bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Class IIa Bacteriocin Resistance in Enterococcus faecium
Authors: Geldart Kathryn , Kaznessis Yiannis N. 
Published: January 2017

ABSTRACT

Vancomycin-resistant enterococci, particularly resistant
Enterococcus faecium
, pose an escalating threat in nosocomial environments because of their innate resistance to many antibiotics, including vancomycin, a treatment of last resort. Many class IIa bacteriocins strongly target these enterococci and may offer a potential alternative for the management of this pathogen. However,
E. faecium
's resistance to these peptides remains relatively uncharacterized. Here, we explored the development of resistance of
E. faecium
to a cocktail of three class IIa bacteriocins: enterocin A, enterocin P, and hiracin JM79. We started by quantifying the frequency of resistance to these peptides in four clinical isolates of
E. faecium
. We then investigated the levels of resistance of
E. faecium
6E6 mutants as well as their fitness in different carbon sources. In order to elucidate the mechanism of resistance of
E. faecium
to class IIa bacteriocins, we completed whole-genome sequencing of resistant mutants and performed reverse transcription-quantitative PCR (qRT-PCR) of a suspected target mannose phosphotransferase (ManPTS). We then verified this ManPTS's role in bacteriocin susceptibility by showing that expression of the ManPTS in
Lactococcus lactis
results in susceptibility to the peptide cocktail. Based on the evidence found from these studies, we conclude that, in accord with other studies in
E. faecalis
and
Listeria monocytogenes
, resistance to class IIa bacteriocins in
E. faecium
6E6 is likely caused by the disruption of a particular ManPTS, which we believe we have identified.
Management of Multiple Nitrogen Sources during Wine Fermentation by Saccharomyces cerevisiae
Authors: Crépin Lucie , Truong Nhat My , Bloem Audrey , Sanchez Isabelle , Dequin Sylvie , Camarasa Carole 
Published: January 2017

ABSTRACTDuring fermentative growth in natural and industrial environments,Saccharomyces cerevisiaemust redistribute the available nitrogen from multiple exogenous sources to amino acids in order to suitably fulfill anabolic requirements. To exhaustively explore the management of this complex resource, we developed an advanced strategy based on the reconciliation of data from a set of stable isotope tracer experiments with labeled nitrogen sources. Thus, quantifying the partitioning of the N compounds through the metabolism network during fermentation, we demonstrated that, contrary to the generally accepted view, only a limited fraction of most of the consumed amino acids is directly incorporated into proteins. Moreover, substantial catabolism of these molecules allows for efficient redistribution of nitrogen, supporting the operativede novosynthesis of proteinogenic amino acids. In contrast, catabolism of consumed amino acids plays a minor role in the formation of volatile compounds. Another important feature is that the α-keto acid precursors required for thede novosyntheses originate mainly from the catabolism of sugars, with a limited contribution from the anabolism of consumed amino acids. This work provides a comprehensive view of the intracellular fate of consumed nitrogen sources and the metabolic origin of proteinogenic amino acids, highlighting a strategy of distribution of metabolic fluxes implemented by yeast as a means of adapting to environments with changing and scarce nitrogen resources.IMPORTANCEA current challenge for the wine industry, in view of the extensive competition in the worldwide market, is to meet consumer expectations regarding the sensory profile of the product while ensuring an efficient fermentation process. Understanding the intracellular fate of the nitrogen sources available in grape juice is essential to the achievement of these objectives, since nitrogen utilization affects both the fermentative activity of yeasts and the formation of flavor compounds. However, little is known about how the metabolism operates when nitrogen is provided as a composite mixture, as in grape must. Here we quantitatively describe the distribution through the yeast metabolic network of the N moieties and C backbones of these nitrogen sources. Knowledge about the management of a complex resource, which is devoted to improvement of the use of the scarce N nutrient for growth, will be useful for better control of the fermentation process and the sensory quality of wines.
Formulation of Biocides Increases Antimicrobial Potency and Mitigates the Enrichment of Nonsusceptible Bacteria in Multispecies Biofilms
Authors: Forbes Sarah , Cowley Nicola , Humphreys Gavin , Mistry Hitesh , Amézquita Alejandro , McBain Andrew J. 
Published: January 2017

ABSTRACT
The current investigation aimed to generate data to inform the development of risk assessments of biocide usage. Stabilized domestic drain biofilm microcosms were exposed daily over 6 months to increasing concentrations (0.01% to 1%) of the biocide benzalkonium chloride (BAC) in a simple aqueous solution (BAC-s) or in a complex formulation (BAC-f) representative of a domestic cleaning agent. Biofilms were analyzed by culture, differentiating by bacterial functional group and by BAC or antibiotic susceptibility. Bacterial isolates were identified by 16S rRNA sequencing, and changes in biofilm composition were assessed by high-throughput sequencing. Exposure to BAC-f resulted in significantly larger reductions in levels of viable bacteria than exposure to BAC-s, while bacterial diversity greatly decreased during exposure to both BAC-s and BAC-f, as evidenced by sequencing and viable counts. Increases in the abundance of bacteria exhibiting reduced antibiotic or BAC susceptibility following exposure to BAC at 0.1% were significantly greater for BAC-s than BAC-f. Bacteria with reduced BAC and antibiotic susceptibility were generally suppressed by higher BAC concentrations, and formulation significantly enhanced this effect. Significant decreases in the antimicrobial susceptibility of bacteria isolated from the systems before and after long-term BAC exposure were not detected. In summary, dose-dependent suppression of bacterial viability by BAC was enhanced by formulation. Biocide exposure decreased bacterial diversity and transiently enriched populations of organisms with lower antimicrobial susceptibility, and the effects were subsequently suppressed by exposure to 1% BAC-f, the concentration most closely reflecting deployment in formulated products.

IMPORTANCE
Assessment of the risks of biocide use has been based mainly on the exposure of axenic cultures of bacteria to biocides in simple aqueous solutions. The current investigation aimed to assess the effects of formulation on the outcome of biocide exposure in multispecies biofilms. Formulation of the cationic biocide BAC significantly increased antimicrobial potency. Bacteria with lower antimicrobial susceptibility whose populations were enriched after low-level biocide exposure were more effectively suppressed by the biocide at in-use concentrations (1% [wt/vol]) in a formulation than in a simple aqueous solution. These observations underline the importance of simulating normal deployment conditions in considering the risks and benefits of biocide use.
Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss
Authors: Zhang Xian , Liu Xueduan , Liang Yili , Guo Xue , Xiao Yunhua , Ma Liyuan , Miao Bo , Liu Hongwei , Peng Deliang , Huang Wenkun , Zhang Yuguang , Yin Huaqun 
Published: January 2017

ABSTRACT

Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with
Sulfobacillus
thermosulfidooxidans
. Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the
Sulfobacillus
genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The
Sulfobacillus
strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of
Sulfobacillus
strains.

IMPORTANCE
Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.
In Vivo
Single-Cell Fluorescence and Size Scaling of Phytoplankton Chlorophyll Content
Authors: Álvarez Eva , Nogueira Enrique , López-Urrutia Ángel 
Published: January 2017

ABSTRACT
In unicellular phytoplankton, the size scaling exponent of chlorophyll content per cell decreases with increasing light limitation. Empirical studies have explored this allometry by combining data from several species, using average values of pigment content and cell size for each species. The resulting allometry thus includes phylogenetic and size scaling effects. The possibility of measuring single-cell fluorescence with imaging-in-flow cytometry devices allows the study of the size scaling of chlorophyll content at both the inter- and intraspecific levels. In this work, the changing allometry of chlorophyll content was estimated for the first time for single phytoplankton populations by using data from a series of incubations with monocultures exposed to different light levels. Interspecifically, our experiments confirm previous modeling and experimental results of increasing size scaling exponents with increasing irradiance. A similar pattern was observed intraspecifically but with a larger variability in size scaling exponents. Our results show that size-based processes and geometrical approaches explain variations in chlorophyll content. We also show that the single-cell fluorescence measurements provided by imaging-in-flow devices can be applied to field samples to understand the changes in the size dependence of chlorophyll content in response to environmental variables affecting primary production.

IMPORTANCE
The chlorophyll concentrations in phytoplankton register physiological adjustments in cellular pigmentation arising mainly from changes in light conditions. The extent of these adjustments is constrained by the size of the phytoplankton cells, even within single populations. Hence, variations in community chlorophyll derived from photoacclimation are also dependent on the phytoplankton size distribution.
Differential Gene Expression by Lactobacillus plantarum WCFS1 in Response to Phenolic Compounds Reveals New Genes Involved in Tannin Degradation
Authors: Reverón Inés , Jiménez Natalia , Curiel José Antonio , Peñas Elena , López de Felipe Félix , de las Rivas Blanca , Muñoz Rosario 
Published: January 2017

ABSTRACT

Lactobacillus plantarum
is a lactic acid bacterium that can degrade food tannins by the successive action of tannase and gallate decarboxylase enzymes. In the
L. plantarum
genome, the gene encoding the catalytic subunit of gallate decarboxylase (
lpdC
, or
lp_2945
) is only 6.5 kb distant from the gene encoding inducible tannase (
L. plantarum
tanB
[

tanB
Lp

], or
lp_2956
). This genomic context suggests concomitant activity and regulation of both enzymatic activities. Reverse transcription analysis revealed that subunits B (
lpdB
, or
lp_0271
) and D (
lpdD
, or
lp_0272
) of the gallate decarboxylase are cotranscribed, whereas subunit C (
lpdC
, or
lp_2945
) is cotranscribed with a gene encoding a transport protein (
gacP
, or
lp_2943
). In contrast, the tannase gene is transcribed as a monocistronic mRNA. Investigation of knockout mutations of genes located in this chromosomal region indicated that only mutants of the gallate decarboxylase (subunits B and C), tannase, GacP transport protein, and TanR transcriptional regulator (
lp_2942
) genes exhibited altered tannin metabolism. The expression profile of genes involved in tannin metabolism was also analyzed in these mutants in the presence of methyl gallate and gallic acid. It is noteworthy that inactivation of
tanR
suppresses the induction of all genes overexpressed in the presence of methyl gallate and gallic acid. This transcriptional regulator was also induced in the presence of other phenolic compounds, such as kaempferol and myricetin. This study complements the catalog of
L. plantarum
expression profiles responsive to phenolic compounds, which enable this bacterium to adapt to a plant food environment.

IMPORTANCE
Lactobacillus plantarum
is a bacterial species frequently found in the fermentation of vegetables when tannins are present.
L. plantarum
strains degrade tannins to the less-toxic pyrogallol by the successive action of tannase and gallate decarboxylase enzymes. The genes encoding these enzymes are located close to each other in the chromosome, suggesting concomitant regulation. Proteins involved in tannin metabolism and regulation, such GacP (gallic acid permease) and TanR (tannin transcriptional regulator), were identified by differential gene expression in knockout mutants with mutations in genes from this region. This study provides insights into the highly coordinated mechanisms that enable
L. plantarum
to adapt to plant food fermentations.
Identification of Mycobacterial RplJ/L10 and RpsA/S1 Proteins as Novel Targets for CD4+T Cells
Authors: Johnson Alison J. , Kennedy Steven C. , Lindestam Arlehamn Cecilia S. , Goldberg Michael F. , Saini Neeraj K. , Xu Jiayong , Paul Sinu , Hegde Subray S. , Blanchard John S. , Chan John , Jacobs William R. , Sette Alessandro , Porcelli Steven A. 
Published: January 2017

ABSTRACTTuberculosis (TB) due toMycobacterium tuberculosisremains a major global infectious disease problem, and a more efficacious vaccine is urgently needed for the control and prevention of disease caused by this organism. We previously reported that a genetically modified strain ofMycobacterium smegmatiscalled IKEPLUS is a promising TB vaccine candidate. Since protective immunity induced by IKEPLUS is dependent on antigen-specific CD4+T cell memory, we hypothesized that the specificity of the CD4+T cell response was a critical feature of this protection. Usingin vitroassays of interferon gamma production (enzyme-linked immunosorbent spot [ELISPOT] assays) by splenocytes from IKEPLUS-immunized C57BL/6J mice, we identified an immunogenic peptide within the mycobacterial ribosomal large subunit protein RplJ, encoded by the Rv0651 gene. In a complementary approach, we generated major histocompatibility complex (MHC) class II-restricted T cell hybridomas from IKEPLUS-immunized mice. Screening of these T cell hybridomas against IKEPLUS and ribosomes enriched from IKEPLUS suggested that the CD4+T cell response in IKEPLUS-immunized mice was dominated by the recognition of multiple components of the mycobacterial ribosome. Importantly, CD4+T cells specific for mycobacterial ribosomes accumulate to significant levels in the lungs of IKEPLUS-immunized mice following aerosol challenge with virulentM. tuberculosis, consistent with a role for these T cells in protective host immunity in TB. The identification of CD4+T cell responses to defined ribosomal protein epitopes expands the range of antigenic targets for adaptive immune responses toM. tuberculosisand may help to inform the design of more effective vaccines against tuberculosis.
A previously unrecognized high-temperature impactite from the Steen River impact structure, Alberta, Canada
Authors: Walton E. , Hughes A. , MacLagan E. , Herd C.D.K. , Dence M. 
Published: January 2017

Abstract
Here, we report a previously unrecognized impactite from the Steen River impact structure in Alberta, Canada, which was intersected by continuous diamond drill core into the allochthonous proximal deposits of this buried 25-km-diameter complex crater. A suite of high-temperature minerals defines the matrix, formed by grain growth in a solid state by static recrystallization of an originally clastic matrix, deposited at temperatures ≥800 °C. This rock type is predominantly a result of the recrystallization of target material driven by the acceleration of hot gasses from volatilized sedimentary cover mixed with variably shocked crystalline basement. Approximately one-third of terrestrial impact structures occur in mixed target rocks; therefore, this type of impactite may be more common than previously realized. Contact metamorphism between entrained sedimentary target rocks and the juxtaposed hot matrix resulted in carbonate decomposition to form a rare spinel-group mineral, magnesioferrite. In crater environments, magnesioferrite has been found in the distal Chicxulub (Mexico) ejecta and may prove a novel indicator mineral for impact into carbonate-bearing target rocks.
Seismic array constraints on reach-scale bedload transport
Authors: Schmandt B. , Gaeuman D. , Stewart R. , Hansen S.M. , Tsai V.C. , Smith J. 
Published: January 2017

Abstract
Measurements and mechanical models of heterogeneous bedload transport in rivers remain basic challenges for studies of landscape evolution and watershed management. A 700 m reach of the Trinity River (northern California, USA), a large gravel-bed river, was instrumented with an array of 76 seismographs during a dam-controlled flood and gravel augmentation to investigate the potential for out-of-stream monitoring. The temporal response to gravel augmentation during constant discharge provides strong evidence of seismic sensitivity to bedload transport and aids in identification of the seismic frequencies most sensitive to bedload in the study area. Following gravel augmentations, the seismic array reveals a period of enhanced transport that spans most or all of the reach for ∼7–10 h. Neither the duration nor the downstream extent of enhanced transport would have been constrained without the seismic array. Sensitivity to along-stream transport variations is further demonstrated by seismic amplitudes that decrease between the upper and lower halves of the reach consistent with decreased bedload flux constrained by time-lapse bathymetry. Insight into the magnitude of impact energy that reaches the bed is also gained from the seismic array. Observed peak seismic power is ∼1%–5% of that predicted by a model of saltation over exposed bedrock. Our results suggest that dissipation of impact energy due to cover effects needs to be considered to seismically constrain bedload transport rates, and that noninvasive constraints from seismology can be used to test and refine mechanical models of bedload transport.
Risk of cardiovascular events, arrhythmia and all-cause mortality associated with clarithromycin versus alternative antibiotics prescribed for respiratory tract infections: a retrospective cohort study
Authors: Berni Ellen , de Voogd Hanka , Halcox Julian P , Butler Christopher C , Bannister Christian A , Jenkins-Jones Sara , Jones Bethan , Ouwens Mario , Currie Craig J 
Published: January 2017

ObjectiveTo determine whether treatment with clarithromycin for respiratory tract infections was associated with an increased risk of cardiovascular (CV) events, arrhythmias or all-cause mortality compared with other antibiotics.DesignRetrospective cohort design comparing clarithromycin monotherapy for lower (LRTI) or upper respiratory tract infection (URTI) with other antibiotic monotherapies for the same indication.SettingRoutine primary care data from the UK Clinical Practice Research Datalink and inpatient data from the Hospital Episode Statistics (HES).ParticipantsPatients aged ≥35 years prescribed antibiotic monotherapy for LRTI or URTI 1998–2012 and eligible for data linkage to HES.Main outcome measuresThe main outcome measures were: adjusted risk of first-ever CV event, within 37 days of initiation, in commonly prescribed antibiotics compared with clarithromycin. Secondarily, adjusted 37-day risks of first-ever arrhythmia and all-cause mortality.ResultsOf 700 689 treatments for LRTI and eligible for the CV analysis, there were 2071 CV events (unadjusted event rate: 29.6 per 10 000 treatments). Of 691 998 eligible treatments for URTI, there were 688 CV events (9.9 per 10 000 treatments). In LRTI and URTI, there were no significant differences in CV risk between clarithromycin and all other antibiotics combined: OR=1.00 (95% CI 0.82 to 1.22) and 0.82 (0.54 to 1.25), respectively. Adjusted CV risk in LRTI versus clarithromycin ranged from OR=1.42 (cefalexin; 95% CI 1.08 to 1.86) to 0.92 (doxycycline; 0.64 to 1.32); in URTI, from 1.17 (co-amoxiclav; 0.68 to 2.01) to 0.67 (erythromycin; 0.40 to 1.11). Adjusted mortality risk versus clarithromycin in LRTI ranged from 0.42 to 1.32; in URTI, from 0.75 to 1.43. For arrhythmia, adjusted risks in LRTI ranged from 0.68 to 1.05; in URTI, from 0.70 to 1.22.ConclusionsCV events were more likely after LRTI than after URTI. When analysed by specific indication, CV risk associated with clarithromycin was no different to other antibiotics.