bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Genetic Bases of
Vibrio fluvialis
Species-Specific Biochemical Pathways and Potential Virulence Factors by Comparative Genomic Analysis
Authors: Lu Xin , Liang Weili , Wang Yunduan , Xu Jialiang , Zhu Jun , Kan Biao 
Published: January 2014

ABSTRACT

Vibrio fluvialis
is an important food-borne pathogen that causes diarrheal illness and sometimes extraintestinal infections in humans. In this study, we sequenced the genome of a clinical
V. fluvialis
strain and determined its phylogenetic relationships with other
Vibrio
species by comparative genomic analysis. We found that the closest relationship was between
V. fluvialis
and
V. furnissii
, followed by those with
V. cholerae
and
V. mimicus
. Moreover, based on genome comparisons and gene complementation experiments, we revealed genetic mechanisms of the biochemical tests that differentiate
V. fluvialis
from closely related species. Importantly, we identified a variety of genes encoding potential virulence factors, including multiple hemolysins, transcriptional regulators, and environmental survival and adaptation apparatuses, and the type VI secretion system, which is indicative of complex regulatory pathways modulating pathogenesis in this organism. The availability of
V. fluvialis
genome sequences may promote our understanding of pathogenic mechanisms for this emerging pathogen.
A Rice Gene for Microbial Symbiosis,
Oryza sativa
CCaMK
, Reduces CH
4
Flux in a Paddy Field with Low Nitrogen Input
Authors: Bao Zhihua , Watanabe Aya , Sasaki Kazuhiro , Okubo Takashi , Tokida Takeshi , Liu Dongyan , Ikeda Seishi , Imaizumi-Anraku Haruko , Asakawa Susumu , Sato Tadashi , Mitsui Hisayuki , Minamisawa Kiwamu 
Published: January 2014

ABSTRACT

Plants have mutualistic symbiotic relationships with rhizobia and fungi by the common symbiosis pathway, of which Ca
2+
/calmodulin-dependent protein kinase (encoded by
CCaMK
) is a central component. Although
Oryza sativa
CCaMK
(
OsCCaMK
) is required for fungal accommodation in rice roots, little is known about the role of
OsCCaMK
in rice symbiosis with bacteria. Here, we report the effect of a
Tos17
-induced
OsCCaMK
mutant (NE1115) on CH
4
flux in low-nitrogen (LN) and standard-nitrogen (SN) paddy fields compared with wild-type (WT) Nipponbare. The growth of NE1115 was significantly decreased compared with that of the WT, especially in the LN field. The CH
4
flux of NE1115 in the LN field was significantly greater (156 to 407% in 2011 and 170 to 816% in 2012) than that of the WT, although no difference was observed in the SN field. The copy number of
pmoA
(encodes methane monooxygenase in methanotrophs) was significantly higher in the roots and rhizosphere soil of the WT than in those of NE1115. However, the
mcrA
(encodes methyl coenzyme M reductase in methanogens) copy number did not differ between the WT and NE1115. These results were supported by a
13
C-labeled CH
4
-feeding experiment. In addition, the natural abundance of
15
N in WT shoots (3.05‰) was significantly lower than in NE1115 shoots (3.45‰), suggesting greater N
2
fixation in the WT because of dilution with atmospheric N
2
(0.00‰). Thus, CH
4
oxidation and N
2
fixation were simultaneously activated in the root zone of WT rice in the LN field and both processes are likely controlled by
OsCCaMK
.
Temporal Alterations in the Secretome of the Selective Ligninolytic Fungus Ceriporiopsis subvermispora during Growth on Aspen Wood Reveal This Organism's Strategy for Degrading Lignocellulose
Authors: Hori Chiaki , Gaskell Jill , Igarashi Kiyohiko , Kersten Phil , Mozuch Michael , Samejima Masahiro , Cullen Dan 
Published: January 2014

ABSTRACTThe white-rot basidiomycetes efficiently degrade all wood cell wall polymers. Generally, these fungi simultaneously degrade cellulose and lignin, but certain organisms, such asCeriporiopsis subvermispora, selectively remove lignin in advance of cellulose degradation. However, relatively little is known about the mechanism of selective ligninolysis. To address this issue,C. subvermisporawas grown in liquid medium containing ball-milled aspen, and nano-liquid chromatography-tandem mass spectrometry was used to identify and estimate extracellular protein abundance over time. Several manganese peroxidases and an aryl alcohol oxidase, both associated with lignin degradation, were identified after 3 days of incubation. A glycoside hydrolase (GH) family 51 arabinofuranosidase was also identified after 3 days but then successively decreased in later samples. Several enzymes related to cellulose and xylan degradation, such as GH10 endoxylanase, GH5_5 endoglucanase, and GH7 cellobiohydrolase, were detected after 5 days. Peptides corresponding to potential cellulose-degrading enzymes GH12, GH45, lytic polysaccharide monooxygenase, and cellobiose dehydrogenase were most abundant after 7 days. This sequential production of enzymes provides a mechanism consistent with selective ligninolysis byC. subvermispora.
The Global Response Regulator ExpA Controls Virulence Gene Expression through RsmA-Mediated and RsmA-Independent Pathways in
Pectobacterium wasabiae
SCC3193
Authors: Broberg M. , Lee G. W. , Nykyri J. , Lee Y. H. , Pirhonen M. , Palva E. T. 
Published: January 2014

ABSTRACT

ExpA (GacA) is a global response regulator that controls the expression of major virulence genes, such as those encoding plant cell wall-degrading enzymes (PCWDEs) in the model soft rot phytopathogen
Pectobacterium wasabiae
SCC3193. Several studies with pectobacteria as well as related phytopathogenic gammaproteobacteria, such as
Dickeya
and
Pseudomonas
, suggest that the control of virulence by ExpA and its homologues is executed partly by modulating the activity of RsmA, an RNA-binding posttranscriptional regulator. To elucidate the extent of the overlap between the ExpA and RsmA regulons in
P. wasabiae
, we characterized both regulons by microarray analysis. To do this, we compared the transcriptomes of the wild-type strain, an
expA
mutant, an
rsmA
mutant, and an
expA rsmA
double mutant. The microarray data for selected virulence-related genes were confirmed through quantitative reverse transcription (qRT-PCR). Subsequently, assays were performed to link the observed transcriptome differences to changes in bacterial phenotypes such as growth, motility, PCWDE production, and virulence
in planta
. An extensive overlap between the ExpA and RsmA regulons was observed, suggesting that a substantial portion of ExpA regulation appears to be mediated through RsmA. However, a number of genes involved in the electron transport chain and oligogalacturonide metabolism, among other processes, were identified as being regulated by ExpA independently of RsmA. These results suggest that ExpA may only partially impact fitness and virulence via RsmA.
Animal Rennets as Sources of Dairy Lactic Acid Bacteria
Authors: Cruciata Margherita , Sannino Ciro , Ercolini Danilo , Scatassa Maria L. , De Filippis Francesca , Mancuso Isabella , La Storia Antonietta , Moschetti Giancarlo , Settanni Luca 
Published: January 2014

ABSTRACT

The microbial composition of artisan and industrial animal rennet pastes was studied by using both culture-dependent and -independent approaches. Pyrosequencing targeting the 16S rRNA gene allowed to identify 361 operational taxonomic units (OTUs) to the genus/species level. Among lactic acid bacteria (LAB),
Streptococcus thermophilus
and some lactobacilli, mainly
Lactobacillus crispatus
and
Lactobacillus reuteri
, were the most abundant species, with differences among the samples. Twelve groups of microorganisms were targeted by viable plate counts revealing a dominance of mesophilic cocci. All rennets were able to acidify ultrahigh-temperature-processed (UHT) milk as shown by pH and total titratable acidity (TTA). Presumptive LAB isolated at the highest dilutions of acidified milks were phenotypically characterized, grouped, differentiated at the strain level by randomly amplified polymorphic DNA (RAPD)-PCR analysis, and subjected to 16S rRNA gene sequencing. Only 18 strains were clearly identified at the species level, as
Enterococcus casseliflavus
,
Enterococcus faecium
,
Enterococcus faecalis
,
Enterococcus lactis
,
Lactobacillus delbrueckii
, and
Streptococcus thermophilus
, while the other strains, all belonging to the genus
Enterococcus
, could not be allotted into any previously described species. The phylogenetic analysis showed that these strains might represent different unknown species. All strains were evaluated for their dairy technological performances. All isolates produced diacetyl, and 10 of them produced a rapid pH drop in milk, but only 3 isolates were also autolytic. This work showed that animal rennet pastes can be sources of LAB, mainly enterococci, that might contribute to the microbial diversity associated with dairy productions.
Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves
Authors: Malmuthuge Nilusha , Griebel Philip J. , Guan Le Luo 
Published: January 2014

ABSTRACT

Bacterial colonization in the gastrointestinal tracts (GIT) of preweaned calves is very important, since it can influence early development and postweaning performance and health. This study investigated the composition of the bacteria along the GIT (rumen, jejunum, ileum, cecum, and colon) of preweaned bull calves (3 weeks old) using pyrosequencing to understand the segregation of bacteria between the mucosal surface and digesta. Phylogenetic analysis revealed that a total of 83 genera belonging to 13 phyla were distributed throughout the GIT of preweaned calves, with the
Firmicutes
,
Bacteroidetes
, and
Proteobacteria
predominating. Quantitative PCR (qPCR) analysis of selected abundant bacterial genera (
Prevotella
,
Bacteroides
,
Lactobacillus
, and
Faecalibacterium
) revealed that their prevalence was significantly different among the GIT regions and between mucosa- and digesta-associated communities. Rumens contained the most diverse bacterial population, consisting of 47 genera, including 16 rumen-specific genera, followed by the large intestine and then the small intestine. Bacterial species richness was higher at the mucosal surface than in the local digesta, with the exception of the rumen. The majority of bacteria found on the rumen epithelial surface and within the small intestine could not be identified due to a lack of known genus-level information. Thus, future studies will be required to fully characterize the microbiome during the development of the rumens and the mucosal immune systems of newborn calves. This is the first study to analyze in depth the bacterial composition of the GIT microbiome in preweaned calves, which extends previous findings regarding early rumen colonization and bacterial segregation between mucosa- and digesta-associated microbial communities.
Occurrence of Diarrheagenic Virulence Genes and Genetic Diversity in
Escherichia coli
Isolates from Fecal Material of Various Avian Hosts in British Columbia, Canada
Authors: Chandran Abhirosh , Mazumder Asit 
Published: January 2014

ABSTRACT

Contamination of surface water by fecal microorganisms originating from human and nonhuman sources is a public health concern. In the present study,
Escherichia coli
isolates (
n
= 412) from the feces of various avian host sources were screened for various virulence genes:
stx
1
and
stx
2
(Shiga toxin-producing
E. coli
[STEC]),
eae
(enteropathogenic
E. coli
[EPEC]),
est
-h,
est
-p, and
elt
(encoding heat-stable toxin [ST] variants STh and STp and heat-labile toxin [LT], respectively) (enterotoxigenic
E. coli
[ETEC]), and
ipaH
(enteroinvasive
E. coli
[EIEC]). None of the isolates were found to be positive for
stx
1
, while 23% (
n
= 93) were positive for only
stx
2
, representing STEC, and 15% (
n
= 63) were positive for only
eae
, representing EPEC. In addition, five strains obtained from pheasant were positive for both
stx
2
and
eae
and were confirmed as non-O157 by using an
E. coli
O157
rfb
(
rfb
O157
) TaqMan assay. Isolates positive for the virulence genes associated with ETEC and EIEC were not detected in any of the hosts. The repetitive element palindromic PCR (rep-PCR) fingerprint analysis identified 143 unique fingerprints, with an overall Shannon diversity index of 2.36. Multivariate analysis of variance (MANOVA) showed that the majority of the STEC and EPEC isolates were genotypically distinct from nonpathogenic
E. coli
and clustered independently. MANOVA analysis also revealed spatial variation among the
E. coli
isolates, since the majority of the isolates clustered according to the sampling locations. Although the presence of virulence genes alone cannot be used to determine the pathogenicity of strains, results from this study show that potentially pathogenic STEC and EPEC strains can be found in some of the avian hosts studied and may contaminate surface water and potentially impact human health.
Hot-Alkaline DNA Extraction Method for Deep-Subseafloor Archaeal Communities
Authors: Morono Yuki , Terada Takeshi , Hoshino Tatsuhiko , Inagaki Fumio 
Published: January 2014

ABSTRACT
A prerequisite for DNA-based microbial community analysis is even and effective cell disruption for DNA extraction. With a commonly used DNA extraction kit, roughly two-thirds of subseafloor sediment microbial cells remain intact on average (i.e., the cells are not disrupted), indicating that microbial community analyses may be biased at the DNA extraction step, prior to subsequent molecular analyses. To address this issue, we standardized a new DNA extraction method using alkaline treatment and heating. Upon treatment with 1 M NaOH at 98°C for 20 min, over 98% of microbial cells in subseafloor sediment samples collected at different depths were disrupted. However, DNA integrity tests showed that such strong alkaline and heat treatment also cleaved DNA molecules into short fragments that could not be amplified by PCR. Subsequently, we optimized the alkaline and temperature conditions to minimize DNA fragmentation and retain high cell disruption efficiency. The best conditions produced a cell disruption rate of 50 to 80% in subseafloor sediment samples from various depths and retained sufficient DNA integrity for amplification of the complete 16S rRNA gene (i.e., ∼1,500 bp). The optimized method also yielded higher DNA concentrations in all samples tested compared with extractions using a conventional kit-based approach. Comparative molecular analysis using real-time PCR and pyrosequencing of bacterial and archaeal 16S rRNA genes showed that the new method produced an increase in archaeal DNA and its diversity, suggesting that it provides better analytical coverage of subseafloor microbial communities than conventional methods.
Calcineurin Controls Hyphal Growth, Virulence, and Drug Tolerance of Candida tropicalis
Authors: Chen Ying-Lien , Yu Shang-Jie , Huang Hsin-Yu , Chang Ya-Lin , Lehman Virginia N. , Silao Fitz Gerald S. , Bigol Ursela G. , Bungay Alice Alma C. , Averette Anna , Heitman Joseph 
Published: January 2014

ABSTRACT

Candida tropicalis
, a species closely related to
Candida albicans
, is an emerging fungal pathogen associated with high mortality rates of 40 to 70%. Like
C. albicans
and
Candida dubliniensis
,
C. tropicalis
is able to form germ tubes, pseudohyphae, and hyphae, but the genes involved in hyphal growth machinery and virulence remain unclear in
C. tropicalis
. Recently, echinocandin- and azole-resistant
C. tropicalis
isolates have frequently been isolated from various patients around the world, making treatment difficult. However, studies of the
C. tropicalis
genes involved in drug tolerance are limited. Here, we investigated the roles of calcineurin and its potential target, Crz1, for core stress responses and pathogenesis in
C. tropicalis
. We demonstrate that calcineurin and Crz1 are required for hyphal growth, micafungin tolerance, and virulence in a murine systemic infection model, while calcineurin but not Crz1 is essential for tolerance of azoles, caspofungin, anidulafungin, and cell wall-perturbing agents, suggesting that calcineurin has both Crz1-dependent and -independent functions in
C. tropicalis
. In addition, we found that calcineurin and Crz1 have opposite roles in controlling calcium tolerance. Calcineurin serves as a negative regulator, while Crz1 plays a positive role for calcium tolerance in
C. tropicalis
.
High-Throughput Chemical Screening for Antivirulence Developmental Phenotypes in Trypanosoma brucei
Authors: MacGregor Paula , Ivens Alasdair , Shave Steven , Collie Iain , Gray David , Auer Manfred , Matthews Keith R. 
Published: January 2014

ABSTRACT

In the bloodstream of mammalian hosts, the sleeping sickness parasite,
Trypanosoma brucei
, exists as a proliferative slender form or a nonproliferative, transmissible, stumpy form. The transition between these developmental forms is controlled by a density-dependent mechanism that is important for the parasite's infection dynamics, immune evasion via ordered antigenic variation, and disease transmissibility. However, stumpy formation has been lost in most laboratory-adapted trypanosome lines, generating monomorphic parasites that proliferate uncontrolled as slender forms
in vitro
and
in vivo
. Nonetheless, these forms are readily amenable to cell culture and high-throughput screening for trypanocidal lead compounds. Here, we have developed and exploited a high-throughput screen for developmental phenotypes using a transgenic monomorphic cell line expressing a reporter under the regulation of gene control signals from the stumpy-specific molecule PAD1. Using a whole-cell fluorescence-based assay to screen over 6,000 small molecules from a kinase-focused compound library, small molecules able to activate stumpy-specific gene expression and proliferation arrest were assayed in a rapid assay format. Independent follow-up validation identified one hit able to induce modest, yet specific, changes in mRNA expression indicative of a partial differentiation to stumpy forms in monomorphs. Further, in pleomorphs this compound induced a stumpy-like phenotype, entailing growth arrest, morphological changes, PAD1 expression, and enhanced differentiation to procyclic forms. This not only provides a potential tool compound for the further understanding of stumpy formation but also demonstrates the use of high-throughput screening in the identification of compounds able to induce specific phenotypes, such as differentiation, in African trypanosomes.
Regulatory and Functional Diversity of Methylmercaptopropionate Coenzyme A Ligases from the Dimethylsulfoniopropionate Demethylation Pathway in Ruegeria pomeroyi DSS-3 and Other Proteobacteria
Authors: Bullock Hannah A. , Reisch Chris R. , Burns Andrew S. , Moran Mary Ann , Whitman William B. 
Published: January 2014

ABSTRACT

The organosulfur compound dimethylsulfoniopropionate (DMSP) is produced by phytoplankton and is ubiquitous in the surface ocean. Once released from phytoplankton, marine bacteria degrade DMSP by either the cleavage pathway to form the volatile gas dimethylsulfide (DMS) or the demethylation pathway, yielding methanethiol (MeSH), which is readily assimilated or oxidized. The enzyme DmdB, a methylmercaptopropionate (MMPA)-coenzyme A (CoA) ligase, catalyzes the second step in the demethylation pathway and is a major regulatory point. The two forms of DmdB present in the marine roseobacter
Ruegeria pomeroyi
DSS-3, RPO_DmdB1 and RPO_DmdB2, and the single form in the SAR11 clade bacterium “
Candidatus
Pelagibacter ubique” HTCC1062, PU_DmdB1, were characterized in detail. DmdB enzymes were also examined from
Ruegeria lacuscaerulensis
ITI-1157,
Pseudomonas aeruginosa
PAO1, and
Burkholderia thailandensis
E264. The DmdB enzymes separated into two phylogenetic clades. All enzymes had activity with MMPA and were sensitive to inhibition by salts, but there was no correlation between the clades and substrate specificity or salt sensitivity. All
Ruegeria
species enzymes were inhibited by physiological concentrations (70 mM) of DMSP. However, ADP reversed the inhibition of RPO_DmdB1, suggesting that this enzyme was responsive to cellular energy charge. MMPA reversed the inhibition of RPO_DmdB2 as well as both
R. lacuscaerulensis
ITI-1157 DmdB enzymes, suggesting that a complex regulatory system exists in marine bacteria. In contrast, the DmdBs of the non-DMSP-metabolizing
P. aeruginosa
PAO1 and
B. thailandensis
E264 were not inhibited by DMSP, suggesting that DMSP inhibition is a specific adaptation of DmdBs from marine bacteria.
Salinity-Dependent Impacts of ProQ, Prc, and Spr Deficiencies on Escherichia coli Cell Structure
Authors: Kerr Craig H. , Culham Doreen E. , Marom David , Wood Janet M. 
Published: January 2014

ABSTRACT

ProQ is a cytoplasmic protein with RNA chaperone activities that reside in FinO- and Hfq-like domains. Lesions at
proQ
decrease the level of the osmoregulatory glycine betaine transporter ProP. Lesions at
proQ
eliminated ProQ and Prc, the periplasmic protease encoded by the downstream gene
prc
. They dramatically slowed the growth of
Escherichia coli
populations and altered the morphologies of
E. coli
cells in high-salinity medium. ProQ and Prc deficiencies were associated with different phenotypes. ProQ-deficient bacteria were elongated unless glycine betaine was provided. High-salinity cultures of Prc-deficient bacteria included spherical cells with an enlarged periplasm and an eccentric nucleoid. The nucleoid-containing compartment was bounded by the cytoplasmic membrane and peptidoglycan. This phenotype was not evident in bacteria cultivated at low or moderate salinity, nor was it associated with murein lipoprotein (Lpp) deficiency, and it differed from those elicited by the MreB inhibitor A-22 or the FtsI inhibitor aztreonam at low or high salinity. It was suppressed by deletion of
spr
, which encodes one of three murein hydrolases that are redundantly essential for enlargement of the murein sacculus. Prc deficiency may alter bacterial morphology by impairing control of Spr activity at high salinity. ProQ and Prc deficiencies lowered the ProP activity of bacteria cultivated at moderate salinity by approximately 70% and 30%, respectively, but did not affect other osmoregulatory functions. The effects of ProQ and Prc deficiencies on ProP activity are indirect, reflecting their roles in the maintenance of cell structure.