bluuebunny/crossref_metadata_2025_split huggingface dataset:
The putative Agrobacterium transcriptional activator‐like virulence protein VirD5 may target T‐complex to prevent the degradation of coat proteins in the plant cell nucleus
Authors: Wang Yafei , Peng Wei , Zhou Xu , Huang Fei , Shao Lingyun , Luo Meizhong 
Published: May 2014

Summary

Agrobacterium exports at least five virulence proteins (VirE2, VirE3, VirF, VirD2, VirD5) into host cells and hijacks some host plant factors to facilitate its transformation process.

Random DNA binding selection assays (RDSAs), electrophoretic mobility shift assays (EMSAs) and yeast one‐hybrid systems were used to identify protein‐bound DNA elements. Bimolecular fluorescence complementation, glutathione S‐transferase pull‐down and yeast two‐hybrid assays were used to detect protein interactions. Protoplast transformation, coprecipitation, competitive binding and cell‐free degradation assays were used to analyze the relationships among proteins.

We found that Agrobacterium VirD5 exhibits transcriptional activation activity in yeast, is located in the plant cell nucleus, and forms homodimers. A specific VirD5‐bound DNA element designated D5RE (VirD5 response element) was identified. VirD5 interacted directly with Arabidopsis VirE2 Interacting Protein 1 (AtVIP1). However, the ternary complex of VirD5–AtVIP1–VirE2 could be detected, whereas that of VirD5–AtVIP1–VBF (AtVIP1 Binding F‐box protein) could not. We demonstrated that VirD5 competes with VBF for binding to AtVIP1 and stabilizes AtVIP1 and VirE2 in the cell‐free degradation system.

Our results indicated that VirD5 may act as both a transcriptional activator‐like effector to regulate host gene expression and a protector preventing the coat proteins of the T‐complex from being quickly degraded by the host's ubiquitin proteasome system (UPS).
Novel applications of fluid inclusions and isotope geochemistry in unravelling the genesis of fossil travertine systems
Authors: Desouky Hamdy El , Soete Jeroen , Claes Hannes , Özkul Mehmet , Vanhaecke Frank , Swennen Rudy 
Published: May 2014

AbstractThe Denizli Basin is a fault‐bounded Neogene–Quaternary depression located in the Western Anatolian Extensional Province, Western Turkey. The basin is a unique geological site with abundant active and fossil (Quaternary) travertine and tufa deposits. Fluid inclusion microthermometry and isotopic analysis were applied to study the genesis of the Ballık fossil travertine deposits, located in the south‐eastern part of the basin. Microthermometry on fluid inclusions indicates that the main travertine precipitating and cementing fluids are characterized by low salinity (<0·7 wt% NaCl equivalent) and variable temperatures that cluster at <50°C and ca 100°C. Fluids of meteoric origin have been heated by migration to the deeper subsurface, possibly in a local high geothermal gradient setting. A later uncommon cementation phase is related to a fluid with a significantly higher salinity (25·5 to 26·0 wt% bulk). The fluid obtained its salinity by interaction with Late Triassic evaporite layers. Strontium isotopes indicate that the parent carbonate source rock of the different travertine precipitates is very likely to be the Triassic limestone of the Lycian Nappes. Carbon isotopes suggest that the parent CO2 gas originated from thermal decarbonation of the Lycian limestones with minor contributions of magmatic degassing and organic soil CO2. Oxygen isotopes confirm the meteoric origin of the fluids and indicate disequilibrium precipitation because of evaporation and degassing. Results were integrated within the available geological data of the Denizli Basin in a generalized travertine precipitation model, which enhanced the understanding of fossil travertine systems. The study highlights the novel application of fluid inclusion research in unravelling the genesis of continental carbonates and provides several recommendations for hydrocarbon exploration in travertine‐bearing sedimentary basins. The findings suggest that travertine bodies and their parent carbonate source rocks have the potential to constitute interesting subsurface hydrocarbon reservoirs.
The biochemical relationships in anaerobic digestion after thermal hydrolysis at Davyhulme
Authors: Jolly Martin , Belshaw Dave , Telfer Jack 
Published: May 2014

AbstractThe commissioning of the largest thermal hydrolysis plant in the world at Davyhulme, Manchester involved detailed analysis of the digestion process. The plant consists of eight digesters, 20 thermal hydrolysis reactors and a maximum throughput of 121 000 tDS/year.The plant was converted from conventional digestion with a loading rate of 1.25 kgVS/m3/day to digestion fed with thermally hydrolysed sludge with a loading rate of 4.16 kgVS/m3/day. At the start of the commissioning and ramp‐up of the loading rate, control actions were based on acid/alkalinity, pH and foaming; however, it was found that the methane concentration was the parameter that changed quickest during digester instability. The monitoring was changed during commissioning to use methane concentration as the primary control parameter.It was found that the rate of increased organic loading is dependent on the availability of seed biomass already acclimatised to thermally hydrolysed feed sludge and the presence of a high alkalinity buffer.
Bordetella pertussis Lipid A Glucosamine Modification Confers Resistance to Cationic Antimicrobial Peptides and Increases Resistance to Outer Membrane Perturbation
Authors: Shah Nita R. , Hancock Robert E. W. , Fernandez Rachel C. 
Published: May 2014

ABSTRACT

Bordetella pertussis
, the causative agent of whooping cough, has many strategies for evading the human immune system. Lipopolysaccharide (LPS) is an important Gram-negative bacterial surface structure that activates the immune system via Toll-like receptor 4 and enables susceptibility to cationic antimicrobial peptides (CAMPs). We show modification of the lipid A region of LPS with glucosamine increased resistance to numerous CAMPs, including LL-37. Furthermore, we demonstrate that this glucosamine modification increased resistance to outer membrane perturbation.
Activity of Daptomycin or Linezolid in Combination with Rifampin or Gentamicin against Biofilm-Forming Enterococcus faecalis or E. faecium in an
In Vitro
Pharmacodynamic Model Using Simulated Endocardial Vegetations and an
In Vivo
Survival Assay Using Galleria mellonella Larvae
Authors: Luther Megan K. , Arvanitis Marios , Mylonakis Eleftherios , LaPlante Kerry L. 
Published: May 2014

ABSTRACT

Enterococci are the third most frequent cause of infective endocarditis. A high-inoculum stationary-phase
in vitro
pharmacodynamic model with simulated endocardial vegetations was used to simulate the human pharmacokinetics of daptomycin at 6 or 10 mg/kg of body weight/day or linezolid at 600 mg every 12 h (q12h), alone or in combination with gentamicin at 1.3 mg/kg q12h or rifampin at 300 mg q8h or 900 mg q24h. Biofilm-forming, vancomycin-susceptible
Enterococcus faecalis
and vancomycin-resistant
Enterococcus faecium
(vancomycin-resistant enterococcus [VRE]) strains were tested. At 24, 48, and 72 h, all daptomycin-containing regimens demonstrated significantly more activity (decline in CFU/g) than any linezolid-containing regimen against biofilm-forming
E. faecalis
. The addition of gentamicin to daptomycin (at 6 or 10 mg/kg) in the first 24 h significantly improved bactericidal activity. In contrast, the addition of rifampin delayed the bactericidal activity of daptomycin against
E. faecalis
, and the addition of rifampin antagonized the activities of all regimens against VRE at 24 h. Also, against VRE, the addition of gentamicin to linezolid at 72 h improved activity and was bactericidal. Rifampin significantly antagonized the activity of linezolid against VRE at 72 h. In
in vivo
Galleria mellonella
survival assays, linezolid and daptomycin improved survival. Daptomycin at 10 mg/kg improved survival significantly over that with linezolid against
E. faecalis
. The addition of gentamicin improved the efficacy of daptomycin against
E. faecalis
and those of linezolid and daptomycin against VRE. We conclude that in enterococcal infection models, daptomycin has more activity than linezolid alone. Against biofilm-forming
E. faecalis
, the addition of gentamicin in the first 24 h causes the most rapid decline in CFU/g. Of interest, the addition of rifampin decreased the activity of daptomycin against both
E. faecalis
and VRE.
β-Lactam Resistance in Methicillin-Resistant Staphylococcus aureus USA300 Is Increased by Inactivation of the ClpXP Protease
Authors: Bæk Kristoffer T. , Gründling Angelika , Mogensen René G. , Thøgersen Louise , Petersen Andreas , Paulander Wilhelm , Frees Dorte 
Published: May 2014

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) has acquired the
mecA
gene encoding a peptidoglycan transpeptidase, penicillin binding protein 2a (PBP2a), which has decreased affinity for β-lactams. Quickly spreading and highly virulent community-acquired (CA) MRSA strains recently emerged as a frequent cause of infection in individuals without exposure to the health care system. In this study, we found that the inactivation of the components of the ClpXP protease substantially increased the β-lactam resistance level of a CA-MRSA USA300 strain, suggesting that the proteolytic activity of ClpXP controls one or more pathways modulating β-lactam resistance. These pathways do not involve the control of
mecA
expression, as the cellular levels of PBP2a were unaltered in the
clp
mutants. An analysis of the cell envelope properties of the
clpX
and
clpP
mutants revealed a number of distinct phenotypes that may contribute to the enhanced β-lactam tolerance. Both mutants displayed significantly thicker cell walls, increased peptidoglycan cross-linking, and altered composition of monomeric muropeptide species compared to those of the wild types. Moreover, changes in Sle1-mediated peptidoglycan hydrolysis and altered processing of the major autolysin Atl were observed in the
clp
mutants. In conclusion, the results presented here point to an important role for the ClpXP protease in controlling cell wall metabolism and add novel insights into the molecular factors that determine strain-dependent β-lactam resistance.
Interspecies Mixed-Effect Pharmacokinetic Modeling of Penicillin G in Cattle and Swine
Authors: Li Mengjie , Gehring Ronette , Tell Lisa , Baynes Ronald , Huang Qingbiao , Riviere Jim E. 
Published: May 2014

ABSTRACT
Extralabel drug use of penicillin G in food-producing animals may cause an excess of residues in tissue which will have the potential to damage human health. Of all the antibiotics, penicillin G may have the greatest potential for producing allergic responses to the consumer of food animal products. There are, however, no population pharmacokinetic studies of penicillin G for food animals. The objective of this study was to develop a population pharmacokinetic model to describe the time-concentration data profile of penicillin G across two species. Data were collected from previously published pharmacokinetic studies in which several formulations of penicillin G were administered to diverse populations of cattle and swine. Liver, kidney, and muscle residue data were also used in this study. Compartmental models with first-order absorption and elimination were fit to plasma and tissue concentrations using a nonlinear mixed-effect modeling approach. A 3-compartment model with extra tissue compartments was selected to describe the pharmacokinetics of penicillin G. Typical population parameter estimates (interindividual variability) were central volumes of distribution of 3.45 liters (12%) and 3.05 liters (8.8%) and central clearance of 105 liters/h (32%) and 16.9 liters/h (14%) for cattle and swine, respectively, with peripheral clearance of 24.8 liters/h (13%) and 9.65 liters/h (23%) for cattle and 13.7 liters/h (85%) and 0.52 liters/h (40%) for swine. Body weight and age were the covariates in the final pharmacokinetic models. This study established a robust model of penicillin for a large and diverse population of food-producing animals which could be applied to other antibiotics and species in future analyses.
Plasmodium falciparum Founder Populations in Western Cambodia Have Reduced Artemisinin Sensitivity
In Vitro
Authors: Amaratunga Chanaki , Witkowski Benoit , Dek Dalin , Try Vorleak , Khim Nimol , Miotto Olivo , Ménard Didier , Fairhurst Rick M. 
Published: May 2014

ABSTRACT

Reduced
Plasmodium falciparum
sensitivity to short-course artemisinin (ART) monotherapy manifests as a long parasite clearance half-life. We recently defined three parasite founder populations with long half-lives in Pursat, western Cambodia, where reduced ART sensitivity is prevalent. Using the ring-stage survival assay, we show that these founder populations have reduced ART sensitivity
in vitro
at the early ring stage of parasite development and that a genetically admixed population contains subsets of parasites with normal or reduced ART sensitivity.
Alternative Screening Approaches for Discovery of Middle East Respiratory Syndrome Coronavirus Inhibitors
Authors: LaFemina Robert L. 
Published: May 2014

ABSTRACT

Two coronaviruses causing severe respiratory disease and high mortality rates emerging within the past dozen years reinforces the need for clinically efficacious antivirals targeting coronaviruses. Alternative screening approaches for antivirals against the recently emergent Middle East respiratory syndrome coronavirus (MERS-CoV) may provide lead compounds to address this need. Two
Antimicrobial Agents and Chemotherapy
(AAC) papers screened libraries of approved compounds that may potentially be repurposed as MERS-CoV antivirals. A third AAC paper showed that a previously described severe acute respiratory syndrome coronavirus (SARS-CoV) helicase inhibitor also has activity against MERS-CoV.
Nuclear Factor of Activated T Cells Regulates Neutrophil Recruitment, Systemic Inflammation, and T-Cell Dysfunction in Abdominal Sepsis
Authors: Zhang Su , Luo Lingtao , Wang Yongzhi , Gomez Maria F. , Thorlacius Henrik 
Published: May 2014

ABSTRACT

The signaling mechanisms regulating neutrophil recruitment, systemic inflammation, and T-cell dysfunction in polymicrobial sepsis are not clear. This study explored the potential involvement of the calcium/calcineurin-dependent transcription factor, nuclear factor of activated T cells (NFAT), in abdominal sepsis. Cecal ligation and puncture (CLP) triggered NFAT-dependent transcriptional activity in the lung, spleen, liver, and aorta in NFAT-luciferase reporter mice. Treatment with the NFAT inhibitor A-285222 prior to CLP completely prevented sepsis-induced NFAT activation in all these organs. Inhibition of NFAT activity reduced sepsis-induced formation of CXCL1, CXCL2, and CXCL5 chemokines and edema as well as neutrophil infiltration in the lung. Notably, NFAT inhibition efficiently reduced the CLP-evoked increases in HMBG1, interleukin 6 (IL-6), and CXCL5 levels in plasma. Moreover, administration of A-285222 restored sepsis-induced T-cell dysfunction, as evidenced by markedly decreased apoptosis and restored proliferative capacity of CD4 T cells. Along these lines, treatment with A-285222 restored gamma interferon (IFN-γ) and IL-4 levels in the spleen, which were markedly reduced in septic mice. CLP-induced formation of regulatory T cells (CD4
+
CD25
+
Foxp3
+
) in the spleen was also abolished in A-285222-treated animals. All together, these novel findings suggest that NFAT is a powerful regulator of pathological inflammation and T-cell immune dysfunction in abdominal sepsis. Thus, our data suggest that NFAT signaling might be a useful target to protect against respiratory failure and immunosuppression in patients with sepsis.
CD14 Influences Host Immune Responses and Alternative Activation of Macrophages during Schistosoma mansoni Infection
Authors: Tundup Smanla , Srivastava Leena , Nagy Tamas , Harn Donald 
Published: May 2014

ABSTRACT

Antigen-presenting cell (APC) plasticity is critical for controlling inflammation in metabolic diseases and infections. The roles that pattern recognition receptors (PRRs) play in regulating APC phenotypes are just now being defined. We evaluated the expression of PRRs on APCs in mice infected with the helminth parasite
Schistosoma mansoni
and observed an upregulation of CD14 expression on macrophages. Schistosome-infected
Cd14
−/−
mice showed significantly increased alternative activation of (M2) macrophages in the livers compared to infected wild-type (wt) mice. In addition, splenocytes from infected
Cd14
−/−
mice exhibited increased production of CD4
+
-specific interleukin-4 (IL-4), IL-5, and IL-13 and CD4
+
Foxp3
+
IL-10
+
regulatory T cells compared to cells from infected wt mice.
S. mansoni
-infected
Cd14
−/−
mice also presented with smaller liver egg granulomas associated with increased collagen deposition compared to granulomas in infected wt mice. The highest expression of CD14 was found on liver macrophages in infected mice. To determine if the
Cd14
−/−
phenotype was in part due to increased M2 macrophages, we adoptively transferred wt macrophages into
Cd14
−/−
mice and normalized the M2 and CD4
+
Th cell balance close to that observed in infected wt mice. Finally, we demonstrated that CD14 regulates STAT6 activation, as
Cd14
−/−
mice had increased STAT6 activation
in vivo
, suggesting that lack of CD14 impacts the IL-4Rα-STAT6 pathway, altering macrophage polarization during parasite infection. Collectively, these data identify a previously unrecognized role for CD14 in regulating macrophage plasticity and CD4
+
T cell biasing during helminth infection.
The Borrelia hermsii Factor H Binding Protein FhbA Is Not Required for Infectivity in Mice or for Resistance to Human Complement
In Vitro
Authors: Fine Lindy M. , Miller Daniel P. , Mallory Katherine L. , Tegels Brittney K. , Earnhart Christopher G. , Marconi Richard T. 
Published: May 2014

ABSTRACT

The primary causative agent of tick-borne relapsing fever in North America is
Borrelia hermsii
. It has been hypothesized that
B. hermsii
evades complement-mediated destruction by binding factor H (FH), a host-derived negative regulator of complement.
In vitro
,
B. hermsii
produces a single FH binding protein designated FhbA (FH binding protein A). The properties and ligand binding activity of FhbA suggest that it plays multiple roles in pathogenesis. It binds plasminogen and has been identified as a significant target of a B1b B cell-mediated IgM response in mice. FhbA has also been explored as a potential diagnostic antigen for
B. hermsii
infection in humans. The ability to test the hypothesis that FhbA is a critical virulence factor
in vivo
has been hampered by the lack of well-developed systems for the genetic manipulation of the relapsing fever spirochetes. In this report, we have successfully generated a
B. hermsii
fhbA
deletion mutant (the
B. hermsii
YORΔ
fhbA
strain) through allelic exchange mutagenesis. Deletion of
fhbA
abolished FH binding by the YORΔ
fhbA
strain and eliminated cleavage of C3b on the cell surface. However, the YORΔ
fhbA
strain remained infectious in mice and retained resistance to killing
in vitro
by human complement. Collectively, these results indicate that
B. hermsii
employs an FhbA/FH-independent mechanism of complement evasion that allows for resistance to killing by human complement and persistence in mice.
Functional Genomics with a Comprehensive Library of Transposon Mutants for the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20
Authors: Kuehl Jennifer V. , Price Morgan N. , Ray Jayashree , Wetmore Kelly M. , Esquivel Zuelma , Kazakov Alexey E. , Nguyen Michelle , Kuehn Raquel , Davis Ronald W. , Hazen Terry C. , Arkin Adam P. , Deutschbauer Adam 
Published: May 2014

ABSTRACT

The genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacterium
Desulfovibrio alaskensis
G20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5′ RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, the
D. alaskensis
G20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical gene
Dde_3007
is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group to
O
-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance.

IMPORTANCE
Sulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants in
Desulfovibrio alaskensis
G20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria.