1,649 research outputs found
Transcriptional analysis of temporal gene expression in germinating Clostridium difficile 630 endospores.
Clostridium difficile is the leading cause of hospital acquired diarrhoea in industrialised countries. Under conditions that are not favourable for growth, the pathogen produces metabolically dormant endospores via asymmetric cell division. These are extremely resistant to both chemical and physical stress and provide the mechanism by which C. difficile can evade the potentially fatal consequences of exposure to heat, oxygen, alcohol, and certain disinfectants. Spores are the primary infective agent and must germinate to allow for vegetative cell growth and toxin production. While spore germination in Bacillus is well understood, little is known about C. difficile germination and outgrowth. Here we use genome-wide transcriptional analysis to elucidate the temporal gene expression patterns in C. difficile 630 endospore germination. We have optimized methods for large scale production and purification of spores. The germination characteristics of purified spores have been characterized and RNA extraction protocols have been optimized. Gene expression was highly dynamic during germination and outgrowth, and was found to involve a large number of genes. Using this genome-wide, microarray approach we have identified 511 genes that are significantly up- or down-regulated during C. difficile germination (p≤0.01). A number of functional groups of genes appeared to be co-regulated. These included transport, protein synthesis and secretion, motility and chemotaxis as well as cell wall biogenesis. These data give insight into how C. difficile re-establishes its metabolism, re-builds the basic structures of the vegetative cell and resumes growth
Understanding and exploiting plant beneficial microbes
After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant–microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant–microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture
Winegrowers’ decision-making: A pan-European perspective on pesticide use and inter-row management
European viticultural landscapes not only support a significant share of rural livelihoods and cultural traditions, but also conserve biodiversity and sustain various ecosystem services. Winegrowers' practices of inter-row management (including whether to have vegetation in the inter-rows, type of vegetation, duration of vegetation cover, and soil tillage) and pesticide use (including herbicides in the inter-rows, fungicides, insecticides, and pheromone dispensers as an alternative) can affect these services. This study aims to understand winegrowers' decision-making driven by their personal characteristics, attitudes and beliefs towards viticultural practices, physical properties of vineyards, and farm management characteristics in five European winegrowing regions. These include Palatinate in Germany, Leithaberg in Austria, Tarnave in Romania, Bordeaux in France, and Montilla-Moriles in Spain. Based on a questionnaire survey, we constructed decision trees for each behaviour per case study as well as in a generic European model. We found factors that best explain how winegrowers manage their inter-rows and use pesticides. Results showed that not only do behaviours of winegrowers vary drastically across the case studies, but also the factors that explain most behaviours: farmers' attitudes and beliefs and farm management characteristics. This implies the importance of attitudes and beliefs – which are under-researched as compared to other factors – in understanding farmers’ behaviour. With the driving factors found to vary per case study, our results also imply the need for locally-adapted policies. Furthermore, our results suggest that the effects of climate change on European viticultural landscapes concern not only shifting production regions and changes in yields, but also changing pressure of pests and diseases. Any long-term behavioural change requires efforts from many stakeholders.This research was funded by the research project SECBIVIT which was funded through the 2017–2018 Belmont Forum and BiodivERsA joint call for research proposals, under the BiodivScen ERA-Net COFUND programme, with the funding organisations: Agencia Estatal de Investigación (Ministerio de ciencia e innovación/Spain), Austrian Science Fund (FWF) (grant number I 4025-B32), Federal Ministry of Education and Research (BMBF/Germany) through VDI/VDE Innovation + Technik GmbH, DLR Projektträger, French National Research Agency (ANR), Netherlands Organisation for Scientific Research (NWO), National Science Foundation (Grant #1850943) and Romanian Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI). We would like to thank all winegrowers who participated in the focus groups, online questionnaires and personal interviews and the extension services who distributed our online questionnaire through their e-mail distribution list (DLR-Rheinpfalz)
Design of synthetic bacterial communities for predictable plant phenotypes
Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant–bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation–responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities
Primary herpes simplex virus type 1 infection with acute liver failure in solid organ transplantation: Report of three cases and review
Herpes virus infections is not uncommon in solid organ transplantation patients. We report 3 cases with primary Herpes simplex virus type-1 (HSV1) infection with acute liver failure (ALF). This is a rare and potentially fatal entity that could be a donor-derived infection. Although the initial clinical presentation is non-specific, it should be considered as a differential diagnosis in HSV-negative serology patients with liver failure and empirical treatment must be started in combination with a drastic reduction of immunosuppression. A strategy of HSV prophylaxis for pre-transplant HSV seronegative patients must be stablished in order to reduce the risk of clinical disease.© 2022 Published by Elsevier Ltd
Discovery of the Optical Transient of the Gamma Ray Burst 990308
The optical transient of the faint Gamma Ray Burst 990308 was detected by the
QUEST camera on the Venezuelan 1-m Schmidt telescope starting 3.28 hours after
the burst. Our photometry gives , , , and for times ranging from 3.28 to 3.47
hours after the burst. The colors correspond to a spectral slope of close to
. Within the standard synchrotron fireball model,
this requires that the external medium be less dense than , the
electrons contain of the shock energy, and the magnetic field energy
must be less than 24% of the energy in the electrons for normal interstellar or
circumstellar densities. We also report upper limits of at 132 s
(with LOTIS), from 132-1029s (with LOTIS), at 28.2 min
(with Super-LOTIS), and a 8.5 GHz flux of at 110 days (with the
Very Large Array). WIYN 3.5-m and Keck 10-m telescopes reveal this location to
be empty of any host galaxy to and . The lack of a host
galaxy likely implies that it is either substantially subluminous or more
distant than a red shift of .Comment: ApJ Lett submitted, 5 pages, 2 figures, no space for 12 coauthor
Detection of bridge emission above 50 GeV from the Crab pulsar with the MAGIC telescopes
The Crab pulsar is the only astronomical pulsed source detected at very high
energy (VHE, E>100GeV) gamma-rays. The emission mechanism of VHE pulsation is
not yet fully understood, although several theoretical models have been
proposed. In order to test the new models, we measured the light curve and the
spectra of the Crab pulsar with high precision by means of deep observations.
We analyzed 135 hours of selected MAGIC data taken between 2009 and 2013 in
stereoscopic mode. In order to discuss the spectral shape in connection with
lower energies, 4.6 years of {\it Fermi}-LAT data were also analyzed. The known
two pulses per period were detected with a significance of and
. In addition, significant emission was found between the two
pulses with . We discovered the bridge emission above 50 GeV
between the two main pulses. This emission can not be explained with the
existing theories. These data can be used for testing new theoretical models.Comment: 5 pages, 4 figure
Detection of very high energy gamma-ray emission from the gravitationally-lensed blazar QSO B0218+357 with the MAGIC telescopes
Context. QSO B0218+357 is a gravitationally lensed blazar located at a
redshift of 0.944. The gravitational lensing splits the emitted radiation into
two components, spatially indistinguishable by gamma-ray instruments, but
separated by a 10-12 day delay. In July 2014, QSO B0218+357 experienced a
violent flare observed by the Fermi-LAT and followed by the MAGIC telescopes.
Aims. The spectral energy distribution of QSO B0218+357 can give information on
the energetics of z ~ 1 very high energy gamma- ray sources. Moreover the
gamma-ray emission can also be used as a probe of the extragalactic background
light at z ~ 1. Methods. MAGIC performed observations of QSO B0218+357 during
the expected arrival time of the delayed component of the emission. The MAGIC
and Fermi-LAT observations were accompanied by quasi-simultaneous optical data
from the KVA telescope and X-ray observations by Swift-XRT. We construct a
multiwavelength spectral energy distribution of QSO B0218+357 and use it to
model the source. The GeV and sub-TeV data, obtained by Fermi-LAT and MAGIC,
are used to set constraints on the extragalactic background light. Results.
Very high energy gamma-ray emission was detected from the direction of QSO
B0218+357 by the MAGIC telescopes during the expected time of arrival of the
trailing component of the flare, making it the farthest very high energy
gamma-ray sources detected to date. The observed emission spans the energy
range from 65 to 175 GeV. The combined MAGIC and Fermi-LAT spectral energy
distribution of QSO B0218+357 is consistent with current extragalactic
background light models. The broad band emission can be modeled in the
framework of a two zone external Compton scenario, where the GeV emission comes
from an emission region in the jet, located outside the broad line region.Comment: 11 pages, 6 figures, accepted for publication in A&
Measurement of the Crab Nebula spectrum over three decades in energy with the MAGIC telescopes
The MAGIC stereoscopic system collected 69 hours of Crab Nebula data between
October 2009 and April 2011. Analysis of this data sample using the latest
improvements in the MAGIC stereoscopic software provided an unprecedented
precision of spectral and night-by-night light curve determination at gamma
rays. We derived a differential spectrum with a single instrument from 50 GeV
up to almost 30 TeV with 5 bins per energy decade. At low energies, MAGIC
results, combined with Fermi-LAT data, show a flat and broad Inverse Compton
peak. The overall fit to the data between 1 GeV and 30 TeV is not well
described by a log-parabola function. We find that a modified log-parabola
function with an exponent of 2.5 instead of 2 provides a good description of
the data (). Using systematic uncertainties of red the MAGIC and
Fermi-LAT measurements we determine the position of the Inverse Compton peak to
be at (53 3stat + 31syst -13syst) GeV, which is the most precise
estimation up to date and is dominated by the systematic effects. There is no
hint of the integral flux variability on daily scales at energies above 300 GeV
when systematic uncertainties are included in the flux measurement. We consider
three state- of-the-art theoretical models to describe the overall spectral
energy distribution of the Crab Nebula. The constant B-field model cannot
satisfactorily reproduce the VHE spectral measurements presented in this work,
having particular difficulty reproducing the broadness of the observed IC peak.
Most probably this implies that the assumption of the homogeneity of the
magnetic field inside the nebula is incorrect. On the other hand, the
time-dependent 1D spectral model provides a good fit of the new VHE results
when considering a 80 {\mu}G magnetic field. However, it fails to match the
data when including the morphology of the nebula at lower wavelengths.Comment: accepted by JHEAp, 9 pages, 6 figure
First broadband characterization and redshift determination of the VHE blazar MAGIC J2001+439
We aim to characterize the broadband emission from 2FGL J2001.1+4352, which
has been associated with the unknown-redshift blazar MG4 J200112+4352. Based on
its gamma-ray spectral properties, it was identified as a potential very high
energy (VHE; E > 100 GeV) gamma-ray emitter. The source was observed with MAGIC
first in 2009 and later in 2010 within a multi-instrument observation campaign.
The MAGIC observations yielded 14.8 hours of good quality stereoscopic data.
The object was monitored at radio, optical and gamma-ray energies during the
years 2010 and 2011. The source, named MAGIC J2001+439, is detected for the
first time at VHE with MAGIC at a statistical significance of 6.3 {\sigma} (E >
70 GeV) during a 1.3-hour long observation on 2010 July 16. The
multi-instrument observations show variability in all energy bands with the
highest amplitude of variability in the X-ray and VHE bands. We also organized
deep imaging optical observations with the Nordic Optical Telescope in 2013 to
determine the source redshift. We determine for the first time the redshift of
this BL Lac object through the measurement of its host galaxy during low blazar
activity. Using the observational evidence that the luminosities of BL Lac host
galaxies are confined to a relatively narrow range, we obtain z = 0.18 +/-
0.04. Additionally, we use the Fermi-LAT and MAGIC gamma-ray spectra to provide
an independent redshift estimation, z = 0.17 +/- 0.10. Using the former (more
accurate) redshift value, we adequately describe the broadband emission with a
one-zone SSC model for different activity states and interpret the few-day
timescale variability as produced by changes in the high-energy component of
the electron energy distribution.Comment: 17 pages, 15 figures, Accepted for publication in A&
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