bluuebunny/crossref_metadata_2025 huggingface dataset:
Toward Automatic Reconstruction of a Highly Resolved Tree of Life
Authors: Ciccarelli Francesca D. , Doerks Tobias , von Mering Christian , Creevey Christopher J. , Snel Berend , Bork Peer
Published: March 2006

We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of δ-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.
Architecture of Mammalian Fatty Acid Synthase at 4.5 Å Resolution
Authors: Maier Timm , Jenni Simon , Ban Nenad
Published: March 2006

The homodimeric mammalian fatty acid synthase is one of the most complex cellular multienzymes, in that each 270-kilodalton polypeptide chain carries all seven functional domains required for fatty acid synthesis. We have calculated a 4.5 angstrom–resolution x-ray crystallographic map of porcine fatty acid synthase, highly homologous to the human multienzyme, and placed homologous template structures of all individual catalytic domains responsible for the cyclic elongation of fatty acid chains into the electron density. The positioning of domains reveals the complex architecture of the multienzyme forming an intertwined dimer with two lateral semicircular reaction chambers, each containing a full set of catalytic domains required for fatty acid elongation. Large distances between active sites and conformational differences between the reaction chambers demonstrate that mobility of the acyl carrier protein and general flexibility of the multienzyme must accompany handover of the reaction intermediates during the reaction cycle.
The Rotational Spectrum of the Water-Hydroperoxy Radical (H
2
O-HO
2
) Complex
Authors: Suma Kohsuke , Sumiyoshi Yoshihiro , Endo Yasuki
Published: March 2006

Peroxy radicals and their derivatives are elusive but important intermediates in a wide range of oxidation processes. We observed pure rotational transitions of the water–hydroperoxy radical complex, H
2
O–HO
2
, in a supersonic jet by means of a Fourier transform microwave spectrometer combined with a double-resonance technique. The observed rotational transitions were found to split into two components because of the internal rotation of the water moiety. The molecular constants for the two components were determined precisely, supporting a molecular structure in which HO
2
acts as a proton donor to form a nearly planar five-membered ring, and one hydrogen atom of water sticks out from the ring plane. The structure and the spectral splittings due to internal rotation provide information on the nature of the bonding interaction between open- and closed-shell species, and they also provide accurate transition frequencies that are applicable to remote sensing of this complex, which may elucidate its potential roles in atmospheric and combustion chemistry.
Of Microbes, Medicine, and Ecology
Authors: Strick James
Published: March 2006

René Dubos, Friend of the Good Earth
. Microbiologist, Medical Scientist, Environmentalist.
By Carol L. Moberg
. American Society for Microbiology, Washington, DC, 2005. 292 pp. $29.95. ISBN 1-55581-340-2.

The author discusses Dubos's life and science in the context of microbiology, ecology, medicine, and environmentalism.
Basaltic Rocks Analyzed by the Spirit Rover in Gusev Crater
Authors: McSween H. Y. , Arvidson R. E. , Bell J. F. , Blaney D. , Cabrol N. A. , Christensen P. R. , Clark B. C. , Crisp J. A. , Crumpler L. S. , Des Marais D. J. , Farmer J. D. , Gellert R. , Ghosh A. , Gorevan S. , Graff T. , Grant J. , Haskin L. A. , Herkenhoff K. E. , Johnson J. R. , Jolliff B. L. , Klingelhoefer G. , Knudson A. T. , McLennan S. , Milam K. A. , Moersch J. E. , Morris R. V. , Rieder R. , Ruff S. W. , de Souza P. A. , Squyres S. W. , WaÌnke H. , Wang A. , Wyatt M. B. , Yen A. , Zipfel J.
Published: March 2006

The Spirit landing site in Gusev Crater on Mars contains dark, fine-grained, vesicular rocks interpreted as lavas. Pancam and MiniâThermal Emission Spectrometer (Mini-TES) spectra suggest that all of these rocks are similar but have variable coatings and dust mantles. Magnified images of brushed and abraded rock surfaces show alteration rinds and veins. Rock interiors contain â¤25% megacrysts. Chemical analyses of rocks by the Alpha Particle X-ray Spectrometer are consistent with picritic basalts, containing normative olivine, pyroxenes, plagioclase, and accessory FeTi oxides. MoÌssbauer, Pancam, and Mini-TES spectra confirm the presence of olivine, magnetite, and probably pyroxene. These basalts extend the known range of rock compositions composing the martian crust.
Mga Is Sufficient To Activate Transcription In Vitro ofsof-sfbXand Other Mga-Regulated Virulence Genes in the Group A Streptococcus
Authors: Almengor Audry C. , Walters Matthew S. , McIver Kevin S.
Published: March 2006

The group A streptococcus (GAS), orStreptococcus pyogenes, is a strict human pathogen of medical significance, causing infections ranging from pharyngitis (strep throat) to necrotizing fasciitis (flesh-eating disease). Several virulence genes that encode factors important for colonization, internalization, and immune evasion are under the control of the multiple gene regulator of the GAS, or Mga. Mga functions as a DNA-binding protein that interacts with sites both proximal (Pemmand PscpA) and distal (PsclA) to the start of transcription for the genes that it regulates. The genes encoding serum opacity factor,sof, and a novel fibronectin-binding protein,sfbX, are cotranscribed and represent two uncharacterized Mga-regulated virulence genes in the GAS. Analysis of the promoter region ofsof-sfbXidentified a putative Mga-binding site 278 bp upstream of the regulated start of transcription as determined by primer extension. Electrophoretic mobility shift assays demonstrated that Mga is able to bind specifically to the single distal site in a fashion similar to the previously characterized PsclA. In order to better understand the events that take place at this and other Mga-regulated promoters, an in vitro transcription assay was established. Using this assay, we showed that Mga is sufficient to activate transcription in vitro for Mga-regulated promoters containing both proximal (Pemm) and distal (PsclAand Psof-sfbX) binding sites. These results indicate that additional factors are not required for Mga-specific activation at diverse promoters in vitro, although they do not rule out the potential influence of other components on the Mga virulence regulon in vivo.
Requirement of
Staphylococcus aureus
ATP-Binding Cassette-ATPase FhuC for Iron-Restricted Growth and Evidence that It Functions with More than One Iron Transporter
Authors: Speziali Craig D. , Dale Suzanne E. , Henderson James A. , Vinés Enrique D. , Heinrichs David E.
Published: March 2006

In
Staphylococcus aureus, fhuCBG
encodes an ATP-binding cassette (ABC) transporter that is required for the transport of iron(III)-hydroxamates; mutation of either
fhuB
or
fhuG
eliminates transport. In this paper, we describe construction and characterization of an
S. aureus fhuCBG
deletion strain. The Δ
fhuCBG
::
ermC
mutation not only resulted in a strain that was incapable of growth on iron(III)-hydroxamates as a sole source of iron but also resulted in a strain which had a profound growth defect in iron-restricted laboratory media. The growth defect was not a result of the inability to transport iron(III)-hydroxamates since
S. aureus fhuG
::Tn
917
and
S. aureus fhuD1
::Km
fhuD2
::Tet mutants, which are also unable to transport iron(III)-hydroxamates, do not have similar iron-restricted growth defects. Complementation experiments demonstrated that the growth defect of the Δ
fhuCBG
::
ermC
mutant was the result of the inability to express FhuC and that this was the result of an inability to transport iron complexed to the
S. aureus
siderophore staphylobactin. Transport of iron(III)-staphylobactin is dependent upon SirA (binding protein), SirB (permease), and SirC (permease).
S. aureus
expressing FhuC with a Walker A K42N mutation could not utilize iron(III)-hydroxamates or iron(III)-staphylobactin as a sole source of iron, supporting the conclusion that FhuC, as expected, functions with FhuB, FhuG, and FhuD1 or FhuD2 to transport iron(III)-hydroxamates and is the “genetically unlinked” ABC-ATPase that functions with SirA, SirB, and SirC to transport iron(III)-staphylobactin. Finally, we demonstrated that the Δ
fhuCBG
::
ermC
strain had decreased virulence in a murine kidney abscess model.
Abundance of the δ Subunit of RNA Polymerase Is Linked to the Virulence ofStreptococcus agalactiae
Authors: Seepersaud Ravin , Needham Rachel H. V. , Kim Cathy S. , Jones Amanda L.
Published: March 2006

Group B streptococcus (GBS) remains a major cause of morbidity and mortality among newborn children. The bacterium is a commensal organism colonizing the rectum and the gastrointestinal and urogenital tracts of adults, but it can be transmitted to neonates by an ascending infection of the maternal genital tract or during parturition. We previously reported that a transposon insertion disruptingrpoEresulted in the decreased survival of the mutant in the neonatal rat sepsis model of GBS infection.rpoEencodes the δ protein, a subunit of RNA polymerase (RNAP) that has been characterized inBacillusspecies. In this study, we confirm the association of the δ protein with purified GBS RNAP and show that it is expressed in strains representing all nine serotypes. Flow cytometric analysis of a reporter strain containing a transcriptional fusion of therpoEpromoter togfprevealed that, in vitro, this gene is continuously expressed. Analysis of δ expression in the transposon mutant by quantitative Western blotting revealed a 10-fold reduction in relative abundance (which was linked to the attenuation in virulence that was observed for this mutant) compared to that for the wild-type strain. These data suggest that a minimum intracellular concentration of δ is necessary for this organism to cause disease.
Transcriptional and Biochemical Analysis of Starch Metabolism in the Hyperthermophilic Archaeon
Pyrococcus furiosus
Authors: Lee Han-Seung , Shockley Keith R. , Schut Gerrit J. , Conners Shannon B. , Montero Clemente I. , Johnson Matthew R. , Chou Chung-Jung , Bridger Stephanie L. , Wigner Nathan , Brehm Scott D. , Jenney Francis E. , Comfort Donald A. , Kelly Robert M. , Adams Michael W. W.
Published: March 2006

Pyrococcus furiosus
utilizes starch and its degradation products, such as maltose, as primary carbon sources, but the pathways by which these α-glucans are processed have yet to be defined. For example, its genome contains genes proposed to encode five amylolytic enzymes (including a cyclodextrin glucanotransferase [CGTase] and amylopullulanase), as well as two transporters for maltose and maltodextrins (Mal-I and Mal-II), and a range of intracellular enzymes have been purified that reportedly metabolize maltodextrins and maltose. However, precisely which of these enzymes are involved in starch processing is not clear. In this study, starch metabolism in
P. furiosus
was examined by biochemical analyses in conjunction with global transcriptional response data for cells grown on a variety of glucans. In addition, DNA sequencing led to the correction of two key errors in the genome sequence, and these change the predicted properties of amylopullulanase (now designated PF1935*) and CGTase (PF0478*). Based on all of these data, a pathway is proposed that is specific for starch utilization that involves one transporter (Mal-II [PF1933 to PF1939]) and only three enzymes, amylopullulanase (PF1935*), 4-α-glucanotransferase (PF0272), and maltodextrin phosphorylase (PF1535). Their expression is upregulated on starch, and together they generate glucose and glucose-1-phosphate, which then feed into the novel glycolytic pathway of this organism. In addition, the results indicate that several hypothetical proteins encoded by three gene clusters are also involved in the transport and processing of α-glucan substrates by
P. furiosus
.
The Pea Nodule Environment Restores the Ability of a
Rhizobium leguminosarum
Lipopolysaccharide
acpXL
Mutant To Add 27-Hydroxyoctacosanoic Acid to Its Lipid A
Authors: Vedam Vinata , Kannenberg Elmar , Datta Anup , Brown Dusty , Haynes-Gann Janine G. , Sherrier D. Janine , Carlson Russell W.
Published: March 2006

Members of the
Rhizobiaceae
contain 27-hydroxyoctacosanoic acid (27OHC
28:0
) in their lipid A. A
Rhizobium leguminosarum 3841 acpXL
mutant (named here Rlv22) lacking a functional specialized acyl carrier lacked 27OHC
28:0
in its lipid A, had altered growth and physiological properties (e.g., it was unable to grow in the presence of an elevated salt concentration [0.5% NaCl]), and formed irregularly shaped bacteroids, and the synchronous division of this mutant and the host plant-derived symbiosome membrane was disrupted. In spite of these defects, the mutant was able to persist within the root nodule cells and eventually form, albeit inefficiently, nitrogen-fixing bacteroids. This result suggested that while it is in a host root nodule, the mutant may have some mechanism by which it adapts to the loss of 27OHC
28:0
from its lipid A. In order to further define the function of this fatty acyl residue, it was necessary to examine the lipid A isolated from mutant bacteroids. In this report we show that addition of 27OHC
28:0
to the lipid A of Rlv22 lipopolysaccharides is partially restored in Rlv22
acpXL
mutant bacteroids. We hypothesize that
R. leguminosarum
bv. viciae 3841 contains an alternate mechanism (e.g., another
acp
gene) for the synthesis of 27OHC
28:0
, which is activated when the bacteria are in the nodule environment, and that it is this alternative mechanism which functionally replaces
acpXL
and is responsible for the synthesis of 27OHC
28:0
-containing lipid A in the Rlv22
acpXL
bacteroids.
MprAB Is a Stress-Responsive Two-Component System That Directly Regulates Expression of Sigma Factors SigB and SigE in
Mycobacterium tuberculosis
Authors: He Hongjun , Hovey Raymond , Kane Jason , Singh Vineet , Zahrt Thomas C.
Published: March 2006

The genetic mechanisms mediating the adaptation of
Mycobacterium tuberculosis
within the host are poorly understood. The best-characterized regulatory systems in this organism include sigma factors and two-component signal transduction systems.
mprAB
is a two-component system required by
M. tuberculosis
for growth in vivo during the persistent stage of infection. In this report, we demonstrate that MprAB is stress responsive and regulates the expression of numerous stress-responsive genes in
M. tuberculosis
. With DNA microarrays and quantitative real-time reverse transcription-PCR, genes regulated by MprA in
M. tuberculosis
that included two stress-responsive sigma factors were identified. Response regulator MprA bound to conserved motifs in the upstream regions of both
sigB
and
sigE
in vitro and regulated the in vivo expression of
sigB
and
sigE
in
M. tuberculosis
. In addition,
mprA
itself was induced following exposure to stress, establishing a direct role for this regulatory system in stress response pathways of
M. tuberculosis
. Induction of
mprA
and
sigE
by MprA in response to stress was mediated through the cognate sensor kinase MprB and required expression of the extracytoplasmic loop domain. These results provide the first evidence that recognition of and adaptation to specific stress in
M. tuberculosis
are mediated through activation of a two-component signal transduction system that directly regulates the expression of stress-responsive determinants.
Regulation of Long-Chain
N
-Acyl-Homoserine Lactones in
Agrobacterium vitis
Authors: Hao Guixia , Burr Thomas J.
Published: March 2006

Homologs of quorum-sensing
luxR
and
luxI
regulatory genes,
avsR
and
avsI
, were identified in
Agrobacterium vitis
strain F2/5. Compared to other LuxI proteins from related species, the deduced AvsI shows the greatest identity to SinI (71%) from
Sinorhizobium meliloti
Rm1021. AvsR possesses characteristic autoinducer binding and helix-turn-helix DNA binding domains and shares a high level of identity with SinR (38%) from Rm1021. Site-directed mutagenesis of
avsR
and
avsI
was performed, and both genes are essential for hypersensitive-like response (HR) and necrosis. Two hypothetical proteins (ORF1 and ORF2) that are positioned downstream of
avsR-avsI
are also essential for the phenotypes. Profiles of
N
-acyl-homoserine lactones (AHLs) isolated from the wild type and mutants revealed that disruption of
avsI
, ORF1, or ORF2 abolished the production of long-chain AHLs. Disruption of
avsR
reduces long-chain AHLs. Expression of a cloned
avsI
gene in
A. tumefaciens
strain NT1 resulted in synthesis of long-chain AHLs. The necrosis and HR phenotypes of the
avsI
and
avsR
mutants were fully complemented with cloned
avsI
. The addition of synthetic AHLs (C
16:1
and 3-O-C
16:1
) complemented grape necrosis in the
avsR
,
avsI
, ORF1, and ORF2 mutants. It was determined by reverse transcriptase PCR that the expression level of
avsI
is regulated by
avsR
but not by
aviR
or
avhR
, two other luxR homologs which were previously shown to be associated with induction of a tobacco hypersensitive response and grape necrosis. We further verified that
avsR
regulates
avsI
by measuring the expression of an
avsI
::
lacZ
fusion construct.
YtkD and MutT Protect Vegetative Cells but Not Spores of
Bacillus subtilis
from Oxidative Stress
Authors: Castellanos-Juárez Francisco X. , Álvarez-Álvarez Carlos , Yasbin Ronald E. , Setlow Barbara , Setlow Peter , Pedraza-Reyes Mario
Published: March 2006

ytkD
and
mutT
of
Bacillus subtilis
encode potential 8-oxo-dGTPases that can prevent the mutagenic effects of 8-oxo-dGTP. Loss of YtkD but not of MutT increased the spontaneous mutation frequency of growing cells. However, cells lacking both YtkD and MutT had a higher spontaneous mutation frequency than cells lacking YtkD. Loss of either YtkD or MutT sensitized growing cells to hydrogen peroxide (H
2
O
2
) and
t
-butylhydroperoxide (
t
-BHP), and the lack of both proteins sensitized growing cells to these agents even more. In contrast,
B. subtilis
spores lacking YtkD and MutT were not sensitized to H
2
O
2
,
t
-BHP, or heat. These results suggest (i) that YtkD and MutT play an antimutator role and protect growing cells of
B. subtilis
against oxidizing agents, and (ii) that neither YtkD nor MutT protects spores against potential DNA damage induced by oxidative stress or heat.
Genomic Comparison of
Mycobacterium avium
subsp.
paratuberculosis
Sheep and Cattle Strains by Microarray Hybridization
Authors: Marsh Ian B. , Bannantine John P. , Paustian Michael L. , Tizard Mark L. , Kapur Vivek , Whittington Richard J.
Published: March 2006

Microarray-based comparisons of three
Mycobacterium avium
subsp.
paratuberculosis
isolates, including one sheep strain and two cattle strains, identified three large genomic deletions in the sheep strain, totaling 29,208 bp and involving 24 open reading frames. These deletions may help explain some of the differences in pathogenicity and host specificity observed between the cattle and sheep strains of
Mycobacterium avium
subsp.
paratuberculosis
.
CORRECTED BLACK HOLE THERMODYNAMICS FROM A MODIFIED WAVE-PARTICLE DUALITY
Authors: LI XIANG , SHEN YOU-GEN
Published: March 2006

In this paper, we argue that the log-area type correction to black hole entropy is also obtained from a gravitationally-induced modification to de Broglie wave-particle duality. A formula for the corrected temperature is presented. The negative temperature might be an interesting hint, although its meaning is still unclear. We make comparisons between our work and relevant literatures.
EMBEDDING GÖDEL'S UNIVERSE IN FIVE DIMENSIONS
Authors: FONSECA-NETO J. B. , ROMERO C. , DAHIA F.
Published: March 2006

According to the Campbell–Magaard theorem, any analytical spacetime can be locally and analytically embedded into a five-dimensional pseudo-Riemannian Ricci-flat manifold. This embedding for Gödel's universe can be found. The embedding space is Ricci-flat and has a non-Lorentzian signature of type (+ + - - -). We also show that the embedding found is global.
REMARKS ON E11 APPROACH
Authors: MKRTCHYAN H. , MKRTCHYAN R.
Published: March 2006

We consider a few topics in E11 approach to superstrings/M-theory: even subgroups (Z2 orbifolds) of En, n = 11, 10, 9 and their connection to Kac–Moody algebras, particularly to EE11 subgroup of E11; possible form of supersymmetry relation in E11; decomposition of first fundamental representation l1 w.r.t. the SO (10, 10) and its square-root at first few levels; particle orbit of l1 ⋉ E11. Possible relevance of coadjoint orbits method is noticed, based on a self-duality form of equations of motion in E11.
Freeze-thaw increases adeno-associated virus transduction of cells
Authors: Chen Sifeng , Wasserfall Clive , Kapturczak Matthias H. , Atkinson Mark , Agarwal Anupam
Published: March 2006

A combination of gene and cell-based therapies may provide significant advantages over existing treatments in terms of their effectiveness. However, long-term efficient gene delivery has been difficult to achieve in many cell types, including endothelial cells. We developed a freeze-thaw technique which significantly increases the transduction efficiency of recombinant adeno-associated virus vectors in human aortic endothelial cells (23-fold) and in human renal proximal tubular epithelial cells (128-fold) in comparison to current methods for transduction. Freeze-thaw resulted in a transient but significant increase in cell surface area by 1,174 ± 69.8 μM2 per cell. Reduction of cryogenic medium volume and repeated freeze-thaw further increased transduction efficiency by 2.8- and 2.4-fold, respectively. Trypsinization, dimethylsulfoxide, and cold temperatures, which are also involved in cell preservation, had no significant impact on transduction efficiency. Increased transduction was also observed in mesenchymal stem cells (42-fold) by the freeze-thaw method. The potential mechanism of this novel technique likely involves an increase in the net permeable area of biological membranes caused by water crystallization. These findings provide a new approach for gene delivery in various cell types, particularly in those resistant to transduction by conventional methods.
Hop functions downstream of Nkx2.1 and GATA6 to mediate HDAC-dependent negative regulation of pulmonary gene expression
Authors: Yin Zhan , Gonzales Linda , Kolla Venkatadri , Rath Nibedita , Zhang Yuzhen , Lu Min Min , Kimura Shioko , Ballard Philip L. , Beers Michael F. , Epstein Jonathan A. , Morrisey Edward E.
Published: March 2006

Hop is an unusual homeodomain protein that was first identified in the developing heart where it functions downstream of Nkx2.5 to modulate cardiac gene expression. Hop functions through interactions with histone deacetylase (HDAC) 2 to mediate repression of cardiac-specific genes, and recent studies show that HDAC activity and HDAC2 expression are decreased in people with chronic obstructive pulmonary disease. Here, we show that Hop is expressed in airway epithelium coincident with HDAC2, and expression is induced by the combination of dexamethasone and cAMP in parallel with induction of surfactant protein gene expression. Hop functions in the developing pulmonary airway, acting downstream of Nkx2.1 and GATA6, to negatively regulate surfactant protein expression. Loss of Hop expression in vivo results in defective type 2 pneumocyte development with increased surfactant production and disrupted alveolar formation. Thus Hop represents a novel regulator of pulmonary maturation that is induced by glucocorticoids to mediate functionally important HDAC-dependent negative feedback regulation.
Postexercise hypotension causes a prolonged perturbation in esophageal and active muscle temperature recovery
Authors: Kenny Glen P. , Jay Ollie , Zaleski Wytek M. , Reardon Mark L. , Sigal Ronald J. , Journeay W. Shane , Reardon Francis D.
Published: March 2006

We examined the effect of two levels of exercise-induced hypotension on esophageal (Tes) and active and nonactive muscle temperatures during and following exercise. Seven males performed an incremental isotonic test on a Kin-Com isokinetic apparatus to determine their peak oxygen consumption during bilateral knee extensions (V̇o2sp). This was followed on separate days by 15-min of isolated bilateral knee extensions at moderate (60% V̇o2sp) (MEI) and high (80% V̇o2sp) (HEI) exercise intensities, followed by 90 min of recovery. Muscle temperature was measured with an intramuscular probe inserted in the left vastus medialis (Tvm) and triceps brachii (Ttb) muscles under ultrasound guidance. The deepest sensor (tip) was located ∼10 mm from the femur and deep femoral artery and from the superior ulnar collateral artery and humerus for the Tvm and Ttb, respectively. Additional sensors were located 15 and 30 mm from the tip with an additional sensor located at 45 mm for the Tvm measurements only. Following exercise, mean arterial pressure (MAP) remained significantly below preexercise rest for the initial 60 min of recovery after MEI and for the duration of the postexercise recovery period after HEI ( P ≤ 0.05). After HEI, significantly greater elevations from preexercise rest were recorded for Tes and all muscle temperatures paralleled a greater decrease in MAP compared with MEI (all P ≤ 0.05). By the end of 90-min postexercise recovery, MAP, Tes, and all muscle temperatures remained significantly greater after HEI than MEI. Furthermore, a significantly shallower muscle temperature profile across Tvm, relative to preexercise rest, was observed at the end of exercise for both HEI and MEI ( P ≤ 0.05), and for 30 min of recovery for MEI and throughout 90 min of recovery for HEI. No significant differences in muscle temperature profile were observed for Ttb. Thus we conclude that the increase in the postexercise hypotensive response, induced by exercise of increasing intensity, was paralleled by an increase in the magnitude and recovery time of the postexercise esophageal and active muscle temperatures.
Selective cerebral vascular dysfunction in Mn-SOD-deficient mice
Authors: Faraci F. M. , Modrick M. L. , Lynch C. M. , Didion L. A. , Fegan P. E. , Didion S. P.
Published: March 2006

We tested the hypothesis that the mitochondrial form of superoxide dismutase [manganese superoxide dismutase (Mn-SOD)] protects the cerebral vasculature. Basilar arteries (baseline diameter ∼140 μm) from mice were isolated, cannulated, and pressurized to measure vessel diameter. In arteries from C57BL/6 mice preconstricted with U-46619, acetylcholine (ACh; an endothelium-dependent vasodilator) produced dilation that was similar in male and female mice and abolished by an inhibitor of nitric oxide synthase. Vasodilation to ACh was not altered in heterozygous male or female Mn-SOD-deficient (Mn-SOD+/−) mice compared with wild-type littermate controls (Mn-SOD+/+). Constriction of the basilar artery to arginine vasopressin, but not KCl or U-46619, was increased in Mn-SOD+/− mice ( P < 0.05), and this effect was prevented by tempol, a scavenger of superoxide. We also examined responses of cerebral (pial) arterioles (branches of the middle cerebral artery, control diameter ∼30 μm) to ACh in anesthetized mice using a cranial window. Responses to ACh, but not nitroprusside (an endothelium-independent agonist), were reduced ( P < 0.05) in cerebral arterioles in Mn-SOD+/− mice, and this effect was prevented by tempol. Thus these are the first data on the role of Mn-SOD in cerebral circulation. In the basilar artery, ACh produced nitric oxide-mediated dilation that was similar in male and female mice. Under normal conditions in cerebral arteries, responses to ACh were not altered but constrictor responses were selectively enhanced in Mn-SOD+/− mice. In the cerebral microcirculation, there was superoxide-mediated impairment of responses to ACh.
Low-Threshold Ca2+-Associated Bursts Are Rare Events in the LGN of the Awake Behaving Monkey
Authors: Ruiz Octavio , Royal David , Sáry Gyula , Chen Xin , Schall Jeffrey D. , Casagrande Vivien A.
Published: March 2006

It has been proposed that low-threshold Ca2+ (LT)-associated bursts in the lateral geniculate nucleus (LGN) of awake animals communicate significant or unexpected visual events to cortex. The present study investigated this hypothesis by examining the incidence of LT bursts in 146 cells recorded from the LGN of three macaque monkeys. Bursts were defined as clusters of two or more action potentials separated by not more than 4 ms and preceded by a ≥100-ms quiescent interval. The incidence of bursts was examined in several intensive-training Go-NoGo and target selection tasks as well as in training-free tasks where natural scenes with both familiar and novel contents were shown. Our chief findings were as follows. 1) Bursts occur in the majority of cells under every condition tested, 2) burst incidence is very low (<1 burst every 10 s), 3) bursts occur in association with a receptive field stimulus on average only once every 23 times in 65% of cells tested, 4) cells responding with bursts to the stimulus also tended to exhibit higher levels of spontaneous bursting, 5) the presence of bursts did not depend on the novelty of the stimulus or its behavioral relevance. When the monkeys explored static natural scenes, 6) bursts were not correlated with short-term changes in the image sampled by the cell's receptive field during saccades. Burst incidence 7) did not increase when images were novel or when they evoked an emotional reaction, and 8) bursts did not decrease when images were familiar. 9) Bursts were not correlated with saccades in the dark, but 10) more spikes participated in bursts in the dark. Although these results confirm the occurrence of LT bursts in LGN cells of awake monkeys, they do not support the hypothesis that these bursts are a privileged means of transferring sensory information, that they signal unexpected or significant visual events, or that they are involved uniquely in the coding of natural scenes.
Conduction Deficits and Membrane Disruption of Spinal Cord Axons as a Function of Magnitude and Rate of Strain
Authors: Shi Riyi , Whitebone Jim
Published: March 2006

White matter strips extracted from adult guinea pig spinal cords were subjected to tensile strain (stretch) injury ex vivo. Strain was carried out at three magnitudes (25, 50, and 100%) and two strain rate regimens: slow (0.006–0.008 s−1) and fast (355–519 s−1). The cord samples were monitored physiologically using a double sucrose-gap technique and anatomically using a horseradish peroxidase assay. It seems that a higher magnitude of strain inflicted significantly more functional and structural damage within each strain rate group. Likewise, a higher strain rate inflicted more damage when the strain magnitude was maintained. It is evident that axons have remarkable tolerance to strain injury at a slow strain rate. Even a 100% strain at the slow rate only eliminated two-thirds of the compound action potential amplitude and resulted in almost no membrane damage when examined 30 min after strain. It is also clear that the spontaneous recovery is evident yet not complete compared with preinjury levels at the fast strain rate. To examine the factors that might influence the vulnerability of axons to strain, we have shown that the axonal diameters did not play a significant role in dictating the susceptibility of axons to strain. Rather, it is speculated that the location of axons might be a more important factor in this regard. The knowledge gained from this study is likely to be informative in elucidating the spinal cord biomechanical response to strain and strain rate.
Modulation of V1 Activity by Shape: Image-Statistics or Shape-Based Perception?
Authors: Dumoulin Serge O. , Hess Robert F.
Published: March 2006

It is current dogma that neurons in primary visual cortex extract local edges from the scene from which later visual areas reconstruct more meaningful shapes. Recent neuroimaging studies, however, have shown V1 modulations by the degree of structure in the image (shape). These V1 modulations due to the level of shape coherence have been explained in one of two possible ways: due to changes in image statistics or shape-based perceptual influences from higher visual areas. Here we compare both hypotheses using stimuli composed of Gabor arrays constructed to form circular shapes that can be successively degraded by manipulating the orientations of individual Gabors while maintaining local and global statistics. In a first experiment, we confirm that V1 responses are inversely correlated with the degree of structure in the image. In a second experiment, stimulus predictions are compared based on the degree of circular shape or change in the image statistic varied (orientation variance) in the image. We find that these V1 modulations to shape change are correlated with low-level changes in orientation contrast rather than shape perception per se.
Concurrent Encoding of Frequency and Amplitude Modulation in Human Auditory Cortex: MEG Evidence
Authors: Luo Huan , Wang Yadong , Poeppel David , Simon Jonathan Z.
Published: March 2006

A natural sound can be described by dynamic changes in envelope (amplitude) and carrier (frequency), corresponding to amplitude modulation (AM) and frequency modulation (FM), respectively. Although the neural responses to both AM and FM sounds are extensively studied in both animals and humans, it is uncertain how they are corepresented when changed simultaneously but independently, as is typical for ecologically natural signals. This study elucidates the neural coding of such sounds in human auditory cortex using magnetoencephalography (MEG). Using stimuli with both sinusoidal modulated envelope (ƒAM, 37 Hz) and carrier frequency (ƒFM, 0.3–8 Hz), it is demonstrated that AM and FM stimulus dynamics are corepresented in the neural code of human auditory cortex. The stimulus AM dynamics are represented neurally with AM encoding, by the auditory steady-state response (aSSR) at ƒAM. For sounds with slowly changing carrier frequency (ƒFM <5 Hz), it is shown that the stimulus FM dynamics are tracked by the phase of the aSSR, demonstrating neural phase modulation (PM) encoding of the stimulus carrier frequency. For sounds with faster carrier frequency change (ƒFM ≥ 5 Hz), it is shown that modulation encoding of stimulus FM dynamics persists, but the neural encoding is no longer purely PM. This result is consistent with the recruitment of additional neural AM encoding over and above the original neural PM encoding, indicating that both the amplitude and phase of the aSSR at ƒAM track the stimulus FM dynamics. A neural model is suggested to account for these observations.
Loss of Fragile Histidine Triad Gene Expression in Advanced Lung Cancer Is Consequent to Allelic Loss at 3p14 Locus and Promoter Methylation
Authors: Wali Anjilna , Srinivasan Radhika , Shabnam Mir Snober , Majumdar Siddhartha , Joshi Kusum , Behera Digambar
Published: March 2006

The fragile histidine triad (FHIT) gene located at the 3p14.2 locus plays an important role in the pathogenesis of lung cancer. The objective of this study was to analyze loss of heterozygosity and FHIT gene methylation status and correlate them to fhit expression. Bronchoscopically obtained lung biopsies from 30 cases of histologically proven carcinoma of the lung in stage III were assessed for the alterations in the FHIT gene. Fhit protein expression was determined by immunohistochemistry, and transcript levels were determined by reverse transcription-PCR. Microsattelite alterations and methylation status of the Fhit gene promoter was determined by PCR. Loss of heterozygosity at the 3p14 locus was observed in all the 30 cases at least by one of the three microsatellite polymorphic markers. The FHIT gene promoter showed complete methylation in 37% cases and partial methylation in 47% cases, and 16% cases showed no promoter methylation. FHIT full-length coding region (exons 5-9) transcripts were present in eight cases (26.6%), and aberrant transcripts were additionally seen in four cases. Loss of FHIT mRNA expression correlated to FHIT promoter methylation but not to loss of heterozygosity at the 3p14 locus. There was a strong correlation between the expression of FHIT at the transcript and protein level. The apoptotic index estimated by the terminal deoxynucleotidyl transferase–mediated nick end labeling assay was significantly correlated to the fhit protein expression. The results of this study indicate that in locally advanced carcinoma of the lung, there is frequent loss of FHIT expression, and methylation of the FHIT gene promoter is an important mechanism of its inactivation. (Mol Cancer Res 2006;4(2):93–9)
Mechanisms of Cell Death Induced by Histone Deacetylase Inhibitors in Androgen Receptor–Positive Prostate Cancer Cells
Authors: Rokhlin Oskar W. , Glover Rebecca B. , Guseva Natalya V. , Taghiyev Agshin F. , Kohlgraf Karl G. , Cohen Michael B.
Published: March 2006

Histone deacetylase inhibitors (HDACI) are potential therapeutic agents that inhibit tumor cell growth and survival. Although there are several publications regarding the effects of HDACIs on prostate cancer cell growth, their mechanism(s) of action remains undefined. We treated several human prostate cancer cell lines with the HDACI trichostatin A and found that trichostatin A induced cell death in androgen receptor (AR)–positive cell lines to higher extent compared with AR-negative cell lines. We then discovered that trichostatin A and other HDACIs suppressed AR gene expression in prostate cancer cell lines as well as in AR-positive breast carcinoma cells and in mouse prostate. Trichostatin A also induced caspase activation, but trichostatin A–induced AR suppression and cell death were caspase independent. In addition, we found that doxorubicin inhibited AR expression, and p21 protein completely disappeared after simultaneous treatment with trichostatin A and doxorubicin. This effect may be attributed to the induction of protease activity under simultaneous treatment with these two agents. Further, simultaneous treatment with trichostatin A and doxorubicin increased cell death in AR-positive cells even after culturing in steroid-free conditions. The protease/proteasome inhibitor MG132 protected AR and p21 from the effects of trichostatin A and doxorubicin and inhibited trichostatin A–induced cell death in AR-positive prostate cells. Taken together, our data suggest that the main mechanism of trichostatin A–induced cell death in AR-positive prostate cancer is inhibition of AR gene expression. The synergistic effect of simultaneous treatment with trichostatin A and doxorubicin is mediated via inhibition of AR expression, induction of protease activity, increased expression of p53, and proteolysis of p21. (Mol Cancer Res 2006;4(2):113–23)
Involvement of the ATR- and ATM-Dependent Checkpoint Responses in Cell Cycle Arrest Evoked by Pierisin-1
Authors: Shiotani Bunsyo , Kobayashi Masahiko , Watanabe Masahiko , Yamamoto Ken-ichi , Sugimura Takashi , Wakabayashi Keiji
Published: March 2006

Pierisin-1 identified from the cabbage butterfly, Pieris rapae, is a novel mono-ADP-ribosylating toxin that transfers the ADP-ribose moiety of NAD at N2 of dG in DNA. Resulting mono-ADP-ribosylated DNA adducts cause mutations and the induction of apoptosis. However, little is known about checkpoint responses elicited in mammalian cells by the formation of such bulky DNA adducts. In the present study, it was shown that DNA polymerases were blocked at the specific site of mono-ADP-ribosylated dG, which might lead to the replication stress. Pierisin-1 treatment of HeLa cells was found to induce an intra-S-phase arrest through both ataxia telangiectasia mutated (ATM) and Rad3-related (ATR) and ATM pathways, and ATR pathway also contributes to a G2-M-phase delay. In the colony survival assays, Rad17−/− DT40 cells showed greater sensitivity to pierisin-1-induced cytotoxicity than wild-type and ATM−/− DT40 cells, possibly due to defects of checkpoint responses, such as the Chk1 activation. Furthermore, apoptotic 50-kb DNA fragmentation was observed in the HeLa cells, which was well correlated with occurrence of phosphorylation of Chk2. These results thus suggest that pierisin-1 treatment primarily activates ATR pathway and eventually activates ATM pathway as a result of the induction of apoptosis. From these findings, it is suggested that mono-ADP-ribosylation of DNA causes a specific type of fork blockage that induces checkpoint activation and signaling. (Mol Cancer Res 2006;4(2):125–33)
Regulation of NADPH Oxidases
Authors: Hordijk Peter L.
Published: March 2006

The role for reactive oxygen species (ROS) in cellular (patho)physiology, in particular in signal transduction, is increasingly recognized. The family of NADPH oxidases (NOXes) plays an important role in the production of ROS in response to receptor agonists such as growth factors or inflammatory cytokines that signal through the Rho-like small GTPases Rac1 or Rac2. The phagocyte oxidase (gp91

phox

/NOX2) is the best characterized family member, and its mode of activation is relatively well understood. Recent work has uncovered novel and increasingly complex modes of control of the NOX2-related proteins. Some of these, including NOX2, have been implicated in various aspects of (cardio)vascular disease, including vascular smooth muscle and endothelial cell hypertrophy and proliferation, inflammation, and atherosclerosis. This review focuses on the role of the Rac1 and Rac2 GTPases in the activation of the various NOX family members.
Disarmament without Agreements?
Authors: Rydell Randy
Published: March 2006

The literature on arms control and disarmament is replete with studies demonstrating the numerous difficulties in negotiating agreements for the control or elimination of nuclear weapons. These studies stress the time consumed during negotiations, the complexity of the emerging agreements, the trade-offs required to achieve agreement, the political difficulties of treaty ratification, and the alleged advantages of alternative approaches to arms control and disarmament not involving treaties. This essay examines whether treaties and negotiations are in fact dispensable in achieving agreed multilateral disarmament objectives. It surveys recent multilateral efforts in the field of nuclear disarmament and identifies six basic criteria that enjoy broad international support as standards for assessing the merits of disarmament agreements. The essay concludes that tacit understandings and other informal political arrangements offer no substitute for legally-binding treaty obligations. This conclusion leads to several implications affecting the conduct of multilateral negotiations, and the kinds of institutional support required in the negotiating process and for the maintenance of key commitments by the relevant multilateral regimes.
Negotiating Multilateral Instruments Against Missile Proliferation
Authors: Mistry Dinshaw , Smith Mark
Published: March 2006

The absence of a major multilateral treaty banning missiles is explained by the limited scope of the two main instruments against missile proliferation – the Missile Technology Control Regime (MTCR) and the Hague Code of Conduct against Ballistic Missile Proliferation (HCOC). In the MTCR's case, limiting the scope to supply-side technology controls facilitated progress during its negotiations. In the Hague Code, limiting the scope to transparency, and keeping out additional items such as incentives to renounce ballistic missiles and the topic of cruise missiles, made negotiations easier. The trade-off from a limited scope in both instruments is that there is still no significant worldwide treaty banning missiles.
The Limited Test Ban Negotiations, 1954–63: How a Negotiator Viewed the Proceedings
Authors: Goodby James
Published: March 2006

The test ban treaty negotiations had their origins in a larger-than-expected U.S. thermonuclear explosion in the Pacific in 1954. Nearly a decade later, in 1963, Great Britain, the Soviet Union, and the United States concluded a treaty that permitted underground explosions but banned them in other environments. It was the first treaty of the Cold War to place limits on nuclear operations, but it was not what the negotiators had originally sought – a complete ban on tests. A substantial amount of pre-negotiations on the limited test ban treaty occurred during the Eisenhower administration. The idea itself first surfaced very early in these pre-negotiations. The willingness of two U.S. presidents and a British prime minister to persevere in the face of domestic opposition and foreign difficulties shows the importance of individuals in the negotiating process. The effect on negotiations of world events not directly related to the talks is demonstrated by the impact of the Sino-Soviet split, the unsettled status of Berlin and Germany, and the Cuban Missile Crisis. Single-issue lobbyists, representing the interests of weapons laboratories and the views of those opposed to U.S.-Soviet cooperation, caused major difficulties during the years of negotiations, as reflected in the interagency bargaining that preceded policy decisions. This included the use of scientific information both to advance and to block the negotiations. As a leading member of the advisory and negotiating teams during much of the period discussed in this article, the author pays tribute to professionals in the Eisenhower and Kennedy administrations whose dedication and ingenuity kept the negotiations alive until circumstances finally crowned the effort with success.
Shear and Static Instability of Inertia–Gravity Wave Packets: Short-Term Modal and Nonmodal Growth
Authors: Achatz Ulrich , Schmitz Gerhard
Published: March 2006

The problem of nonmodal instabilities of inertia–gravity waves (IGW) in the middle atmosphere is addressed, within the framework of a Boussinesq model with realistic molecular viscosity and thermal diffusion, by singular-vector analysis of horizontally homogeneous vertical profiles of wind and buoyancy obtained from IGW packets at their statically least stable or most unstable horizontal location. Nonmodal growth is always found to be significantly stronger than that of normal modes, most notably at wave amplitudes below the static instability limit where normal-mode instability is very weak, whereas the energy gain between the optimal perturbation and singular vector after one Brunt–Väisälä period can be as large as two orders of magnitude. Among a multitude of rapidly growing singular vectors for this optimization time, small-scale (wavelengths of a few 100 m) perturbations propagating in the horizontal parallel to the IGW are most prominent. These parallel optimal perturbations are amplified by a roll mechanism, while transverse perturbations (with horizontal scales of a few kilometers) are to a large part subject to an Orr mechanism, both controlled by the transverse wind shear in the IGW at its statically least stable altitude, but further enhanced by reduced static stability. The elliptic polarization of the IGW leaves its traces in an additional impact of the roll mechanism via the parallel wind shear on the leading transverse optimal perturbation.