bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Bacillus thuringiensis δ-Endotoxin Active against Locusta migratoria manilensis
Authors: Wu Yan , Lei Cheng-Feng , Yi Dan , Liu Peng-Ming , Gao Mei-Ying 
Published: March 2011

ABSTRACT

A novel δ-endotoxin gene was cloned from a
Bacillus thuringiensis
strain with activity against
Locusta migratoria manilensis
by PCR-based genome walking. The sequence of the
cry
gene was 3,432 bp long, and it encoded a Cry protein of 1,144 amino acid residues with a molecular mass of 129,196.5 kDa, which exhibited 62% homology with Cry7Ba1 in the amino acid sequence. The δ-endotoxin with five conserved sequence blocks in the amino-terminal region was designated Cry7Ca1 (GenBank accession no.
EF486523
). Protein structure analysis suggested that the activated toxin of Cry7Ca1 has three domains: 227 residues forming 7 α-helices (domain I); 213 residues forming three antiparallel β-sheets (domain II); and 134 residues forming a β-sandwich (domain III). The three domains, respectively, exhibited 47, 44, and 34% sequence identity with corresponding domains of known Cry toxins. SDS-PAGE and Western blot analysis showed that Cry7Ca1, encoded by the full-length open reading frame of the
cry
gene, the activated toxin 1, which included three domains but without the N-terminal 54 amino acid residues and the C terminus, and the activated toxin 2, which included three domains and N-terminal 54 amino acid residues but without the C terminus, could be expressed in
Escherichia coli
. Bioassay results indicated that the expressed proteins of Cry7Ca1 and the activated toxins (toxins 1 and 2) showed significant activity against 2nd instar locusts, and after 7 days of infection, the estimated 50% lethal concentrations (LC
50
s) were 8.98 μg/ml for the expressed Cry7Ca1, 0.87 μg/ml for the activated toxin 1, and 4.43 μg/ml for the activated toxin 2. The δ-endotoxin also induced histopathological changes in midgut epithelial cells of adult
L. migratoria manilensis
.
Transcriptomic Responses of the Softwood-Degrading White-Rot Fungus Phanerochaete carnosa during Growth on Coniferous and Deciduous Wood
Authors: MacDonald Jacqueline , Doering Matt , Canam Thomas , Gong Yunchen , Guttman David S. , Campbell Malcolm M. , Master Emma R. 
Published: March 2011

ABSTRACT

To identify enzymes that could be developed to reduce the recalcitrance of softwood resources, the transcriptomes of the softwood-degrading white-rot fungus
Phanerochaete carnosa
were evaluated after growth on lodgepole pine, white spruce, balsam fir, and sugar maple and compared to the transcriptome of
P. carnosa
after growth on liquid nutrient medium. One hundred fifty-two million paired-end reads were obtained, and 63% of these reads were mapped to 10,257 gene models from
P. carnosa.
Five-hundred thirty-three of these genes had transcripts that were at least four times more abundant during growth on at least one wood medium than on nutrient medium. The 30 transcripts that were on average over 100 times more abundant during growth on wood than on nutrient medium included 6 manganese peroxidases, 5 cellulases, 2 hemicellulases, a lignin peroxidase, glyoxal oxidase, and a P450 monooxygenase. Notably, among the genes encoding putative cellulases, one encoding a glycosyl hydrolase family 61 protein had the highest relative transcript abundance during growth on wood. Overall, transcripts predicted to encode lignin-degrading activities were more abundant than those predicted to encode carbohydrate-active enzymes. Transcripts predicted to encode three MnPs represented the most highly abundant transcripts in wood-grown cultivations compared to nutrient medium cultivations. Gene set enrichment analyses did not distinguish transcriptomes resulting from softwood and hardwood cultivations, suggesting that similar sets of enzyme activities are elicited by
P. carnosa
grown on different wood substrates, albeit to different expression levels.
Root-Associated Ectomycorrhizal Fungi Shared by Various Boreal Forest Seedlings Naturally Regenerating after a Fire in Interior Alaska and Correlation of Different Fungi with Host Growth Responses
Authors: Bent Elizabeth , Kiekel Preston , Brenton Rebecca , Taylor D. Lee 
Published: March 2011

ABSTRACT

The role of common mycorrhizal networks (CMNs) in postfire boreal forest successional trajectories is unknown. We investigated this issue by sampling a 50-m by 40-m area of naturally regenerating black spruce (
Picea mariana
), trembling aspen (
Populus tremuloides
), and paper birch (
Betula papyrifera
) seedlings at various distances from alder (
Alnus viridis
subsp.
crispa
), a nitrogen-fixing shrub, 5 years after wildfire in an Alaskan interior boreal forest. Shoot biomasses and stem diameters of 4-year-old seedlings were recorded, and the fungal community associated with ectomycorrhizal (ECM) root tips from each seedling was profiled using molecular techniques. We found distinct assemblages of fungi associated with alder compared with those associated with the other tree species, making the formation of CMNs between them unlikely. However, among the spruce, aspen, and birch seedlings, there were many shared fungi (including members of the
Pezoloma ericae
[
Hymenoscyphus ericae
] species aggregate,
Thelephora terrestris
, and
Russula
spp.), raising the possibility that these regenerating seedlings may form interspecies CMNs. Distance between samples did not influence how similar ECM root tip-associated fungal communities were, and of the fungal groups identified, only one of them was more likely to be shared between seedlings that were closer together, suggesting that the majority of fungi surveyed did not have a clumped distribution across the small scale of this study. The presence of some fungal ribotypes was associated with larger or smaller seedlings, suggesting that these fungi may play a role in the promotion or inhibition of seedling growth. The fungal ribotypes associated with larger seedlings were different between spruce, aspen, and birch, suggesting differential impacts of some host-fungus combinations. One may speculate that wildfire-induced shifts in a given soil fungal community could result in variation in the growth response of different plant species after fire and a shift in regenerating vegetation.
Formyltetrahydrofolate Synthetase Gene Diversity in the Guts of Higher Termites with Different Diets and Lifestyles
Authors: Ottesen Elizabeth A. , Leadbetter Jared R. 
Published: March 2011

ABSTRACT

In this study, we examine gene diversity for formyl-tetrahydrofolate synthetase (FTHFS), a key enzyme in homoacetogenesis, recovered from the gut microbiota of six species of higher termites. The “higher” termites (family
Termitidae
), which represent the majority of extant termite species and genera, engage in a broader diversity of feeding and nesting styles than the “lower” termites. Previous studies of termite gut homoacetogenesis have focused on wood-feeding lower termites, from which the preponderance of FTHFS sequences recovered were related to those from acetogenic treponemes. While sequences belonging to this group were present in the guts of all six higher termites examined, treponeme-like FTHFS sequences represented the majority of recovered sequences in only two species (a wood-feeding
Nasutitermes
sp. and a palm-feeding
Microcerotermes
sp.). The remaining four termite species analyzed (a
Gnathamitermes
sp. and two
Amitermes
spp. that were recovered from subterranean nests with indeterminate feeding strategies and a litter-feeding
Rhynchotermes
sp.) yielded novel FTHFS clades not observed in lower termites. These termites yielded two distinct clusters of probable purinolytic
Firmicutes
and a large group of potential homoacetogens related to sequences previously recovered from the guts of omnivorous cockroaches. These findings suggest that the gut environments of different higher termite species may select for different groups of homoacetogens, with some species hosting treponeme-dominated homoacetogen populations similar to those of wood-feeding, lower termites while others host
Firmicutes
-dominated communities more similar to those of omnivorous cockroaches.
Antifungal Activity of Wickerhamomyces anomalus and Lactobacillus plantarum during Sourdough Fermentation: Identification of Novel Compounds and Long-Term Effect during Storage of Wheat Bread
Authors: Coda Rossana , Cassone Angela , Rizzello Carlo G. , Nionelli Luana , Cardinali Gianluigi , Gobbetti Marco 
Published: March 2011

ABSTRACT

This study aimed at investigating the antifungal activity of
Wickerhamomyces anomalus
and sourdough lactic acid bacteria to extend the shelf life of wheat flour bread. The antifungal activity was assayed by agar diffusion, growth rate inhibition, and conidial germination assays, using
Penicillium roqueforti
DPPMAF1 as the indicator fungus. Sourdough fermented by
Lactobacillus plantarum
1A7 (S1A7) and dough fermented by
W. anomalus
LCF1695 (D1695) were selected and characterized. The water/salt-soluble extract of S1A7 was partially purified, and several novel antifungal peptides, encrypted into sequences of
Oryza sativa
proteins, were identified. The water/salt-soluble extract of D1695 contained ethanol and, especially, ethyl acetate as inhibitory compounds. As shown by growth inhibition assays, both water/salt-soluble extracts had a large inhibitory spectrum, with some differences, toward the most common fungi isolated from bakeries. Bread making at a pilot plant was carried out with S1A7, D1695, or a sourdough started with a combination of both strains (S1A7-1695). Slices of the bread manufactured with S1A7-1695 did not show contamination by fungi until 28 days of storage in polyethylene bags at room temperature, a level of protection comparable to that afforded by 0.3% (wt/wt) calcium propionate. The effect of sourdough fermentation with
W. anomalus
LCF1695 was also assessed based on rheology and sensory properties.
Quantification and Evaluation of Infectivity of Shiga Toxin-Encoding Bacteriophages in Beef and Salad
Authors: Imamovic Lejla , Muniesa Maite 
Published: March 2011

ABSTRACT

Stx bacteriophages in 68 samples of beef and salad were quantified by real-time quantitative PCR (qPCR). Stx phages from the samples were propagated in
Escherichia coli
C600,
E. coli
O157:H7, and
Shigella
strains and further quantified. Fifty percent of the samples carried infectious Stx phages that were isolated from plaques generated by lysis.
Bacteriophage-Mediated Dispersal of Campylobacter jejuni Biofilms
Authors: Siringan Patcharin , Connerton Phillippa L. , Payne Robert J. H. , Connerton Ian F. 
Published: March 2011

ABSTRACTBacteria in their natural environments frequently exist as mixed surface-associated communities, protected by extracellular material, termed biofilms. Biofilms formed by the human pathogenCampylobacter jejunimay arise in the gastrointestinal tract of animals but also in water pipes and other industrial situations, leading to their possible transmission into the human food chain either directly or via farm animals. Bacteriophages are natural predators of bacteria that usually kill their prey by cell lysis and have potential application for the biocontrol and dispersal of target bacteria in biofilms. The effects of virulentCampylobacterspecific-bacteriophages CP8 and CP30 onC. jejunibiofilms formed on glass by strains NCTC 11168 and PT14 at 37°C under microaerobic conditions were investigated. Independent bacteriophage treatments (n≥ 3) led to 1 to 3 log10CFU/cm2reductions in the viable count 24 h postinfection compared with control levels. In contrast, bacteriophages applied under these conditions effected a reduction of less than 1 log10CFU/ml in planktonic cells. Resistance to bacteriophage in bacteria surviving bacteriophage treatment ofC. jejuniNCTC 11168 biofilms was 84% and 90% for CP8 and CP30, respectively, whereas bacteriophage resistance was not found in similarly recoveredC. jejuniPT14 cells. Dispersal of the biofilm matrix by bacteriophage was demonstrated by crystal violet staining and transmission electron microscopy. Bacteriophage may play an important role in the control of attachment and biofilm formation byCampylobacterin situations where biofilms occur in nature, and they have the potential for application in industrial situations leading to improvements in food safety.
New Method Using a Positively Charged Microporous Filter and Ultrafiltration for Concentration of Viruses from Tap Water
Authors: Ikner Luisa A. , Soto-Beltran Marcela , Bright Kelly R. 
Published: March 2011

ABSTRACTThe methods used to concentrate enteric viruses from water have remained largely unchanged for nearly 30 years, with the most common technique being the use of 1MDS Virozorb filters followed by organic flocculation for secondary concentration. Recently, a few studies have investigated alternatives; however, many of these methods are impractical for use in the field or share some of the limitations of this traditional method. In the present study, the NanoCeram virus sampler, an electropositive pleated microporous filter composed of microglass filaments coated with nanoalumina fibers, was evaluated. Test viruses were first concentrated by passage of 20 liters of seeded water through the filter (average filter retention efficiency was ≥99.8%), and then the viruses were recovered using various salt-based or proteinaceous eluting solutions. A 1.0% sodium polyphosphate solution with 0.05 M glycine was determined to be the most effective. The recovered viruses were then further concentrated using Centricon Plus-70 centrifugal ultrafilters to a final volume of 3.3 (±0.3 [standard deviation]) ml; this volume compares quite favorably to that of previously described methods, such as organic flocculation (∼15 to 40 ml). The overall virus recovery efficiencies were 66% for poliovirus 1, 83% for echovirus 1, 77% for coxsackievirus B5, 14% for adenovirus 2, and 56% for MS2 coliphage. In addition, this method appears to be compatible with both cell culture and PCR assays. This new approach for the recovery of viruses from water is therefore a viable alternative to currently used methods when small volumes of final concentrate are an advantage.
Transient Fecal Shedding and Limited Animal-to-Animal Transmission of Clostridium difficile by Naturally Infected Finishing Feedlot Cattle
Authors: Rodriguez-Palacios Alexander , Pickworth Carrie , Loerch Steve , LeJeune Jeffrey T. 
Published: March 2011

ABSTRACT

To longitudinally assess fecal shedding and animal-to-animal transmission of
Clostridium difficile
among finishing feedlot cattle as a risk for beef carcass contamination, we tested 186 ± 12 steers (mean ± standard deviation; 1,369 samples) in an experimental feedlot facility during the finishing period and at harvest.
Clostridium difficile
was isolated from 12.9% of steers on arrival (24/186; 0 to 33% among five suppliers). Shedding decreased to undetectable levels a week later (0%;
P
< 0.001), and remained low (<3.6%) until immediately prior to shipment for harvest (1.2%). Antimicrobial use did not increase fecal shedding, despite treatment of 53% of animals for signs of respiratory disease. Animals shedding
C. difficile
on arrival, however, had 4.6 times higher odds of receiving antimicrobials for respiratory signs than nonshedders (95% confidence interval for the odds ratio, 1.4 to 14.8;
P
= 0.01). Neither the toxin genes nor toxin A or B was detected in most (39/42) isolates based on two complementary multiplex PCRs and enzyme-linked immunosorbent assay testing, respectively. Two linezolid- and clindamycin-resistant PCR ribotype 078 (
tcdA
+
/
tcdB
+
/
cdtB
+
/39-bp-type deletion in
tcdC
) isolates were identified from two steers (at arrival and week 20), but these ribotypes did not become endemic. The other toxigenic isolate (
tcdA
+
/
tcdB
+
/
cdtB
+
/classic
tcdC
; PCR ribotype 078-like) was identified in the cecum of one steer at harvest. Spatio-temporal analysis indicated transient shedding with no evidence of animal-to-animal transmission. The association between
C. difficile
shedding upon arrival and the subsequent need for antimicrobials for respiratory disease might indicate common predisposing factors. The isolation of toxigenic
C. difficile
from bovine intestines at harvest highlights the potential for food contamination in meat processing plants.
Core and Intact Polar Glycerol Dibiphytanyl Glycerol Tetraether Lipids of Ammonia-Oxidizing Archaea Enriched from Marine and Estuarine Sediments
Authors: Pitcher Angela , Hopmans Ellen C. , Mosier Annika C. , Park Soo-Je , Rhee Sung-Keun , Francis Christopher A. , Schouten Stefan , Sinninghe Damsté Jaap S. 
Published: March 2011

ABSTRACT

Glycerol dibiphytanyl glycerol tetraether (GDGT)-based intact membrane lipids are increasingly being used as complements to conventional molecular methods in ecological studies of ammonia-oxidizing archaea (AOA) in the marine environment. However, the few studies that have been done on the detailed lipid structures synthesized by AOA in (enrichment) culture are based on species enriched from nonmarine environments, i.e., a hot spring, an aquarium filter, and a sponge. Here we have analyzed core and intact polar lipid (IPL)-GDGTs synthesized by three newly available AOA enriched directly from marine sediments taken from the San Francisco Bay estuary (“
Candidatus
Nitrosoarchaeum limnia”), and coastal marine sediments from Svalbard, Norway, and South Korea. Like previously screened AOA, the sedimentary AOA all synthesize crenarchaeol (a GDGT containing a cyclohexane moiety and four cyclopentane moieties) as a major core GDGT, thereby supporting the hypothesis that crenarchaeol is a biomarker lipid for AOA. The IPL headgroups synthesized by sedimentary AOA comprised mainly monohexose, dihexose, phosphohexose, and hexose-phosphohexose moieties. The hexose-phosphohexose headgroup bound to crenarchaeol was common to all enrichments and, in fact, the only IPL common to every AOA enrichment analyzed to date. This apparent specificity, in combination with its inferred lability, suggests that it may be the most suitable biomarker lipid to trace living AOA. GDGTs bound to headgroups with a mass of 180 Da of unknown structure appear to be specific to the marine group I.1a AOA: they were synthesized by all three sedimentary AOA and “
Candidatus
Nitrosopumilus maritimus”; however, they were absent in the group I.1b AOA “
Candidatus
Nitrososphaera gargensis.”
Improvement of Fitness and Efficacy of a Fire Blight Biocontrol Agent via Nutritional Enhancement Combined with Osmoadaptation
Authors: Cabrefiga J. , Francés J. , Montesinos E. , Bonaterra A. 
Published: March 2011

ABSTRACT

The efficacy of
Pseudomonas fluorescens
EPS62e in the biocontrol of
Erwinia amylovora
was improved by a procedure of physiological adaptation to increase colonization and survival in the phytosphere of rosaceous plants. The procedure consisted of osmoadaptation (OA) and nutritional enhancement (NE). OA was based on saline stress and osmolyte amendment of the growth medium during inoculum preparation. NE consisted of addition of glycine and Tween 80 to the formulation. NE and OA increased the growth rate and carrying capacity of EPS62e under high-relative-humidity (RH) conditions and improved survival at low RH on flowers under controlled environmental conditions. NE did not promote growth or affect infection capacity of
E. amylovora
. The effect of both methods was tested in the field by following the population of EPS62e using quantitative PCR (Q-PCR) (total population) and CFU counting (culturable population) methods. Following field application, EPS62e colonized blossoms, but it was stressed, as indicated by a sharp decrease in culturable compared to total population levels. However, once established in flowers and at the end of bloom, almost all the total population was culturable. The physiological adaptation treatments increased population levels of EPS62e over those of nonadapted cells during the late stage of the flowering period. Control of fire blight infections in flowers and immature fruits was tested by field application of EPS62e and subsequent inoculation with
E. amylovora
under controlled-environment conditions. The efficacy of fire blight control increased significantly with the combination of nutritional enhancement and osmoadaptation, in comparison with the absence of physiological adaptation.
Integrated Regulation of Acetoin Fermentation by Quorum Sensing and pH in Serratia plymuthica RVH1
Authors: Moons Pieter , Van Houdt Rob , Vivijs Bram , Michiels Chris M. , Aertsen Abram 
Published: March 2011

ABSTRACT

During fermentation of sugars, a number of bacterial species are able to switch from mixed acid production to acetoin and 2,3-butanediol production in order to avoid lethal acidification of their environment, although the regulation of this switch is only poorly understood. In this study, we report the identification of the
budAB
structural operon, involved in acetoin production in
Serratia plymuthica
RVH1, and its activation by a LysR-type regulator encoded by
budR
, immediately upstream of this operon. In addition, the regulation of
budR
transcription was elucidated and found to be subject to negative control by BudR itself and to positive control by external stimuli such as
N
-(3-oxohexanoyl)-
l
-homoserine lactone (OHHL) quorum sensing signaling molecules and acetate. Interestingly, however, we observed that induction of
budR
transcription by OHHL or acetate did not require BudR, indicating the involvement of additional regulatory factors in relaying these environmental signals to the
budR
promoter.
Binding Sites for Bacillus thuringiensis Cry2Ae Toxin on Heliothine Brush Border Membrane Vesicles Are Not Shared with Cry1A, Cry1F, or Vip3A Toxin
Authors: Gouffon C. , Van Vliet A. , Van Rie J. , Jansens S. , Jurat-Fuentes J. L. 
Published: March 2011

ABSTRACT

The use of combinations of
Bacillus thuringiensis
(Bt) toxins with diverse modes of action for insect pest control has been proposed as the most efficient strategy to increase target range and delay the onset of insect resistance. Considering that most cases of cross-resistance to Bt toxins in laboratory-selected insect colonies are due to alteration of common toxin binding sites, independent modes of action can be defined as toxins sharing limited or no binding sites in brush border membrane vesicles (BBMV) prepared from the target insect larvae. In this paper, we report on the specific binding of Cry2Ae toxin to binding sites on BBMV from larvae of the three most commercially relevant heliothine species,
Heliothis virescens
,
Helicoverpa zea
, and
Helicoverpa armigera
. Using chromatographic purification under reducing conditions before labeling, we detected specific binding of radiolabeled Cry2Ae, which allowed us to perform competition assays using Cry1Ab, Cry1Ac, Cry1Fa, Vip3A, Cry2Ae, and Cry2Ab toxins as competitors. In these assays, Cry2Ae binding sites were shared with Cry2Ab but not with the tested Cry1 or Vip3A toxins. Our data support the use of Cry2Ae toxin in combination with Cry1 or Vip3A toxins in strategies to increase target range and delay the onset of heliothine resistance.