bluuebunny/crossref_metadata_2025 huggingface dataset:
Putative Role of Cellulosomal Protease Inhibitors in Clostridium cellulovorans Based on Gene Expression and Measurement of Activities
Authors: Meguro Hirokazu , Morisaka Hironobu , Kuroda Kouichi , Miyake Hideo , Tamaru Yutaka , Ueda Mitsuyoshi
Published: July 2011

This study is the first to demonstrate the activity of putative cellulosomal protease/peptidase inhibitors (named cyspins) ofClostridium cellulovorans, using theSaccharomyces cerevisiaedisplay system. Cyspins exhibited inhibitory activities against several representative plant proteases. This suggests that these inhibitors protect their microbe and cellulosome from external attack by plant proteases.
Complete Genome and Proteome of Acholeplasma laidlawii
Authors: Lazarev V. N. , Levitskii S. A. , Basovskii Y. I. , Chukin M. M. , Akopian T. A. , Vereshchagin V. V. , Kostrjukova E. S. , Kovaleva G. Y. , Kazanov M. D. , Malko D. B. , Vitreschak A. G. , Sernova N. V. , Gelfand M. S. , Demina I. A. , Serebryakova M. V. , Galyamina M. A. , Vtyurin N. N. , Rogov S. I. , Alexeev D. G. , Ladygina V. G. , Govorun V. M.
Published: July 2011

We present the complete genome sequence and proteogenomic map for
Acholeplasma laidlawii
PG-8A (class
Mollicutes
, order
Acholeplasmatales
, family
Acholeplasmataceae
). The genome of
A. laidlawii
is represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the
Mollicutes
with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress.
Acholeplasma laidlawii
and phytoplasmas are the only
Mollicutes
known to use the universal genetic code, in which UGA is a stop codon. Within the
Mollicutes
group, only the sterol-nonrequiring
Acholeplasma
has the capacity to synthesize saturated fatty acids
de novo
. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of
A. laidlawii
proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to
A. laidlawii
, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.
Provirus Induction in Hyperthermophilic Archaea: Characterization of Aeropyrum pernix Spindle-Shaped Virus 1 and Aeropyrum pernix Ovoid Virus 1
Authors: Mochizuki Tomohiro , Sako Yoshihiko , Prangishvili David
Published: July 2011

By
in silico
analysis, we have identified two putative proviruses in the genome of the hyperthermophilic archaeon
Aeropyrum pernix
, and under special conditions of
A. pernix
growth, we were able to induce their replication. Both viruses were isolated and characterized. Negatively stained virions of one virus appeared as pleomorphic spindle-shaped particles, 180 to 210 nm by 40 to 55 nm, with tails of heterogeneous lengths in the range of 0 to 300 nm. This virus was named
Aeropyrum pernix
spindle-shaped virus 1 (APSV1). Negatively stained virions of the other virus appeared as slightly irregular oval particles with one pointed end, while in cryo-electron micrographs, the virions had a regular oval shape and uniform size (70 by 55 nm). The virus was named
Aeropyrum pernix
ovoid virus 1 (APOV1). Both viruses have circular, double-stranded DNA genomes of 38,049 bp for APSV1 and 13,769 bp for APOV1. Similarities to proteins of other archaeal viruses were limited to the integrase and Dna1-like protein. We propose to classify APOV1 into the family
Guttaviridae
.
Identification and Characterization of a
Re
-Citrate Synthase in Dehalococcoides Strain CBDB1
Authors: Marco-Urrea Ernest , Paul Steffanie , Khodaverdi Viola , Seifert Jana , von Bergen Martin , Kretzschmar Utta , Adrian Lorenz
Published: July 2011

The genome annotations of all sequenced
Dehalococcoides
strains lack a citrate synthase, although physiological experiments have indicated that such an activity should be encoded. We here report that a
Re
face-specific citrate synthase is synthesized by
Dehalococcoides
strain CBDB1 and that this function is encoded by the gene cbdbA1708 (NCBI accession number
CAI83711
), previously annotated as encoding homocitrate synthase. Gene cbdbA1708 was heterologously expressed in
Escherichia coli
, and the recombinant enzyme was purified. The enzyme catalyzed the condensation of oxaloacetate and acetyl coenzyme A (acetyl-CoA) to citrate. The protein did not have homocitrate synthase activity and was inhibited by citrate, and Mn
2+
was needed for full activity. The stereospecificity of the heterologously expressed citrate synthase was determined by electrospray ionization liquid chromatography-mass spectrometry (ESI LC/MS). Citrate was synthesized from [2-
13
C]acetyl-CoA and oxaloacetate by the
Dehalococcoides
recombinant citrate synthase and then converted to acetate and malate by commercial citrate lyase plus malate dehydrogenase. The formation of unlabeled acetate and
13
C-labeled malate proved the
Re
face-specific activity of the enzyme. Shotgun proteome analyses of cell extracts of strain CBDB1 demonstrated that cbdbA1708 is expressed in strain CBDB1.
Quantifying Aggregation Dynamics during Myxococcus xanthus Development
Authors: Zhang Haiyang , Angus Stuart , Tran Michael , Xie Chunyan , Igoshin Oleg A. , Welch Roy D.
Published: July 2011

Under starvation conditions, a swarm of
Myxococcus xanthus
cells will undergo development, a multicellular process culminating in the formation of many aggregates called fruiting bodies, each of which contains up to 100,000 spores. The mechanics of symmetry breaking and the self-organization of cells into fruiting bodies is an active area of research. Here we use microcinematography and automated image processing to quantify several transient features of developmental dynamics. An analysis of experimental data indicates that aggregation reaches its steady state in a highly nonmonotonic fashion. The number of aggregates rapidly peaks at a value 2- to 3-fold higher than the final value and then decreases before reaching a steady state. The time dependence of aggregate size is also nonmonotonic, but to a lesser extent: average aggregate size increases from the onset of aggregation to between 10 and 15 h and then gradually decreases thereafter. During this process, the distribution of aggregates transitions from a nearly random state early in development to a more ordered state later in development. A comparison of experimental results to a mathematical model based on the traffic jam hypothesis indicates that the model fails to reproduce these dynamic features of aggregation, even though it accurately describes its final outcome. The dynamic features of
M. xanthus
aggregation uncovered in this study impose severe constraints on its underlying mechanisms.
Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp
Authors: Bogdanove Adam J. , Koebnik Ralf , Lu Hong , Furutani Ayako , Angiuoli Samuel V. , Patil Prabhu B. , Van Sluys Marie-Anne , Ryan Robert P. , Meyer Damien F. , Han Sang-Wook , Aparna Gudlur , Rajaram Misha , Delcher Arthur L. , Phillippy Adam M. , Puiu Daniela , Schatz Michael C. , Shumway Martin , Sommer Daniel D. , Trapnell Cole , Benahmed Faiza , Dimitrov George , Madupu Ramana , Radune Diana , Sullivan Steven , Jha Gopaljee , Ishihara Hiromichi , Lee Sang-Won , Pandey Alok , Sharma Vikas , Sriariyanun Malinee , Szurek Boris , Vera-Cruz Casiana M. , Dorman Karin S. , Ronald Pamela C. , Verdier Valérie , Dow J. Maxwell , Sonti Ramesh V. , Tsuge Seiji , Brendel Volker P. , Rabinowicz Pablo D. , Leach Jan E. , White Frank F. , Salzberg Steven L.
Published: July 2011

Xanthomonas
is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of
Xanthomonas campestris
pv. raphani strain 756C and
X. oryzae
pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology,
Arabidopsis thaliana
and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete
Xanthomonas
genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.
The RpiR-Like Repressor IolR Regulates Inositol Catabolism in Sinorhizobium meliloti
Authors: Kohler Petra R. A. , Choong Ee-Leng , Rossbach Silvia
Published: July 2011

Sinorhizobium meliloti
, the nitrogen-fixing symbiont of alfalfa, has the ability to catabolize
myo
-,
scyllo
-, and
d
-
chiro
-inositol. Functional inositol catabolism (
iol
) genes are required for growth on these inositol isomers, and they play a role during plant-bacterium interactions. The inositol catabolism genes comprise the chromosomally encoded
iolA
(
mmsA
) and the
iolY
(
smc01163
)
RCDEB
genes, as well as the
idhA
gene located on the pSymB plasmid. Reverse transcriptase assays showed that the
iolYRCDEB
genes are transcribed as one operon. The
iol
genes were weakly expressed without induction, but their expression was strongly induced by
myo
-inositol. The putative transcriptional regulator of the
iol
genes, IolR, belongs to the RpiR-like repressor family. Electrophoretic mobility shift assays demonstrated that IolR recognized a conserved palindromic sequence (5′-GGAA-N
6
-TTCC-3′) in the upstream regions of the
idhA
,
iolY
,
iolR
, and
iolC
genes. Complementation assays found IolR to be required for the repression of its own gene and for the downregulation of the
idhA
-encoded
myo
-inositol dehydrogenase activity in the presence and absence of inositol. Further expression studies indicated that the late pathway intermediate 2-keto-5-deoxy-
d
-gluconic acid 6-phosphate (KDGP) functions as the true inducer of the
iol
genes. The
iolA
(
mmsA
) gene encoding methylmalonate semialdehyde dehydrogenase was not regulated by IolR. The
S. meliloti iolA
(
mmsA
) gene product seems to be involved in more than only the inositol catabolic pathway, since it was also found to be essential for valine catabolism, supporting its more recent annotation as
mmsA
.
Osmotically Controlled Synthesis of the Compatible Solute Proline Is Critical for Cellular Defense of Bacillus subtilis against High Osmolarity
Authors: Brill Jeanette , Hoffmann Tamara , Bleisteiner Monika , Bremer Erhard
Published: July 2011

Bacillus subtilis
is known to accumulate large amounts of the compatible solute proline via
de novo
synthesis as a stress protectant when it faces high-salinity environments. We elucidated the genetic determinants required for the osmoadaptive proline production from the precursor glutamate. This proline biosynthesis route relies on the
proJ
-encoded γ-glutamyl kinase, the
proA
-encoded γ-glutamyl phosphate reductase, and the
proH
-encoded Δ
1
-pyrroline-5-caboxylate reductase. Disruption of the
proHJ
operon abolished osmoadaptive proline production and strongly impaired the ability of
B. subtilis
to cope with high-osmolarity growth conditions. Disruption of the
proA
gene also abolished osmoadaptive proline biosynthesis but caused, in contrast to the disruption of
proHJ
, proline auxotrophy. Northern blot analysis demonstrated that the transcription of the
proHJ
operon is osmotically inducible, whereas that of the
proBA
operon is not. Reporter gene fusion studies showed that
proHJ
expression is rapidly induced upon an osmotic upshift. Increased expression is maintained as long as the osmotic stimulus persists and is sensitively linked to the prevalent osmolarity of the growth medium. Primer extension analysis revealed the osmotically controlled
proHJ
promoter, a promoter that resembles typical SigA-type promoters of
B. subtilis
. Deletion analysis of the
proHJ
promoter region identified a 126-bp DNA segment carrying all sequences required in
cis
for osmoregulated transcription. Our data disclose the presence of ProA-interlinked anabolic and osmoadaptive proline biosynthetic routes in
B. subtilis
and demonstrate that the synthesis of the compatible solute proline is a central facet of the cellular defense to high-osmolarity surroundings for this soil bacterium.
Characterization of a Glucosamine/Glucosaminide
N
-Acetyltransferase of Clostridium acetobutylicum
Authors: Reith Jan , Mayer Christoph
Published: July 2011

Many bacteria, in particular Gram-positive bacteria, contain high proportions of non-
N
-acetylated amino sugars, i.e., glucosamine (GlcN) and/or muramic acid, in the peptidoglycan of their cell wall, thereby acquiring resistance to lysozyme. However, muramidases with specificity for non-
N
-acetylated peptidoglycan have been characterized as part of autolytic systems such as of
Clostridium acetobutylicum
. We aim to elucidate the recovery pathway for non-
N
-acetylated peptidoglycan fragments and present here the identification and characterization of an acetyltransferase of novel specificity from
C. acetobutylicum
, named GlmA (for
gl
ucosa
m
ine/glucosaminide
N
-
a
cetyltransferase). The enzyme catalyzes the specific transfer of an acetyl group from acetyl coenzyme A to the primary amino group of GlcN, thereby generating
N
-acetylglucosamine. GlmA is also able to
N
-acetylate GlcN residues at the nonreducing end of glycosides such as (partially) non-
N-
acetylated peptidoglycan fragments and β-1,4-glycosidically linked chitosan oligomers.

K
m

values of 114, 64, and 39 μM were determined for GlcN, (GlcN)
2
, and (GlcN)
3
, respectively, and a 3- to 4-fold higher catalytic efficiency was determined for the di- and trisaccharides. GlmA is the first cloned and biochemically characterized glucosamine/glucosaminide
N
-acetyltransferase and a member of the large GCN5-related
N
-acetyltransferases (GNAT) superfamily of acetyltransferases. We suggest that GlmA is required for the recovery of non-
N
-acetylated muropeptides during cell wall rescue in
C. acetobutylicum
.
The Fimbrial Usher FimD Follows the SurA-BamB Pathway for Its Assembly in the Outer Membrane of Escherichia coli
Authors: Palomino Carmen , Marín Elvira , Fernández Luis Ángel
Published: July 2011

Fimbrial ushers are the largest β-barrel outer membrane proteins (OMPs) known to date, which function in the polymerization of fimbriae and their translocation to the bacterial surface. Folding and assembly of these complex OMPs are not characterized. Here, we investigate the role of periplasmic chaperones (SurA, Skp, DegP, and FkpA) and individual components of the β-barrel assembly machinery (BAM) complex (BamA, BamB, BamC, and BamE) in the folding of the
Escherichia coli
FimD usher. The FimD level is dramatically reduced (∼30-fold) in a
surA
null mutant, but a strong cell envelope stress is constitutively activated with upregulation of DegP (∼10-fold). To demonstrate a direct role of SurA, FimD folding was analyzed in a conditional
surA
mutant in which SurA expression was controlled. In this strain, FimD is depleted from bacteria in parallel to SurA without significant upregulation of DegP. Interestingly, the dependency on SurA is higher for FimD than for other OMPs. We also demonstrate that a functional BAM complex is needed for folding of FimD. In addition, FimD levels were strongly reduced (∼5-fold) in a mutant lacking the accessory lipoprotein BamB. The critical role of BamB for FimD folding was confirmed by complementation and BamB depletion experiments. Similar to SurA dependency, FimD showed a stronger dependency on BamB than OMPs. On the other hand, folding of FimD was only marginally affected in
bamC
and
bamE
mutants. Collectively, our results indicate that FimD usher follows the SurA-BamB pathway for its assembly. The preferential use of this pathway for the folding of OMPs with large β-barrels is discussed.
Electrical modulation of the sympathetic nervous system in order to augment cerebral blood flow: a protocol for an experimental study
Authors: Ter Laan Mark , van Dijk J Marc C , Staal Michiel J , Elting Jan-Willem J
Published: July 2011

Introduction

Cerebral blood flow (CBF) is regulated by several mechanisms. Neurogenic control has been a matter of debate, even though several publications reported the effects of changes in sympathetic tone on CBF. Transcutaneous electrical nerve stimulation and spinal-cord stimulation have been shown to influence peripheral and cerebral blood flow through a sympathetic pathway. The authors hypothesise that certain pathological conditions result in a relative increase in the neurogenic regulation of CBF and that this regulation can be modulated electrically.

Methods and analysis

Patients with cerebral vasospasm after subarachnoid haemorrhage will be included. The experimental set-up measures several parameters that are involved in cerebral blood flow regulation in patients with cerebral vasospasm after subarachnoid haemorrhage. Measurements are taken at baseline and with stimulation in several frequencies. An ad hoc statistical analysis is used to evaluate different settings of the electrical stimulation. Autoregulation is evaluated with transfer function analysis and autoregulatory index calculations.

Ethics and dissemination

Ethical registration was granted by Medical Review Ethics Committee Groningen (ID METc 2010.123). All participants provide written informed consent on participation. Upon finishing a pilot study to investigate feasibility and effect, either future prospective (randomised) studies will be designed, or other modalities of electrical stimulation will be explored using the same set-up.

Trial Registration

Dutch Trial Registry: NTR2358.
Effects of mechanical limitation of apical rotation on left ventricular relaxation and end-diastolic pressure
Authors: Iwasaki Mariko , Masuda Kasumi , Asanuma Toshihiko , Nakatani Satoshi
Published: July 2011

Left ventricular (LV) twist is thought to play an important role in cardiac function. However, how twist affects systolic or diastolic function is not understood in detail. We acquired apical and basal short-axis images of dogs undergoing open-chest procedures ( n = 15) using a GE Vivid 7 at baseline and during the use of an apical suction device (Starfish) to limit apical rotation. We measured LV pressure and stroke volume using a micromanometer-tipped catheter and an ultrasonic flow probe, respectively. Peak radial strain, peak rotation, peak twist, peak systolic twisting rate (TR), peak untwisting rate during isovolumic relaxation period (URIVR), and peak early diastolic untwisting rate after mitral valve opening (URE) were determined using speckle tracking echocardiography. Immobilizing the apex with gentle suction significantly decreased apical rotation (−50 ± 27%) and slightly increased basal rotation, resulting in a significant decrease in twist. The time constant of LV relaxation (τ) was prolonged, and LV end-diastolic pressure increased. TR and URIVR decreased. LV systolic pressure, peak positive and negative first derivative of LV pressure (±dP/d t), stroke volume, radial strain, and URE were not changed. The correlation between τ and URIVR ( r = 0.63, P = 0.0006) was stronger than that between peak +dP/d t and TR ( r = 0.46, P = 0.01). Diastolic function was impaired with reduced apical rotation and URIVR when the apex of the heart was immobilized using an apical suction device.
Mechanisms of ATP-mediated vasodilation in humans: modest role for nitric oxide and vasodilating prostaglandins
Authors: Crecelius Anne R. , Kirby Brett S. , Richards Jennifer C. , Garcia Leora J. , Voyles Wyatt F. , Larson Dennis G. , Luckasen Gary J. , Dinenno Frank A.
Published: July 2011

ATP is an endothelium-dependent vasodilator, and findings regarding the underlying signaling mechanisms are equivocal. We sought to determine the independent and interactive roles of nitric oxide (NO) and vasodilating prostaglandins (PGs) in ATP-mediated vasodilation in young, healthy humans and determine whether any potential role was dependent on ATP dose or the timing of inhibition. In protocol 1 ( n = 18), a dose-response curve to intrabrachial infusion of ATP was performed before and after both single and combined inhibition of NO synthase [ NG-monomethyl-l-arginine (l-NMMA)] and cyclooxygenase (ketorolac). Forearm blood flow (FBF) was measured via venous occlusion plethysmography and forearm vascular conductance (FVC) was calculated. In this protocol, neither individual nor combined NO/PG inhibition had any effect on the vasodilatory response ( P = 0.22–0.99). In protocol 2 ( n = 16), we determined whether any possible contribution of both NO and PGs to ATP vasodilation was greater at low vs. high doses of ATP and whether inhibition during steady-state infusion of the respective dose of ATP impacted the dilation. FBF in this protocol was measured via Doppler ultrasound. In protocol 2, infusion of low ( n = 8)- and high-dose ( n = 8) ATP for 5 min evoked a significant increase in FVC above baseline (low = 198 ± 24%; high = 706 ± 79%). Infusion of l-NMMA and ketorolac together reduced steady-state FVC during both low- and high-dose ATP ( P < 0.05), and in a subsequent trial with continuous NO/PG blockade, the vasodilator response from baseline to 5 min of steady-state infusion was similarly reduced for both low (ΔFVC = −31 ± 11%)- and high-dose ATP (ΔFVC −25 ± 11%; P = 0.70 low vs. high dose). Collectively, our findings indicate a potential modest role for NO and PGs in the vasodilatory response to exogenous ATP in the human forearm that does not appear to be dose or timing dependent; however, this is dependent on the method for assessing forearm vascular responses. Importantly, the majority of ATP-mediated vasodilation is independent of these putative endothelium-dependent pathways in humans.
The impact of baseline artery diameter on flow-mediated vasodilation: a comparison of brachial and radial artery responses to matched levels of shear stress
Authors: Jazuli F. , Pyke K. E.
Published: July 2011

An inverse relationship between baseline artery diameter (BAD) and flow-mediated vasodilation (FMD) has been identified using reactive hyperemia (RH) to create a shear stress (SS) stimulus in human conduit arteries. However, RH creates a SS stimulus that is inversely related to BAD. The purpose of this study was to compare FMD in response to matched levels of SS in two differently sized upper limb arteries [brachial (BA) and radial (RA) artery]. With the use of exercise, three distinct, shear rate (SR) stimuli were created (SR = blood velocity/vessel diameter; estimate of SS) in the RA and BA. Artery diameter and mean blood velocity were assessed with echo and Doppler ultrasound in 15 healthy male subjects (19–25 yr). Data are means ± SE. Subjects performed 6 min of adductor pollicis and handgrip exercise to increase SR in the RA and BA, respectively. Exercise intensity was modulated to achieve uniformity in SR between arteries. The three distinct SR levels were as follows: steady-state exercise 39.8 ± 0.6, 57.3 ± 0.7, and 72.4 ± 1.2 s−1 ( P < 0.001). %FMD and AbsFMD (mm) at the end of exercise were greater in the RA vs. the BA at each shear level [at the highest level: RA = 15.7 ± 1.5%, BA = 5.4 ± 0.8% ( P < 0.001)]. The mean slope of the within-subject SR-%FMD regression line was greater in the RA (RA = 0.33 ± 0.04, BA = 0.13 ± 0.02, P < 0.001), and a strong within-subjects relationship between %FMD and SR was observed in both arteries (RA: r2 = 0.92 ± 0.02; BA: r2 = 0.90 ± 0.03). Within the RA, there was a significant relationship between baseline diameter and %FMD; however, this relationship was not present in the BA (RA: r2 = 0.76, P < 0.001; BA: r2 = 0.03, P = 0.541). These findings suggest that the response to SS is not uniform across differently sized vessels, which is in agreement with previous studies.
Desmin-related cardiomyopathy: an unfolding story
Authors: McLendon Patrick M. , Robbins Jeffrey
Published: July 2011

The intermediate filament protein desmin is an integral component of the cardiomyocyte and serves to maintain the overall structure and cytoskeletal organization within striated muscle cells. Desmin-related myopathy can be caused by mutations in desmin or associated proteins, which leads to intracellular accumulation of misfolded protein and production of soluble pre-amyloid oligomers, which leads to weakened skeletal and cardiac muscle. In this review, we examine the cellular phenotypes in relevant animal models of desmin-related cardiomyopathy. These models display characteristic sarcoplasmic protein aggregates. Aberrant protein aggregation leads to mitochondrial dysfunction, abnormal metabolism, and altered cardiomyocyte structure. These deficits to cardiomyocyte function may stem from impaired cellular proteolytic mechanisms. The data obtained from these models allow a more complete picture of the pathology in desmin-related cardiomyopathy to be described. Moreover, these studies highlight the importance of desmin in maintaining cardiomyocyte structure and illustrate how disrupting this network can be deleterious to the heart. We emphasize the similarities observed between desmin-related cardiomyopathy and other protein conformational disorders and speculate that therapies to treat this disease may be broadly applicable to diverse protein aggregation-based disorders.
Thyroid transcription factor-1 (TTF-1) gene: identification of ZBP-89, Sp1, and TTF-1 sites in the promoter and regulation by TNF-α in lung epithelial cells
Authors: Das Aparajita , Acharya Sunil , Gottipati Koteswara Rao , McKnight James B. , Chandru Hemakumar , Alcorn Joseph L. , Boggaram Vijay
Published: July 2011

Thyroid transcription factor-1 (TTF-1/Nkx2.1/TITF1) is a homeodomain-containing transcription factor essential for the morphogenesis and differentiation of the lung. In the lung, TTF-1 controls the expression of surfactant proteins that are essential for lung stability and lung host defense. In this study, we identified functionally important transcription factor binding sites in the TTF-1 proximal promoter and studied tumor necrosis factor-α (TNF-α) regulation of TTF-1 expression. TNF-α, a proinflammatory cytokine, has been implicated in the pathogenesis of acute respiratory distress syndrome (ARDS) and inhibits surfactant protein levels. Deletion analysis of TTF-1 5′-flanking DNA indicated that the TTF-1 proximal promoter retained high-level activity. Electrophoretic mobility shift assay, chromatin immunoprecipitation, and mutational analysis experiments identified functional ZBP-89, Sp1, Sp3, and TTF-1 sites in the TTF-1 proximal promoter. TNF-α inhibited TTF-1 protein levels in H441 and primary alveolar type II cells. TNF-α inhibited TTF-1 gene transcription and promoter activity, indicating that transcriptional mechanisms play important roles in the inhibition of TTF-1 levels. TNF-α inhibited TTF-1 but not Sp1 or hepatocyte nuclear factor-3 DNA binding to TTF-1 promoter. Transactivation experiments in A549 cells indicated that TNF-α inhibited TTF-1 promoter activation by exogenous Sp1 and TTF-1 without altering their levels, suggesting inhibition of transcriptional activities of these proteins. TNF-α inhibition of TTF-1 expression was associated with increased threonine, but not serine, phosphorylation of Sp1. Because TTF-1 serves as a positive regulator for surfactant protein gene expression, TNF-α inhibition of TTF-1 expression could have important implications for the reduction of surfactant protein levels in diseases such as ARDS.
Surfactant protein A is defective in abrogating inflammation in asthma
Authors: Wang Ying , Voelker Dennis R. , Lugogo Njira L. , Wang Guirong , Floros Joanna , Ingram Jennifer L. , Chu Hong Wei , Church Tony D. , Kandasamy Pitchaimani , Fertel Daniel , Wright Jo Rae , Kraft Monica
Published: July 2011

Surfactant protein A (SP-A) regulates a variety of immune cell functions. We determined the ability of SP-A derived from normal and asthmatic subjects to modulate the inflammatory response elicited by Mycoplasma pneumoniae , a pathogen known to exacerbate asthma. Fourteen asthmatic and 10 normal control subjects underwent bronchoscopy with airway brushing and bronchoalveolar lavage (BAL). Total SP-A was extracted from BAL. The ratio of SP-A1 to total SP-A (SP-A1/SP-A) and the binding of total SP-A to M. pneumoniae membranes were determined. Airway epithelial cells from subjects were exposed to either normal or asthmatic SP-A before exposure to M. pneumoniae . IL-8 protein and MUC5AC mRNA were measured. Total BAL SP-A concentration did not differ between groups, but the percentage SP-A1 was significantly increased in BAL of asthmatic compared with normal subjects. SP-A1/SP-A significantly correlated with maximum binding of total SP-A to M. pneumoniae , but only in asthma. SP-A derived from asthmatic subjects did not significantly attenuate IL-8 and MUC5AC in the setting of M. pneumoniae infection compared with SP-A derived from normal subjects. We conclude that SP-A derived from asthmatic subjects does not abrogate inflammation effectively, and this dysfunction may be modulated by SP-A1/SP-A.
Bcl-2 Family Genetic Profiling Reveals Microenvironment-Specific Determinants of Chemotherapeutic Response
Authors: Pritchard Justin R. , Gilbert Luke A. , Meacham Corbin E. , Ricks Jennifer L. , Jiang Hai , Lauffenburger Douglas A. , Hemann Michael T.
Published: July 2011

The Bcl-2 family encompasses a diverse set of apoptotic regulators that are dynamically activated in response to various cell-intrinsic and -extrinsic stimuli. An extensive variety of cell culture experiments have identified effects of growth factors, cytokines, and drugs on Bcl-2 family functions, but in vivo studies have tended to focus on the role of one or two particular members in development and organ homeostasis. Thus, the ability of physiologically relevant contexts to modulate canonical dependencies that are likely to be more complex has yet to be investigated systematically. In this study, we report findings derived from a pool-based shRNA assay that systematically and comprehensively interrogated the functional dependence of leukemia and lymphoma cells upon various Bcl-2 family members across many diverse in vitro and in vivo settings. This approach permitted us to report the first in vivo loss of function screen for modifiers of the response to a front-line chemotherapeutic agent. Notably, our results reveal an unexpected role for the extrinsic death pathway as a tissue-specific modifier of therapeutic response. In particular, our findings show that particular tissue sites of tumor dissemination play critical roles in demarcating the nature and extent of cancer cell vulnerabilities and mechanisms of chemoresistance. Cancer Res; 71(17); 5850–8. ©2011 AACR.
BIM Expression in Treatment-Naïve Cancers Predicts Responsiveness to Kinase Inhibitors
Authors: Faber Anthony C. , Corcoran Ryan B. , Ebi Hiromichi , Sequist Lecia V. , Waltman Belinda A. , Chung Euiheon , Incio Joao , Digumarthy Subba R. , Pollack Sarah F. , Song Youngchul , Muzikansky Alona , Lifshits Eugene , Roberge Sylvie , Coffman Erik J. , Benes Cyril H. , Gómez Henry L. , Baselga José , Arteaga Carlos L. , Rivera Miguel N. , Dias-Santagata Dora , Jain Rakesh K. , Engelman Jeffrey A.
Published: July 2011

Cancers with specific genetic mutations are susceptible to selective kinase inhibitors. However, there is a wide spectrum of benefit among cancers harboring the same sensitizing genetic mutations. Herein, we measured apoptotic rates among cell lines sharing the same driver oncogene following treatment with the corresponding kinase inhibitor. There was a wide range of kinase inhibitor-induced apoptosis despite comparable inhibition of the target and associated downstream signaling pathways. Surprisingly, pretreatment RNA levels of the BH3-only pro-apoptotic BIM strongly predicted the capacity of EGFR, HER2, and PI3K inhibitors to induce apoptosis in EGFR-mutant, HER2-amplified, and PIK3CA-mutant cancers, respectively, but BIM levels did not predict responsiveness to standard chemotherapies. Furthermore, BIM RNA levels in EGFR-mutant lung cancer specimens predicted response and duration of clinical benefit from EGFR inhibitors. These findings suggest assessment of BIM levels in treatment-naïve tumor biopsies may indicate the degree of benefit from single-agent kinase inhibitors in multiple oncogene-addiction paradigms.

Significance: In several oncogene-addiction paradigms, assessment of BIM RNA levels identifies those cancers that fail to have substantial apoptotic responses to kinase inhibitors. BIM RNA levels may be assessed in diagnostic cancer specimens to predict which patients will receive less benefit from single-agent kinase inhibitors. Cancer Discovery: 1(4); 352–65. ©2011 AACR.

Read the Commentary on this article by Yoshida and Haura, p. 289

This article is highlighted in the In This Issue feature, p. 275
Discourse studies in the 21st century: A response to Mats Alvesson and Dan Kärreman’s ‘Decolonializing discourse’
Authors: Iedema Rick
Published: July 2011

This article reflects on some of the definitions and practices that fall under the heading ‘discourse studies’. The springboard for my reflections is Mats Alvesson’s and Dan Kärreman’s retrospective piece, ‘Decolonializing discourse’, published in this issue. In responding to their piece, I’ll address some of the ‘big’ issues they raise: discourse as conceptual frame; discourse as language; the agency of discourse, and discourse as opposed to non-discourse.
Discourse(s), social construction and language practices: In conversation with Alvesson and Kärreman
Authors: Bargiela-Chiappini Francesca
Published: July 2011

This piece seeks to extend a conversation that Alvesson and Kärreman started in 2000 from the pages of Human Relations and are continuing in their 2011 article; a conversation that is of great interest well beyond management and organization studies. Through a linguistics perspective that is attentive to the peculiarities of the discourse vocabulary but also seeks to probe aspects of its conceptual import, I will explore the significance of understandings of discourse circulating within the social sciences. I will continue with reflections on select difficulties raised by ‘social construction-unlimited’ before highlighting some of the benefits of a social semiotic approach to ethnographic research centred on the concept of indexicality. I will conclude with an invitation to ‘bring the researcher back’, in an embodied engagement with the field that can help put discourse in ‘its right place’.
What’s cooking in organizational discourse studies? A response to Alvesson and Kärreman
Authors: Mumby Dennis K
Published: July 2011

While Alvesson and Kärreman’s (2000) ‘Varieties of Discourse’ essay was an important and oft-cited marker in the field of organizational discourse studies, I argue in this response that their rather gloomy, even curmudgeonly, updated reading of the field is not only misplaced but also rooted in their own reductionist conception of discourse — a charge that they themselves level against contemporary organizational discourse research. As a communication scholar who makes his interdisciplinary home in the area of organizational communication/organization studies, I argue that much of Alvesson and Kärreman’s critique has its origin in a rather anemic, even wrongheaded, reading of the ‘linguistic turn’ — a reading that limits the generative and analytic possibilities of post-linguistic turn organizational discourse studies.
Organizational discourse analysis - well done or too rare? A reply to our critics
Authors: Alvesson Mats , Kärreman Dan
Published: July 2011

In this article we respond to Bargiela-Chiappini, Iedema and Mumby.We notice that there is considerable agreement concerning the state of the art of organizational discourse analysis, while also discussing the disagreements. We expand on some of the ontological issues inherent in our argument, further discuss the character of reductionism in organizational discourse analysis, the trappings of a priori assumptions, and, finally, argue that our critics themselves, perhaps inadvertently, tend to repeat the problematic moves we identified in our original article.
Laminated plate formulation for photostrictive actuators and sensors
Authors: Luo Quantian , Tong Liyong
Published: July 2011

This paper presents a model for a laminated plate with surface mounted photostrictive materials. The photo-induced electrical, thermal, and mechanical fields in lanthanum zirconate titanate (PLZT) ceramics with 0-3 polarization are considered as the coupled multi-physics fields in PLZT ceramics. The formulation is presented for general multi-physics fields in PLZT ceramics. The actuating and sensing equations are formulated for a 0-3 polarized PLZT laminated plate and they are also applicable to other photostrictive materials such as polymers and semiconductors. The actuated behaviors of a 0-3 polarized PLZT laminated plate subjected to light illumination are investigated and the numerical results calculated using the present formulations are compared with those available in the literatures.
Investigation of Science Inquiry Items for Use on an Alternate Assessment Based on Modified Achievement Standards Using Cognitive Lab Methodology
Authors: Dickenson Tammiee S. , Gilmore Joanna A. , Price Karen J. , Bennett Heather L.
Published: July 2011

This study evaluated the benefits of item enhancements applied to science-inquiry items for incorporation into an alternate assessment based on modified achievement standards for high school students. Six items were included in the cognitive lab sessions involving both students with and without disabilities. The enhancements (e.g., use of visuals, reading support) were intended to improve access to the items for students who had grade-level science content knowledge, but whose disability may impact their ability to answer the items in the original form. Students were asked to think aloud while answering items and answer follow-up questions about specific item-enhancement features. Achievement did not show much improvement but reported cognitive effort suggests reduction in perceived difficulty of enhanced items.
Understanding African American Adolescents’ Identity Development
Authors: Brittian Aerika S.
Published: July 2011

This article examines the development of African American adolescents’ identity using a relational developmental systems theory framework, which led to the expectation that identity development is linked to both the reduction of risk behaviors and the promotion of African American adolescents’ healthy development. Different personological theories of identity development were discussed, including Erikson’s theory of psychosocial development and Marcia’s theory of identity statuses. Developmental systems theory was used to further the literature on African American adolescents’ identity development, by integrating various views of identity development as they pertain to these youth. Furthermore, the formation of many aspects of identity may be an important coping and resilience process for such youth. In addition, directions for future research are discussed, including a consideration of the complexity of diversity that exists within the African American adolescent population, and a call for more longitudinal assessments of identity development is presented.
The importance of peer-support for teaching staff when including children with special educational needs
Authors: Boyle Christopher , Topping Keith , Jindal-Snape Divya , Norwich Brahm
Published: July 2011

Policies of inclusion in schools now transcend national boundaries; but much less is known about how teachers interact best with each other in order to establish a successful inclusion environment. School psychologists cannot work in isolation and require being fully conversant with this perennially polemic topic. This article reports on a study in which 43 teachers in three secondary schools across one local authority in Scotland were interviewed on a range of topics related to inclusion. One of the important themes to emerge was the importance of peer-support within staff groups. It was found that teachers could still hold positive attitudes towards inclusion, even if the management team and heads of department within the same school were not regarded as being particularly supportive. Peer support was highlighted as a valuable component enabling teachers to feel that they were able successfully to include children with special needs. Moreover, the importance of peer support was perceived as superseding other support across the three high schools. Some implications for a possible role for school psychologists in helping to establish peer support networks for teachers are considered.
Perception of social relationships with classmates and social support in adolescents with Asperger syndrome attending mainstream schools in Poland
Authors: Pisula Ewa , Łukowska Ewa
Published: July 2011

One of the factors affecting successful inclusion of adolescents with Asperger syndrome (AS) in mainstream schools is positive relationships with classmates. The present study investigates how adolescents with AS: (1) perceive their classmates' attitude towards them; (2) what attitude towards classmates they declare, and (3) how they assess the effectiveness of social support received from parents, teachers, and classmates. The relationship between social support received by adolescents with AS and their perception of their relationships with classmates was also analysed. There were 50 participants in the study: Two groups with equal numbers of participants, one with adolescents with AS and the other with typically developing adolescents (age 12- to 17-years-old). All participants attended mainstream schools. A set of questionnaires measuring perception of social relationships in class and perceived social support was used. Adolescents with AS gave poorer assessments of their classmates’ attitude towards them and their attitude to their classmates. They also claimed to receive less support from classmates. Moreover, that type of support was significantly correlated with their evaluation of their peers attitude towards them and declared behaviour towards their peers.
Strengthening classroom emotional support for children following a family member’s death
Authors: Heath Melissa Allen , Cole Beth Vaughan
Published: July 2011

National and international organizations have identified schools as having an unparalleled potential to offer supportive services for children’s mental health needs. This article reviews research and practice related to children’s grief and specifies strategies for classroom-based interventions. In particular, school psychologists are encouraged to assist teachers in addressing the needs of children following the death of a family member. A list of resources is included to assist school psychologists in sharing critical information with teachers, preparing them to implement suggested strategies. Additionally, two ready-to-use classroom lesson plans integrate classroom discussion and activities with grief-themed children’s literature.
Hardt, Negri, and Antagonism
Authors: Nicholls Brett
Published: July 2011

At first glance, Hardt and Negri.FN”s brief excursion into the sociology of media in Empire is hardly earth shattering; in fact it is quite disappointing. In Empire the media occupies a fraught and complex space between the past (civil society) and the emergence of the neoliberal consensus in which capitalism is considered the only social and economic option. Popular instrument or lackey for corporate capital, this is the tension that marks institutional forms of media. But by looking more closely at Hardt and Negri’s diagram of Empire, we find that there is a second and more expansive sense of the operation of media. Media works as the glue that holds the heterogeneous components of Empire in place. This glue (media operation), however, serves a double function. On the one hand, it works as communication that connects and information is exchanged, but, on the other, it connects in such a way that it maintains heterogeneity and distance. The double function of media as communication, the article contends, should be understood in terms of the logic of connection without connectivity. This logic is central in mechanisms of control in the context of Empire, and, the article maintains, crucial for any analysis of contemporary media today.
Constitutive Communications and the Shimmering Project of the Multitude
Authors: Wolfson Todd
Published: July 2011

In Multitude: War and Democracy in the Age of Empire (2004), Michael Hardt and Antonio Negri analyze the major shifts in the inner workings of capitalism and class that have taken place across the last forty years. Building on these global transformations they offer a compelling vision for a new political project, which relies on the growing power of a new political subject, the multitude. They argue that this new political subject is irreducible to a singular identity or project, and therefore demands new horizontal networked, organizational forms, held together by communication technologies, in an effort to forge a radical democratic praxis. In this essay I argue that while their vision for a new logic of contemporary class-based social movements takes us in important new directions ultimately they are unable to deliver on the pledge of a meaningful political program because they rely to heavily on communications as a tool to bind the multitude.
Is there an Autonomist Model of Political Communication?
Authors: Thoburn Nicholas
Published: July 2011

This article explores the different models of political communication that inhere in Hardt and Negri’s Empire trilogy, models that are explicit and implicit, intended and accidental, dominant and latent. From their existence tangled up in Hardt and Negri’s work, I draw out for consideration the communicative models of the rhizome-book, manifesto, textbook, mass-market book, autonomous language, and political journal. My aim is less to evaluate the relative dominance of these models in the trilogy, than to take the opportunity this work offers for thinking political communication as specifically communist problematic, a somewhat neglected field of inquiry.
Empire, Biopolitics, and Communication
Authors: Macmillan Alexandre
Published: July 2011

Hardt and Negri’s description of Empire is in a large part based on Michel Foucault’s account of biopolitics. For Hardt and Negri, the biopolitical nature of Empire means that social forms and modes of subjectivity are considered as the result of communication processes, and that imperial domination is exercised through networks of communication. However, this reading of Foucault is problematic inasmuch as he never reduced communication or modes of subjectivity to a product of biopolitical society. As a consequence of this partial reading, Hardt and Negri fail to consider the specificities of biopolitical communication. Furthermore, by taking the Internet as the model for communication and social forms in Empire, Hardt and Negri seem to ignore the constitutive nature of communication and address the role communication could take in the liberation process of the multitude.