bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compensatory Growth of Olive Flounder, Paralichthys olivaceus, Fed the Extruded Pellet with Different Feeding Regimes
Authors: Cho Young Jin , Cho Sung Hwoan 
Published: July 2009

Abstract This study was performed to determine compensatory growth of juvenile olive flounder fed the extruded pellet (EP) with different feeding regimes. Seven treatments with triplicates of different feeding regimes were prepared; α fish was daily fed for 6 d a week throughout 8 wk (8WF); α fish was starved for 1 wk and then fed for 3 wk twice [(1WS + 3WF) × 2]; β fish was starved for 2 wk and then fed for 6 wk (2WS + 6WF); χ fish was starved for 5 d and then fed for 9 d four times [(5DS + 9DF) × 4]; δ fish was starved for 10 d and then fed for 18 d twice [(10DS + 18DF) × 2]; δ fish was starved for 2 d, fed for 5 d, starved for 3 d, and then fed for 4 d four times [(2DS + 5DF + 3DS + 4DF) × 4]; and φ fish was starved for 4 d, fed for 10 d, starved for 6 d, and then fed for 8 d twice [(4DS + 10DF + 6DS + 8DF) × 2], respectively. Total feeding day was all same, 36 d except for control group (48 d). Weight gain of flounder in the 8WF treatment was higher than that of fish in other treatments. And weight gain of flounder in the 2WS + 6WF treatment was higher than that of fish in the (5DS + 9DF) × 4 and (4DS + 10DF + 6DS + 8DF) × 2 treatments. Feed consumption of flounder in the 8WF treatment was higher than that of fish experienced feed deprivation. Feed efficiency ratio (FER), protein efficiency ratio (PER), and protein retention (PR) were not significantly different among treatments. Chemical composition of the whole body of fish with and without liver, except for moisture content of liver, was not different among treatments. T3 level of fish in the 8WF and 2WS + 6WF treatments was higher than that of fish in the (5DS + 9DF) × 4 treatment. It can be concluded that juvenile olive flounder achieved better compensatory growth at 6‐wk refeeding after 2‐wk feed deprivation compared with that of fish with different feeding regimes. And T3 level of fish seemed to partially play an important role in achieving compensatory growth.
Effects of the Prebiotics GroBiotic®‐A and Inulin on the Intestinal Microbiota of Red Drum, Sciaenops ocellatus
Authors: Burr Gary , Gatlin Delbert M. , Hume Michael 
Published: July 2009

Abstract Two separate feeding trials examined the effects of dietary supplementation of the prebiotics GroBiotic®‐A and inulin on growth performance and gastrointestinal tract microbiota of the red drum, Sciaenops ocellatus. In the first feeding trial, fish meal‐based diets without prebiotics or supplemented with either GroBiotic®‐A or inulin at 1% of dry weight were fed to triplicate groups of juvenile red drum (initial weight of 2.6 g) in 110‐L aquaria operated as a brackish water (7 ppt) recirculating system for 8 wk. In the second feeding trial, soybean meal/fish meal‐based diets supplemented with either GroBiotic®‐A or inulin at 1% of dry weight were fed to triplicate groups of red drum (initial weight of 15.8 g) in 110‐L aquaria operated as either a common recirculating water system or closed system with individual biofilters (independent aquaria) for 6 wk. Supplementation of the prebiotics in either feeding trial did not alter weight gain, feed efficiency ratio, or protein efficiency ratio of red drum fed the various diets. In the second feeding trial, the culture system significantly affected weight gain, feed efficiency ratio, and protein efficiency ratio although there were no effects of dietary treatments on fish performance or whole‐body protein, lipid, moisture, or ash. Denaturing gradient gel electrophoresis (DGGE) analysis of the gastrointestinal tract microbial community showed no effect of the dietary prebiotics as the microbial community appeared to be dominated by a single organism with very low diversity when compared with other livestock and fish species. DGGE of the microbial community in the biofilters of the independent aquariums showed a diverse microbial community that was not affected by the dietary prebiotics.
Adhesion determinants of the Streptococcus species
Authors: Moschioni Monica , Pansegrau Werner , Barocchi Michèle A. 
Published: July 2009

SummaryStreptococci are clinically important Gram‐positive bacteria that are capable to cause a wide variety of diseases in humans and animals. Phylogenetic analyses based on 16S rRNA sequences of the streptococcal species reveal a clustering pattern, reflecting, with a few exceptions, their pathogenic potential and ecological preferences. Microbial adhesion to host tissues is the initial critical event in the pathogenesis of most infections. Streptococci use multiple adhesins to attach to the epithelium, and their expression is regulated in response to environmental and growth conditions. Bacterial adhesins recognize and bind cell surface molecules and extracellular matrix components through specific domains that for certain adhesin families have been well defined and found conserved across the streptococcal species. In this review, we present the different streptococcal adhesin families categorized on the basis of their adhesive properties and structural characteristics, and, when available, we focus the attention on conserved functional domains.
Nature versus nurture in two highly enantioselective esterases fromBacillus cereusandThermoanaerobacter tengcongensis
Authors: Grosse Stephan , Bergeron Hélène , Imura Akihiro , Boyd Jason , Wang Shaozhao , Kubota Kazuo , Miyadera Akihiko , Sulea Traian , Lau Peter C. K. 
Published: July 2009

SummaryThere is an increasing need for the use of biocatalysis to obtain enantiopure compounds as chiral building blocks for drug synthesis such as antibiotics. The principal findings of this study are: (i) the complete sequenced genomes ofBacillus cereusATCC 14579 andThermoanaerobacter tengcongensisMB4 contain a hitherto undescribed enantioselective and alkaliphilic esterase (BcEST and TtEST respectively) that is specific for the production of (R)‐2‐benzyloxy‐propionic acid ethyl ester, a key intermediate in the synthesis of levofloxacin, a potent antibiotic; and (ii) directed evolution targeted for increased thermostability of BcEST produced two improved variants, but in either case the 3–5°C increase in the apparent melting temperature (Tm) of the mutants over the native BcEST that has aTmof 50°C was outperformed by TtEST, a naturally occurring homologue with aTmof 65°C. Protein modelling of BcEST mapped the S148C and K272R mutations at protein surface and the I88T and Q110L mutations at more buried locations. This work expands the repertoire of characterized members of the α/β‐fold hydrolase superfamily. Further, it shows that genome mining is an economical option for new biocatalyst discovery and we provide a rare example of a naturally occurring thermostable biocatalyst that outperforms experimentally evolved homologues that carry out the same hydrolysis.
ORIGINAL ARTICLE: Propensity of marine reserves to reduce the evolutionary effects of fishing in a migratory species
Authors: Dunlop Erin S. , Baskett Marissa L. , Heino Mikko , Dieckmann Ulf 
Published: July 2009

AbstractEvolutionary effects of fishing can have unwanted consequences diminishing a fishery’s value and sustainability. Reserves, or no‐take areas, have been proposed as a management tool for reducing fisheries‐induced selection, but their effectiveness for migratory species has remained unexplored. Here we develop an eco‐genetic model to predict the effects of marine reserves on fisheries‐induced evolution under migration. To represent a stock that undergoes an annual migration between feeding and spawning grounds, we draw model parameters from Atlantic cod (Gadus morhua) in the northern part of its range. Our analysis leads to the following conclusions: (i) a reserve in a stock’s feeding grounds, protecting immature and mature fish alike, reduces fisheries‐induced evolution, even though protected and unprotected population components mix on the spawning grounds; (ii) in contrast, a reserve in a stock’s spawning grounds, protecting only mature fish, has little mitigating effects on fisheries‐induced evolution and can sometimes even exacerbate its magnitude; (iii) evolutionary changes that are already underway may be difficult to reverse with a reserve; (iv) directly after a reserve is created or enlarged, most reserve scenarios result in yield losses; and (v) timescale is very important: short‐term yield losses immediately after a reserve’s creation can give way to long‐term gains.
Western Australian cigarette smokers have fewer small lung nodules than North Americans on CT screening for lung cancer
Authors: Murray CP , Wong PM , Louw J , Waterer GW 
Published: July 2009

SummaryTo determine the prevalence of small lung nodules on low‐dose helical computed tomography (CT) in a Western Australian cohort of asymptomatic long‐term cigarette smokers and to compare this with a large, similarly derived cohort of North Americans from the Mayo Clinic Lung Cancer Screening Trial. Forty‐nine asymptomatic long‐term cigarette smokers of minimum age 50 years underwent a low‐dose 64‐slice helical CT of the lungs. Images were viewed on a soft copy reporting station with thin section axial and coronal images, maximum intensity projection images, and advanced image manipulation tools. The prevalence of all nodules was 39%, significantly lower than the Mayo Clinic cohort prevalence of 51% (P < 0.01, Fisher's exact test), despite the use of more advanced imaging technology and image manipulation designed to increase the sensitivity for nodules. The prevalence of small nodules in asymptomatic long‐term cigarette smokers in Western Australia is high, though significantly less than that found in a large study in North America. The authors postulate this is due to the relatively low rates of mycobacterium tuberculosis and soil‐derived fungal pulmonary infections in Western Australia, as well as a lower degree of urban air pollution.
The Geneva prognostic score and mortality in patients diagnosed with pulmonary embolism by CT pulmonary angiogram
Authors: Subramaniam RM , Mandrekar J , Blair D , Peller PJ , Karalus N 
Published: July 2009

SummaryThis study prospectively evaluates whether a previously established adverse outcome score (the Geneva prognostic score) predicts 3 and 12‐month overall mortality among the patients diagnosed with pulmonary embolism (PE) by a CT pulmonary angiogram (CTPA). Five hundred twenty‐three consecutive patients who had CTPA for suspected PE were recruited prospectively from March 2003 to October 2004. The Geneva prognostic score was calculated for all patients. Twelve‐month follow up was completed in all patients in December 2005. There were 105 patients diagnosed with PE. The mean score was 2.71 (standard deviation (SD) 1.25) for those patients who had died (n = 7) and 1.14 (SD 1.19) for those patients who were alive (n = 98) at 3‐month follow up (P < 0.001). The mean scores were 2.69 (SD 0.95) for those who had died (n = 13) and 1.04 (SD 1.15) for those patients who were alive (n = 92) at 12‐month follow up (P < 0.001). At 3‐month follow up, among the 88 patients with a score of 2 or less, three patients (3.4%) died and among 17 patients with a score of greater than 2, four patients (23.5%) died (P = 0.01). At 12‐month follow up, five patients (5.7%) with a score of 2 or less died and eight patients (47.1%) with a score of three or more died (P < 0.0001). The Geneva prognostic score stratifies patients with low and high risk for overall mortality at 3 and 12 months among patients diagnosed with PE by CTPA.
Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence
Authors: CASTOE TODD A. , POOLE ALEXANDER W. , GU WANJUN , JASON de KONING A. P. , DAZA JUAN M. , SMITH ERIC N. , POLLOCK DAVID D. 
Published: July 2009

AbstractOptimal integration of next‐generation sequencing into mainstream research requires re‐evaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic and chromosome linkage mapping research on non‐model and not previously sequenced organisms. Here, we report on results using high‐throughput sequencing to obtain a large number of microsatellite loci from the venomous snake Agkistrodon contortrix, the copperhead. We used the 454 Genome Sequencer FLX next‐generation sequencing platform to sample randomly ∼27 Mbp (128 773 reads) of the copperhead genome, thus sampling about 2% of the genome of this species. We identified microsatellite loci in 11.3% of all reads obtained, with 14 612 microsatellite loci identified in total, 4564 of which had flanking sequences suitable for polymerase chain reaction primer design. The random sequencing‐based approach to identify microsatellites was rapid, cost‐effective and identified thousands of useful microsatellite loci in a previously unstudied species.
Mallard ducks – a waterfowl species with high risk of distributing Escherichia coli pathogenic for humans
Authors: Ewers Christa , Guenther Sebastian , Wieler Lothar H. , Schierack Peter 
Published: July 2009

SummaryMallard ducks may pose a so far underestimated risk to human and animal health by transmitting pathogenic Escherichia coli via their faecal deposits to various environmental sources. We processed Mallard duck faecal samples for E. coli and unique clones, as defined by pulsed‐field gel electrophoresis (PFGE), were subsequently investigated for their virulence genotype and phylogenetic background. Multilocus sequence typing and in vivo experiments were performed for selected clones. Of 60 clones identified among 142 E. coli isolated from 175 samples, 15 (25%) were recovered from multiple individuals (up to 23 per clone). None of the clones harboured stx1 and stx2 genes and other intestinal pathogenic E. coli virulence‐associated genes were only occasionally identified in the collection. In contrast, the clones possessed considerable numbers of VAGs (up to 30) linked with extraintestinal pathogenic E. coli (ExPEC). Their pathogenic potential was confirmed in chicken infection experiments. Moreover, selected clones were assigned to sequence types (STs) being most prominent for human ExPEC strains, including ST95 and ST73. One clone exhibited a multi‐resistant phenotype against several antibiotics including beta‐lactams, tetracyclines and sulfonamides. Mallard ducks have therefore to be considered as an important reservoir for zoonotic E. coli strains, thus serving as a substantial non‐point source especially of strains capable of causing extraintestinal diseases.
Identification of Novel
Mycobacterium bovis
Antigens by Dissection of Crude Protein Fractions
Authors: Meikle V. , Alito A. , Llera A. S. , Gioffré A. , Peralta A. , Buddle B. M. , Cataldi A. 
Published: July 2009

ABSTRACT

Culture filtrate and cell extracts from
Mycobacterium bovis
cultures contain molecules which could promote protective immunity to tuberculosis in animals. Different protein fractions of
M. bovis
cultures were obtained by elution electrophoresis and were tested in experimentally infected cattle. The fractions that elicited gamma interferon (IFN-γ) responses were resolved by two-dimensional gel electrophoresis, and individual proteins were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The open reading frames were cloned, expressed as their recombinant forms, and retested with naturally and experimentally infected animals. Eleven protein fractions were highly reactive, from which the Rv1636, HspX, Rv0138, Rv2524, EsxI, and Rv3740 recombinant proteins were obtained. EsxI and HspX were the antigens most recognized by the IFN-γ release assay. In summary, a proteomic approach allowed the identification of novel antigens useful for the diagnosis of bovine tuberculosis.
Seroprevalence of Human Toxocariasis in Denmark
Authors: Stensvold Christen R. , Skov Jakob , Møller Lone N. , Jensen Per M. , Kapel Christian M. O. , Petersen Eskild , Nielsen Henrik V. 
Published: July 2009

ABSTRACT

The seroprevalence of
Toxocara
in the Danish population was assessed from 3,247 sera from individuals originally screened for toxoplasmosis. Of 87 enzyme-linked immunosorbent assay-positive sera, 79 were confirmed by Western blotting, yielding a crude seroprevalence of 2.4%. This indicates that the seroprevalence of toxocariasis in Denmark is low compared to those in other European countries.
Discarding the Initial Aliquot of Blood Does Not Reduce Contamination Rates in Intravenous-Catheter-Drawn Blood Cultures
Authors: Dwivedi Sukrut , Bhalla Rohit , Hoover Donald R. , Weinstein Melvin P. 
Published: July 2009

ABSTRACT

Although venipuncture is the preferred method for obtaining blood cultures, specimens often are obtained from intravenous catheters (IVC). For IVC-drawn blood cultures, some authorities recommend discarding the initial 5 to 10 ml of blood to reduce contamination and remove potential inhibitory substances. To determine whether this practice reduced contamination rates (CR), we assessed the results of IVC-drawn blood cultures for adults. Thirty milliliters of blood was obtained aseptically. The first 10 ml, rather than being discarded, was inoculated into an aerobic culture vial. Using a second sterile syringe, 20 ml of blood was obtained and inoculated in 10-ml aliquots to aerobic and anaerobic culture vials. Positive cultures were evaluated to assess clinical significance (true versus contaminant). Out of 653 IVC-drawn blood culture pairs, both vials were contaminated in 38 pairs (5.8%); only the “discard” vial was contaminated in 33 (5.1%); and only the “standard” vial was contaminated in 31 (4.7%). Overall CR were 10.9% for the discard vial versus 10.5% for the standard vial (
P
= 0.90). We conclude that discarding an initial aliquot of blood when obtaining blood cultures from IVCs does not reduce CR.
Rapid Semiautomated Subtyping of Influenza Virus Species during the 2009 Swine Origin Influenza A H1N1 Virus Epidemic in Milwaukee, Wisconsin
Authors: Bose Michael E. , Beck Eric T. , Ledeboer Nate , Kehl Sue C. , Jurgens Lisa A. , Patitucci Teresa , Witt Lorraine , LaGue Elizabeth , Darga Patrick , He Jie , Fan Jiang , Kumar Swati , Henrickson Kelly J. 
Published: July 2009

ABSTRACT
In the spring of 2009, a novel influenza A (H1N1) virus (swine origin influenza virus [S-OIV]) emerged and began causing a large outbreak of illness in Milwaukee, WI. Our group at the Midwest Respiratory Virus Program laboratory developed a semiautomated real-time multiplex reverse transcription-PCR assay (Seasonal), employing the NucliSENS easyMAG system (bioMérieux, Durham, NC) and a Raider thermocycler (HandyLab Inc., Ann Arbor, MI), that typed influenza A virus, influenza B virus, and respiratory syncytial virus (RSV) and subtyped influenza A virus into the currently circulating H1 and H3 subtypes, as well as a similar assay that identified H1 of S-OIV. The Seasonal and H1 S-OIV assays demonstrated analytical limits of detection of <50 50% tissue culture infective doses/ml and 3 to 30 input copies, respectively. Testing of the analytical specificities revealed no cross-reactivity with 41 and 26 different common organisms and demonstrated outstanding reproducibility of results. Clinical testing showed 95% sensitivity for influenza A virus and influenza B virus and 95 and 97% specificity compared to tissue culture. Comparisons of results from other molecular tests showed levels of positive agreement with the Seasonal and H1 S-OIV assay results of 99 and 100% and levels of negative agreement of 98 and 100%. This study has demonstrated the use of a semiautomated system for sensitive, specific, and rapid detection of influenza A virus, influenza B virus, and RSV and subtyping of influenza A virus into human H1 and H3 and S-OIV strains. This assay/system performed well in clinical testing of regular seasonal influenza virus subtypes and was outstanding during the 2009 Milwaukee S-OIV infection outbreak. This recent outbreak of infection with a novel influenza A (H1N1) virus also demonstrates the importance of quickly distributing information on new agents and of having rapid influenza virus subtyping assays widely available for clinical and public health decisions.
Mycoplasma hominis
-Associated Parapharyngeal Abscess following Acute Epstein-Barr Virus Infection in a Previously Immunocompetent Adult
Authors: Kennedy Karina J. , Prince Sam , Makeham Timothy 
Published: July 2009

ABSTRACT

Mycoplasma hominis
most frequently causes diseases of the genitourinary tract. Extragenital infections are uncommon, with almost all occurring in immunosuppressed persons or those predisposed due to trauma or surgery. We present the case of a previously well man who developed an
M. hominis
-associated parapharyngeal abscess following acute Epstein-Barr virus infection.
Rapid, Point-of-Care Extraction of Human Immunodeficiency Virus Type 1 Proviral DNA from Whole Blood for Detection by Real-Time PCR
Authors: Jangam Sujit R. , Yamada Douglas H. , McFall Sally M. , Kelso David M. 
Published: July 2009

ABSTRACT
PCR detection of human immunodeficiency virus type 1 (HIV-1) proviral DNA is the method recommended for use for the diagnosis of HIV-1 infection in infants in limited-resource settings. Currently, testing must be performed in central laboratories, which are usually located some distance from health care facilities. While the collection and transportation of samples, such as dried blood spots, has improved test accessibility, the results are often not returned for several weeks. To enable PCR to be performed at the point of care while the mothers wait, we have developed a vertical filtration method that uses a separation membrane and an absorbent pad to extract cellular DNA from whole blood in less than 2 min. Cells are trapped in the separation membrane as the specimen is collected, and then a lysis buffer is added. The membrane retains the DNA, while the buffer washes away PCR inhibitors, which get wicked into the absorbent blotter pad. The membrane containing the entrapped DNA is then added to the PCR mixture without further purification. The method demonstrates a high degree of reproducibility and analytical sensitivity and allows the quantification of as few as 20 copies of HIV-1 proviral DNA from 100 μl of blood. In a blinded study with 182 longitudinal samples from infants (ages, 0 to 72 weeks) obtained from the Women and Infants Transmission Study, our assay demonstrated a sensitivity of 99% and a specificity of 100%.