bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting novel chemical and constitutive primed metabolites against Plectosphaerella cucumerina
Authors: Gamir Jordi , Pastor Victoria , Kaever Alexander , Cerezo Miguel , Flors Victor 
Published: February 2014

SummaryPriming is a physiological state for protection of plants against a broad range of pathogens, and is achieved through stimulation of the plant immune system. Various stimuli, such as beneficial microbes and chemical induction, activate defense priming. In the present study, we demonstrate that impairment of the high‐affinity nitrate transporter 2.1 (encoded by NRT2.1) enables Arabidopsis to respond more quickly and strongly to Plectosphaerella cucumerina attack, leading to enhanced resistance. The Arabidopsis thaliana mutant lin1 (affected in NRT2.1) is a priming mutant that displays constitutive resistance to this necrotroph, with no associated developmental or growth costs. Chemically induced priming by β–aminobutyric acid treatment, the constitutive priming mutant ocp3 and the constitutive priming present in the lin1 mutant result in a common metabolic profile within the same plant–pathogen interactions. The defense priming significantly affects sugar metabolism, cell‐wall remodeling and shikimic acid derivatives levels, and results in specific changes in the amino acid profile and three specific branches of Trp metabolism, particularly accumulation of indole acetic acid, indole‐3–carboxaldehyde and camalexin, but not the indolic glucosinolates. Metabolomic analysis facilitated identification of three metabolites in the priming fingerprint: galacturonic acid, indole‐3–carboxylic acid and hypoxanthine. Treatment of plants with the latter two metabolites by soil drenching induced resistance against P. cucumerina, demonstrating that these compounds are key components of defense priming against this necrotrophic fungus. Here we demonstrate that indole‐3–carboxylic acid induces resistance by promoting papillae deposition and H2O2 production, and that this is independent of PR1, VSP2 and PDF1.2 priming.
Management of roadside populations of invasive Ambrosia artemisiifolia by mowing
Authors: Milakovic I , Fiedler K , Karrer G 
Published: February 2014

SummaryAmbrosia artemisiifolia (common ragweed) is a highly allergenic alien weed in Europe, which spreads rapidly along roadsides. Road verges are subject to frequent mowing, which further increases the spreading of the plants' seeds. Ambrosia artemisiifolia reacts to cutting by producing new shoots, which are able to develop flowers and ultimately new seeds. An effective mowing regime that would decrease the production of seeds and their dispersal is desirable to control the spread of the plant, but an appropriate way of mowing has yet to be found. In this study, we explored how the reproductive traits of A. artemisiifolia plants in seven spontaneous roadside populations reacted to the application of different mowing regimes over 3 years. The mowing regimes that were applied differed in the timing and frequency of cuttings. We found that the cutting regime, if appropriately timed, can strongly influence the production of male inflorescences (i.e. allergenic pollen), of female flowers (i.e. seeds) and had an impact on the phenological development of the plant. Based on our findings, we suggest that the optimal management of the plant along roadsides must be adjusted to its phenological development. The most effective mowing method of control consists of a first cut shortly before male flowering, to limit the quantities of released pollen, followed by subsequent cuts before the onset of new flowers on the resprouting lateral shoots.
Pharmacokinetics of Isoniazid in Low-Birth-Weight and Premature Infants
Authors: Bekker A. , Schaaf H. S. , Seifart H. I. , Draper H. R. , Werely C. J. , Cotton M. F. , Hesseling A. C. 
Published: February 2014

ABSTRACT

Isoniazid (INH) is recommended for use as posttuberculosis exposure preventive therapy in children. However, no pharmacokinetic data are available for INH treatment in low-birth-weight (LBW) infants, who undergo substantial developmental and physiological changes. Our objectives in this study were to determine the pharmacokinetic parameters of INH at a dose of 10 mg/kg of body weight/day and to define its pharmacokinetics relative to the arylamine
N
-acetyltransferase-2 (
NAT2
) genotype. An intensive prospective pharmacokinetic sampling study was conducted at Tygerberg Children's Hospital, South Africa, in which we measured INH blood plasma concentrations at 2, 3, 4 and 5 h postdose. Twenty LBW infants (14 male, 16 exposed to HIV) were studied. The median birth weight was 1,575 g (interquartile range, 1,190 to 2,035 g) and the median gestational age was 35 weeks (interquartile range, 34 to 38 weeks). The
NAT2
acetylation statuses of the infants were homozygous slow (SS) (5 infants), heterozygous intermediate (FS) (11 infants), and homozygous fast (FF) (4 infants). Using a noncompartmental analysis approach, the median maximum drug concentration in blood serum (
C
max
) was 5.63 μg/ml, the time after drug administration to reach
C
max
T
max
) was 2 h, the area under the concentration-time curve from 2 to 5 h (AUC
2–5
) was 13.56 μg · h/ml, the half-life (
t
1/2
) was 4.69 h, and the elimination constant rate (
k
el
) was 0.15 h
−1
. The alanine aminotransferase levels were normal, apart from 2 isolated values at two and three times above the normal levels. Only the three-times-elevated value was repeated at 6 months and normalized. All LBW infants achieved target INH blood plasma concentrations comparable to the adult values. Reduced elimination was observed in smaller and younger infants and in slow acetylators, cautioning against higher doses. The safety data, although limited, were reassuring. More data, however, are required for newborn infants.
Interspecific Quorum Sensing Mediates the Resuscitation of Viable but Nonculturable Vibrios
Authors: Ayrapetyan Mesrop , Williams Tiffany C. , Oliver James D. 
Published: February 2014

ABSTRACT

Entry and exit from dormancy are essential survival mechanisms utilized by microorganisms to cope with harsh environments. Many bacteria, including the opportunistic human pathogen
Vibrio vulnificus
, enter a form of dormancy known as the viable but nonculturable (VBNC) state. VBNC cells can resuscitate when suitable conditions arise, yet the molecular mechanisms facilitating resuscitation in most bacteria are not well understood. We discovered that bacterial cell-free supernatants (CFS) can awaken preexisting dormant vibrio populations within oysters and seawater, while CFS from a quorum sensing mutant was unable to produce the same resuscitative effect. Furthermore, the quorum sensing autoinducer AI-2 could induce resuscitation of VBNC
V. vulnificus in vitro
, and VBNC cells of a mutant unable to produce AI-2 were unable to resuscitate unless the cultures were supplemented with exogenous AI-2. The quorum sensing inhibitor cinnamaldehyde delayed the resuscitation of wild-type VBNC cells, confirming the importance of quorum sensing in resuscitation. By monitoring AI-2 production by VBNC cultures over time, we found quorum sensing signaling to be critical for the natural resuscitation process. This study provides new insights into the molecular mechanisms stimulating VBNC cell exit from dormancy, which has significant implications for microbial ecology and public health.
Viruses in a 14th-Century Coprolite
Authors: Appelt Sandra , Fancello Laura , Le Bailly Matthieu , Raoult Didier , Drancourt Michel , Desnues Christelle 
Published: February 2014

ABSTRACT

Coprolites are fossilized fecal material that can reveal information about ancient intestinal and environmental microbiota. Viral metagenomics has allowed systematic characterization of viral diversity in environmental and human-associated specimens, but little is known about the viral diversity in fossil remains. Here, we analyzed the viral community of a 14th-century coprolite from a closed barrel in a Middle Ages site in Belgium using electron microscopy and metagenomics. Viruses that infect eukaryotes, bacteria, and archaea were detected, and we confirmed the presence of some of them by
ad hoc
suicide PCR. The coprolite DNA viral metagenome was dominated by sequences showing homologies to phages commonly found in modern stools and soil. Although their phylogenetic compositions differed, the metabolic functions of the viral communities have remained conserved across centuries. Antibiotic resistance was one of the reconstructed metabolic functions detected.
Growth of Myxococcus xanthus in Continuous-Flow-Cell Bioreactors as a Method for Studying Development
Authors: Smaldone Gregory T. , Jin Yujie , Whitfield Damion L. , Mu Andrew Y. , Wong Edward C. , Wuertz Stefan , Singer Mitchell 
Published: February 2014

ABSTRACT

Nutrient sensors and developmental timers are two classes of genes vital to the establishment of early development in the social soil bacterium
Myxococcus xanthus
. The products of these genes trigger and regulate the earliest events that drive the colony from a vegetative state to aggregates, which ultimately leads to the formation of fruiting bodies and the cellular differentiation of the individual cells. In order to more accurately identify the genes and pathways involved in the initiation of this multicellular developmental program in
M. xanthus
, we adapted a method of growing vegetative populations within a constant controllable environment by using flow cell bioreactors, or flow cells. By establishing an
M. xanthus
community within a flow cell, we are able to test developmental responses to changes in the environment with fewer concerns for effects due to nutrient depletion or bacterial waste production. This approach allows for greater sensitivity in investigating communal environmental responses, such as nutrient sensing. To demonstrate the versatility of our growth environment, we carried out time-lapse confocal laser scanning microscopy to visualize
M. xanthus
biofilm growth and fruiting body development, as well as fluorescence staining of exopolysaccharides deposited by biofilms. We also employed the flow cells in a nutrient titration to determine the minimum concentration required to sustain vegetative growth. Our data show that by using a flow cell,
M. xanthus
can be held in a vegetative growth state at low nutrient concentrations for long periods, and then, by slightly decreasing the nutrient concentration, cells can be allowed to initiate the developmental program.
Conventional and Real-Time PCRs for Detection of Erwinia piriflorinigrans Allow Its Distinction from the Fire Blight Pathogen, Erwinia amylovora
Authors: Barbé Silvia , Bertolini Edson , Roselló Montserrat , Llop Pablo , López María M. 
Published: February 2014

ABSTRACT

Erwinia piriflorinigrans
is a new pathogenic species of the bacterial genus
Erwinia
that has been described recently in Spain. Accurate detection and identification of
E. piriflorinigrans
are challenging because its symptoms on pear blossoms are similar to those caused by
Erwinia amylovora
, the causal agent of fire blight. Moreover, these two species share phenotypic and molecular characteristics. Two specific and sensitive conventional and real-time PCR protocols were developed to identify and detect
E. piriflorinigrans
and to differentiate it from
E. amylovora
and other species of this genus. These protocols were based on sequences from plasmid pEPIR37, which is present in all strains of
E. piriflorinigrans
analyzed. After the stability of the plasmid was demonstrated, the specificities of the protocols were confirmed by the amplification of all
E. piriflorinigrans
strains tested, whereas 304 closely related pathogenic and nonpathogenic
Erwinia
strains and microbiota from pear trees were not amplified. In sensitivity assays, 10
3
cells/ml extract were detected in spiked plant material by conventional or real-time PCR, and 10
2
cells/ml were detected in DNA extracted from spiked plant material by real-time PCR. The protocols developed here succeeded in detecting
E. piriflorinigrans
in 102 out of 564 symptomatic and asymptomatic naturally infected pear samples (flowers, cortex stem tissue, leaves, shoots, and fruitlets), in necrotic
Pyracantha
sp. blossoms, and in necrotic pear and apple tissues infected with both
E. amylovora
and
E. piriflorinigrans
. Therefore, these new tools can be used in epidemiological studies that will enhance our understanding of the life cycle of
E. piriflorinigrans
in different hosts and plant tissues and its interaction with
E. amylovora
.
Farm Management, Environment, and Weather Factors Jointly Affect the Probability of Spinach Contamination by Generic Escherichia coli at the Preharvest Stage
Authors: Park Sangshin , Navratil Sarah , Gregory Ashley , Bauer Arin , Srinath Indumathi , Szonyi Barbara , Nightingale Kendra , Anciso Juan , Jun Mikyoung , Han Daikwon , Lawhon Sara , Ivanek Renata 
Published: February 2014

ABSTRACT

The National Resources Information (NRI) databases provide underutilized information on the local farm conditions that may predict microbial contamination of leafy greens at preharvest. Our objective was to identify NRI weather and landscape factors affecting spinach contamination with generic
Escherichia coli
individually and jointly with farm management and environmental factors. For each of the 955 georeferenced spinach samples (including 63 positive samples) collected between 2010 and 2012 on 12 farms in Colorado and Texas, we extracted variables describing the local weather (ambient temperature, precipitation, and wind speed) and landscape (soil characteristics and proximity to roads and water bodies) from NRI databases. Variables describing farm management and environment were obtained from a survey of the enrolled farms. The variables were evaluated using a mixed-effect logistic regression model with random effects for farm and date. The model identified precipitation as a single NRI predictor of spinach contamination with generic
E. coli
, indicating that the contamination probability increases with an increasing mean amount of rain (mm) in the past 29 days (odds ratio [OR] = 3.5). The model also identified the farm's hygiene practices as a protective factor (OR = 0.06) and manure application (OR = 52.2) and state (OR = 108.1) as risk factors. In cross-validation, the model showed a solid predictive performance, with an area under the receiver operating characteristic (ROC) curve of 81%. Overall, the findings highlighted the utility of NRI precipitation data in predicting contamination and demonstrated that farm management, environment, and weather factors should be considered jointly in development of good agricultural practices and measures to reduce produce contamination.
Guanidination of Soluble Lysine-Rich Cyanophycin Yields a Homoarginine-Containing Polyamide
Authors: Frommeyer Maja , Bergander Klaus , Steinbüchel Alexander 
Published: February 2014

ABSTRACT

Soluble cyanobacterial granule polypeptide (CGP), especially that isolated from recombinant
Escherichia coli
strains, consists of aspartic acid, arginine, and a greater amount of lysine than that in insoluble CGP isolated from cyanobacteria or various other recombinant bacteria.
In vitro
guanidination of lysine side chains of soluble CGP with
o
-methylisourea (OMIU) yielded the nonproteinogenic amino acid homoarginine. The modified soluble CGP consisted of 51 mol% aspartate, 14 mol% arginine, and 35 mol% homoarginine. The complete conversion of lysine residues to homoarginine was confirmed by (i) nuclear magnetic resonance spectrometry, (ii) coupled liquid chromatography-mass spectrometry, and (iii) high-performance liquid chromatography. Unlike soluble CGP, this new homoarginine-containing polyamide was soluble only under acidic or alkaline conditions and was insoluble in water or at a neutral pH. Thus, it showed solubility behavior similar to that of the natural insoluble polymer isolated from cyanobacteria, consisting of aspartic acid and arginine only. Polyacrylamide gel electrophoresis revealed similar degrees of polymerization of the native (12- to 40-kDa) and modified (10- to 35-kDa) polymers. This study showed that the chemical structure and properties of a biopolymer could be changed by
in vitro
introduction of a new functional group after biosynthesis of the native polymer. In addition, the modified CGP could be digested
in vitro
using the cyanophycinase from
Pseudomonas alcaligenes
strain DIP1, yielding a new dipeptide consisting of aspartate and homoarginine.
ExpR Coordinates the Expression of Symbiotically Important, Bundle-Forming Flp Pili with Quorum Sensing in Sinorhizobium meliloti
Authors: Zatakia Hardik M. , Nelson Cassandra E. , Syed Umair J. , Scharf Birgit E. 
Published: February 2014

ABSTRACT

Type IVb pili in enteropathogenic bacteria function as a host colonization factor by mediating tight adherence to host cells, but their role in bacterium-plant symbiosis is currently unknown. The genome of the symbiotic soil bacterium
Sinorhizobium meliloti
contains two clusters encoding proteins for type IVb pili of the Flp (fimbrial low-molecular-weight protein) subfamily. To establish the role of Flp pili in the symbiotic interaction of
S. meliloti
and its host,
Medicago sativa
, we deleted
pilA1
, which encodes the putative pilin subunit in the chromosomal
flp-1
cluster and conducted competitive nodulation assays. The
pilA1
deletion strain formed 27% fewer nodules than the wild type. Transmission electron microscopy revealed the presence of bundle-forming pili protruding from the polar and lateral region of
S. meliloti
wild-type cells. The putative pilus assembly ATPase CpaE1 fused to mCherry showed a predominantly unilateral localization. Transcriptional reporter gene assays demonstrated that expression of
pilA1
peaks in early stationary phase and is repressed by the quorum-sensing regulator ExpR, which also controls production of exopolysaccharides and motility. Binding of acyl homoserine lactone-activated ExpR to the
pilA1
promoter was confirmed with electrophoretic mobility shift assays. A 17-bp consensus sequence for ExpR binding was identified within the 28-bp protected region by DNase I footprinting analyses. Our results show that Flp pili are important for efficient symbiosis of
S. meliloti
with its plant host. The temporal inverse regulation of exopolysaccharides and pili by ExpR enables
S. meliloti
to achieve a coordinated expression of cellular processes during early stages of host interaction.
Autotrophic Carbon Dioxide Fixation via the Calvin-Benson-Bassham Cycle by the Denitrifying Methanotroph “Candidatus Methylomirabilis oxyfera”
Authors: Rasigraf Olivia , Kool Dorien M. , Jetten Mike S. M. , Sinninghe Damsté Jaap S. , Ettwig Katharina F. 
Published: February 2014

ABSTRACT

Methane is an important greenhouse gas and the most abundant hydrocarbon in the Earth's atmosphere. Methanotrophic microorganisms can use methane as their sole energy source and play a crucial role in the mitigation of methane emissions in the environment. “
Candidatus
Methylomirabilis oxyfera” is a recently described intra-aerobic methanotroph that is assumed to use nitric oxide to generate internal oxygen to oxidize methane via the conventional aerobic pathway, including the monooxygenase reaction. Previous genome analysis has suggested that, like the verrucomicrobial methanotrophs, “
Ca.
Methylomirabilis oxyfera” encodes and transcribes genes for the Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. Here we provide multiple independent lines of evidence for autotrophic carbon dioxide fixation by “
Ca.
Methylomirabilis oxyfera” via the CBB cycle. The activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), a key enzyme of the CBB cycle, in cell extracts from an “
Ca.
Methylomirabilis oxyfera” enrichment culture was shown to account for up to 10% of the total methane oxidation activity. Labeling studies with whole cells in batch incubations supplied with either
13
CH
4
or [
13
C]bicarbonate revealed that “
Ca.
Methylomirabilis oxyfera” biomass and lipids became significantly more enriched in
13
C after incubation with
13
C-labeled bicarbonate (and unlabeled methane) than after incubation with
13
C-labeled methane (and unlabeled bicarbonate), providing evidence for autotrophic carbon dioxide fixation. Besides this experimental approach, detailed genomic and transcriptomic analysis demonstrated an operational CBB cycle in “
Ca.
Methylomirabilis oxyfera.” Altogether, these results show that the CBB cycle is active and plays a major role in carbon assimilation by “
Ca.
Methylomirabilis oxyfera” bacteria. Our results suggest that autotrophy might be more widespread among methanotrophs than was previously assumed and implies that a methanotrophic community in the environment is not necessarily revealed by
13
C-depleted lipids.
Evaluation of a Loop-Mediated Isothermal Amplification Suite for the Rapid, Reliable, and Robust Detection of Shiga Toxin-Producing Escherichia coli in Produce
Authors: Wang Fei , Yang Qianru , Qu Yinzhi , Meng Jianghong , Ge Beilei 
Published: February 2014

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) strains are a leading cause of produce-associated outbreaks in the United States. Rapid, reliable, and robust detection methods are needed to better ensure produce safety. We recently developed a loop-mediated isothermal amplification (LAMP) suite for STEC detection. In this study, the STEC LAMP suite was comprehensively evaluated against real-time quantitative PCR (qPCR) using a large panel of bacterial strains (
n
= 156) and various produce items (several varieties of lettuce, spinach, and sprouts). To simulate real-world contamination events, produce samples were surface inoculated with a low level (1.2 to 1.8 CFU/25 g) of individual STEC strains belonging to seven serogroups (O26, O45, O103, O111, O121, O145, and O157) and held at 4°C for 48 h before testing. Six DNA extraction methods were also compared using produce enrichment broths. All STEC targets and their subtypes were accurately detected by the LAMP suite. The detection limits were 1 to 20 cells per reaction in pure culture and 10
5
to 10
6
CFU per 25 g (i.e., 10
3
to 10
4
CFU per g) in produce, except for strains harboring the
stx
2c
,
eae
-β, and
eae
-θ subtypes. After 6 to 8 h of enrichment, the LAMP suite achieved accurate detection of low levels of STEC strains of various
stx
2
and
eae
subtypes in lettuce and spinach varieties but not in sprouts. A similar trend of detection was observed for qPCR. The PrepMan Ultra sample preparation reagent yielded the best results among the six DNA extraction methods. This research provided a rapid, reliable, and robust method for detecting STEC in produce during routine sampling and testing. The challenge with sprouts detection by both LAMP and qPCR calls for special attention to further analysis.