bluuebunny/crossref_metadata_2025 huggingface dataset:
Catabolic Pathway for the Production of Skatole and Indoleacetic Acid by the Acetogen
Clostridium drakei
,
Clostridium scatologenes
, and Swine Manure
Authors: Whitehead Terence R. , Price Neil P. , Drake Harold L. , Cotta Michael A.
Published: January 2008

Skatole (3-methylindole) is a malodorous chemical in stored swine manure and is implicated as a component of foul-tasting pork. Definitive evidence for the skatole pathway is lacking. Deuterium-labeled substrates were employed to resolve this pathway in the acetogenic bacterium
Clostridium drakei
and
Clostridium scatologenes
and to determine if a similar pathway is used by microorganisms present in stored swine manure. Indoleacetic acid (IAA) was synthesized from tryptophan by both bacteria, and skatole was synthesized from both IAA and tryptophan. Microorganisms in swine manure produced skatole and other oxidation products from tryptophan, but IAA yielded only skatole. A catabolic mechanism for the synthesis of skatole is proposed.
Glycogen Phosphorylase in
Acanthamoeba
spp.: Determining the Role of the Enzyme during the Encystment Process Using RNA Interference
Authors: Lorenzo-Morales Jacob , Kliescikova Jarmila , Martinez-Carretero Enrique , De Pablos Luis Miguel , Profotova Bronislava , Nohynkova Eva , Osuna Antonio , Valladares Basilio
Published: January 2008

Acanthamoeba
infections are difficult to treat due to often late diagnosis and the lack of effective and specific therapeutic agents. The most important reason for unsuccessful therapy seems to be the existence of a double-wall cyst stage that is highly resistant to the available treatments, causing reinfections. The major components of the
Acanthamoeba
cyst wall are acid-resistant proteins and cellulose. The latter has been reported to be the major component of the inner cyst wall. It has been demonstrated previously that glycogen is the main source of free glucose for the synthesis of cellulose in
Acanthamoeba
, partly as glycogen levels fall during the encystment process. In other lower eukaryotes (e.g.,
Dictyostelium discoideum
), glycogen phosphorylase has been reported to be the main tool used for glycogen breakdown in order to maintain the free glucose levels during the encystment process. Therefore, it was hypothesized that the regulation of the key processes involved in the
Acanthamoeba
encystment may be similar to the previously reported regulation mechanisms in other lower eukaryotes. The catalytic domain of the glycogen phosphorylase was silenced using RNA interference methods, and the effect of this phenomenon was assessed by light and electron microscopy analyses, calcofluor staining, expression zymogram assays, and Northern and Western blot analyses of both small interfering RNA-treated and control cells. The present report establishes the role of glycogen phosphorylase during the encystment process of
Acanthamoeba
. Moreover, the obtained results demonstrate that the enzyme is required for cyst wall assembly, mainly for the formation of the cell wall inner layer.
Key Function for the CCAAT-Binding Factor Php4 To Regulate Gene Expression in Response to Iron Deficiency in Fission Yeast
Authors: Mercier Alexandre , Watt Stephen , Bähler Jürg , Labbé Simon
Published: January 2008

The fission yeast
Schizosaccharomyces pombe
responds to the deprivation of iron by inducing the expression of the
php4

+

gene, which encodes a negative regulatory subunit of the heteromeric CCAAT-binding factor. Once formed, the Php2/3/4/5 transcription complex is required to inactivate a subset of genes encoding iron-using proteins. Here, we used a pan-
S. pombe
microarray to study the transcriptional response to iron starvation and identified 86 genes that exhibit
php4

+

-dependent changes on a genome-wide scale. One of these genes encodes the iron-responsive transcriptional repressor Fep1, whose mRNA levels were decreased after treatment with the permeant iron chelator 2,2′-dipyridyl. In addition, several genes encoding the components of iron-dependent biochemical pathways, including the tricarboxylic acid cycle, mitochondrial respiration, amino acid biosynthesis, and oxidative stress defense, were downregulated in response to iron deficiency. Furthermore, Php4 repressed transcription when brought to a promoter using a yeast DNA-binding domain, and iron deprivation was required for this repression. On the other hand, Php4 was constitutively active when glutathione levels were depleted within the cell. Based on these and previous results, we propose that iron-dependent inactivation of Php4 is regulated at two distinct levels: first, at the transcriptional level by the iron-responsive GATA factor Fep1 and second, at the posttranscriptional level by a mechanism yet to be identified, which inhibits Php4-mediated repressive function when iron is abundant.
Role of
Staphylococcus aureus
Catalase in Niche Competition against
Streptococcus pneumoniae
Authors: Park Bonggoo , Nizet Victor , Liu George Y.
Published: January 2008

Nasal colonization by
Staphylococcus aureus
is a major predisposing factor for subsequent infection. Recent reports of increased
S. aureus
colonization among children receiving pneumococcal vaccine implicate
Streptococcus pneumoniae
as an important competitor for the same niche. Since
S. pneumoniae
uses H
2
O
2
to kill competing bacteria, we hypothesized that oxidant defense could play a significant role in promoting
S. aureus
colonization of the nasal mucosa. Using targeted mutagenesis, we showed that
S. aureus
expression of catalase contributes significantly to the survival of this pathogen in the presence of
S. pneumoniae
both in vitro and in a murine model of nasal cocolonization.
Staphylococcus aureus
Pathogenicity Island DNA Is Packaged in Particles Composed of Phage Proteins
Authors: Tormo María Ángeles , Ferrer María Desamparados , Maiques Elisa , Úbeda Carles , Selva Laura , Lasa Íñigo , Calvete Juan J. , Novick Richard P. , Penadés José R.
Published: January 2008

Staphylococcus aureus
pathogenicity islands (SaPIs) have an intimate relationship with temperate staphylococcal phages. During phage growth, SaPIs are induced to replicate and are efficiently encapsidated into special small phage heads commensurate with their size. We have analyzed by amino acid sequencing and mass spectrometry the protein composition of the specific SaPI particles. This has enabled identification of major capsid and tail proteins and a putative portal protein. As expected, all these proteins were phage encoded. Additionally, these analyses suggested the existence of a protein required for the formation of functional phage but not SaPI particles. Mutational analysis demonstrated that the phage proteins identified were involved only in the formation and possibly the function of SaPI or phage particles, having no role in other SaPI or phage functions.
Cyclic AMP-Dependent Catabolite Repression Is the Dominant Control Mechanism of Metabolic Fluxes under Glucose Limitation in
Escherichia coli
Authors: Nanchen Annik , Schicker Alexander , Revelles Olga , Sauer Uwe
Published: January 2008

Although a whole arsenal of mechanisms are potentially involved in metabolic regulation, it is largely uncertain when, under which conditions, and to which extent a particular mechanism actually controls network fluxes and thus cellular physiology. Based on
13
C flux analysis of
Escherichia coli
mutants, we elucidated the relevance of global transcriptional regulation by ArcA, ArcB, Cra, CreB, CreC, Crp, Cya, Fnr, Hns, Mlc, OmpR, and UspA on aerobic glucose catabolism in glucose-limited chemostat cultures at a growth rate of 0.1 h
−1
. The by far most relevant control mechanism was cyclic AMP (cAMP)-dependent catabolite repression as the inducer of the phosphoenolpyruvate (PEP)-glyoxylate cycle and thus low tricarboxylic acid cycle fluxes. While all other mutants and the reference
E. coli
strain exhibited high glyoxylate shunt and PEP carboxykinase fluxes, and thus high PEP-glyoxylate cycle flux, this cycle was essentially abolished in both the Crp and Cya mutants, which lack the cAMP-cAMP receptor protein complex. Most other mutations were phenotypically silent, and only the Cra and Hns mutants exhibited slightly altered flux distributions through PEP carboxykinase and the tricarboxylic acid cycle, respectively. The Cra effect on PEP carboxykinase was probably the consequence of a specific control mechanism, while the Hns effect appears to be unspecific. For central metabolism, the available data thus suggest that a single transcriptional regulation process exerts the dominant control under a given condition and this control is highly specific for a single pathway or cycle within the network.
Binding of the Major Phasin, PhaP1, fromRalstonia eutrophaH16 to Poly(3-Hydroxybutyrate) Granules
Authors: Neumann Liv , Spinozzi Francesco , Sinibaldi Raffaele , Rustichelli Franco , Pötter Markus , Steinbüchel Alexander
Published: January 2008

The surface of polyhydroxybutyrate (PHB) storage granules in bacteria is covered mainly by proteins referred to as phasins. The layer of phasins stabilizes the granules and prevents coalescence of separated granules in the cytoplasm and nonspecific binding of other proteins to the hydrophobic surfaces of the granules. Phasin PhaP1Reuis the major surface protein of PHB granules inRalstonia eutrophaH16 and occurs along with three homologues (PhaP2, PhaP3, and PhaP4) that have the capacity to bind to PHB granules but are present at minor levels. All four phasins lack a highly conserved domain but share homologous hydrophobic regions. To identify the region of PhaP1Reuwhich is responsible for the binding of the protein to the granules, N-terminal and C-terminal fusions of enhanced green fluorescent protein with PhaP1Reuor various regions of PhaP1Reuwere generated by recombinant techniques. The fusions were localized in the cells of various recombinant strains by fluorescence microscopy, and their presence in different subcellular protein fractions was determined by immunodetection of blotted proteins. The fusions were also analyzed to determine their capacities to bind to isolated PHB granules in vitro. The results of these studies indicated that unlike the phasin ofRhodococcus ruber, there is no discrete binding motif; instead, several regions of PhaP1Reucontribute to the binding of this protein to the surface of the granules. The conclusions are supported by the results of a small-angle X-ray scattering analysis of purified PhaP1Reu, which revealed that PhaP1Reuis a planar, triangular protein that occurs as trimer. This study provides new insights into the structure of the PHB granule surface, and the results should also have an impact on potential biotechnological applications of phasin fusion proteins and PHB granules in nanobiotechnology.
Identification of Genes Associated with the Long-Gut-Persistence Phenotype of the Probiotic
Lactobacillus johnsonii
Strain NCC533 Using a Combination of Genomics and Transcriptome Analysis
Authors: Denou Emmanuel , Pridmore Raymond David , Berger Bernard , Panoff Jean-Michel , Arigoni Fabrizio , Brüssow Harald
Published: January 2008

Lactobacillus johnsonii
strains NCC533 and ATCC 33200 (the type strain of this species) differed significantly in gut residence time (12 versus 5 days) after oral feeding to mice. Genes affecting the long gut residence time of the probiotic strain NCC533 were targeted for analysis. We hypothesized that genes specific for this strain, which are expressed during passage of the bacterium through the gut, affect the phenotype. When the DNA of the type strain was hybridized against a microarray of the sequenced NCC533 strain, we identified 233 genes that were specific for the long-gut-persistence isolate. Whole-genome transcription analysis of the NCC533 strain using the microarray format identified 174 genes that were strongly and consistently expressed in the jejunum of mice monocolonized with this strain. Fusion of the two microarray data sets identified three gene loci that were both expressed in vivo and specific to the long-gut-persistence isolate. The identified genes included LJ1027 and LJ1028, two glycosyltransferase genes in the exopolysaccharide synthesis operon; LJ1654 to LJ1656, encoding a sugar phosphotransferase system (PTS) transporter annotated as mannose PTS; and LJ1680, whose product shares 30% amino acid identity with immunoglobulin A proteases from pathogenic bacteria. Knockout mutants were tested in vivo. The experiments revealed that deletion of LJ1654 to LJ1656 and LJ1680 decreased the gut residence time, while a mutant with a deleted exopolysaccharide biosynthesis cluster had a slightly increased residence time.
Comparative Genomics and an Insect Model Rapidly Identify Novel Virulence Genes of
Burkholderia mallei
Authors: Schell Mark A. , Lipscomb Lyla , DeShazer David
Published: January 2008

Burkholderia pseudomallei
and its host-adapted deletion clone
Burkholderia mallei
cause the potentially fatal human diseases melioidosis and glanders, respectively. The antibiotic resistance profile and ability to infect via aerosol of these organisms and the absence of protective vaccines have led to their classification as major biothreats and select agents. Although documented infections by these bacteria date back over 100 years, relatively little is known about their virulence and pathogenicity mechanisms. We used in silico genomic subtraction to generate their virulome, a set of 650 putative virulence-related genes shared by
B. pseudomallei
and
B. mallei
but not present in five closely related nonpathogenic
Burkholderia
species. Although most of these genes are clustered in putative operons, the number of targets for mutant construction and verification of reduced virulence in animal models is formidable. Therefore,
Galleria mellonella
(wax moth) larvae were evaluated as a surrogate host; we found that
B. pseudomallei
and
B. mallei
, but not other phylogenetically related bacteria, were highly pathogenic for this insect. More importantly, four previously characterized
B. mallei
mutants with reduced virulence in hamsters or mice had similarly reduced virulence in
G. mellonella
larvae. Site-specific inactivation of selected genes in the computationally derived virulome identified three new potential virulence genes, each of which was required for rapid and efficient killing of larvae. Thus, this approach may provide a means to quickly identify high-probability virulence genes in
B. pseudomallei, B. mallei
, and other pathogens.
Genetic Interaction Screens with Ordered Overexpression and Deletion Clone Sets Implicate the
Escherichia coli
GTPase YjeQ in Late Ribosome Biogenesis
Authors: Campbell Tracey L. , Brown Eric D.
Published: January 2008

The
Escherichia coli
protein YjeQ is a circularly permuted GTPase that is broadly conserved in bacteria. An emerging body of evidence, including cofractionation and in vitro binding to the ribosome, altered polysome profiles after YjeQ depletion, and stimulation of GTPase activity by ribosomes, suggests that YjeQ is involved in ribosome function. The growth of strains lacking YjeQ in culture is severely compromised. Here, we probed the cellular function of YjeQ with genetic screens of ordered
E. coli
genomic libraries for suppressors and enhancers of the slow-growth phenotype of a Δ
yjeQ
strain. Screening for suppressors using an ordered library of 374 clones overexpressing essential genes and genes associated with ribosome function revealed that two GTPases, Era and initiation factor 2, ameliorated the growth and polysome defects of the Δ
yjeQ
strain. In addition, seven bona fide enhancers of slow growth were identified (Δ
tgt
, Δ
ksgA
, Δ
ssrA
, Δ
rimM
, Δ
rluD
, Δ
trmE/mnmE
, and Δ
trmU/mnmA
) among 39 deletions (in genes associated with ribosome function) that we constructed in the Δ
yjeQ
genetic background. Taken in context, our work is most consistent with the hypothesis that YjeQ has a role in late 30S subunit biogenesis.
Quorum Sensing Controls Biofilm Formation in
Vibrio cholerae
through Modulation of Cyclic Di-GMP Levels and Repression of
vpsT
Authors: Waters Christopher M. , Lu Wenyun , Rabinowitz Joshua D. , Bassler Bonnie L.
Published: January 2008

Two chemical signaling systems, quorum sensing (QS) and 3′,5′-cyclic diguanylic acid (c-di-GMP), reciprocally control biofilm formation in
Vibrio cholerae
. QS is the process by which bacteria communicate via the secretion and detection of autoinducers, and in
V. cholerae
, QS represses biofilm formation. c-di-GMP is an intracellular second messenger that contains information regarding local environmental conditions, and in
V. cholerae
, c-di-GMP activates biofilm formation. Here we show that HapR, a major regulator of QS, represses biofilm formation in
V. cholerae
through two distinct mechanisms. HapR controls the transcription of 14 genes encoding a group of proteins that synthesize and degrade c-di-GMP. The net effect of this transcriptional program is a reduction in cellular c-di-GMP levels at high cell density and, consequently, a decrease in biofilm formation. Increasing the c-di-GMP concentration at high cell density to the level present in the low-cell-density QS state restores biofilm formation, showing that c-di-GMP is epistatic to QS in the control of biofilm formation in
V. cholerae
. In addition, HapR binds to and directly represses the expression of the biofilm transcriptional activator,
vpsT
. Together, our results suggest that
V. cholerae
integrates information about the vicinal bacterial community contained in extracellular QS autoinducers with the intracellular environmental information encoded in c-di-GMP to control biofilm formation.
Analysis of the
Campylobacter jejuni
FlgR Response Regulator Suggests Integration of Diverse Mechanisms To Activate an NtrC-Like Protein
Authors: Joslin Stephanie N. , Hendrixson David R.
Published: January 2008

Flagellar motility in
Campylobacter jejuni
mediates optimal interactions with human or animal hosts. σ
54
and the FlgSR two-component system are necessary for the expression of many
C. jejuni
flagellar genes. The FlgR response regulator is homologous to the NtrC family of transcriptional activators. These regulators usually contain an N-terminal receiver domain, a central domain that interacts with σ
54
and hydrolyzes ATP, and a DNA-binding C-terminal domain. Most often, phosphorylation of the receiver domain influences its inherent ability to either positively or negatively control the activity of the regulator. In this study, we performed genetic and biochemical analyses to understand how FlgR activity is controlled to culminate in the expression of σ
54
-dependent flagellar genes. Our data suggest that the FlgR receiver domain has the capacity for both positive and negative regulation in controlling the activation of the protein. Analysis of the C-terminal domain of FlgR revealed that it lacks a DNA-binding motif and is not required for σ
54
-dependent flagellar gene expression. Further analysis of FlgR lacking the C-terminal domain indicates that this protein is partially functional in the absence of the cognate sensor kinase, FlgS, but its activity is still dependent on the phosphorylated residue in the receiver domain, D51. We hypothesize that the C-terminal domain may not function to bind DNA but may ensure the specificity of the phosphorylation of FlgR by FlgS. Our results demonstrate that FlgR activation mechanisms are unusual among characterized NtrC-like proteins and emphasize that various means are utilized by the NtrC family of proteins to control the transcription of target genes.
Analysis of Tryptophan Residues in the Staphylococcal Multidrug Transporter QacA Reveals Long-Distance Functional Associations of Residues on Opposite Sides of the Membrane
Authors: Hassan Karl A. , Souhani Talal , Skurray Ronald A. , Brown Melissa H.
Published: January 2008

Tryptophan residues can possess a multitude of functions within a multidrug transport protein, e.g., mediating interactions with substrates or distal parts of the protein, or fulfilling a structural requirement, such as guiding the depth of membrane insertion. In this study, the nine tryptophan residues of the staphylococcal QacA multidrug efflux protein were individually mutated to alanine and phenylalanine, and the functional consequences of these changes were determined. Phenylalanine substitutions for each tryptophan residue were functionally tolerated. However, alanine modifications revealed an important functional role for three tryptophan residues, W58, W149, and W173, each of which is well conserved among QacA-related transport proteins in the major facilitator superfamily. The most functionally compromising mutation, an alanine substitution for W58, likely to be located at the extracellular interface of transmembrane segment 2, abolished all detectable QacA-mediated resistance and transport function. Second-site suppressor analyses identified several mutations that rescued the function of the W58A QacA mutant. Remarkably, all of these suppressor mutations were shown to be located in cytoplasmic loops between transmembrane helices 2 and 3 or 12 and 13, demonstrating novel functional associations between amino acid positions on opposite sides of the membrane and in distal N- and C-terminal regions of the QacA protein.
Signal Integration by the Two-Component Signal Transduction Response Regulator CpxR
Authors: Wolfe Alan J. , Parikh Niyati , Lima Bruno P. , Zemaitaitis Bozena
Published: January 2008

The CpxAR two-component signal transduction system in
Escherichia coli
and other pathogens senses diverse envelope stresses and promotes the transcription of a variety of genes that remedy these stresses. An important member of the CpxAR regulon is
cpxP
. The CpxA-dependent transcription of
cpxP
has been linked to stresses such as misfolded proteins and alkaline pH. It also has been proposed that acetyl phosphate, the intermediate of the phosphotransacetylase (Pta)-acetate kinase (AckA) pathway, can activate the transcription of
cpxP
in a CpxA-independent manner by donating its phosphoryl group to CpxR. We tested this hypothesis by measuring the transcription of
cpxP
using mutants with mutations in the CpxAR pathway, mutants with mutations in the Pta-AckA pathway, and mutants with a combination of both types of mutations. From this epistasis analysis, we learned that CpxR integrates diverse stimuli. The stimuli that originate in the envelope depend on CpxA, while those associated with growth and central metabolism depend on the Pta-AckA pathway. While CpxR could receive a phosphoryl group from acetyl phosphate, this global signal was not the primary trigger for CpxR activation associated with the Pta-AckA pathway. On the strength of these results, we contend that the interactions between central metabolism and signal transduction can be quite complex and that successful investigations of such interactions must include a complete epistatic analysis.
Heavy metal pollution and Pb isotopes in urban soils of Napoli, Italy
Authors: Cicchella D. , De Vivo B. , Lima A. , Albanese S. , McGill R.A.R. , Parrish R.R.
Published: January 2008

Lead isotope analysis is an increasingly widespread tool in the study of environmental pollution as Pb isotope compositions do not change during industrial and environmental processes, and always reflect their source origin. In this study we present the results of R-mode factor analysis for associations between chemical elements in Neapolitan soils, combined with the distribution of Pb concentrations and Pb isotope compositions in order to differentiate natural from anthropogenic metal sources. Results show Neapolitan urban soils to be significantly enriched in Pb, Hg, Zn, Sb, and to a lesser extent in Cu, Cd, Cr and Ni. Lead isotope measurements form a trend suggesting mixing between two end-member compositions, one of clear natural origin (geogenic) and another related to human activities (anthropogenic). Lead isotope investigations demonstrate that road traffic is one of the main sources of metal pollution.
Platinum group element distribution in the soils from urban areas of the Campania region (Italy)
Authors: Cicchella D. , Fedele L. , De Vivo B. , Albanese S. , Lima A.
Published: January 2008

This paper represents a detailed study to assess the platinum group element (PGE) content of topsoils from urban areas in the Campania region (Italy), following on from previous work. Samples were collected from residual and non-residual soils from flowerbeds in the urban areas of Avellino, Benevento and Caserta (characterized by low population density, LPD), and in Salerno (a city with high population and high automobile traffic densities).

The soils (<100-mesh size fraction, i.e. <150 μm) were analysed for Pt, Pd and Rh by fire assay ICP-MS and for 37 other elements by ICP-AES and ICP-MS after a modified aqua regia digestion. In LPD cities, PGE concentrations were close to background values (with the exception of the industrial areas), but Salerno proved to be contaminated by PGEs. Platinum, Pd and Rh concentrations are in the <0.1–278, <0.5–432 and 0.07–47 ppb range, respectively. Moreover, a high correlation among Pt, Pd and Rh (R=0.98), and between PGEs and other typical traffic-emitted metals such as Cr, Cu, Sb and Sn has been detected only in Salerno. Finally, the statistical analysis pointed out a lower background for PGEs in soils formed on sedimentary rocks (in the eastern sector of Caserta, in Benevento and Salerno) compared to those formed on volcanic rocks (Avellino and the western area of Caserta).
Low-dose aspirin prevents age-related endothelial dysfunction in a mouse model of physiological aging
Authors: Bulckaen Hélène , Prévost Gaétan , Boulanger Eric , Robitaille Géraldine , Roquet Valérie , Gaxatte Cédric , Garçon Guillaume , Corman Bruno , Gosset Pierre , Shirali Pirouz , Creusy Colette , Puisieux François
Published: January 2008

The age-related impairment of endothelium-dependent vasodilatation contributes to increased cardiovascular risk in the elderly. For primary and secondary prevention, aspirin can reduce the incidence of cardiovascular events in this patient population. The present work evaluated the effect of low-dose aspirin on age-related endothelial dysfunction in C57B/J6 aging mice and investigated its protective antioxidative effect. Age-related endothelial dysfunction was assessed by the response to acetylcholine of phenylephrine-induced precontracted aortic segments isolated from 12-, 36-, 60-, and 84-wk-old mice. The effect of low-dose aspirin was examined in mice presenting a decrease in endothelial-dependent relaxation (EDR). The effects of age and aspirin treatment on structural changes were determined in mouse aortic sections. The effect of aspirin on the oxidative stress markers malondialdehyde and 8-hydroxy-2′-deoxyguanosine (8-OhdG) was also quantified. Compared with that of 12-wk-old mice, the EDR was significantly reduced in 60- and 84-wk-old mice ( P < 0.05); 68-wk-old mice treated with aspirin displayed a higher EDR compared with control mice of the same age (83.9 ± 4 vs. 66.3 ± 5%; P < 0.05). Aspirin treatment decreased 8-OHdG levels ( P < 0.05), but no significant effect on intima/media thickness ratio was observed. The protective effect of aspirin was not observed when treatment was initiated in older mice (96 wk of age). It was found that low-dose aspirin is able to prevent age-related endothelial dysfunction in aging mice. However, the absence of this effect in the older age groups demonstrates that treatment should be initiated early on. The underlying mechanism may involve the protective effect of aspirin against oxidative stress.
Delayed cardioprotection afforded by the glycogen synthase kinase 3 inhibitor SB-216763 occurs via a KATP- and MPTP-dependent mechanism at reperfusion
Authors: Gross Eric R. , Hsu Anna K. , Gross Garrett J.
Published: January 2008

Previous studies in our laboratory suggest that an acute inhibition of glycogen synthase kinase 3 (GSK3) by SB-216763 (SB21) is cardioprotective when administered just before reperfusion. However, it is unknown whether the GSK inhibitor SB21 administered 24 h before ischemia is cardioprotective and whether the mechanism involves ATP-sensitive potassium (KATP) channels and the mitochondrial permeability transition pore (MPTP). Male Sprague-Dawley rats were administered the GSK inhibitor SB21 (0.6 mg/kg) or vehicle 24 h before ischemia. Subsequently, the rats were acutely anesthetized with Inactin and underwent 30 min of ischemia and 2 h of reperfusion followed by infarct size determination. Subsets of rats received either the sarcolemmal KATP channel blocker HMR-1098 (6 mg/kg), the mitochondrial KATP channel blocker 5-hydroxydecanoic acid (5-HD; 10 mg/kg), or the MPTP opener atractyloside (5 mg/kg) either 5 min before SB21 administration or 5 min before reperfusion 24 h later. The infarct size was reduced in SB21 compared with vehicle (44 ± 2% vs. 61 ± 2%, respectively; P < 0.01). 5-HD administered either before SB21 treatment or 5 min before reperfusion the following day abrogated SB21-induced protection (54 ± 4% and 61 ± 2%, respectively). HMR-1098 did not affect the SB21-induced infarct size reduction when administered before the SB21 treatment (43 ± 1%); however, HMR-1098 partially abrogated the SB21-induced infarct size reduction when administered just before reperfusion 24 h later (52 ± 1%). The MPTP opening either before SB21 administration or 5 min before reperfusion abrogated the infarct size reduction produced by SB21 (61 ± 2% and 62 ± 2%, respectively). Hence, GSK inhibition reduces infarct size when given 24 h before the administration via the opening KATP channels and MPTP closure.
T3 increases Na-K-ATPase activity via a MAPK/ERK1/2-dependent pathway in rat adult alveolar epithelial cells
Authors: Lei Jianxun , Mariash Cary N. , Bhargava Maneesh , Wattenberg Elizabeth V. , Ingbar David H.
Published: January 2008

Thyroid hormone (T3) increases Na-K-ATPase activity in rat adult alveolar type II cells via a PI3K-dependent pathway. In these cells, dopamine and β-adrenergic agonists can stimulate Na-K-ATPase activity through either PI3K or MAPK pathways. We assessed the role of the MAPK pathway in the stimulation of Na-K-ATPase by T3. In the adult rat alveolar type II-like cell line MP48, T3 enhanced MAPK/ERK1/2 activity in a dose-dependent manner. Increased ERK1/2 phosphorylation was observed within 5 min, peaked at 20 min, and then decreased. Two MEK1/2 inhibitors, U0126 and PD-98059, each abolished the T3-induced increase in the quantity of Na-K-ATPase α1-subunit plasma membrane protein and Na-K-ATPase activity. T3 also increased the phosphorylation of MAPK/p38; however, SB-203580, a specific inhibitor of MAPK/p38 activity, did not prevent the T3-induced Na-K-ATPase activity. SP-600125, a specific inhibitor of the MAPK/JNK pathway, also did not block the T3-induced Na-K-ATPase activity. Phorbol 12-myristate 13-acetate (PMA) significantly increased ERK1/2 phosphorylation and Na-K-ATPase activity. The PMA-induced Na-K-ATPase activity was inhibited by U0126. These data indicate that activation of MAPK-ERK1/2 was required for the T3-induced increase in Na-K-ATPase activity in addition to the requirement for the PI3K pathway.
Mechanisms of cigarette smoke-induced COPD: insights from animal models
Authors: Churg Andrew , Cosio Manuel , Wright Joanne L.
Published: January 2008

Cigarette smoke-induced animal models of chronic obstructive pulmonary disease support the protease-antiprotease hypothesis of emphysema, although which cells and proteases are the crucial actors remains controversial. Inhibition of either serine or metalloproteases produces significant protection against emphysema, but inhibition is invariably accompanied by decreases in the inflammatory response to cigarette smoke, suggesting that these inhibitors do more than just prevent matrix degradation. Direct anti-inflammatory interventions are also effective against the development of emphysema, as are antioxidant strategies; the latter again decrease smoke-induced inflammation. There is increasing evidence for autoimmunity, perhaps directed against matrix components, as a driving force in emphysema. There is intriguing but controversial animal model evidence that failure to repair/failure of lung maintenance also plays a role in the pathogenesis of emphysema. Cigarette smoke produces small airway remodeling in laboratory animals, possibly by direct induction of fibrogenic growth factors in the airway wall, and also produces pulmonary hypertension, at least in part through direct upregulation of vasoactive mediators in the intrapulmonary arteries. Smoke exposure causes goblet cell metaplasia and excess mucus production in the small airways and proximal trachea, but these changes are not good models of either chronic bronchitis or acute exacerbations. Emphysema, small airway remodeling, pulmonary hypertension, and mucus production appear to be at least partially independent processes that may require different therapeutic approaches.
The Basis of an Intracrine Pharmacology
Authors: Re Richar N. , Cook Juli L.
Published: January 2008

Intracrines are extracellular signaling peptide factors that can act in the intracellular space after either internalization or retention in the cells that synthesize them. They are structurally diverse and include hormones, growth factors, enzymes, DNA‐binding proteins, and other peptide moieties. We have suggested principles of intracrine action and have applied those principles to forms of cellular and tissue differentiation, hormonal responsiveness, and memory. Moreover, recent findings make clear that some currently available pharmaceuticals act via the alteration of intracrine function. Thus, the beginnings of an intracrine pharmacology are at hand and we here review principles applicable to the design of such agents. The intracrine pharmacology of the renin‐angiotensin system, angiogenesis, and stem cell development is discussed.
Perceived Organizational Support: Reducing the Negative Influence of Coworker Withdrawal Behavior
Authors: Eder Paul , Eisenberger Robert
Published: January 2008

When employees' coworkers exhibit higher levels of withdrawal, individual employees are more likely to withdraw from their own work. The authors explored whether this relation would be curbed by a positive exchange relationship with one's organization, as suggested by organizational support theory (Eisenberger, Huntington, Hutchison, & Sowa, 1986). Among 23 work groups in a manufacturing organization (Study 1), high perceived organizational support (POS) eliminated the relation between work group and individual tardiness. Among 94 work groups in a retail sales organization (Study 2), POS reduced the relation between work group withdrawal and individual withdrawal.
Residuals of Death
Authors: Lapum Jennifer L.
Published: January 2008

This is a poem about living and how people construct certain things to provide them with a sense of comfort in life. It lends itself to the idea of how death shapes living in prereflexive ways, sometimes before death is even on the horizon. The crafting of this poetry attempts to bring forth how comfort and what people think provides comfort can be transformed by the abstraction of death and the reality of death.
Preserved and Impaired Aspects of Feed-Forward Grip Force Control After Chronic Somatosensory Deafferentation
Authors: Hermsdörfer J. , Elias Z. , Cole J. D. , Quaney B. M. , Nowak D. A.
Published: January 2008

Background. Although feed-forward mechanisms of grip force control are a prerequisite for skilled object manipulation, somatosensory feedback is essential to acquire, maintain, and adapt these mechanisms. Objective. Individuals with complete peripheral deafferentation provide the unique opportunity to study the function of the motor system deprived of somatosensory feedback. Methods. Two individuals (GL and IW) with complete chronic deafferentation of the trunk and limbs were tested during cyclic vertical movements of a hand-held object. Such movements induce oscillating loads that are typically anticipated by parallel modulations of the grip force. Load magnitude was altered by varying either the movement frequency or object weight. Results. GL and IW employed excessive grip forces probably reflecting a compensatory mechanism. Despite this overall force increase, both deafferented participants adjusted their grip force level according to the load magnitude, indicating preserved scaling of the background grip force to physical demands. The dynamic modulation of the grip force with the load force was largely absent in GL, whereas in IW only slower movements were clearly affected. Conclusions. The authors hypothesize that the deafferented patients may have utilized visual and vestibular cues and/or an efferent copy of the motor command of the arm movement to scale the grip force level. Severely impaired grip force-load coupling in GL suggests that sensory information is important for maintaining a precise internal model of dynamic grip force control. However, comparably better performance in IW argues for the possibility that alternative cues can be used to trigger a residual internal model.
Hardness improvement of surface alloyed materials fabricated with Fe based metamorphic powders by high energy electron beam irradiation
Authors: Nam D.-H. , Lee K. , Lee S. , Kim C. P.
Published: January 2008

In the present study, surface alloyed materials were fabricated with Fe based metamorphic powders by the high energy electron beam irradiation. A surface alloyed layer was fabricated by depositing metamorphic powders on a carbon steel substrate and by irradiating with high energy electron beam. On top of this surface alloyed layer, metamorphic powders were deposited once again and irradiated with electron beam to fabricate a two layered surface alloyed material. In the surface alloyed layers, 53–64 vol.-%Cr1·65Fe0·35B0·96 borides were densely precipitated in the martensitic matrix. A large amount of hard borides improved the hardness of the surface alloyed layers 2–3 times greater than that of the substrate. In addition, they showed high hardness of ∼500 VHN even at 450°C, because borides were thermally stable at high temperatures. These results suggested potentials of the fabricated surface alloyed materials for applications requiring good wear and thermal resistance.
Formation of fine grained globular microstructures during isothermal annealing of PM T42 high speed steel: Role of nanometric proeutectoid carbides
Authors: Trabadelo V. , Iturriza I.
Published: January 2008

The microstructure of powder metallurgy T42 high speed steel has been analysed after isothermal annealing. The heat treatment parameters (austenitising temperature, annealing time and annealing temperature) have been chosen aiming at obtaining a moderate hardness (50 HRC) adequate for structural applications. It has been demonstrated that it is possible to attain the targeted hardness through a globular pearlitic matrix microstructure at temperatures markedly lower than A1 and by short time annealing cycles. The key factor for the generation of such microstructure is the precipitation of a homogeneous distribution of nanometric tungsten rich M6C proeutectoid carbides in the austenite. The presence of these carbides avoids the growing of lamellar pearlite independently of the annealing time.
Efficient refinement of spherical grains by LSPSF rheocasting process
Authors: Guo H.-M. , Yang X.-J.
Published: January 2008

A new rheocasting process, low superheat pouring with a shear field (LSPSF), to achieve sound semisolid slurry is reported. Results show that a fully grain refined spherical structure can be obtained using proper processing conditions within 25 s. The efficient grain refinement should be attributed to the continuous nucleation events, enhanced crystal separation from the nucleation sites and crystal survival, as a consequence of low superheat pouring combined with localised rapid cooling and positive mixing–shearing during the initial stage of solidification. The discussion based on the morphological instability theory indicates that the combined effects of both low cooling and high grain density can enhance the stabilisation of solid/liquid interface and promote grains to grow spherically to a larger size scale. Suppressing dendrite growth and coarsening through the overlapping of diffusion fields and the Gibbs–Thomson effect are the main dynamic conditions that lead to the formation of spherical primary a α-Al particles.
Mechanical and hardness evaluations of Fe–18Cr–18Mn alloys
Authors: Rawers J. , Duttlinger N.
Published: January 2008

A series of Fe–18Cr–18Mn–N–C alloys was produced and evaluated to determine their mechanical and hardness properties. In one group, different levels of nitrogen and carbon were added to a base composition of Fe–18Cr–18Mn. The base Fe–18Cr–18Mn alloy had a fcc–bcc duplex microstructure. The addition of nitrogen and carbon stabilised the fcc phase. These alloys had increasing room temperature hardness, strength, and failure energy with increasing interstitial concentrations. At cryogenic and elevated temperatures, these alloys had increasing hardness (and by implication, increased strength) with increasing interstitial concentrations. In a second group, different levels of nitrogen and carbon were added to the base Fe–18Cr–18Mn composition to which minor solid solution additions of silicon, molybdenum, and nickel had been added. Minor alloy additions made only nominal improvement to mechanical and hardness properties. Nitrogen remained interstitial. However, these minor solid solution additions reduced carbon solubility resulting in the formation of M23C6 precipitates that, while increasing alloy hardness and strength, greatly reduced fracture toughness. The present study suggests that replacing nickel with manganese in stainless steels results not only in more economical alloys but also in alloys with higher strength and hardness.
Deformation behaviour in superplastic 5083 Al alloy during biaxial gas pressure forming with lubrication
Authors: Chen H.-H. , Wu H.-Y. , Lee W.-S. , Lee S.
Published: January 2008

Effect of lubrication on deformation behaviour of a superplastic material has been given little attention, although it is important for industrial application. In this paper, a superplastic 5083 Al alloy under biaxial deformation was investigated by deforming the sheet into a cylindrical die cavity with and without lubrication. Several interrupted tests were performed to bulge the sheets to various depths for two different strain rates, the formed parts were then utilised to evaluate the effect of lubrication on metal flow, thickness distribution and cavitation. It was found that reducing the interfacial friction by use of a lubricant improved the metal flow after the deformed sheet had made contact with the bottom surface of die. Changes of the metal flow during forming not only developed a better thickness distribution of the formed part, but also reduced cavitation levels.
Role of zinc coat in friction stir lap welding Al and zinc coated steel
Authors: Chen Y. C. , Komazaki T. , Tsumura T. , Nakata K.
Published: January 2008

AC4C cast Al alloy and Zn coated steel were successfully lap welded using friction stir welding technology. Full strength joints could be obtained and the joints fractured at Zn coated steel base metal side, while Al alloy and unzinced steel could not be welded in the same welding conditions. The joining mechanism and the role of Zn coat on friction stir lap welding of Al alloy and Zn coated steel were put forward. The intervention of Zn coat promoted the formation of Al–Zn low melting point eutectic structure at the interface, which significantly improved the weldability of Al and steel.
Development of microstructure and mechanical properties of as cast Al–Mg–Mn alloy during high temperature ECAP
Authors: Ning J. L. , Jiang D. M.
Published: January 2008

A large scale billet with diameter of 58·5 mm of an as cast Al–Mg–Mn alloy was processed by equal channel angular pressing (ECAP) at 350°C up to six passes. A significant refinement of the grains was observed after six pressings to ∼2 μm. And the selected area electron diffraction (SAED) pattern showed that almost all of the grains were separated by boundaries with high angles of misorientation. A banded substructure was not observed during the hot ECAP, and a reasonably equiaxed structure was obtained just after one single pressing. Both the strength and the elongation increased abruptly in a single passage through the die, but thereafter, the increase was more gradual and exhibited a saturation effect after the fourth pressing. The good combination of strength and ductility of the Al–Mg–Mn alloy attained by the hot ECAP appeared to be attractive properties for industrial applications. Moreover, hot ECAP could possibly be used as an alternative step to hot extrusion or hot rolling in industrial processing, to break down an initial coarse as cast structure in a quite large scale billet.
A Faster Index Algorithm and a Computational Study for Bandits with Switching Costs
Authors: Niño-Mora José
Published: January 2008

We address the intractable multi-armed bandit problem with switching costs, for which an index that partially characterizes optimal policies was introduced (Asawa, M., D. Teneketzis. 1996. Multi-armed bandits with switching penalties. IEEE Trans. Automatic Control 41 328–348), attaching to each project state a “continuation index” (its Gittins index) and a “switching index.” Asawa and Teneketzis proposed to jointly compute both as the Gittins index of a project with 2n states—when the original project has n states—resulting in an eightfold increase in O(n3) arithmetic operations relative to those to compute the continuation index. We present a faster decoupled computation method, which in a first stage computes the continuation index and then, in a second stage, computes the switching index an order of magnitude faster in at most n2+ O(n) arithmetic operations, achieving overall a fourfold reduction in arithmetic operations and substantially reduced memory operations. The analysis exploits the fact that the Asawa and Teneketzis index is the marginal productivity index of the project in its restless reformulation, using methods introduced by the author. Extensive computational experiments are reported, which demonstrate the dramatic runtime speedups achieved by the new algorithm, as well as the near optimality of the resultant index policy and its substantial gains against the benchmark Gittins index policy across a wide range of randomly generated two- and three-project instances.
Risk Minimization and Minimum Description for Linear Discriminant Functions
Authors: Aytug Haldun , Koehler Gary J. , He Ling
Published: January 2008

Statistical learning theory provides a formal criterion for learning a concept from examples. This theory addresses directly the trade-off in empirical fit and generalization. In practice, this leads to the structural risk-minimization principle where one minimizes a bound on the overall risk functional. For learning linear discriminant functions, this bound is impacted by the minimum of two terms—the dimension and the inverse of the margin. A popular and powerful learning mechanism, support vector machines, focuses on maximizing the margin. We compare this to methods that focus on minimizing the dimensionality, which, coincidentally, fulfills another useful criterion—the minimum description length principle.