bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Five Structurally Unrelated Quorum-Sensing Inhibitors of Pseudomonas aeruginosa from a Natural-Derivative Database
Authors: Tan Sean Yang-Yi , Chua Song-Lin , Chen Yicai , Rice Scott A. , Kjelleberg Staffan , Nielsen Thomas E. , Yang Liang , Givskov Michael 
Published: September 2013

ABSTRACT

Bacteria communicate by means of small signal molecules in a process termed quorum sensing (QS). QS enables bacteria to organize their activities at the population level, including the coordinated secretion of virulence factors. Certain small-molecule compounds, known as quorum-sensing inhibitors (QSIs), have been shown to effectively block QS and subsequently attenuate the virulence of
Pseudomonas aeruginosa
, as well as increasing its susceptibility to both antibiotics and the immune system. In this study, a structure-based virtual screening (SB-VS) approach was used for the discovery of novel QSI candidates. Three-dimensional structures of 3,040 natural compounds and their derivatives were obtained, after which molecular docking was performed using the QS receptor LasR as a target. Based on docking scores and molecular masses, 22 compounds were purchased to determine their efficacies as quorum-sensing inhibitors. Using a live reporter assay for quorum sensing, 5 compounds were found to be able to inhibit QS-regulated gene expression in
P. aeruginosa
in a dose-dependent manner. The most promising compound, G1, was evaluated by isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis, and it was found to significantly affect the abundance of 46 proteins (19 were upregulated; 27 were downregulated) in
P. aeruginosa
PAO1. It specifically reduced the expression of several quorum-sensing-regulated virulence factors, such as protease IV, chitinase, and pyoverdine synthetases. G1 was also able to reduce extracellular DNA release and inhibited the secretion of the virulence factor, elastase, whose expression is regulated by LasR. These results demonstrate the utility of SB-VS for the discovery of target-specific QSIs.
Isavuconazole Pharmacodynamic Target Determination for Candida Species in an
In Vivo
Murine Disseminated Candidiasis Model
Authors: Lepak Alexander J. , Marchillo Karen , VanHecker Jamie , Diekema Daniel , Andes David R. 
Published: September 2013

ABSTRACT

Pharmacodynamic (PD) studies with triazoles in the neutropenic murine disseminated candidiasis model have been performed extensively for
Candida albicans
. They have consistently shown that the pharmacodynamic index most closely correlated with efficacy is the ratio of the 24-h area under the concentration-time curve (AUC) to the MIC, and a target 24-h free-drug AUC/MIC ratio near 25 is associated with 50% of maximal microbiologic efficacy. We utilized this model to investigate the pharmacodynamics of isavuconazole. Isavuconazole pharmacokinetics were linear over the dose range studied. Oral-gastric doses of 640, 160, 40, and 10 mg of prodrug/kg of body weight produced peak levels of 0.51 to 25.4 mg/liter, an elimination half-life of 1 to 5 h, and an AUC from 0 h to infinity (AUC
0-∞
) of 0.9 to 287 mg · h/liter. The AUC/MIC ratio was the pharmacodynamic index that correlated best with efficacy (
R
2
, 0.84). Pharmacodynamic target studies were performed using 4
C. albicans
isolates with both a 24-h and a 96-h treatment duration. The strains were chosen to include previously characterized fluconazole-resistant strains. The mean 50% effective doses (ED
50
) (expressed in mg/kg of body weight/12 h) and associated 24-h free-drug AUC/MIC ratios were 89.3 ± 46.7 and 67.7 ± 35 for the 24-h treatment and 59.6 ± 22 and 33.3 ± 25.5 for the 96-h treatment. These differences were not statistically significant. Pharmacodynamic targets for two non-
albicans Candida
species were also explored. The mean ED
50
(expressed in mg/kg/12 h) and associated 24-h free-drug AUC/MIC ratios were 31.2 and 6.2 for
Candida tropicalis
(
n
= 1) and 50.5 and 1.6 for
Candida glabrata
(
n
= 2). These PD targets were significantly different from
C. albicans
targets (
P
, 0.04). Isavuconazole PD targets for
C. albicans
are similar to those observed in this model with other triazoles. However, the PD targets for non-
albicans Candida
species were more than 10-fold lower than those for
C. albicans
(
P
, 0.04). This difference is similar to the species-specific PD relationships for the echinocandins. The lower PD targets for these species in this model will be important to consider in the analysis of clinical trial data and during the development of susceptibility breakpoints.
Deciphering the Contribution of Human Meningothelial Cells to the Inflammatory and Antimicrobial Response at the Meninges
Authors: Royer Pierre-Joseph , Rogers Andrew J. , Wooldridge Karl G. , Tighe Patrick , Mahdavi Jafar , Rittig Michael G. , Ala'Aldeen Dlawer 
Published: September 2013

ABSTRACT

We have investigated the response of primary human meningothelial cells to
Neisseria meningitidis
. Through a transcriptome analysis, we provide a comprehensive examination of the response of meningothelial cells to bacterial infection. A wide range of chemokines are elicited which act to attract and activate the main players of innate and adaptive immunity. We showed that meningothelial cells expressed a high level of Toll-like receptor 4 (TLR4), and, using a gene silencing strategy, we demonstrated the contribution of this pathogen recognition receptor in meningothelial cell activation. Secretion of interleukin-6 (IL-6), CXCL10, and CCL5 was almost exclusively TLR4 dependent and relied on MyD88 and TRIF adaptor cooperation. In contrast, IL-8 induction was independent of the presence of TLR4, MyD88, and TRIF. Transcription factors NF-κB p65, p38 mitogen-activated protein kinase (MAPK), Jun N-terminal protein kinase (JNK1), IRF3, and IRF7 were activated after contact with bacteria. Interestingly, the protein kinase IRAK4 was found to play a minor role in the meningothelial cell response to
Neisseria
infection. Our work highlights the role of meningothelial cells in the development of an immune response and inflammation in the central nervous system (CNS) in response to meningococcal infection. It also sheds light on the complexity of intracellular signaling after TLR triggering.
Mutation of the Conserved Calcium-Binding Motif in Neisseria gonorrhoeae PilC1 Impacts Adhesion but Not Piliation
Authors: Cheng Yuan , Johnson Michael D. L. , Burillo-Kirch Christine , Mocny Jeffrey C. , Anderson James E. , Garrett Christopher K. , Redinbo Matthew R. , Thomas Christopher E. 
Published: September 2013

ABSTRACT

Neisseria gonorrhoeae
PilC1 is a member of the PilC family of type IV pilus-associated adhesins found in
Neisseria
species and other type IV pilus-producing genera. Previously, a calcium-binding domain was described in the C-terminal domains of PilY1 of
Pseudomonas aeruginosa
and in PilC1 and PilC2 of
Kingella kingae
. Genetic analysis of
N. gonorrhoeae
revealed a similar calcium-binding motif in PilC1. To evaluate the potential significance of this calcium-binding region in
N. gonorrhoeae
, we produced recombinant full-length PilC1 and a PilC1 C-terminal domain fragment. We show that, while alterations of the calcium-binding motif disrupted the ability of PilC1 to bind calcium, they did not grossly affect the secondary structure of the protein. Furthermore, we demonstrate that both full-length wild-type PilC1 and full-length calcium-binding-deficient PilC1 inhibited gonococcal adherence to cultured human cervical epithelial cells, unlike the truncated PilC1 C-terminal domain. Similar to PilC1 in
K. kingae
, but in contrast to the calcium-binding mutant of
P. aeruginosa
PilY1, an equivalent mutation in
N. gonorrhoeae
PilC1 produced normal amounts of pili. However, the
N. gonorrhoeae
PilC1 calcium-binding mutant still had partial defects in gonococcal adhesion to ME180 cells and genetic transformation, which are both essential virulence factors in this human pathogen. Thus, we conclude that calcium binding to PilC1 plays a critical role in pilus function in
N. gonorrhoeae
.
Control of Bacterial Virulence by the RalR Regulator of the Rabbit-Specific Enteropathogenic Escherichia coli Strain E22
Authors: Srikhanta Yogitha N. , Hocking Dianna M. , Wakefield Matthew J. , Higginson Ellen , Robins-Browne Roy M. , Yang Ji , Tauschek Marija 
Published: September 2013

ABSTRACT

Atypical enteropathogenic
Escherichia coli
(aEPEC) causes endemic diarrhea, diarrheal outbreaks, and persistent diarrhea in humans, but the mechanism by which aEPEC causes disease is incompletely understood. Virulence regulators and their associated regulons, which often include adhesins, play key roles in the expression of virulence factors in enteric pathogenic bacteria. In this study we identified a transcriptional regulator, RalR, in the rabbit-specific aEPEC strain, E22 (O103:H2) and examined its involvement in the regulation of virulence. Microarray analysis and quantitative real-time reverse transcription-PCR demonstrated that RalR enhances the expression of a number of genes encoding virulence-associated factors, including the Ral fimbria, the Aap dispersin, and its associated transport system, and downregulates several housekeeping genes, including
fliC
. These observations were confirmed by proteomic analysis of secreted and heat-extracted surface-associated proteins and by adherence and motility assays. To investigate the mechanism of RalR-mediated activation, we focused on its most highly upregulated target operons,
ralCDEFGHI
and
aap
. By using primer extension, electrophoretic mobility shift assay, and mutational analysis, we identified the promoter and operator sequences for these two operons. By employing promoter-
lacZ
reporter systems, we demonstrated that RalR activates the expression of its target genes by binding to one or more 8-bp palindromic sequences (with the consensus of TGTGCACA) located immediately upstream of the promoter core regions. Importantly, we also demonstrated that RalR is essential for virulence since infection of rabbits with E22 carrying a knockout mutation in the
ralR
gene completely abolished its ability to cause disease.
B Cell Production of Tumor Necrosis Factor in Response to Pneumocystis murina Infection in Mice
Authors: Opata Michael M. , Ye Zhan , Hollifield Melissa , Garvy Beth A. 
Published: September 2013

ABSTRACTPneumocystisspecies are opportunistic fungal pathogens that induce tumor necrosis factor (TNF) production by alveolar macrophages. Here we report that B cells from the draining lymph nodes as well as lung CD4+T cells are important producers of TNF uponPneumocystis murinainfection. To determine the importance of B cell-derived TNF in the primary response toP. murina, we generated bone marrow chimeras whose B cells were unable to produce TNF. The lungP. murinaburden at 10 days postinfection in TNF knockout (TNFKO) chimeras was significantly higher than that in wild-type (WT) chimeras, which corresponded to reduced numbers of activated CD4+T cells in the lungs at this early time point. Furthermore, CD4+T cells isolated fromP. murina-infected TNFKO chimeras were unable to stimulate clearance ofP. murinaupon adoptive transfer to recombinase-deficient (RAG1KO) hosts. Together, these data indicate that B cell-derived TNF plays an important function in promoting CD4+T cell expansion and production of TNF and facilitating protection againstP. murinainfection.
YaxAB, a Yersinia enterocolitica Pore-Forming Toxin Regulated by RovA
Authors: Wagner Nikki J. , Lin Carolina P. , Borst Luke B. , Miller Virginia L. 
Published: September 2013

ABSTRACT

The transcriptional regulator RovA positively regulates transcription of the
Yersinia enterocolitica
virulence gene
inv
. Invasin, encoded by
inv
, is important for establishment of
Y. enterocolitica
infection. However, a
rovA
mutant is more attenuated for virulence than an
inv
mutant, implying that RovA regulates additional virulence genes. When the
Y. enterocolitica
RovA regulon was defined by microarray analysis, YE1984 and YE1985 were among the genes identified as being upregulated by RovA. Since these genes are homologous to
Xenorhabdus nematophila
cytotoxin genes
xaxA
and
xaxB
, we named them
yaxA
and
yaxB
, respectively. In this work, we demonstrate the effects of YaxAB on the course of infection in the murine model. While a
yaxAB
mutant (Δ
yaxAB
) is capable of colonizing mice at the same level as the wild type, it slightly delays the course of infection and results in differing pathology in the spleen. Further, we found that
yaxAB
encode a probable cytotoxin capable of lysing mammalian cells, that both YaxA and YaxB are required for cytotoxic activity, and that the two proteins associate. YaxAB-mediated cell death occurs via osmotic lysis through the formation of distinct membrane pores.
In silico
tertiary structural analysis identified predicted structural homology between YaxA and proteins in pore-forming toxin complexes from
Bacillus cereus
(HBL-B) and
Escherichia coli
(HlyE). Thus, it appears that YaxAB function as virulence factors by inducing cell lysis through the formation of pores in the host cell membrane. This characterization of YaxAB supports the hypothesis that RovA regulates expression of multiple virulence factors in
Y. enterocolitica
.
LtpD Is a Novel Legionella pneumophila Effector That Binds Phosphatidylinositol 3-Phosphate and Inositol Monophosphatase IMPA1
Authors: Harding Clare R. , Mattheis Corinna , Mousnier Aurélie , Oates Clare V. , Hartland Elizabeth L. , Frankel Gad , Schroeder Gunnar N. 
Published: September 2013

ABSTRACT

The Dot/Icm type IV secretion system (T4SS) of
Legionella pneumophila
is crucial for the pathogen to survive in protozoa and cause human disease. Although more than 275 effector proteins are delivered into the host cell by the T4SS, the function of the majority is unknown. Here we have characterized the Dot/Icm effector LtpD. During infection, LtpD localized to the cytoplasmic face of the membrane of the
Legionella
-containing vacuole (LCV). In A549 lung epithelial cells, ectopically expressed LtpD localized to large vesicular structures that contained markers of endosomal compartments. Systematic analysis of LtpD fragments identified an internal 17-kDa fragment, LtpD
471-626
, which was essential for targeting ectopically expressed LtpD to vesicular structures and for the association of translocated LtpD with the LCV. LtpD
471-626
bound directly to phosphatidylinositol 3-phosphate [PtdIns(3)P]
in vitro
and colocalized with the PtdIns(3)P markers FYVE and SetA in cotransfected cells. LtpD was also found to bind the host cell enzyme inositol (
myo
)-1 (or 4)-monophosphatase 1, an important phosphatase involved in phosphoinositide production. Analysis of the role of LtpD in infection showed that LtpD is involved in bacterial replication in THP-1 macrophages, the larvae of
Galleria mellonella
, and mouse lungs. Together, these data suggest that LtpD is a novel phosphoinositide-binding
L. pneumophila
effector that has a role in intracellular bacterial replication.
Evidence for a Structural Role for Acid-Fast Lipids in Oocyst Walls of
Cryptosporidium
,
Toxoplasma
, and
Eimeria
Authors: Bushkin G. Guy , Motari Edwin , Carpentieri Andrea , Dubey Jitender P. , Costello Catherine E. , Robbins Phillips W. , Samuelson John 
Published: September 2013

ABSTRACT

Coccidia are protozoan parasites that cause significant human disease and are of major agricultural importance.
Cryptosporidium
spp. cause diarrhea in humans and animals, while
Toxoplasma
causes disseminated infections in fetuses and untreated AIDS patients.
Eimeria
is a major pathogen of commercial chickens. Oocysts, which are the infectious form of
Cryptosporidium
and
Eimeria
and one of two infectious forms of
Toxoplasma
(the other is tissue cysts in undercooked meat), have a multilayered wall. Recently we showed that the inner layer of the oocyst walls of
Toxoplasma
and
Eimeria
is a porous scaffold of fibers of β-1,3-glucan, which are also present in fungal walls but are absent from
Cryptosporidium
oocyst walls. Here we present evidence for a structural role for lipids in the oocyst walls of
Cryptosporidium
,
Toxoplasma
, and
Eimeria
. Briefly, oocyst walls of each organism label with acid-fast stains that bind to lipids in the walls of mycobacteria. Polyketide synthases similar to those that make mycobacterial wall lipids are abundant in oocysts of
Toxoplasma
and
Eimeria
and are predicted in
Cryptosporidium
. The outer layer of oocyst wall of
Eimeria
and the entire oocyst wall of
Cryptosporidium
are dissolved by organic solvents. Oocyst wall lipids are complex mixtures of triglycerides, some of which contain polyhydroxy fatty acyl chains like those present in plant cutin or elongated fatty acyl chains like mycolic acids. We propose a two-layered model of the oocyst wall (glucan and acid-fast lipids) that resembles the two-layered walls of mycobacteria (peptidoglycan and acid-fast lipids) and plants (cellulose and cutin).

IMPORTANCE
Oocysts, which are essential for the fecal-oral spread of coccidia, have a wall that is thought responsible for their survival in the environment and for their transit through the stomach and small intestine. While oocyst walls of
Toxoplasma
and
Eimeria
are strengthened by a porous scaffold of fibrils of β-1,3-glucan and by proteins cross-linked by dityrosines, both are absent from walls of
Cryptosporidium
. We show here that all oocyst walls are acid fast, have a rigid bilayer, dissolve in organic solvents, and contain a complex set of triglycerides rich in polyhydroxy and long fatty acyl chains that might be synthesized by an abundant polyketide synthase. These results suggest the possibility that coccidia build a waxy coat of acid-fast lipids in the oocyst wall that makes them resistant to environmental stress.
A Strategy To Estimate Unknown Viral Diversity in Mammals
Authors: Anthony Simon J. , Epstein Jonathan H. , Murray Kris A. , Navarrete-Macias Isamara , Zambrana-Torrelio Carlos M. , Solovyov Alexander , Ojeda-Flores Rafael , Arrigo Nicole C. , Islam Ariful , Ali Khan Shahneaz , Hosseini Parviez , Bogich Tiffany L. , Olival Kevin J. , Sanchez-Leon Maria D. , Karesh William B. , Goldstein Tracey , Luby Stephen P. , Morse Stephen S. , Mazet Jonna A. K. , Daszak Peter , Lipkin W. Ian 
Published: September 2013

ABSTRACTThe majority of emerging zoonoses originate in wildlife, and many are caused by viruses. However, there are no rigorous estimates of total viral diversity (here termed “virodiversity”) for any wildlife species, despite the utility of this to future surveillance and control of emerging zoonoses. In this case study, we repeatedly sampled a mammalian wildlife host known to harbor emerging zoonotic pathogens (the Indian Flying Fox,Pteropus giganteus) and used PCR with degenerate viral family-level primers to discover and analyze the occurrence patterns of 55 viruses from nine viral families. We then adapted statistical techniques used to estimate biodiversity in vertebrates and plants and estimated the total viral richness of these nine families inP. giganteusto be 58 viruses. Our analyses demonstrate proof-of-concept of a strategy for estimating viral richness and provide the first statistically supported estimate of the number of undiscovered viruses in a mammalian host. We used a simple extrapolation to estimate that there are a minimum of 320,000 mammalian viruses awaiting discovery within these nine families, assuming all species harbor a similar number of viruses, with minimal turnover between host species. We estimate the cost of discovering these viruses to be ~$6.3 billion (or ~$1.4 billion for 85% of the total diversity), which if annualized over a 10-year study time frame would represent a small fraction of the cost of many pandemic zoonoses.IMPORTANCERecent years have seen a dramatic increase in viral discovery efforts. However, most lack rigorous systematic design, which limits our ability to understand viral diversity and its ecological drivers and reduces their value to public health intervention. Here, we present a new framework for the discovery of novel viruses in wildlife and use it to make the first-ever estimate of the number of viruses that exist in a mammalian host. As pathogens continue to emerge from wildlife, this estimate allows us to put preliminary bounds around the potential size of the total zoonotic pool and facilitates a better understanding of where best to allocate resources for the subsequent discovery of global viral diversity.
Imaging Mass Spectrometry Reveals Highly Specific Interactions between Actinomycetes To Activate Specialized Metabolic Gene Clusters
Authors: Hopwood David A. 
Published: September 2013

ABSTRACTThe genomes of actinomycetes contain numerous gene clusters potentially able to encode the production of many antibiotics and other specialized metabolites that are not expressed during growth under typical laboratory conditions. Undoubtedly, this reflects the soil habitat of these organisms, which is highly complex physically, chemically, and biotically; the majority of the compounds that make up the specialized metabolome are therefore adaptive only under specific conditions. While there have been numerous previous reports of “waking up” the “sleeping” gene clusters, many involving genetic interventions or nutritional challenges, the role of competing microorganisms has been comparatively little studied. Now, Traxler et al. [M. F. Traxler, J. D. Watrous, T. Alexandrov, P. C. Dorrestein, and R. Kolter, mBio 4(4):e00459-13, 2013, doi:10.1128/mBio.00459-13] have used the recently described technique of microscale imaging mass spectrometry to analyze in detail the stimulation of specialized metabolite production by the model actinomyceteStreptomyces coelicolorA3(2) by growth in proximity to other actinomycetes. The striking finding from these experiments was that growth ofS. coelicolorclose to each of the five other actinomycetes studied caused it to produce many specialized metabolites that were not made when it was grown in isolation and that the majority of the compounds were interaction specific, i.e., they occurred only in one of the five pairwise combinations, emphasizing the highly specific nature of the interactions. These observations contribute substantially to the increasing awareness of communication between microorganisms in complex natural communities, as well as auguring well for the discovery of useful specialized metabolites based on microbial interactions.
Patterns and Processes of Microbial Community Assembly
Authors: Nemergut Diana R. , Schmidt Steven K. , Fukami Tadashi , O'Neill Sean P. , Bilinski Teresa M. , Stanish Lee F. , Knelman Joseph E. , Darcy John L. , Lynch Ryan C. , Wickey Phillip , Ferrenberg Scott 
Published: September 2013

SUMMARY

Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol.
85
:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.