bluuebunny/crossref_metadata_2025 huggingface dataset:
Methicillin-Resistant Staphylococcus Aureus and Antimicrobial Use in Belgian Hospitals
Authors: Crowcroft Natasha S. , Ronveaux Olivier , Monnet Dominique L. , Mertens Raf
Published: February 2006

Objective:

To investigate relationships between the incidence of methicillin-resistant Staphylococcus aureus (MRSA) and the use of different classes of antimicrobials in Belgian hospitals.

Design:

Using Pearson correlation coefficients, the number of new nosocomial MRSA-colonized or -infected patients in the second half of 1994 and the first half of 1995 reported by the national MRSA surveillance program was compared with use of various antimicrobial classes as reported by the National Institute for Sickness and Disability Insurance. Relationships between different classes of antimicrobials were evaluated in a correlation matrix. MRSA incidence, antimicrobial use, and potential confounding factors were included in a multiple linear regression analysis.

Setting:

50 hospitals in Belgium.

Results:

The use of a number of different classes of antimicrobials was interrelated. In the multivariate analysis, the incidence of nosocomial MRSA increased with increasing use of ceftazidime and cefsulodin (P=.0003), amoxicillin with clavulanic acid (P=.02), and quinolones (P=.005). No association was found between MRSA incidence and total antimicrobial use.

Conclusions:

The relationships between antimicrobial use and MRSA are complex. Interventions aimed at promoting more rational prescribing patterns should be supported by adequate experimental and epidemiological evidence. Advice for preventing and controlling MRSA has focused mainly on hygienic measures and precautions to avoid cross-transmission; the role of relieving antimicrobial pressure needs to be clarified.
Risk Factors for Colonization or Infection Due to Methicillin-Resistant Staphylococcus Aureus in HIV-Positive Patients A Retrospective Case-Control Study
Authors: Onorato Michelle , Borucki Michael J. , Baillargeon Gwen , Paar David P. , Freeman Daniel H. , Cole C. Pat , Mayhall C. Glen
Published: February 2006

Objective:

To determine the risk factors for colonization or infection with methicillin-resistantStaphylococcus aureusin human immunodeficiency virus (HIV)-infected patients.

Design:

Retrospective matched-pair case-control study.

Setting:

Continuity clinic and inpatient HIV service of a university medical center.

Population:

Patients with HIV infection from the general population of eastern and coastal Texas and from the Texas Department of Criminal Justice.

Data Collection:

Patient charts and the AIDS Care and Clinical Research Program Database were reviewed for the following: age, race, number of admissions, total hospital days, presence of a central venous catheter, serum albumin, total white blood cell count and absolute neutrophil count, invasive or surgical procedures, any cultures positive forS aureus, and a history of opportunistic illnesses, diabetes, or dermatologie diagnoses. Data also were collected on the administration of antibiotics, antiretroviral therapy, steroids, cancer chemotherapy, and subcutaneous medications.

Results:

In the univariate analysis, the presence of a central venous catheter, an underlying dermatologie disease, lower serum albumin, prior steroid therapy, and prior antibiotic therapy, particularly antistaphylococcal therapy or multiple courses of antibiotics, were associated with increased risk for colonization or infection with methicillin-resistantS aureus. Multivariate analysis yielded a model that included presence of a central venous catheter, underlying dermatologie disease, broad-spectrum antibiotic exposure, and number of hospital days as independent risk factors for colonization or infection with methicillin-resistantS aureus.

Conclusions:

In our HIV-infected patient population, prior hospitalization, exposure to broad-spectrum antibiotics, presence of a central venous catheter, and dermatologie disease were risk factors for acquisition of methicillin-resistantS aureus
A Nosocomial Outbreak of Malaria Associated With Contaminated Catheters and Contrast Medium of a Computed Tomographic Scanner
Authors: Chen Kow-Tong , Chen Chein-Jen , Chang Po-Ya , Morse Dale L.
Published: February 2006

Objective:

To identify the risk factors associated with an unexpected outbreak of malaria that occurred among seven patients in a general teaching hospital in Taipei in October 1995.

Design:

A three-stage case-control study was conducted to identify risk factors.

Patients:

We identified all 7 patients who were diagnosed as malaria cases and 69 controls from those undergoing computed tomography (CT) examination.

Methods:

Malaria was diagnosed by demonstrating the presence ofPlasmodium falciparumon either thick or thin blood smears. Clinical characteristics and exposure information were collected from medical records and patient interviews.

Results:

The index case was infected by malaria when he visited Nigeria in early September and was diagnosed when he was hospitalized in hospital A in October. Among 10 patients examined with the Imatron scanner after the index case, all 6 who were injected with contrast medium were infected, but none of 4 examined without contrast medium were infected (P=.005).

Conclusions:

This nosocomial outbreak of malaria was most likely due to transmission via a contaminated catheter and contrast medium used for CT scanning. Use of disposable catheters may avoid such nosocomial outbreaks in the future.
Rubella Immunity in a Cohort of Pregnant Women
Authors: McElhaney Robert D. , Ringer Marilyn , DeHart Del J. , Vasilenko Peter
Published: February 2006

To assess the rubella immune status of a cohort of high-risk pregnant women visiting a Midwestern clinic, we retrospectively studied 50 random pregnancies per year from 1990 through 1996. Of 350 patients analyzed, 53 (15.1%) were not immune to rubella, and vaccination opportunities were missed.
Incidence of Pertussis Infection in Healthcare Workers
Authors: Wright Seth W. , Decker Michael D. , Edwards Kathryn M.
Published: February 2006

Objective:

To determine the incidence of pertussis infection in two groups of healthcare workers.

Design:

Retrospective cohort study.

Setting:

660-bed, urban, tertiary-care university hospital.

Participants:

106 resident physicians and 39 emergency department employees.

Interventions:

Antibodies to pertussis toxin and filamentous hemagglutinin were determined in fresh serum specimens and in stored sera collected 1 to 3 years previously. A 50% rise in both the pertussis toxin and filamentous hemagglutinin from the initial to the follow-up specimen was considered diagnostic of a pertussis infection.

Results:

Two of 106 residents had serological evidence of a pertussis infection during 151.3 subject-observation years, for an annual incidence rate of 1.3% (95% confidence interval [CI95], 0%-3.5%). Three of 39 emergency department employees had serological evidence of a pertussis infection during 81.2 subject-observation years, for an annual incidence of 3.6% (CI95,, 0%-9.6%). Of these 5 subjects, 2 had symptomatic disease.

Conclusion:

We found both symptomatic and asymptomatic pertussis infections in two cohorts of healthcare workers. Although the incidence rates were somewhat lower than found in other studies, they nonetheless were higher than for almost all other diseases for which we vaccinate healthcare workers. Our results would support the use of acellular pertussis vaccine in healthcare workers.
The Continuing Evolution of Methicillin-Resistant Staphylococcus aureus in Western Australia
Authors: Torvaldsen Siranda , Roberts Christine , Riley Thomas V.
Published: February 2006

Methicillin-resistantStaphylococcus aureus(MRSA) has been notifiable in Western Australia since 1985. This article reviews the notification data from 1994 to 1997, focusing on increases in MRSA notifications and the proportion that are local strains; changes in the geographical distribution of MRSA; and changes in antibiotic-resistance patterns.
Transmission of Measles Virus in Healthcare Settings During a Communitywide Outbreak
Authors: Steingart Karen R. , Thomas Ann R. , Dykewicz Clare A. , Redd Stephen C.
Published: February 2006

Objective:

To describe the epidemiology of measles in medical settings and to evaluate the implementation and effectiveness of the 1989 Advisory Committee on Immunization Practices (ACIP) guidelines for measles immunization in healthcare workers (HCWs).

Design:

Confirmed cases of measles reported in Clark County, Washington, from March 14 to June 2,1996, were analyzed for characteristics of cases occurring in medical settings. A questionnaire was used to assess employee immunization (95% response rate).

Setting and Participants:

Reported measles cases and HCWs at community hospitals, primary-care medical facilities, a health-maintenance organization, and a multispecialty group practice.

Results:

Of 31 cases of measles, 8 (26%) occurred in HCWs, and 5 (16%) occurred in patients or visitors to medical facilities. Cases of measles occurred in HCWs who were not required to have proof of measles immunity as defined by the 1989 ACIP guidelines. The relative risk of measles in HCWs compared to Clark County adults was 18.6 (95% confidence interval, 7.4-45.8;P<.001).

A survey of medical facilities revealed that 47% had an employee measles immunization policy; only 21% met ACIP recommendations and enforced their policies.

Conclusions:

HCWs were at higher risk of measles than the adult population. Transmission of measles in medical settings was related to both deficiencies in, and lack of implementation of, the ACIP guidelines.
Infusion Therapy Team and Dressing Changes of Central Venous Catheters
Authors: Abi-Said Dima , Raad Issam , Umphrey Jan , Gonzalez Virginia , Richardson Deborah , Marts Kathy , Hohn David
Published: February 2006

Objective:

To determine whether central venous catheter (CVC) dressing changes could be performed by ward nurses rather than by the infusion therapy team (ITT) nurses without increasing the risk of catheter-related infection.

Design:

Retrospective cohort study using prospectively collected data. The study extended from January 1995 to June 1996.

Setting:

The University of Texas M.D. Anderson Cancer Center, a referral cancer center.

Patients:

The study group was a random sample of 483 patients who received CVC dressing changes by ward nurses during the study period. A random sample of 483 patients who received CVC dressing changes by the ITT constituted the control group.

Results:

The risks of catheter-related septicemia were 1.7% among cases and 1.4% among controls (risk ratio, 1.14; 95% confidence interval [CI95], 0.26-6.42;P=.70). There also were no significant differences between the two groups in the risks of catheter-related site infection (risk ratio, 0.50; CI95, 0.02-4.12;P=.25) or any catheter-related infection (risk ratio=1.00; CI95, 0.27-3.64;P=.59).

Conclusions:

Provided that aseptic techniques (including maximal barrier precautions during insertion) are maintained, the responsibility of CVC dressing changes could be delegated to the ward nurses without increasing the low risk of CVC-related infection, resulting in an estimated cost saving in excess of $90,000 per year.
Control of Vancomycin-Resistant Enterococci at a Community Hospital: Efficacy of Patient and Staff Cohorting
Authors: Jochimsen Elise M. , Fish Laurie , Manning Kelly , Young Sally , Singer Daniel A. , Baker Robert , Jarvis William R.
Published: February 2006

Objective:

To evaluate the efficacy of patient and staff cohorting to control vancomycin-resistant enterococci (VRE) at an Indianapolis community hospital.

Design:

To interrupt transmission of VRE, a VRE point-prevalence survey of hospital inpatients was conducted, and VRE-infected or -colonized patients were cohorted on a single ward with dedicated nursing staff and patient-care equipment. To assess the impact of the intervention, staff compliance with contact isolation procedures was observed, and the VRE point-prevalence survey was repeated 2 months after the cohort ward was established.

Results:

Following the establishment of the cohort ward, VRE prevalence among all hospitalized inpatients decreased from 8.1% to 4.7% (25 positive cultures among 310 patients compared to 13 positive cultures among 276 patients,P=.14); VRE prevalence among patients whose VRE status was unknown before cultures were obtained decreased from 5.9% to 0.8% (18 positive cultures among 303 patients compared to 2 positive cultures among 262 patients,P=.002); and observed staff-patient interactions compliant with published isolation recommendations increased (5 [22%] of 23 interactions compared to 36 [88%] of 41 interactions,P<.0001).

Conclusions:

Our data suggest that, in hospitals with endemic VRE or continued VRE transmission despite implementation of contact isolation measures, establishing a VRE cohort ward may be a practical and effective method to improve compliance with infection control measures and thereby to control epidemic or endemic VRE transmission.
Investigation of Suspected Nosocomial Clusters of Staphylococcus haemolyticus Infections
Authors: Perl Trish M. , Krüger Wolfgang A. , Houston Alison , Boyken Linda D. , Pfaller Michael A. , Herwaldt Loreen A.
Published: February 2006

Objective:

To determine whether typing methods can discriminate amongStaphylococcus haemolyticusisolates.

Design:

Molecular epidemiological evaluation of Shaemolyticusisolates obtained from patients hospitalized on a hematology service and in a surgical intensive-care unit (SICU).

Setting:

A large Midwestern teaching hospital.

Interventions:

None.

Results:

Over 22 days,S haemolyticuswas isolated from five patients on the hematology service. Isolates from four patients had the same unusual antibiogram and biotype. Ribotyping, restriction endonuclease digestion of plasmid DNA (REAP), and whole chromosomal DNA analysis by pulsed-field gel electrophoresis (PFGE) confirmed that these isolates were identical and different from the fifth patient's isolate and from 6 control isolates. In a second cluster, 11S haemolyticusisolates obtained from eight patients in the SICU had similar antibiograms and biotypes. By REAP and ribotype analysis, isolates from four patients were identical. However, PFGE indicated that only two of these patients shared a common strain.

Conclusions:

Antibiograms or biotyping may discriminate among isolates ofS haemolyticusif the results of these tests are unusual. Many clinical isolates can be differentiated by REAP analysis, ribotyping, or PFGE. However, some isolates are identical by all of these methods, suggesting that they may have been transmitted nosocomially.
How Many Nosocomial Infections Are Missed If Identification Is Restricted to Patients With Either Microbiology Reports or Antibiotic Administration?
Authors: Gastmeier Petra , Bräuer Helga , Hauer Thomas , Schumacher Martin , Daschner Franz , Rüden Henning
Published: February 2006

Objective:

To investigate how many nosocomial infections would be missed if surveillance activities were restricted to patients having either microbiology reports or antibiotic administration.

Design:

Analysis of data from a large prevalence study on nosocomial infections (Nosocomial Infections in Germany— Surveillance and Prevention).

Setting:

A total of 14,966 patients were investigated in medical, surgical, obstetric-gynecologic, and intensive-care units of 72 German hospitals representatively selected according to size. Five hundred eighteen patients (3.5%) had at least one nosocomial infection. Microbiology reports were available for 56.6% of these patients on the prevalence day, and 86.3% received antibiotics.

Results:

Only 31 nosocomially infected patients (6%) would have been missed by using either microbiology reports or antibiotic treatment as an indicator. These indicators of nosocomial infections had a high diagnostic sensitivity for nosocomial pneumonia (98.8%), urinary tract infections (96.3%), and primary bloodstream infections (95.3%), but a lower sensitivity for wound infections (85.4%). Thus, 97.4% of all nosocomial infections were found with this method in intensive-care units and 96.1% in medicine units, but only 89.7% in surgical departments. In 9 (12.5%) of 72 hospitals, the overall sensitivity would have been <80% using a combination of the two indicators. For this reason, the situation in one's own hospital should be checked before using this method.

Conclusions:

After checking the situation in one's own hospital, the “either-or” approach using the two indicators “microbiology report” and “antibiotic administration” can be recommended as a time-saving measure to diagnose pneumonia, urinary tract, and primary bloodstream infections. For wound infections, additional information obtained by changing dressings or participating in ward rounds is necessary to achieve satisfactory sensitivity in the surveillance of nosocomial infections. Of course, it is necessary that the surveillance staff discard all false positives to ensure a satisfactory specificity.
Use of Personal Protective Equipment and Operating Room Behaviors in Four Surgical Subspecialties: Personal Protective Equipment and Behaviors in Surgery
Authors: Akduman Deniz , Kim Lynn E. , Parks Rodney L. , L'Ecuyer Paul B. , Mutha Sunita , Jeffe Donna B. , Evanoff Bradley A , Fraser Victoria J.
Published: February 2006

Objective:

To evaluate Universal Precautions (UP) compliance in the operating room (OR).

Design:

Prospective observational cohort. Trained observers recorded information about (1) personal protective equipment used by OR staff; (2) eyewear, glove, or gown breaks; (3) the nature of sharps transfers; (4) risk-taking behaviors of the OR staff; and (5) needlestick injuries and other blood and body-fluid exposures.

Setting:

Barnes-Jewish Hospital, a 1,000-bed, tertiary-care hospital affiliated with Washington University School of Medicine, St Louis, Missouri.

Participants:

OR personnel in four surgical specialties (gynecologic, orthopedic, cardiothoracic, and general). Procedures eligible for the study were selected randomly. Hand surgery and procedures requiring no or a very small incision (eg, arthroscopy, laparoscopy) were excluded.

Results:

A total of 597 healthcare workers' procedures were observed in 76 surgical cases (200 hours). Of the 597 healthcare workers, 32% wore regular glasses, and 24% used no eye protection. Scrub nurses and medical students were more likely than other healthcare workers to wear goggles. Only 28% of healthcare workers double gloved, with orthopedic surgery personnel being the most compliant. Sharps passages were not announced in 91% of the surgical procedures. In 65 cases (86%), sharps were adjusted manually. Three percutaneous and 14 cutaneous exposures occurred, for a total exposure rate of 22%.

Conclusion:

OR personnel had poor compliance with UP. Although there was significant variation in use of personal protective equipment between groups, the total exposure rate was high (22%), indicating the need for further training and reinforcement of UP to reduce occupational exposures.
Donor-to-Recipient Transmission of Bacteria as an Unusual Cause of Mediastinitis in a Heart Transplant Recipient
Authors: Burket Jeffrey S. , Chenoweth Carol E. , Meyer Thomas L. , Barg Neil L.
Published: February 2006

We present a 54-year-old male heart transplant recipient who developed mediastinitis caused byKlebsiella oxytocaandVeillonellaspecies. Culture of the donor's bronchus also grewK oxytocaand aVeillonellaspecies. Pulsed-field gel electrophoresis revealed that theK oxytocaisolates had identical banding patterns. This case illustrates transmission of pathogenic bacteria via a contaminated organ.
Cell Surface Transglutaminase Promotes RhoA Activation via Integrin Clustering and Suppression of the Src–p190RhoGAP Signaling Pathway
Authors: Janiak Anna , Zemskov Evgeny A. , Belkin Alexey M.
Published: February 2006

Tissue transglutaminase (tTG) is a multifunctional protein that serves as cross-linking enzyme and integrin-binding adhesion coreceptor for fibronectin on the cell surface. Previous work showed activation of small GTPase RhoA via enzymatic transamidation by cytoplasmic tTG. Here, we report an alternative nonenzymatic mechanism of RhoA activation by cell surface tTG. Direct engagement of surface tTG with specific antibody or the fibronectin fragment containing modules I6II1,2I7-9increases RhoA-GTP levels. Integrin-dependent signaling to RhoA and its downstream target Rho-associated coiled-coil containing serine/threonine protein kinase (ROCK) is amplified by surface tTG. tTG expression on the cell surface elevates RhoA-GTP levels in nonadherent and adherent cells, delays maximal RhoA activation upon cell adhesion to fibronectin and accelerates a rise in RhoA activity after binding soluble integrin ligands. These data indicate that surface tTG induces integrin clustering regardless of integrin–ligand interactions. This notion is supported by visualization of integrin clusters, increased susceptibility of integrins to chemical cross-linking, and biochemical detection of large integrin complexes in cells expressing tTG. In turn, integrin aggregation by surface tTG inhibits Src kinase activity and decreases activation of the Src substrate p190RhoGAP. Moreover, pharmacological inhibition of Src kinase reveals inactivation of Src signaling as the primary cause of elevated RhoA activity in cells expressing tTG. Together, these findings show that surface tTG amplifies integrin-mediated signaling to RhoA/ROCK via integrin clustering and down-regulation of the Src–p190RhoGAP regulatory pathway.
Involvement of Mitochondrial Complex II Defects in Neuronal Death Produced by N-Terminus Fragment of Mutated Huntingtin
Authors: Benchoua Alexandra , Trioulier Yaël , Zala Diana , Gaillard Marie-Claude , Lefort Nathalie , Dufour Noelle , Saudou Frederic , Elalouf Jean-Marc , Hirsch Etienne , Hantraye Philippe , Déglon Nicole , Brouillet Emmanuel
Published: February 2006

Alterations of mitochondrial function may play a central role in neuronal death in Huntington's disease (HD). However, the molecular mechanisms underlying such functional deficits of mitochondria are not elucidated yet. We herein showed that the expression of two important constituents of mitochondrial complex II, the 30-kDa iron-sulfur (Ip) subunit and the 70-kDa FAD (Fp) subunit, was preferentially decreased in the striatum of HD patients compared with controls. We also examined several mitochondrial proteins in striatal neurons that were infected with lentiviral vectors coding for the N-terminus part of huntingtin (Htt) with either a pathological (Htt171-82Q) or physiological (Htt171-19Q) polyglutamine tract. Compared with Htt171-19Q, expression of Htt171-82Q preferentially decreased the levels of Ip and Fp subunits and affected the dehydrogenase activity of the complex. The Htt171-82Q–induced preferential loss of complex II was not associated with a decrease in mRNA levels, suggesting the involvement of a posttranscriptional mechanism. Importantly, the overexpression of either Ip or Fp subunit restored complex II levels and blocked mitochondrial dysfunction and striatal cell death induced by Htt171-82Q in striatal neurons. The present results strongly suggest that complex II defects in HD may be instrumental in striatal cell death.
GSK-3 Is Activated by the Tyrosine Kinase Pyk2 during LPA1-mediated Neurite Retraction
Authors: Sayas C. Laura , Ariaens Aafke , Ponsioen Bas , Moolenaar Wouter H.
Published: February 2006

Glycogen synthase kinase-3 (GSK-3) is a multifunctional serine/threonine kinase that is usually inactivated by serine phosphorylation in response to extracellular cues. However, GSK-3 can also be activated by tyrosine phosphorylation, but little is known about the upstream signaling events and tyrosine kinase(s) involved. Here we describe a G protein signaling pathway leading to GSK-3 activation during lysophosphatidic acid (LPA)-induced neurite retraction. Using neuronal cells expressing the LPA1receptor, we show that LPA1mediates tyrosine phosphorylation and activation of GSK-3 with subsequent phosphorylation of the microtubule-associated protein tau via the Gi-linked PIP2hydrolysis-Ca2+mobilization pathway. LPA concomitantly activates the Ca2+-dependent tyrosine kinase Pyk2, which is detected in a complex with GSK-3β. Inactivation or knockdown of Pyk2 inhibits LPA-induced (but not basal) tyrosine phosphorylation of GSK-3 and partially inhibits LPA-induced neurite retraction, similar to what is observed following GSK-3 inhibition. Thus, Pyk2 mediates LPA1-induced activation of GSK-3 and subsequent phosphorylation of microtubule-associated proteins. Pyk2-mediated GSK-3 activation is initiated by PIP2hydrolysis and may serve to destabilize microtubules during actomyosin-driven neurite retraction.
The Gcs1 Arf-GAP Mediates Snc1,2 v-SNARE Retrieval to the Golgi in Yeast
Authors: Robinson Micah , Poon Pak Phi , Schindler Christina , Murray Lois E. , Kama Rachel , Gabriely Galina , Singer Richard A. , Spang Anne , Johnston Gerald C. , Gerst Jeffrey E.
Published: February 2006

Gcs1 is an Arf GTPase-activating protein (Arf-GAP) that mediates Golgi-ER and post-Golgi vesicle transport in yeast. Here we show that the Snc1,2 v-SNAREs, which mediate endocytosis and exocytosis, interact physically and genetically with Gcs1. Moreover, Gcs1 and the Snc v-SNAREs colocalize to subcellular structures that correspond to the trans-Golgi and endosomal compartments. Studies performed in vitro demonstrate that the Snc-Gcs1 interaction results in the efficient binding of recombinant Arf1Δ17N-Q71L to the v-SNARE and the recruitment of purified coatomer. In contrast, the presence of Snc had no effect on Gcs1 Arf-GAP activity in vitro, suggesting that v-SNARE binding does not attenuate Arf1 function. Disruption of both the SNC and GCS1 genes results in synthetic lethality, whereas overexpression of either SNC gene inhibits the growth of a distinct subset of COPI mutants. We show that GFP-Snc1 recycling to the trans-Golgi is impaired in gcs1Δ cells and these COPI mutants. Together, these results suggest that Gcs1 facilitates the incorporation of the Snc v-SNAREs into COPI recycling vesicles and subsequent endosome-Golgi sorting in yeast.
Loss of P4 ATPases Drs2p and Dnf3p Disrupts Aminophospholipid Transport and Asymmetry in Yeast Post-Golgi Secretory Vesicles
Authors: Alder-Baerens Nele , Lisman Quirine , Luong Lambert , Pomorski Thomas , Holthuis Joost C.M.
Published: February 2006

Eukaryotic plasma membranes generally display asymmetric lipid distributions with the aminophospholipids concentrated in the cytosolic leaflet. This arrangement is maintained by aminophospholipid translocases (APLTs) that use ATP hydrolysis to flip phosphatidylserine (PS) and phosphatidylethanolamine (PE) from the external to the cytosolic leaflet. The identity of APLTs has not been established, but prime candidates are members of the P4 subfamily of P-type ATPases. Removal of P4 ATPases Dnf1p and Dnf2p from budding yeast abolishes inward translocation of 6-[(7-nitrobenz-2-oxa-1,3-diazol-4-yl)aminocaproyl] (NBD)-labeled PS, PE, and phosphatidylcholine (PC) across the plasma membrane and causes cell surface exposure of endogenous PE. Here, we show that yeast post-Golgi secretory vesicles (SVs) contain a translocase activity that flips NBD-PS, NBD-PE, and NBD-PC to the cytosolic leaflet. This activity is independent of Dnf1p and Dnf2p but requires two other P4 ATPases, Drs2p and Dnf3p, that reside primarily in the trans-Golgi network. Moreover, SVs have an asymmetric PE arrangement that is lost upon removal of Drs2p and Dnf3p. Our results indicate that aminophospholipid asymmetry is created when membrane flows through the Golgi and that P4-ATPases are essential for this process.
Versican Mediates Mesenchymal-Epithelial Transition
Authors: Sheng Wang , Wang Guizhi , La Pierre David P. , Wen Jianping , Deng Zhaoqun , Wong Chung-Kwun Amy , Lee Daniel Y. , Yang Burton B.
Published: February 2006

Versican is a large extracellular chondroitin sulfate proteoglycan that belongs to the family of lecticans. Alternative splicing of versican generates at least four isoforms named V0, V1, V2, and V3. We show here that ectopic expression of versican V1 isoform induced mesenchymal-epithelial transition (MET) in NIH3T3 fibroblasts, and inhibition of endogenous versican expression abolished the MET in metanephric mesenchyme. MET in NIH3T3 cells was demonstrated by morphological changes and dramatic alterations in both membrane and cytoskeleton architecture. Molecular analysis showed that V1 promoted a “switch” in cadherin expression from N- to E-cadherin, resulting in epithelial specific adhesion junctions. V1 expression reduced vimentin levels and induced expression of occludin, an epithelial-specific marker, resulting in polarization of V1-transfected cells. Furthermore, an MSP (methylation-specific PCR) assay showed that N-cadherin expression was suppressed through methylation of its DNA promoter. Exogenous expression of N-cadherin in V1-transfected cells reversed V1's effect on cell aggregation. Reduction of E-cadherin expression by Snail transfection and siRNA targeting E-cadherin abolished V1-induced morphological alteration. Transfection of an siRNA construct targeting versican also reversed the changed morphology induced by V1 expression. Silencing of endogenous versican prevented MET of metanephric mesenchyme. Taken together, our results demonstrate the involvement of versican in MET: expression of versican is sufficient to induce MET in NIH3T3 fibroblasts and reduction of versican expression decreased MET in metanephric mesenchyme.
EDEM Is Involved in Retrotranslocation of Ricin from the Endoplasmic Reticulum to the Cytosol
Authors: Slominska-Wojewodzka Monika , Gregers Tone F. , Wälchli Sébastien , Sandvig Kirsten
Published: February 2006

The plant toxin ricin is transported retrogradely from the cell surface to the endoplasmic reticulum (ER) from where the enzymatically active part is retrotranslocated to the cytosol, presumably by the same mechanism as used by misfolded proteins. The ER degradation enhancing α-mannosidase I-like protein, EDEM, is responsible for directing aberrant proteins for ER-associated protein degradation. In this study, we have investigated whether EDEM is involved in ricin retrotranslocation. Overexpression of EDEM strongly protects against ricin. However, when the interaction between EDEM and misfolded proteins is inhibited by kifunensin, EDEM promotes retrotranslocation of ricin from the ER to the cytosol. Furthermore, puromycin, which inhibits synthesis and thereby transport of proteins into the ER, counteracted the protection seen in EDEM-transfected cells. Coimmunoprecipitation studies revealed that ricin can interact with EDEM and with Sec61α, and both kifunensin and puromycin increase these interactions. Importantly, vector-based RNA interference against EDEM, which leads to reduction of the cellular level of EDEM, decreased retrotranslocation of ricin A-chain to the cytosol. In conclusion, our results indicate that EDEM is involved in retrotranslocation of ricin from the ER to the cytosol.
Domains within the GARP Subunit Vps54 Confer Separate Functions in Complex Assembly and Early Endosome Recognition
Authors: Quenneville Nicole R. , Chao Tzu-Yuan , McCaffery J. Michael , Conibear Elizabeth
Published: February 2006

Tethering complexes contribute to the specificity of membrane fusion by recognizing organelle features on both donor and acceptor membranes. The Golgi-associated retrograde protein (GARP) complex is required for retrograde traffic from both early and late endosomes to the trans-Golgi network (TGN), presenting a paradox as to how a single complex can interact specifically with vesicles from multiple upstream compartments. We have found that a subunit of the GARP complex, Vps54, can be separated into N- and C-terminal regions that have different functions. Whereas the N-terminus of Vps54 is important for GARP complex assembly and stability, a conserved C-terminal domain mediates localization to an early endocytic compartment. Mutation of this C-terminal domain has no effect on retrograde transport from late endosomes. However, a specific defect in retrieval of Snc1 from early endosomes is observed when recycling from late endosomes to the Golgi is blocked. These data suggest that separate domains recruit tethering complexes to different upstream compartments to regulate individual trafficking pathways.
Differential Requirements for Actin Polymerization, Calmodulin, and Ca2+Define Distinct Stages of Lysosome/Phagosome Targeting
Authors: Stockinger Walter , Zhang Shao C. , Trivedi Vishal , Jarzylo Larissa A. , Shieh Eugenie C. , Lane William S. , Castoreno Adam B. , Nohturfft Axel
Published: February 2006

Fusion of phagosomes with late endocytic organelles is essential for cellular digestion of microbial pathogens, senescent cells, apoptotic bodies, and retinal outer segment fragments. To further elucidate the biochemistry of the targeting process, we developed a scintillation proximity assay to study the stepwise association of lysosomes and phagosomes in vitro. Incubation of tritium-labeled lysosomes with phagosomes containing scintillant latex beads led to light emission in a reaction requiring cytosol, ATP, and low Ca2+concentrations. The nascent complex was sensitive to disruption by alkaline carbonate, indicating that the organelles had “docked” but not fused. Through inhibitor studies and fluorescence microscopy we show that docking is preceded by a tethering step that requires actin polymerization and calmodulin. In the docked state ongoing actin polymerization and calmodulin are no longer necessary. The tethering/docking activity was purified to near homogeneity from rat liver cytosol. Major proteins in the active fractions included actin, calmodulin and IQGAP2. IQGAPs are known to bind calmodulin and cross-link F-actin, suggesting a key coordinating role during lysosome/phagosome attachment. The current results support the conclusion that lysosome/phagosome interactions proceed through distinct stages and provide a useful new approach for further experimental dissection.
Memory efficient folding algorithms for circular RNA secondary structures
Authors: Hofacker Ivo L. , Stadler Peter F.
Published: February 2006

Background: A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from ‘internal’ and ‘external’ substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only.

Result: Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of ‘post-processing’ of the linear structures.

Availability: The circular folding algorithm is implemented in the current version of the of RNAfold program of the Vienna RNA Package, which can be downloaded from

Contact:  ivo@tbi.univie.ac.at
Efficient estimation of graphlet frequency distributions in protein–protein interaction networks
Authors: Pržulj N. , Corneil D. G. , Jurisica I.
Published: February 2006

Motivation: Algorithmic and modeling advances in the area of protein–protein interaction (PPI) network analysis could contribute to the understanding of biological processes. Local structure of networks can be measured by the frequency distribution of graphlets, small connected non-isomorphic induced subgraphs. This measure of local structure has been used to show that high-confidence PPI networks have local structure of geometric random graphs. Finding graphlets exhaustively in a large network is computationally intensive. More complete PPI networks, as well as PPI networks of higher organisms, will thus require efficient heuristic approaches.

Results: We propose two efficient and scalable heuristics for finding graphlets in high-confidence PPI networks. We show that both PPI and their model geometric random networks, have defined boundaries that are sparser than the ‘inner parts’ of the networks. In addition, these networks exhibit ‘uniformity’ of local structure inside the networks. Our first heuristic exploits these two structural properties of PPI and geometric random networks to find good estimates of graphlet frequency distributions in these networks up to 690 times faster than the exhaustive searches. Our second heuristic is a variant of a more standard sampling technique and it produces accurate approximate results up to 377 times faster than the exhaustive searches. We indicate how the combination of these approaches may result in an even better heuristic.

Availability: Supplementary information is available at Software implementing the algorithms is available at

Contact:  juris@cs.toronto.edu; natasha@igor.ics.uci.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
MAMMOT—a set of tools for the design, management and visualization of genomic tiling arrays
Authors: Ryder E. , Jackson R. , Ferguson-Smith A. , Russell S.
Published: February 2006

Summary: The MAMMOT software suite is a collection of Perl and PHP scripts for designing, annotating and visualizing genome tiling arrays to, for example, facilitate studies into the epigenetics of gene regulation. The web design allows rapid experimental data entry from multiple users, and results can easily be shared between groups and individuals.

Availability:  

Contact:  e.ryder@gen.cam.ac.uk
A Review of the Biochemistry, Metabolism and Clinical Benefits of Thiamin(e) and Its Derivatives
Authors: Lonsdale Derrick
Published: February 2006

Thiamin(e), also known as vitamin B1, is now known to play a fundamental role in energy metabolism. Its discovery followed from the original early research on the ‘anti‐beriberi factor’ found in rice polishings. After its synthesis in 1936, it led to many years of research to find its action in treating beriberi, a lethal scourge known for thousands of years, particularly in cultures dependent on rice as a staple. This paper refers to the previously described symptomatology of beriberi, emphasizing that it differs from that in pure, experimentally induced thiamine deficiency in human subjects. Emphasis is placed on some of the more unusual manifestations of thiamine deficiency and its potential role in modern nutrition. Its biochemistry and pathophysiology are discussed and some of the less common conditions associated with thiamine deficiency are reviewed. An understanding of the role of thiamine in modern nutrition is crucial in the rapidly advancing knowledge applicable to Complementary Alternative Medicine. References are given that provide insight into the use of this vitamin in clinical conditions that are not usually associated with nutritional deficiency. The role of allithiamine and its synthetic derivatives is discussed. Thiamine plays a vital role in metabolism of glucose. Thus, emphasis is placed on the fact that ingestion of excessive simple carbohydrates automatically increases the need for this vitamin. This is referred to as high calorie malnutrition.
Women′s Health Among the Chumash
Authors: Adams James D. , Garcia Cecilia
Published: February 2006

Plants were, and still are, widely used for a number of conditions affecting women in California. This article discusses traditional remedies of the Chumash for dysmenorrhea, premenstrual syndrome, feminine hygiene, heavy menstruation, urinary tract infections, parturition, lactation, infant care, menopause, sexually transmitted diseases, fertility, contraception and abortions. Many plants are presented including Artemisia douglasiana, Paeonia californica, Trichostema lanatum, Salvia apiana, Ephedra viridis, Leymus condensatus, Vitis californica, Eschscholzia californica, Rosa californica, Scirpus acutus, Anemopsis californica and Phoradendron macrophyllum. By providing the specific uses of plants for specific diseases and discussing chemistry, efficacy and safety concerns for each plant, we hope that this article gives direction to women seeking to use plants in their health care.
Shirking on the Court: Testing for the Incentive Effects of Guaranteed Pay
Authors: Berri David J. , Krautmann Anthony C.
Published: February 2006

Prior work on long‐term contracts and the incentive to shirk has focused almost exclusively on Major League Baseball. The current inquiry is the first to examine shirking in the National Basketball Association. We employed two different measures of player productivity. When the NBA's measure is used, we find evidence consistent with allegations of shirking behavior. But when productivity is measured in a fashion more consistent with economists' definition of marginal product, the evidence of shirking evaporates. (JEL J41, J44, L83)
Incidence of Crohn Disease in the Czech Republic in the Years 1990 to 2001 and Assessment of Pediatric Population with Inflammatory Bowel Disease
Authors: Pozler Oldrich , Maly Jan , Bonova Oldriska , Dedek Petr , Frühauf Pavel , Havlickova Alena , Janatova Tatiana , Jimramovsky Frantisek , Klimova Lenka , Klusacek Dalibor , Kocourkova Dana , Kolek Antonin , Kotalova Radka , Marx David , Nevoral Jiri , Petro Radim , Petru Ondrej , Plasilova Ivana , Seidl Zbynek , Sekyrova Ivana , Semendak Norbert , Schreierova Irena , Stanek Jan , Sykora Josef , Sulakova Astrid , Toukalkova Lenka , Travnickova Radka , Volf Vladimir , Zahradnicek Lubomir , Zenisková Ivana ,   Czech Collaborative Group for the Study of Chronic Illnesses of the Gastrointestinal Tract in Children
Published: February 2006

Background:

The aim of this study was to assess the pediatric population that suffered from inflammatory bowel disease (IBD) in the Czech Republic and to determine the incidence of Crohn disease (CD) in children up to 15 years age between 1990 and 2001.

Methods:

Diagnostic criteria for CD, ulcerative colitis (UC), and indeterminate colitis (IC) were defined. Medical records provided a source of basic information about the children. A standardized protocol was filled out and sent to the coordinator of the study. All protocols were checked to see whether the data corresponded to the defined criteria and then were processed further. The study was retrospective in character for the years 1990 to 1999 and prospective for the years 2000 and 2001.

Results:

Diagnostic criteria were met in 470 patients with IBD; 201 of them turned 18 years old during the study period. CD was diagnosed in 223 patients. The incidence of CD in children up to 15 years of age increased from 0.25/100,000 in 1990 to 1.25/100,000 in 2001. Eighty‐two percent of children with CD were treated with aminosalicylates in combination with corticosteroids; 29% of patients received azathioprine. Severe growth retardation was recorded in 6.4% of adolescents with CD at the age of 18. UC was diagnosed in 202 patients. Therapy with aminosalicylates only was sufficient for control of the disease in 23% patients; 68% children were treated with corticosteroids, 15 of them (23% of the whole group) received additional azathioprine. Criteria for IC were met in 9.8% of all patients with IBD.

Conclusion:

This study confirmed an increase in incidence of CD in children younger than 15 years in the Czech Republic.
Clinical Safety of Lactobacillus casei shirota as a Probiotic in Critically Ill Children
Authors: Srinivasan Ramesh , Meyer Rosan , Padmanabhan Ramnarayan , Britto Joseph
Published: February 2006

Objective:

Diarrhea is frequently observed among critically ill children (CIC) admitted for intensive care. There is increasing evidence that probiotics decrease the incidence of acute infectious and nosocomial and antibiotic induced diarrhea amongst children hospitalized in nonintensive care settings. Despite theoretic advantages for the use of probiotics in CIC, safety has remained a concern in this vulnerable group. The objective of this study was to establish clinical safety (invasive infection/colonization) of Lactobacillus casei shirota (LCS) used as a probiotic in CIC.

Methods:

Prospective, descriptive pilot study on children admitted to a pediatric intensive care unit. Data regarding safety were collected on the initial recruits to a randomized controlled trial aimed to study the effects of LCS on stool frequency and consistency in CIC. Safety was assessed by bacteriologic surveillance for LCS in surface swabs and endotracheal aspirates (colonization) as well as blood, urine, and sterile body fluid cultures (invasive infection/bacteremia).

Results:

Safety data were available on 28 patients. LCS was cultured from the feces of five of the six study subjects who opened bowels during their stay on the pediatric intensive care unit. There was no evidence of either colonization or bacteremia with LCS in bacteriologic cultures obtained from study subjects. The preparation was well tolerated with no apparent side effects.

Conclusions:

Our pilot safety study suggests that the use of LCS as a probiotic in enterally fed CIC is safe.
Serologic and Genetic Markers of Celiac Disease: A Sequential Study in the Screening of First Degree Relatives
Authors: Bonamico Margherita , Ferri Mirella , Mariani Paolo , Nenna Raffaella , Thanasi Enina , Luparia Rita P. L , Picarelli Antonio , Magliocca Fabio M , Mora Barbara , Bardella Maria Teresa , Verrienti Antonella , Fiore Benedetta , Uccini Stefania , Megiorni Francesca , Mazzilli Maria Cristina , Tiberti Claudio
Published: February 2006

Objectives:

The prevalence of celiac disease (CD) among the relatives and the complications of an undiagnosed CD prompted us to identify a useful disease screening strategy.

Methods:

We studied 441 first degree relatives of 208 CD patients by immunoglobulin (Ig)A antiendomysium antibodies (EMA) and radioimmunoprecipitation assay (RIA) IgA antitransglutaminase autoantibodies (TGAA). Of these, 364 were typed for human leukocyte antigen‐DRB1, ‐DQA1, and ‐DQB1 genes by the polymerase chain reaction sequence specific primers method. It was suggested to the autoantibody‐positive subjects that they should undergo intestinal biopsy.

Results:

TGAA were positive in 46 of 439 relatives, EMA in 38; intestinal lesions related to CD were present in 40 subjects. We also found two immunodeficient fathers with duodenal villous atrophy. In three serology‐positive subjects, permission for intestinal biopsy was refused; for another three serology‐positive cases, duodenal mucosa was normal. Thus, the strict CD prevalence resulted 9.5%, the enlarged prevalence 10.9%. The DQ2/DQ8 heterodimers were carried in 231 of 364 subjects and in 38 of 40 biopsy‐proven celiac patients. Three DQ2‐positive parents became positive to the serology during a long‐lasting follow‐up.

Conclusions:

On the basis of a carefully conducted study, CD prevalence in our series was seen as very high. These data suggest an accurate algorithm to select candidates for intestinal biopsy among CD high‐risk subjects. First, an evaluation of the sensitive RIA TGAA and of total IgA (in IgA deficiency RIA IgG anti‐tissue transglutaminase assay) should be performed. Then, an evaluation of the TGAA and the genetic study would be advisable 2 to 3 years later in negative subjects. Those carrying the DQ2/DQ8 heterodimers should continue the serologic follow‐up; the others need a clinical follow‐up.