bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities
Authors: Colin Y. , Nicolitch O. , Turpault M.-P. , Uroz S. 
Published: December 2016

ABSTRACT

Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of
Betaproteobacteria
and effective mineral-weathering bacteria related to the
Burkholderia
and
Collimonas
genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.

IMPORTANCE
Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.
Transcriptomic Responses in the Bloom-Forming Cyanobacterium Microcystis Induced during Exposure to Zooplankton
Authors: Harke Matthew J. , Jankowiak Jennifer G. , Morrell Brooke K. , Gobler Christopher J. 
Published: December 2016

ABSTRACT

The bloom-forming, toxic cyanobacterium
Microcystis
synthesizes multiple secondary metabolites and has been shown to deter zooplankton grazing. However, the biochemical and/or molecular basis by which
Microcystis
deters zooplankton remains unclear. This global transcriptomic study explored the response of
Microcystis
to direct and indirect exposures to multiple densities of two cladoceran grazers,
Daphnia pulex
and
D. magna
. Higher densities of both daphnids significantly reduced
Microcystis
cell densities and elicited a stronger transcriptional response in
Microcystis
. While many putative grazer deterrence genes (encoding microcystin, aeruginosin, cyanopeptolin, and microviridin) were largely unaffected by zooplankton, transcripts for heat shock proteins (
hsp
) increased in abundance. Beyond metabolites and
hsp
, large increases in the abundances of transcripts from photosynthetic processes were observed, evidencing energy acquisition pathways were stimulated by grazing. In addition, transcripts of genes associated with the production of extracellular polysaccharides and gas vesicles significantly increased in abundance. These genes have been associated with colony formation and may have been invoked to deter grazers. Collectively, this study demonstrates that daphnid grazers induce a significant transcriptomic response in
Microcystis
, suggesting this cyanobacterium upregulates specific biochemical pathways to adapt to predation.

IMPORTANCE
This work explores the transcriptomic responses of
Microcystis aeruginosa
following exposure to grazing by two cladocerans,
Daphnia magna
and
D. pulex
. Contrary to previous hypotheses,
Microcystis
did not employ putative grazing deterrent secondary metabolites in response to the cladocerans, suggesting they may have other roles within the cell, such as oxidative stress protection. The transcriptional metabolic signature during intense grazing was largely reflective of a growth and stress response, although increasing abundances of transcripts encoding extracellular polysaccharides and gas vesicles were potentially related to predator avoidance.
Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes
Authors: Sikora Per , Andersson Sofia , Winiecka-Krusnell Jadwiga , Hallström Björn , Alsmark Cecilia , Troell Karin , Beser Jessica , Arrighi Romanico B. G. 
Published: December 2016

ABSTRACT

In order to improve genotyping and epidemiological analysis of
Cryptosporidium
spp., genomic data need to be generated directly from a broad range of clinical specimens. Utilizing a robust method that we developed for the purification and generation of amplified target DNA, we present its application for the successful isolation and whole-genome sequencing of 14 different
Cryptosporidium hominis
patient specimens. Six isolates of subtype IbA10G2 were analyzed together with a single representative each of 8 other subtypes: IaA20R3, IaA23R3, IbA9G3, IbA13G3, IdA14, IeA11G3T3, IfA12G1, and IkA18G1. Parasite burden was measured over a range of more than 2 orders of magnitude for all samples, while the genomes were sequenced to mean depths of between 17× and 490× coverage. Sequence homology-based functional annotation identified several genes of interest, including the gene encoding
Cryptosporidium
oocyst wall protein 9 (COWP9), which presented a predicted loss-of-function mutation in all the sequence subtypes, except for that seen with IbA10G2, which has a sequence identical to the
Cryptosporidium parvum
reference Iowa II sequence. Furthermore, phylogenetic analysis showed that all the IbA10G2 genomes form a monophyletic clade in the
C. hominis
tree as expected and yet display some heterogeneity within the IbA10G2 subtype. The current report validates the aforementioned method for isolating and sequencing
Cryptosporidium
directly from clinical stool samples. In addition, the analysis demonstrates the potential in mining data generated from sequencing multiple whole genomes of
Cryptosporidium
from human fecal samples, while alluding to the potential for a higher degree of genotyping within
Cryptosporidium
epidemiology.
Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Combined Species Identification and Drug Sensitivity Testing in Mycobacteria
Authors: Ceyssens Pieter-Jan , Soetaert Karine , Timke Markus , Van den Bossche An , Sparbier Katrin , De Cremer Koen , Kostrzewa Markus , Hendrickx Marijke , Mathys Vanessa 
Published: December 2016

ABSTRACT

Species identification and drug susceptibility testing (DST) of mycobacteria are important yet complex processes traditionally reserved for reference laboratories. Recent technical improvements in matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has started to facilitate routine mycobacterial identifications in clinical laboratories. In this paper, we investigate the possibility of performing phenotypic MALDI-based DST in mycobacteriology using the recently described MALDI Biotyper antibiotic susceptibility test rapid assay (MBT-ASTRA). We randomly selected 72 clinical
Mycobacterium tuberculosis
and nontuberculous mycobacterial (NTM) strains, subjected them to MBT-ASTRA methodology, and compared its results to current gold-standard methods. Drug susceptibility was tested for rifampin, isoniazid, linezolid, and ethambutol (
M. tuberculosis
,
n
= 39), and clarithromycin and rifabutin (NTM,
n
= 33). Combined species identification was performed using the Biotyper Mycobacteria Library 4.0.
Mycobacterium
-specific MBT-ASTRA parameters were derived (calculation window,
m/z
5,000 to 13,000, area under the curve [AUC] of >0.015, relative growth [RG] of <0.5; see the text for details). Using these settings, MBT-ASTRA analyses returned 175/177
M. tuberculosis
and 65/66 NTM drug resistance profiles which corresponded to standard testing results. Turnaround times were not significantly different in
M. tuberculosis
testing, but the MBT-ASTRA method delivered on average a week faster than routine DST in NTM. Databases searches returned 90.4% correct species-level identifications, which increased to 98.6% when score thresholds were lowered to 1.65. In conclusion, the MBT-ASTRA technology holds promise to facilitate and fasten mycobacterial DST and to combine it directly with high-confidence species-level identifications. Given the ease of interpretation, its application in NTM typing might be the first in finding its way to current diagnostic workflows. However, further validations and automation are required before routine implementation can be envisioned.
Progress towards Rapid Detection of Measles Vaccine Strains: a Tool To Inform Public Health Interventions
Authors: Hacker Jill K. 
Published: December 2016

ABSTRACT

Rapid differentiation of vaccine from wild-type strains in suspect measles cases is a valuable epidemiological tool that informs the public health response to this highly infectious disease. Few public health laboratories sequence measles virus-positive specimens to determine genotype, and the vaccine-specific real-time reverse transcriptase PCR (rRT-PCR) assay described by F. Roy et al. (J. Clin. Microbiol. 55:735–743, 2017,
https://doi.org/10.1128/JCM.01879-16
) offers a rapid, easily adoptable method to identify measles vaccine strains in suspect cases.
Nonstructural Protein 4 of Porcine Reproductive and Respiratory Syndrome Virus Modulates Cell Surface Swine Leukocyte Antigen Class I Expression by Downregulating β2-Microglobulin Transcription
Authors: Qi Pengfei , Liu Ke , Wei Jianchao , Li Yuming , Li Beibei , Shao Donghua , Wu Zhuanchang , Shi Yuanyuan , Tong Guangzhi , Qiu Yafeng , Ma Zhiyong 
Published: December 2016

ABSTRACT

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of PRRS, which has important impacts on the pig industry. PRRSV infection results in disruption of the swine leukocyte antigen class I (SLA-I) antigen presentation pathway. In this study, highly pathogenic PRRSV (HP-PRRSV) infection inhibited transcription of the β2-microglobulin (β2M) gene (
B2M
) and reduced cellular levels of β2M, which forms a heterotrimeric complex with the SLA-I heavy chain and a variable peptide and plays a critical role in SLA-I antigen presentation. HP-PRRSV nonstructural protein 4 (Nsp4) was involved in the downregulation of β2M expression. Exogenous expression of Nsp4 downregulated β2M expression at both the mRNA and the protein level and reduced SLA-I expression on the cell surface. Nsp4 bound to the porcine
B2M
promoter and inhibited its transcriptional activity. Domain III of Nsp4 and the enhancer
PAM
element of the porcine
B2M
promoter were identified as essential for the interaction between Nsp4 and
B2M
. These findings demonstrate a novel mechanism whereby HP-PRRSV may modulate the SLA-I antigen presentation pathway and provide new insights into the functions of HP-PRRSV Nsp4.

IMPORTANCE
PRRSV modulates the host response by disrupting the SLA-I antigen presentation pathway. We show that HP-PRRSV downregulates SLA-I expression on the cell surface via transcriptional inhibition of
B2M
expression by viral Nsp4. The interaction between domain III of Nsp4 and the enhancer
PAM
element of the porcine
B2M
promoter is essential for inhibiting
B2M
transcription. These observations reveal a novel mechanism whereby HP-PRRSV may modulate SLA-I antigen presentation and provide new insights into the functions of viral Nsp4.
Disruption of Stress Granule Formation by the Multifunctional Cricket Paralysis Virus 1A Protein
Authors: Khong Anthony , Kerr Craig H. , Yeung Clarence H. L. , Keatings Kathleen , Nayak Arabinda , Allan Douglas W. , Jan Eric 
Published: December 2016

ABSTRACT

Stress granules (SGs) are cytosolic ribonucleoprotein aggregates that are induced during cellular stress. Several viruses modulate SG formation, suggesting that SGs have an impact on virus infection. However, the mechanisms and impact of modulating SG assembly in infected cells are not completely understood. In this study, we identify the dicistrovirus cricket paralysis virus 1A (CrPV-1A) protein that functions to inhibit SG assembly during infection. Moreover, besides inhibiting RNA interference, CrPV-1A also inhibits host transcription, which indirectly modulates SG assembly. Thus, CrPV-1A is a multifunctional protein. We identify a key R146A residue that is responsible for these effects, and mutant CrPV(R146A) virus infection is attenuated in
Drosophila melanogaster
S2 cells and adult fruit flies and results in increased SG formation. Treatment of CrPV(R146A)-infected cells with actinomycin D, which represses transcription, restores SG assembly suppression and viral yield. In summary, CrPV-1A modulates several cellular processes to generate a cellular environment that promotes viral translation and replication.

IMPORTANCE
RNA viruses encode a limited set of viral proteins to modulate an array of cellular processes in order to facilitate viral replication and inhibit antiviral defenses. In this study, we identified a viral protein, called CrPV-1A, within the dicistrovirus cricket paralysis virus that can inhibit host transcription, modulate viral translation, and block a cellular process called stress granule assembly. We also identified a specific amino acid within CrPV-1A that is important for these cellular processes and that mutant viruses containing mutations of CrPV-1A attenuate virus infection. We also demonstrate that the CrPV-1A protein can also modulate cellular processes in human cells, suggesting that the mode of action of CrPV-1A is conserved. We propose that CrPV-1A is a multifunctional, versatile protein that creates a cellular environment in virus-infected cells that permits productive virus infection.
Systematic review and meta-analysis of the effects of football heading
Authors: Kontos Anthony P , Braithwaite Rock , Chrisman Sara P D , McAllister-Deitrick Jamie , Symington Larissa , Reeves Valerie L , Collins Michael W 
Published: December 2016

Aim/objectiveThe objective of this study was to provide a meta-analysis examining the effects of football heading.DesignMeta-analytical review on football heading effects on neurocognitive performance, cognition and symptom reports.Data sourcesCombinations of the key terms were entered into the following electronic database search engines: Cochrane Libraries, PyscARTICLE, PyscINFO, PubMed, ProQuest, SPORTDiscus and Web of Science on 7 July 2016.Eligibility criteria for selecting studiesThe following inclusion criteria were used to determine eligibility for studies: (1) the study examined and reported on soccer athletes; (2) the population's age, sex and sport position was described; (3) cognitive function, symptoms, balance or other outcomes were quantitatively measured; (4) football heading exposure was quantitatively measured between at least two groups and (5) the study was written in the English language after December 1979.ResultsThe literature search process identified 467 unique studies. After applying exclusion criteria, 28 studies remained. Included studies had a total of 2288 participants (female participants =933, male participants =1355), aged 13–70 years. The overall results of random effects modelling of football heading were found to be inconclusive across all outcomes, groups and time points. No moderating variables related to methodological, sample or study characteristics were supported in the analysis; age was a potential moderating variable.Summary/conclusionsWe provide the first meta-analytical review of football heading effects aggregated from multiple studies and extended findings from a recent systematic review of the effects of football heading. Our analysis indicates no overall effect for heading a football on adverse outcomes.
Calculating acute:chronic workload ratios using exponentially weighted moving averages provides a more sensitive indicator of injury likelihood than rolling averages
Authors: Murray Nicholas B , Gabbett Tim J , Townshend Andrew D , Blanch Peter 
Published: December 2016

ObjectiveTo determine if any differences exist between the rolling averages and exponentially weighted moving averages (EWMA) models of acute:chronic workload ratio (ACWR) calculation and subsequent injury risk.MethodsA cohort of 59 elite Australian football players from 1 club participated in this 2-year study. Global positioning system (GPS) technology was used to quantify external workloads of players, and non-contact ‘time-loss’ injuries were recorded. The ACWR were calculated for a range of variables using 2 models: (1) rolling averages, and (2) EWMA. Logistic regression models were used to assess both the likelihood of sustaining an injury and the difference in injury likelihood between models.ResultsThere were significant differences in the ACWR values between models for moderate (ACWR 1.0–1.49; p=0.021), high (ACWR 1.50–1.99; p=0.012) and very high (ACWR >2.0; p=0.001) ACWR ranges. Although both models demonstrated significant (p<0.05) associations between a very high ACWR (ie, >2.0) and an increase in injury risk for total distance ((relative risk, RR)=6.52–21.28) and high-speed distance (RR=5.87–13.43), the EWMA model was more sensitive for detecting this increased risk. The variance (R2) in injury explained by each ACWR model was significantly (p<0.05) greater using the EWMA model.ConclusionsThese findings demonstrate that large spikes in workload are associated with an increased injury risk using both models, although the EWMA model is more sensitive to detect increases in injury risk with higher ACWR.
Top-down Infliximab Study in Kids with Crohn's disease (TISKids): an international multicentre randomised controlled trial
Authors: Cozijnsen M A , van Pieterson M , Samsom J N , Escher J C , de Ridder L 
Published: December 2016

IntroductionCrohn's disease (CD) is a chronic inflammatory disease predominantly affecting the gastrointestinal tract. CD usually requires lifelong medication and is accompanied by severe complications, such as fistulae and strictures, resulting in surgery. Infliximab (IFX) is very effective for treating paediatric patients with CD, but is currently only registered for therapy refractory patients—the so-called step-up strategy. We hypothesise that using IFX first-line, that is, top-down, will give more mucosal healing, fewer relapses, less complications, need for surgery and hospitalisation.Methods and analysisThis international multicentre open-label randomised controlled trial includes children, aged 3–17 years, with new-onset, untreated CD with moderate-to-severe disease activity (weighted Paediatric Crohn's Disease Activity Index (wPCDAI)>40). Eligible patients will be randomised to top-down or step-up treatment. Top-down treatment consists of 5 IFX infusions combined with azathioprine (AZA). After these 5 infusions, patients will continue AZA. Patients randomised to step-up will receive standard induction treatment, either oral prednisolone or exclusive enteral nutrition, combined with AZA as maintenance treatment. The primary outcome is clinical remission (wPCDAI<12.5) at 52 weeks without need for additional CD-related therapy or surgery. Total follow-up is 5 years. Secondary outcomes include clinical disease activity, mucosal healing by endoscopy (at week 10 and optionally week 52), faecal calprotectin, growth, quality of life, medication use and adverse events.Ethics and disseminationConducted according to the Declaration of Helsinki and Good Clinical Practice. Medical-ethical approval will be obtained for each site.Trial registration numberNCT02517684; Pre-results.
Association between reported sleep need and sleepiness at the wheel: comparative study on French highways between 1996 and 2011
Authors: Quera-Salva M A , Hartley S , Sauvagnac-Quera R , Sagaspe P , Taillard J , Contrand B , Micoulaud J A , Lagarde E , Barbot F , Philip P 
Published: December 2016

ObjectiveTo investigate the evolution over 15 years of sleep schedules, sleepiness at the wheel and driving risk among highway drivers.MethodsComparative survey including questions on usual sleep schedules and before the trip, sleepiness at the wheel, the Epworth sleepiness scale, Basic Nordic Sleep Questionnaire (BNSQ) and a travel questionnaire.Results80% of drivers stopped by the highway patrol agreed to participate in both studies with a total of 3545 drivers in 2011 and 2196 drivers in 1996 interviewed. After standardisation based on sex, age and mean annual driving distance, drivers in 2011 reported shorter sleep time on week days (p<0.0001), and week-ends (p<0.0001) and shorter optimal sleep time (p<0.0001) compared to 1996 drivers. There were more drivers sleepy at the wheel in 2011 than in 1996 (p<0.0001) and 2.5 times more drivers in 2011 than in 1996 had an Epworth sleepiness score >15 indicating severe sleepiness.ConclusionsEven if drivers in 2011 reported good sleep hygiene prior to a highway journey, drivers have reduced their mean weekly sleep duration over 15 years and have a higher risk of sleepiness at the wheel. Sleep hygiene for automobile drivers remains an important concept to address.