bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orf virus interleukin‐10 and vascular endothelial growth factor‐E modulate gene expression in cultured equine dermal fibroblasts
Authors: Wise Lyn M. , Bodaan Christa J. , Mercer Andrew A. , Riley Christopher B. , Theoret Christine L. 
Published: August 2016

BackgroundWounds in horses often exhibit sustained inflammation and inefficient vascularization, leading to excessive fibrosis and clinical complications such as “proud flesh”. Orf virus‐derived proteins, vascular endothelial growth factor (VEGF)‐E and interleukin (ovIL)‐10, enhance angiogenesis and control inflammation and fibrosis in skin wounds of laboratory animals.Hypothesis/ObjectivesThe study aimed to determine if equine dermal cells respond to VEGF‐E and ovIL‐10. Equine dermal cells are expected to express VEGF and IL‐10 receptors, so viral protein treatment is likely to alter cellular gene expression and behaviour in a manner conducive to healing.AnimalsSkin samples were harvested from the lateral thoracic wall of two healthy thoroughbred horses.MethodsEquine dermal cells were isolated using a skin explant method and their phenotype assessed by immunofluorescence. Cells were treated with recombinant proteins, with or without inflammatory stimuli. Gene expression was examined using standard and quantitative reverse transcriptase PCR. Cell behaviour was evaluated in a scratch assay.ResultsCultured cells were half vimentin+ve fibroblasts and half alpha smooth muscle actin+ve and vimentin+ve myofibroblasts. VEGF‐E increased basal expression of IL‐10 mRNA, whereas VEGF‐A and collagenase‐1 mRNA expression was increased by ovIL‐10. In cells exposed to inflammatory stimulus, both treatments dampened tumour necrosis factor mRNA expression, and ovIL‐10 exacerbated expression of monocyte chemoattractant protein. Neither viral protein influenced cell migration greatly.Conclusions and clinical importanceThis study shows that VEGF‐E and ovIL‐10 are active on equine dermal cells and exert anti‐inflammatory and anti‐fibrotic effects that may enhance skin wound healing in horses.
Histopathological and biochemical effects of cyanobacterial cells containing microcystin‐LR on Tilapia fish
Authors: Preeti T. , Hariharan G. , Rajarajeswari G.R. 
Published: August 2016

AbstractBlooms of Microcystis aeruginosa, commonly observed in many lakes of Tamil Nadu, produce the cyanobacterial toxin Microcystin, which has tumor promoting property in fish. Strains of Microcystis aeruginosa species have the same morphology but may vary in their toxicity. In the present study, Microcystin produced by Microcystis aeruginosa from Thenneri lake in Kancheepuram district of Tamil Nadu, was isolated and characterized by high‐performance liquid chromatography and electron spray ionization mass spectroscopy. Based on spectroscopic results the toxin was identified as Microcystin‐LR. Toxicogenicity was evident from the alteration in the activity of antioxidant enzymes [Glutathione S‐transferase and Catalase] and increase of protein and lipid peroxidation contents in Oreochromis niloticus, a fresh water fish species, after controlled exposure to Microcystis aeruginosa cells. Toxicity was further confirmed by histopathological changes in gill, liver and intestine of exposed fish.
Technical Note: plastimatch mabs, an open source tool for automatic image segmentation
Authors: Zaffino Paolo , Raudaschl Patrik , Fritscher Karl , Sharp Gregory C. , Spadea Maria Francesca 
Published: August 2016

Purpose:Multiatlas based segmentation is largely used in many clinical and research applications. Due to its good performances, it has recently been included in some commercial platforms for radiotherapy planning and surgery guidance. Anyway, to date, a software with no restrictions about the anatomical district and image modality is still missing. In this paper we introduce plastimatch mabs, an open source software that can be used with any image modality for automatic segmentation.Methods:plastimatch mabs workflow consists of two main parts: (1) an offline phase, where optimal registration and voting parameters are tuned and (2) an online phase, where a new patient is labeled from scratch by using the same parameters as identified in the former phase. Several registration strategies, as well as different voting criteria can be selected. A flexible atlas selection scheme is also available. To prove the effectiveness of the proposed software across anatomical districts and image modalities, it was tested on two very different scenarios: head and neck (H&N) CT segmentation for radiotherapy application, and magnetic resonance image brain labeling for neuroscience investigation.Results:For the neurological study, minimum dice was equal to 0.76 (investigated structures: left and right caudate, putamen, thalamus, and hippocampus). For head and neck case, minimum dice was 0.42 for the most challenging structures (optic nerves and submandibular glands) and 0.62 for the other ones (mandible, brainstem, and parotid glands). Time required to obtain the labels was compatible with a real clinical workflow (35 and 120 min).Conclusions:The proposed software fills a gap in the multiatlas based segmentation field, since all currently available tools (both for commercial and for research purposes) are restricted to a well specified application. Furthermore, it can be adopted as a platform for exploring MABS parameters and as a reference implementation for comparing against other segmentation algorithms.
A particle filter based autocontouring algorithm for lung tumor tracking using dynamic magnetic resonance imaging
Authors: Bourque Alexandra E. , Bedwani Stéphane , Filion Édith , Carrier Jean‐François 
Published: August 2016

Purpose:This study introduces a novel autocontouring algorithm based on particle filter for lung tumors. It is validated on dynamic magnetic resonance (MR) images and is developed in the context of MR‐linac treatments.Methods:A sequential Monte Carlo method called particle filter is used as the main structure of the algorithm and is combined with Otsu's thresholding technique to contour lung tumors on dynamic MR images. Four non‐small cell lung cancer (NSCLC) patients were imaged with a 1.5 T MR for 60 s at a rate of 4 images/s and were asked to breathe normally. Prior to treatment, some image processing is required by the proposed algorithm, which includes a manual contour of the tumor, the tumor's displacement, and its descriptive statistics. During treatment, the contours are automatically generated by thresholding around the center of mass of the particles. A comparison with the expert's contours is obtained by calculating the Dice similarity coefficient (DSC), the precision, the recall, the Hausdorff distance, and the difference in centroid positions (Δd).Results:This autocontouring algorithm is independent of pretreatment training and presents continuous adaptability as provided by the nature of particle filters. The number of particles is proportional to the area of the tumor and increases the computational time at a rate of 2 ms for every 500 particles, whereas the contouring step adds a constant 14 ms. The contours’ comparison is obtained with a mean DSC of 0.89–0.91, mean precision of 0.88–0.91, mean recall of 0.89–0.95, and mean Δd of 0.6–2.0 mm.Conclusions:This work presents a proof of concept of a new autocontouring algorithm for NSCLC patients on dynamic MR images. The contours were generated in good agreement with the expert's contours.
Dual Targeting of Cell Wall Precursors by Teixobactin Leads to Cell Lysis
Authors: Homma Tomoyuki , Nuxoll Austin , Gandt Autumn Brown , Ebner Patrick , Engels Ina , Schneider Tanja , Götz Friedrich , Lewis Kim , Conlon Brian P. 
Published: August 2016

ABSTRACT

Teixobactin represents the first member of a newly discovered class of antibiotics that act through inhibition of cell wall synthesis. Teixobactin binds multiple bactoprenol-coupled cell wall precursors, inhibiting both peptidoglycan and teichoic acid synthesis. Here, we show that the impressive bactericidal activity of teixobactin is due to the synergistic inhibition of both targets, resulting in cell wall damage, delocalization of autolysins, and subsequent cell lysis. We also find that teixobactin does not bind mature peptidoglycan, further increasing its activity at high cell densities and against vancomycin-intermediate
Staphylococcus aureus
(VISA) isolates with thickened peptidoglycan layers. These findings add to the attractiveness of teixobactin as a potential therapeutic agent for the treatment of infection caused by antibiotic-resistant Gram-positive pathogens.
Population Pharmacokinetics and Safety of Ceftolozane-Tazobactam in Adult Cystic Fibrosis Patients Admitted with Acute Pulmonary Exacerbation
Authors: Monogue Marguerite L. , Pettit Rebecca S. , Muhlebach Marianne , Cies Jeffrey J. , Nicolau David P. , Kuti Joseph L. 
Published: August 2016

ABSTRACT

Ceftolozane-tazobactam has potent activity against
Pseudomonas aeruginosa
, a pathogen associated with cystic fibrosis (CF) acute pulmonary exacerbations (APE). Due to the rapid elimination of many antibiotics, CF patients frequently have altered pharmacokinetics. In this multicenter, open-label study, we described the population pharmacokinetics and safety of ceftolozane-tazobactam at 3 g every 8 h (q8h) in 20 adult CF patients admitted with APE. Population pharmacokinetics were determined using the nonparametric adaptive grid program in Pmetrics for R. A 5,000-patient Monte Carlo simulation was performed to determine the probability of target attainment (PTA) for the ceftolozane component at 1.5 g and 3 g of ceftolozane-tazobactam q8h across a range of MICs using a primary threshold exposure of 60% free time above the MIC (
fT
>MIC). In these 20 adult CF patients, ceftolozane and tazobactam concentration data were best described by 2-compartment models, and ceftolozane clearance (CL) was significantly correlated with creatinine clearance (
r
= 0.71,
P
< 0.001). These data suggest that ceftolozane and tazobactam clearance estimates in CF patients are similar to those in adults without CF (ceftolozane CF CL, 4.76 ± 1.13 liter/h; tazobactam CF CL, 20.51 ± 4.41 liter/h). However, estimates of the volume of the central compartment (

V
c

) were lower than those for adults without CF (ceftolozane CF

V
c

, 7.51 ± 2.05 liters; tazobactam CF

V
c

, 7.85 ± 2.66 liters). Using a threshold of 60%
fT
>MIC, ceftolozane-tazobactam regimens of 1.5 g and 3 g q8h should achieve PTAs of ≥90% at MICs up to 4 and 8 μg/ml, respectively. Ceftolozane-tazobactam at 3 g q8h was well tolerated. These observations support additional studies of ceftolozane-tazobactam for
Pseudomonas aeruginosa
APE in CF patients. (This study has been registered at ClinicalTrials.gov under identifier NCT02421120.)
Transposon-Sequencing Analysis Unveils Novel Genes Involved in the Generation of Persister Cells in Uropathogenic Escherichia coli
Authors: Molina-Quiroz Roberto C. , Lazinski David W. , Camilli Andrew , Levy Stuart B. 
Published: August 2016

ABSTRACT
Persister cells are highly tolerant to different antibiotics and are associated with relapsing infections. In order to understand this phenomenon further, we exposed a transposon library to a lethal concentration of ampicillin, and mutants that survived were identified by transposon sequencing (Tn-Seq). We determined that mutations related to carbon metabolism, cell envelope (cell wall generation and membrane proteins), and stress response have a role in persister cell generation.
Polysaccharide Capsule Composition of Pneumococcal Serotype 19A Subtypes Is Unaltered among Subtypes and Independent of the Nutritional Environment
Authors: Brugger Silvio D. , Troxler Lukas J. , Rüfenacht Susanne , Frey Pascal M. , Morand Brigitte , Geyer Rudolf , Mühlemann Kathrin , Höck Stefan , Thormann Wolfgang , Furrer Julien , Christen Stephan , Hilty Markus 
Published: August 2016

ABSTRACT

Serotype 19A strains have emerged as a cause of invasive pneumococcal disease after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7), and serotype 19A has now been included in the recent 13-valent vaccine (PCV13). Genetic analysis has revealed at least three different capsular serotype 19A subtypes, and nutritional environment-dependent variation of the 19A capsule structure has been reported. Pneumococcal vaccine effectiveness and serotyping accuracy might be impaired by structural differences in serotype 19A capsules. We therefore analyzed the distribution of 19A subtypes collected within a Swiss national surveillance program and determined capsule composition under different nutritional conditions with high-performance liquid chromatography (HPLC), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR) spectroscopy. After the introduction of PCV7, a significant relative increase of subtype 19A-II and decrease of 19A-I occurred. Chemical analyses showed no difference in the composition as well as the linkage of 19A subtype capsular saccharides grown in defined and undefined growth media, which is consistent with a trisaccharide repeat unit composed of rhamnose,
N
-acetyl-mannosamine, and glucose. In summary, our study suggests that no structural variance dependent of the nutritional environment or the subtype exists. The serotype 19A subtype shift observed after the introduction of the PCV7 can therefore not be explained by selection of a capsule structure variant. However, capsule composition analysis of emerging 19A clones is recommended in cases where there is no other explanation for a selective advantage, such as antibiotic resistance or loss or acquisition of other virulence factors.
Yersinia enterocolitica YopH-Deficient Strain Activates Neutrophil Recruitment to Peyer's Patches and Promotes Clearance of the Virulent Strain
Authors: Dave Mabel N. , Silva Juan E. , Eliçabe Ricardo J. , Jeréz María B. , Filippa Verónica P. , Gorlino Carolina V. , Autenrieth Stella , Autenrieth Ingo B. , Di Genaro María S. 
Published: August 2016

ABSTRACT

Yersinia enterocolitica
evades the immune response by injecting
Yersinia
outer proteins (Yops) into the cytosol of host cells. YopH is a tyrosine phosphatase critical for
Yersinia
virulence. However, the mucosal immune mechanisms subverted by YopH during
in vivo
orogastric infection with
Y. enterocolitica
remain elusive. The results of this study revealed neutrophil recruitment to Peyer's patches (PP) after infection with a YopH-deficient mutant strain (
Y. enterocolitica
Δ
yopH
). While the
Y. enterocolitica
wild-type (WT) strain in PP induced the major neutrophil chemoattractant CXCL1 mRNA and protein levels, infection with the
Y. enterocolitica
Δ
yopH
mutant strain exhibited a higher expression of the CXCL1 receptor, CXCR2, in blood neutrophils, leading to efficient neutrophil recruitment to the PP. In contrast, migration of neutrophils into PP was impaired upon infection with
Y. enterocolitica
WT strain.
In vitro
infection of blood neutrophils revealed the involvement of YopH in CXCR2 expression. Depletion of neutrophils during
Y. enterocolitica
Δ
yopH
infection raised the bacterial load in PP. Moreover, the clearance of WT
Y. enterocolitica
was improved when an equal mixture of
Y. enterocolitica
WT and
Y. enterocolitica
Δ
yopH
strains was used in infecting the mice. This study indicates that
Y. enterocolitica
prevents early neutrophil recruitment in the intestine and that the effector protein YopH plays an important role in the immune evasion mechanism. The findings highlight the potential use of the
Y. enterocolitica
YopH-deficient strain as an oral vaccine carrier.
Vitamin D and Lung Infection
Authors: Cantorna Margherita T. 
Published: August 2016

ABSTRACT

Available data suggest that vitamin D plays a role in controlling inflammation in the lungs. However, to date vitamin D-induced production of cathelicidin has not been shown to have an effect on the burden of either viruses or bacteria. Future work should continue to determine the effects of vitamin D-regulated mechanisms in the lung and the possible role of cathelicidin against different pulmonary pathogens
in vivo
.
ZpdN, a Plasmid-Encoded Sigma Factor Homolog, Induces pBS32-Dependent Cell Death in Bacillus subtilis
Authors: Myagmarjav B.-E. , Konkol M. A. , Ramsey J. , Mukhopadhyay S. , Kearns D. B. 
Published: August 2016

ABSTRACT

The ancestral
Bacillus subtilis
strain 3610 contains an 84-kb plasmid called pBS32 that was lost during domestication of commonly used laboratory derivatives. Here we demonstrate that pBS32, normally present at 1 or 2 copies per cell, increases in copy number nearly 100-fold when cells are treated with the DNA-damaging agent mitomycin C. Mitomycin C treatment also caused cell lysis dependent on pBS32-borne prophage genes. ZpdN, a sigma factor homolog encoded by pBS32, was required for the plasmid response to DNA damage, and artificial expression of ZpdN was sufficient to induce pBS32 hyperreplication and cell death. Plasmid DNA released by cell death was protected by the capsid protein ZpbH, suggesting that the plasmid was packaged into a phagelike particle. The putative particles were further indicated by CsCl sedimentation but were not observed by electron microscopy and were incapable of killing
B. subtilis
cells extracellularly. We hypothesize that pBS32-mediated cell death releases a phagelike particle that is defective and unstable.

IMPORTANCE
Prophages are phage genomes stably integrated into the host bacterium's chromosome and less frequently are maintained as extrachromosomal plasmids. Here we report that the extrachromosomal plasmid pBS32 of
Bacillus subtilis
encodes a prophage that, when activated, kills the host. pBS32 also encodes both the sigma factor homolog ZpdN that is necessary and sufficient for prophage induction and the protein ComI, which is a potent inhibitor of DNA uptake by natural transformation. We provide evidence that the entire pBS32 sequence may be part of the prophage and thus that competence inhibition may be linked to lysogeny.
Neisseria gonorrhoeae Crippled Its Peptidoglycan Fragment Permease To Facilitate Toxic Peptidoglycan Monomer Release
Authors: Chan Jia Mun , Dillard Joseph P. 
Published: August 2016

ABSTRACT

Neisseria gonorrhoeae
(gonococci) and
Neisseria meningitidis
(meningococci) are human pathogens that cause gonorrhea and meningococcal meningitis, respectively. Both
N. gonorrhoeae
and
N. meningitidis
release a number of small peptidoglycan (PG) fragments, including proinflammatory PG monomers, although
N. meningitidis
releases fewer PG monomers. The PG fragments released by
N. gonorrhoeae
and
N. meningitidis
are generated in the periplasm during cell wall remodeling, and a majority of these fragments are transported into the cytoplasm by an inner membrane permease, AmpG; however, a portion of the PG fragments are released into the extracellular environment through unknown mechanisms. We previously reported that the expression of meningococcal
ampG
in
N. gonorrhoeae
reduced PG monomer release by gonococci. This finding suggested that the efficiency of AmpG-mediated PG fragment recycling regulates the amount of PG fragments released into the extracellular milieu. We determined that three AmpG residues near the C-terminal end of the protein modulate AmpG's efficiency. We also investigated the association between PG fragment recycling and release in two species of human-associated nonpathogenic
Neisseria
:
N. sicca
and
N. mucosa
. Both
N. sicca
and
N. mucosa
release lower levels of PG fragments and are more efficient at recycling PG fragments than
N. gonorrhoeae
. Our results suggest that
N. gonorrhoeae
has evolved to increase the amounts of toxic PG fragments released by reducing its PG recycling efficiency.

IMPORTANCE
Neisseria gonorrhoeae
and
Neisseria meningitidis
are human pathogens that cause highly inflammatory diseases, although
N. meningitidis
is also frequently found as a normal member of the nasopharyngeal microbiota. Nonpathogenic
Neisseria
, such as
N. sicca
and
N. mucosa
, also colonize the nasopharynx without causing disease. Although all four species release peptidoglycan fragments,
N. gonorrhoeae
is the least efficient at recycling and releases the largest amount of proinflammatory peptidoglycan monomers, partly due to differences in the recycling permease AmpG. Studying the interplay between bacterial physiology (peptidoglycan metabolism) and pathogenesis (release of toxic monomers) leads to an increased understanding of how different bacterial species maintain asymptomatic colonization or cause disease and may contribute to efforts to mitigate disease.
Chromatin Immunoprecipitation Sequencing Technology Reveals Global Regulatory Roles of Low-Cell-Density Quorum-Sensing Regulator AphA in the Pathogen Vibrio alginolyticus
Authors: Gu Dan , Liu Huan , Yang Zhen , Zhang Yuanxing , Wang Qiyao 
Published: August 2016

ABSTRACT

Quorum sensing (QS) is an important regulatory system in virulence expression and environmental adaptation in bacteria. The master QS regulators (MQSR) LuxR and AphA reciprocally control QS gene expression in vibrios. However, the molecular basis for the regulatory functions of AphA remains undefined. In this study, we characterized its regulatory roles in
Vibrio alginolyticus
, an important zoonotic pathogen causing diseases in marine animals as well as in humans. AphA is involved in the motility ability, biofilm formation, and
in vivo
survival of
V. alginolyticus
. Specifically, AphA is expressed at low-cell-density growth phases. In addition, AphA negatively regulates the expression of the main virulence factor, alkaline serine protease (Asp), through LuxR. Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) detected 49 enriched loci harboring AphA-binding peaks across the
V. alginolyticus
genome. An AphA-specific binding motif was identified and further confirmed by electrophoretic mobility shift assay (EMSA) and mutagenesis analysis. A quantitative real-time PCR (qRT-PCR) assay further validated the regulation of AphA on these genes. AphA binds directly to the
aphA
promoter and negatively regulates its own expression. Moreover, AphA directly regulates genes encoding adenylate cyclase, anti-σ
D
, FabR, and the small RNA CsrB, revealing versatile regulatory roles of AphA in its physiology and virulence. Furthermore, our data indicated that AphA modulates motility through the coordinated function of LuxR and CsrB. Collectively, the findings of this work contribute to better understanding of the regulatory roles of AphA in QS and non-QS genes.

IMPORTANCE
In this work, we determined that AphA, the master regulator of QS at low cell density, plays essential roles in expression of genes associated with physiology and virulence in
V. alginolyticus
, a Gram-negative pathogen for humans and marine animals. We further uncovered that 49 genes could be directly regulated by AphA and a 19-bp consensus binding sequence was identified. Among the 49 genes, the QS and other non-QS-associated genes were identified to be regulated by AphA. Besides, the small RNA CsrB was negatively regulated by AphA, and AphA regulate motility abilities through both CsrB and LuxR. Taken together, the findings of this study improve our understanding of the complex regulation network of AphA and QS.