brain-type sodium channels in coupling of cell surface depolarization to contraction in the heart
Authors: Maier Sebastian K. G. , Westenbroek Ruth E. , Schenkman Kenneth A. , Feigl Eric O. , Scheuer Todd , Catterall William A.
Published: July 2002

Voltage-gated sodium channels composed of pore-forming α and auxiliary β subunits are responsible for the rising phase of the action potential in cardiac muscle, but the functional roles of distinct sodium channel subtypes have not been clearly defined. Immunocytochemical studies show that the principal cardiac pore-forming α subunit isoform Na
v
1.5 is preferentially localized in intercalated disks, whereas the brain α subunit isoforms Na
v
1.1, Na
v
1.3, and Na
v
1.6 are localized in the transverse tubules. Sodium currents due to the highly tetrodotoxin (TTX)-sensitive brain isoforms in the transverse tubules are small and are detectable only after activation with β scorpion toxin. Nevertheless, they play an important role in coupling depolarization of the cell surface membrane to contraction, because low TTX concentrations reduce left ventricular function. Our results suggest that the principal cardiac isoform in the intercalated disks is primarily responsible for action potential conduction between cells and reveal an unexpected role for brain sodium channel isoforms in the transverse tubules in coupling electrical excitation to contraction in cardiac muscle.
Potent immunogenicity of the B subunits of Escherichia coli heat-labile enterotoxin: receptor binding is essential and induces differential modulation of lymphocyte subsets.
Authors: Nashar T O , Webb H M , Eaglestone S , Williams N A , Hirst T R
Published: July 2002

The importance of receptor binding in the potent immunogenicity of Escherichia coli heat-labile enterotoxin B subunit (EtxB) was tested by comparing its immunogical properties with those of a receptor binding mutant, EtxB(G33D). Subcutaneous immunization of EtxB(G33D) resulted in 160-fold reduction in antibody titer compared with wild-type EtxB, whereas its oral delivery failed to provoke any detectable secretory or serum anti-B subunit responses. Moreover, the two proteins induced strikingly different effects on lymphocyte cultures in vitro. EtxB, in comparison with EtxB(G33D), caused an increase in the proportion of B cells, many of which were activated (CD25+); the complete depletion of CD8+ T cells; an increase in the activation of CD4+ T cells; and an increase in interleukin 2 and a decrease in interferon gamma. These data indicate that EtxB exerts profound effects on immune cells, suggesting that its potent immunogenicity is dependent not only on efficient receptor-mediated uptake, but also on direct receptor-mediated immunomodulation of lymphocyte subsets.
The yeast and mammalian isoforms of phosphatidylinositol transfer protein can all restore phospholipase C-mediated inositol lipid signaling in cytosol-depleted RBL-2H3 and HL-60 cells.
Authors: Cunningham E , Tan S K , Swigart P , Hsuan J , Bankaitis V , Cockcroft S
Published: July 2002

The mammalian phosphatidylinositol transfer proteins (PITP) and the yeast Saccharomyces cerevisiae PITP (SEC14p) that show no sequence homology both catalyze exchange of phosphatidylinositol (PI) between membranes compartments in vitro. In HL-60 cells where the cytosolic proteins are depleted by permeabilization, exogenously added PITPalpha is required to restore G protein-mediated phospholipase Cbeta (PLCbeta) signaling. Recently, a second mammalian PITPbeta form has been described that shows 77% identity to rat PITPalpha. We have examined the ability of the two mammalian PITPs and SEC14p to restore PLC-mediated signaling in cytosol-depleted HL-60 and RBL-2H3 cells. Both PITPalpha and PITPbeta isoforms as well as SEC14p restore G protein-mediated PLCbeta signaling with a similar potency. In RBL-2H3 cells, crosslinking of the IgE receptor by antigen stimulates inositol lipid hydrolysis by tyrosine phosphorylation of PLCgamma1. Permeabilization of RBL cells leads to loss of PLCgamma1 as well as PITP into the extracellular medium and this coincides with loss of antigen-stimulated lipid hydrolysis. Both PLCgamma1 and PITP were required to restore inositol lipid signaling. We conclude that (i) because the PI binding/transfer activities of PITP/SEC14p is the common feature shared by all three transfer proteins, it must be the relevant activity that determines their abilities to restore inositol lipid-mediated signaling and (ii) PITP is a general requirement for inositol lipid hydrolysis regardless of how and which isoform of PLC is activated by the appropriate agonist.