bluuebunny/crossref_metadata_2025_split huggingface dataset:
Field Evaluation of Arbuscular Mycorrhizal Fungal Colonization in Bacillus thuringiensis Toxin-Expressing (Bt) and Non-Bt Maize
Authors: Cheeke Tanya E. , Cruzan Mitchell B. , Rosenstiel Todd N. 
Published: April 2013

ABSTRACT

The cultivation of genetically engineered
Bacillus thuringiensis
toxin-expressing (Bt) maize continues to increase worldwide, yet the effects of Bt crops on arbuscular mycorrhizal fungi (AMF) in soil are poorly understood. In this field experiment, we investigated the impact of seven different genotypes of Bt maize and five corresponding non-Bt parental cultivars on AMF and evaluated plant growth responses at three different physiological time points. Plants were harvested 60 days (active growth), 90 days (tasseling and starting to produce ears), and 130 days (maturity) after sowing, and data on plant growth responses and percent AMF colonization of roots at each harvest were collected. Spore abundance and diversity were also evaluated at the beginning and end of the field season to determine whether the cultivation of Bt maize had a negative effect on AMF propagules in the soil. Plant growth and AMF colonization did not differ between Bt and non-Bt maize at any harvest period, but AMF colonization was positively correlated with leaf chlorophyll content at the 130-day harvest. Cultivation of Bt maize had no effect on spore abundance and diversity in Bt versus non-Bt plots over one field season. Plot had the most significant effect on total spore counts, indicating spatial heterogeneity in the field. Although previous greenhouse studies demonstrated that AMF colonization was lower in some Bt maize lines, our field study did not yield the same results, suggesting that the cultivation of Bt maize may not have an impact on AMF in the soil ecosystem under field conditions.
Linked Expressions of
nap
and
nos
Genes in a Bradyrhizobium japonicum Mutant with Increased N
2
O Reductase Activity
Authors: Sánchez Cristina , Itakura Manabu , Mitsui Hisayuki , Minamisawa Kiwamu 
Published: April 2013

ABSTRACT

To understand the mechanisms underlying the increased N
2
O reductase activity in the
Bradyrhizobium japonicum
5M09 mutant from enrichment culture under N
2
O respiration, we analyzed the expression of genes encoding denitrification reductases and regulators. Our results suggest a common regulation of
nap
(encoding periplasmic nitrate reductase) and
nos
(encoding N
2
O reductase).
Nitrate-Dependent Ferrous Iron Oxidation by Anaerobic Ammonium Oxidation (Anammox) Bacteria
Authors: Oshiki M. , Ishii S. , Yoshida K. , Fujii N. , Ishiguro M. , Satoh H. , Okabe S. 
Published: April 2013

ABSTRACT

We examined nitrate-dependent Fe
2+
oxidation mediated by anaerobic ammonium oxidation (anammox) bacteria. Enrichment cultures of “
Candidatus
Brocadia sinica” anaerobically oxidized Fe
2+
and reduced NO
3
−
to nitrogen gas at rates of 3.7 ± 0.2 and 1.3 ± 0.1 (mean ± standard deviation [SD]) nmol mg protein
−1
min
−1
, respectively (37°C and pH 7.3). This nitrate reduction rate is an order of magnitude lower than the anammox activity of “
Ca
. Brocadia sinica” (10 to 75 nmol NH
4
+
mg protein
−1
min
−1
). A
15
N tracer experiment demonstrated that coupling of nitrate-dependent Fe
2+
oxidation and the anammox reaction was responsible for producing nitrogen gas from NO
3
−
by “
Ca
. Brocadia sinica.” The activities of nitrate-dependent Fe
2+
oxidation were dependent on temperature and pH, and the highest activities were seen at temperatures of 30 to 45°C and pHs ranging from 5.9 to 9.8. The mean half-saturation constant for NO
3
−
± SD of “
Ca
. Brocadia sinica” was determined to be 51 ± 21 μM. Nitrate-dependent Fe
2+
oxidation was further demonstrated by another anammox bacterium, “
Candidatus
Scalindua sp.,” whose rates of Fe
2+
oxidation and NO
3
−
reduction were 4.7 ± 0.59 and 1.45 ± 0.05 nmol mg protein
−1
min
−1
, respectively (20°C and pH 7.3). Co-occurrence of nitrate-dependent Fe
2+
oxidation and the anammox reaction decreased the molar ratios of consumed NO
2
−
to consumed NH
4
+
(ΔNO
2
−
/ΔNH
4
+
) and produced NO
3
−
to consumed NH
4
+
(ΔNO
3
−
/ΔNH
4
+
). These reactions are preferable to the application of anammox processes for wastewater treatment.
Predicting Salmonella Populations from Biological, Chemical, and Physical Indicators in Florida Surface Waters
Authors: McEgan Rachel , Mootian Gabriel , Goodridge Lawrence D. , Schaffner Donald W. , Danyluk Michelle D. 
Published: April 2013

ABSTRACT

Coliforms,
Escherichia coli
, and various physicochemical water characteristics have been suggested as indicators of microbial water quality or index organisms for pathogen populations. The relationship between the presence and/or concentration of
Salmonella
and biological, physical, or chemical indicators in Central Florida surface water samples over 12 consecutive months was explored. Samples were taken monthly for 12 months from 18 locations throughout Central Florida (
n
= 202). Air and water temperature, pH, oxidation-reduction potential (ORP), turbidity, and conductivity were measured. Weather data were obtained from nearby weather stations. Aerobic plate counts and most probable numbers (MPN) for
Salmonella
,
E. coli
, and coliforms were performed. Weak linear relationships existed between biological indicators (
E. coli
/coliforms) and
Salmonella
levels (
R
2
< 0.1) and between physicochemical indicators and
Salmonella
levels (
R
2
< 0.1). The average rainfall (previous day, week, and month) before sampling did not correlate well with bacterial levels. Logistic regression analysis showed that
E. coli
concentration can predict the probability of enumerating selected
Salmonella
levels. The lack of good correlations between biological indicators and
Salmonella
levels and between physicochemical indicators and
Salmonella
levels shows that the relationship between pathogens and indicators is complex. However,
Escherichia coli
provides a reasonable way to predict
Salmonella
levels in Central Florida surface water through logistic regression.
Distribution of cp32 Prophages among Lyme Disease-Causing Spirochetes and Natural Diversity of Their Lipoprotein-Encoding
erp
Loci
Authors: Brisson Dustin , Zhou Wei , Jutras Brandon L. , Casjens Sherwood , Stevenson Brian 
Published: April 2013

ABSTRACT

Lyme disease spirochetes possess complex genomes, consisting of a main chromosome and 20 or more smaller replicons. Among those small DNAs are the cp32 elements, a family of prophages that replicate as circular episomes. All complete cp32s contain an
erp
locus, which encodes surface-exposed proteins. Sequences were compared for all 193
erp
alleles carried by 22 different strains of Lyme disease-causing spirochete to investigate their natural diversity and evolutionary histories. These included multiple isolates from a focus where Lyme disease is endemic in the northeastern United States and isolates from across North America and Europe. Bacteria were derived from diseased humans and from vector ticks and included members of 5 different
Borrelia
genospecies. All
erp
operon 5′-noncoding regions were found to be highly conserved, as were the initial 70 to 80 bp of all
erp
open reading frames, traits indicative of a common evolutionary origin. However, the majority of the protein-coding regions are highly diverse, due to numerous intra- and intergenic recombination events. Most
erp
alleles are chimeras derived from sequences of closely related and distantly related
erp
sequences and from unknown origins. Since known functions of Erp surface proteins involve interactions with various host tissue components, this diversity may reflect both their multiple functions and the abilities of Lyme disease-causing spirochetes to successfully infect a wide variety of vertebrate host species.
Enumeration of Salmonella and Campylobacter spp. in Environmental Farm Samples and Processing Plant Carcass Rinses from Commercial Broiler Chicken Flocks
Authors: Berghaus Roy D. , Thayer Stephan G. , Law Bibiana F. , Mild Rita M. , Hofacre Charles L. , Singer Randall S. 
Published: April 2013

ABSTRACT

A prospective cohort study was performed to evaluate the prevalences and loads of
Salmonella
and
Campylobacter
spp. in farm and processing plant samples collected from 55 commercial broiler chicken flocks. Environmental samples were collected from broiler houses within 48 h before slaughter, and carcass rinses were performed on birds from the same flocks at 4 different stages of processing.
Salmonella
was detected in farm samples of 50 (90.9%) flocks and in processing samples of 52 (94.5%) flocks.
Campylobacter
was detected in farm samples of 35 (63.6%) flocks and in processing samples of 48 (87.3%) flocks. There was a significant positive relationship between environmental farm samples and processing plant carcass rinses with respect to both
Salmonella
and
Campylobacter
prevalences and loads.
Campylobacter
loads were significantly higher than
Salmonella
loads, and the correlations between samples collected from the same flocks were higher for
Campylobacter
than they were for
Salmonella
. Boot socks were the most sensitive sample type for detection of
Salmonella
on the farm, whereas litter samples had the strongest association with
Salmonella
loads in pre- and postchill carcass rinses. Boot socks, drag swabs, and fecal samples all had similar sensitivities for detecting
Campylobacter
on the farm, and all were more strongly associated with
Campylobacter
loads in carcass rinses than were litter samples. Farm samples explained a greater proportion of the variability in carcass rinse prevalences and loads for
Campylobacter
than they did for
Salmonella. Salmonella
and
Campylobacter
prevalences and loads both decreased significantly as birds progressed through the processing plant.
Novel PCR-Based Methods Enhance Characterization of Vaginal Microbiota in a Bacterial Vaginosis Patient before and after Treatment
Authors: Lambert Janet A. , Kalra Apoorv , Dodge Cristina T. , John Susan , Sobel Jack D. , Akins Robert A. 
Published: April 2013

ABSTRACT
Deep characterization, even by next-generation sequencing, of the vaginal microbiota in healthy women or posttreatment bacterial vaginosis patients is limited by the dominance of lactobacilli. To improve detection, we offer two approaches: quantitative PCR (qPCR) using phylogenetic branch-inclusive primers and sequencing of broad-spectrum amplicons generated with oligomers that block amplification of lactobacilli.
Inactivation of the Pta-AckA Pathway Causes Cell Death in Staphylococcus aureus
Authors: Sadykov Marat R. , Thomas Vinai C. , Marshall Darrell D. , Wenstrom Christopher J. , Moormeier Derek E. , Widhelm Todd J. , Nuxoll Austin S. , Powers Robert , Bayles Kenneth W. 
Published: April 2013

ABSTRACT

During growth under conditions of glucose and oxygen excess,
Staphylococcus aureus
predominantly accumulates acetate in the culture medium, suggesting that the phosphotransacetylase-acetate kinase (Pta-AckA) pathway plays a crucial role in bacterial fitness. Previous studies demonstrated that these conditions also induce the
S. aureus
CidR regulon involved in the control of cell death. Interestingly, the CidR regulon is comprised of only two operons, both encoding pyruvate catabolic enzymes, suggesting an intimate relationship between pyruvate metabolism and cell death. To examine this relationship, we introduced
ackA
and
pta
mutations in
S. aureus
and tested their effects on bacterial growth, carbon and energy metabolism,
cid
expression, and cell death. Inactivation of the Pta-AckA pathway showed a drastic inhibitory effect on growth and caused accumulation of dead cells in both
pta
and
ackA
mutants. Surprisingly, inactivation of the Pta-AckA pathway did not lead to a decrease in the energy status of bacteria, as the intracellular concentrations of ATP, NAD
+
, and NADH were higher in the mutants. However, inactivation of this pathway increased the rate of glucose consumption, led to a metabolic block at the pyruvate node, and enhanced carbon flux through both glycolysis and the tricarboxylic acid (TCA) cycle. Intriguingly, disruption of the Pta-AckA pathway also induced the CidR regulon, suggesting that activation of alternative pyruvate catabolic pathways could be an important survival strategy for the mutants. Collectively, the results of this study demonstrate the indispensable role of the Pta-AckA pathway in
S. aureus
for maintaining energy and metabolic homeostasis during overflow metabolism.
Mutations in the Escherichia coli Ribosomal Protein L22 Selectively Suppress the Expression of a Secreted Bacterial Virulence Factor
Authors: Mee-Ngan Yap F. , Bernstein Harris D. 
Published: April 2013

ABSTRACTMutations in the ribosomal protein L22 that impair peptide-mediated translation arrest inEscherichia colihave been shown to reduce the expression of several genes, includingsecA, which encodes an ATPase that drives protein export via the Sec pathway. Here, we used a comparative proteomic approach to obtain insight into the global effects of the L22(Δ82-84) mutation on gene expression and protein synthesis. While the mutation did not affect or modestly affected the level of most soluble proteins, it dramatically reduced the level of antigen 43 (Ag43), a secreted virulence factor that promotes autoaggregation. The reduced protein concentration correlated with a sharp decrease in the abundance and stability of Ag43 mRNA. We found that the overexpression ofsecAor the inactivation of genes that encode presecretory and membrane proteins restored Ag43 production in the L22 mutant strain. Furthermore, impairment of the Sec pathway in a wild-type strain reduced Ag43 production but did not significantly affect the synthesis of other presecretory proteins. Taken together, these results indicate that Ag43 gene expression is exquisitely sensitive to the status of the Sec machinery and strongly suggest that the L22 mutation decreases the Ag43 concentration indirectly by reducingsecAexpression. Our results imply the existence of a novel regulatory mechanism in which the efficiency of protein export is coupled to gene expression and help to explain the modulation of SecA synthesis that has been observed in response to secretion stress.
Identification of New Proteins That Modulate the Germination of Spores of Bacillus Species
Authors: Ramirez-Peralta Arturo , Gupta Srishti , Butzin Xuan Yi , Setlow Barbara , Korza George , Leyva-Vazquez Marco-Antonio , Christie Graham , Setlow Peter 
Published: April 2013

ABSTRACT

A number of operons encoding the nutrient germinant receptors (GRs) in dormant spores of
Bacillus megaterium
and
Bacillus subtilis
species have small open reading frames (ORFs) of unknown function within or immediately adjacent to the operons. Inactivation of the genes in these ORFs, encoding proteins now termed D proteins, either significantly increased or decreased spore germination via the associated GR but had no effects on germination via non-GR-dependent germinants. These effects on GR-dependent germination were complemented by ectopic expression of the appropriate
D
gene (gene encoding D protein). However, substitution of noncognate
D
genes in two GR operons resulted in inhibition of germination via the GR manipulated, although ectopic overexpression of a
D
gene had no effect on overall GR-dependent germination. The various
D
genes studied were expressed in the forespore during sporulation in parallel with the associated GR operon, and transcription of a
B. subtilis
D
gene was controlled by RNA polymerase sigma factor σ
G
. These results indicate that proteins encoded by small ORFs within or adjacent to operons encoding GRs play major roles in modulating GR function in spores of
Bacillus
species. In
B. subtilis
, deletion of a
D
gene (
B. subtilis
gerKD
[
gerKDbs
]) adjacent to the
gerK
operon encoding the GerK GR or ectopic expression or overexpression of
gerKDbs
had no major effect on the levels of GR subunits or of two other germination proteins.
A Putative Transmembrane Leucine Zipper of Agrobacterium VirB10 Is Essential for T-Pilus Biogenesis but Not Type IV Secretion
Authors: Garza Isaac , Christie Peter J. 
Published: April 2013

ABSTRACT

The
Agrobacterium tumefaciens
VirB/VirD4 type IV secretion system is composed of a translocation channel and an extracellular T pilus. Bitopic VirB10, the VirB7 lipoprotein, and VirB9 interact to form a cell envelope-spanning structural scaffold termed the “core complex” that is required for the assembly of both structures. The related pKM101-encoded core complex is composed of 14 copies each of these VirB homologs, and the transmembrane (TM) α helices of VirB10-like TraF form a 55-Å-diameter ring at the inner membrane. Here, we report that the VirB10 TM helix possesses two types of putative dimerization motifs, a GxxxA (GA
4
) motif and two leucine (Leu1, Leu2) zippers. Mutations in the Leu1 motif disrupted T-pilus biogenesis, but these or other mutations in the GA
4
or Leu2 motif did not abolish substrate transfer. Replacement of the VirB10 TM domain with a nondimerizing poly-Leu/Ala TM domain sequence also blocked pilus production but not substrate transfer or formation of immunoprecipitable complexes with the core subunits VirB7 and VirB9 and the substrate receptor VirD4. The VirB10 TM helix formed weak homodimers in
Escherichia coli
, as determined with the TOXCAT assay, whereas replacement of the VirB10 TM helix with the strongly dimerizing TM helix from glycophorin A blocked T-pilus biogenesis in
A. tumefaciens
. Our findings support a model in which VirB10's TM helix contributes to the assembly or activity of the translocation channel as a weakly self-interacting membrane anchor but establishes a heteromeric TM-TM helix interaction via its Leu1 motif that is critical for T-pilus biogenesis.
Investigating the Functional Hierarchy of Bacillus megaterium PV361 Spore Germinant Receptors
Authors: Gupta Srishti , Üstok Fatma Işık , Johnson Christian L. , Bailey David M. D. , Lowe Christopher R. , Christie Graham 
Published: April 2013

ABSTRACT

Spores of
Bacillus megaterium
QM B1551 germinate rapidly when exposed to a number of single-trigger germinant compounds, including glucose, proline, leucine, and certain inorganic salts. However, spores of strain PV361, a plasmidless QM B1551 derivative that lacks the GerU germinant receptor (GR) responsible for mediating germination in response to single-trigger compounds, can germinate efficiently when incubated in nutritionally rich media, presumably via activation of additional germinant receptors. In this work, we have identified five chromosomally encoded GRs and attempted to characterize, by mutational analysis, germinant recognition profiles associated with the respective receptors in strain PV361. Of strains engineered with single GR insertion-deletions, only GerK-null spores displayed significant defective germination phenotypes when incubated in 5% (wt/vol) beef extract or plated on rich solid medium. Cumulative decreases in viability were observed in GerK-null spores that also lacked GerA or GerA
2
, indicating that these GRs, which exerted little effect on spore germination when disrupted individually, have a degree of functionality. Unexpectedly, an efficient germination response to combinations of germinants was restored in GerA
+
spores, which lack all other functional GRs, providing evidence for negative cooperativity between some GRs within the spore. Tetrazolium-based germinative assays conducted with purified spores indicated that these newly characterized
B. megaterium
GRs are cognate for a wide and chemically diverse range of germinant molecules, but unlike GerU, can only be induced to trigger germination when stimulated by at least two different germinants.
Functional Properties and Structural Requirements of the Plasmid pMV158-Encoded MobM Relaxase Domain
Authors: Fernández-López Cris , Pluta Radoslaw , Pérez-Luque Rosa , Rodríguez-González Lorena , Espinosa Manuel , Coll Miquel , Lorenzo-Díaz Fabián , Boer D. Roeland 
Published: April 2013

ABSTRACT

A crucial element in the horizontal transfer of mobilizable and conjugative plasmids is the relaxase, a single-stranded endonuclease that nicks the origin of transfer (
oriT
) of the plasmid DNA. The relaxase of the pMV158 mobilizable plasmid is MobM (494 residues). In solution, MobM forms a dimer through its C-terminal domain, which is proposed to anchor the protein to the cell membrane and to participate in type 4 secretion system (T4SS) protein-protein interactions. In order to gain a deeper insight into the structural MobM requirements for efficient DNA catalysis, we studied two endonuclease domain variants that include the first 199 or 243 amino acid residues (MobMN199 and MobMN243, respectively). Our results confirmed that the two proteins behaved as monomers in solution. Interestingly, MobMN243 relaxed supercoiled DNA and cleaved single-stranded oligonucleotides harboring
oriT
pMV158
, whereas MobMN199 was active only on supercoiled DNA. Protein stability studies using gel electrophoresis and mass spectrometry showed increased susceptibility to degradation at the domain boundary between the N- and C-terminal domains, suggesting that the domains change their relative orientation upon DNA binding. Overall, these results demonstrate that MobMN243 is capable of nicking the DNA substrate independently of its topology and that the amino acids 200 to 243 modulate substrate specificity but not the nicking activity
per se
. These findings suggest that these amino acids are involved in positioning the DNA for the nuclease reaction rather than in the nicking mechanism itself.
Stress-Induced Outer Membrane Vesicle Production by Pseudomonas aeruginosa
Authors: MacDonald Ian A. , Kuehn Meta J. 
Published: April 2013

ABSTRACT

As an opportunistic Gram-negative pathogen,
Pseudomonas aeruginosa
must be able to adapt and survive changes and stressors in its environment during the course of infection. To aid survival in the hostile host environment,
P. aeruginosa
has evolved defense mechanisms, including the production of an exopolysaccharide capsule and the secretion of a myriad of degradative proteases and lipases. The production of outer membrane-derived vesicles (OMVs) serves as a secretion mechanism for virulence factors as well as a general bacterial response to envelope-acting stressors. This study investigated the effect of sublethal physiological stressors on OMV production by
P. aeruginosa
and whether the
Pseudomonas
quinolone signal (PQS) and the MucD periplasmic protease are critical mechanistic factors in this response. Exposure to some environmental stressors was determined to increase the level of OMV production as well as the activity of AlgU, the sigma factor that controls MucD expression. Overexpression of AlgU was shown to be sufficient to induce OMV production; however, stress-induced OMV production was not dependent on activation of AlgU, since stress caused increased vesiculation in strains lacking
algU
. We further determined that MucD levels were not an indicator of OMV production under acute stress, and PQS was not required for OMV production under stress or unstressed conditions. Finally, an investigation of the response of
P. aeruginosa
to oxidative stress revealed that peroxide-induced OMV production requires the presence of B-band but not A-band lipopolysaccharide. Together, these results demonstrate that distinct mechanisms exist for stress-induced OMV production in
P. aeruginosa
.