bluuebunny/crossref_metadata_2025 huggingface dataset:
Heritability of post-mixing aggressiveness in grower-stage pigs and its relationship with production traits
Authors: Turner S.P. , White I. M. S. , Brotherstone S. , Farnworth M. J. , Knap P. W. , Penny P. , Mendl M. , Lawrence A. B.
Published: August 2009

Mixing of commercial pigs frequently leads to intense aggression. Considerable phenotypic variation exists between individuals and selection against aggressiveness may offer a long-term reduction in aggression without incurring additional costs to the primary producer. The genetic contribution to aggressiveness was quantified in this study using the number of skin lesions as an indicator of involvement in aggression. A sample of 1132 pigs were mixed at an average weight of 27·9 (s.d. 4·6) kg into 96 pens on a commercial sire line nucleus unit. Post-mixing aggressiveness of pigs was assessed using the lesion score (LS) approach. Growth rate, between 27·9 and 91·9 kg, and backfat depth at 91·9 kg were recorded for a subsample of 658 pigs. With a pedigree file of 1947 animals, a heritability of 0·22 was estimated for the LS trait. No significant genetic or phenotypic correlations were found between LS and growth rate or backfat depth, but standard errors of estimates were large. The response to selection, when all selection pressure was placed on the LS trait, was a 25% reduction in LS per generation. It is therefore technically possible to select for a reduced LS without substantially inhibiting genetic progress in growth rate or backfat depth through antagonistic genetic relationships.
The effect of feeding a low- or a high-starch diet on thein vitrofermentative capacity of equine faecal inocula
Authors: Murray J. M. D. , Longland A. , Moore-Colyer M. , Dunnett C.
Published: August 2009

Seven mature Welsh-cross pony geldings provided the faecal inocula in a cross-over design experiment, consisting of two 14-day periods. In period 1, four ponies (group 1) were offered a low-starch fibre mix (LS), and three (group 2) were offered a conventional high-starch coarse mix (HS). Both groups were offered these mixes in a 50:50 ratio with mature grass hay, to give a total daily dry-matter intake of 17·5 g/kg live weight per day. Diets were then switched in period 2. At the end of each experimental period freshly voided faeces were collected from each animal and assessed for their ability to ferment grass hay (H), fibre mix (FMix) or starch-based coarse mix (SMix) using the gas production (GP) technique of Theodorouet al.(1994). Donor animal diet and donor animal had no effect on any end-point measurements. Lag times recorded for the SMix were significantly (P<0·001) greater in LS-inoculated bottles compared with the HS inocula (1·74v.2·25 h, respectively). Lag times for FMix and SMix varied significantly (P<0·001) between ponies (0·82 to 1·78 h in the FMix and 1·64 to 2·51 h in the SMix). The degradation rate of H also differed significantly (P<0·001) between ponies with the time taken to reach 50% of GP (T50) ranging from 12·70 to 17·30 h. Consequently, it would appear that the effect of feeding LS or HS on thein vitrofermentative capacity of equine faecal inocula is minimal; moreover, the GP technique appears to be valuable tool for evaluating such effects.
Comparison of fresh and ensiled white and red clover added to ryegrass on energy and protein utilization of lactating cows
Authors: van Dorland H. A. , Wettstein H.-R. , Leuenberger H. , Kreuzer M.
Published: August 2009

Two respiratory chamber experiments were conducted with dairy cows to compare metabolizable energy and protein utilization when feeding white or red clover with ryegrass. In experiment 1, fresh ryegrass was mixed with fresh white (WF) or red clover (RF) (60/40, on dry matter (DM) basis). Experiment 2 involved similar mixed diets in ensiled form (WS and RS, respectively), and two ryegrass silage diets, without (GS) or with supplementary maize gluten (GS+). Barley was supplemented according to requirements for milk production. Voluntary forage DM intake remained unaffected in experiment 1 and was higher (P<0·01) in experiment 2 for WS than for GS and GS+(128 v. 98 and 106 g/kg M0·75). Within experiments, no treatment effects occurred for apparent nutrient digestibilities, milk yield, and composition. Protein utilization (milk-N/N-intake) was numerically lower on all clover-based diets (0·24 to 0·25) versus GS (0·29). With added maize gluten (GS+), protein utilization decreased to 0·23, indicating that ryegrass silage (plus barley) alone provided sufficient metabolizable protein. Consequently, higher (P<0·01) urinary energy losses occurred in GS+ compared with GS, despite similar metabolizable energy intakes, and a trend for the highest plasma urea levels was found for GS+ cows (7·59 mmol/l;P<0·1). Overall, this study illustrates that the white and red clovers investigated were equivalent in energy and protein supply, also in comparison to the ryegrass. It remains open whether these forage legumes, when supplemented to a moderate-protein ryegrass, would have contributed to metabolizable protein supply or would have merely increased metabolic nitrogen load.
Influence of provision of toys during transport and lairage on stress responses and meat quality of pigs
Authors: Peeters E. , Geers R.
Published: August 2009

Transport and accompanying mixing of pigs causes fights among pigs and stress resulting in decreased welfare and reduced meat quality. This study investigates the effect of toys available during transport and lairage on behaviour, stress responses, and meat quality of slaughter pigs. Cross-bred (Piétrain×Hypor) pigs (109·1±10·1 kg) were allocated to one of three treatments during transport and lairage: 1) no toys (control) 2) rubber toys and 3) balls. The rubber toy consisted of two fixed rubber sticks; the plastic ball was filled with pieces of maize, which became available for the pigs in small amounts by manipulating the ball. Per group of 11 pigs, two toys were provided. Totally, divided over 4 replicates, 144 pigs were involved, of which 72 were used for blood sampling and meat quality measurements. Five minutes scans during lairage revealed that treatment did not affect the percentage of pigs that lay (P=0·20), stood (P=0·83) or sat (P=0·12) and that in almost all scans at least one pigs was manipulating a ball, compared with half of the scans in which at least one animal was manipulating a rubber toy (P=0·02). However both toys resulted in a lower incidence of shoulder lesions compared with the control group (P=0·06; 31·1% and 28·9% of the pigs for the rubber toys and balls respectively, versus 51·1% for the control group). Blood sampling at sticking showed that pigs with the balls during transport and lairage tended to have lower cortisol concentrations (P=0·07) than pigs with the rubber toys. Also, a decrease in plasma lactate concentration was observed for these pigs in comparison with the control group (P=0·08), and a higher pH of the m. longissimus dorsi 45 min post mortem for the pigs with the balls was found than for the pigs with the rubber toys (P=0·01). These results indicate that enrichment of compartments during transport and lairage with balls reduced glycolysis in muscle resulting in a lower lactate production and a slower pH decline. The pH 45 min post mortem of the m. biceps femoris and the pH, electrical conductivity, colour, and water-holding capacity of the loin 48 h post mortem were not affected by treatment. In conclusion, environmental enrichment with toys during transport and lairage can decrease shoulder lesions and lower the pH decline 45 min post mortem, especially by provision of plastic balls filled with maize.
Long-term effect of selection for litter size and feeding programme on the performance of reproductive rabbit does 2. Lactation and growing period
Authors: Quevedo F. , Cervera C. , Blas E. , Baselga M. , Pascual J. J.
Published: August 2009

A total of 166 crossbred does were used to study the possible long-term effect of two types of crossbred does (H1v.H2, old and current generations, respectively) from the cross of different generations of lines selected for litter size, the use of a rearing programme based on a low-energy diet, and the administration of a high-energy diet during reproductive life, on the performance and body condition of lactating rabbit does and their litters until slaughter. The body condition of the reproductive rabbit does increased in the successive cycles to the fourth parturition, being maintained from this moment on. Animals more selected for litter size at weaning presented a greater food intake (+3%;P<0·05) and milk yield (+6%;P<0·05) during the first 21 days of lactation, which could be related to greater maternal aptitude. The difference in the weight of pups at slaughter time (+24 g for H2 respect to H1 pups) was one third lower than that expected from the generation response of the paternal line (0·45 g/day), perhaps related to the different enteropathy incidence depending on the genetic type. The use of a high-energy diet during the reproduction period increased the milk yield (+22%;P<0·05) of does, as the growth (+16 g at weaning day;P<0·05) and survival index (+2%;P<0·05) of the litters during lactation, but could produce a more sudden weaning of pups as a consequence of their lower pre-weaning food intake (−42%;P<0·05), which has been related with a greater health risk index during the growing period (+4·2%;P<0·05). Reproductive does given a high fibre diet during the rearing period (from 3 kg live weight to 28th day of the first pregnancy) reached parturition with a higher live weight than does that received a moderate energy diet restricted during this same period (+142 g;P<0·05). All other parameters controlled for the lactating does and their litters were not affected by the type of diet received during the rearing period. Females that were not effectively mated at first AI (11 dayspost partum) showed a greater increase in their perirenal fat thickness between partum and the 11th day of lactation than those lactating females that showed an effective mating (+0·22v.+0·37 mm, respectively;P<0·05).
Oral administration of spermine advances intestinal maturation in sucking piglets
Authors: Cheng Z. B. , Li D. F. , Xing J. J. , Guo X. Y. , Li Z. J.
Published: August 2009

The objective of this study was to investigate the effect of orally administered spermine at various doses on intestinal maturation in sucking piglets. Thirty-six 11-day-old sucking piglets were assigned randomly to one of six treatments to receive via a stomach tube 0, 0·1, 0·2, 0·3, 0·4, or 0·5 mmol spermine per kg live weight (LW) per day for 3 days. At day 14 of age, duodenum, jejunum and ileum were obtained for biochemical and morphological analysis. Increasing the dose of orally administered spermine increased intestinal weight (linear effect, P<0·01), mucosal weight (linear effect, P<0·05), and mucosal protein, DNA and RNA contents of the duodenum (linear effect, P≤0·01) and jejunum (linear effect, P<0·01). Elevating spermine doses also enhanced (linear effect, P≤0·02) the specific activities of maltase and sucrase but decreased (linear effect, P<0·01) lactase specific activity in the jejunum and duodenum. Furthermore, augmenting oral doses of spermine increased crypt depth and villus width but reduced villus height in the jejunum (linear effect, P<0·05) and duodenum (linear effect, P<0·01). For most measurements, the effects were observed at the oral spermine doses of 0·3 to 0·5 mmol/kg LW per day. Collectively, the results show that oral administration of optimal doses of spermine to 11-day-old sucking piglets induces precocious intestinal maturation and promotes intestinal growth.
T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm
Authors: Jorda Julien , Kajava Andrey V.
Published: August 2009

Motivation: Over the last years a number of evidences have been accumulated about high incidence of tandem repeats in proteins carrying fundamental biological functions and being related to a number of human diseases. At the same time, frequently, protein repeats are strongly degenerated during evolution and, therefore, cannot be easily identified. To solve this problem, several computer programs which were based on different algorithms have been developed. Nevertheless, our tests showed that there is still room for improvement of methods for accurate and rapid detection of tandem repeats in proteins.

Results: We developed a new program called T-REKS for ab initio identification of the tandem repeats. It is based on clustering of lengths between identical short strings by using a K-means algorithm. Benchmark of the existing programs and T-REKS on several sequence datasets is presented. Our program being linked to the Protein Repeat DataBase opens the way for large-scale analysis of protein tandem repeats. T-REKS can also be applied to the nucleotide sequences.

Availability: The algorithm has been implemented in JAVA, the program is available upon request at http://bioinfo.montp.cnrs.fr/?r=t-reks. Protein Repeat DataBase generated by using T-REKS is accessible at http://bioinfo.montp.cnrs.fr/?r=repeatDB.

Contact:  julien.jorda@crbm.cnrs.fr; andrey.kajava@crbm.cnrs.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Determination of Atlantic bluefin tuna (Thunnus thynnus) spawning time within a transport cage in the western Mediterranean
Authors: Gordoa Ana , Olivar Maria Pilar , Arevalo Raquel , Viñas Jordi , Molí Balbina , Illas Xenia
Published: August 2009

Gordoa, A., Olivar, M. P., Arevalo, R., Viñas, J., Molí, B., and Illas, X. 2009. Determination of Atlantic bluefin tuna (Thunnus thynnus) spawning time within a transport cage in the western Mediterranean. – ICES Journal of Marine Science, 66: 2205–2210. For the first time, tuna spawning in a transport cage being towed from the western Mediterranean spawning ground to a fattening facility off the coast of northeastern Spain was examined during the 2008 fishing season. Daylight and night surface plankton samples were collected using bongo nets located in front of and behind the transport cage. The results for the different time intervals revealed clear and massive nocturnal spawning from 03:00 to 05:00, when the rear bongo was completely jammed with eggs (up to 250 000–300 000 eggs per 1000 m3). Egg size and morphology were consistent with the features of Thunnus thynnus eggs, and identification was confirmed by genetic analysis. Microscopic examination showed the eggs to be in the very early developmental stages. Spawning took place every night over the entire journey. The study showed that neither captivity nor handling/environmental changes along the route inhibited T. thynnus spawning to a very precise biological clock. The study also revealed the diel temporal concurrence of T. thynnus spawning and jellyfish larvae at the sea surface.
Remarks on “Comment on: Williams et al. (2009) Australia's deep-water reserve network: implications of false homogeneity for classifying abiotic surrogates of biodiversity, ICES Journal of Marine Science, 66: 214–224” by Peter T. Harris, Andrew D. Heap, Tara J. Anderson, and Brendan Brooke
Authors: Williams Alan , Bax Nicholas J. , Kloser Rudy J.
Published: August 2009

Williams, A., Bax, N. J., and Kloser, R. J. 2009. Remarks on “Comment on: Williams et al. (2009) Australia's deep-water reserve network: implications of false homogeneity for classifying abiotic surrogates of biodiversity, ICES Journal of Marine Science, 66: 214–224” by Peter T. Harris, Andrew D. Heap, Tara J. Anderson, and Brendan Brooke. – ICES Journal of Marine Science, 66: 2086–2088. Commitment by many nations at the 2002 World Summit on Sustainable Development to complete national networks of Marine Protected Areas (MPAs) by 2012 focused attention on MPA design and implementation, especially for the deep waters that make up the majority of many national EZs. Further, there is a focus on conservation in the High Seas through the Convention on Biological Biodiversity and the FAO, e.g. for seamounts and other vulnerable benthic habitats. Any manuscript that raises basic issues on one identified area for conservation is therefore a prospectively useful addition to the international debate. The Comment by Harris et al. (2009) on a paper authored by myself and colleagues (Williams et al., 2009) is a potentially useful contribution. The authors provide data, examples, and insights into aspects of the design and planning process for Australia's SE network of reserves. Here, we address the main question of how geological descriptions can be used or modified to provide the most information on marine biodiversity patterns for use in conservation planning—in the context of the major points raised by Harris et al. (2009).
Spatial segregation among fishing vessels in a multispecies fishery
Authors: Poos J. J. , Quirijns F. J. , Rijnsdorp A. D.
Published: August 2009

Poos, J. J., Quirijns, F. J., and Rijnsdorp, A. D. 2010. Spatial segregation among fishing vessels in a multispecies fishery. – ICES Journal of Marine Science, 67: 155–164. Individual decisions of fishers on where to fish in heterogeneous environments may shape the relation between fishing effort and fishing mortality. Fishers may be viewed as individual foragers, whose decisions are aimed at optimizing short-term gain, as in ideal free distribution (IFD) theory. Although IFD assumes all foragers to be equal, they are likely to differ in competitive abilities for different prey types or target species. Here, we present an IFD-like model of a fishing fleet consisting of two components with different competitive abilities for two target species, showing that spatial segregation can result from unequal interference competition, but also in the absence of interference competition. Differences in catch efficiency between vessels for target species in combination with differences in the spatial distribution of target species can result in spatial segregation among vessel groups. The theoretical results are used to interpret the observed spatial segregation of two components within the Dutch beam trawl fleet using observations from a vessel monitoring by satellite system. However, this study cannot pinpoint which of the processes included in the theoretical model is the prime cause of the segregation within the Dutch beam trawl fleet.
Mhcpolymorphisms fail to explain the heritability of phytohaemagglutinin-induced skin swelling in a wild passerine
Authors: Bonneaud Camille , Sinsheimer Janet S. , Richard Murielle , Chastel Olivier , Sorci Gabriele
Published: August 2009

Genetic estimates of the variability of immune responses are rarely examined in natural populations because of confounding environmental effects. As a result, and because of the difficulty of pinpointing the genetic determinants of immunity, no study has to our knowledge examined the contribution of specific genes to the heritability of an immune response in wild populations. We cross-fostered nestling house sparrows to disrupt the association between genetic and environmental effects and determine the heritability of the response to a classic immunological test, the phytohaemagglutinin (PHA)-induced skin swelling. We detected significant heritability estimates of the response to PHA, of body mass and tarsus length when nestlings were 5 and 10 days old. Variation atMhcgenes, however, did not explain a significant portion of the genetic variation of nestling swelling to PHA. Our results suggest that while PHA-induced swelling is influenced by the nest of origin, the importance of additive genetic variation relative to non-additive genetic variation and the genetic factors that influence the former in wild populations still need to be identified for this trait.
Neonatal bacterial meningitis caused by Streptococcus gallolyticus subsp. pasteurianus
Authors: Onoyama Sagano , Ogata Reina , Wada Akihito , Saito Mitsumasa , Okada Kenji , Harada Tatsuo
Published: August 2009

This report describes a case of neonatal bacteraemia and meningitis due toStreptococcus gallolyticussubsp.pasteurianus. Based on the identification kit results, this species may have been reported asStreptococcus bovisorS. bovisbiotype II. The accurate identification of this organism is mandatory for evaluating the aetiology of neonatal meningitis.
Reduced susceptibility to carbapenems in Klebsiella pneumoniae clinical isolates associated with plasmid-mediated β-lactamase production and OmpK36 porin deficiency
Authors: Wang Xuan Ding , Cai Jia Chang , Zhou Hong Wei , Zhang Rong , Chen Gong-Xiang
Published: August 2009

Two carbapenem-non-susceptibleKlebsiella pneumoniaeisolates, Z2554 and Z2110, were collected from a hospital in China and analysed by PFGE.K. pneumoniaeZ2554 and Z2110 were genetically unrelated and showed resistance to ertapenem, and reduced susceptibility to imipenem and meropenem. Analysis of theirβ-lactamases indicated thatK. pneumoniaeZ2554 produced TEM-1 and CTX-M-14β-lactamases, whilst Z2110 produced a plasmid-mediated AmpCβ-lactamase, DHA-1, in addition to TEM-1 and CTX-M-14. SDS-PAGE analysis of the outer-membrane proteins (OMPs) revealed that both isolates lacked an OMP of ∼39 kDa (OmpK36), whilst Z2110 had an additional protein with an approximate molecular mass of 26 kDa. Analysis of the OMP-encoding genes demonstrated that theompK35sequence ofK. pneumoniaeZ2554 and Z2110 contained a number of silent mutations. InompK36, several insertions and deletions of short DNA fragments (1–6 bp) were detected in both isolates. The N-terminal sequence of the ∼26 kDa protein band identified in Z2110 had no similarity to the sequence of OmpK36. Instead, it shared high similarity with hypothetical protein KPN_03267 originating fromK. pneumoniae subsp.pneumoniaeMGH 78578. It was concluded thatβ-lactamase production combined with OmpK36 deficiency results in ertapenem resistance, and reduced imipenem and meropenem susceptibility, inK. pneumoniaeZ2554 and Z2110. OmpK36 may play an important role in the resistance or reduced susceptibility to carbapenems inK. pneumoniaeproducing AmpC, extended-spectrumβ-lactamase or broad-spectrumβ-lactamase.
In vivo activity of anprocide alone, and in vitro activity in combination with conventional antibiotics against Staphylococcus aureus and Staphylococcus epidermidis biofilms
Authors: Pettit Robin K. , Weber Christine A. , Lawrence Stacey B. , Pettit George R. , Kean Melissa J. , Cage Gary D.
Published: August 2009

The alarming spread of multiple drug resistance inStaphylococcus aureus, combined with the frequent occurrence ofS. aureusandStaphylococcus epidermidisin biofilm-type infections, indicates a growing need for new therapies. The experimental steroidal amide anprocide [3β-acetoxy-17β-(l-prolyl)amino-5α-androstane] significantly reduced c.f.u. ml−1per suture (P<0.0001) in a murine model of topicalS. aureusinfection. In chequerboard assays with planktonic-grownS. aureusandS. epidermidis, anprocide was synergistic with bacitracin, oxacillin, clindamycin or ceftriaxone. Anprocide was also synergistic in combination with bacitracin or oxacillin against some isolates of biofilm-grownS. aureusandS. epidermidis.
Detection of virulence-associated and regulatory protein genes in association with phage typing of human Vibrio cholerae from several geographical regions of the world
Authors: Bhowmick Tushar Suvra , Das Mayukh , Ruppitsch Werner , Stoeger Anna , Pietzka Ariane Tatjana , Allerberger Franz , Rodrigues D. P. , Sarkar B. L.
Published: August 2009

Vibrio cholerae O1, O139 and occasionally non-O1/non-O139 serogroups are most often responsible for epidemic and pandemic cholera. This study used genotypic patterns of PCR-based detection of virulence-associated and regulatory protein genes, along with phage typing, to characterize 86 V. cholerae strains. Thirty-eight of 53 O1 biotype El Tor strains harboured both tcpA classical and tcpA El Tor genes, and three El Tor strains lacked the V. cholerae O1-specific gene (Vc-O1); three O139 strains contained both Vc-O1 and Vc-O139 genes and seven out of ten non-O1/non-O139 strains possessed the Vc-O1 gene. The latter strains all harboured the virulence-associated genes ctxA, zot, ace, RS1, hlyA, ompU, rtxA and sxt. Two phage types, T27 and T25, were predominant in strains from different geographical regions of India, whereas more variation in phage susceptibility was observed for tetracycline-resistant strains from Kolkata. These results suggest that the pattern and distribution of virulence genes and phage types of V. cholerae are equally useful and discriminatory in tracing the origin of newly emerging strains.
Distribution of the leptospiral immunoglobulin-like (lig) genes in pathogenic Leptospira species and application of ligB to typing leptospiral isolates
Authors: Cerqueira Gustavo M. , McBride Alan J. A. , Picardeau Mathieu , Ribeiro Samuel G. , Moreira Ângela N. , Morel Viviane , Reis Mitermayer G. , Ko Albert I. , Dellagostin Odir A.
Published: August 2009

The family of leptospiral immunoglobulin-like (lig) genes comprises ligA, ligB and ligC. This study used PCR to demonstrate the presence of lig genes among serovars from a collection of leptospiral strains and clinical isolates. Whilst ligA and ligC appeared to be present in a limited number of pathogenic serovars, the ligB gene was distributed ubiquitously among all pathogenic strains. None of the lig genes were detected among intermediate or saprophytic Leptospira species. It was also shown that, similar to the previously characterized secY gene, a short specific PCR fragment of ligB could be used to correctly identify pathogenic Leptospira species. These findings demonstrate that ligB is widely present among pathogenic strains and may be useful for their reliable identification and classification.
Sphingomonas paucimobilis bacteraemia and septic arthritis in a diabetic patient presenting with septic pulmonary emboli
Authors: Kuo I-Ching , Lu Po-Liang , Lin Wei-Ru , Lin Chun-Yu , Chang Yu-Wei , Chen Tun-Chieh , Chen Yen-Hsu
Published: August 2009

Sphingomonas paucimobilis, a yellow-pigmented, aerobic, glucose non-fermenting, Gram-negative bacillus, is a rare cause of human infection normally associated with immunocompromised hosts. We report a case of bacteraemia and septic arthritis in a 47-year-old diabetic man who presented with septic pulmonary emboli due toS. paucimobilis. The patient had an initial presentation of fever, right knee pain, coughing, dyspnoea and chest pain. The infection was treated successfully by surgical debridement combined with meropenem plus ciprofloxacin, based on the patient's antibiotic susceptibility profile. To our knowledge, this is the first case report for septic pulmonary emboli having arisen from anS. paucimobilisinfection.
Distribution of meticillin-resistant Staphylococcus aureus spa types isolated from health-care workers and patients in a Scottish university teaching hospital
Authors: Soliman Reham S. , Phillips Gabby , Whitty Patrick , Edwards David H.
Published: August 2009

Our study was aimed at comparing the meticillin-resistantStaphylococcus aureus(MRSA) strains isolated from an anonymous group of health-care workers (HCWs) with those obtained from patient samples during a 3-month time interval. We employedspatyping and virulence gene profiling to characterize the MRSA strains. Our data revealed that a total of 14 discretespatypes were circulating in both patients and HCWs. The t032spatype, characteristic of EMRSA15 and the Barnim EMRSA ST 22 clones, accounted for over 70 % of isolates, and was equally distributed between patients and HCW groups. In addition, a number of epidemic and sporadic strains were identified, which highlighted the diversity ofspatypes that can be found within a health-care setting. Virulence profiling for the carriage of 7 genes by the 14 differentspatypes demonstrated that 10 types carried thefnbA,cna,sdrE,hlgandicavirulence factors. We concluded that there was no significant difference between the MRSA strains found circulating in the patients and the HCWs, and noted that the dominantspatypes carried an identical set of virulence genes that included the key adhesinsfnbA,cnaandsdrE.
Bacterial colonization and granulocyte activation in chronic maxillary sinusitis in asthmatics and non-asthmatics
Authors: Zurak Kreso , Vagić Davor , Drvis Petar , Prohaska Potocnik Carmen , Dzidic Senka , Kalogjera Livije
Published: August 2009

The impact of bacterial colonization on the severity and pattern of chronic inflammation in rhinosinusitis is not clear. In this study, it was hypothesized that bacterial colonization of the sinus mucosa would have a greater impact on inflammatory response modulation in asthmatic patients than in non-asthmatic patients with chronic rhinosinusitis. In order to test this hypothesis, granulocyte activation was measured and related to bacteria identified in the sinus lavage. Lavages from the maxillary sinuses of 21 asthmatic and 19 non-asthmatic patients with chronic rhinosinusitis (CRS) were microbiologically examined for aerobic and anaerobic growth. Eosinophil cationic protein (ECP), an eosinophil activation marker, and myeloperoxidase (MPO), a neutrophil activation marker, were measured in the sinus lavages. Bacteria were recovered in 20/32 samples from the asthmatics and in 21/33 samples from the non-asthmatics. Gram-positive aerobes and anaerobes were slightly more common than Gram-negative bacteria. A different bacterial profile was found when comparing Gram-negatives between the groups. Concentrations of MPO were significantly higher in samples with bacterial recovery from asthmatic patients, compared to sterile samples of both groups. Concentrations of ECP in the samples from asthmatic patients were significantly higher than in the controls, with no significant difference related to bacterial colonization. Bacterial colonization in chronically inflamed sinuses may have an impact on neutrophil granulocyte activation in patients with bronchial asthma, which was not confirmed for patients with CRS without asthma.
Evaluation of real-time nucleic acid sequence-based amplification for detection of Chikungunya virus in clinical samples
Authors: Telles J.-N. , Le Roux K. , Grivard P. , Vernet G. , Michault A.
Published: August 2009

The Chikungunya virus (CHIKV) is a member of the genus Alphavirus that is transmitted to humans by Aedes mosquitoes. In 2005 and 2006, the Indian Ocean island of La Réunion was hit with an unprecedented CHIKV fever outbreak that infected 300 000 people. In the present study, we describe the evaluation of real-time nucleic acid sequence-based amplification (RT-NASBA) for the detection of CHIKV in clinical samples. A co-extracted and co-amplified chimerical CHIKV RNA sequence was used as an internal control to eliminate false-negative results. The detection threshold of the assay was determined from quantified CHIKV-positive plasma, and estimated to be 200 copies per NASBA reaction. The specificity of the assay was determined using blast analyses and non-cross-reactivity using an O'nyong-nyong virus culture and 250 CHIKV RT-PCR-negative plasma samples. A 100 % specificity was found and no invalid result was obtained, showing the good quality of the nucleic acid extraction. The assay was then evaluated using 252 CHIKV-positive RT-PCR plasma samples. The samples were all tested positive, including those with low viral load. This evaluation showed that the RT-NASBA is a rapid (5 h from sample nucleic acid extraction to detection), sensitive, specific and reliable method for the routine diagnosis of CHIKV in clinical samples.
Assessment of East Asian-type cagA-positive Helicobacter pylori using stool specimens from asymptomatic healthy Japanese individuals
Authors: Hirai Itaru , Sasaki Tadahiro , Kimoto Ai , Fujimoto Saori , Moriyama Toshiki , Yamamoto Yoshimasa
Published: August 2009

Recent investigations have suggested that CagA, a virulence factor of Helicobacter pylori and known to have multiple genotypes, plays a critical role in the development of stomach cancer. However, the prevalence of cagA-positive H. pylori strains and the cagA genotypes have not been well studied in healthy individuals because of the difficulty in collecting gastric specimens. In the present study, we assessed the prevalence of infection with H. pylori, particularly the strains with the East Asian cagA genotype (which is more potent in causing gastric diseases), among healthy asymptomatic Japanese individuals by a noninvasive method using stool specimens. The H. pylori antigen was detected in 40.3 % of healthy asymptomatic adult individuals (n=186) enrolled in the study. For the detection and genotyping of the cagA gene, DNA was extracted from the stool specimens of these individuals and analysed by PCR. We detected the East Asian cagA genotype in the DNA samples of a significantly high number (63.1 %) of healthy asymptomatic Japanese individuals. These results indicate that a significant number of asymptomatic healthy Japanese individuals were infected with highly virulent H. pylori.
Quest for a broad-range vaccine against Neisseria meningitidis serogroup B: implications of genetic variations of the surface-exposed proteins
Authors: de Filippis Ivano
Published: August 2009

Despite the development of new vaccine formulations using new biotechnology resources to combat emerging and re-emerging diseases, serogroup B meningococcal disease is still a worldwide burden, accounting for many deaths and disabilities every year. The successful approach of coupling a polysaccharide (PS) with a carrier protein in order to increase long-lasting immunity could not be exploited againstNeisseria meningitidisB because of the limitations of using the capsular PS of serogroup B meningococci. Tailor-made vaccines based on exposed proteins were shown to be a promising approach to overcome these flaws. However, the continuous adaptation of surface meningococcal structures to the external environment has led to genetic shifts of potential vaccine-target epitopes, hampering the quest for a broad-range vaccine that could be used against all serogroups, especially against serogroup B.
Characterization of meticillin-resistant Staphylococcus aureus isolates from hospitals in KwaZulu-Natal province, Republic of South Africa
Authors: Shittu Adebayo , Nübel Ulrich , Udo Edet , Lin Johnson , Gaogakwe Sedio
Published: August 2009

Epidemiological data based on phenotypic and molecular characterization of meticillin-resistantStaphylococcus aureus(MRSA) in sub-Saharan Africa are limited. This investigation studied 61 MRSA isolates obtained from 13 health-care institutions in KwaZulu-Natal (KZN) province, South Africa, from March 2001 to August 2003. More than 80 % of the isolates were resistant to at least four classes of antibiotics and six isolates were resistant to the aminoglycoside, macrolide-lincosamide and tetracycline groups of antibiotics, heavy metals and nucleic acid-binding compounds. PFGE ofSmaI-digested genomic DNA revealed seven types, designated A–G. Type A was the main pulsotype (62.3 %) and was identified in 11 of the 13 health-care institutions, suggesting that it represented a major clone in health-care institutions in KZN province. Analysis of representative members of the three major pulsotypes byspa, multilocus sequence typing and SCCmectyping revealed the types t064-ST1173-SCCmecIV and t064-ST1338-SCCmecIV (PFGE type A, single-locus and double-locus variants of ST8), t037-ST239-SCCmecIII (PFGE type F) and t045-ST5-SCCmecIII (PFGE type G). The combination of various typing methods provided useful information on the geographical dissemination of MRSA clones in health-care institutions in KZN province. The observation of major clones circulating in health-care facilities in KZN province indicates that adequate infection control measures are urgently needed.
Human leptospirosis cases and the prevalence of rats harbouring Leptospira interrogans in urban areas of Tokyo, Japan
Authors: Koizumi Nobuo , Muto Maki , Tanikawa Tsutomu , Mizutani Hiroshi , Sohmura Yoshiko , Hayashi Eiji , Akao Nobuaki , Hoshino Mayu , Kawabata Hiroki , Watanabe Haruo
Published: August 2009

Thirteen patients with leptospirosis were identified, as confirmed by laboratory analysis during the last 5 years in our laboratory, who came from urban areas of Tokyo, Japan. All of the patients came into contact with rats before the onset of illness. Seventeen per cent of Norway rats captured in the inner cities of Tokyo carried leptospires in their kidneys. Most of these rat isolates wereLeptospira interrogansserovar Copenhageni/Icterohaemorrhagiae. Antibodies against these serovars and their DNA were detected in the patients. This suggests that rats are important reservoirs of leptospirosis, and that rat-borne leptospires occur in urban areas of Tokyo.
Proteolysis of a Negative Regulator of Innate Immunity Is Dependent on Resistance Genes in Tomato and Nicotiana benthamiana and Induced by Multiple Bacterial Effectors
Authors: Luo Yao , Caldwell Katherine S. , Wroblewski Tadeusz , Wright Michael E. , Michelmore Richard W.
Published: August 2009

RPM1-interacting protein 4 (RIN4), a negative regulator of the basal defense response in plants, is targeted by multiple bacterial virulence effectors. We show that RIN4 degradation is induced by the effector AvrPto from Pseudomonas syringae and that this degradation in Solanaceous plants is dependent on the resistance protein, Pto, a protein kinase, and Prf, a nucleotide binding site–leucine-rich repeat protein. Our data demonstrate overlap between two of the best-characterized pathways for recognition of pathogen virulence effectors in plants. RIN4 interacts with multiple plant signaling components and bacterial effectors in yeast and in planta. AvrPto induces an endogenous proteolytic activity in both tomato (Solanum lycopersicum) and Nicotiana benthamiana that degrades RIN4 and requires the consensus site cleaved by the protease effector AvrRpt2. The interaction between AvrPto and Pto, but not the kinase activity of Pto, is required for proteolysis of RIN4. Analysis of many of the effectors comprising the secretome of P. syringae pv tomato DC3000 led to the identification of two additional sequence-unrelated effectors that can also induce degradation of RIN4. Therefore, multiple bacterial effectors besides AvrRpt2 elicit proteolysis of RIN4 in planta.
The Mediator Complex Subunit PFT1 Is a Key Regulator of Jasmonate-Dependent Defense inArabidopsis
Authors: Kidd Brendan N. , Edgar Cameron I. , Kumar Krish K. , Aitken Elizabeth A. , Schenk Peer M. , Manners John M. , Kazan Kemal
Published: August 2009

Jasmonate signaling plays an important role in both plant defense and development. Here, we have identified a subunit of the Mediator complex as a regulator of the jasmonate signaling pathway in Arabidopsis thaliana. The Mediator complex is a conserved multiprotein complex that acts as a universal adaptor between transcription factors and the RNA polymerase II transcriptional machinery. We report that the PHYTOCHROME AND FLOWERING TIME1 (PFT1) gene, which encodes the MEDIATOR25 subunit of Mediator, is required for jasmonate-dependent defense gene expression and resistance to leaf-infecting necrotrophic fungal pathogens. Conversely, PFT1 appears to confer susceptibility to Fusarium oxysporum, a root-infecting hemibiotrophic fungal pathogen known to hijack jasmonate responses for disease development. Consistent with this, jasmonate gene expression was suppressed in the pft1 mutant during infection with F. oxysporum. In addition, a wheat (Triticum aestivum) homolog of PFT1 complemented the defense and the developmental phenotypes of the pft1 mutant, suggesting that the jasmonate signaling functions of PFT1 may be conserved in higher plants. Overall, our results identify an important control point in the regulation of the jasmonate signaling pathway within the transcriptional machinery.
Covalent bonded Gag multimers in human immunodeficiency virus type‐1 particles
Authors: Kitagawa Yoshinori , Maeda‐Sato Masae , Tanaka Keiko , Tobiume Minoru , Sawa Hirofumi , Hasegawa Hideki , Kojima Asato , Hall William W. , Kurata Takeshi , Sata Tetsutaro , Takahashi Hidehiro
Published: August 2009

The oligomerization of HIV‐1 Gag and Gag‐Pol proteins, which are assembled at the plasma membrane, leads to viral budding. The budding generally places the viral components under non‐reducing conditions. Here the effects of non‐reducing conditions on Gag structures and viral RNA protection were examined. Using different reducing conditions and SDS‐PAGE, it was shown that oligomerized Gag possesses intermolecular covalent bonds under non‐reducing conditions. In addition, it was demonstrated that the mature viral core contains a large amount of covalent bonded Gag multimers, as does the immature core. Viral genomic RNA becomes sensitive to ribonuclease in reducing conditions. These results suggest that, under non‐reducing conditions, covalent bonded Gag multimers are formed within the viral particles and play a role in protection of the viral genome.
Characterization of integrons and antimicrobial resistance genes in clinical isolates of Gram‐negative bacteria from Palestinian hospitals
Authors: Hussein Amjad I. A. , Ahmed Ashraf M. , Sato Maiko , Shimamoto Tadashi
Published: August 2009

Sixty Gram‐negative bacterial isolates were collected from Palestinian hospitals in 2006. Thirty‐two (53.3%) isolates showed multidrug resistance phenotypes. PCR and DNA sequencing were used to characterize integrons and antimicrobial resistance genes. PCR screening showed that 19 (31.7%) and five (8.3%) isolates were positive for class 1 and class 2 integrons, respectively. DNA‐sequencing results for the captured antimicrobial resistance gene cassettes within class 1 integrons identified the following genes: dihydrofolate reductases, dfrA1, dfrA5, dfrA7, dfrA12, dfrA17 and dfrA25; aminoglycoside adenyltransferases, aadA1, aadA2, aadA5, aadA12 and aadB; aminoglycoside acetyltransferase, aac(6′)‐Ib; and chloramphenicol resistance gene, cmlA1. ESBL were identified in 25 (41.7%) isolates. The identified ESBL were blaCTX‐M‐15, blaCTX‐M‐56, blaOXA‐1, blaSHV‐1, blaSHV‐12, blaSHV‐32 and blaTEM‐1 genes. Moreover, we characterized the plasmid‐mediated quinolone resistance genes, aac(6′)‐Ib‐cr and qnrB2, which were detected in seven (11.7%) and two (3.3%) isolates, respectively. In this study various types of antibiotic resistance genes have been identified in Gram‐negative bacteria from Palestinian hospitals, many of which are reported in the Middle East area for the first time.
Review article: the modern management of portal vein thrombosis
Authors: CHAWLA Y. , DUSEJA A. , DHIMAN R. K.
Published: August 2009

Background  Portal vein thrombosis (PVT) is an important cause of portal hypertension. It may occur as such with or without associated cirrhosis and hepatocellular carcinoma. Information on its management is scanty.

Aim  To provide an update on the modern management of portal vein thrombosis. Information on portal vein thrombosis in patients with and without cirrhosis and hepatocellular carcinoma is also updated.

Methods  A pubmed search was performed to identify the literature using search items portal vein thrombosis‐aetiology and treatment and portal vein thrombosis in cirrhosis and hepatocellular carcinoma.

Results  Portal vein thrombosis occurs because of local inflammatory conditions in the abdomen and prothrombotic factors. Acute portal vein thrombosis is usually symptomatic when associated with cirrhosis and/or superior mesenteric vein thrombosis. Anticoagulation should be given for 3–6 months if detected early. If prothrombotic factors are identified, anticoagulation should be given lifelong. Chronic portal vein thrombosis usually presents with well tolerated upper gastrointestinal bleed. It is diagnosed by imaging, which demonstrates a portal cavernoma in place of a portal vein. Anticoagulation does not have a definite role, but bleeds can be treated with endotherapy or shunt surgery. Rarely liver transplantation may be considered.

Conclusion  Role of anticoagulation in chronic portal vein thrombosis needs to be further studied.
Clinical trial: ulcerative colitis maintenance treatment with 5‐ASA: a 1‐year, randomized multicentre study comparing MMX® with Asacol®
Authors: PRANTERA C. , KOHN A. , CAMPIERI M. , CAPRILLI R. , COTTONE M. , PALLONE F. , SAVARINO V. , STURNIOLO G. C. , VECCHI M. , ARDIA A. , BELLINVIA S.
Published: August 2009

Background  5‐ASA‐MMX® (1.2 g/tablet) is a 5‐aminosalicylic acid formulation, designed for once‐daily dosing in the treatment of ulcerative colitis.

Aim  To evaluate the efficacy and safety of 5‐ASA‐MMX (2.4 g/day, once daily), compared with Asacol® (2.4 g/day, twice daily) in the maintenance of left‐sided UC, through a double‐blind, double‐dummy, parallel‐group, randomized, comparator study.

Methods  In all, 331 patients with UC were randomized to receive either 5‐ASA‐MMX 2.4 g/day, once daily, or Asacol 2.4 g/day, twice daily, for 12 months. All patients were in remission for ≥1 month prior to the trial, with ≥1 documented relapse in the previous year. The co‐primary endpoints of this study were the proportion of patients in clinical, and clinical and endoscopic remission following 12 months’ treatment.

Results  In the intent‐to‐treat population, excluding those with major protocol deviations, 68.0 and 65.9% patients in the 5‐ASA‐MMX and Asacol groups, respectively, were in clinical remission (P = 0.69), and 60.9 and 61.7% of patients, respectively, were in clinical and endoscopic remission (P = 0.89). Diary card data revealed statistically significant treatment differences favouring 5‐ASA‐MMX. Both treatments were similarly tolerated.

Conclusions  Once‐daily 5‐ASA‐MMX is similarly effective with a comparable safety profile to Asacol administered twice daily, for the maintenance treatment of ulcerative colitis.
Effects of bisacodyl on ascending colon emptying and overall colonic transit in healthy volunteers
Authors: MANABE N. , CREMONINI F. , CAMILLERI M. , SANDBORN W. J. , BURTON D. D.
Published: August 2009

Background The mechanism of action of bisacodyl in the unprepared human colon remains unclear.

Aim To evaluate the effect of oral bisacodyl on the overall and regional colonic transit in humans.

Methods In a double‐blind, randomized, placebo‐controlled study of 25 healthy participants, effects of oral bisacodyl (5 mg p.o. per day) and placebo on colonic transit were compared. A validated scintigraphy method was used to measure colonic transit. The primary transit endpoints, ascending colon emptyingt1/2and geometric centre of colon isotope at 24 h (overall transit), were compared (Wilcoxon rank sum test).

Results There were significant treatment effects on ascending colont1/2, with the bisacodyl group demonstrating accelerated emptying [median 6.5 h, interquartile range 5.0–8.0 h] relative to the placebo group [11.0 h (7.0–17.1);P = 0.03]. Numerical differences in colonic geometric centre 24 h [bisacodyl median 3.0 (2.2–3.8), placebo 4.0 (3.1–4.6)] were not significant (P = 0.19). There were no significant differences observed in geometric centre 4 h.

Conclusion Oral 5 mg bisacodyl accelerates ascending colon in the unprepared colon in healthy adults; this action may contribute to the drug’s efficacy in constipation.