bluuebunny/crossref_metadata_2025_split huggingface dataset:
LuxR- and LuxI-Type Quorum-Sensing Circuits Are Prevalent in Members of the Populus deltoides Microbiome
Authors: Schaefer Amy L. , Lappala Colin R. , Morlen Ryan P. , Pelletier Dale A. , Lu Tse-Yuan S. , Lankford Patricia K. , Harwood Caroline S. , Greenberg E. Peter 
Published: July 2013

ABSTRACT

We are interested in the root microbiome of the fast-growing Eastern cottonwood tree,
Populus deltoides
. There is a large bank of bacterial isolates from
P. deltoides
, and there are 44 draft genomes of bacterial endophyte and rhizosphere isolates. As a first step in efforts to understand the roles of bacterial communication and plant-bacterial signaling in
P. deltoides
, we focused on the prevalence of acyl-homoserine lactone (AHL) quorum-sensing-signal production and reception in members of the
P. deltoides
microbiome. We screened 129 bacterial isolates for AHL production using a broad-spectrum bioassay that responds to many but not all AHLs, and we queried the available genome sequences of microbiome isolates for homologs of AHL synthase and receptor genes. AHL signal production was detected in 40% of 129 strains tested. Positive isolates included members of the
Alpha
-,
Beta
-, and
Gammaproteobacteria
. Members of the
luxI
family of AHL synthases were identified in 18 of 39 proteobacterial genomes, including genomes of some isolates that tested negative in the bioassay. Members of the
luxR
family of transcription factors, which includes AHL-responsive factors, were more abundant than
luxI
homologs. There were 72 in the 39 proteobacterial genomes. Some of the
luxR
homologs appear to be members of a subfamily of LuxRs that respond to as-yet-unknown plant signals rather than bacterial AHLs. Apparently, there is a substantial capacity for AHL cell-to-cell communication in proteobacteria of the
P. deltoides
microbiota, and there are also
Proteobacteria
with LuxR homologs of the type hypothesized to respond to plant signals or cues.
Core Fluxome and Metafluxome of Lactic Acid Bacteria under Simulated Cocoa Pulp Fermentation Conditions
Authors: Adler Philipp , Bolten Christoph Josef , Dohnt Katrin , Hansen Carl Erik , Wittmann Christoph 
Published: July 2013

ABSTRACT

In the present work, simulated cocoa fermentation was investigated at the level of metabolic pathway fluxes (fluxome) of lactic acid bacteria (LAB), which are typically found in the microbial consortium known to convert nutrients from the cocoa pulp into organic acids. A comprehensive
13
C labeling approach allowed to quantify carbon fluxes during simulated cocoa fermentation by (i) parallel
13
C studies with [
13
C
6
]glucose, [1,2-
13
C
2
]glucose, and [
13
C
6
]fructose, respectively, (ii) gas chromatography-mass spectrometry (GC/MS) analysis of secreted acetate and lactate, (iii) stoichiometric profiling, and (iv) isotopomer modeling for flux calculation. The study of several strains of
L. fermentum
and
L. plantarum
revealed major differences in their fluxes. The
L. fermentum
strains channeled only a small amount (4 to 6%) of fructose into central metabolism, i.e., the phosphoketolase pathway, whereas only
L. fermentum
NCC 575 used fructose to form mannitol. In contrast,
L. plantarum
strains exhibited a high glycolytic flux. All strains differed in acetate flux, which originated from fractions of citrate (25 to 80%) and corresponding amounts of glucose and fructose. Subsequent, metafluxome studies with consortia of different
L. fermentum
and
L. plantarum
strains indicated a dominant (96%) contribution of
L. fermentum
NCC 575 to the overall flux in the microbial community, a scenario that was not observed for the other strains. This highlights the idea that individual LAB strains vary in their metabolic contribution to the overall fermentation process and opens up new routes toward streamlined starter cultures.
L. fermentum
NCC 575 might be one candidate due to its superior performance in flux activity.
Assimilation of Cellulose-Derived Carbon by Microeukaryotes in Oxic and Anoxic Slurries of an Aerated Soil
Authors: Chatzinotas Antonis , Schellenberger Stefanie , Glaser Karin , Kolb Steffen 
Published: July 2013

ABSTRACT

Soil microeukaryotes may trophically benefit from plant biopolymers. However, carbon transfer from cellulose into soil microeukaryotes has not been demonstrated so far. Microeukaryotes assimilating cellulose-derived carbon in oxic and anoxic soil slurries were therefore examined by rRNA-based stable-isotope probing. Bacteriovorous flagellates and ciliates and, likely, mixotrophic algae and saprotrophic fungi incorporated carbon from supplemental [U-
13
C]cellulose under oxic conditions. A previous study using the same soil suggested that cellulolytic
Bacteria
assimilated
13
C of supplemental cellulose. Thus, it can be assumed that ciliates, cercozoa, and chrysophytes assimilated carbon by grazing upon and utilizing metabolic products of
Bacteria
that hydrolyzed cellulose in the soil slurries.
Differential Growth of and Nanoscale TiO
2
Accumulation in Tetrahymena thermophila by Direct Feeding versus Trophic Transfer from Pseudomonas aeruginosa
Authors: Mielke Randall E. , Priester John H. , Werlin Rebecca A. , Gelb Jeff , Horst Allison M. , Orias Eduardo , Holden Patricia A. 
Published: July 2013

ABSTRACT

Nanoscale titanium dioxide (TiO
2
) is increasingly used in consumer goods and is entering waste streams, thereby exposing and potentially affecting environmental microbes. Protozoans could either take up TiO
2
directly from water and sediments or acquire TiO
2
during bactivory (ingestion of bacteria) of TiO
2
-encrusted bacteria. Here, the route of exposure of the ciliated protozoan
Tetrahymena thermophila
to TiO
2
was varied and the growth of, and uptake and accumulation of TiO
2
by,
T. thermophila
were measured. While TiO
2
did not affect
T. thermophila
swimming or cellular morphology, direct TiO
2
exposure in rich growth medium resulted in a lower population yield. When TiO
2
exposure was by bactivory of
Pseudomonas aeruginosa
, the
T. thermophila
population yield and growth rate were lower than those that occurred during the bactivory of non-TiO
2
-encrusted bacteria. Regardless of the feeding mode,
T. thermophila
cells internalized TiO
2
into their food vacuoles. Biomagnification of TiO
2
was not observed; this was attributed to the observation that TiO
2
appeared to be unable to cross the food vacuole membrane and enter the cytoplasm. Nevertheless, our findings imply that TiO
2
could be transferred into higher trophic levels within food webs and that the food web could be affected by the decreased growth rate and yield of organisms near the base of the web.
Impact of Manure Fertilization on the Abundance of Antibiotic-Resistant Bacteria and Frequency of Detection of Antibiotic Resistance Genes in Soil and on Vegetables at Harvest
Authors: Marti Romain , Scott Andrew , Tien Yuan-Ching , Murray Roger , Sabourin Lyne , Zhang Yun , Topp Edward 
Published: July 2013

ABSTRACT
Consumption of vegetables represents a route of direct human exposure to bacteria found in soil. The present study evaluated the complement of bacteria resistant to various antibiotics on vegetables often eaten raw (tomato, cucumber, pepper, carrot, radish, lettuce) and how this might vary with growth in soil fertilized inorganically or with dairy or swine manure. Vegetables were sown into field plots immediately following fertilization and harvested when of marketable quality. Vegetable and soil samples were evaluated for viable antibiotic-resistant bacteria by plate count on Chromocult medium supplemented with antibiotics at clinical breakpoint concentrations. DNA was extracted from soil and vegetables and evaluated by PCR for the presence of 46 gene targets associated with plasmid incompatibility groups, integrons, or antibiotic resistance genes. Soil receiving manure was enriched in antibiotic-resistant bacteria and various antibiotic resistance determinants. There was no coherent corresponding increase in the abundance of antibiotic-resistant bacteria enumerated from any vegetable grown in manure-fertilized soil. Numerous antibiotic resistance determinants were detected in DNA extracted from vegetables grown in unmanured soil. A smaller number of determinants were additionally detected on vegetables grown only in manured and not in unmanured soil. Overall, consumption of raw vegetables represents a route of human exposure to antibiotic-resistant bacteria and resistance determinants naturally present in soil. However, the detection of some determinants on vegetables grown only in freshly manured soil reinforces the advisability of pretreating manure through composting or other stabilization processes or mandating offset times between manuring and harvesting vegetables for human consumption.
Interaction of Lactobacillus fermentum BGHI14 with Rat Colonic Mucosa: Implications for Colitis Induction
Authors: Lukic Jovanka , Strahinic Ivana , Milenkovic Marina , Golic Natasa , Kojic Milan , Topisirovic Ljubisa , Begovic Jelena 
Published: July 2013

ABSTRACT

The present study was carried out to test the colonic mucosal response of rats to oral supplementation with
Lactobacillus fermentum
BGHI14 and to correlate the tissue reaction to trinitrobenzenesulfonate (TNBS)-induced colitis with mucosal barrier alterations caused by bacterial ingestion. An immune cell-mediated reaction of healthy colonic tissue was noticed after bacterial feeding. After prolonged bacterial treatment, the observed reaction had retreated to normality, but the mRNA levels of proinflammatory cytokines interleukin-1β (IL-1β) and tumor necrosis factor alpha (TNF-α) remained elevated. These data point to the chronic low-grade inflammation that could be caused by long-term probiotic consumption. Although no detrimental effects of bacterial pretreatment were noticed in colitic rats, at least in the acute state of disease, the results obtained in our study point to the necessity of reassessment of existing data on the safety of probiotic preparations. Additionally, probiotic effects in experimental colitis models might depend on time coordination of disease induction with treatment duration.
Prevalence of Gastrointestinal Clostridium difficile Carriage in Australian Sheep and Lambs
Authors: Knight Daniel R. , Riley Thomas V. 
Published: July 2013

ABSTRACT

Recently,
Clostridium difficile
has been isolated from a wide variety of animals, particularly production animals, mainly cattle and pigs. Concurrently, the incidence of
C. difficile
infection (CDI) in humans has increased in the community, with some suggestions that food-borne transmission of
C. difficile
is occurring. Interestingly, sheep and lambs appear not to have been investigated for carriage/colonization with
C. difficile
. The aim of this project was to determine the prevalence of carriage of
C. difficile
in sheep and lambs in Australia by culturing fecal samples. A total of 371 sheep and lamb fecal samples were received in seven batches from three different geographic areas in eastern Australia and two in Western Australia. The overall rate of detection in sheep and lambs was low (4.0%); however, carriage/colonization in lambs (6.5%) was statistically significantly higher than that in sheep (0.6%) (
P
= 0.005). Seven distinct PCR ribotype patterns were observed, three of which were known international ribotypes (UK 056 [
n
= 1], UK 101 [
n
= 6], and UK 137 [
n
= 2]), while the remainder were unable to be matched with our available reference library. This low rate of carriage/colonization in Australian ovines suggests they are unlikely to be a major source/reservoir of human infections.
CMF22 Is a Broadly Conserved Axonemal Protein and Is Required for Propulsive Motility in Trypanosoma brucei
Authors: Nguyen HoangKim T. , Sandhu Jaspreet , Langousis Gerasimos , Hill Kent L. 
Published: July 2013

ABSTRACT

The eukaryotic flagellum (or cilium) is a broadly conserved organelle that provides motility for many pathogenic protozoa and is critical for normal development and physiology in humans. Therefore, defining core components of motile axonemes enhances understanding of eukaryotic biology and provides insight into mechanisms of inherited and infectious diseases in humans. In this study, we show that component of motile flagella 22 (CMF22) is tightly associated with the flagellar axoneme and is likely to have been present in the last eukaryotic common ancestor. The CMF22 amino acid sequence contains predicted IQ and
A
TPase
a
ssociated with a variety of cellular
a
ctivities (AAA) motifs that are conserved among CMF22 orthologues in diverse organisms, hinting at the importance of these domains in CMF22 function. Knockdown by RNA interference (RNAi) and rescue with an RNAi-immune mRNA demonstrated that CMF22 is required for propulsive cell motility in
Trypanosoma brucei
. Loss of propulsive motility in CMF22-knockdown cells was due to altered flagellar beating patterns, rather than flagellar paralysis, indicating that CMF22 is essential for motility regulation and likely functions as a fundamental regulatory component of motile axonemes. CMF22 association with the axoneme is weakened in mutants that disrupt the nexin-dynein regulatory complex, suggesting potential interaction with this complex. Our results provide insight into the core machinery required for motility of eukaryotic flagella.
The Calcineurin Pathway Inhibitor Tacrolimus Enhances the
In Vitro
Activity of Azoles against Mucorales via Apoptosis
Authors: Shirazi F. , Kontoyiannis D. P. 
Published: July 2013

ABSTRACT

The calcineurin pathway regulates antifungal drug resistance and the virulence of several major human-pathogenic fungi, including the recalcitrant
Mucorales
. We hypothesized that the fungistatic triazoles posaconazole (PCZ) and itraconazole (ICZ) become fungicidal in the setting of the calcineurin inhibitor tacrolimus (TCR) and that such an effect is mediated through apoptosis. Fungicidal activity and apoptosis were studied using standard microbiological techniques and hyphal metabolic and vital dye reduction assays at 37°C in RPMI 1640. Apoptosis was characterized by detecting intracellular Ca
2+
, phosphatidylserine (PS) externalization, DNA fragmentation, plasma membrane integrity, chromatin condensation, reactive oxygen species (ROS) generation, caspase-like activity, ATP, and cytochrome
c
release. MICs for PCZ and ICZ alone were significantly higher (8 to 128 μg/ml) than those of PCZ or ICZ plus TCR (0.25 to 4 μg/ml) for
Rhizopus oryzae
,
Cunninghamella bertholletiae
, and
Mucor circinelloides
. Both PCZ and ICZ in combination with TCR became fungicidal, and their activity was mediated through increased apoptotic cell death of
R. oryzae
(10 to 50%),
C. bertholletiae
(5 to 50%), and
M. circinelloides
(5 to 55%) germlings, with morphological apoptotic changes characterized by externalization of PS, nuclear condensation, and DNA fragmentation. Moreover, activation of the caspase-like activity was correlated with cell death induced by TCR plus PCZ or ICZ. These changes correlated with elevated intracellular Ca
2+
and ROS levels and disturbance of mitochondrial potential. We found that PCZ or ICZ in combination with TCR renders
Mucorales
sensitive to triazoles via apoptotic death. These observations could serve as a new paradigm for the development of new therapeutic strategies.
Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei
Authors: Yang Ence , Wang Gang , Woo Patrick C. Y. , Lau Susanna K. P. , Chow Wang-Ngai , Chong Ken T. K. , Tse Herman , Kao Richard Y. T. , Chan Che-Man , Che Xiaoyan , Yuen Kwok-Yung , Cai James J. 
Published: July 2013

ABSTRACT

Penicillium marneffei
is an opportunistic fungal pathogen endemic in Southeast Asia, causing lethal systemic infections in immunocompromised patients.
P. marneffei
grows in a mycelial form at the ambient temperature of 25°C and transitions to a yeast form at 37°C. The ability to alternate between the mycelial and yeast forms at different temperatures, namely, thermal dimorphism, has long been considered critical for the pathogenicity of
P. marneffei
, yet the underlying genetic mechanisms remain elusive. Here we employed high-throughput sequencing to unravel global transcriptional profiles of
P. marneffei
PM1 grown at 25 and 37°C. Among ∼11,000 protein-coding genes, 1,447 were overexpressed and 1,414 were underexpressed at 37°C. Counterintuitively, heat-responsive genes, predicted in
P. marneffei
through sequence comparison, did not tend to be overexpressed at 37°C. These results suggest that
P. marneffei
may take a distinct strategy of genetic regulation at the elevated temperature; the current knowledge concerning fungal heat response, based on studies of model fungal organisms, may not be applicable to
P. marneffei
. Our results further showed that the tandem repeat sequences (TRSs) are overrepresented in coding regions of
P. marneffei
genes, and TRS-containing genes tend to be overexpressed at 37°C. Furthermore, genomic sequences and expression data were integrated to characterize gene clusters, multigene families, and species-specific genes of
P. marneffei
. In sum, we present an integrated analysis and a comprehensive resource toward a better understanding of temperature-dependent genetic regulation in
P. marneffei
.
Mutations in
hemG
Mediate Resistance to Salicylidene Acylhydrazides, Demonstrating a Novel Link between Protoporphyrinogen Oxidase (HemG) and Chlamydia trachomatis Infectivity
Authors: Engström Patrik , Nguyen Bidong D. , Normark Johan , Nilsson Ingela , Bastidas Robert J. , Gylfe Åsa , Elofsson Mikael , Fields Kenneth A. , Valdivia Raphael H. , Wolf-Watz Hans , Bergström Sven 
Published: July 2013

ABSTRACT

Salicylidene acylhydrazides (SAHs) inhibit the type III secretion system (T3S) of
Yersinia
and other Gram-negative bacteria. In addition, SAHs restrict the growth and development of
Chlamydia
species. However, since the inhibition of
Chlamydia
growth by SAH is suppressed by the addition of excess iron and since SAHs have an iron-chelating capacity, their role as specific T3S inhibitors is unclear. We investigated here whether SAHs exhibit a function on
C. trachomatis
that goes beyond iron chelation. We found that the iron-saturated SAH INP0341 (IS-INP0341) specifically affects
C. trachomatis
infectivity with reduced generation of infectious elementary body (EB) progeny. Selection and isolation of spontaneous SAH-resistant mutant strains revealed that mutations in
hemG
suppressed the reduced infectivity caused by IS-INP0341 treatment. Structural modeling of
C. trachomatis
HemG predicts that the acquired mutations are located in the active site of the enzyme, suggesting that IS-INP0341 inhibits this domain of HemG and that protoporphyrinogen oxidase (HemG) and heme metabolism are important for
C. trachomatis
infectivity.
Duplex Molecular Assay Intended for Point-of-Care Diagnosis of Influenza A/B Virus Infection
Authors: Wu Liang-Ta , Thomas Isabelle , Curran Martin D. , Ellis Joanna S. , Parmar Surendra , Goel Neha , Sharma Pia I. , Allain Jean-Pierre , Lee Helen H. 
Published: July 2013

ABSTRACT

Early diagnosis and management of influenza virus infection directly correlates with the effectiveness in disease control. Current molecular influenza virus tests were designed for use in diagnostic testing facilities, where sophisticated equipment and highly trained technicians are available. A longer turnaround time for the centralized testing than when testing near the sample source could delay the initiation of medical intervention, thereby reducing the efficacy of antiviral treatment. The new assay, the SAMBA (
s
imple
am
plification-
b
ased
a
ssay) Flu duplex test, is a dipstick-based molecular assay developed to provide a simple, accurate, and cost-effective solution for the diagnosis of influenza A/B viruses intended for near-patient testing. The test presents an alternative format of influenza virus molecular testing that utilizes isothermal amplification and visual detection of nucleic acid on a test strip. The entire test procedure (extraction, amplification, and detection) is integrated into an enclosed semiautomated system. Analytically, the SAMBA Flu duplex test detects 95 and 85 copies of viral genomes for influenza A and B viruses, respectively, with no cross-reactivity observed against other common respiratory pathogens. The clinical performance was established by blind testing of 328 nasal/throat and nasopharyngeal swab specimens from the United Kingdom and Belgium and comparing the results with the quantitative reverse transcription-PCR method routinely used in two public health laboratories. The SAMBA Flu duplex test showed a clinical sensitivity and specificity of 100% and 97.9% for influenza virus A and 100% and 100% for influenza virus B. The test provides a new technology that could facilitate simple and timely identification of influenza virus infection, potentially resulting in more efficient control measures.
Evaluation of Luminex xTAG Gastrointestinal Pathogen Analyte-Specific Reagents for High-Throughput, Simultaneous Detection of Bacteria, Viruses, and Parasites of Clinical and Public Health Importance
Authors: Navidad Jose F. , Griswold David J. , Gradus M. Stephen , Bhattacharyya Sanjib 
Published: July 2013

ABSTRACTAcute diarrheal disease (ADD) can be caused by a range of pathogens, including bacteria, viruses, and parasites. Conventional diagnostic methods, such as culture, microscopy, biochemical assays, and enzyme-linked immunosorbent assays (ELISA), are laborious and time-consuming and lack sensitivity. Combined, the array of tests performed on a single specimen can increase the turnaround time (TAT) significantly. We validated a 19plex laboratory-developed gastrointestinal pathogen panel (GPP) using Luminex xTAG analyte-specific reagents (ASRs) to simultaneously screen directly in fecal specimens for diarrhea-causing pathogens, including bacteria (Campylobacter jejuni,Salmonellaspp.,Shigellaspp., enterotoxigenicEscherichia coli[ETEC], Shiga toxin-producingE. coli[STEC],E. coliO157:H7,Vibrio cholerae,Yersinia enterocolitica, and toxigenicClostridium difficile), parasites (Giardia lamblia,Cryptosporidiumspp., andEntamoeba histolytica), and viruses (norovirus GI and GII, adenovirus 40/41, and rotavirus A). Performance characteristics of GPP ASRs were determined using 48 reference isolates and 254 clinical specimens. Stool specimens from individuals with diarrhea were tested for pathogens using conventional and molecular methods. Using the predictive methods as standards, the sensitivities of the GPP ASRs were 100% for adenovirus 40/41, norovirus, rotavirus A,Vibrio cholerae,Yersinia enterocolitica,Entamoeba histolytica,Cryptosporidiumspp., andE. coliO157:H7; 95% forGiardia lamblia; 94% for ETEC and STEC; 93% forShigellaspp.; 92% forSalmonellaspp.; 91% forC. difficileA/B toxins; and 90% forCampylobacter jejuni. The overall comparative performance of the GPP ASRs with conventional methods in clinical samples was 94.5% (range, 90% to 97%), with 99% (99.0% to 99.9%) specificity. Implementation of the GPP ASRs enables our public health laboratory to offer highly sensitive and specific screening and identification of the major ADD-causing pathogens.