bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of Aqueous Metathesis Catalysts
Authors: Zaman Shazia , Curnow Owen J. , Abell Andrew D.
Published: February 2009

Recent developments (and some historical aspects) of protic solvent metathesis using ill-defined catalysts [e.g., RuCl3·H2O and Ru(H2O)6(tos)2] and also the more easily handled, well-defined ruthenium-based alkylidene complexes (based on 15, 16, and 17) are highlighted. Modification of these catalysts has been achieved for applications in protic solvents with the introduction of water-solubilizing ligands and by immobilization onto a suitable support. The introduction of water-solubilizing cationic and anionic phosphines is synthetically straightforward with various catalysts having been prepared in this way (see 18, 19, 29–32, 36). Immobilzation methods include tethering to a water-soluble polymeric support (see 39, 40) and modification of the benzylidene group (see 43–46). Ionic tags have also been attached to the benzylidene group (see 48–50, 52, 53). Several other approaches have also been reported as discussed here to prepare modified catalysts that display good activity in protic media (see 54–59).
Synthesis of Quinoline Derivatives as 5-HT4 Receptor Ligands
Authors: Hanna-Elias Amir , Manallack David T. , Berque-Bestel Isabelle , Irving Helen R. , Coupar Ian M. , Iskander Magdy N.
Published: February 2009

A general and convenient synthesis of 6-methoxyquinoline-3-carboxamides commencing with a cyclization step that involves ρ-anisidine and diethyl (ethoxymethylene)malonate is described. An additional tetrahydroquinoline scaffold 19 is prepared from 6-methoxyquinoline-3-carboxamide and this represents a novel serotinergic lead structure. These compounds show reasonable affinity at 1 × 10–6 M, and docking experiments suggest that they may bind in a similar manner to serotonin.
Enhanced selection of FoxP3
+
T-regulatory cells protects CTLA-4-deficient mice from CNS autoimmune disease
Authors: Verhagen Johan , Gabryšová Leona , Minaee Sophie , Sabatos Catherine A. , Anderson Graham , Sharpe Arlene H. , Wraith David C.
Published: February 2009

It is generally acknowledged that cytotoxic T-lymphocyte–associated antigen-4 (CTLA-4/CD152) plays a pivotal role in the regulation of T-cell activation and the establishment of self-tolerance in the periphery. CTLA-4–deficient (CTLA-4KO) mice develop a lymphoproliferative disorder and die within 4 weeks of birth, suggesting a role for CTLA-4 in T-cell homeostasis or the development and activity of T-regulatory (Treg) cells. To study the role of CTLA-4 in the control of experimental autoimmune encephalomyelitis (EAE), we have generated a CTLA-4KO mouse in which >90% of all CD4
+
T cells bear a Vβ8.2 transgenic T-cell receptor that is specific for myelin basic protein peptide Ac1–9 (ASQKRPSQR). These mice do not develop spontaneous lymphoproliferative disease or EAE and are resistant to disease induction. This correlates with a higher frequency of functional FoxP3
+
Treg cells in the spleen and thymus of CTLA-4KO mice. The absence of CTLA-4–mediated suppression of CD28 signaling resulted in the early expression of FoxP3 on double-positive cells in the thymic cortex. We conclude that CTLA-4 is not essential for the peripheral function of FoxP3
+
Treg cells but plays a pivotal role in their thymic selection.
Murine epidermal Langerhans cells and langerin-expressing dermal dendritic cells are unrelated and exhibit distinct functions
Authors: Nagao Keisuke , Ginhoux Florent , Leitner Wolfgang W. , Motegi Sei-Ichiro , Bennett Clare L. , Clausen Björn E. , Merad Miriam , Udey Mark C.
Published: February 2009

A new langerin
+
DC subset has recently been identified in murine dermis (langerin
+
dDC), but the lineage and functional relationships between these cells and langerin
+
epidermal Langerhans cells (LC) are incompletely characterized. Selective expression of the cell adhesion molecule EpCAM by LC allowed viable LC to be easily distinguished from langerin
+
dDC in skin and lymphoid tissue and ex vivo as well. Differential expression of EpCAM and langerin revealed the presence of at least 3 distinct skin DC subsets. We determined that LC and langerin
+
dDC exhibit different migratory capabilities in vitro and repopulate distinct anatomic compartments in skin at different rates after conditional depletion in vivo. Langerin
+
dDC, in contrast to LC, did not require TGFβ1 for development. Carefully timed gene gun immunization studies designed to take advantage of the distinct repopulation kinetics of langerin
+
dDC and LC revealed that langerin
+
dDC were required for optimal production of β-galactosidase-specific IgG2a/c and IgG2b in the acute phase. In contrast, immunization via LC-deficient skin resulted in persistent and strikingly reduced IgG1 and enhanced IgG2a Ab production. Our data support the concepts that LC and langerin
+
dDC represent distinct DC subsets that have specialized functions and that LC are important immunoregulatory cells. The presence of at least 3 functionally distinct skin DC subsets may have particular relevance for vaccines that are administered epicutaneously.
Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
Authors: Yang Sichun , Banavali Nilesh K. , Roux Benoît
Published: February 2009

The Src-family kinases are allosteric enzymes that play a key role in the regulation of cell growth and proliferation. In response to cellular signals, they undergo large conformational changes to switch between distinct inactive and active states. A computational strategy for characterizing the conformational transition pathway is presented to bridge the inactive and active states of the catalytic domain of Hck. The information from a large number (78) of independent all-atom molecular dynamics trajectories with explicit solvent is combined together to assemble a connectivity map of the conformational transition. Two intermediate states along the activation pathways are identified, and their structural features are characterized. A coarse free-energy landscape is built in terms of the collective motions corresponding to the opening of the activation loop (A-loop) and the rotation of the αC helix. This landscape shows that the protein can adopt a multitude of conformations in which the A-loop is partially open, while the αC helix remains in the orientation characteristic of the inactive conformation. The complete transition leading to the active conformation requires a concerted movement involving further opening of the A-loop, the relative alignment of N-lobe and C-lobe, and the rotation of the αC helix needed to recruit the residues necessary for catalysis in the active site. The analysis leads to a dynamic view of the full-length kinase activation, whereby transitions of the catalytic domain to intermediate configurations with a partially open A-loop are permitted, even while the SH2-SH3 clamp remains fully engaged. These transitions would render Y416 available for the transphosphorylation event that ultimately locks down the active state. The results provide a broad framework for picturing the conformational transitions leading to kinase activation.
Control of
Arabidopsis
meristem development by thioredoxin-dependent regulation of intercellular transport
Authors: Benitez-Alfonso Yoselin , Cilia Michelle , Roman Adrianna San , Thomas Carole , Maule Andy , Hearn Stephen , Jackson David
Published: February 2009

Cell-to-cell transport in plants occurs through cytoplasmic channels called “plasmodesmata” and is regulated by developmental and environmental factors. Callose deposition modulates plasmodesmal transport in vivo, but little is known about the mechanisms that regulate this process. Here we report a genetic approach to identify mutants affecting plasmodesmal transport. We isolated 5 mutants, named
gfp arrested trafficking
(
gat
), affected in GFP unloading from the phloem into the meristem.
gat1
mutants were seedling lethal and carried lesions in an
m
-type thioredoxin that is expressed in non-green plastids of meristems and organ primordia. Callose and hydrogen peroxide accumulated in
gat1
mutants, and WT plants subjected to oxidative conditions phenocopied the
gat1
trafficking defects. Ectopic expression of GAT1 in mature leaves increased plasmodesmal permeability and led to a delay in senescence and flowering time. We propose a role for the GAT1 thioredoxin in the redox regulation of callose deposition and symplastic permeability that is essential for meristem maintenance in
Arabidopsis
.
Synchronization of chaotic early afterdepolarizations in the genesis of cardiac arrhythmias
Authors: Sato Daisuke , Xie Lai-Hua , Sovari Ali A. , Tran Diana X. , Morita Norishige , Xie Fagen , Karagueuzian Hrayr , Garfinkel Alan , Weiss James N. , Qu Zhilin
Published: February 2009

The synchronization of coupled oscillators plays an important role in many biological systems, including the heart. In heart diseases, cardiac myocytes can exhibit abnormal electrical oscillations, such as early afterdepolarizations (EADs), which are associated with lethal arrhythmias. A key unanswered question is how cellular EADs partially synchronize in tissue, as is required for them to propagate. Here, we present evidence, from computational simulations and experiments in isolated myocytes, that irregular EAD behavior is dynamical chaos. We then show in electrically homogeneous tissue models that chaotic EADs synchronize globally when the tissue is smaller than a critical size. However, when the tissue exceeds the critical size, electrotonic coupling can no longer globally synchronize EADs, resulting in regions of partial synchronization that shift in time and space. These regional partially synchronized EADs then form premature ventricular complexes that propagate into recovered tissue without EADs. This process creates multiple hat propagate “shifting” foci resembling polymorphic ventricular tachycardia. Shifting foci encountering shifting repolarization gradients can also develop localized wave breaks leading to reentry and fibrillation. As predicted by the theory, rabbit hearts exposed to oxidative stress (H
2
O
2
) exhibited multiple shifting foci causing polymorphic tachycardia and fibrillation. This mechanism explains how collective cellular behavior integrates at the tissue scale to generate lethal cardiac arrhythmias over a wide range of heart rates.
Donor Toll-like receptor 4 contributes to ischemia and reperfusion injury following human kidney transplantation
Authors: Krüger Bernd , Krick Stefanie , Dhillon Navdeep , Lerner Susan M. , Ames Scott , Bromberg Jonathan S. , Lin Marvin , Walsh Liron , Vella John , Fischereder Michael , Krämer Bernhard K. , Colvin Robert B. , Heeger Peter S. , Murphy Barbara T. , Schröppel Bernd
Published: February 2009

While studies in animal models have linked Toll-like receptor (TLR) 4 signaling to kidney injury induced by ischemia and reperfusion, the relevance of TLR4 activation to allograft injury in human kidney transplants is unknown. Here we show that TLR4 is constitutively expressed within all donor kidneys but is significantly higher in deceased-, compared with living-donor organs. Tubules from deceased- but not living-donor kidneys also stained positively for high-mobility group box-1 (HMGB1), a known endogenous TLR4 ligand. In vitro stimulation of human tubular cells with HMGB1, in a TLR4-dependent system, confirmed that HMGB1 can stimulate proinflammatory responses through TLR4. To assess the functional significance of TLR4 in human kidney transplantation, we determined whether TLR4 mutations that confer diminished affinity for HMGB1 influence intragraft gene-expression profiles and immediate graft function. Compared with kidneys expressing WT alleles, kidneys with a TLR4 loss-of-function allele contained less TNFα, MCP-1, and more heme oxygenase 1 (HO-1), and exhibited a higher rate of immediate graft function. These results represent previously undetected evidence that donor TLR4 contributes to graft inflammation and sterile injury following cold preservation and transplantation in humans. Targeting TLR4 signaling may have value in preventing or treating postischemic acute kidney injury after transplantation.
Sigma factor mimicry involved in regulation of general stress response
Authors: Francez-Charlot Anne , Frunzke Julia , Reichen Christian , Ebneter Judith Zingg , Gourion Benjamin , Vorholt Julia A.
Published: February 2009

Bacteria have evolved regulatory traits to rapidly adapt to changing conditions. Two principal regulatory mechanisms to modulate gene expression consist of regulation via alternative sigma factors and phosphorylation-dependent response regulators. PhyR represents a recently discovered protein family combining parts of both systems: a sigma factor-like domain of the extracytoplasmic function (ECF) subfamily linked to a receiver domain of a response regulator. Here we investigated the mode of action of this key regulator of general stress response in
Methylobacterium extorquens
. Our results indicate that PhyR does not act as a genuine sigma factor but instead controls gene expression indirectly through protein-protein interactions. This is evident from the analysis of additional proteins involved in PhyR-dependent gene regulation. We demonstrated that the ECF sigma factor-like domain of PhyR interacts with a protein, designated NepR, upon phosphorylation of the PhyR receiver domain. Using transcriptome analysis and phenotypic assays, we showed that NepR is a negative regulator of PhyR response. Furthermore, we provide biochemical and genetic evidence that NepR exerts this inhibitory effect through sequestration of the ECF sigma factor σ
EcfG1
. Our data support an unprecedented model according to which PhyR acts as a mimicry protein triggering a partner-switching mechanism. Such a regulation of general stress response clearly differs from the two known models operating via σ
S
and σ
B
. Given the absence of these master regulators and the concomitant conservation of PhyR in Alphaproteobacteria, the novel mechanism presented here is most likely central to the control of general stress response in this large subclass of Proteobacteria.
Scaling and self-organized criticality in proteins I
Authors: Phillips J. C.
Published: February 2009

The complexity of proteins is substantially simplified by regarding them as archetypical examples of self-organized criticality (SOC). To test this idea and elaborate on it, this article applies the Moret–Zebende SOC hydrophobicity scale to the large-scale scaffold repeat protein of the HEAT superfamily, PR65/A. Hydrophobic plasticity is defined and used to identify docking platforms and hinges from repeat sequences alone. The difference between the MZ scale and conventional hydrophobicity scales reflects long-range conformational forces that are central to protein functionality.
A mitochondrial DNA mutation linked to colon cancer results in proton leaks in cytochrome
c
oxidase
Authors: Namslauer Ida , Brzezinski Peter
Published: February 2009

An increasing number of cancer types have been found to be linked to specific mutations in the mitochondrial DNA, which result in specific structural changes of the respiratory enzyme complexes. In this study, we have investigated the effect of 2 such mutations identified in colon cancer patients, leading to the amino acid substitutions Ser458Pro and Gly125Asp in subunit I of cytochrome
c
oxidase (complex IV) [Greaves
et al.
(2006)
Proc Natl Acad Sci USA
103:714–719]. We introduced these mutations in
Rhodobacter sphaeroides
, which carries an oxidase that serves as a model of the mitochondrial counterpart. The lack of expression of the former variant indicates that the amino acid substitution results in severely altered overall structure of the enzyme. The latter mutation (Gly171Asp in the bacterial oxidase) resulted in a structurally intact enzyme, but with reduced activity (approximately 30%), mainly due to slowed reduction of the redox site heme
a
. Furthermore, even though the Gly171Asp Cyt
c
O pumps protons, an intrinsic proton leak was identified, which would lead to a decreased overall energy-conversion efficiency of the respiratory chain, and would also perturb transport processes such as protein, ion, and metabolite trafficking. Furthermore, the specific leak may act to alter the balance between the electrical and chemical components of the proton electrochemical gradient.
Persistent elimination of ErbB-2/HER2-overexpressing tumors using combinations of monoclonal antibodies: Relevance of receptor endocytosis
Authors: Ben-Kasus Tsipi , Schechter Bilha , Lavi Sara , Yarden Yosef , Sela Michael
Published: February 2009

Monoclonal antibodies (mAbs) to ErbB-2/HER2 or to its sibling, the epidermal growth factor receptor (EGFR), prolong survival of cancer patients, especially when combined with cytotoxic therapies. However, low effectiveness of therapeutic mAbs and the evolution of patient resistance call for improvements. Here we test in animals pairs of anti-ErbB-2 mAbs and report that pairs comprising an antibody reactive with the dimerization site of ErbB-2 and an antibody recognizing another distinct epitope better inhibit ErbB-2-overexpressing tumors than other pairs or the respective individual mAbs. Because the superiority of antibody combinations extends to tumor cell cultures, we assume that nonimmunological mechanisms contribute to mAb synergy. One potential mechanism, namely the ability of mAb combinations to instigate ErbB-2 endocytosis, is demonstrated. Translation of these lessons to clinical applications may enhance patient response and delay acquisition of resistance.
A manganese transporter, BB0219 (BmtA), is required for virulence by the Lyme disease spirochete,
Borrelia burgdorferi
Authors: Ouyang Zhiming , He Ming , Oman Tara , Yang X. Frank , Norgard Michael V.
Published: February 2009

Borrelia burgdorferi
(
Bb
), the causative agent of Lyme disease, is transmitted to mammalian hosts through an arthropod (tick) vector. To establish infection,
Bb
must acquire essential nutrients, including transition metals, from its mammalian and tick hosts. Thus far, no metal transporter has been identified in
Bb
. Here, we report the identification of the first metal transporter, BmtA (BB0219), in
Bb
. BmtA-deficient mutants of virulent
Bb
were readily generated, and the mutants grew slightly slower than wild-type
Bb
in vitro. However, BmtA mutants were sensitive to the chelating actions of EDTA, suggesting a role for BmtA in metal utilization. Intracellular accumulation of manganese (Mn) was substantially diminished in the
bmtA
mutant, indicating that BmtA was operative in Mn uptake. Given that BmtA lacks homology to any known Mn transporter, we postulate that BmtA is part of a novel mechanism for Mn acquisition by a bacterial pathogen. BmtA also was essential to the infectious life cycle of
Bb
in ticks and mammals, thereby qualifying BmtA as a new borrelial virulence factor. In addition, the
bmtA
mutant was sensitive to treatment with
t
-butyl hydroperoxide, implying that BmtA, and thus Mn, is important to
Bb
for detoxifying reactive oxygen species, including those potentially liberated by immune effector cells during the innate immune response. Our discovery of the first molecule involved in metal transport in
Bb
provides a foundation for further elucidating metal homeostasis in this important human pathogen, which may lead to new strategies for thwarting Lyme disease.
Interaction forces and adhesion of supported myelin lipid bilayers modulated by myelin basic protein
Authors: Min Younjin , Kristiansen Kai , Boggs Joan M. , Husted Cynthia , Zasadzinski Joseph A. , Israelachvili Jacob
Published: February 2009

Force–distance measurements between supported lipid bilayers mimicking the cytoplasmic surface of myelin at various surface coverages of myelin basic protein (MBP) indicate that maximum adhesion and minimum cytoplasmic spacing occur when each negative lipid in the membrane can bind to a positive arginine or lysine group on MBP. At the optimal lipid/protein ratio, additional attractive forces are provided by hydrophobic, van der Waals, and weak dipolar interactions between zwitterionic groups on the lipids and MBP. When MBP is depleted, the adhesion decreases and the cytoplasmic space swells; when MBP is in excess, the bilayers swell even more. Excess MBP forms a weak gel between the surfaces, which collapses on compression. The organization and proper functioning of myelin can be understood in terms of physical noncovalent forces that are optimized at a particular combination of both the amounts of and ratio between the charged lipids and MBP. Thus loss of adhesion, possibly contributing to demyelination, can be brought about by either an excess or deficit of MBP or anionic lipids.
Receptor-mediated phagocytosis elicits cross-presentation in nonprofessional antigen-presenting cells
Authors: Giodini Alessandra , Rahner Christoph , Cresswell Peter
Published: February 2009

In cross-presentation by dendritic cells (DCs), internalized proteins are retrotranslocated into the cytosol, degraded by the proteasome, and the generated antigenic peptides bind to MHC class I molecules for presentation on the cell surface. Endoplasmic reticulum (ER) contribution to phagosomal membranes is thought to provide antigen access to the ER-associated degradation (ERAD) machinery, allowing cytosolic dislocation. Because the ERAD pathway is present in all cell types and exogenous antigens encounter an ER-containing compartment during phagocytosis, we postulated that forcing phagocytosis in cell types other than DCs would render them competent for cross-presentation. Indeed, FcRγIIA expression endowed 293T cells with the capacity for both phagocytosis and ERAD-mediated cross-presentation of an antigen provided as an immune complex. The acquisition of this ability by nonprofessional antigen-presenting cells suggests that a function potentially available in all cell types has been adapted by DCs for presentation of exogenous antigens by MHC class I molecules.
A panel of isogenic human cancer cells suggests a therapeutic approach for cancers with inactivated p53
Authors: Sur Surojit , Pagliarini Raymond , Bunz Fred , Rago Carlo , Diaz Luis A. , Kinzler Kenneth W. , Vogelstein Bert , Papadopoulos Nickolas
Published: February 2009

Through targeted homologous recombination, we developed a panel of matched colorectal cancer cell lines that differ only with respect to their endogenousTP53status. We then used these lines to define the genes whose expression was altered after DNA damage induced by ionizing radiation. Transcriptome analyses revealed a consistent up-regulation of polo-like kinase 1 (PLK1) as well as other genes controlling the G2/M transition in the cells whoseTP53genes were inactivated compared with those with WTTP53genes. This led to the hypothesis that the viability of stressed cells without WTTP53depended onPLK1. This hypothesis was validated by demonstrating that stressed cancer cells without WTTP53alleles were highly sensitive to PLK1 inhibitors, both in vivo and in vitro.
Discordant memory B cell and circulating anti-Env antibody responses in HIV-1 infection
Authors: Guan Yongjun , Sajadi Mohammad M. , Kamin-Lewis Roberta , Fouts Timothy R. , Dimitrov Anthony , Zhang Zhixin , Redfield Robert R. , DeVico Anthony L. , Gallo Robert C. , Lewis George K.
Published: February 2009

Long-lived memory B cells (B
Mem
) provide an archive of historic Ab responses. By contrast, circulating Abs typically decline once the immunogen is cleared. Consequently, circulating Abs can underestimate the nature of cognate humoral immunity. On the other hand, the B
Mem
pool should provide a comprehensive picture of Ab specificities that arise over the entire course of infection. To test this hypothesis, we compared circulating Ab and B
Mem
from natural virus suppressors who control HIV-1 without therapy and maintain a relatively intact immune system. We found high frequencies of B
Mem
specific for the conserved neutralizing CD4 induced or CD4 binding site epitopes of gp120, whereas low Ab titers to these determinants were detected in contemporaneous plasma. These data suggest that plasma Ab repertoires can underestimate the breadth of humoral immunity, and analyses of B
Mem
should be included in studies correlating Ab specificity with protective immunity to HIV-1.
A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle
Authors: Yao Qing , Cui Jixin , Zhu Yongqun , Wang Guolun , Hu Liyan , Long Chengzu , Cao Ran , Liu Xinqi , Huang Niu , Chen She , Liu Liping , Shao Feng
Published: February 2009

Pathogenic bacteria deliver effector proteins into host cells through the type III secretion apparatus to modulate the host function. We identify a family of proteins, homologous to the type III effector Cif from enteropathogenic
Escherichia coli
, in pathogens including
Yersinia
,
Photorhabdus
, and
Burkholderia
that contain functional type III secretion systems. Like Cif, this family of proteins is capable of arresting the host cell cycle at G
2
/M. Structure of one of the family members, Cif homolog in
Burkholderia pseudomallei
(CHBP), reveals a papain-like fold and a conserved Cys-His-Gln catalytic triad despite the lack of primary sequence identity. For CHBP and Cif, only the putative catalytic Cys is susceptible to covalent modification by E-64, a specific inhibitor of papain-like cysteine proteases. Unlike papain-like enzymes where the S2 site is the major determinant of cleavage-site specificity, CHBP has a characteristic negatively charged pocket occupying surface areas corresponding to the S1/S1′ site in papain-like proteases. The negative charge is provided by a conserved aspartate, and the pocket best fits an arginine, as revealed by molecular docking analysis. Mutation analysis establishes the essential role of the catalytic triad and the negatively charged pocket in inducing cell cycle arrest in host cells. Our results demonstrate that bacterial pathogens have evolved a unique papain-like hydrolytic activity to block the normal host cell cycle progression.
The Fifth Estate Emerging through the Network of Networks
Authors: Dutton William H.
Published: February 2009

The rise of the press, radio, television and other mass media enabled the development of an independent institution: the ‘Fourth Estate’, central to pluralist democratic processes. The growing use of the Internet and related digital technologies is creating a space for networking individuals in ways that enable a new source of accountability in government, politics and other sectors. This paper explains how this emerging ‘Fifth Estate’ is being established and why this could challenge the influence of other more established bases of institutional authority. It discusses approaches to the governance of this new social and political phenomenon that could nurture the Fifth Estate’s potential for supporting the vitality of liberal democratic societies.
Services, ICTs and the Changing Nature of Economic Development Processes in the KBE Era
Authors: Mandeville Tom , Kardoyo Hadi
Published: February 2009

We present a concise, exploratory, discussion paper that provides some promising hypotheses concerning how economic development processes may be evolving in the KBE era. Emerging roles for ICTs and services in the economy are driving these changes. Developing countries may be able to leapfrog stages of growth, or structural change, that presently developed nations historically went through. Case studies of India and Indonesia are utilized.
Anxiety Sensitivity as a Moderator of the Association between Smoking Rate and Panic‐Relevant Symptoms among a Community Sample of Middle‐aged Adult Daily Smokers
Authors: McLeish Alison C. , Zvolensky Michael J. , Del Ben Kevin S. , Burke Randy S.
Published: February 2009

The aim of the present investigation was to evaluate the moderating role of anxiety sensitivity (AS) in the relation between smoking rate and panic vulnerability variables among a community‐based sample of adults. Results indicated that the interaction between AS and smoking rate significantly predicted anxious arousal, agoraphobic avoidance, and anticipatory anxiety. Specifically, participants who reported higher levels of AS and heavier smoking rates reported the highest levels of panic vulnerability. These data suggest that this combination of high AS and heavier smoking is particularly problematic in regard to panic symptoms.
Treatment Challenges Associated with Comorbid Substance Use and Posttraumatic Stress Disorder: Clinicians' Perspectives
Authors: Back Sudie E. , Waldrop Angela E. , Brady Kathleen T.
Published: February 2009

A significant proportion of individuals with substance use disorders (SUDs) meet criteria for comorbid posttraumatic stress disorder (PTSD). This comorbidity confers a more complicated clinical presentation that carries with it formidable treatment challenges for practitioners. The current study examined sources of difficulty and gratification among clinicians (N = 423) from four national organizations who completed an anonymous questionnaire. As expected, the findings revealed that comorbid SUD/PTSD was rated as significantly more difficult to treat than either disorder alone. The most common challenges associated with treating SUD/PTSD patients included knowing how to best prioritize and integrate treatment components, patient self‐destructiveness and severe symptomatology, and helping patients abstain from substance use. The findings increase understanding of SUD/PTSD treatment challenges, and may be useful for enhancing therapist training programs, supervision effectiveness, and designing optimal SUD/PTSD interventions.
Oral Tolerance Induced by Enterobacteria Altered the Process of Lymphocyte Recruitment to Intestinal Microvessels: Roles of Endothelial Cell Adhesion Molecules, TGF‐beta and Negative Regulators of TLR Signaling
Authors: TAKEBAYASHI KOICHI , HOKARI RYOTA , KURIHARA CHIE , OKADA YOSHIKIYO , OKUDAIRA KEISUKE , MATSUNAGA HISAYUKI , KOMOTO SYUNSUKE , WATANABE CHIKAKO , KAWAGUCHI ATSUSHI , NAGAO SHIGEAKI , TSUZUKI YOSHIKAZU , MIURA SOICHIRO
Published: February 2009

Objective: Although enterobacteria are implicated in intestinal immune response, there has been no report on how intraluminal pathogens affect lymphocyte recruitment. The aim of this study was to determine how the presence of intestinal flora affects lymphocyte migration to intestine under physiological and lipopolysaccharide (LPS)‐induced inflammatory conditions.

Methods: Interaction of T‐cells with ileal microvessels was monitored by using an intravital microscope in mice under germ‐free (GF) and specific pathogen‐free (SPF) conditions. LPS was administered into either the peritoneal cavity or duodenum before lymphocyte injection.

Results: Adherence of T‐cells was greater in SPF than in GF mice, indicating that the presence of enterobacteria upregulated migration under physiological conditions. Intraperitoneally administered LPS significantly increased the adherence of T‐cells in both GF and SPF mice accompanied by the expression of adhesion molecules and proinflammatory cytokines. However, intraluminally administered LPS did not enhance the adherence of T‐cells in SPF mice. A significant induction of increase in mRNA expression of IRAK‐M, a negative regulator of TLR4 signaling, and transforming growth factor beta (TGF‐beta), a regulatory cytokine, was observed in SPF mice after luminal LPS treatment.

Conclusions: Tolerance to intraluminally administered LPS in the lymphocyte recruitment process was induced by enterobacteria, possibly via the induction of IRAK‐M and TGF‐beta.
3D MHD VDE and disruptions simulations of tokamaks plasmas including some ITER scenarios
Authors: Paccagnella R. , Strauss H.R. , Breslau J.
Published: February 2009

Tokamaks vertical displacement events (VDEs) and disruptions simulations in toroidal geometry by means of a single fluid visco-resistive magneto-hydro-dynamic (MHD) model are presented in this paper. The plasma model is completed with the presence of a 2D wall with finite resistivity which allows the study of the relatively slowly growing magnetic perturbation, the resistive wall mode (RWM), which is, in this paper, the main drive of the disruption evolution. Amplitudes and asymmetries of the halo currents pattern at the wall are also calculated and comparisons with tokamak experimental databases and predictions for ITER are given.
Mutants of the Paf1 Complex Alter Phenotypic Expression of the Yeast Prion [PSI+]
Authors: Strawn Lisa A. , Lin Changyi A. , Tank Elizabeth M.H. , Osman Morwan M. , Simpson Sarah A. , True Heather L.
Published: February 2009

The yeast [PSI+] prion is an epigenetic modifier of translation termination fidelity that causes nonsense suppression. The prion [PSI+] forms when the translation termination factor Sup35p adopts a self-propagating conformation. The presence of the [PSI+] prion modulates survivability in a variety of growth conditions. Nonsense suppression is essential for many [PSI+]-mediated phenotypes, but many do not appear to be due to read-through of a single stop codon, but instead are multigenic traits. We hypothesized that other global mechanisms act in concert with [PSI+] to influence [PSI+]-mediated phenotypes. We have identified one such global regulator, the Paf1 complex (Paf1C). Paf1C is conserved in eukaryotes and has been implicated in several aspects of transcriptional and posttranscriptional regulation. Mutations in Ctr9p and other Paf1C components reduced [PSI+]-mediated nonsense suppression. The CTR9 deletion also alters nonsense suppression afforded by other genetic mutations but not always to the same extent as the effects on [PSI+]-mediated read-through. Our data suggest that the Paf1 complex influences mRNA translatability but not solely through changes in transcript stability or abundance. Finally, we demonstrate that the CTR9 deletion alters several [PSI+]-dependent phenotypes. This provides one example of how [PSI+] and genetic modifiers can interact to uncover and regulate phenotypic variability.
Core Exosome-independent Roles for Rrp6 in Cell Cycle Progression
Authors: Graham Amy C. , Kiss Daniel L. , Andrulis Erik D.
Published: February 2009

Exosome complexes are 3′ to 5′ exoribonucleases composed of subunits that are critical for numerous distinct RNA metabolic (ribonucleometabolic) pathways. Several studies have implicated the exosome subunits Rrp6 and Dis3 in chromosome segregation and cell division but the functional relevance of these findings remains unclear. Here, we report that, in Drosophila melanogaster S2 tissue culture cells, dRrp6 is required for cell proliferation and error-free mitosis, but the core exosome subunit Rrp40 is not. Micorarray analysis of dRrp6-depleted cell reveals increased levels of cell cycle– and mitosis-related transcripts. Depletion of dRrp6 elicits a decrease in the frequency of mitotic cells and in the mitotic marker phospho-histone H3 (pH3), with a concomitant increase in defects in chromosome congression, separation, and segregation. Endogenous dRrp6 dynamically redistributes during mitosis, accumulating predominantly but not exclusively on the condensed chromosomes. In contrast, core subunits localize predominantly to MTs throughout cell division. Finally, dRrp6-depleted cells treated with microtubule poisons exhibit normal kinetochore recruitment of the spindle assembly checkpoint protein BubR1 without restoring pH3 levels, suggesting that these cells undergo premature chromosome condensation. Collectively, these data support the idea that dRrp6 has a core exosome-independent role in cell cycle and mitotic progression.
Mislocalized Scaffolding by the Na-H Exchanger NHE1 Dominantly Inhibits Fibronectin Production and TGF-β Activation
Authors: Karydis Anastasios , Jimenez-Vidal Maite , Denker Sheryl P. , Barber Diane L.
Published: February 2009

Secretion and assembly of the extracellular matrix protein fibronectin regulates a number of normal cell and tissue functions and is dysregulated in disease states such as fibrosis, diabetes, and cancer. We found that mislocalized scaffolding by the plasma membrane Na-H exchanger NHE1 suppresses fibronectin expression, secretion, and assembly. In fibroblasts, wild-type NHE1 localizes to the distal margin of membrane protrusions or lamellipodia but a mutant NHE1-KRA2 lacking binding sites for PI(4,5)P2 and the ERM proteins ezrin, radixin, and moesin is mislocalized and found uniformly along the plasma membrane. Although NHE1 regulates intracellular pH homeostasis, fibronectin production is not regulated by changes in intracellular pH, nor is it attenuated in NHE1-deficient cells, indicating fibronectin expression is independent of NHE1 activity. However, fibronectin production is nearly absent in cells expressing NHE1-KRA2 because scaffolding by NHE1 is mislocalized. Additionally, secretion of active but not latent TGF-β is reduced and exogenous TGF-β restores fibronectin secretion and assembly. Our data indicate that scaffolding by NHE1-KRA2 dominantly suppresses fibronectin synthesis and TGF-β activation, and they suggest that NHE1-KRA2 can be used for obtaining a mechanistic understanding of how fibronectin production is regulated and speculatively for therapeutic control of dysregulated production in pathological conditions.
An Atg1/Atg13 Complex with Multiple Roles in TOR-mediated Autophagy Regulation
Authors: Chang Yu-Yun , Neufeld Thomas P.
Published: February 2009

The TOR kinases are conserved negative regulators of autophagy in response to nutrient conditions, but the signaling mechanisms are poorly understood. Here we describe a complex containing the protein kinase Atg1 and the phosphoprotein Atg13 that functions as a critical component of this regulation in Drosophila. We show that knockout of Atg1 or Atg13 results in a similar, selective defect in autophagy in response to TOR inactivation. Atg1 physically interacts with TOR and Atg13 in vivo, and both Atg1 and Atg13 are phosphorylated in a nutrient-, TOR- and Atg1 kinase-dependent manner. In contrast to yeast, phosphorylation of Atg13 is greatest under autophagic conditions and does not preclude Atg1-Atg13 association. Atg13 stimulates both the autophagic activity of Atg1 and its inhibition of cell growth and TOR signaling, in part by disrupting the normal trafficking of TOR. In contrast to the effects of normal Atg13 levels, increased expression of Atg13 inhibits autophagosome expansion and recruitment of Atg8/LC3, potentially by decreasing the stability of Atg1 and facilitating its inhibitory phosphorylation by TOR. Atg1-Atg13 complexes thus function at multiple levels to mediate and adjust nutrient-dependent autophagic signaling.
PASS: a program to align short sequences
Authors: Campagna Davide , Albiero Alessandro , Bilardi Alessandra , Caniato Elisa , Forcato Claudio , Manavski Svetlin , Vitulo Nicola , Valle Giorgio
Published: February 2009

Summary: Standard DNA alignment programs are inadequate to manage the data produced by new generation DNA sequencers. To answer this problem, we developed PASS with the objective of improving execution time and sensitivity when compared with other available programs. PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of ‘seed’ words (typically 11 and 12 bases) as well as an index of the precomputed scores of short words (typically seven and eight bases) aligned against each other. After building the genomic index, the program scans every query sequence performing three steps: (1) it finds matching seed words in the genome; (2) for every match checks the precomputed alignment of the short flanking regions; (3) if passes step 2, then it performs an exact dynamic alignment of a narrow region around the match. The performance of the program is very striking both for sensitivity and speed. For instance, gap alignment is achieved hundreds of times faster than BLAST and several times faster than SOAP, especially when gaps are allowed. Furthermore, PASS has a higher sensitivity when compared with the other available programs.

Availability and implementation: Source code and binaries are freely available for download at http://pass.cribi.unipd.it, implemented in C++and supported on Linux and Windows.

Contact:  pass@cribi.unipd.it
Medialization Thyroplasty Window Creation Using an Ultrasonic Surgical Aspirator
Authors: Halum Stacey , Patel Nalin , Hoffman Raymond G. , Simpson C Blake , Merati Albert L.
Published: February 2009

Objectives/Hypothesis: The aim of the study was to investigate the use of an ultrasonic surgical aspirator for creation of the laryngeal cartilage window during medialization thyroplasty.

Study Design: Basic science.

Methods: Forty thyroplasty windows were constructed in fresh, unpreserved cadaver larynges. A 6 × 13‐mm rectangular window and a 4 × 4‐mm round window were created on each side of the larynges in a symmetrical fashion. A standard surgical drill with a 3‐mm cutting burr was used on one side; the ultrasonic surgical aspirator was used on the contralateral side. The time required for window construction was recorded, as was the status of the inner perichondrium at window completion.

Results: For creation of the 6 × 13‐mm window, a mean time of 128 seconds was required using a standard surgical drill. The mean time using the ultrasonic aspirator device was 91 seconds for the window of the same size (P < .008). For the 4‐mm round window, drilling completed the task in a mean time of 63 seconds, compared with 40 seconds (P < .016) for the ultrasonic aspirator. On creation of the 6 × 13‐mm window, there were 4 of 10 perichondrial violations in the drilled specimens, and there were no violations in creation of the window of the same size with the ultrasonic aspirator (P = .12). The 4‐mm round window had no perichondrium violations in the standard drill group and only 1 of 10 violations in the ultrasonic aspirator group (P = .99).

Conclusion: The study suggested that the ultrasonic surgical aspirator device may be an effective, efficient alternative to the standard drill for medialization thyroplasty window creation. Prospective clinical trials are warranted to better characterize its applicability.
Effects of a Twenty‐Four Hour Call Period on Resident Performance During Simulated Endoscopic Sinus Surgery in an Accreditation Council for Graduate Medical Education–Compliant Training Program
Authors: Jakubowicz David M. , Price Erin M. , Glassman Harrison J. , Gallagher Anthony J.G. , Mandava Neil , Ralph Walter P. , Fried Marvin P.
Published: February 2009

Objectives/Hypothesis: Since the early 1990s, extended resident work hours have undergone increasing scrutiny. Although previous studies have demonstrated conflicting results regarding cognitive decline secondary to fatigue, few studies have specifically examined the effects of fatigue on surgical performance. No previous studies have examined resident performance under current Accreditation Council for Graduate Medical Education (ACGME) work‐hour guidelines that limit residents to an average number of work hours of 80 hours per week. The study sought to determine whether an endoscopic sinus surgery simulator (ES3) measured performance changes before and after a 24‐hour on‐call period in residents following mandated work‐hour limitations.

Study Design: Case control, crossover trial at a Level I trauma center.

Methods: Eight general surgical residents were trained on the novice mode of the ES3. These residents were then tested twice both before and after on‐call duties. Performance and hazard scores were compared using a paired t test.

Results: No statistically significant change in the number of errors, time to task completion, or overall performance was identified in the study between the precall and postcall groups. There was a trend toward improved speed at the expense of accuracy in the postcall group. Postcall score between the two trials improved, on average, by 3.3 (P = .045).

Conclusion: In the study of residents following current ACGME work‐hour mandates, there was no diminution in performance before and after a 24‐hour on‐call period. There was a trend toward improved speed at the expense of accuracy. Furthermore, repetition on the ES3 in the postcall period can result in improved ES3 proficiency.
Atomic Force Microscopy Investigation of Vocal Fold Collagen
Authors: Sivasankar Mahalakshmi , Ivanisevic Albena
Published: February 2009

Objectives: Collagen is an important constituent of the vocal fold extracellular matrix and is necessary for providing tensile strength and maintaining tissue geometry. Traditional investigations of vocal fold collagen using light and electron microscopy do not provide information on the organization and mechanical properties of collagen in native topographic state. The primary objective of this study was to use Atomic Force Microscopy (AFM) to examine the surface characteristics and organization of collagen in the deep layer of the lamina propria at nanoscale resolution.

Study Design: Experimental in vitro design.

Methods: Freshly dissected porcine vocal folds were mounted on AFM discs and imaged under contact and tapping mode to obtain information on topographic distribution of collagen.

Results: AFM imaging of the deep layer of the lamina propria revealed dense, abundant collagen fibers with a characteristic banding pattern. The distribution of collagen was heterogeneous, with both hydrophilic and hydrophobic regions within a sample.

Conclusions: AFM offers a useful tool to obtain topographic information about biologic samples at nanoscale resolution with minimal sample preparation. Mapping the topography and mechanical properties of vocal fold collagen is necessary for designing rheologically compatible bioimplants for the treatment of dysphonia resulting from vocal fold scarring and bowing.
Oncostatin‐M Enhances Osteoinduction in a Rabbit Critical Calvarial Defect Model
Authors: Moxham J Paul
Published: February 2009

Introduction: Oncostatin‐M (OSM) is a member of the interleukin‐6 family of cytokines with controversial roles in bone homeostasis. Evidence supports a role in bone regulation, but the balance between healing promotion and acceleration of bone destruction is unclear. It is also uncertain as to whether these varied responses may be dose dependent or related to interactions with other growth factors within the bone microenvironment.

Objective: To determine whether OSM enhances osteoinduction in a rabbit critical calvarial defect model and whether there is a dose response curve.

Hypothesis: OSM enhances osteoinduction, and there is a dose response curve favoring lower doses over higher doses.

Study Design: Controlled animal study using arms of increasing concentrations of OSM in an inactive demineralized bone matrix (DBM) carrier to assess the degree of osteoinduction through standard histomorphometric analysis and a variant of the radiodensitometry technique.

Methods: Twenty‐five skeletally mature New Zealand white rabbits were randomized into control and experimental arms. Incremental doses of OSM (30 μg, 100 μg, and 300 μg/g) in an inactivated guanidine‐extracted DBM (Gu‐DBM) carrier were implanted into a critically sized (13 mm) calvarial defect. Arms of carrier alone and no carrier served as controls. The animals were sacrificed at 4 weeks, and histomorphometry and radiodensitometry analyses were then performed.

Results: All OSM arms showed a statistically significant increase in bone formation and bone density compared with either control arm. There was also a statistically significant increase in bone area by histomorphometry between each OSM group, showing an inverse relationship to dose. Radiodensitometry analysis confirmed a significant bone density difference when comparing experimental groups with controls and also showed a significant difference between the low dose and the higher doses of OSM. It failed to show any significance between the higher two doses when compared with each other.

Conclusions: OSM enhances osteoinduction in vivo and will close a critically sized calvarial defect in a rabbit model when delivered in a Gu‐DBM carrier. There appears to be an inverse dose relationship with new bone formation.