bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abundance of Ammonia-Oxidizing
Archaea
and
Bacteria
along an Estuarine Salinity Gradient in Relation to Potential Nitrification Rates
Authors: Bernhard Anne E. , Landry Zachary C. , Blevins Alison , de la Torre José R. , Giblin Anne E. , Stahl David A. 
Published: December 2009

ABSTRACT

Abundance of ammonia-oxidizing
Archaea
(AOA) was found to be always greater than that of ammonia-oxidizing
Bacteria
along an estuarine salinity gradient, and AOA abundance was highest at intermediate salinity. However, AOA abundance did not correlate with potential nitrification rates. This lack of correlation may be due to methodological limitations or alternative energy sources.
Bibersteinia trehalosiInhibits the Growth ofMannheimia haemolyticaby a Proximity-Dependent Mechanism
Authors: Dassanayake Rohana P. , Call Douglas R. , Sawant Ashish A. , Casavant N. Carol , Weiser Glen C. , Knowles Donald P. , Srikumaran Subramaniam 
Published: December 2009

ABSTRACTMannheimia(Pasteurella)haemolyticais the only pathogen that consistently causes severe bronchopneumonia and rapid death of bighorn sheep (BHS;Ovis canadensis) under experimental conditions. Paradoxically,Bibersteinia(Pasteurella)trehalosiandPasteurella multocidahave been isolated from BHS pneumonic lungs much more frequently thanM. haemolytica. These observations suggest that there may be an interaction between these bacteria, and we hypothesized thatB. trehalosiovergrows or otherwise inhibits the growth ofM. haemolytica. Growth curves (monoculture) demonstrated thatB. trehalosihas a shorter doubling time (∼10 min versus ∼27 min) and consistently achieves 3-log higher cell density (CFU/ml) compared toM. haemolytica. During cocultureM. haemolyticagrowth was inhibited whenB. trehalosientered stationary phase (6 h) resulting in a final cell density forM. haemolyticathat was 6 to 9 logs lower than expected with growth in the absence ofB. trehalosi. Coculture supernatant failed to inhibitM. haemolyticagrowth on agar or in broth, indicating no obvious involvement of lytic phages, bacteriocins, or quorum-sensing systems. This observation was confirmed by limited growth inhibition ofM. haemolyticawhen both pathogens were cultured in the same media but separated by a filter (0.4-μm pore size) that limited contact between the two bacterial populations. There was significant growth inhibition ofM. haemolyticawhen the populations were separated by membranes with a pore size of 8 μm that allowed free contact. These observations demonstrate thatB. trehalosican both outgrow and inhibitM. haemolyticagrowth with the latter related to a proximity- or contact-dependent mechanism.
Reliable Detection of Dead Microbial Cells by Using Fluorescent Hydrazides
Authors: Saint-Ruf Claude , Cordier Corinne , Mégret Jérome , Matic Ivan 
Published: December 2009

ABSTRACT
We have developed a new method for accurate quantification of dead microbial cells. This technique employs the simultaneous use of fluorescent hydrazides and nucleic acid dyes. Fluorescent hydrazides allow detection of cells that cannot be detected with currently used high-affinity nucleic acid dyes. This is particularly important for nongrowing bacterial populations and for multicellular communities containing physiologically heterogeneous cell populations, such as colonies and biofilms.
Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of
Desulfovibrio vulgaris
Hildenborough to Salt Adaptation
Authors: He Zhili , Zhou Aifen , Baidoo Edward , He Qiang , Joachimiak Marcin P. , Benke Peter , Phan Richard , Mukhopadhyay Aindrila , Hemme Christopher L. , Huang Katherine , Alm Eric J. , Fields Matthew W. , Wall Judy , Stahl David , Hazen Terry C. , Keasling Jay D. , Arkin Adam P. , Zhou Jizhong 
Published: December 2009

ABSTRACT

The response of
Desulfovibrio vulgaris
Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). The expression of genes involved in carbon metabolism, cell growth, and phage structures was decreased. Transcriptome profiles of
D. vulgaris
responses to salt adaptation were compared with transcriptome profiles of
D. vulgaris
responses to salt shock (short-term NaCl exposure). Metabolite assays showed that glutamate and alanine accumulated under salt adaptation conditions, suggesting that these amino acids may be used as osmoprotectants in
D. vulgaris
. Addition of amino acids (glutamate, alanine, and tryptophan) or yeast extract to the growth medium relieved salt-related growth inhibition. A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of
D. vulgaris
adaptation to elevated NaCl levels.
Effect of Growth Phase Feeding Strategies on Succinate Production by Metabolically Engineered
Escherichia coli
Authors: Jiang Min , Liu Shu-wen , Ma Jiang-feng , Chen Ke-quan , Yu Li , Yue Fang-fang , Xu Bing , Wei Ping 
Published: December 2009

ABSTRACT

Aerobic growth conditions significantly influenced anaerobic succinate production in two-stage fermentation by
Escherichia coli
AFP111 with knockouts in
rpoS
,
pflAB
,
ldhA
, and
ptsG
genes. At a low cell growth rate limited by glucose, enzymes involved in the reductive arm of the tricarboxylic acid cycle and the glyoxylate shunt showed elevated activities, providing AFP111 with intracellular redox balance and increased succinic acid yield and productivity.
Identification of the Main Promoter Directing Cereulide Biosynthesis in Emetic
Bacillus cereus
and Its Application for Real-Time Monitoring of
ces
Gene Expression in Foods
Authors: Dommel Monica K. , Frenzel Elrike , Strasser Bernd , Blöchinger Claudia , Scherer Siegfried , Ehling-Schulz Monika 
Published: December 2009

ABSTRACT

Cereulide, the emetic
Bacillus cereus
toxin, is synthesized by cereulide synthetase via a nonribosomal peptide synthetase (NRPS) mechanism. Previous studies focused on the identification, structural organization, and biochemical characterization of the
ces
gene locus encoding cereulide synthetase; however, detailed information about the transcriptional organization of the
ces
genes was lacking. The present study shows that the
cesPTABCD
genes are transcribed as a 23-kb polycistronic transcript, while
cesH
, encoding a putative hydrolase, is transcribed from its own promoter. Transcription initiation was mapped by primer extension and rapid amplification of cDNA ends (RACE). Deletion analysis of promoter elements revealed a main promoter located upstream of the
cesP
coding sequence, encoding a 4′-phosphopantetheinyl transferase. This promoter drives transcription of
cesPTABCD
. In addition, intracistronic promoter regions in proximity to the translational start sites of
cesB
and
cesT
were identified but were only weakly active under the chosen assay conditions. The identified main promoter was amplified from the emetic reference strain
B. cereus
F4810/72 and fused to luciferase genes in order to study promoter activity in complex environments and to establish a biomonitoring system to assess cereulide production in different types of foods.
ces
promoter activity was strongly influenced by the food matrix and varied by 5 orders of magnitude. The amount of cereulide toxin extracted from spiked foods correlated well with the bioluminescence data, thus illustrating the potential of the established reporter system for monitoring of
ces
gene expression in complex matrices.
Indigenous and Environmental Modulation of Frequencies of Mutation in
Lactobacillus plantarum
Authors: Machielsen Ronnie , van Alen-Boerrigter Ingrid J. , Koole Lucy A. , Bongers Roger S. , Kleerebezem Michiel , Van Hylckama Vlieg Johan E. T. 
Published: December 2009

ABSTRACT

Reliability of microbial (starter) strains in terms of quality, functional properties, growth performance, and robustness is essential for industrial applications. In an industrial fermentation process, the bacterium should be able to successfully withstand various adverse conditions during processing, such as acid, osmotic, temperature, and oxidative stresses. Besides the evolved defense mechanisms, stress-induced mutations participate in adaptive evolution for survival under stress conditions. However, this may lead to accumulation of mutant strains, which may be accompanied by loss of desired functional properties. Defining the effects of specific fermentation or processing conditions on the mutation frequency is an important step toward preventing loss of genome integrity and maintaining the productivity of industrial strains. Therefore, a set of
Lactobacillus plantarum
mutator reporter strains suitable for qualitative and quantitative analysis of low-frequency mutation events was developed. The mutation reporter system constructed was validated by using chemical mutagenesis (
N
-methyl-
N
′-nitro-
N
-nitrosoguanidine) and by controlled expression of endogenous candidate mutator genes (e.g., a truncated derivative of the
L. plantarum hexA
gene). Growth at different temperatures, under low-pH conditions, at high salt concentrations, or under starvation conditions did not have a significant effect on the mutation frequency. However, incubation with sublethal levels of hydrogen peroxide resulted in a 100-fold increase in the mutation frequency compared to the background mutation frequency. Importantly, when cells of
L. plantarum
were adapted to 42°C prior to treatment with sublethal levels of hydrogen peroxide, there was a 10-fold increase in survival after peroxide treatment, and there was a concomitant 50-fold decrease in the mutation frequency. These results show that specific environmental conditions encountered by bacteria may significantly influence the genetic stability of strains, while protection against mutagenic conditions may be obtained by pretreatment of cultures with other, nonmutagenic stress conditions.
The Lactococcin G Immunity Protein Recognizes Specific Regions in Both Peptides Constituting the Two-Peptide Bacteriocin Lactococcin G
Authors: Oppegård Camilla , Emanuelsen Linda , Thorbek Lisbeth , Fimland Gunnar , Nissen-Meyer Jon 
Published: December 2009

ABSTRACT

Lactococcin G and enterocin 1071 are two homologous two-peptide bacteriocins. Expression vectors containing the gene encoding the putative lactococcin G immunity protein (
lagC
) or the gene encoding the enterocin 1071 immunity protein (
entI
) were constructed and introduced into strains sensitive to one or both of the bacteriocins. Strains that were sensitive to lactococcin G became immune to lactococcin G when expressing the putative lactococcin G immunity protein, indicating that the
lagC
gene in fact encodes a protein involved in lactococcin G immunity. To determine which peptide or parts of the peptide(s) of each bacteriocin that are recognized by the cognate immunity protein, combinations of wild-type peptides and hybrid peptides from the two bacteriocins were assayed against strains expressing either of the two immunity proteins. The lactococcin G immunity protein rendered the enterococcus strain but not the lactococcus strains resistant to enterocin 1071, indicating that the functionality of the immunity protein depends on a cellular component. Moreover, regions important for recognition by the immunity protein were identified in both peptides (Lcn-α and Lcn-β) constituting lactococcin G. These regions include the N-terminal end of Lcn-α (residues 1 to 13) and the C-terminal part of Lcn-β (residues 14 to 24). According to a previously proposed structural model of lactococcin G, these regions will be positioned adjacent to each other in the transmembrane helix-helix structure, and the model thus accommodates the present results.
Development of a Common Oligonucleotide Reference Standard for Microarray Data Normalization and Comparison across Different Microbial Communities
Authors: Liang Yuting , He Zhili , Wu Liyou , Deng Ye , Li Guanghe , Zhou Jizhong 
Published: December 2009

ABSTRACT

High-density functional gene arrays have become a powerful tool for environmental microbial detection and characterization. However, microarray data normalization and comparison for this type of microarray remain a challenge in environmental microbiology studies because some commonly used normalization methods (e.g., genomic DNA) for the study of pure cultures are not applicable. In this study, we developed a common oligonucleotide reference standard (CORS) method to address this problem. A unique 50-mer reference oligonucleotide probe was selected to co-spot with gene probes for each array feature. The complementary sequence was synthesized and labeled for use as the reference target, which was then spiked and cohybridized with each sample. The signal intensity of this reference target was used for microarray data normalization and comparison. The optimal amount or concentration were determined to be ca. 0.5 to 2.5% of a gene probe for the reference probe and ca. 0.25 to 1.25 fmol/μl for the reference target based on our evaluation with a pilot array. The CORS method was then compared to dye swap and genomic DNA normalization methods using the
Desulfovibrio vulgaris
whole-genome microarray, and significant linear correlations were observed. This method was then applied to a functional gene array to analyze soil microbial communities, and the results demonstrated that the variation of signal intensities among replicates based on the CORS method was significantly lower than the total intensity normalization method. The developed CORS provides a useful approach for microarray data normalization and comparison for studies of complex microbial communities.
Aspergillus fumigatus Survival in Alkaline and Extreme Zinc-Limiting Environments Relies on the Induction of a Zinc Homeostasis System Encoded by the
zrfC
and
aspf2
Genes
Authors: Amich Jorge , Vicentefranqueira Rocío , Leal Fernando , Calera José Antonio 
Published: December 2009

ABSTRACT

Aspergillus fumigatus
has three zinc transporter-encoding genes whose expression is regulated by both pH and the environmental concentration of zinc. We have previously reported that the
zrfA
and
zrfB
genes of
A. fumigatus
are transcribed at higher levels and are required for fungal growth under acidic zinc-limiting conditions whereas they are dispensable for growth in neutral or alkaline zinc-limiting media. Here we report that the transporter of the zinc uptake system that functions in
A. fumigatus
growing in neutral or alkaline environments is encoded by
zrfC
. The transcription of
zrfC
occurs divergently with respect to the adjacent
aspf2
gene, which encodes an immunodominant antigen secreted by
A. fumigatus
. The two genes—
zrfC
and
aspf2
—are required to different extents for fungal growth in alkaline and extreme zinc-limiting media. Indeed, these environmental conditions induce the simultaneous transcription of both genes mediated by the transcriptional regulators ZafA and PacC. ZafA upregulates the expression of
zrfC
and
aspf2
under zinc-limiting conditions regardless of the ambient pH, whereas PacC represses the expression of these genes under acidic growth conditions. Interestingly, the mode of action of PacC for
zrfC-aspf2
transcription contrasts with the more widely accepted model for PacC function, according to which under alkaline growth conditions PacC would activate the transcription of alkaline-expressed genes but would repress the transcription of acid-expressed genes. In sum, this report provides a good framework for investigating several important aspects of the biology of species of
Aspergillus
, including the repression of alkaline genes by PacC at acidic pH and the interrelationship that must exist between tissue pH, metal availability in the host tissue, and fungal virulence.
Immunization with a Combination of Three Pneumococcal Proteins Confers Additive and Broad Protection against
Streptococcus pneumoniae
Infections in Mice
Authors: Wu Kaifeng , Zhang Xuemei , Shi Jing , Li Nan , Li Dairong , Luo Miao , Cao Ju , Yin Nanlin , Wang Hong , Xu Wenchun , He Yujuan , Yin Yibing 
Published: December 2009

ABSTRACT

Pneumococcal polysaccharide-based vaccines are effective in preventing pneumococcus infection; however, some drawbacks preclude their widespread use in developing and undeveloped countries. Here, we evaluated the protective effects of ATP-dependent caseinolytic protease (ClpP), pneumolysin mutant (ΔA146 Ply), putative lipoate-protein ligase (Lpl), or combinations thereof against pneumococcal infections in mice. Vaccinated mice were intraperitoneally and/or intranasally challenged with different pneumococcal strains. In intraperitoneal challenge models with pneumococcal strain D39 (serotype 2), the most striking protection was obtained with the combination of the three antigens. Similarly, with the intranasal challenge models, (i) additive clearance of bacteria in lungs was observed for the combination of the three antigens and (ii) a combination vaccine conferred complete protection against intranasal infections of three of the four most common pneumococcal strains (serotypes 14, 19F, and 23F) and 80% protection for pneumococcal strain 6B. Even so, immunity to this combination could confer protection against pneumococcal infection with a mixture of four serotypes. Our results showed that the combination vaccine was as effective as the currently used vaccines (PCV7 and PPV23). These results indicate that system immunization with the combination of pneumococcal antigens could provide an additive and broad protection against
Streptococcus pneumoniae
in pneumonia and sepsis infection models.
Assessment of Live Candidate Vaccines for Paratuberculosis in Animal Models and Macrophages
Authors: Scandurra Gabriella M. , de Lisle Geoffrey W. , Cavaignac Sonia M. , Young May , Kawakami R. Pamela , Collins Desmond M. 
Published: December 2009

ABSTRACT

Mycobacterium avium
subsp.
paratuberculosis
(basonym
M. paratuberculosis
) is the causative agent of paratuberculosis, a chronic enteritis of ruminants. To control the considerable economic effect that paratuberculosis has on the livestock industry, a vaccine that induces protection with minimal side effects is required. We employed transposon mutagenesis and allelic exchange to develop three potential vaccine candidates, which were then tested for virulence with macrophages, mice, and goats. All three models identified the WAg906 mutant as being the most attenuated, but some differences in the levels of attenuation were evident among the models when testing the other strains. In a preliminary mouse vaccine experiment, limited protection was induced by WAg915, as evidenced by a reduced bacterial load in spleens and livers 12 weeks following intraperitoneal challenge with
M. paratuberculosis
K10. While we found macrophages and murine models to be rapid and cost-effective alternatives for the initial screening of
M. paratuberculosis
mutants for attenuation, it appears necessary to do the definitive assessment of attenuation with a ruminant model.
Increase in NF-κB Binding Affinity of the Variant C Allele of the Toll-Like Receptor 9 −1237T/C Polymorphism Is Associated with
Helicobacter pylori
-Induced Gastric Disease
Authors: Ng Mike Tsz Hin , van't Hof Rob , Crockett Julie C. , Hope Mairi E. , Berry Susan , Thomson John , McLean Mairi H. , McColl Kenneth E. L. , El-Omar Emad M. , Hold Georgina L. 
Published: December 2009

ABSTRACT

Colonization of the gastric mucosa by
Helicobacter pylori
can lead to serious clinical outcomes, including gastric cancer. Toll-like receptors (TLRs) play an important role in the host response to
H. pylori
through the recognition of pathogen-associated molecular patterns. TLR9, in particular, is partly responsible for initiating bacterial induced immunity by binding unmethylated CpG-DNA, which is abundant in bacteria. A well-documented single nucleotide polymorphism (SNP) within the
TLR9
promoter (
TLR9
−1237T/C), is associated with a variety of inflammatory disorders, including allergic asthma, inflammatory bowel disease, and atopy. Analysis of the
TLR9
promoter gene sequence has shown that carriage of the variant “C” allele at position −1237 creates a potential NF-κB binding site that would theoretically increase the transcriptional activity of the gene. In this study, we report that the
TLR9
−1237 C allele was significantly associated with the development of
H. pylori
-induced premalignant gastric changes. Functional analysis of the SNP, supporting the data generated from the genetic association study, showed that carriage of the C allele increased
TLR9
transcriptional activity driven mainly by activation of NF-κB. Collectively, these findings confirm that the
TLR9
−1237T/C polymorphism is a risk factor for the development of
H. pylori
-induced premalignant gastric changes and provide a plausible mechanistic explanation.
Lost in Translation—Basic Science in the Era of Translational Research
Authors: Fang Ferric C. , Casadevall Arturo 
Published: December 2009

ABSTRACT
The concept of translational research, which aims to facilitate the application of basic scientific discoveries in clinical and community settings, is currently in vogue. While there are powerful forces driving this trend, support for translational research must be accompanied by a robust investment in basic science, which provides the essential raw material for translation and continues to represent humanity's best hope to meet a wide range of public health challenges.
Proteolytic Regulation of Toxin-Antitoxin Systems by ClpPC in
Staphylococcus aureus
Authors: Donegan Niles P. , Thompson Earl T. , Fu Zhibiao , Cheung Ambrose L. 
Published: December 2009

ABSTRACT

Bacterial toxin-antitoxin (TA) systems typically consist of a small, labile antitoxin that inactivates a specific longer-lived toxin. In
Escherichia coli
, such antitoxins are proteolytically regulated by the ATP-dependent proteases Lon and ClpP. Under normal conditions, antitoxin synthesis is sufficient to replace this loss from proteolysis, and the bacterium remains protected from the toxin. However, if TA production is interrupted, antitoxin levels decrease, and the cognate toxin is free to inhibit the specific cellular component, such as mRNA, DnaB, or gyrase. To date, antitoxin degradation has been studied only in
E. coli
, so it remains unclear whether similar mechanisms of regulation exist in other organisms. To address this, we followed antitoxin levels over time for the three known TA systems of the major human pathogen
Staphylococcus aureus
,
mazEF
,
axe1
-
txe1
, and
axe2
-
txe2
. We observed that the antitoxins of these systems, MazE

sa

, Axe1, and Axe2, respectively, were all degraded rapidly (half-life [
t
1/2
], ∼18 min) at rates notably higher than those of their
E. coli
counterparts, such as MazE (
t
1/2
, ∼30 to 60 min). Furthermore, when
S. aureus
strains deficient for various proteolytic systems were examined for changes in the half-lives of these antitoxins, only strains with
clpC
or
clpP
deletions showed increased stability of the molecules. From these studies, we concluded that ClpPC serves as the functional unit for the degradation of all known antitoxins in
S. aureus
.