bluuebunny/crossref_metadata_2025 huggingface dataset:
Urban aerosols harbor diverse and dynamic bacterial populations
Authors: Brodie Eoin L. , DeSantis Todd Z. , Parker Jordan P. Moberg , Zubietta Ingrid X. , Piceno Yvette M. , Andersen Gary L.
Published: December 2006

Considering the importance of its potential implications for human health, agricultural productivity, and ecosystem stability, surprisingly little is known regarding the composition or dynamics of the atmosphere's microbial inhabitants. Using a custom high-density DNA microarray, we detected and monitored bacterial populations in two U.S. cities over 17 weeks. These urban aerosols contained at least 1,800 diverse bacterial types, a richness approaching that of some soil bacterial communities. We also reveal the consistent presence of bacterial families with pathogenic members including environmental relatives of select agents of bioterrorism significance. Finally, using multivariate regression techniques, we demonstrate that temporal and meteorological influences can be stronger factors than location in shaping the biological composition of the air we breathe.
How personal experience modulates the neural circuitry of memories of September 11
Authors: Sharot Tali , Martorella Elizabeth A. , Delgado Mauricio R. , Phelps Elizabeth A.
Published: December 2006

Brown and Kulik [Brown R, Kulik J (1977)
Cognition
5:73–99] introduced the term “flashbulb memory” to describe the recall of shocking, consequential events such as hearing news of a presidential assassination. They proposed that the vivid detail of such memories results from the action of a unique neural mechanism. In the present study of personal recollections of the terrorist attacks of September 11, 2001 (9/11) in New York City, we combine behavioral and brain imaging techniques, with two goals: (
i
) to explore the neural basis of such memories and (
ii
) to clarify the characteristics of the emotional events that may give rise to them. Three years after the terrorist attacks, participants were asked to retrieve memories of 9/11, as well as memories of personally selected control events from 2001. At the time of the attacks, some participants were in Downtown Manhattan, close to the World Trade Center; others were in Midtown, a few miles away. The Downtown participants exhibited selective activation of the amygdala as they recalled events from 9/11, but not while they recalled control events. This was not the case for the Midtown participants. Moreover, only the Downtown participants reported emotionally enhanced recollective experiences while recalling events from 9/11, as compared with control events. These results suggest that close personal experience may be critical in engaging the neural mechanisms that underlie the emotional modulation of memory and thus in producing the vivid recollections to which the term flashbulb memory is often applied.
Monoalkyl sulfates as alkylating agents in water, alkylsulfatase rate enhancements, and the “energy-rich” nature of sulfate half-esters
Authors: Wolfenden Richard , Yuan Yang
Published: December 2006

Alkyl sulfate monoesters are involved in cell signaling and structure. Alkyl sulfates are also present in many commercial detergents. Here, we show that monomethyl sulfate acts as an efficient alkylating agent in water, reacting spontaneously with oxygen nucleophiles >100-fold more rapidly than do alkylsulfonium ions, the usual methyl donors in living organisms. These reactions of methyl sulfate, which are much more rapid than its hydrolysis, are insensitive to the nature of the attacking nucleophile, with a Brønsted β
nuc
value of −0.01. Experiments at elevated temperatures indicate a rate constant of 2 × 10
−11
s
−1
for the uncatalyzed hydrolysis of methyl sulfate at 25°C (
t
1/2
= 1,100 y), corresponding to a rate enhancement of ≈10
11
-fold by a human alkylsulfatase. Equilibria of formation of methyl sulfate from methanol and sodium hydrogen sulfate indicate a group transfer potential (Δ
G′
pH7
) of −8.9 kcal/mol for sulfate ester hydrolysis. The magnitude of that value, involving release of the strong acid HSO
4
−
, helps to explain the need for harnessing the free energy of hydrolysis of two ATP molecules in activating sulfate for the biosynthesis of sulfate monoesters. The “energy-rich” nature of monoalkyl sulfate esters, coupled with their marked resistance to hydrolysis, renders them capable of acting as sulfating or alkylating agents under relatively mild conditions. These findings raise the possibility that, under appropriate circumstances, alkyl groups may undergo transfer from alkyl sulfate monoesters to biological target molecules.
The 1′,4′-iminopyrimidine tautomer of thiamin diphosphate is poised for catalysis in asymmetric active centers on enzymes
Authors: Nemeria Natalia , Chakraborty Sumit , Baykal Ahmet , Korotchkina Lioubov G. , Patel Mulchand S. , Jordan Frank
Published: December 2006

Thiamin diphosphate, a key coenzyme in sugar metabolism, is comprised of the thiazolium and 4′-aminopyrimidine aromatic rings, but only recently has participation of the 4′-aminopyrimidine moiety in catalysis gained wider acceptance. We report the use of electronic spectroscopy to identify the various tautomeric forms of the 4′-aminopyrimidine ring on four thiamin diphosphate enzymes, all of which decarboxylate pyruvate: the E1 component of human pyruvate dehydrogenase complex, the E1 subunit of
Escherichia coli
pyruvate dehydrogenase complex, yeast pyruvate decarboxylase, and pyruvate oxidase from
Lactobacillus plantarum
. It is shown that, according to circular dichroism spectroscopy, both the 1′,4′-iminopyrimidine and the 4′-aminopyrimidine tautomers coexist on the E1 component of human pyruvate dehydrogenase complex and pyruvate oxidase. Because both tautomers are seen simultaneously, these two enzymes provide excellent evidence for nonidentical active centers (asymmetry) in solution in these multimeric enzymes. Asymmetry of active centers can also be induced upon addition of acetylphosphinate, an excellent electrostatic pyruvate mimic, which participates in an enzyme-catalyzed addition to form a stable adduct, resembling the common predecarboxylation thiamin-bound intermediate, which exists in its 1′,4′-iminopyrimidine form. The identification of the 1′,4′-iminopyrimidine tautomer on four enzymes is almost certainly applicable to all thiamin diphosphate enzymes: this tautomer is the intramolecular trigger to generate the reactive ylide/carbene at the thiazolium C2 position in the first fundamental step of thiamin catalysis.
Personality Risk Factors Associated with Trajectories of Tobacco Use
Authors: Brook Judith S. , Ning Yuming , Brook David W.
Published: December 2006

The purpose of this longitudinal, prospective study was to evaluate trajectories of smoking in a cohort of African‐American and Puerto Rican young adults and describe personality and behavioral factors associated with specific smoking trajectory group membership. Participants consisted of African‐American and Puerto Rican male and female young adults (n = 451, mean age 26) from an inner‐city community. Data were collected at four time points over a period of 13 years using structured interviews. Interviews took place within the schools and the participants' homes. Scales with adequate psychometric properties were adapted from previously validated measures. Variables that were examined for this study came from the domains of internalizing behaviors, externalizing behaviors, drug use, and demographic information. Data were analyzed using latent growth mixture modeling to explore discrete smoking trajectories. Logistic regression analyses were then used to examine the risk factors associated with the various smoking trajectory groups. Four trajectory groups were determined to best fit the data: nonsmokers, maturing‐out smokers, late‐starting smokers, and early‐starting continuous smokers. Subjects who were unconventional, experienced intrapersonal distress, and used alcohol and illegal drugs were more likely to belong to one of the smoking trajectory groups than to the nonsmoking group. The early‐starting continuous group scored highest on these personal risk attributes. The long‐term impact of unconventional behavior, intrapersonal distress, and drug use on developmental trajectories of smoking support the importance of early intervention and prevention.
Outcome Predictors in Cocaine Dependence Treatment Trials
Authors: Ahmadi Jamshid , Kampman Kyle , Dackis Charles
Published: December 2006

Finding the predictors of outcome in outpatient cocaine dependence treatment trials may be useful for the development of both psychosocial as well as pharmacological treatments for cocaine dependence. Among the most powerful predictors of response to psychosocial treatment are cocaine withdrawal symptom severity and the results of a urine drug screen (UDS) collected at study entry. The present trial seeks to extend these findings by examining outcome predictors in a large number of subjects participating in a series of outpatient cocaine pharmacotherapy trials while selecting three separate criteria to define successful outcome. The ability of several baseline variables were tested to predict treatment outcome in a series of cocaine medication trials that included 402 cocaine‐dependent subjects. Predictor variables included results from the baseline Addiction Severity Index (ASI), initial UDS results, and cocaine withdrawal symptom severity at treatment entry, as measured by scores on the Cocaine Selective Severity Assessment (CSSA). Outcome measures included UDS results obtained during the trials and results from the ASI gathered at the end of the trials. Baseline variables that most consistently predicted treatment outcome were the initial UDS results and initial CSSA scores. These findings indicate that baseline UDS results and CSSA scores are powerful predictors of outcome and should be used as stratifying variables in outpatient cocaine medication trials.
More Severe Violence Exposure Associated with Poly‐Pharmaceutical Use
Authors: Kubiak Sheryl Pimlott , Arfken Cynthia L. , Boyd Carol , Cortina Lilia M.
Published: December 2006

Exposure to emotional, physical, and sexual abuse carries varying psychological and somatic sequelae, including the increased use of alcohol and illicit drugs. Less studied is the association between violence exposure and prescription drug use. Using previously determined lifetime exposure profiles of 16,000 men and women, the current use of three specific drug categories was assessed and a strong relationship between victimization severity and prescription drugs used within the last month was found. Victimization screening has important implications in health care settings.
Abstinence and Initiation of Treatment Following Inpatient Detoxification
Authors: Blondell Richard D. , Smith Susan J. , Canfield Marta C. , Servoss Timothy J.
Published: December 2006

This prospective cohort study compared in‐patients who remained abstinent and initiated aftercare treatment following detoxification with those who did not. Of 110 patients enrolled, 58% (46/79) were totally abstinent and 72% (67/93) initiated treatment during the first 30 days following hospital discharge. Patients who relapsed after hospital discharge were more likely than those who remained abstinent to have a primary drug‐use disorder (p = 0.05), prior mental health treatment (p = .007), or previous incarceration (p = 0.035). Those who initiated aftercare treatment were less likely to have had prior mental health treatment than those who did not (p = .046).
Demographic Characteristics and Antisocial Personality Disorder of Early and Late Onset Alcoholics Identified in a Primary Care Clinic
Authors: Huang David B. , Kamat Paresh P. , Wang Jay
Published: December 2006

A total of 1,734 persons were prospectively screened in a primary care clinic to examine the demographic characteristics and presence or absence of antisocial personality disorder among early onset alcoholics (EOA) and late onset alcoholics (LOA). A total of 76 EOA (male −58 and female −18) and 80 LOA (male −56 and female −24), as determined by the Comprehensive Drinking Profile Scale, participated in the study. EOA tended to be single and were younger, in a lower socioeconomic class, raised by non‐biological parents, more likely to have antisocial personality disorder, and more likely to commit certain convicted offenses compared to LOA (p<.05). This study found that EOA identified in a primary care clinic have a different demographic profile and are more likely to have antisocial personality disorder compared to LOA.
Adolescent and Therapist Perception of Barriers to Outpatient Substance Abuse Treatment
Authors: Lynn Mensinger Janell , Diamond Guy S. , Kaminer Yifrah , Wintersteen Matthew B.
Published: December 2006

Attrition is one of the most vexing problems for the effective delivery of behavioral health services. Most prior studies focus on patient demographics and psychopathology factors predicting dropout. We examined patient and therapist post‐treatment reports of barriers to attending treatment. Six hundred adolescents and their therapists completed the Perceived Barriers to Treatment scale (PBT) at discharge from a brief substance abuse intervention. After adjusting for covariates, results suggest that perceived barriers, in particular, practical obstacles, lack of treatment readiness, relevance, and compatibility, are related to sessions attended. Shifting to a more patient‐centered approach for understanding treatment retention is discussed.
Absence of Iatrogenic or Contagion Effects in Adolescent Group Therapy: Findings from the Cannabis Youth Treatment (CYT) Study
Authors: Burleson Joseph A. , Kaminer Yifrah , Dennis Michael L.
Published: December 2006

Though widely used and presumed effective in practice, some scholars (Dishion et al., 1999) have raised the concern that group therapy for adolescents with substance use disorder and a range of deviancy has the potential for causing iatrogenic effects (e.g., increased substance use, behavior and legal problems) for those with low deviancy. Using data from 400 youth in the largest adolescent treatment experiment conducted to date (Dennis et al., 2004), this study shows that group composition in terms of conduct disorder symptoms is not associated with worse substance use, psychological, environmental or legal treatment outcomes. The results actually indicated that there was a slight advantage for youth with high conduct disorder to be included in the groups with less symptoms. The results appear consistent with recent meta‐analyses of delinquency studies (Lipsey, 2006) which have found no evidence of iatrogenic effects. These results support the common clinical belief that group therapy for youths with substance use disorders is a safe and effective treatment modality.
Early Therapeutic Alliance as a Predictor of Treatment Outcome for Adolescent Cannabis Users in Outpatient Treatment
Authors: Diamond Guy S. , Liddle Howard A. , Wintersteen Matthew B. , Dennis Michael L. , Godley Susan H. , Tims Frank
Published: December 2006

The association of early alliance to treatment attendance and longitudinal outcomes were examined in 356 adolescents participating in a randomized clinical trial targeting cannabis use. Both patient and therapist views of alliance were examined, and outcomes were evaluated over 12 months after numerous other sources of variance were controlled. Patient‐rated alliance predicted a reduction in cannabis use at three and six months and a reduction in substance‐related problem behaviors at six months. Therapist‐rated alliance did not predict outcomes. Neither patient nor therapist alliance ratings were associated with attendance. The findings support the important and often overlooked role that alliance can play in treating substance abusing, often delinquent, adolescents.
Effects of Motivational Interviewing for Incarcerated Adolescents on Driving Under the Influence after Release
Authors: Stein L. A. R. , Colby Suzanne M. , Barnett Nancy P. , Monti Peter M. , Golembeske Charles , Lebeau‐Craven Rebecca
Published: December 2006

Motivational Interviewing (MI) to reduce alcohol and marijuana‐related driving events among incarcerated adolescents was evaluated. Adolescents were randomly assigned to receive MI or Relaxation Training. Follow‐up assessment showed that, as compared to RT, adolescents who received MI had lower rates of drinking and driving, and being a passenger in a car with someone who had been drinking. Effects were moderated by levels of depression. At low levels of depression, MI evidenced lower rates of these behaviors; at high levels of depression, effects for MI and RT were equivalent. Similar patterns were found for marijuana‐related risky driving, but effects were nonsignificant.
Impact of Victimization on Substance Abuse Treatment Outcomes for Adolescents in Outpatient and Residential Substance Abuse Treatment
Authors: Shane Patricia , Diamond Guy S. , Lynn Mensinger Janell , Shera David , Wintersteen Matthew B.
Published: December 2006

This paper considers whether victimization moderates adolescents’ outcomes in substance abuse treatment. Adolescents (N—975) in outpatient and residential settings were assessed at intake, three, six, nine, and 12 months. Differential outcomes by gender and degree of victimization were analyzed. Dependent variables were marijuana use and substance‐related problems. The residential sample reported higher baseline marijuana use and victimization. Both samples significantly reduced marijuana use and associated problems during treatment. Victimization was significantly related to more substance‐related problems at intake and follow‐up. More severe trauma histories in residential females were associated with significantly greater persistence in substance‐related problems post‐discharge.
The Construct and Predictive Validity of Different Approaches to Combining Urine and Self‐Reported Drug Use Measures among Older Adolescents after Substance Abuse Treatment
Authors: Lennox Richard , Dennis Michael L. , Ives Melissa , White Michelle K.
Published: December 2006

Reconciling urine results and self‐reports is a classic challenge in substance abuse treatment research in general. For adolescents, the problems are compounded by the facts that they are more likely to use marijuana (which takes longer to metabolize) and to be coerced into treatment (which may increase lying). This article examines the construct and predictive validity of several different approaches for combining urine and self reported drug use including using common individual measures (urine tests and self‐reported recency, frequency, and peak use), taking either as positive, using a summary scale, and using a latent model. Data are from 819 older adolescents 24 to 42 months after intake in seven sites. Days of use, the GAIN's substance frequency scale, and a latent model were the three best methods in terms of construct and predictive validity. Implications for treatment and longitudinal evaluation will be discussed.
Health Care Services Use by Adolescents with Intakes into an Outpatient Alcohol and Drug Treatment Program
Authors: Parthasarathy Sujaya , Weisner Constance
Published: December 2006

We examined utilization and cost in the 1 year pre‐ and post‐intake among a sample of adolescents (N—419) entering chemical dependency (CD) treatment. Multivariate analyses showed that these youth used significantly more medical services than a demographically matched sample of members without substance use (SU) problems. Their utilization and costs were higher than matched members, and they did not show the same reductions in post‐treatment costs that adults do. This is of concern since it would appear that the medical and mental health problems of adolescents entering CD treatment may be so severe that there are no short‐term reductions in post‐treatment cost, including ER and hospitalizations.
Activated Cdc42-associated Kinase 1 Is a Component of EGF Receptor Signaling Complex and Regulates EGF Receptor Degradation
Authors: Shen Feng , Lin Qiong , Gu Yan , Childress Chandra , Yang Wannian
Published: December 2006

Cdc42-associated tyrosine kinase 1 (ACK1) is a specific down-stream effector of Cdc42, a Rho family small G-protein. Previous studies have shown that ACK1 interacts with clathrin heavy chain and is involved in clathrin-coated vesicle endocytosis. Here we report that ACK1 interacted with epidermal growth factor receptor (EGFR) upon EGF stimulation via a region at carboxy terminus that is highly homologous to Gene-33/Mig-6/RALT. The interaction of ACK1 with EGFR was dependent on the kinase activity or tyrosine phosphorylation of EGFR. Immunofluorescent staining using anti-EGFR and GFP-ACK1 indicates that ACK1 was colocalized with EGFR on EEA-1 positive vesicles upon EGF stimulation. Suppression of the expression of ACK1 by ACK-RNAi inhibited ligand-induced degradation of EGFR upon EGF stimulation, suggesting that ACK1 plays an important role in regulation of EGFR degradation in cells. Furthermore, we identified ACK1 as an ubiquitin-binding protein. Through an ubiquitin-association (Uba) domain at the carboxy terminus, ACK1 binds to both poly- and mono-ubiquitin. Overexpression of the Uba domain-deletion mutant of ACK1 blocked the ligand-dependent degradation of EGFR, suggesting that ACK1 regulates EGFR degradation via its Uba domain. Taken together, our studies suggest that ACK1 senses signal of EGF and regulates ligand-induced degradation of EGFR.
Villin Severing Activity Enhances Actin-based Motility In Vivo
Authors: Revenu Céline , Courtois Matthieu , Michelot Alphée , Sykes Cécile , Louvard Daniel , Robine Sylvie
Published: December 2006

Villin, an actin-binding protein associated with the actin bundles that support microvilli, bundles, caps, nucleates, and severs actin in a calcium-dependant manner in vitro. We hypothesized that the severing activity of villin is responsible for its reported role in enhancing cell plasticity and motility. To test this hypothesis, we chose a loss of function strategy and introduced mutations in villin based on sequence comparison with CapG. By pyrene-actin assays, we demonstrate that this mutant has a strongly reduced severing activity, whereas nucleation and capping remain unaffected. The bundling activity and the morphogenic effects of villin in cells are also preserved in this mutant. We thus succeeded in dissociating the severing from the three other activities of villin. The contribution of villin severing to actin dynamics is analyzed in vivo through the actin-based movement of the intracellular bacteria Shigella flexneri in cells expressing villin and its severing variant. The severing mutations abolish the gain of velocity induced by villin. To further analyze this effect, we reconstituted an in vitro actin-based bead movement in which the usual capping protein is replaced by either the wild type or the severing mutant of villin. Confirming the in vivo results, villin-severing activity enhances the velocity of beads by more than two-fold and reduces the density of actin in the comets. We propose a model in which, by severing actin filaments and capping their barbed ends, villin increases the concentration of actin monomers available for polymerization, a mechanism that might be paralleled in vivo when an enterocyte undergoes an epithelio-mesenchymal transition.
Critical Role of DNA Checkpoints in Mediating Genotoxic-Stress–induced Filamentous Growth inCandida albicans
Authors: Shi Qing-Mei , Wang Yan-Ming , Zheng Xin-De , Teck Ho Lee Raymond , Wang Yue
Published: December 2006

The polymorphic fungus Candida albicans switches from yeast to filamentous growth in response to a range of genotoxic insults, including inhibition of DNA synthesis by hydroxyurea (HU) or aphidicolin (AC), depletion of the ribonucleotide-reductase subunit Rnr2p, and DNA damage induced by methylmethane sulfonate (MMS) or UV light (UV). Deleting RAD53, which encodes a downstream effector kinase for both the DNA-replication and DNA-damage checkpoint pathways, completely abolished the filamentous growth caused by all the genotoxins tested. Deleting RAD9, which encodes a signal transducer of the DNA-damage checkpoint, specifically blocked the filamentous growth induced by MMS or UV but not that induced by HU or AC. Deleting MRC1, the counterpart of RAD9 in the DNA-replication checkpoint, impaired DNA synthesis and caused cell elongation even in the absence of external genotoxic insults. Together, the results indicate that the DNA-replication/damage checkpoints are critically required for the induction of filamentous growth by genotoxic stress. In addition, either of two mutations in the FHA1 domain of Rad53p, G65A, and N104A, nearly completely blocked the filamentous-growth response but had no significant deleterious effect on cell-cycle arrest. These results suggest that the FHA domain, known for its ability to bind phosphopeptides, has an important role in mediating genotoxic-stress–induced filamentous growth and that such growth is a specific, Rad53p-regulated cellular response in C. albicans.
The Karyopherin Kap95 Regulates Nuclear Pore Complex Assembly into Intact Nuclear Envelopes In Vivo
Authors: Ryan Kathryn J. , Zhou Yingna , Wente Susan R.
Published: December 2006

Nuclear pore complex (NPC) assembly in interphase cells requires that new NPCs insert into an intact nuclear envelope (NE). Our previous work identified the Ran GTPase as an essential component in this process. We proposed that Ran is required for targeting assembly factors to the cytoplasmic NE face via a novel, vesicular intermediate. Although the molecular target was not identified, Ran is known to function by modulating protein interactions for karyopherin (Kap) β family members. Here we characterize loss-of-function Saccharomyces cerevisiae mutants in KAP95 with blocks in NPC assembly. Similar to defects in Ran cycle mutants, nuclear pore proteins are no longer localized properly to the NE in kap95 mutants. Also like Ran cycle mutants, the kap95-E126K mutant displayed enhanced lethality with nic96 and nup170 mutants. Thus, Kap95 and Ran are likely functioning at the same stage in assembly. However, although Ran cycle mutants accumulate small cytoplasmic vesicles, cells depleted of Kap95 accumulated long stretches of cytoplasmic membranes and had highly distorted NEs. We conclude that Kap95 serves as a key regulator of NPC assembly into intact NEs. Furthermore, both Kap95 and Ran may provide spatial cues necessary for targeting of vesicular intermediates in de novo NPC assembly.
N-WASP Involvement in Dorsal Ruffle Formation in Mouse Embryonic Fibroblasts
Authors: Legg John A. , Bompard Guillaume , Dawson John , Morris Hannah L. , Andrew Natalie , Cooper Lisa , Johnston Simon A. , Tramountanis Giorgos , Machesky Laura M.
Published: December 2006

The Wiskott–Aldrich syndrome protein (WASP) family activates the Arp2/3 complex leading to the formation of new actin filaments. Here, we study the involvement of Scar1, Scar2, N-WASP, and Arp2/3 complex in dorsal ruffle formation in mouse embryonic fibroblasts (MEFs). Using platelet-derived growth factor to stimulate circular dorsal ruffle assembly in primary E13 and immortalized E9 Scar1+/+and Scar1 null MEFs, we establish that Scar1 loss does not impair the formation of dorsal ruffles. Reduction of Scar2 protein levels via small interfering RNA (siRNA) also did not affect dorsal ruffle production. In contrast, wiskostatin, a chemical inhibitor of N-WASP, potently suppressed dorsal ruffle formation in a dose-dependent manner. Furthermore, N-WASP and Arp2 siRNA treatment significantly decreased the formation of dorsal ruffles in MEFs. In addition, the expression of an N-WASP truncation mutant that cannot bind Arp2/3 complex blocked the formation of these structures. Finally, N-WASP−/−fibroblast-like cells generated aberrant dorsal ruffles. These ruffles were highly unstable, severely depleted of Arp2/3 complex, and diminished in size. We hypothesize that N-WASP and Arp2/3 complex are part of a multiprotein assembly important for the generation of dorsal ruffles and that Scar1 and Scar2 are dispensable for this process.
Mad2-independent Spindle Assembly Checkpoint Activation and Controlled Metaphase–Anaphase Transition inDrosophilaS2 Cells
Authors: Orr Bernardo , Bousbaa Hassan , Sunkel Claudio E.
Published: December 2006

The spindle assembly checkpoint is essential to maintain genomic stability during cell division. We analyzed the role of the putative Drosophila Mad2 homologue in the spindle assembly checkpoint and mitotic progression. Depletion of Mad2 by RNAi from S2 cells shows that it is essential to prevent mitotic exit after spindle damage, demonstrating its conserved role. Mad2-depleted cells also show accelerated transit through prometaphase and premature sister chromatid separation, fail to form metaphases, and exit mitosis soon after nuclear envelope breakdown with extensive chromatin bridges that result in severe aneuploidy. Interestingly, preventing Mad2-depleted cells from exiting mitosis by a checkpoint-independent arrest allows congression of normally condensed chromosomes. More importantly, a transient mitotic arrest is sufficient for Mad2-depleted cells to exit mitosis with normal patterns of chromosome segregation, suggesting that all the associated phenotypes result from a highly accelerated exit from mitosis. Surprisingly, if Mad2-depleted cells are blocked transiently in mitosis and then released into a media containing a microtubule poison, they arrest with high levels of kinetochore-associated BubR1, properly localized cohesin complex and fail to exit mitosis revealing normal spindle assembly checkpoint activity. This behavior is specific for Mad2 because BubR1-depleted cells fail to arrest in mitosis under these experimental conditions. Taken together our results strongly suggest that Mad2 is exclusively required to delay progression through early stages of prometaphase so that cells have time to fully engage the spindle assembly checkpoint, allowing a controlled metaphase–anaphase transition and normal patterns of chromosome segregation.
Direct Binding to Rsp5 Mediates Ubiquitin-independent Sorting of Sna3 via the Multivesicular Body Pathway
Authors: McNatt Matthew W. , McKittrick Ian , West Matthew , Odorizzi Greg
Published: December 2006

The sorting of most integral membrane proteins into the lumenal vesicles of multivesicular bodies (MVBs) is dependent on the attachment of ubiquitin (Ub) to their cytosolic domains. However, Ub is not required for sorting of Sna3, an MVB vesicle cargo protein in yeast. We show that Sna3 circumvents Ub-mediated recognition by interacting directly with Rsp5, an E3 Ub ligase that catalyzes monoubiquitination of MVB vesicle cargoes. The PPAY motif in the C-terminal cytosolic domain of Sna3 binds the WW domains in Rsp5, and Sna3 is polyubiquitinated as a consequence of this association. However, Ub does not appear to be required for transport of Sna3 via the MVB pathway because its sorting occurs under conditions in which its ubiquitination is impaired. Consistent with Ub-independent function of the MVB pathway, we show by electron microscopy that the formation of MVB vesicles does not require Rsp5 E3 ligase activity. However, cells expressing a catalytically disabled form of Rsp5 have a greater frequency of smaller MVB vesicles compared with the relatively broad distribution of vesicles seen in MVBs of wild-type cells, suggesting that the formation of MVB vesicles is influenced by Rsp5-mediated ubiquitination.
The Unique-5 and -6 Motifs of ZO-1 Regulate Tight Junction Strand Localization and Scaffolding Properties
Authors: Fanning Alan S. , Little Brent P. , Rahner Christoph , Utepbergenov Darkhan , Walther Zenta , Anderson James M.
Published: December 2006

The proper cellular location and sealing of tight junctions is assumed to depend on scaffolding properties of ZO-1, a member of the MAGUK protein family. ZO-1 contains a conserved SH3-GUK module that is separated by a variable region (unique-5), which in other MAGUKs has proven regulatory functions. To identify motifs in ZO-1 critical for its putative scaffolding functions, we focused on the SH3-GUK module including unique-5 (U5) and unique-6 (U6), a motif immediately C-terminal of the GUK domain. In vitro binding studies reveal U5 is sufficient for occludin binding; U6 reduces the affinity of this binding. In cultured cells, U5 is required for targeting ZO-1 to tight junctions and removal of U6 results in ectopically displaced junction strands containing the modified ZO-1, occludin, and claudin on the lateral cell membrane. These results provide evidence that ZO-1 can control the location of tight junction transmembrane proteins and reveals complex protein binding and targeting signals within its SH3-U5-GUK-U6 region. We review these findings in the context of regulated scaffolding functions of other MAGUK proteins.
BLOC-1 Is Required for Cargo-specific Sorting from Vacuolar Early Endosomes toward Lysosome-related Organelles
Authors: Setty Subba Rao Gangi , Tenza Danièle , Truschel Steven T. , Chou Evelyn , Sviderskaya Elena V. , Theos Alexander C. , Lamoreux M. Lynn , Di Pietro Santiago M. , Starcevic Marta , Bennett Dorothy C. , Dell'Angelica Esteban C. , Raposo Graça , Marks Michael S.
Published: December 2006

Hermansky-Pudlak syndrome (HPS) is a genetic disorder characterized by defects in the formation and function of lysosome-related organelles such as melanosomes. HPS in humans or mice is caused by mutations in any of 15 genes, five of which encode subunits of biogenesis of lysosome-related organelles complex (BLOC)-1, a protein complex with no known function. Here, we show that BLOC-1 functions in selective cargo exit from early endosomes toward melanosomes. BLOC-1–deficient melanocytes accumulate the melanosomal protein tyrosinase-related protein-1 (Tyrp1), but not other melanosomal proteins, in endosomal vacuoles and the cell surface due to failed biosynthetic transit from early endosomes to melanosomes and consequent increased endocytic flux. The defects are corrected by restoration of the missing BLOC-1 subunit. Melanocytes from HPS model mice lacking a different protein complex, BLOC-2, accumulate Tyrp1 in distinct downstream endosomal intermediates, suggesting that BLOC-1 and BLOC-2 act sequentially in the same pathway. By contrast, intracellular Tyrp1 is correctly targeted to melanosomes in melanocytes lacking another HPS-associated protein complex, adaptor protein (AP)-3. The results indicate that melanosome maturation requires at least two cargo transport pathways directly from early endosomes to melanosomes, one pathway mediated by AP-3 and one pathway mediated by BLOC-1 and BLOC-2, that are deficient in several forms of HPS.
Clustering threshold gradient descent regularization: with applications to microarray studies
Authors: Ma Shuangge , Huang Jian
Published: December 2006

Motivation: An important goal of microarray studies is to discover genes that are associated with clinical outcomes, such as disease status and patient survival. While a typical experiment surveys gene expressions on a global scale, there may be only a small number of genes that have significant influence on a clinical outcome. Moreover, expression data have cluster structures and the genes within a cluster have correlated expressions and coordinated functions, but the effects of individual genes in the same cluster may be different. Accordingly, we seek to build statistical models with the following properties. First, the model is sparse in the sense that only a subset of the parameter vector is non-zero. Second, the cluster structures of gene expressions are properly accounted for.

Results: For gene expression data without pathway information, we divide genes into clusters using commonly used methods, such as K-means or hierarchical approaches. The optimal number of clusters is determined using the Gap statistic. We propose a clustering threshold gradient descent regularization (CTGDR) method, for simultaneous cluster selection and within cluster gene selection. We apply this method to binary classification and censored survival analysis. Compared to the standard TGDR and other regularization methods, the CTGDR takes into account the cluster structure and carries out feature selection at both the cluster level and within-cluster gene level. We demonstrate the CTGDR on two studies of cancer classification and two studies correlating survival of lymphoma patients with microarray expressions.

Availability: R code is available upon request.

Contact:  shuangge.ma@yale.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
URec: a system for unrooted reconciliation
Authors: Górecki Pawel , Tiuryn Jerzy
Published: December 2006

Summary: URec is a software based on a concept of unrooted reconciliation. It can be used to reconcile a set of unrooted gene trees with a rooted species tree or a set of rooted species trees. Moreover, it computes detailed distribution of gene duplications and gene losses in a species tree. It can be used to infer optimal species phylogenies for a given set of gene trees. URec is implemented in C++ and can be easily compiled under Unix and Windows systems.

Availability: Software is freely available for download from our website at . This webpage also contains Windows executables and a number of advanced examples with explanations.

Contact:  gorecki@mimuw.edu.pl
The Demand Attributes of Assurance Services Providers and the Role of Independent Accountants
Authors: Knechel W. Robert , Wallage Philip , Eilifsen Aasmund , Van Praag Bart
Published: December 2006

This study reports on desirable attributes of assurance services providers for assurance services based on responses from a sample of Dutch senior accounting and financial officers. In general, overall expertise and objectivity are perceived as the most important attributes for selecting an assurance service provider. Cost is perceived as the least important attribute. In general, accountants are perceived as more likely to be the preferred service provider for assurance over information systems and/or when professional reputation and integrity is important for providing a service. These attributes are in line with the projected image of the profession. An accountant is less likely to be the preferred provider when cost and independence are not important. We interpret this result as an indication that independence in the audit is important and, thus, other services are acceptable only when independence is not an issue.
External Auditors’ Decisions in EU Credit Institutions: A Multicriteria Approach
Authors: Gaganis Chrysovalantis , Pasiouras Fotios , Zopounidis Constantin
Published: December 2006

In this paper we develop classification models that could assist auditors in their decision to issue a qualified or unqualified opinion during the auditing of EU credit institutions. The models are developed with the Utilites Additives Discriminantes (UTADIS) multicriteria technique and incorporate financial and non‐financial variables. Discriminant analysis is also employed for comparison purposes. The dataset consists of 80 qualified financial statements and 2,631 unqualified ones, from 446 credit institutions operating in eight EU countries over the period 1995–2002. The models are developed and tested using a ten‐fold cross‐validation approach. The results show that the developed auditing models can discriminate between financial statements that should receive qualified opinions from the ones that should receive unqualified opinions. The overall accuracy is 73.55% in the validation sample for a general model and increases up to 88.49% in the case of a model developed specifically for commercial banks.
Anti‐p200 pemphigoid: A novel autoimmune subepidermal blistering disease
Authors: DILLING Amrei , ROSE Christian , HASHIMOTO Takashi , ZILLIKENS Detlef , SHIMANOVICH Iakov
Published: December 2006

Anti‐p200 pemphigoid is a recently defined autoimmune subepidermal blistering disease characterized by circulating and tissue‐bound autoantibodies to a 200‐kDa protein (p200) of the dermal–epidermal junction (DEJ). This DEJ constituent is thought to be important for adhesion of basal keratinocytes to the underlying dermis. While the exact identity of p200 remains unknown, it has been demonstrated to be immunologically and biochemically distinct from all major autoantigens of the DEJ, including bullous pemphigoid antigens 180 and 230, laminin 1, 5 and 6, α6β4 integrin, and type VII collagen. Clinically, most reported cases present with tense blisters as well as urticarial papules and plaques, closely resembling bullous pemphigoid. Histopathological examination of lesional skin biopsies shows subepidermal split formation and superficial inflammatory infiltrate typically dominated by neutrophils. Immunopathologically, linear deposits of immunoglobulin (Ig)G and C3 are detected along the DEJ by direct immunofluorescence microscopy of perilesional skin. Indirect immunofluorescence microscopy of patients’ sera on NaCl‐split human skin demonstrates circulating IgG autoantibodies labeling the dermal side of the split. By immunoblotting, these autoantibodies recognize a 200‐kDa protein of human dermis. Biochemical characterization of the p200 molecule revealed a noncollagenous N‐glycosylated acidic protein with an isoelectric point of approximately 5.5. We present an overview of the pathogenesis, clinical features, diagnosis and treatment of this new disease entity.
Efficacy and safety of serial glycolic acid peels and a topical regimen in the treatment of recalcitrant melasma
Authors: ERBIL Hakan , SEZER Engin , TAŞTAN Bülent , ARCA Ercan , KURUMLU Zafer
Published: December 2006

Melasma is a common acquired disorder of facial hyperpigmentation. In this study we investigated the efficacy and safety of a combined treatment regimen including serial glycolic acid peels, topical azelaic acid cream and adapalene gel in the treatment of recalcitrant melasma. Twenty‐eight patients with recalcitrant melasma were enrolled in a prospective, randomized, controlled trial lasting 20 weeks. The patients of the group receiving chemical peels underwent serial glycolic acid peels in combination with topical azelaic acid 20% cream (b.i.d.) and adapalene 0.1% gel (q.i.d., applied at night). The control group received only topical treatment including topical azelaic acid and adapalene. The clinical improvement was assessed with the Melasma Area Severity Index (MASI) at baseline and monthly during the 20‐week treatment period. The results showed a prominent decrease in MASI scores at the end of the treatment in both groups, although the results were better in the group receiving chemical peels (P = 0.048). All patients tolerated the topical agents well with minimal irritation observed in the first few weeks of the therapy. Three patients in the glycolic acid peel group developed a mild‐degree postinflammatory hyperpigmentation with total clearance at the end of the treatment period. Therefore, the present study suggests that combined treatment with serial glycolic acid peels, azelaic acid cream and adapalene gel should be considered as an effective and safe therapy in recalcitrant melasma.
Case of keratosis lichenoides chronica with atypical sarcoidal granulomatous inflammation
Authors: MANSUR Ayşe Tülin , AYDINGÖZ İkbal Esen , KOCAAYAN Nurhan , GÜNDÜZ Sevil , ÖZŞEKER Nihal , HAZAR Armağan , YILDIZ Kürşat
Published: December 2006

Keratosis lichenoides chronica (KLC) is a rare chronic disease characterized by violaceous, papular and nodular lesions typically arranged in a linear and reticulate pattern. The etiology of KLC is unknown, but it may be associated with internal diseases such as hypothyroidism, glomerulonephritis and lymphoproliferative disorders. Herein, we describe the case of 44‐year‐old male patient with characteristic lesions of KLC on the trunk and extremities, present for 12 years. The clinical diagnosis was proven by histopathological examination on several occasions. In the years following the diagnosis of KLC, he developed bilateral hilar and multiple mediastinal, cervical and inguinal lymphadenopathies and hepatosplenomegaly. In 2000, diffuse interstitial and then reticulonodular pulmonary infiltrates associated with fever, weight loss, malaise and subcutaneous nodules developed. Biopsies taken from peripheral and mediastinal lymph nodes, pulmonary parenchyma, pleural tissue, bone marrow and skin showed non‐necrotizing granulomas, indicating a sarcoidal granulomatous reaction. Characteristic histopathological findings and the absence of atypical cells, clonality and a high proliferative index excluded lymphomas. Furthermore, detailed tests showed no evidence of an infectious granulomatous disease. As far as we know, this is the first reported case of KLC associated with a sarcoidal granulomatous reaction.
Neurofibromatosis type 2 in an infant with multiple plexiform schwannomas as first symptom
Authors: MIYAKAWA Takehiko , KAMADA Noriaki , KOBAYASHI Takashi , HIRANO Keiko , FUJII Katsunori , SASAHARA Yoshitaro , NAGAI Yuichiro , SHINKAI Hiroshi
Published: December 2006

Neurofibromatosis type 2 (NF2) is an autosomal dominant disorder that is caused by inactivating mutations or a loss of both alleles in the NF2 tumor‐suppressor gene. Bilateral vestibular schwannomas are considered to be the hallmark of this disease, with hearing loss and tinnitus which are caused by these tumors, usually presenting as the initial symptoms. In addition to other tumors and ocular findings, skin abnormalities also occur in NF2, however, they are not so characteristic as neurofibromatosis type 1 (NF1). We herein report a case of NF2 which occurred in a 5‐year‐old boy. He had multiple cutaneous tumors but did not have any symptoms related to vestibular schwannomas. He also had multiple depigmented spots. A histopathological examination revealed these tumors to be plexiform schwannomas; we therefore suspected NF2. As a result of magnetic resonance imaging with gadolinium enhancement, bilateral vestibular schwannomas were detected and a final diagnosis of NF2 was thus made. The association between NF2 and multiple depigmented spots is unknown, we therefore consider that multiple cutaneous plexiform schwannomas may strongly suggest an association with NF2.
Zosteriform skin involvement of nodal T‐cell lymphoma: A review of the published work of cutaneous malignancies mimicking herpes zoster
Authors: NIIYAMA Shiro , SATOH Kanji , KANEKO Satoshi , AIBA Shinsaku , TAKAHASHI Mari , MUKAI Hideki
Published: December 2006

A 77‐year‐old Japanese woman initially presented with non‐Hodgkin's lymphoma involving her neck, axillary and inguen lymph nodes. She had edematous erythema and nodules limited to the skin in zosteriform distribution on the left side chest wall along the T4–5 dermatome. In addition, since 1970, we have mainly been collecting English‐language articles on malignant skin tumors and skin metastasis described as zosteriform in the title, and we have reviewed a total of 29 cases, including our own. It should be mentioned that 59% of the cases reported had been diagnosed with herpes zoster at the time of the initial examination and that many of them had received drug therapy (e.g. acyclovir). We wish to add the dermatomic eruption mimicking zoster sine herpete to the list of possible presentations of cutaneous malignancies.
Drug eruption caused by ranitidine hydrochloride (Zantac) which showed a strong reaction in a drug‐induced lymphocyte stimulation test
Authors: OKAMOTO Osamu , FUJIWARA Sakuhei
Published: December 2006

An 80‐year‐old male who developed a generalized papular erythema‐type drug eruption after being treated with ranitidine hydrochloride is herein reported. The duration from the intake of the medicine to the onset of the eruption was 3 days, and the eruption remained unchanged for a week after withdrawal of the medicine and even after the eruption itself was treated. A diagnosis of drug eruption by ranitidine hydrochloride was confirmed based on a strongly‐positive reaction of a drug‐induced lymphocyte stimulation test (DLST).