bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of puerperal diseases in sows on their fertility and health up to next farrowing
Authors: Hoy S.
Published: August 2009

Investigations utilizing a total number of 3998 farrowings from 1558 sows on two farms have shown a frequency of puerperal diseases (periparturient hypogalactia syndrome=PHS) of 32·7% and 27·0% respectively with significant differences between gilts and sows. Sows without PHS after farrowing (farm A) had a lower frequency of animals without oestrus after weaning of the piglets (0·3 V. 1·1%), a lower rate of late onset of oestrus (3·4% V. 5·9%,P<0·05), fewer sows had abortions (0·9 V. 2·3%,P<0·05) and a lower mortality rate (1·2 V. 4·1%,P<0·05) compared with sows which contracted puerperal diseases. The return rate was significantly lower in sows without PHS (12·4%, 16·1% in herds A and B) when compared with sows with puerperal diseases (15·8%, 21·7%,P<0·05). Also, the litter size of live born piglets was lower in sows with PHS when compared with healthy sows (farm A: 10·42 V. 10·66,P>0·05; farm B: 10·44 V. 10·80,P<0·05)
The effect of hot season and nutrition on the oxidative status and metabolic profile in dairy goats during mid lactation
Authors: Di Trana A. , Celi P. , Claps S. , Fedele V. , Rubino R.
Published: August 2009

The aim of this study was to evaluate the effects of the hot season and nutrition on the oxidative status and metabolic profile of lactating goats during mid lactation. Twenty-four Red Syrian goats were allocated into three groups that were offered the following diets: natural pasture (P), pasture+500 g/h per day of concentrate (PC) and hay plus 500 g/h per day of concentrate (HC). Blood samples were taken in spring (85±7 days in milk (DIM)) and summer (120±7 DIM) and assayed for reactive oxygen metabolites (ROMs), α-tocopherol, glucose, triglycerides, cholesterol, non-esterified fatty acids, total protein, albumin and globulin concentrations and glutathione peroxidase (GHS-Px) and superoxide dismutase (SOD) activities. Milk yield and milk composition were also measured. SOD, GSH-Px and ROMs levels increased during summer when temperature humidity index values were high. The increase in ROMs in the PC and HC groups could be ascribed to the improved nutritional regime and to their higher production level. The markers of the oxidative status and of the metabolic profile measured in this study indicate that goats may have experienced moderate oxidative stress. It seems that, seasonal rather than nutritional factors have a more pronounced effect on oxidative status markers. Concentrate supplementation sustained milk yield and may represent a useful means to extend the lactation period in dairy goats during late spring and summer.
Growth, carcass characteristics and meat quality of rabbits given maize ears or maize plant
Authors: Pla M. , Martínez M. , Cervera C.
Published: August 2009

Three hundred young rabbits were divided into three groups at weaning and given ad libitum a control diet (C), or an experimental diet in which 0·20 of control diet was substituted by maize ear (E) or by whole maize plant (P) in order to examine their effects on fattening rabbits performance, carcass characteristics and meat quality. No significant differences were found in live-weight gain (45 g/day) or in food intake between diets but food conversion ratio was higher in the P group (2·4 g dry matter (DM) per g gain) than in E group (2·2 g DM per g gain). The rate of mortality was similar in the three groups. No differences between groups on live weight (2152 g) or in the digestive tract weight (437 g) were found and the dressing yield was similar in the three groups. At constant carcass weight, the carcasses of rabbits of the P group had lesser lumbar circumference and higher length to circumference ratio (P<0·0001) than of the C or E groups. No differences were found in the weights of liver or thoracic viscera, but kidneys of rabbits of P group were lighter than of the C or E groups. No differences between groups were found in the weights of scapular fat, perirenal fat, forelegs or thoracic cage, but the loin of rabbits of P group was heavier (291 v. 286 g) than in the other groups. Meat of rabbits P had higher L* and b* parameters of colour and higher water-holding capacity (P=0·003) but the meat of rabbits of the control group had less lipids (31 v. 36 g/kg meat) and more moisture (739 v. 735 g/kg meat) than of the experimental groups. The proportion of protein was higher in E group than in P group. Intra and intermuscular fat of hind leg meat from rabbits ‘maize’ substituted was more monounsaturated than control rabbits (34·2 v. 32·5 g·100 g lipids) and had lesser saturated: monounsaturated ratio (1·2 v. 1·3) indicating a more desirable meat from a nutritional point of view, but had less n-3 fatty acid content. Loin meat of the rabbits given E and P diets seems more tender than one fed conventionally (10·4 v. 11·4 kg) and meat of the rabbits ‘whole maize plant’ had more grass flavour (P=0·009) which is a positive factor for acceptability of consumers.
Soya-bean agglutinin induced both direct and cholecystokinin-mediated pancreatic enzyme synthesis in rats
Authors: Zang J. J. , Li D. F. , Wang J. R. , Tang S. S. , Li X. L. , Guo P. F.
Published: August 2009

This study was conducted to examine the relationship between soya-bean agglutinin and cholecystokinin in stimulating pancreatic enzyme synthesis in rats. In experiment 1, 30 rats were given daily gastric infusions of 0, 3·5, 7·0, 10·5, or 14·0 mg of soya-bean agglutinin (no.=6) for 14 days. Compared with the control group, soya-bean agglutinin reduced weight gains, enhanced absolute and relative dry pancreatic weights, elevated serum cholecystokinin levels, and stimulated cholecystokinin mRNA expression in the intestine (P<0·001). Pancreatic nucleic acid composition and the pancreatic activities of the enzymes amylase, trypsin and chymotrypsin all increased in response to increasing levels of soya-bean agglutinin (P<0·001). In experiment 2, duodenal cells obtained from two rats were incubated at 37°C with either saline, 100 μg/ml soya-bean agglutinin, or a mixture of 100 μg/ml soya-bean agglutinin and 10 mmol/m of the L-type, calcium channel antagonist verapamil. Soya-bean agglutinin stimulated cholecystokinin mRNA expression and cholecystokinin release from small intestinal mucosal cells, and the effect was attenuated by verapamil. In experiment 3, pancreatic acinar cells, obtained from three rats, were incubated at 37 °C with either saline, or cholecystokinin (100 fmol/ml) and soya-bean agglutinin (1000 fmol/ml), either alone or in combination. Amylase, trypsin, and chymotrypsin activities from both culture media and acini cells were stimulated by both the soya-bean agglutinin and the cholecystokinin treatments. Enzyme activities, when the two factors were incubated in combination, were intermediate to those obtained when the factors were incubated alone. This suggesting that soya-bean agglutinin may depress the action of cholecystokinin on pancreatic enzymatic activities. In summary, soya-bean agglutinin appears to stimulate pancreatic enzyme synthesis both directly and also through a cholecystokinin-mediated pathway.
Effects of nutrition on hormone profiles and patterns of deiodinase activity in the skin and associated patterns of hair follicle activity and moult in cashmere goats
Authors: Rhind S. M. , Kyle C. E. , Riach D. J. , Duff E. I.
Published: August 2009

The effects of nutrition on patterns of live-weight change, hair follicle activity, moult, hormone profiles and associated activities of monodeiodinase enzyme types II and III (MDII and MDIII) in cashmere goats were investigated. From 1 week before the winter solstice (mid December), one group of 15 animals was given a ration designed to provide 2·0 × live weight maintenance requirements (high; H) while a second, similar, group was given 0·8 × live weight maintenance requirements (low; L). After approximately 3 months, L animals had significantly lower mean live weights (P<0·01) than H animals. This was associated with lower (P<0·05) overall mean hair follicle activity in L than H animals during the March to May period and a lower overall mean moult score during March and April in L animals (P<0·01) but a similar mean date of moult onset. Mean concentrations of all of the hormones measured exhibited significant changes (P<0·01) with date of sampling. Overall mean concentrations of insulin, tri-iodothyronine and thyroxine did not differ with treatment but, compared with L animals, H animals exhibited higher mean concentrations of prolactin in April and May (P<0·05) and of insulin-like growth factor-1 in December and January (P<0·001). Rates of activity of MDII and MDIII in skin differed with date (P<0·001) but were not significantly affected by nutritional treatment. The MDIII/MDII ratio differed (P=0·05) with month but was significantly higher (P<0·05) in L than H animals in January, only. It is concluded that the reduction in hair follicle activity and the slower onset of moult associated with reduced nutrition were unlikely to be controlled, directly, by differences in activities of MDII or MDIII in skin tissue.
Effects of monensin and yeast supplementation on blood acid-base balance in finishing feedlot steers fed a high-grain, high-protein diet
Authors: Castillo C. , Hernández J. , Méndez J. , García-Partida P. , Pereira V. , Vázquez P. , Alonso M. López , Benedito J. L.
Published: August 2009

The aim of this study was to evaluate the effects of two dietary supplements (monensin and a live yeast culture) on acid-base balance in steers maintained in a commercial feedlot system, considering effects over the finishing productive cycle. Steers (no. =42) were allotted randomly to one of the three study groups: (1) control group (no supplementation, C), (2) monensin supplementation (MON), and (3) live Saccharomyces cerevisiae strain 47 supplementation (SACC). Venous blood samples were collected for the measurement of acid-base parameters and l-lactate. Production parameters were also used as a complementary tool for understanding the internal changes associated with supplementation. During the finishing period, MON steers tended to gain more efficiently than C and SACC steers. In the C group, the finishing-period diet caused a progressive decline in blood bases, in line with the high-grain diet consumption. In contrast, supplemented animals did not show this trend, although lower HCO3− and base excess values were registered in SACC steers than in MON, indicating that ionophore supplementation is less effective for reducing blood base consumption than yeast supplementation. In our study, the lack of the expected response to yeast supplementation may be attributable to the high crude protein content of the ration, a common feature of commercial feedlot industries.
Holo-analysis of the efficacy of Bio-Mos® in pig nutrition
Authors: Rosen G. D.
Published: August 2009

This exploratory holo-analysis of the efficacy of Bio-Mos®, (BM), an outer cell wall derivative of a strain ofSaccharomyces cerevisiae, is part of an empirical modelling research programme comparing the efficacies of potential replacements for veterinary prescription-free pronutrient antibiotics in pig production. The data resource was mined from 128 saccharide publications of which 31/97 on BM (1997 to 2003) provided 69 negatively controlled start-to-finish tests from 10 countries (USA 71%) using 3778 pigs(30·5 per treatment). Respective food intake, live-weight gain and food conversion responses of 0·0075 kg/day (0·99%), 0·0145 kg/day (3·58%) and −0·0526 (3·07%) have coefficients of variation of 511, 163 and 229% and beneficial gain and conversion frequencies of 73 and 68%, 54% jointly. Holo-analytical multiple regression models of BM food intake, live-weight gain and food conversion effects using conventional and less stringent probabilities contain significant independent variables for negative control performances, dosage, discontinuous dosage, test duration, year of test, non-USA test, male, grower-finisher, slatted floor, processed food, antibacterial foods, animal protein food, main vegetable protein not soya bean, added oil/fat food and factorial data, which account for 11 to 68% of variations in response. The models quantify differences in research and praxis and indicate areas for future modelling research on BM dose-response relations, effects of ration ingredient and nutrient contents, other saccharide efficacy comparisons, including lactose, and BM comparisons and interactions with other proposed antibiotic replacements.
Institutionalizing Water Governance in England and Wales: Potential and Limitations
Authors: Wong Sam
Published: August 2009

This paper evaluates the neo-institutional perspective in conceptualizing the public-private partnership in water provision in England and Wales. It questions the simplistic assumptions that effective water governance lies in getting institutions, incentives, and authority right. Drawing upon Mary Douglas's social embeddedness of institutions, this paper demonstrates that use of water is both individually-pursued and socially-shaped. This paper calls for a reorganization of the institutional arrangements to tackle power asymmetries between the regulators, water companies, and the public. It suggests that the design of the regulatory structures needs to cohere with the cultural meaning of water.
Testing the hypothesis of tissue selectivity: the intersection–union test and a Bayesian approach
Authors: Van Deun K. , Hoijtink H. , Thorrez L. , Van Lommel L. , Schuit F. , Van Mechelen I.
Published: August 2009

Motivation: Finding genes that are preferentially expressed in a particular tissue or condition is a problem that cannot be solved by standard statistical testing procedures. A relatively unknown procedure that can be used is the intersection–union test (IUT). However, two disadvantages of the IUT are that it is conservative and it conveys only the information of the least differing target tissue–other tissue pair.

Results: We propose a Bayesian procedure that quantifies how much evidence there is in the overall expression profile for selective over-expression. In a small simulation study, it is shown that the proposed method outperforms the IUT when it comes to finding selectively expressed genes. An application to publicly available data consisting of 22 tissues shows that the Bayesian method indeed selects genes with functions that reflect the specific tissue functions. The proposed method can also be used to find genes that are underexpressed in a particular tissue.

Availability: Both MATLAB and R code that implement the IUT and the Bayesian procedure in an efficient way, can be downloaded at http://ppw.kuleuven.be/okp/software/BayesianIUT/.

Contact:  katrijn.vandeun@psy.kuleuven.be
Partition function and base pairing probabilities for RNA–RNA interaction prediction
Authors: Huang Fenix W. D. , Qin Jing , Reidys Christian M. , Stadler Peter F.
Published: August 2009

Motivation: The RNA–RNA interaction problem (RIP) consists in finding the energetically optimal structure of two RNA molecules that bind to each other. The standard model allows secondary structures in both partners as well as additional base pairs between the two RNAs subject to certain restrictions that ensure that RIP is solvabale by a polynomial time dynamic programming algorithm. RNA–RNA binding, like RNA folding, is typically not dominated by the ground state structure. Instead, a large ensemble of alternative structures contributes to the interaction thermodynamics.

Results: We present here an O(N6) time and O(N4) dynamics programming algorithm for computing the full partition function for RIP which is based on the combinatorial notion of ‘tight structures’. Albeit equivalent to recent work by H. Chitsaz and collaborators, our approach in addition provides a full-fledged computation of the base pairing probabilities, which relies on the notion of a decomposition tree for joint structures. In practise, our implementation is efficient enough to investigate, for instance, the interactions of small bacterial RNAs and their target mRNAs.

Availability: The program rip is implemented in C. The source code is available for download from http://www.combinatorics.cn/cbpc/rip.html and http://www.bioinf.uni-leipzig.de/Software/rip.html.

Contact:  duck@santafe.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Comment on ‘MeSH-up: effective MeSH text classification for improved document retrieval’
Authors: Névéol Aurélie , Mork James G. , Aronson Alan R.
Published: August 2009

Contact:  neveola@ncbi.nlm.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ethical Guidelines in Pandemic Influenza: Recommendations of the Ethics Subcommittee of the Advisory Committee of the Director, Centers for Disease Control and Prevention
Authors: Kinlaw Kathy , Barrett Drue H. , Levine Robert J.
Published: August 2009

Because of the importance of including ethical considerations in planning efforts for pandemic influenza, in February 2005 the Centers for Disease Control and Prevention requested that the Ethics Subcommittee of the Advisory Committee to the Director develop guidance that would serve as a foundation for decision making in preparing for and responding to pandemic influenza. Specifically, the ethics subcommittee was asked to make recommendations regarding ethical considerations relevant to decision making about vaccine and antiviral drug distribution prioritization and development of interventions that would limit individual freedom and create social distancing. The ethics subcommittee identified a number of general ethical considerations including identification of clear goals for pandemic planning, responsibility to maximize preparedness, transparency and public engagement, sound science, commitment to the global community, balancing individual liberty and community interests, diversity in ethical decision making, and commitment to justice. These general ethical considerations are applied to the issues of vaccine and antiviral drug distribution and use of community mitigation interventions. (Disaster Med Public Health Preparedness. 2009;3(Suppl 2):S185–S192)
Systemic phaeohyphomycosis resembling primary sclerosing cholangitis caused by Exophiala dermatitidis
Authors: Oztas Erkin , Odemis Bulent , Kekilli Murat , Kurt Mevlut , Dinc Bedia Mert , Parlak Erkan , Kalkanci Ayse , Sasmaz Nurgul
Published: August 2009

Exophiala dermatitidis, one of the saprophytic dematiaceous fungi, is a cause of local and disseminated phaeohyphomycosis. We report a case of systemic phaeohyphomycosis resembling sclerosing cholangitis caused by E. dermatitidis in a 24-year-old woman.
Pseudomonas aeruginosa – a phenomenon of bacterial resistance
Authors: Strateva Tanya , Yordanov Daniel
Published: August 2009

Pseudomonas aeruginosais one of the leading nosocomial pathogens worldwide. Nosocomial infections caused by this organism are often hard to treat because of both the intrinsic resistance of the species (it has constitutive expression of AmpCβ-lactamase and efflux pumps, combined with a low permeability of the outer membrane), and its remarkable ability to acquire further resistance mechanisms to multiple groups of antimicrobial agents, includingβ-lactams, aminoglycosides and fluoroquinolones.P. aeruginosarepresents a phenomenon of bacterial resistance, since practically all known mechanisms of antimicrobial resistance can be seen in it: derepression of chromosomal AmpC cephalosporinase; production of plasmid or integron-mediatedβ-lactamases from different molecular classes (carbenicillinases and extended-spectrumβ-lactamases belonging to class A, class D oxacillinases and class B carbapenem-hydrolysing enzymes); diminished outer membrane permeability (loss of OprD proteins); overexpression of active efflux systems with wide substrate profiles; synthesis of aminoglycoside-modifying enzymes (phosphoryltransferases, acetyltransferases and adenylyltransferases); and structural alterations of topoisomerases II and IV determining quinolone resistance. Worryingly, these mechanisms are often present simultaneously, thereby conferring multiresistant phenotypes. This review describes the known resistance mechanisms inP. aeruginosato the most frequently administrated antipseudomonal antibiotics:β-lactams, aminoglycosides and fluoroquinolones.
Rapid electrochemical identification of pathogenic Candida species
Authors: Muir Alastair , Jenkins A. Toby A. , Forrest Gordon , Clarkson John , Wheals Alan
Published: August 2009

This study describes the development of a novel assay to detect fungal DNA and identify the most clinically relevant invasive human pathogenic fungi to the species level using oligonucleotide probes, labelled with electrochemically active groups, and solid-state electrodes. A panfungal probe designed against the 18S rRNA gene region, capable of detecting all fungal pathogens tested, and species-specific probes, designed against the ITS2 region for detection of the five Candida species most commonly encountered in the clinical setting (Candida albicans, Candida glabrata, Candida parapsilosis species complex, Candida krusei and Candida tropicalis), are described. When tested with PCR-amplified DNA from both type and clinical strains of the relevant species, the probes were able to positively identify the relevant fungi, indicated by production of a current significantly elevated above the background reading. No cross-reactivity was observed with any of the species-specific probes when compared with nine non-target Candida species or in the presence of human DNA equivalent to an equal number of ITS2 targets. The panfungal probe gave results that were similarly positive against 15 other fungal species and also did not cross-react with human DNA. The limit of detection of the assay was shown to be approximately 1 genome equivalent for all probes using extracted genomic DNA.
Rapid and cost-effective identification of Bartonella species using mass spectrometry
Authors: Fournier Pierre-Edouard , Couderc Carine , Buffet Sylvain , Flaudrops Christophe , Raoult Didier
Published: August 2009

Bacteria of the genus Bartonella are emerging zoonotic bacteria recognized in a variety of human diseases. Due to their poor chemical reactivity, these fastidious bacteria are poorly characterized using routine phenotypic laboratory tests. Identification is usually achieved using molecular techniques that are time-consuming, expensive and technically demanding. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a new technique for bacterial species identification. This study evaluated the use of MALDI-TOF MS for rapid genus and species identification of Bartonella species. Reference strains representing 17 recognized Bartonella species were studied. For each species, MS spectra for four colonies were analysed. The consensus spectrum obtained for each species was unique among spectra obtained for 2843 bacteria within the Bruker database, including 109 alphaproteobacteria. Thirty-nine additional blind-coded Bartonella strains were correctly identified at the species level, including 36 with a significant score. Altogether, these data demonstrate that MS is an accurate and reproducible tool for rapid and inexpensive identification of Bartonella species.
Septic shock induced by Lecythophora mutabilis in a patient with mitochondrial encephalomyopathy
Authors: Taniguchi Yuki , Taketani Takeshi , Moriyama Hidehiko , Moriki Shoji , Nishimura Kazuko , Sato Emi , Notsu Yasuko , Higuchi Tsuyoshi , Sugitani Yuichiro , Yasuda Kenji , Nagai Atsushi , Yamaguchi Seiji , Shibata Hiroshi , Masuda Junichi
Published: August 2009

Invasive fungal infection (IFI) caused by Lecythophora mutabilis occasionally occurs in patients with impaired host immunity; such patients had eosinophilia at onset, and surviving patients were treated with fungal cell-membrane-targeted drugs. An 18-year-old man with mitochondrial encephalomyopathy accompanied with refractory anaemia and chronic renal failure developed septic shock caused by L. mutabilis, which was detected from a blood culture, and was identified morphologically and genetically. During the course of the infection, he had eosinophilia, although β-d-glucan levels were within the normal range. He was treated with micafungin, but deteriorated and died, despite his treatment being changed to liposomal amphotericin B. On the basis of this we suggest that IFI caused by L. mutabilis should be suspected when a compromised host develops infection and eosinophilia, and that antifungal drugs that target β-d-glucan are not advisable.
Central nervous system invasion by community-acquired meticillin-resistant Staphylococcus aureus
Authors: Naesens Reinout , Ronsyn Mark , Druwé Patrick , Denis Olivier , Ieven Margareta , Jeurissen Axel
Published: August 2009

We report a case of community-acquired meticillin-resistant Staphylococcus aureus (CA-MRSA) bacteraemia with cavernous sinus thrombosis, meningitis and brain abscess in a previously healthy American, who was employed in Belgium. We consecutively reviewed all published cases of CA-MRSA with central nervous system (CNS) involvement. A total of 12 similar cases were found, of which 11 were published in the last 4 years. Predominantly, young previously healthy subjects were affected (median age 28 years). The cases involved brain abscesses (5/12), disseminated disease (4/12), cavernous sinus thrombosis (2/12) and other (1/12). Infection origins were superficial skin infections (5/12), mostly of the face, sinusitis (1/12), otitis media (1/12), other or unknown (5/12). Although, in our review of the literature patients treated with linezolid had a better outcome compared to patients treated with vancomycin, the latter is still the mainstay of therapy for CNS infections associated with MRSA.
Characteristics of community- and hospital-acquired meticillin-resistant Staphylococcus aureus strains carrying SCCmec type IV isolated in Malaysia
Authors: Ahmad Norazah , Ruzan Izayu Nurfarha , Abd Ghani Mohamed Kamel , Hussin Azura , Nawi Salbiah , Aziz Mohamad Nazri , Maning Nurahan , Eow Victor Lim Kok
Published: August 2009

Community-acquired meticillin-resistantStaphylococcus aureus(CA-MRSA) occurring among hospital isolates in Malaysia has not been reported previously. As CA-MRSA reported worldwide has been shown to carry SCCmectypes IV and V, the aim of this study was to determine the SCCmectypes of MRSA strains collected in Malaysia from November 2006 to June 2008. From a total of 628 MRSA isolates, 20 were SCCmectype IV, whilst the rest were type III. Further characterization of SCCmectype IV strains revealed 11 sequence types (STs), including ST22, with the majority being ST30/Panton–Valentine leukocidin positive. Eight out of nine CA-MRSA were ST30, one was ST80, and all were sensitive to co-trimoxazole and gentamicin. Five new STs designated ST1284, ST1285, ST1286, ST1287 and ST1288 were discovered, suggesting the emergence of novel clones of MRSA circulating in Malaysian hospitals. The discovery of the ST22 strain is a cause for concern because of its ability to replace existing predominant clones in certain geographical regions.
Prevalence of Chlamydophila psittaci infections in a human population in contact with domestic and companion birds
Authors: Harkinezhad Taher , Verminnen Kristel , De Buyzere Marc , Rietzschel Ernst , Bekaert Sofie , Vanrompay Daisy
Published: August 2009

Chlamydophila psittaciinfections in humans are underestimated. We investigated the occurrence ofC. psittaciin a Belgian population of 540 individuals. Data were from a population survey (n=2524) of apparently healthy community-dwelling subjects aged 35–55 years. Pharyngeal swabs and blood were taken. Individuals completed a questionnaire on professional and nonprofessional activities, smoking habits, medical history and contact frequency with different bird species. Swabs were analysed by aC. psittaci-specific and aChlamydophila pneumoniae-specific PCR. Sera were tested by a recombinantC. psittacimajor outer-membrane protein-based ELISA, aC. psittaciwhole organism-based ELISA (Serion) and a micro-immunofluorescence test (Focus Diagnostics). Results confirmed our suspicion about the underestimation of psittacosis in Belgium. Psittaciformes and racing pigeons were the main infection source. Women with excessive alcohol intake defined as a mean intake of >2 units daily were more frequently infected than men. We analysed the effect of seropositivity and/or PCR positivity on inflammation (white blood cell count, high-sensitivity C-reactive protein, fibrinogen). In general, seropositivity showed a trend to slightly higher levels of inflammatory variables (all non-significant), whilst PCR positivity showed a trend to no effect or even lower inflammatory levels.
Salmonella expressing a T-cell epitope from Sendai virus are able to induce anti-infection immunity
Authors: Huang He , Wang Ye-Jun , White Aaron P. , Meng Jia-Zi , Liu Gui-Rong , Liu Shu-Lin , Wang Yue-Dan
Published: August 2009

Bacterial fimbriae can accept foreign peptides and display them on the cell surface. A highly efficient gene replacement method was used to generate peptide vaccines based onSalmonella entericasubsp.entericaserovar Typhimurium LT2. DNA encoding an epitope from Sendai virus, SV9 (Sendai virus nucleoprotein peptide 324–332, FAPGNYPAL), which is known to induce cytotoxic T lymphocytes, was incorporated into the gene encoding AgfA (the major subunit protein of thin aggregative fimbriae ofSalmonella) by replacing an equal length DNA segment. To improve cytotoxic T lymphocyte recognition, both termini of the peptide were flanked by double alanine (AA) or arginine (RR) residues. Western blotting and immunofluorescence microscopy using AgfA-specific antiserum verified the expression of chimeric AgfA; expression was also proved by a Congo red binding assay. Oral immunizations of C57BL/6 mice with the four strains induced an epitope-specific T-cell response (detected by enzyme-linked immunosorbent spot assay). When the mice were challenged with the Sendai virus, the magnitude of the infection was significantly reduced in the immunized groups compared with the controls. TheSalmonellafimbrial display system efficiently induces a cellular immune response and anti-infection immunityin vivo, providing a new strategy for the development of efficient peptide vaccination.
Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs
Authors: Rechavi Oded , Erlich Yaniv , Amram Hila , Flomenblit Lena , Karginov Fedor V. , Goldstein Itamar , Hannon Gregory J. , Kloog Yoel
Published: August 2009

In some organisms, small RNA pathways can act nonautonomously, with responses spreading from cell to cell. Dedicated intercellular RNA delivery pathways have not yet been characterized in mammals, although secretory compartments have been found to contain RNA. Here we show that, upon cell contact, T cells acquire from B cells small RNAs that can impact the expression of target genes in the recipient T cells. Synthetic microRNA (miRNA) mimetics, viral miRNAs expressed by infected B cells, and endogenous miRNAs could all be transferred into T cells. These mechanisms may allow small RNA-mediated communication between immune cells. The documented transfer of viral miRNAs raises the possible exploitation of these pathways for viral manipulation of the host immune response.
A mechanism for cell cycle regulation of sporulation initiation in Bacillus subtilis
Authors: Veening Jan-Willem , Murray Heath , Errington Jeff
Published: August 2009

Coordination of DNA replication with cellular development is a crucial problem in most living organisms. Bacillus subtilis cells switch from vegetative growth to sporulation when starved. Sporulation normally occurs in cells that have stopped replicating DNA and have two completed chromosomes: one destined for the prespore and the other for the mother cell. It has long been recognized that there is a sensitive period in the cell cycle during which the initiation of spore development can be triggered, presumably to allow for the generation of exactly two complete chromosomes. However, the mechanism responsible for this has remained unclear. Here we show that the sda gene, previously identified as a checkpoint factor preventing sporulation in response to DNA damage, exerts cell cycle control over the initiation of sporulation. Expression of sda occurs in a pulsatile manner, with a burst of expression each cell cycle at the onset of DNA replication. Up-regulation of the intrinsically unstable Sda protein, which is dependent on the active form of the DNA replication initiator protein, DnaA, transiently inhibits the initiation of sporulation. This regulation avoids the generation of spore formers with replicating chromosomes, which would result in diploid or polyploid spores that we show have reduced viability.
Comorbid personality disorder predicts suicide after major depression: a 10‐year follow‐up
Authors: Hansen P. E. B. , Wang A. G. , Stage K. B. , Kragh‐Sorensen P. ,   The Danish University Antidepressant Group
Published: August 2009

Objective:  To identify psychopathological predictors for suicide in a population of major depressed Diagnostic Statistical Manual‐III (DSM‐III) in‐patients.

Method:  A total of 210 previous participants in multicentre antidepressant drug trials, carried out in a randomized double‐blind design, were followed prospectively through a maximum of 10 years. Patients with a drug or alcohol abuse were excluded. The association between suicide and the pretreatment psychopathological profile was analysed using survival statistics.

Results:  The suicide rate for non‐melancholic depressed patients was significantly higher than for melancholic depressed patients. Comorbid personality disorder was independently associated with an increased suicide rate [relative hazard 3.41(CI: 1.15–10.10)].

Conclusion:  The study indicates that the non‐melancholic aspect of depression, and especially comorbid personality disorder, is associated with an increased suicidal vulnerability.
Archetype JC virus efficiently propagates in kidney‐derived cells stably expressing HIV‐1 Tat
Authors: Nukuzuma Souichi , Kameoka Masanori , Sugiura Shigeki , Nakamichi Kazuo , Nukuzuma Chiyoko , Miyoshi Isao , Takegami Tsutomu
Published: August 2009

Pathogenic JCV with rearranged regulatory regions (PML‐type) causes PML, a demyelinating disease, in the brains of immunocompromised patients. On the other hand, archetype JCV persistently infecting the kidney is thought to be converted to PML‐type virus during JCV replication in the infected host under immunosuppressed conditions. In addition, Tat protein, encoded by HIV‐1, markedly enhances the expression of a reporter gene under control of the JCV late promoter.

In order to examine the influence of Tat on JCV propagation, we used kidney‐derived COS‐7 cells, which only permit archetype JCV, and established COS‐tat cells, which express HIV‐1 Tat stably. We found that the extent of archetype JCV propagation in COS‐tat cells is significantly greater than in COS‐7 cells. On the other hand, COS‐7 cells express SV40 T antigen, which is a strong stimulator of archetype JCV replication. The expression of SV40 T antigen was enhanced by HIV‐1 Tat slightly according to real‐time RT‐PCR, this was not closely related to JCV replication in COS‐tat cells. The efficiency of JCV propagation depended on the extent of expression of functional Tat. To our knowledge, this is the first report of increased production of archetype JCV in a culture system using cell lines stably expressing HIV‐1 Tat. We propose here that COS‐tat cells are a useful tool for studying the role of Tat in archetype JCV replication in the development of PML.
N‐linked glycan‐dependent interaction of CD63 with CXCR4 at the Golgi apparatus induces downregulation of CXCR4
Authors: Yoshida Takeshi , Ebina Hirotaka , Koyanagi Yoshio
Published: August 2009

Efficient downregulation of CXCR4 cell surface expression by introduction of the CD63 gene has previously been reported by us. In the present study, it was found that CD63 and its mutant efficiently interact with CXCR4 in live cells and that CD63‐induced downregulation and interaction are significantly abrogated by the N‐linked glycosylation inhibitor, TM. Furthermore, the downregulation and interaction were clearly attenuated by alternation of all three N‐linked glycosylation sites in CD63. Either CD63 or CD63ΔN formed a complex with CXCR4 at the Golgi apparatus and the late endosomes, while CD63 GD mutants lost the ability to form a complex with CXCR4 exclusively at the Golgi apparatus. These findings suggest that CD63 interacts with CXCR4 through the N‐linked glycans‐portion of the CD63 protein and that the complex induces direction of CXCR4 trafficking to the endosomes/lysosomes, rather than to the plasma membrane. At the Golgi apparatus, there may be lysosome protein (CD63)‐associated machinery that influences trafficking of other membrane proteins.
A new lineage sheds light on the evolutionary history of Potato virus Y
Authors: MOURY BENOIT
Published: August 2009

Potato virus Y (PVY) is one of the rare plant viruses for which some biological traits (host range and symptomatology) are highly correlated with phylogeny, allowing the reconstruction of the evolutionary history of these traits. In this article, a new lineage of PVY isolates from Chile is described, showing unique genomic and biological properties. This lineage was found to be the sister group of all other PVY isolates and helped in the reconstruction of the ancestral traits and evolutionary history of PVY, suggesting that veinal necrosis in tobacco is an ancestral state and that adaptation to pepper (Capsicum spp.) and potato (Solanum tuberosum) has been modified several times during PVY history.
A novel population of human CD56+ human leucocyte antigen D-related (HLA-DR+) colonic lamina propria cells is associated with inflammation in ulcerative colitis
Authors: Ng S C , Plamondon S , Al-Hassi H O , English N , Gellatly N , Kamm M A , Knight S C , Stagg A J
Published: August 2009

Ulcerative colitis (UC) involves inappropriate mucosal immune responses to intestinal microbiota. Gut dendritic cells (DC) are central immunoregulators of the response to commensal bacteria, and the subset of CD11c+ cells within the human leucocyte antigen D-related (HLA-DR+) lineage (lin)–/dim population are activated in inflammatory bowel disease. We hypothesized that CD11c- cells within this population may also be involved in intestinal inflammation. HLA-DR+ lin–/dim cells were identified in freshly isolated lamina propria mononuclear cells by multi-colour flow cytometry in 54 UC patients and 22 controls. Proportion and number of CD11c+ and CD11c- cells, and surface expression of activation markers CD40, CD86, Toll-like receptor (TLR)-2, TLR-4, and CD56+[natural killer (NK) marker], were determined. Cytokine production was assessed by intracellular staining. Lamina propria colonic CD11c- HLA-DR+ lin–/dim cells were increased significantly in inflamed and ‘non-inflamed’ UC tissue, compared with control tissue. CD11c+ HLA-DR+ lin–/dim cells were unchanged. Fewer CD11c- cells expressed activation markers and produced intracellular cytokines than their CD11c+ counterparts, and they were weakly stimulatory in mixed leucocyte reactions. Few CD11c- cells expressed blood plasmacytoid DC markers, but a major subset expressed high levels of CD56. CD11c- cells decreased after inflammation resolved. Intestinal inflammation in UC is associated with the presence of cells that share phenotypic features of both DC and NK cells. This novel population of human colonic CD56+ HLA-DR+ cells may play a role in immune regulation or tissue repair. Their increase in quiescent UC may be a marker of subclinical inflammation.
Interactive effects of mycorrhizal fungi, salt stress, and competition on the herbivores of Baccharis halimifolia
Authors: YOUNGINGER BRETT , BARNOUTI JWAN , MOON DANIEL C.
Published: August 2009

1. Plant stress and association with mycorrhizal fungi have been shown to significantly influence plant quality, yet their roles in influencing plant–insect interactions remain unclear. Even less is known about how these factors might interact with or be modified by within‐trophic level interactions.

2. In the present study, the results of a factorial field experiment are reported in which the effects of within‐trophic‐level interactions, plant stress, and mycorrhizae on three herbivores of Baccharis halimifolia were examined.

3. Plant stress was increased by adding salt to the soil, and availability of mycorrhizal fungi was increased by inoculating plant roots. These treatments were applied to plants with either low or high densities of a competitor (Trirhabda baccharidis).

4. For the two leaf miners, Amauromyza maculosa and Liriomyza trifolii, increased soil salinity and high densities of the competitor Trirhabdabaccharidis resulted in significant decreases in density. Neither of these treatments affected the gall maker Neolasioptera lathami.

5. Mycorrhizal fungi increased the densities of all three herbivores, possibly by increasing foliar nitrogen levels. For the two leaf miners, there was also evidence that mycorrhizae ameliorated the negative effects of salt stress. There was also evidence that high levels of competition dampened the positive effects of mycorrhizae on the two leaf miners.
Unravelling complexities in benthic food webs using a dual stable isotope (hydrogen and carbon) approach
Authors: DEINES PETER , WOOLLER MATTHEW J. , GREY JONATHAN
Published: August 2009

1. Stable carbon isotope studies have been an essential component of research regarding the contribution of methane (CH4)‐derived carbon to freshwater food webs and results have suggested that benthic macroinvertebrates in billabongs, streams and lakes may be partially, and in some instances, significantly ‘fuelled’ by methanotrophic biomass. However, the singular use of carbon isotopes can lead to ambiguous interpretations concerning the origin of carbon, especially in systems where phototrophs are likely to be using carbon respired sources and hence show more 13C‐depleted values.

2. These uncertainties can be further resolved by the inclusion of additional isotopic data. Stable hydrogen isotopes are being increasingly used in food web studies with a marked advantage that sources may be isotopically distinct by one or two orders of magnitude greater than stable carbon or nitrogen, the isotopes most commonly used to delineate trophic interactions. By using hydrogen as a second biogeochemical tracer we provide further supportive evidence for the assimilation of methanotrophic microbial biomass by chironomid larvae.

3. Moreover, the hydrogen and carbon isotope values we found in chironomid tissues appear to reflect the original substrate used during methanogenesis; either acetate fermentation or carbonate reduction. Use of the former tends to result in relatively heavy carbon and light hydrogen isotope values due to kinetic isotope effects, whereas use of the latter results in relatively lighter carbon and heavier hydrogen isotope values.

4. We provide preliminary evidence to suggest that hydrogen and carbon isotope values in macroinvertebrates may be used to distinguish between CH4 formation pathways and help to explain inter‐depth and inter‐specific differences between co‐existing chironomid species found in the same lake.
Direct and indirect effects of viral pathogens and the environment on invasive grass fecundity in Pacific Coast grasslands
Authors: Seabloom Eric W. , Borer Elizabeth T. , Jolles Anna , Mitchell Charles E.
Published: August 2009

1.  Pathogens can have strong effects on their hosts and can be important determinants of biological invasions. In natural systems, host–pathogen interactions may be mediated by direct environmental effects on pathogen communities and host fitness.

2.  While environmental mediation of host–pathogen interactions has been investigated experimentally and at single sites, there have been few studies tracking pathogen effects on lifetime host fecundity across large naturally occurring environmental gradients.

3.  If environmental factors directly mediate both pathogen transmission and host fecundity, laboratory and local‐scale studies may not predict pathogen effects across large spatial scales.

4.  Here we investigate the relationship between host fecundity and infection by a suite of RNA viral pathogens, by surveying two invasive annual grasses at 18 locations along a 1200‐km latitudinal gradient on the west coast of North America.

5.  Infected hosts of both species had 28–30% lower fecundity than uninfected hosts in our field surveys. However, the correlation of reduced fecundity to infection arose from indirect effects of the environment on both host fecundity and pathogen prevalence, rather than direct effects of the pathogen on the host. Pathogen prevalence was highest at sites where uninfected hosts had lowest fecundity.

6.
 Synthesis. In past experimental inoculations, virus infection reduced fecundity of these host species. Against this background, the results of our geographic‐scale survey demonstrate the challenges not only of inferring cause from correlation, but also of extrapolating from local studies and experimental inoculations to larger spatial scales. Our results highlight a need for experimentally manipulating infection across environmental gradients. Such an integrated approach would allow quantification of the fitness impacts of infection, even when the environment directly affects both prevalence and host fecundity.
Trade‐offs in resource allocation that favour resprouting affect the competitive ability of woody seedlings in grassy communities
Authors: Clarke Peter J. , Knox Kirsten J. E.
Published: August 2009

1.  Differences in the competitive ability of plant functional groups at early life‐history stages can have important consequences for community structure. In particular, trade‐offs in allocation to roots by woody plant seedlings may influence competitive ability with grasses in fire‐prone vegetation.

2.
 We followed post‐fire survival of seedlings of facultative resprouter and obligate seeder (fire‐killed) shrubs for 3 years in adjacent communities with a grassy/graminoid ground stratum (54 plots, 20 m2) or a non‐graminoid ground stratum (54 plots, 20 m2).

3.
 The competitive effect of a grass (Poa) on seedlings of three congeneric pairs of resprouters and obligate seeder shrubs was tested in a factorial experiment where nutrients and the grass competitor were manipulated. The effects of grass (+,−) and nutrients (+,−) on the growth response, biomass allocation and root carbohydrate storage were measured after harvest at 26 weeks and the relative neighbour effect calculated.

4.  Post‐fire shrub seedling survival was high with about 50% (2163 seedlings) surviving over 3 years, but this varied between habitats and functional groups. In the grassy/graminoid ground layer communities 27% of shrub seedlings survived, whereas in the habitats with a more open ground stratum 55% of seedlings survived. In grassy habitats, obligate seeder survival was lower (23% survival) than that of resprouter seedlings (35% survival). Similarly, in open habitats, obligate seeder seedling survival was lower (51%) than that of resprouter seedlings (64% survival).

5.  Growth of both resprouters and obligate seeders in our manipulative experiment was strongly reduced in the presence of a grass competitor. Moreover, the addition of nutrients increased the relative difference in mass and height between those seedlings exposed to a grass competitor and those grown without a competitor. Resprouter species allocated more to roots under competition and were less affected by grass competition than obligate seeders.

6.
 Synthesis. The results of seedling survival and of the experiment on the effects of grass competition on woody plant seedlings suggest that early life‐history trade‐offs in allocation influence seedling survival. Allocation to resprouting appears to enhance the ability of shrub seedlings to survive grass competition. We propose that grass competition across productivity gradients plays an important role in influencing landscape‐level distribution patterns of woody resprouters.