bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations
Authors: Paris Josephine R. , King R. Andrew , Stevens Jamie R. 
Published: April 2015

AbstractHumans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well‐defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal‐impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal‐impacted trout populations have low genetic diversity and have experienced severe population declines. Metal‐river trout populations are genetically distinct from clean‐river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal‐impacted populations from clean‐river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human‐altered landscapes can change the genetic makeup of a species.
The contribution of phenotypic plasticity to the evolution of insecticide tolerance in amphibian populations
Authors: Hua Jessica , Jones Devin K. , Mattes Brian M. , Cothran Rickey D. , Relyea Rick A. , Hoverman Jason T. 
Published: April 2015

AbstractUnderstanding population responses to rapid environmental changes caused by anthropogenic activities, such as pesticides, is a research frontier. Genetic assimilation (GA), a process initiated by phenotypic plasticity, is one mechanism potentially influencing evolutionary responses to novel environments. While theoretical and laboratory research suggests thatGAhas the potential to influence evolutionary trajectories, few studies have assessed its role in the evolution of wild populations experiencing novel environments. Using the insecticide, carbaryl, and 15 wood frog populations distributed across an agricultural gradient, we tested whetherGAcontributed to the evolution of pesticide tolerance. First, we investigated the evidence for evolved tolerance to carbaryl and discovered that population‐level patterns of tolerance were consistent with evolutionary responses to pesticides; wood frog populations living closer to agriculture were more tolerant than populations living far from agriculture. Next, we tested the potential role ofGAin the evolution of pesticide tolerance by assessing whether patterns of tolerance were consistent with theoretical predictions. We found that populations close to agriculture displayed constitutive tolerance to carbaryl whereas populations far from agriculture had low naïve tolerance but high magnitudes of induced tolerance. These results suggestGAcould play a role in evolutionary responses to novel environments in nature.
Prognosis and impact of equine recurrent uveitis
Authors: Gerding J. C. , Gilger B. C. 
Published: April 2015

SummaryReasons for performing studyEquine recurrent uveitis (ERU) is a leading cause of vision loss in horses.ObjectivesTo assess the prognosis and impact ofERUon affected horses and their owners by evaluating the signalment, treatment and outcome (including the loss of use, vision assessment and economic loss).Study designRetrospective impact study.MethodsMedical records of horses presenting to the North Carolina State University Veterinary Health Complex (NCSU‐VHC) withERUbetween 1999 and 2014 were reviewed. Signalment, clinical signs, ophthalmic examination findings, treatments and outcomes were evaluated. Owner questionnaires were completed regarding vision, job/role, monetary value, diagnostic and treatment costs, concurrent illness and outcomes.ResultsRecords of 224 horses (338 eyes) withERUwere reviewed. There was an overrepresentation of Appaloosas (54; 24.1%), Hanoverians (11; 4.9%) and other Warmbloods (13; 5.8%). Ninety‐six eyes (28.4%) were diagnosed as blind and 38 eyes (11.2%) with glaucoma on initial evaluation. Leptospirosis titres of serum and/or aqueous humour were obtained in 88 horses and were positive in 40 horses (45.5%), withL. pomonabeing the most frequently isolated serovar. Globe loss at theNCSU‐VHCoccurred in 41ERUeyes (12.1% of total). Owner questionnaires were evaluated in 194 horses (86.6%) and 91 horses (46.9%) were reported blind in the affected eye(s). Fifty‐seven horses (29.4%) did not return to their previous role, while 61 (31.4%) performed at a reduced level. Equine recurrent uveitis decreased the monetary value of 164 horses. Twenty‐nine horses (14.9%) were euthanised and 37 (19.1%) underwent change in ownership as a direct result ofERU.ConclusionsThe impact ofERUis attributed to the high frequency of blindness, globe loss and loss of function. Euthanasia and change of ownership are common sequelae to the progressive nature ofERU. These factors, along with financial costs of the disease, have a significant impact on affected horses and their owners.The Summary is available in Chinese – see Supporting Information.
CO2 uptake is offset by CH4 and N2O emissions in a poplar short‐rotation coppice
Authors: Zenone Terenzio , Zona Donatella , Gelfand Ilya , Gielen Bert , Camino‐Serrano Marta , Ceulemans Reinhart 
Published: April 2015

AbstractThe need for renewable energy sources will lead to a considerable expansion in the planting of dedicated fast‐growing biomass crops across Europe. These are commonly cultivated as short‐rotation coppice (SRC), and currently poplar (Populus spp.) is the most widely planted. In this study, we report the greenhouse gas (GHG) fluxes of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) measured using eddy covariance technique in an SRC plantation for bioenergy production. Measurements were made during the period 2010–2013, that is, during the first two rotations of the SRC. The overall GHG balance of the 4 years of the study was an emission of 1.90 (±1.37) Mg CO2eq ha−1; this indicated that soil trace gas emissions offset the CO2 uptake by the plantation. CH4 and N2O contributed almost equally to offset the CO2 uptake of −5.28 (±0.67) Mg CO2eq ha−1 with an overall emission of 3.56 (±0.35) Mg CO2eq ha−1 of N2O and of 3.53 (±0.85) Mg CO2eq ha−1 of CH4. N2O emissions mostly occurred during one single peak a few months after the site was converted to SRC; this peak comprised 44% of the total N2O loss during the two rotations. Accurately capturing emission events proved to be critical for deriving correct estimates of the GHG balance. The nitrogen (N) content of the soil and the water table depth were the two drivers that best explained the variability in N2O and CH4, respectively. This study underlines the importance of the ‘non‐CO2 GHGs’ on the overall balance. Further long‐term investigations of soil trace gas emissions should monitor the N content and the mineralization rate of the soil, as well as the microbial community, as drivers of the trace gas emissions.
Intercellular interplay between Sirt1 signalling and cell metabolism in immune cell biology
Authors: Chen Xi , Lu Yun , Zhang Zhengguo , Wang Jian , Yang Hui , Liu Guangwei 
Published: April 2015

SummarySirtuins are evolutionarily conserved class III histone deacetylases that have been the focus of intense scrutiny and interest since the discovery of Sir2 as a yeast longevity factor. Early reports demonstrated an important role of Sirt1 in aging and metabolism, but its critical regulatory role in the immune system has only been unveiled in recent years. In this review we discuss the latest advances in understanding the regulatory role of Sirt1 in immune responses as well as how Sirt1 translates metabolic cues to immune signals, which would bring new insights into both pathogenesis and potential therapeutic strategies of a variety of immune‐related diseases, such as cancer, microbial infection, autoimmune diseases and transplantation.
Anatomy of the larynx and pharynx: effects of age, gender and height revealed by multidetector computed tomography
Authors: Inamoto Y. , Saitoh E. , Okada S. , Kagaya H. , Shibata S. , Baba M. , Onogi K. , Hashimoto S. , Katada K. , Wattanapan P. , Palmer J. B. 
Published: April 2015

SummaryAlthough oropharyngeal and laryngeal structures are essential for swallowing, the three‐dimensional (3D) anatomy is not well understood, due in part to limitations of available measuring techniques. This study uses 3D images acquired by 320‐row area detector computed tomography (‘320‐ADCT’), to measure the pharynx and larynx and to investigate the effects of age, gender and height. Fifty‐four healthy volunteers (30 male, 24 female, 23–77 years) underwent one single‐phase volume scan (0·35 s) with 320‐ADCT during resting tidal breathing. Six measurements of the pharynx and two of larynx were performed. Bivariate statistical methods were used to analyse the effects of gender, age and height on these measurements. Length and volume were significantly larger for men than for women for every measurement (P < 0·05) and increased with height (P < 0·05). Multiple regression analysis was performed to understand the interactions of gender, height and age. Gender, height and age each had significant effects on certain values. The volume of the larynx and hypopharynx was significantly affected by height and age. The length of pharynx was associated with gender and age. Length of the vocal folds and distance from the valleculae to the vocal folds were significantly affected by gender (P < 0·05). These results suggest that age, gender and height have independent and interacting effects on the morphology of the pharynx and larynx. Three‐dimensional imaging and morphometrics using 320‐ADCT are powerful tools for efficiently and reliably observing and measuring the pharynx and larynx.
Local adaptation and oceanographic connectivity patterns explain genetic differentiation of a marine diatom across the North Sea–Baltic Sea salinity gradient
Authors: Sjöqvist C. , Godhe A. , Jonsson P. R. , Sundqvist L. , Kremp A. 
Published: April 2015

AbstractDrivers of population genetic structure are still poorly understood in marine micro‐organisms. We exploited the North Sea–Baltic Sea transition for investigating the seascape genetics of a marine diatom, Skeletonema marinoi. Eight polymorphic microsatellite loci were analysed in 354 individuals from ten locations to analyse population structure of the species along a 1500‐km‐long salinity gradient ranging from 3 to 30 psu. To test for salinity adaptation, salinity reaction norms were determined for sets of strains originating from three different salinity regimes of the gradient. Modelled oceanographic connectivity was compared to directional relative migration by correlation analyses to examine oceanographic drivers. Population genetic analyses showed distinct genetic divergence of a low‐salinity Baltic Sea population and a high‐salinity North Sea population, coinciding with the most evident physical dispersal barrier in the area, the Danish Straits. Baltic Sea populations displayed reduced genetic diversity compared to North Sea populations. Growth optima of low salinity isolates were significantly lower than those of strains from higher native salinities, indicating local salinity adaptation. Although the North Sea–Baltic Sea transition was identified as a barrier to gene flow, migration between Baltic Sea and North Sea populations occurred. However, the presence of differentiated neutral markers on each side of the transition zone suggests that migrants are maladapted. It is concluded that local salinity adaptation, supported by oceanographic connectivity patterns creating an asymmetric migration pattern between the Baltic Sea and the North Sea, determines genetic differentiation patterns in the transition zone.
Giant radiating mafic dyke swarm of the Emeishan Large Igneous Province: Identifying the mantle plume centre
Authors: Li Hongbo , Zhang Zhaochong , Ernst Richard , Lü Linsu , Santosh M. , Zhang Dongyang , Cheng Zhiguo 
Published: April 2015

AbstractIn many continental large igneous provinces, giant radiating dyke swarms are typically interpreted to result from the arrival of a mantle plume at the base of the lithosphere. Mafic dyke swarms in the Emeishan large igneous province (ELIP) have not received much attention prior to this study. We show that the geochemical characteristics and geochronological data of the mafic dykes are broadly similar to those of the spatially associated lavas, suggesting they were derived from a common parental magma. Based on the regional geological data and our field observations, we mapped the spatial distribution patterns of mafic dyke swarms in the ELIP, and recognized six dyke sub‐swarms, forming an overall radiating dyke swarm and converging in the Yongren area, Yunnan province. This location coincides with the maximum pre‐eruptive domal uplift, and is close to the locations of high‐temperature picrites. Our study suggests that the Yongren area may represent the mantle plume centre during the peak of Emeishan magmatism.
Lincosamide resistance is less frequent in Denmark in Staphylococcus pseudintermedius from first‐time canine superficial pyoderma compared with skin isolates from clinical samples with unknown clinical background
Authors: Larsen Rikke , Boysen Lene , Berg June , Guardabassi Luca , Damborg Peter 
Published: April 2015

BackgroundAntimicrobial resistance may be overestimated in bacterial isolates from clinical samples because veterinarians often submit samples in cases of treatment failure or recurrent cases, which are more frequently associated with resistant strains.Hypothesis/ObjectivesTo assess to what extent the prevalence of antimicrobial resistance in Staphylococcus pseudintermedius isolated from first‐time superficial pyoderma differs from canine skin isolates from clinical samples with unknown clinical background.AnimalsTwo study groups were enrolled in Denmark between March 2012 and October 2013: 57 dogs with first‐time superficial pyoderma and no prior antimicrobial treatment (Group A); and 289 different dogs for which skin specimens were submitted for culture during the study (Group B).MethodsOne S. pseudintermedius isolate from each dog was confirmed by MALDI‐TOF mass spectrometry and tested for antimicrobial susceptibility by broth microdilution. Resistance levels in the two groups were compared by Fisher's exact test.ResultsClindamycin resistance was less frequent in Group A (14%) than in Group B (27%) (P = 0.02). Similar trends were observed for amoxicillin–clavulanic acid (1.8 versus 4.8%), chloramphenicol (8.8 versus 14.5%), enrofloxacin (1.8 versus 3.5%), oxacillin (1.8 versus 4.8%) and trimethoprim/sulfamethoxazole (3.5 versus 5.9%). Oxacillin resistance was significantly associated with resistance to six of seven non‐β‐lactams.Conclusions and clinical importanceThe prevalence of lincosamide resistance is markedly influenced by patients’ clinical and antimicrobial treatment history. To limit selection of multidrug‐resistant bacteria, lincosamides are appropriate empirical choices for treatment of first‐time superficial pyoderma even though resistance is not infrequent. Culture and susceptibility testing are, however, recommended for all pyoderma patients.
Characterization of a high‐energy in‐line phase contrast tomosynthesis prototype
Authors: Wu Di , Yan Aimin , Li Yuhua , Wong Molly D. , Zheng Bin , Wu Xizeng , Liu Hong 
Published: April 2015

Purpose:In this research, a high‐energy in‐line phase contrast tomosynthesis prototype was developed and characterized through quantitative investigations and phantom studies.Methods:The prototype system consists of an x‐ray source, a motorized rotation stage, and a CMOS detector with a pixel pitch of 0.05 mm. The x‐ray source was operated at 120 kVp for this study, and the objects were mounted on the rotation stage 76.2 cm (R1) from the source and 114.3 cm (R2) from the detector. The large air gap between the object and detector guarantees sufficient phase‐shift effects. The quantitative evaluation of this prototype included modulation transfer function and noise power spectrum measurements conducted under both projection mode and tomosynthesis mode. Phantom studies were performed including three custom designed phantoms with complex structures: a five‐layer bubble wrap phantom, a fishbone phantom, and a chicken breast phantom with embedded fibrils and mass structures extracted from an ACR phantom. In‐plane images of the phantoms were acquired to investigate their image qualities through observation, intensity profile plots, edge enhancement evaluations, and/or contrast‐to‐noise ratio calculations. In addition, the robust phase‐attenuation duality (PAD)‐based phase retrieval method was applied to tomosynthesis for the first time in this research. It was utilized as a preprocessing method to fully exhibit phase contrast on the angular projection before reconstruction.Results:The resolution and noise characteristics of this high‐energy in‐line phase contrast tomosynthesis prototype were successfully investigated and demonstrated. The phantom studies demonstrated that this imaging prototype can successfully remove the structure overlapping in phantom projections, obtain delineate interfaces, and achieve better contrast‐to‐noise ratio after applying phase retrieval to the angular projections.Conclusions:This research successfully demonstrated a high‐energy in‐line phase contrast tomosynthesis prototype. In addition, the PAD‐based method of phase retrieval was combined with tomosynthesis imaging for the first time, which demonstrated its capability in significantly improving the contrast‐to‐noise ratios in the images.
Selection and Characterization of Phage-Resistant Mutant Strains of Listeria monocytogenes Reveal Host Genes Linked to Phage Adsorption
Authors: Denes Thomas , den Bakker Henk C. , Tokman Jeffrey I. , Guldimann Claudia , Wiedmann Martin 
Published: April 2015

ABSTRACT

Listeria
-infecting phages are readily isolated from
Listeria
-containing environments, yet little is known about the selective forces they exert on their host. Here, we identified that two virulent phages, LP-048 and LP-125, adsorb to the surface of
Listeria monocytogenes
strain 10403S through different mechanisms. We isolated and sequenced, using whole-genome sequencing, 69 spontaneous mutant strains of 10403S that were resistant to either one or both phages. Mutations from 56 phage-resistant mutant strains with only a single mutation mapped to 10 genes representing five loci on the 10403S chromosome. An additional 12 mutant strains showed two mutations, and one mutant strain showed three mutations. Two of the loci, containing seven of the genes, accumulated the majority (
n
= 64) of the mutations. A representative mutant strain for each of the 10 genes was shown to resist phage infection through mechanisms of adsorption inhibition. Complementation of mutant strains with the associated wild-type allele was able to rescue phage susceptibility for 6 out of the 10 representative mutant strains. Wheat germ agglutinin, which specifically binds to
N
-acetylglucosamine, bound to 10403S and mutant strains resistant to LP-048 but did not bind to mutant strains resistant to only LP-125. We conclude that mutant strains resistant to only LP-125 lack terminal
N
-acetylglucosamine in their wall teichoic acid (WTA), whereas mutant strains resistant to both phages have disruptive mutations in their rhamnose biosynthesis operon but still possess
N
-acetylglucosamine in their WTA.
Spatial, Temporal, and Matrix Variability of Clostridium botulinum Type E Toxin Gene Distribution at Great Lakes Beaches
Authors: Wijesinghe Rasanthi U. , Oster Ryan J. , Haack Sheridan K. , Fogarty Lisa R. , Tucker Taaja R. , Riley Stephen C. 
Published: April 2015

ABSTRACT

Clostridium botulinum
type E toxin is responsible for extensive mortality of birds and fish in the Great Lakes. The
C. botulinum bontE
gene that produces the type E toxin was amplified with quantitative PCR from 150 sloughed algal samples (primarily
Cladophora
species) collected during summer 2012 from 10 Great Lakes beaches in five states; concurrently, 74 sediment and 37 water samples from four sites were also analyzed. The
bontE
gene concentration in algae was significantly higher than in water and sediment (
P
< 0.05), suggesting that algal mats provide a better microenvironment for
C. botulinum
. The
bontE
gene was detected most frequently in algae at Jeorse Park and Portage Lake Front beaches (Lake Michigan) and Bay City State Recreation Area beach on Saginaw Bay (Lake Huron), where 77, 100, and 83% of these algal samples contained the
bontE
gene, respectively. The highest concentration of
bontE
was detected at Bay City (1.98 × 10
5
gene copies/ml of algae or 5.21 × 10
6
g [dry weight]). This study revealed that the
bontE
gene is abundant in the Great Lakes but that it has spatial, temporal, and matrix variability. Further, embayed beaches, low wave height, low wind velocity, and greater average water temperature enhance the
bontE
occurrence.
BadR and BadM Proteins Transcriptionally Regulate Two Operons Needed for Anaerobic Benzoate Degradation by Rhodopseudomonas palustris
Authors: Hirakawa Hidetada , Hirakawa Yuko , Greenberg E. Peter , Harwood Caroline S. 
Published: April 2015

ABSTRACT

The bacterium
Rhodopseudomonas palustris
grows with the aromatic acid benzoate and the alicyclic acid cyclohexanecarboxylate (CHC) as sole carbon sources. The enzymatic steps in an oxygen-independent pathway for CHC degradation have been elucidated, but it was unknown how the CHC operon (
badHI aliAB badK
) encoding the enzymes for CHC degradation was regulated.
aliA
and
aliB
encode enzymes for the conversion of CHC to cyclohex-1-enecarboxyl–coenzyme A (CHene-CoA). At this point, the pathway for CHC degradation merges with the pathway for anaerobic benzoate degradation, as CHene-CoA is an intermediate in both degradation pathways. Three enzymes, encoded by
badK
,
badH
, and
badI
, prepare and cleave the alicyclic ring of CHene-CoA to yield pimelyl-CoA. Here, we show that the MarR transcription factor family member, BadR, represses transcription of the CHC operon by binding near the transcription start site of
badH
. 2-Ketocyclohexane-1-carboxyl–CoA, an intermediate of CHC and benzoate degradation, interacts with BadR to abrogate repression. We also present evidence that the transcription factor BadM binds to the promoter of the
badDEFGAB
(Bad) operon for the anaerobic conversion of benzoate to CHene-CoA to repress its expression. Contrary to previous reports, BadR does not appear to control expression of the Bad operon. These data enhance our view of the transcriptional regulation of anaerobic benzoate degradation by
R. palustris
.