bluuebunny/crossref_metadata_2025 huggingface dataset:
Stabilizing the Earth’s climate is not a losing game: Supporting evidence from public goods experiments
Authors: Milinski Manfred , Semmann Dirk , Krambeck Hans-Jürgen , Marotzke Jochem
Published: March 2006

Maintaining the Earth’s climate within habitable boundaries is probably the greatest “public goods game” played by humans. However, with >6 billion “players” taking part, the game seems to rule out individual altruistic behavior. Thus, climate protection is a problem of sustaining a public resource that everybody is free to overuse, a “tragedy of the commons” problem that emerges in many social dilemmas. We perform a previously undescribed type of public goods experiment with human subjects contributing to a public pool. In contrast to the standard protocol, here the common pool is not divided among the participants; instead, it is promised that the pool will be invested to encourage people to reduce their fossil fuel use. Our extensive experiments demonstrate that players can behave altruistically to maintain the Earth’s climate given the right set of circumstances. We find a nonzero basic level of altruistic behavior, which is enhanced if the players are provided with expert information describing the state of knowledge in climate research. Furthermore, personal investments in climate protection increase substantially if players can invest publicly, thus gaining social reputation. This increase occurs because subjects reward other subjects’ contributions to sustaining the climate, thus reinforcing their altruism. Therefore, altruism may convert to net personal benefit and to relaxing the dilemma if the gain in reputation is large enough. Our finding that people reward contributions to sustaining the climate of others is a surprising result. There are obvious ways these unexpected findings can be applied on a large scale.
Gold nanoparticles-based protease assay
Authors: Guarise Cristian , Pasquato Lucia , De Filippis Vincenzo , Scrimin Paolo
Published: March 2006

We describe here a simple assay that allows the visual detection of a protease. The method takes advantage of the high molar absorptivity of the plasmon band of gold colloids and is based on the color change of their solution when treated with dithiols. We used C- and N-terminal cysteinyl derivatives of a peptide substrate exploiting its selective recognition and cleavage by a specific protease. Contrary to the native ones, cleaved peptides are unable to induce nanoparticles aggregation; hence, the color of the solution does not change. The detection of two proteases is reported: thrombin (involved in blood coagulation and thrombosis) and lethal factor (an enzyme component of the toxin produced by
Bacillus anthracis
). The sensitivity of this nanoparticle-based assay is in the low nanomolar range.
Evaluation of a Safety Resheathable Winged Steel Needle for Prevention of Percutaneous Injuries Associated With Intravascular-Access Procedures Among Healthcare Workers
Authors: Mendelson Meryl H. , Lin-Chen Bao Ying , Solomon Robin , Bailey Eileen , Kogan Gene , Goldbold James
Published: March 2006

Objective:

To compare the percutaneous injury rate associated with a standard versus a safety resheathable winged steel (butterfly) needle.

Design:

Before-after trial of winged steel needle injuries during a 33-month period (19-month baseline, 3-month training, and 11-month study intervention), followed by a 31-month poststudy period.

Setting:

A 1,190-bed acute care referral hospital with inpatient and outpatient services in New York City.

Participants:

All healthcare workers performing intravascular-access procedures with winged steel needles.

Intervention:

Safety resheathable winged steel needle.

Results:

The injury rate associated with winged steel needles declined from 13.41 to 6.41 per 100,000 (relative risk [RR], 0.48; 95% confidence interval [CI95], 0.31 to 0.73) following implementation of the safety device. Injuries occurring during or after disposal were reduced most substantially (RR 0.15; CI95, 0.06 to 0.43 Safety winged steel needle injuries occurred most often before activation of the safety mechanism was appropriate (39%); 32% were due to the user choosing not to activate the device, 21% occurred during activation, and 4% were due to improper activation. Preference for the safety winged steel needle over the standard device was 63%. The safety feature was activated in 83% of the samples examined during audits of disposal containers. Following completion of the study, the safety winged steel needle injury rate (7.29 per 100,000) did not differ significantly from the winged steel needle injury rate during the study period.

Conclusion:

Implementation of a safety resheathable winged steel needle substantially reduced injuries among healthcare workers performing vascular-access procedures. The residual risk of injury associated with this device can be reduced further with increased compliance with proper activation procedures.
Recycling of Injection Equipment in Pakistan
Authors: Mujeeb Syed Abdul , Adil Malik Mohummad , Altaf Arshad , Hutin Yvan , Luby Stephen
Published: March 2006

The prevalence of hepatitis C virus (HCV) infection is high in the general population in Pakistan, ranging from 2% to 6%. Reuse of injection equipment in the absence of sterilization is common, particularly in healthcare facilities that serve low-income populations. Studies have identified unsafe injection practices as a major route of transmission of HCV in Pakistan. Changing the behavior of injection providers so that they would use new freshly opened disposable syringes would improve injection safety in Pakistan. However, frequent reports of recycling of injection equipment in the local media question the safety of apparently new syringes. Clinical laboratories are one of the major sources of production of used syringes. To evaluate the resale of used syringes, we followed the course of used syringes from their initial use to their final destination.
Nosocomial Transmission of Hepatitis C Virus Associated With the Use of Multidose Saline Vials
Authors: Krause Gérard , Trepka Mary Jo , Whisenhunt Robert S. , Katz Dolly , Nainan Omana , Wiersma Steven T. , Hopkins Richard S.
Published: March 2006

Objective:

To identify the source of an outbreak of acute hepatitis C virus (HCV) infection among 3 patients occurring within 8 weeks of hospitalization in the same ward of a Florida hospital during November 1998.

Design:

A retrospective cohort study was conducted among 41 patients hospitalized between November 11 and 19, 1998. Patients' blood was tested for antibodies to HCV, and HCV RNA-positive samples were genotyped and sequenced.

Results:

Of the 41 patients, 24 (59%) participated in the study. HCV genotype 1b infections were found in 5 patients. Three of 4 patients who received saline flushes from a multidose saline vial on November 16 had acute HCV infection, whereas none of the 9 patients who did not receive saline flushes had HCV infection (P= .01). No other significant exposures were identified. The HCV sequence was available for 1 case of acute HCV and differed by a single nucleotide (0.3%) from that of the indeterminate case.

Conclusion:

This outbreak of HCV probably occurred when a multidose saline vial was contaminated with blood from an HCV-infected patient. Hospitals should emphasize adherence to standard procedures to prevent blood-borne infections. In addition, the use of single-dose vials or prefilled saline syringes might further reduce the risk for nosocomial transmission of blood-borne pathogens.
Occupationally Acquired Human Immunodeficiency Virus (HIV) Infection: National Case Surveillance Data During 20 Years of the HIV Epidemic in the United States
Authors: Do Ann N. , Ciesielski Carol A. , Metler Russ P. , Hammett Teresa A. , Li Jianmin , Fleming Patricia L.
Published: March 2006

Objective:

To characterize occupationally acquired human immunodeficiency virus (HIV) infection detected through case surveillance efforts in the United States.

Design:

National surveillance systems, based on voluntary case reporting.

Setting:

Healthcare or laboratory (clinical or research) settings.

Patients:

Healthcare workers, defined as individuals employed in healthcare or laboratory settings (including students and trainees), who are infected with HIV.

Methods:

Review of data reported through December 2001 in the HIV/AIDS Reporting System and the National Surveillance for Occupationally Acquired HIV Infection.

Results:

Of 57 healthcare workers with documented occupationally acquired HIV infection, most (86%) were exposed to blood, and most (88%) had percutaneous injuries. The circumstances varied among 51 percutaneous injuries, with the largest proportion (41%) occurring after a procedure, 35% occurring during a procedure, and 20% occurring during disposal of sharp objects. Unexpected circumstances difficult to anticipate during or after procedures accounted for 20% of all injuries. Of 55 known source patients, most (69%) had acquired immunodeficiency syndrome (AIDS) at the time of occupational exposure, but some (11%) had asymptomatic HIV infection. Eight (14%) of the healthcare workers were infected despite receiving postexposure prophylaxis (PEP).

Conclusions:

Prevention strategies for occupationally acquired HIV infection should continue to emphasize avoiding blood exposures. Healthcare workers should be educated about both the benefits and the limitations of PEP, which does not always prevent HIV infection following an exposure. Technologic advances (eg, safety-engineered devices) may further enhance safety in the healthcare workplace
Monsel's Solution: A Potential Vector for Nosocomial Infection?
Authors: Rupp Mark E. , Medcalf Sharon J. , Fey Paul D. , Handke Luke D. , Marion Nedra D.
Published: March 2006

Monsel's solution is a common topically applied hemostatic agent used in minor dermatologic and gynecologic surgery. Clinically, because it is often stored for long periods and dispensed from a common source for multiple patients, Monsel's solution is a potential vector for transmission of infection. However, microbiologic inoculation studies and contamination surveys indicate that Monsel's solution has properties that prohibit microbial growth, making it an unlikely vector for nosocomial infection.
A Cluster of Primary Varicella Cases Among Healthcare Workers With False-Positive Varicella Zoster Virus Titers
Authors: Behrman Amy , Schmid D. Scott , Crivaro Anne , Watson Barbara
Published: March 2006

Background:

Five cases of primary varicella zoster virus (VZV) were diagnosed among hospital healthcare workers (HCWs). All had complied with a pre-employment VZV screening program and had been considered immune.

Objectives:

To summarize the investigation of VZV among un-immunized HCWs and to provide recommendations for avoiding false-positive serologic tests.

Design:

Risk of transmission of VZV to susceptible HCWs is minimized through serologic screening. Varicella vaccine is recommended for susceptible HCWs. A commercially available latex bead agglutination assay (LA) is widely used because it is rapid and easy to perform. LA was compared with the whole-cell varicella ELISA standardized in the Centers for Disease Control and Prevention (CDC) National Herpes Laboratory.

Setting/Population:

Large inner-city, tertiarycare hospital with a diverse employee population.

Results:

In a year, 5 HCWs presented with laboratory-confirmed primary varicella infection. Four had VZV exposures 2 weeks prior to presentation. All had documented positive VZV titers by LA performed at hire. None were offered VZV vaccination. The original LAs were judged false-positives.

Intervention/Follow-Up Investigation:

Fifty-three consecutive VZV LA samples from the hospital laboratory were retested at the CDC. Forty-four samples concurred. Of the remaining 9, 4 were positive by hospital LA but negative by CDC IgG ELISA. Four were equivocal by hospital LA but negative by CDC IgG ELISA and LA. One was positive by hospital LA but negative by LA and equivocal by ELISA at the CDC.

Conclusion:

LA may be prone to false-positive results and inappropriate for screening hospital HCWs.
Modeling the Costs of Hospital-Acquired Infections in New Zealand
Authors: Graves Nicholas , Nicholls Tanya M. , Morris Arthur J.
Published: March 2006

Objective:

To model the economic costs of hospital-acquired infections (HAIs) in New Zealand, by type of HAI.

Design:

Monte Carlo simulation model.

Setting:

Auckland District Health Board Hospitals (DHBH), the largest publicly funded hospital group in New Zealand supplying secondary and tertiary services. Costs are also estimated for predicted HAIs in admissions to all hospitals in New Zealand.

Patients:

All adults admitted to general medical and general surgical services.

Method:

Data on the number of cases of HAI were combined with data on the estimated prolongation of hospital stay due to HAI to produce an estimate of the number of bed days attributable to HAI. A cost per bed day value was applied to provide an estimate of the economic cost. Costs were estimated for predicted infections of the urinary tract, surgical wounds, the lower and upper respiratory tracts, the bloodstream, and other sites, and for cases of multiple sites of infection. Sensitivity analyses were undertaken for input variables.

Results:

The estimated costs of predicted HAIs in medical and surgical admissions to Auckland DHBH were $10.12 (US $4.56) million and $8.64 (US $3.90) million, respectively. They were $51.35 (US $23.16) million and $85.26 (US $38.47) million, respectively, for medical and surgical admissions to all hospitals in New Zealand.

Conclusions:

The method used produces results that are less precise than those of a specifically designed study using primary data collection, but has been applied at a lower cost. The estimated cost of HAIs is substantial, but only a proportion of infections can be avoided. Further work is required to identify the most cost-effective strategies for the prevention of HAI.
Adherence With Hand Hygiene: Does Number of Sinks Matter?
Authors: Vernon Michael O. , Trick William E. , Welbel Sharon F. , Peterson Brian J. , Weinstein Robert A.
Published: March 2006

We observed adherence with hand hygiene in 14 units at 4 hospitals with varying sink-to-bed ratios (range, 1:1 to 1:6). Adherence was less than 50% in all units and there was no significant trend toward improved hand hygiene with increased sink-to-bed ratios.
An Investigation of the Bactericidal Effect of Certain Antiseptics and Disinfectants on Some Hospital Isolates of Gram-Negative Bacteria
Authors: Ekizoglu Melike Tunçay , Özalp Meral , Sultan Nedim , Gür Deniz
Published: March 2006

The effect of widely used antiseptics and disinfectants on some hospital isolates of gram-negative bacteria was assessed by the quantitative suspension test. Chlorhexidine gluconate (4%), savlon (1:100), and 5.25% sodium hypochlorite were tested. Savlon and chlorhexidine gluconate were effective at in-use concentrations and sodium hypochlorite was effective at 1:50 dilution.
Motion Matters: Secretory Granule Motion Adjacent to the Plasma Membrane and Exocytosis
Authors: Allersma Miriam W. , Bittner Mary A. , Axelrod Daniel , Holz Ronald W.
Published: March 2006

Total internal reflection fluorescence microscopy was used to monitor changes in individual granule motions related to the secretory response in chromaffin cells. Because the motions of granules are very small (tens of nanometers), instrumental noise in the quantitation of granule motion was taken into account. ATP and Ca2+, both of which prime secretion before fusion, also affect granule motion. Removal of ATP in permeabilized cells causes average granule motion to decrease. Nicotinic stimulation causes a calcium-dependent increase in average granule motion. This effect is more pronounced for granules that undergo exocytosis than for those that do not. Fusion is not preceded by a reduction in mobility. Granules sometimes move 100 nm or more up to and within a tenth of a second before fusion. Thus, the jittering motion of granules adjacent to the plasma membrane is regulated by factors that regulate secretion and may play a role in secretion. Motion continues until shortly before fusion, suggesting that interaction of granule and plasma membrane proteins is transient. Disruption of actin dynamics did not significantly alter granule motion.
Coordinated Requirements of Human Topo II and Cohesin for Metaphase Centromere Alignment under Mad2-dependent Spindle Checkpoint Surveillance
Authors: Toyoda Yusuke , Yanagida Mitsuhiro
Published: March 2006

Cohesin maintains sister chromatid cohesion until its Rad21/Scc1/Mcd1 is cleaved by separase during anaphase. DNA topoisomerase II (topo II) maintains the proper topology of chromatid DNAs and is essential for chromosome segregation. Here we report direct observations of mitotic progression in individual HeLa cells after functional disruptions of hRad21, NIPBL, a loading factor for hRad21, and topo II α,β by RNAi and a topo II inhibitor, ICRF-193. Mitosis is delayed in a Mad2-dependent manner after disruption of either or both cohesin and topo II. In hRad21 depletion, interphase pericentric architecture becomes aberrant, and anaphase is virtually permanently delayed as preseparated chromosomes are misaligned on the metaphase spindle. Topo II disruption perturbs centromere organization leading to intense Bub1, but no Mad2, on kinetochores and sustains a Mad2-dependent delay in anaphase onset with persisting securin. Thus topo II impinges upon centromere/kinetochore function. Disruption of topo II by RNAi or ICRF-193 overrides the mitotic delay induced by cohesin depletion: sister centromeres are aligned and anaphase spindle movements occur. The ensuing accumulation of catenations in preseparated sister chromatids may overcome the reduced tension arising from cohesin depletion, causing the override. Cohesin and topo II have distinct, yet coordinated functions in metaphase alignment.
MERGERS, CAPITAL GAINS, AND PRODUCTIVITY: EVIDENCE FROM U.S. TELECOMMUNICATIONS MERGERS
Authors: SUNG NAKIL , Gort Michael
Published: March 2006

The article examines the effects of two horizontal mergers on the performance of the respective operating companies. The effects of the mergers are investigated by comparing the performance of the merging companies with a control group of nonmerging companies and also the performance of the merging companies before and after merger. The article concludes that mergers did not produce net economies of scale, did not lead to substantial productivity growth or cost reduction, and did not generate significant shareholder wealth effects. It is, to the authors' knowledge, the first study of mergers that combines the analysis of productivity and cost effects, on one hand, with an examination of the effects on financial variables, on the other hand. (JEL L11, L9)
SELF‐EMPLOYMENT WITH CHINESE CHARACTERISTICS: THE FORGOTTEN ENGINE OF RURAL CHINA'S GROWTH
Authors: ZHANG JIAN , ZHANG LINXIU , ROZELLE SCOTT , BOUCHER STEVE
Published: March 2006

This article sketches a picture of the self‐employment sector in rural China and examines the nature of its emergence. Using a randomly selected, nationally representative household‐level data set that contains detailed information on household self‐employment activities, this article provides evidence that although the self‐employed enterprises are small, they have grown fast, operate as relatively complex businesses, and perform well in a financially healthy way. These results, taken together with the pattern of the emergence of self‐employed enterprises across China's regions, reveal that the expansion of self‐employment is not symptomatic of a failing economy; instead it is a component of the dynamic development process that characterizes rural China during its reform period.(JELJ23, D21, O12)
New Leptospira serovar Sokoine of serogroup Icterohaemorrhagiae from cattle in Tanzania
Authors: Mgode G. F. , Machang'u R. S. , Goris M. G. , Engelbert M. , Sondij S. , Hartskeerl R. A.
Published: March 2006

The prevalence of leptospirosis is generally high in domestic animals and rodents in Tanzania. Identification of Leptospira isolates from cattle was carried out to establish prevalent Leptospira serovars. Serological typing was done based on monoclonal antibodies and the standard cross-agglutination absorption test. Molecular typing involved pathogenic- and saprophytic-specific PCRs and a PCR specifically amplifying DNA from the species Leptospira kirschneri. DNA fingerprinting with primers derived from sequences of insertion elements IS1500 and IS1533 was carried out. Both serological and molecular characterization indicated that one of the Leptospira isolates, coded RM1, represents a new serovar of the species L. kirschneri of serogroup Icterohaemorrhagiae. The serovar name Sokoine is proposed for this new Leptospira isolate.
Ureibacillus suwonensis sp. nov., isolated from cotton waste composts
Authors: Kim Byung-Yong , Lee Seon-Young , Weon Hang-Yeon , Kwon Soon-Wo , Go Seung-Joo , Park Yong-Keun , Schumann Peter , Fritze Dagmar
Published: March 2006

The taxonomic position of two spore-forming strains 6T19Tand 6T29, isolated from cotton composts for the cultivation of oyster mushroom (Pleurotus ostreatus), was investigated by a polyphasic approach. Cells of strains 6T19Tand 6T29 were rod-shaped, Gram-negative and strictly aerobic. Sequencing and comparative analyses for the 16S rRNA genes of these strains clearly showed their phylogenetic affiliation to the genusUreibacillus. Their closest relativesUreibacillus thermosphaericusandUreibacillus terrenushave sequence similarity of 96·9 and 97·5 %, respectively. The isoprenoid quinones of isolate 6T19Twere MK-9, MK-8, MK-7, MK-10 and MK-6 (45 : 27 : 18 : 5 : 4 %), the peptidoglycan type wasl-lys←d-Asp and the main cellular fatty acid was i-C16 : 0. DNA–DNA hybridization experiments resulted in relatedness values of 37 % between 6T19TandU. thermosphaericusDSM 10633Tand 41 % between 6T19TandU. terrenusDSM 12654T. Based on the polyphasic data, strains 6T19Tand 6T29 can be described as members of a novel species of the genusUreibacillus, for which the nameUreibacillus suwonenesissp. nov. is proposed. The type strain is 6T19T(=KACC 11287T=DSM 16752T).
Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen
Authors: Cirne Dores G. , Delgado Osvaldo D. , Marichamy Sankar , Mattiasson Bo
Published: March 2006

A strictly anaerobic, mesophilic, endospore-forming, lipolytic bacterium, designated strain R1T, was isolated from bovine rumen fluid and characterized. Cells of this isolate were Gram-positive, non-motile rods that formed spherical terminal spores. The overall biochemical and physiological characteristics indicated that this strain should be placed in the genus Clostridium. The strain grew at temperatures between 25 and 47 °C (optimum, 37 °C), at pH between 5·0 and 8·5 (optimum pH 5·5–7·0) and in NaCl concentrations of 0–3 % (w/v). The isolate was not able to utilize glucose or other carbohydrates as carbon sources. The DNA G+C content was 31·2 mol%. Sequence analysis of the 16S rRNA gene of R1T revealed that it has the closest match (98 % similarity) with Clostridium tetanomorphum DSM 4474T. The highest levels of DNA–DNA relatedness of the isolate were 61·9 and 54·3 % with Clostridium pascui DSM 10365T and C. tetanomorphum DSM 4474T, respectively. Based on 16S rRNA gene sequence similarity, phylogenetic analysis, DNA G+C content, DNA–DNA hybridization data and distinct phenotypic characteristics, strain R1T (=DSM 17049T=CCUG 50446T) was classified in the genus Clostridium, as a member of a novel species, for which the name Clostridium lundense sp. nov. is proposed.
Brevundimonas kwangchunensis sp. nov., isolated from an alkaline soil in Korea
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Hyun Woo , Lee Jung-Sook , Oh Tae-Kwang
Published: March 2006

Two Gram-negative, rod-shaped bacterial strains, KSL-102Tand KSL-110, were isolated from an alkaline soil in Korea, and their taxonomic positions were investigated by use of a polyphasic study. The two strains grew optimally at pH 7·0–8·0 and 30 °C without NaCl. They contained Q-10 as the predominant ubiquinone. The major fatty acids were C18 : 1ω7cand C16 : 0on trypticase soy agar, but 11-methyl C18 : 1ω7cwas also a major component when the two strains were cultivated on LMG medium no. 221. Their DNA G+C contents were 68·4–68·7 mol%. Strains KSL-102Tand KSL-110 exhibited three nucleotide differences in their 16S rRNA gene sequences and a mean DNA–DNA relatedness value of 85 %. Phylogenetic trees based on 16S rRNA gene sequences showed that the two strains fell within the evolutionary radiation encompassed by the genusBrevundimonas. Levels of 16S rRNA gene sequence similarity between the two strains and the type strains of recognizedBrevundimonasspecies ranged from 96·3 to 98·4 %. DNA–DNA relatedness levels between the two strains and recognizedBrevundimonasspecies were 8–21 %. On the basis of phenotypic, phylogenetic and genetic data, strains KSL-102Tand KSL-110 were classified in the genusBrevundimonasas members of a novel species, for which the nameBrevundimonas kwangchunensissp. nov. is proposed. The type strain is KSL-102T(=KCTC 12380T=DSM 17033T).
Kitasatospora sampliensis sp. nov., a novel actinobacterium isolated from soil of a sugar-cane field in India
Authors: Mayilraj S. , Krishnamurthi S. , Saha P. , Saini H. S.
Published: March 2006

Polyphasic characterization of an actinomycete strain VT-36Tisolated from a sugar-cane field soil sample collected in Punjab State, India, revealed that the strain belongs to the genusKitasatospora. The strain's chemotaxonomic characters and G+C content of DNA (76·5 mol%) were typical of members of the genus. Analysis of the 16S rRNA gene sequence supported the generic affiliation of the strain and showed that its closest phylogenetic relative wasKitasatospora putterlickiaeF18-98T(=DSM 44665T) (98·3 % 16S rRNA gene sequence similarity). The similarities with type strains of all otherKitasatosporaspecies were in the range 95·1–97·0 %. The results of DNA–DNA hybridization showed 54 % relatedness of the isolate andK. putterlickiaeF18-98T. Based on the above data and the phenotypic differences fromK. putterlickiaeand otherKitasatosporaspecies, it is proposed that the isolate should be classified as the type strain of a novel species,Kitasatospora sampliensissp. nov., with strain VT-36T(=MTCC 6546T=DSM 44898T=JCM 13010T) as the type strain.
Pseudonocardia ammonioxydans sp. nov., isolated from coastal sediment
Authors: Liu Zhi-Pei , Wu Jian-Feng , Liu Zhi-Heng , Liu Shuang-Jiang
Published: March 2006

Actinomycete strain H9Twas isolated from coastal sediment of the Jiao-Dong peninsula (near Tsingdao city) in China, and was identified by means of polyphasic taxonomy. The strain grew autotrophically on modified nitrifying medium and heterotrophically on Luria–Bertani medium, with NaCl ranging from 0 to 8 % (w/v) (optimal growth at 3·5 %). The 16S rRNA gene sequence similarities of strain H9Tto members of the genusPseudonocardiaranged from 93·0 to 97·5 %, indicating that strain H9Twas phylogenetically related to members of the genusPseudonocardia. Strain H9Thad type IV cell wall and type PIII phospholipid, and its major menaquinone was MK-8 (H4). DNA–DNA relatedness values between strain H9TandPseudonocardia kongjuensis,Pseudonocardia autotrophicaandPseudonocardia compactawere 42, 13 and 11 %, respectively. These results support the conclusion that H9Trepresents a novel species within the genusPseudonocardia, for which the namePseudonocardia ammonioxydanssp. nov. is proposed, with the type strain H9T(=CGMCC 4.1877T=JCM 12462T).
Microbacterium paludicola sp. nov., a novel xylanolytic bacterium isolated from swamp forest
Authors: Park Hye Yoon , Kim Kwang Kyu , Jin Long , Lee Sung-Taik
Published: March 2006

A xylanolytic bacterium, US15T, was isolated from swamp forest soil in Ulsan, Korea. The cells of the novel strain were Gram-positive, non-motile, short-rod-shaped and showed chemotaxonomic properties that were consistent with its classification in the genus Microbacterium. Chemotaxonomic results showed MK-12 and MK-11 as major menaquinones, predominating iso- and anteiso-branched cellular fatty acids, glucose, galactose and mannose as cell-wall sugars, peptidoglycan-type B2β with glycolyl residues and a DNA G+C content of 66·5 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain US15T was closely related to Microbacterium arborescens IFO 3750T, Microbacterium imperiale IFO 12610T and Microbacterium ulmi LMG 20991T (96·9, 96·8 and 96·2 % similarities, respectively), and formed a separate lineage within the genus Microbacterium. Combined genotypic and phenotypic data showed that strain US15T (=DSM 16915T=KCTC 19080T) merits recognition as the type strain of a novel species within the genus Microbacterium, for which the name Microbacterium paludicola sp. nov. is proposed.
Providencia vermicola sp. nov., isolated from infective juveniles of the entomopathogenic nematode Steinernema thermophilum
Authors: Somvanshi Vishal S. , Lang Elke , Sträubler Bettina , Spröer Cathrin , Schumann Peter , Ganguly Sudershan , Saxena Anil K. , Stackebrandt Erko
Published: March 2006

In the course of isolating bacteria from infective juveniles of the entomopathogenic nematodeSteinernema thermophilumGanguly & Singh, 2000, three isolates were obtained (OP1T, OP29 and VS3). On the basis of 16S rRNA gene sequence analysis and riboprint patterns, these three strains were identical to each other but distinct from the type strains of the five recognized species of the genusProvidencia. Based on biochemical and genomic analysis and supported by the low (<35 %) DNA–DNA relatedness between strain OP1Tand the type strain of its phylogenetically closest relative,Providencia rettgeri(99·5 % 16S rRNA gene sequence similarity), strain OP1Twas considered to be sufficiently distinct from recognizedProvidenciaspecies to warrant the description of a novel species. The nameProvidencia vermicolasp. nov. is proposed, with OP1T(=DSM 17385T=CIP 108829T) as the type strain.
Chromohalobacter nigrandesensis sp. nov., a moderately halophilic, Gram-negative bacterium isolated from Lake Tebenquiche on the Atacama Saltern, Chile
Authors: Prado Bernardo , Lizama Catherine , Aguilera Margarita , Ramos-Cormenzana Alberto , Fuentes Susana , Campos Victoriano , Monteoliva-Sánchez Mercedes
Published: March 2006

A total of 52 strains of moderately halophilic bacteria isolated from hypersaline sediment of Lake Tebenquiche on the Atacama Saltern, Chile, were subjected to a taxonomic study. The morphological, physiological, biochemical and nutritional characteristics of the strains matched those described for the genus Chromohalobacter. Cells were Gram-negative, non-spore-forming, rod-shaped and motile. A black pigmentation was produced. One strain, designated LTS-4NT, grew optimally at 32 °C. Growth occurred in media containing 0·5–25 % (w/v) total salts; the optimum was 7·5 % (w/v) total salts. The pH range for growth was 5–10. The G+C content of the DNA of strain LTS-4NT was 59·8 mol%. Analysis of 16S rRNA gene sequence similarity revealed that strain LTS-4NT was closely related to Chromohalobacter species; however, DNA–DNA hybridization of representative strain LTS-4NT failed to associate the strain with any species of the genus Chromohalobacter with validly published names. Therefore, the name Chromohalobacter nigrandesensis sp. nov. is proposed. The type strain is LTS-4NT (=CECT 5315T=DSM 14323T).
Marinimicrobium koreense gen. nov., sp. nov. and Marinimicrobium agarilyticum sp. nov., novel moderately halotolerant bacteria isolated from tidal flat sediment in Korea
Authors: Lim Jee-Min , Jeon Che Ok , Lee Jae-Chan , Song Sung-Min , Kim Kwang-Yup , Kim Chang-Jin
Published: March 2006

Two moderately halotolerant Gram-negative bacteria were isolated from tidal flat sediment of the South Sea in Korea (the Korea Strait). The strains, designated M9Tand M18T, were strictly aerobic, rod-shaped and non-spore-forming and motile with a flagellum and their major fatty acids were C16 : 0and C19 : 0cycloω8c. Strains M9Tand M18Tcould grow in the presence of up to 13–15 % (w/v) NaCl, but their optimum salt concentrations were relatively low (0–3 %, w/v). The major predominant isoprenoid quinone was Q-8 and the G+C content of the genomic DNA was 57–58 mol%. Phylogenetic analyses and comparative 16S rRNA gene sequence studies revealed that strains M9Tand M18Tformed a phylogenetic lineage distinct from the genusTeredinibacterwithin the classGammaproteobacteriaand were most closely related to the generaMicrobulbifer,SaccharophagusandTeredinibacter, with less than 92·5 % 16S rRNA gene sequence similarity. The level of 16S rRNA gene sequence similarity between the two strains was 96·7 %. On the basis of physiological and phylogenetic properties, strains M9Tand M18Trepresent separate species within a novel genus of the classGammaproteobacteria, for which the namesMarinimicrobium koreensegen. nov., sp. nov. (type species) andMarinimicrobium agarilyticumsp. nov. are proposed. The type strains ofMarinimicrobium koreenseandMarinimicrobium agarilyticumare M9T(=KCTC 12356T=DSM 16974T) and M18T(=KCTC 12357T=DSM 16975T), respectively.
Salegentibacter flavus sp. nov.
Authors: Ivanova Elena P. , Bowman John P. , Christen Richard , Zhukova Natalia V. , Lysenko Anatoly M. , Gorshkova Natalia M. , Mitik-Dineva Natasa , Sergeev Alexander F. , Mikhailov Valery V.
Published: March 2006

A yellow-pigmented, non-motile, Gram-negative bacterium, designated Fg 69T, was isolated from a sediment sample collected in Chazhma Bay (Sea of Japan). The novel organism grew at 10–35 °C, was neutrophilic and required 3–10 % NaCl for optimal growth. Strain Fg 69T was able to degrade starch and to hydrolyse gelatin and Tween 80 weakly but not casein or agar. Predominant cellular fatty acids comprised n-C15 and n-C16 branched-chain and straight-chain saturated and unsaturated fatty acids, including iso-C15 : 0 (5 %), anteiso-C15 : 0 (11 %), C15 : 0 (9 %), iso-C15 : 1 (5 %), iso-C16 : 0 (8 %), C16 : 0 (5 %) and C16 : 1
ω7 (5 %) and iso- and anteiso-branched 2-OH and 3-OH C15 : 0 to C17 : 0 fatty acids (26 % in total). The G+C content of the DNA was 40·4 mol%. 16S rRNA gene sequence data indicated that strain Fg 69T belonged to the genus Salegentibacter but was distinct from recognized Salegentibacter species (94–95 % sequence similarity). Based on these results, a novel species, Salegentibacter flavus sp. nov., is proposed. The type strain is Fg 69T (=KMM 6000T=CIP 107843T).
The Rho3 and Rho4 small GTPases interact functionally with Wsc1p, a cell surface sensor of the protein kinase C cell-integrity pathway in Saccharomyces cerevisiae
Authors: Fernandes Helder , Roumanie Olivier , Claret Sandra , Gatti Xavier , Thoraval Didier , Doignon François , Crouzet Marc
Published: March 2006

Rgd1, a GTPase-activating protein, is the only known negative regulator of the Rho3 and Rho4 small GTPases in the yeastSaccharomyces cerevisiae. Rho3p and Rho4p are involved in regulating cell polarity by controlling polarized exocytosis. Co-inactivation ofRGD1andWSC1, which is a cell wall sensor-encoding gene, is lethal. Another plasma membrane sensor, Mid2p, is known to rescue thergd1Δwsc1Δ synthetic lethality. It has been proposed that Wsc1p and Mid2p act upstream of the protein kinase C (PKC) pathway to function as mechanosensors of cell wall stress. Analysis of the synthetic lethal phenomenon revealed that production of activated Rho3p and Rho4p leads to lethality inwsc1Δ cells. Inactivation ofRHO3orRHO4was able to rescue thergd1Δwsc1Δ synthetic lethality, supporting the idea that the accumulation of GTP-bound Rho proteins, following loss of Rgd1p, is detrimental if the Wsc1 sensor is absent. In contrast, the genetic interaction betweenRGD1andMID2was not due to an accumulation of GTP-bound Rho proteins. It was proposed that simultaneous inactivation ofRGD1andWSC1constitutively activates the PKC–mitogen-activated protein kinase (MAP kinase) pathway. Moreover, it was shown that the activity of this pathway was not involved in the synthetic lethal interaction, which suggests the existence of another mechanism. Consistent with this idea, it was found that perturbations in Rho3-mediated polarized exocytosis specifically impair the abundance and processing of Wsc1 and Mid2 proteins. Hence, it is proposed that Wsc1p participates in the regulation of a Rho3/4-dependent cellular mechanism, and that this is distinct from the role of Wsc1p in the PKC–MAP kinase pathway.
Thermodynamic boundary conditions suggest that a passive transport step suffices for citrate excretion in Aspergillus and Penicillium
Authors: Burgstaller Wolfgang
Published: March 2006

Excretion of organic acids, e.g. citrate, by anamorphic fungi is a frequent phenomenon in natural habitats and in laboratory cultures. In biotechnological processes for citrate production withAspergillus nigerextracellular citrate concentrations up to 1 mol l−1are achieved. Intracellular citrate concentrations are in the millimolar range. Therefore the question arises whether citrate excretion depends on active transport. In this article thermodynamic calculations are presented for citrate excretion byA. nigerat an extracellular pH of 3 and byPenicillium simplicissimumat an extracellular pH of 7. From the results of these calculations it is concluded that in both cases a passive transport step suffices for citrate excretion.
Genetic and phenotypic characterization of Listeria monocytogenes lineage III
Authors: Roberts Angela , Nightingale Kendra , Jeffers Greg , Fortes Esther , Kongo Jose Marcelino , Wiedmann Martin
Published: March 2006

Listeria monocytogeneshas been previously grouped into three evolutionary groups, termed lineages I, II and III. While lineages I and II are commonly isolated from various sources, lineage III isolates are rare and have several atypical and unique phenotypic characteristics. Relative to their prevalence in other sources, lineage III strains are overrepresented among isolates from food-production animals, and underrepresented among isolates from human clinical cases and foods. This work describes an extensive genotypic and phenotypic characterization of 46 lineage III isolates. Phylogenetic analyses of partialsigBandactAsequences showed that lineage III represents three distinct subgroups, which were termed IIIA, IIIB and IIIC. Each of these lineage III subgroups is characterized by differentiating genotypic and phenotypic characteristics. Unlike typicalL. monocytogenes, all subgroup IIIB and IIIC isolates lack the ability to ferment rhamnose. While all IIIC and most IIIB isolates carry the putative virulence genelmaA, the majority of subgroup IIIA isolates lack this gene. All three lineage III subgroups contain isolates from human clinical cases as well as isolates that are cytopathogenic in a cell culture plaque assay, indicating that lineage III isolates have the potential to cause human disease. The identification of specific genotypic and phenotypic characteristics among the three lineage III subgroups suggests that these subgroups may occupy different ecological niches and, therefore, may be transmitted by different pathways.
From genomes to function: haloarchaea as model organisms
Authors: Soppa Jörg
Published: March 2006

Haloarchaea are adapted to high-salt environments and accumulate equally high salt concentrations in the cytoplasm. The genomes of representatives of six haloarchaeal genera have been fully or partially sequenced, allowing the analysis of haloarchaeal propertiesin silico. Transcriptome and proteome analyses have been established forHalobacterium salinarumandHaloferax volcanii. Genetic systems are available including methods that allow the fast in-frame deletion or modification of chromosomal genes. The high-efficiency transformation system ofHf. volcaniiallows the isolation of genes essential for a biological process by complementation of loss-of-function mutants. For the analysis of haloarchaeal biology many molecular genetic, biochemical, structural and cell biological methods have been adapted to application at high salt concentrations. Recently it has become clear that several different mechanisms allow the adaptation of proteins to the high salt concentration of the cytoplasm. Taken together, the wealth of techniques available make haloarchaea excellent archaeal model species.
Expression of botulinum neurotoxins A and E, and associated non-toxin genes, during the transition phase and stability at high temperature: analysis by quantitative reverse transcription-PCR
Authors: Couesnon Aurélie , Raffestin Stéphanie , Popoff Michel R.
Published: March 2006

Production of botulinum neurotoxin A (BoNT/A) and associated non-toxic proteins (ANTPs), which include a non-toxic non-haemagglutinin (NTNH/A) as well as haemagglutinins (HAs), was found previously to be dependent upon an RNA polymerase alternative sigma factor (BotR/A). Expression of thebotR/A,bont/Aandantpgenes, monitored by reverse transcription and real-time PCR analysis, occurred concomitantly at the transition between the exponential and stationary growth phases ofClostridium botulinumA. ThebotR/Aexpression level was about 100-fold less than those of thebont/Aandantpgenes. Therefore, BotR/A is an alternative sigma factor controlling the botulinum A locus genes during the transition phase. The highest toxin concentration was released into the culture supernatant 12 h after maximum expression of thebotR/A,bont/Aandantpgenes, without any apparent bacterial lysis. Toxin levels were then stable over 5 days in cultures at 37 °C, whereas a dramatic decrease in lethal activity was observed between 24 and 48 h in cultures at 44 °C. High temperature did inhibit transcription, since expression levels of thebotR/A,bont/Aandantpgenes were similar in cultures at 37 and 44 °C. However, incubation at 44 °C triggered a calcium-dependent protease that degraded BoNT/A and NTNH/A, but not HAs. InC. botulinumE, which contains no gene related tobotR, thebont/Eandp47genes were also expressed during the transition phase, and no protease activation at 44 °C was evident.
A SitABCD homologue from an avian pathogenic Escherichia coli strain mediates transport of iron and manganese and resistance to hydrogen peroxide
Authors: Sabri Mourad , Léveillé Simon , Dozois Charles M.
Published: March 2006

An operon encoding a member of the family of ATP-binding cassette (ABC) divalent metal ion transporters, homologous to Salmonella enterica SitABCD, has been identified in the avian pathogenic Escherichia coli (APEC) strain χ7122. The sitABCD genes were located on the virulence plasmid pAPEC-1, and were highly similar at the nucleotide level to the chromosomally encoded sitABCD genes present in Shigella spp. A cloned copy of sitABCD conferred increased growth upon a siderophore-deficient E. coli strain grown in nutrient broth supplemented with the chelator 2,2′-dipyridyl. Ion rescue demonstrated that Sit-mediated growth promotion of this strain was due to the transport of iron. SitABCD mediated increased transport of both iron and manganese as demonstrated by uptake of 55Fe, 59Fe or 54Mn in E. coli K-12 strains deficient for the transport of iron (aroB feoB) and manganese (mntH) respectively. Isotope uptake and transport inhibition studies showed that in the iron transport deficient strain, SitABCD demonstrated a greater affinity for iron than for manganese, and SitABCD-mediated transport was higher for ferrous iron, whereas in the manganese transport deficient strain, SitABCD demonstrated greater affinity for manganese than for iron. Introduction of the APEC sitABCD genes into an E. coli K-12 mntH mutant also conferred increased resistance to the bactericidal effects of hydrogen peroxide. APEC strain χ7122 derivatives lacking either a functional SitABCD or a functional MntH transport system were as resistant to hydrogen peroxide as the wild-type strain, whereas a Δsit ΔmntH double mutant was more sensitive to hydrogen peroxide. Overall, the results demonstrate that in E. coli SitABCD represents a manganese and iron transporter that, in combination with other ion transport systems, may contribute to acquisition of iron and manganese, and resistance to oxidative stress.
Phosphoethanolamine substitution in the lipid A of Escherichia coli O157 : H7 and its association with PmrC
Authors: Kim Sang-Hyun , Jia Wenyi , Parreira Valeria R. , Bishop Russell E. , Gyles Carlton L.
Published: March 2006

This study shows that lipid A ofEscherichia coliO157 : H7 differs from that ofE. coliK-12 in that it has a phosphoform at the C-1 position, which is distinctively modified by a phosphoethanolamine (PEtN) moiety, in addition to the diphosphoryl form. ThepmrCgene responsible for the addition of PEtN to the lipid A ofE. coliO157 : H7 was inactivated and the changes in lipid A profiles were assessed. ThepmrCnull mutant still produced PEtN-modified lipid A species, albeit in a reduced amount, indicating that PmrC was not the only enzyme that could be used to add PEtN to lipid A. Natural PEtN substitution was shown to be present in the lipid A of other serotypes of enterohaemorrhagicE. coliand absent from the lipid A ofE. coliK-12. However, the clonedpmrCO157gene in a high-copy-number plasmid generated a large amount of PEtN-substituted lipid A species inE. coliK-12. The occurrence of PEtN-substituted lipid A species was associated with a slight increase in the MICs of cationic peptide antibiotics, suggesting that the lipid A modification with PEtN would be beneficial for survival ofE. coliO157 : H7 in certain environmental niches. However, PEtN substitution in the lipid A profiles was not detected when putative inner-membrane proteins (YhbX/YbiP/YijP/Ecf3) that show significant similarity with PmrC in amino acid sequence were expressed from high-copy-number plasmids inE. coliK-12. This suggests that these potential homologues are not responsible for the addition of PEtN to lipid A in thepmrCmutant ofE. coliO157 : H7. When cells were treated with EDTA, the amount of palmitoylated lipid A from the cells carrying a high-copy-number plasmid clone ofpmrCO157that resulted in significant increase of PEtN substitution was unchanged compared with cells without PEtN substitution, suggesting that the PEtN moiety substituted in lipid A does not compensate for the loss of divalent cations required for bridging neighbouring lipid A molecules.
Evidence for a cytochrome bcc–aa 3 interaction in the respiratory chain of Mycobacterium smegmatis
Authors: Megehee James A. , Hosler Jonathan P. , Lundrigan Michael D.
Published: March 2006

Spectroscopic analysis of membranes isolated fromMycobacterium smegmatis, along with analysis of its genome, indicates that the cytochromecbranch of its respiratory pathway consists of a modifiedbc1complex that contains two cytochromescin itsc1subunit, similar to other acid-fast bacteria, and anaa3-type cytochromecoxidase. A functional association of the cytochromebccandaa3complexes was indicated by the findings that levels of detergent sufficient to completely disrupt isolated membranes failed to inhibit quinol-driven O2reduction, but known inhibitors of thebc1complex did inhibit quinol-driven O2reduction. The gene for subunit II of theaa3-type oxidase indicates the presence of additional charged residues in a predicted extramembrane domain, which could mediate an intercomplex association. However, high concentrations of monovalent salts had no effect on O2reduction, suggesting that ionic interactions between extramembrane domains do not play the major role in stabilizing thebcc–aa3interaction. Divalent cations did inhibit electron transfer, likely by distorting the electron-transfer interface between cytochromec1and subunit II. Soluble cytochromeccannot donate electrons to theaa3-type oxidase, even though key cytochromec-binding residues are conserved, probably because the additional residues of subunit II prevent the binding of soluble cytochromec. The results indicate that hydrophobic interactions are the primary forces maintaining thebcc–aa3interaction, but ionic interactions may assist in aligning the two complexes for efficient electron transfer.