bluuebunny/crossref_metadata_2025 huggingface dataset:
New ways to print living cells promise breakthroughs for engineering complex tissues in vitro
Authors: Withers Ginger S.
Published: March 2006

The ability to control the placement of cells and the assembly of networks in vitro has tremendous potential for understanding the regulation of development as well as for generating artificial tissues. To date, most engineering tools that can place materials with precision are not compatible with the requirements of living cells, and so approaches to tissue engineering have focused on patterning substrates as a way of controlling cell growth rather than patterning cells directly. In this issue of Biochemical Journal, however, Eagles et al. adapt electrohydrodynamic printing technology to ‘print’ living cells from a neuronal cell line on to a substrate. The importance of this approach is that it has the potential for unprecedented control over the position of cells in culture by directly placing them, thus allowing for the systematic assembly of cell networks.
The ubiquitin-associated domain of AMPK-related protein kinases allows LKB1-induced phosphorylation and activation
Authors: Rider Mark H.
Published: March 2006

The AMPK (AMP-activated protein kinase)-related protein kinase subfamily of the human kinome comprises 12 members closely related to the catalytic α1/α2 subunits of AMPK. The precise role of the AMPK-related kinases and their in vivo substrates is rather unclear at present, but some are involved in regulating cell polarity, whereas others appear to control cellular differentiation. Of the 12 human AMPK-related protein kinase family members, 11 can be activated following phosphorylation of their T-loop threonine residue by the LKB1 complex. Nine of these AMPK-related kinases activated by LKB1 contain an UBA (ubiquitin-associated) domain immediately C-terminal to the kinase catalytic domain. In this issue of the Biochemical Journal, Jaleel et al. show that the presence of an UBA domain in AMP-related kinases allows LKB1-induced phosphorylation and activation. The findings have implications for understanding the molecular mechanisms of activation of this fascinating family of protein kinases. Also, mutations in the UBA domains of the AMP-related kinase genes might be present in families with Peutz–Jehgers syndrome and in other cancer patients.
The impact of innovation on beef production in far northern Australia
Authors: Whan I. , Bortolussi G. , Backus R.
Published: March 2006

In this paper we examine the forces that have shaped Australia’s far northern (north of 20° south) beef industry over the past 35 years. This is done for the purpose of tracing its transformation from a state of relative isolation to an integral part of the national beef industry. We note that integration is being accompanied by a greater focus, particularly by corporate producers, on specialised breeding in the far north and this is being assisted by innovations that increase herd fertility and raise the meat quality of the progeny, while retaining adaptation of the breeding herd to the local environment. Among a range of technologies, genetic improvement has significant potential to bring about rapid improvement in the meat quality of tropically adapted cattle. With respect to gene-based technology, however, independent producers will have to be convinced about the rigour of the technology and the prospects of economic gains before they make significant management changes. To this end, innovative marketing systems are needed that will reveal the link between expected meat returns and the offer prices applying to groups of growing cattle in any location. Accordingly, there is an urgent need to develop and introduce a descriptive and informative trading language for growing cattle that incorporates inherent qualities including those that influence meat quality. Innovations that will complement those applying to enhancement of meat quality are more general but will significantly raise herd productivity. We also compare the operating systems of both corporate and independent producers in the region.
Influences of nutrition during pregnancy and lactation on birth weights and growth to weaning of calves sired by Piedmontese or Wagyu bulls
Authors: Cafe L. M. , Hennessy D. W. , Hearnshaw H. , Morris S. G. , Greenwood P. L.
Published: March 2006

The aim of this study was to quantify the effects of nutrition during pregnancy and lactation on birth weight and growth to weaning of Piedmontese and Wagyu sired calves. This research was also conducted to provide animals for long-term studies on the consequences of growth early in life. During 2 breeding cycles, Hereford cows were managed within low or high pasture-based nutritional systems from about 80 days of pregnancy to parturition. During lactation, the calves and their dams remained on the low or high nutritional system or crossed over to the alternative system. From commencement of the nutritional treatment during pregnancy until parturition, and then during lactation, cows on low nutrition lost an average of 45 and 23 kg liveweight, respectively, and those on high nutrition gained 55 and 40 kg, respectively. Calves of Wagyu sires weighed less at birth (31.0 v 35.9 kg, s.e. = 0.31 kg) and weaning (182 v. 189 kg, s.e. = 2.26 kg) than those of Piedmontese sires. Calves of cows on low nutrition during pregnancy weighed less at birth than those of cows on high nutrition (32.5 v. 35.2 kg, s.e. = 0.32 kg). Low nutrition during pregnancy adversely influenced birth to weaning ADG (676 v. 759 g, s.e. = 9.2 g), weight gain (145 v. 160 kg, s.e. = 2.1 kg) and liveweight (177 v. 195 kg, s.e. = 2.3 kg) of calves at weaning. The nutritional system during lactation had greater effects on ADG (618 v. 816 g, s.e. = 9.2 g), weight gain (131 v. 174 kg, s.e. = 2.1 kg) and liveweight (164 v. 207 kg, s.e. = 2.3 kg) of calves at weaning than the nutritional system during pregnancy. Overall, the responses to the nutritional treatments were consistent for the progeny of both sire-genotypes.
Long-term consequences of birth weight and growth to weaning on carcass, yield and beef quality characteristics of Piedmontese- and Wagyu-sired cattle
Authors: Greenwood P. L. , Cafe L. M. , Hearnshaw H. , Hennessy D. W. , Thompson J. M. , Morris S. G.
Published: March 2006

Cattle sired by Piedmontese or Wagyu bulls were bred and grown within pasture-based nutritional systems followed by feedlot finishing. Effects of low (mean 28.6 kg, n = 120) and high (38.8 kg, n = 120) birth weight followed by slow (mean 554 g/day, n = 119) or rapid (875 g/day, n = 121) growth to weaning on carcass, yield and beef quality characteristics at about 30 months of age were examined. Low birth weight calves weighed 56 kg less at 30 months of age, had 32 kg lighter carcasses, and yielded 18 kg less retail beef compared with high birth weight calves. Composition of carcasses differed little due to birth weight when adjusted to an equivalent carcass weight (380 kg). Calves grown slowly to weaning were 40 kg lighter at 30 months of age compared with those grown rapidly to weaning. They had 25 kg smaller carcasses which yielded 12 kg less retail beef than their counterparts at 30 months of age, although at an equivalent carcass weight yielded 5 kg more retail beef and had 5 kg less fat trim. Neither low birth weight nor slow growth to weaning had adverse effects on beef quality measurements. No interactions between sire-genotype and birth weight, or growth to weaning, were evident for carcass, yield and beef quality traits. Although restricted growth during fetal life or from birth to weaning resulted in smaller animals that yield less meat at about 30 months of age, adverse effects on composition due to increased fatness, or on indices of beef quality, were not evident at this age or when data were adjusted to an equivalent carcass weight.
Variance components for birth and carcass traits of crossbred cattle
Authors: Pitchford W. S. , Mirzaei H. M. , Deland M. P. B. , Afolayan R. A. , Rutley D. L. , Verbyla A. P.
Published: March 2006

During a 4-year period (1994–97) of the Australian ‘Southern Crossbreeding Project’, mature Hereford cows (n = 637) were mated to 97 sires from 7 breeds (Jersey, Wagyu, Angus, Hereford, South Devon, Limousin and Belgian Blue), resulting in 1334 calves. Heifers were slaughtered at around 16 months and steers at 23 months. The objective of the study was to quantify between- and within-breed genetic variation for numerous production and quality traits in a southern-Australian production system. Calf survival, birth weight and carcass production traits (carcass weight, fat depth, loin eye area, intramuscular fat) were obtained from these cattle. The carcass traits were loge-transformed because of a scale effect on the variance. Data were analysed using multi-variate animal models containing fixed effects of sex with random effects of management group, sire breed and animal. In addition, birth month and age of dam were included as fixed effects for birth weight. Covariances between survival and other traits could not be estimated from the multi-variate model so they were estimated from a series of bi-variate models. On average, management group and sire breed accounted for similar proportions of variance. Heritability ranged from 0.14 (survival), 0.17 (intramuscular fat), 0.28 (loin eye area), 0.29 (P8 fat depth), 0.31 (birth weight) to 0.50 (carcass weight). In general, environmental (management and residual) correlations between meat (carcass weight and loin eye area) and fat traits (fat depth and intramuscular fat) were positive, but the genetic correlations (both between and within breed) were negative. Management and genetic (co)variation has been quantified and can facilitate production of calves with carcasses suitable for specific market requirements.
Isolation and characterisation of a protein elicitor from Sclerospora graminicola and elicitor-mediated induction of defence responses in cultured cells of Pennisetum glaucum
Authors: Sharathchandra R. G. , Geetha N. P. , Amruthesh K. N. , Kini K. Ramachandra , Sarosh B. R. , Shetty N. P. , Shetty H. S.
Published: March 2006

Sclerospora graminicola (Sacc.) Schroet., an oomycete pathogen of Pennisetum glaucum (L.) R.Br. infects the meristematic tissues of young seedlings. The motile zoospores from the sporangia encyst, germinate and penetrate the plant tissue. Resistance to the invading pathogen is governed by the specific recognition of conserved pathogen-associated proteins or elicitors. In the present study, a zoospore protein was isolated and purified to homogeneity by a combination of size exclusion and high-performance liquid chromatography (HPLC). The crude fractionated protein was able to elicit an array of defence responses in resistant and susceptible cells of pearl millet. Treatment of cultured cells of pearl millet with partially purified elicitor protein resulted in a rapid loss of cell viability in the resistant cells and the percentage of cell death was higher in the resistant than in the susceptible cells. Cultures of resistant cells showed a sharp increase in the extra cellular pH compared with susceptible cells when treated with the crude elicitor. Increased oxidative burst was also recorded in the cells treated with the crude elicitor. The purified elicitor showed unique properties. The purified protein was acidic with a pI of 5.6 as revealed by isoelectric focusing (IEF) and matrix-assisted laser desorption ionisation (MALDI) analysis showed that the elicitor had a molecular mass of 7040 daltons. The primary structure determined by N-terminal Edman degradation and searches with BLAST did not reveal similarities to any known plant pathogenic or oomycete elicitor. Higher activities of the important defence-related enzymes phenylalanine ammonia lyase (PAL) and peroxidase in the resistant cell cultures than in the susceptible cell cultures treated with the purified elicitor were clearly evident. Studies of gene expression by northern blotting with heterologus peroxidase, PAL and oxalate oxidase probes showed that the mRNA transcripts were strongly up-regulated in resistant cell cultures within 30 min of elicitor treatment. The purified elicitor also demonstrated a very strong concentration-dependent sterol binding. The purified elicitor protein belongs to a class of low molecular weight oomycete elicitors with sterol carrier properties. The identified low molecular weight protein elicitor displays unique properties that can be exploited for synthesis of novel molecules for eco-friendly crop protection.
Genetic diversity of Cistus albidus in south-east Spain does not relate to mesoclimate
Authors: Grant Olga M. , McNeilly Tom , Incoll Lynton D.
Published: March 2006

Patterns of variation at selected isozyme loci were examined in populations of Cistus albidus L. in south-east Spain, from areas differing in precipitation and temperature, to determine whether population divergence has occurred. Total genetic diversity was high, with a high percentage of the variation being found between populations. Genetic variation between populations did not relate to climate. Populations exposed to severe summer drought did not show lower genetic diversity than populations from more benign climates. Little genetic variation was found between populations that showed variation in ecophysiological and growth responses in situ and under controlled conditions. Cluster analyses showed different patterns of between-population distances with respect to genetic, physiological and morphological data, and none of these patterns corresponded to that for between-site environmental variation.
Beyond Rayleigh's criterion: A resolution measure with application to single-molecule microscopy
Authors: Ram Sripad , Ward E. Sally , Ober Raimund J.
Published: March 2006

Rayleigh's criterion is extensively used in optical microscopy for determining the resolution of microscopes. This criterion imposes a resolution limit that has long been held as an impediment for studying nanoscale biological phenomenon through an optical microscope. However, it is well known that Rayleigh's criterion is based on intuitive notions. For example, Rayleigh's criterion is formulated in a deterministic setting that neglects the photon statistics of the acquired data. Hence it does not take into account the number of detected photons, which, in turn, raises concern over the use of Rayleigh's criterion in photon-counting techniques such as single-molecule microscopy. Here, we re-examine the resolution problem by adopting a stochastic framework and present a resolution measure that overcomes the limitations of Rayleigh's criterion. This resolution measure predicts that the resolution of optical microscopes is not limited and that it can be improved by increasing the number of detected photons. Experimental verification of the resolution measure is carried out by imaging single-molecule pairs with different distances of separation. The resolution measure provides a quantitative tool for designing and evaluating single-molecule experiments that probe biomolecular interactions.
Gene expression changes in foam cells and the role of chemokine receptor CCR7 during atherosclerosis regression in ApoE-deficient mice
Authors: Trogan Eugene , Feig Jonathan E. , Dogan Snjezana , Rothblat George H. , Angeli Véronique , Tacke Frank , Randolph Gwendalyn J. , Fisher Edward A.
Published: March 2006

Atherosclerosis regression is an important clinical goal. In previous studies of regression in mice, the rapid loss of plaque foam cells was explained by emigration to lymph nodes, a process reminiscent of dendritic cells. In the present study, plaque-containing arterial segments from apoE−/−mice were transplanted into WT recipient normolipidemic mice or apoE−/−mice. Three days after transplant, in the WT regression environment, plaque size decreased by ≈40%, and foam cell content by ≈75%. In contrast, both parameters increased in apoE−/−recipients. Foam cells were isolated by laser capture microdissection. In WT recipients, there were 3- to 6-fold increases in foam cells of mRNA for liver X receptor α and cholesterol efflux factors ABCA1 and SR-BI. Although liver X receptor α was induced, there was no detectable expression of its putative activator, peroxisome proliferator-activated receptor γ. Expression levels of VCAM or MCP-1 were reduced to 25% of levels in pretransplant or apoE−/−recipient samples, but there was induction at the mRNA and protein levels of chemokine receptor CCR7, an essential factor for dendritic cell migration. Remarkably, when CCR7 function was abrogatedin vivoby treatment of WT recipients with antibodies to CCR7 ligands CCL19 and CCL21, lesion size and foam cell content were substantially preserved. In summary, in foam cells during atherosclerosis regression, there is induction of CCR7 and a requirement for its function. Taken with the other gene expression data, these resultsin vivopoint to complex relationships among the immune system, nuclear hormone receptors, and inflammation during regression.
Human Immunodeficiency Virus Knowledge and Attitudes Among Hospital-Based Healthcare Professionals in Guangxi Zhuang Autonomous Region, People's Republic of China
Authors: Anderson Allen F. , Qingsi Zheng , Guanglin Wu , Zhijun Li , Wei Liu
Published: March 2006

Background and Objective:

Since the discovery of human immunodeficiency virus (HIV) on the Chinese mainland in 1985, the virus has spread to all provinces and autonomous regions. Although much research emphasis has been placed on studying behaviors and transmission knowledge among high-risk populations, especially drug abusers and commercial sex workers, little has been done to measure understanding within other risk groups. The objective of this study was to investigate HIV/acquired immunodeficiency syndrome (AIDS) knowledge and attitudes among hospital-based healthcare professionals in Guangxi Zhuang Autonomous Region in southern China.

Methods:

Data were gathered through a questionnaire completed by a convenience sample of individuals from three diverse hospitals.

Results:

Insufficient knowledge of the disease and its transmission resulted in more than 90% of the respondents expressing apprehension about contracting the virus and nearly 24% expressing reservations about caring for infected patients.

Conclusion:

Uncorrected, such attitudes and knowledge deficiencies have the potential to impact negatively on the quality of care, patient-practitioner safety, and proper postexposure prophylaxis.
Sharps-Related Injuries in California Healthcare Facilities: Pilot Study Results From the Sharps Injury Surveillance Registry
Authors: Gillen Marion , McNary Jennifer , Lewis Julieann , Davis Martha , Boyd Alisa , Schuller Mary , Curran Chris , Young Carol A. , Cone James
Published: March 2006

Background and Objectives:

In 1998, the California Department of Health Services invited all healthcare facilities in California (n = 2,532) to participate in a statewide, voluntary sharps injury surveillance project The objectives were to determine whether a low-cost sharps registry could be established and maintained, and to evaluate the circumstances surrounding sharps injuries in California.

Results:

Approximately 450 facilities responded and reported a total of 1,940 sharps-related injuries from January 1998 through January 2000. Injuries occurred in a variety of healthcare workers (80 different job titles). Nurses sustained the highest number of injuries (n = 658). In hospital settings (n = 1,780), approximately 20% of the injuries were associated with drawing venous blood, injections, or assisting with a procedure such as suturing. As expected, injuries were caused by tasks conventionally related to specific job classifications. The overall results approximate those reported by the Centers for Disease Control and Prevention's National Surveillance System for Health Care Workers and the University of Virginia's Exposure Prevention Information Network.

Conclusion:

These data further support findings from previous studies documenting the complex and persistent nature of sharps-related injuries in healthcare workers. In the future, mandated reporting using standardized forms and consistent application of decision rules would facilitate a more thorough analysis of injury events.
Comparison of Waterless Hand Antisepsis Agents at Short Application Times: Raising the Flag of Concern
Authors: Dharan Sasi , Hugonnet Stéphane , Sax Hugo , Pittet Didier
Published: March 2006

Objective:

Although alcohol-based hand rinses and gels have recommended application times of 30 to 60 seconds, healthcare workers usually take much less time for hand hygiene. We compared the efficacies of four alcohol-based hand rubs produced in Europe (hand rinses A, B, and C and one gel formulation) with the efficacy of the European Norm 1500 (EN 1500) reference waterless hand antisepsis agent (60% 2-propanol) at short application times.

Design:

Comparative crossover study.

Setting:

Infection Control Program laboratory of a large tertiary-care teaching hospital.

Participants:

Twelve healthy volunteers.

Intervention:

Measurement of residual bacterial counts and log reduction factors following inoculation of fingertips with Staphylococcus aureus American Type Culture Collection (ATCC) 6538, Pseudomonas aeruginosa ATCC 15442, and a clinical isolate of Enterococcus faecalis.

Results:

All hand rinses satisfied EN 1500 standards following a single application for 15 and 30 seconds, but reduction factors for the gel formulation were significantly lower for all tested organisms (all P < .025).

Conclusions:

Under stringent conditions similar to clinical practice, all three hand rinses proved to be more efficacious than the marketed alcohol-based gel in reducing bacterial counts on hands. Further studies are necessary to determine the in vivo efficacy of alcohol-based gels and whether they are as efficacious as alcohol-based rinses in reducing the transmission of nosocomial infections.
Introduction of a Waterless Alcohol-Based Hand Rub in a Long-Term–Care Facility
Authors: Mody Lona , McNeil Shelly A. , Sun Rongjun , Bradley Suzanne F. , Kauffman Carol A.
Published: March 2006

Objective:

To examine the impact of introduction of an alcohol-based hand rub on hand hygiene knowledge and compliance and hand colonization of healthcare workers (HCWs) in a long-term-care facility (LTCF).

Methods:

Two floors of an LTCF participated. Ward A used the hand rub as an adjunct to soap and water; ward B was the control. HCWs' hands were cultured using the bag-broth technique forStaphylococcus aureus,gram-negative bacilli (GNB),Candida,and vancomycin-resistant enterococci (VRE). HCWs completed a questionnaire at baseline and after an educational intervention and introduction of rub.

Results:

Hand hygiene practices, knowledge, and opinions did not change after the educational or rub intervention. Ward A HCWs thought that the rub was faster (P= .002) and less drying (P= .04) than soap. Hand hygiene frequency did not differ at baseline between the two floors, but increased on ward A by the end of the study (P= .04). HCWs were colonized frequently with GNB (66%),Candida(41%), S.aureus(20%), and VRE (9%). Although colonization did not change from baseline on either ward, the rub was more effective in clearing GNB (P= .03) and S.aureus(P= .003). Nosocomial infection rates did not change.

Conclusion:

The alcohol-based hand rub was a faster, more convenient, less drying method of hand hygiene for HCWs in an LTCF, and it improved compliance. Although microbial colonization did not change, the rub was more efficacious in removing pathogens already present on the hands of HCWs.
Can Whipple's Disease Be Transmitted by Gastroscopes?
Authors: Scola Bernard La , Rolain Jean-Marc , Maurin Max , Raoult Didier
Published: March 2006

Objective:

To determine whether disinfection protocols currently used for gastroscopes are effective against cultures ofTropheryma whipplei.

Design:

The bactericidal activity of 2% glutaraldehyde and two peracetic acids on the Twist-Marseille strain ofT. whippleigrown in cell monolayers was determined.

Patients:

Two patients who were diagnosed as having Whipple's disease 3 years after they had had intestinal biopsies.

Results:

The disinfectants reduced bacteria by approximately 2 log10to 3 log10after 5 to 60 minutes of contact.

Conclusion:

The bactericidal activity of a disinfectant is usually considered significant if it causes a 5 log10or greater reduction in viable bacterial titers. Disinfecting gastroscopes with2%glutaraldehyde or peracetic acids for 20 minutes may be insufficient to prevent transmission ofT. whippleion the instruments or stop false-positive results on polymerase chain reaction.
Hand Antisepsis: Evaluation of a Sprayer System for Alcohol Distribution
Authors: Barrau Karine , Rovery Clarisse , Drancourt Michel , Brouqui Philippe
Published: March 2006

Objective:

To evaluate the usefulness of a new alcohol sprayer by comparing it with an individual bottle of alcohol. Patterns of use and perceptions among healthcare personnel were compared for the two products.

Design:

Observational study recording the volume of alcohol used and the compliance rate (frequency of hand antisepsis per number of opportunities), and a survey of healthcare workers' perceptions of the different hand hygiene strategies.

Setting:

A 20-bed medical unit in a public hospital in Marseille, France.

Participants:

Healthcare workers of an infectious disease unit.

Interventions:

Hand hygiene alcohol systems (sprayer vs individual bottle, 70% ethyl alcohol).

Results:

The sprayer was used more frequently than the individual bottle (12.6 vs 9.7 hand washes per day). With the sprayer system, compliance was 91% for physicians, 28% for nurses, and 8% for housekeeping personnel. Alcohol hand antisepsis was preferred to washing hands with soap and water in low-risk situations such as simple entrance into a room (91% vs 36%;P< 10-6) or simple contact with a patient (69% vs 40%;P< .005). The sprayer system was considered easier to use (95%), more hygienic (90%), and faster (92%), with a better tolerance than the individual bottle.

Conclusion:

The new alcohol sprayer should improve rapid hand antisepsis.
A Decontamination and Sterilization Protocol Employed During Reuse of Cardiac Electrophysiology Catheters Inactivates Human Immunodeficiency Virus
Authors: Druce Julian D. , Russell Jessica S. , Birch Christopher J. , Yates Lynette A. , Harper Richard W. , Smolich Joseph J.
Published: March 2006

Objective:

To assess the effect of a standard decontamination and sterilization protocol employed during reuse of cardiac electrophysiology (EP) catheters on human immunodeficiency virus (HIV).

Setting:

Public health viral research laboratory.

Methods:

Studies were performed on distal, electrode-containing segments of 40 EP catheters previously used in up to 10 clinical EP procedures. EP catheter segments were immersed for 1 hour in blood contaminated with a high titer of HIV. After air drying for 2 hours, subgroups of 8 EP catheters were subjected to either (1) no treatment, (2) washing in general purpose detergent, (3) washing in enzyme cleaner, (4) sterilization in ethylene oxide, or (5) the full protocol of sequential detergent-enzyme cleaner-ethylene oxide exposure. HIV infectivity after treatment was determined by measuring HIV RNA and, in cell culture studies, assessing HIV-induced cytopathic effects (CPEs) and supernatant HIV-specific p24 antigen content.

Results:

With no treatment, all catheters had high HIV RNA levels associated with CPEs and high p24 antigen levels. After washing in detergent, 5 of 8 catheters had HIV RNA detected, but without CPEs or p24 antigen. HIV RNA was detected in all catheters after washing in enzyme cleaner, with CPEs and a high p24 antigen level in 1 of 8 catheters. HIV RNA, CPEs, and p24 antigen were absent after ethylene oxide. After the full protocol, HIV RNA levels were undetectable (n = 7) or low (n = 1), without evidence of CPEs or p24 antigen.

Conclusion:

Appropriate decontamination and sterilization of EP catheters during reuse is highly effective in inactivating HIV.
Factors Related to Hospital Stay Among Patients With Nosocomial Infection Acquired in the Intensive Care Unit
Authors: Olaechea Pedro M. , Ulibarrena Miguel-Angel , Álvarez-Lerma Francisco , Insausti Jesús , Palomar Mercedes , De la Cal Miguel-Angel ,   ENVIN-UCI Study Group
Published: March 2006

Objectives:

To assess the influence of nosocomial infection on length of stay in the intensive care unit (ICU) and to determine the relative effect of other factors on extra length of hospitalization associated with nosocomial infection.

Design:

Prospective cohort multicenter study in the context of the ENVIN-UCI project.

Setting:

Medical or surgical ICUs of 49 different hospitals in Spain.

Methods:

All consecutive patients (N = 6,593) admitted to ICUs of the participating hospitals who stayed for more than 24 hours during a 3-month period (from January 15 to April 15, 1996) were included. Length of ICU stay was compared between patients with and without nosocomial infections.

Results:

Uninfected patients (N = 5,868) had a median stay in the ICU of 3 days, whereas the median for infected patients (N = 725) was 17 days (P < .001). The median for infected patients with one episode of nosocomial infection was 13 days. The greatest length of stay (40 days) was among patients admitted to the ICU because of medical diseases, with an infection acquired before admission to the ICU, and with the largest number of nosocomial infection episodes. In extended stays, nosocomial infection was significantly associated with length of hospitalization (day 21; odds ratio, 22.38; 95% confidence interval, 16.6 to 30.4), whereas an effect of variables related to severity of illness on admission (Acute Physiology and Chronic Health Evaluation II score, urgent surgery, and infection prior to ICU admission) was not found.

Conclusions:

The presence of nosocomial infection and the number of infection episodes were the variables with the strongest association with prolonged hospital stay among ICU patients.
COG-7-deficient Human Fibroblasts Exhibit Altered Recycling of Golgi Proteins
Authors: Steet Richard , Kornfeld Stuart
Published: March 2006

Recently, we reported that two siblings presenting with the clinical syndrome congenital disorders of glycosylation (CDG) have mutations in the gene encoding Cog7p, a member of the conserved oligomeric Golgi (COG) complex. In this study, we analyzed the localization and trafficking of multiple Golgi proteins in patient fibroblasts under a variety of conditions. Although the immunofluorescent staining pattern of several Golgi proteins was indistinguishable from normal, the staining of endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC)-53 and the vesicular-soluble N-ethylmaleimide-sensitive factor attachment protein receptors GS15 and GS28 was abnormal, and the steady-state level of GS15 was greatly decreased. Retrograde transport of multiple Golgi proteins to the ER in patient fibroblasts via brefeldin A-induced tubules was significantly slower than occurs in normal fibroblasts, whereas anterograde protein trafficking was much less affected. After prolonged treatment with brefeldin A, several Golgi proteins were detected in clusters that colocalize with the microtubule-organizing center in patient cells. All of these abnormalities were normalized in COG7-corrected patient fibroblasts. These results serve to better define the role of the COG complex in facilitating protein trafficking between the Golgi and ER and provide a diagnostic framework for the identification of CDG defects involving trafficking proteins.
PIANA: protein interactions and network analysis
Authors: Aragues Ramon , Jaeggi Daniel , Oliva Baldo
Published: March 2006

Summary: We present a software framework and tool called Protein Interactions And Network Analysis (PIANA) that facilitates working with protein interaction networks by (1) integrating data from multiple sources, (2) providing a library that handles graph-related tasks and (3) automating the analysis of protein–protein interaction networks. PIANA can also be used as a stand-alone application to create protein interaction networks and perform tasks such as predicting protein interactions and helping to identify spots in a 2D electrophoresis gel.

Availability: PIANA is under the GNU GPL. Source code, database and detailed documentation may be freely downloaded from .

Contact:  ramon.aragues@upf.edu; boliva@imim.es
GALGO: an R package for multivariate variable selection using genetic algorithms
Authors: Trevino Victor , Falciani Francesco
Published: March 2006

Summary: The development of statistical models linking the molecular state of a cell to its physiology is one of the most important tasks in the analysis of Functional Genomics data. Because of the large number of variables measured a comprehensive evaluation of variable subsets cannot be performed with available computational resources. It follows that an efficient variable selection strategy is required. However, although software packages for performing univariate variable selection are available, a comprehensive software environment to develop and evaluate multivariate statistical models using a multivariate variable selection strategy is still needed. In order to address this issue, we developed GALGO, an R package based on a genetic algorithm variable selection strategy, primarily designed to develop statistical models from large-scale datasets.

Availability: GALGO can be downloaded from

Contact:  vtrevino@itesm.mx; f.falciani@bham.ac.uk

Supplementary information:  Supplementary data are available at
Nesiotobacter exalbescens gen. nov., sp. nov., a moderately thermophilic alphaproteobacterium from an Hawaiian hypersaline lake
Authors: Donachie Stuart P. , Bowman John P. , Alam Maqsudul
Published: March 2006

A Gram-negative bacterium, designated LA33BT, was isolated from water collected from a hypersaline lake on uninhabited Laysan Atoll in the Northwestern Hawaiian Islands. Cells of strain LA33BTare motile, straight rods that grow between 4 and 45 °C and in media containing 1–17·5 % (w/v) NaCl. The strain oxidizes carbohydrates, nucleosides, amino acids and organic acids presented as sole carbon sources and constitutive lipolytic and proteolytic enzymes are expressed. Over 75 % of the fatty acid pool iscis-11-octadecenoic acid (18 : 1ω7c). Comparative sequence analysis of the 16S rRNA gene indicates that the strain forms a new lineage in theα-2 subclass of theProteobacteria, with the closest recognized strains beingStappia aggregataNCIMB 2208TandRoseibium denhamenseJCM 10543T, with which it shares 94–95 % sequence similarity. Strain LA33BTdiffers phenotypically from extantStappiaandRoseibiumspecies, however, in that it is a moderate thermophile, it requires NaCl and tolerates higher NaCl concentrations and it does not expressβ-galactosidase or oxidize glycerol. On the basis of genotypic data and phenotypic characteristics, we propose that strain LA33BTdoes not belong to the generaStappiaorRoseibiumand that it represents the type species of a new genus,Nesiotobacter. Strain LA33BT(=ATCC BAA-994T=CIP 108449T) is proposed as the type strain of the type species of this genus, with the nameNesiotobacter exalbescensgen. nov., sp. nov.
Lactobacillus nantensis sp. nov., isolated from French wheat sourdough
Authors: Valcheva Rosica , Ferchichi Mounir F. , Korakli Maher , Ivanova Iskra , Gänzle Michael G. , Vogel Rudi F. , Prévost Hervé , Onno Bernard , Dousset Xavier
Published: March 2006

A polyphasic taxonomic study of the bacterial flora isolated from traditional French wheat sourdough, using phenotypic characterization and phylogenetic as well as genetic methods, revealed a consistent group of isolates that could not be assigned to any recognized species. These results were confirmed by randomly amplified polymorphic DNA and amplified fragment length polymorphism fingerprinting analyses. Cells were Gram-positive, homofermentative rods. Comparative 16S rRNA gene sequence analysis of the representative strain LP33T indicated that these strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives Lactobacillus farciminis, Lactobacillus alimentarius, Lactobacillus paralimentarius and Lactobacillus mindensis. DNA–DNA reassociation experiments with the three phylogenetically closest Lactobacillus species confirmed that LP33T (=DSM 16982T=CIP 108546T=TMW 1.1265T) represents the type strain of a novel species, for which the name Lactobacillus nantensis sp. nov. is proposed.
Zoogloea oryzae sp. nov., a nitrogen-fixing bacterium isolated from rice paddy soil, and reclassification of the strain ATCC 19623 as Crabtreella saccharophila gen. nov., sp. nov.
Authors: Xie Cheng-Hui , Yokota Akira
Published: March 2006

Two strains of free-living diazotrophs isolated from soil from a rice paddy field were characterized by using a polyphasic approach. The novel strains, A-7Tand A-4, were found to be very closely related, with 99·9 % 16S rRNA gene sequence similarity and a DNA–DNA hybridization value of 89·5 %, suggesting that they represent a single species. 16S rRNA gene sequence analyses indicated that the two strains fell within theZoogloealineage, with less than 96·7 % sequence similarity to otherZoogloeaspecies. Chemotaxonomic characteristics of the novel strains, including DNA G+C content (65·1 mol%), the major quinone system (Q-8), predominant fatty acids (16 : 1ω7cand 16 : 0) and major hydroxy fatty acids (3-OH 10 : 0 and 3-OH 12 : 0), are similar to those of the genusZoogloea. The novel strains showed positive results for floc formation which is accepted as confirmatory for species of the genusZoogloea. However, the novel strains can be distinguished from the other species ofZoogloeaby physiological characteristics. The nameZoogloea oryzaesp. nov. is therefore proposed for the novel strains with strain A-7T(=IAM 15218T=CCTCC AB 2052005T) as the type strain. Phylogenetic and chemotaxonomic analyses indicate that strain ATCC 19623, designated as a reference strain ofZoogloea ramigera, does not belong to the genusZoogloeabut to a new genus ofAlphaproteobacteria. The nameCrabtreella saccharophilagen. nov., sp. nov. is proposed for strain ATCC 19623T(=IAM 12669T).
Leptospira broomii sp. nov., isolated from humans with leptospirosis
Authors: Levett Paul N. , Morey Roger E. , Galloway Renee L. , Steigerwalt Arnold G.
Published: March 2006

Isolates of Leptospira from two human cases of leptospirosis in Denmark and France were studied using DNA–DNA relatedness, G+C content, 16S rRNA gene sequence data and pulsed-field gel electrophoresis. These isolates differed from previously described species of Leptospira and are defined as Leptospira broomii sp. nov. The type strain is 5399T (=ATCC BAA-1107T=KIT 5399T).
Prevotella bergensis sp. nov., isolated from human infections
Authors: Downes Julia , Sutcliffe Iain C. , Hofstad Tor , Wade William G.
Published: March 2006

Eight strains of anaerobic Gram-negative bacilli isolated from infections of the skin and soft tissues were subjected to a comprehensive range of phenotypic and genotypic tests. 16S rRNA gene sequence analysis revealed the strains to constitute a homogeneous group, distinct from species with validly published names but related to a cluster including Prevotella buccae, Prevotella dentalis and Prevotella baroniae. A novel species, Prevotella bergensis sp. nov., is proposed to accommodate these strains. Prevotella bergensis is saccharolytic and produces acetic and succinic acids as end products of fermentation. The G+C content of the DNA of the type strain is 48 mol%. The type strain of Prevotella bergensis is 94067913T (=DSM 17361T=CCUG 51224T).
Methylocystis rosea sp. nov., a novel methanotrophic bacterium from Arctic wetland soil, Svalbard, Norway (78° N)
Authors: Wartiainen Ingvild , Hestnes Anne Grethe , McDonald Ian R. , Svenning Mette M.
Published: March 2006

A Gram-negative, rod-shaped, non-motile, non-spore-forming, pink-pigmented bacterium, SV97T, was isolated from a wetland soil near Ny-Ålesund, Svalbard Islands, Norway (78° N). On the basis of 16S rRNA gene sequence similarity, strain SV97T was shown to belong to the Alphaproteobacteria and was highly related to a number of non-characterized Methylocystis strains with GenBank accession nos AJ458507 and AJ458502 (100 %) and AF177299, AJ458510, AJ458467, AJ458471, AJ431384, AJ458475, AJ458484, AJ458501 and AJ458466 (99 %). The most closely related type strains were Methylocystis parvus OBBPT (97·2 %) and Methylocystis echinoides IMET 10491T (97 %). The closest related recognized species within the genus Methylosinus was Methylosinus sporium NCIMB 11126T (96·0 % similarity). Chemotaxonomic and phenotypic data (C18 : 1
ω8 as the major fatty acid, non-motile, no rosette formation) supported the affiliation of strain SV97T to the genus Methylocystis. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain SV97T from the two recognized Methylocystis species. Strain SV97T therefore represents a novel species, for which the name Methylocystis rosea sp. nov. is proposed, with the type strain SV97T (=DSM 17261T=ATCC BAA-1196T).
Reclassification of Paenibacillus larvae subsp. pulvifaciens and Paenibacillus larvae subsp. larvae as Paenibacillus larvae without subspecies differentiation
Authors: Genersch Elke , Forsgren Eva , Pentikäinen Jaana , Ashiralieva Ainura , Rauch Sandra , Kilwinski Jochen , Fries Ingemar
Published: March 2006

A polyphasic taxonomic study of the two subspecies of Paenibacillus larvae, Paenibacillus larvae subsp. larvae and Paenibacillus larvae subsp. pulvifaciens, supported the reclassification of the subspecies into one species, Paenibacillus larvae, without subspecies separation. Our conclusions are based on the analysis of six reference strains of P. larvae subsp. pulvifaciens and three reference strains and 44 field isolates of P. larvae. subsp. larvae. The latter originated from brood or honey of clinically diseased honey bee colonies or from honey of both clinically diseased and asymptomatic colonies from Sweden, Finland and Germany. Colony and spore morphology, as well as the metabolism of mannitol and salicin, did not allow a clear identification of the two subspecies and SDS-PAGE of whole-cell proteins did not support the subspecies differentiation. For genomic fingerprinting, repetitive element-PCR fingerprinting using ERIC primers and PFGE of bacterial DNA were performed. The latter method is a high-resolution DNA fingerprinting method proven to be superior to most other methods for biochemical and molecular typing and has not previously been used to characterize P. larvae. ERIC-PCR identified four different genotypes, while PFGE revealed two main clusters. One cluster included most of the P. larvae subsp. larvae field isolates, as well as all P. larvae subsp. pulvifaciens reference strains. The other cluster comprised the pigmented variants of P. larvae subsp. larvae. 16S rRNA gene sequences were determined for some strains. Finally, exposure bioassays demonstrated that reference strains of P. larvae subsp. pulvifaciens were pathogenic for honey bee larvae, producing symptoms similar to reference strains of P. larvae subsp. larvae. In comparison with the type strain for P. larvae subsp. larvae, ATCC 9545T, the P. larvae subsp. pulvifaciens strains tested were even more virulent, since they showed a shorter LT100. An emended description of the species is given.
Enterococcus silesiacus sp. nov. and Enterococcus termitis sp. nov.
Authors: Švec Pavel , Vancanneyt Marc , Sedláček Ivo , Naser Sabri M. , Snauwaert Cindy , Lefebvre Karen , Hoste Bart , Swings Jean
Published: March 2006

Three enterococci constituted two aberrant branches after numerical analysis of (GTG)5-PCR fingerprints: analogous patterns were found for two water isolates, strains W213 and W442T, and a separate position was found for an isolate from the gut of a termite, strain LMG 8895T. 16S rRNA gene sequence analysis classified all three strains in the Enterococcus faecalis species group. Further sequencing analysis of the housekeeping gene pheS (encoding the phenylalanyl-tRNA synthase α-subunit) and whole-cell-protein analysis confirmed a distinct position for the two water isolates and the termite strain, respectively. DNA–DNA hybridization experiments and distinct phenotypic features between the strains studied and representatives of the E. faecalis species group confirmed novel species status, respectively, for the two water isolates, strains W213 and W442T, and for strain LMG 8895T. The names Enterococcus silesiacus sp. nov. and Enterococcus termitis sp. nov. are proposed for the novel taxa, with W442T (=CCM 7319T=LMG 23085T) and LMG 8895T (=CCM 7300T) as the respective type strains.
Proposal of Giesbergeria voronezhensis gen. nov., sp. nov. and G. kuznetsovii sp. nov. and reclassification of [Aquaspirillum] anulus, [A.] sinuosum and [A.] giesbergeri as Giesbergeria anulus comb. nov., G. sinuosa comb. nov. and G. giesbergeri comb. nov., and [Aquaspirillum] metamorphum and [A.] psychrophilum as Simplicispira metamorpha gen. nov., comb. nov. and S. psychrophila comb. nov.
Authors: Grabovich Margarita , Gavrish Ekaterina , Kuever Jan , Lysenko Anatoly M. , Podkopaeva Daria , Dubinina Galina
Published: March 2006

Five Gram-negative, motile, spiral-shaped strains were isolated from a sulfide spring (D-412T), active sludge of wastewater (D-419T, D-420, D-424) and industrial wastewater (D-416). Comparative 16S rRNA gene sequence analysis showed that the isolates belong to the family Comamonadaceae, within the class Betaproteobacteria, but fall into a distinct cluster. On the basis of phenotypic, chemotaxonomic and phylogenetic data, a new genus, Giesbergeria gen. nov., is proposed, including five species. The type species of the genus is Giesbergeria voronezhensis sp. nov. (type strain D-419T=DSM 12825T=CIP 107340T=VKM B-2350T) and other novel members of the genus are Giesbergeria kuznetsovii sp. nov. (type strain D-412T=DSM 12827T=VKM B-2352T), Giesbergeria giesbergeri comb. nov. (basonym Aquaspirillum giesbergeri), Giesbergeria sinuosa comb. nov. (basonym Aquaspirillum sinuosum) and Giesbergeria anulus comb. nov. (basonym Aquaspirillum anulus). Using the same criteria, isolate D-416 (=DSM 12826) was identified as a strain of [Aquaspirillum] metamorphum. Strain D-416, the type strain of [A.] metamorphum and the type strain of [Aquaspirillum] psychrophilum form a distinct cluster within the family Comamonadaceae (97–97·2 % 16S rRNA gene sequence similarity) and share phenotypic and chemotaxonomic properties. Therefore, it is proposed that these strains are reclassified as members of a new genus, Simplicispira gen. nov., as Simplicispira metamorpha comb. nov. (the type species) and Simplicispira psychrophila comb. nov., respectively.
Tenacibaculum litoreum sp. nov., isolated from tidal flat sediment
Authors: Choi Dong Han , Kim Yoon-Gon , Hwang Chung Yeon , Yi Hana , Chun Jongsik , Cho Byung Cheol
Published: March 2006

A rod-shaped bacterium, designated CL-TF13T, was isolated from a tidal flat in Ganghwa, Korea. Analysis of the 16S rRNA gene sequence revealed an affiliation with the genusTenacibaculum. The sequence similarities between CL-TF13Tand type strains of members of the genusTenacibaculumwere from 94·2 to 97·4 %. Cells were motile by means of gliding. Strain CL-TF13Tgrew on solid medium as pale-yellow colonies with an irregular spreading edge. The strain was able to grow in NaCl at a range of 3–5 %. They grew within a temperature range of 5–40 °C and at pH range of 6–10. The major fatty acids were summed feature 3 (C16 : 1ω7cand/or iso-C15 : 02-OH, 19·6 %), iso-C15 : 0(18·8 %) and iso-C17 : 03-OH (13·6 %). Fatty acids such as C18 : 3ω6c(6,9,12) (1·5 %) and summed feature 4 (iso I- and/or anteiso B-C17 : 1, 1·3 %) were uniquely found in minor quantities in CL-TF13TamongTenacibaculumspecies. The DNA G+C content was 30 mol%. According to physiological data, fatty-acid composition and 16S rRNA gene sequence, CL-TF13Tcould be assigned to the genusTenacibaculumbut distinguished from the recognized species of the genus. Therefore, strain CL-TF13T(=KCCM 42115T=JCM 13039T) represents a novel species, for which the nameTenacibaculum litoreumsp. nov. is proposed.