bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus PCR Assays Elucidate Vegetative Incompatibility Gene Profiles of Cryphonectria parasitica in the United States
Authors: Short Dylan P. G. , Double Mark , Nuss Donald L. , Stauder Cameron M. , MacDonald William , Kasson Matthew T. 
Published: June 2015

ABSTRACT

Chestnut blight is a devastating disease of
Castanea
spp. Mycoviruses that reduce virulence (hypovirulence) of the causative agent,
Cryphonectria parasitica
, can be used to manage chestnut blight. However, vegetative incompatibility (
vic
) barriers that restrict anastomosis-mediated virus transmission hamper hypovirulence efficacy. In order to effectively determine the vegetative incompatibility genetic structure of
C. parasitica
field populations, we have designed PCR primer sets that selectively amplify and distinguish alleles for each of the six known diallelic
C. parasitica
vic
genetic loci. PCR assay results were validated using a panel of 64 European tester strains with genetically determined
vic
genotypes. Analysis of 116
C. parasitica
isolates collected from five locations in the eastern United States revealed 39 unique
vic
genotypes and generally good agreement between PCR and tester strain coculturing assays in terms of
vic
diversity and genotyping. However, incongruences were observed for isolates from multiple locations and suggested that the coculturing assay can overestimate diversity at the six known
vic
loci. The availability of molecular tools for rapid and precise
vic
genotyping significantly improves the ability to predict and evaluate the efficacy of hypovirulence and related management strategies.
Acetylation Regulates Survival of Salmonella enterica Serovar Typhimurium under Acid Stress
Authors: Ren Jie , Sang Yu , Ni Jinjing , Tao Jing , Lu Jie , Zhao Mingwen , Yao Yu-Feng 
Published: June 2015

ABSTRACT

The ability to acetylate lysine residues is conserved across organisms, and acetylation of lysine residues plays important roles in various cellular functions. Maintaining intracellular pH homeostasis is crucial for the survival of enteric bacteria in the acidic gastric tract. It has been shown that eukaryotes can stabilize the intracellular pH by histone deacetylation. However, it remains unknown whether bacteria can utilize a reversible protein acetylation system to adapt to an acidic environment. Here we demonstrate that protein acetylation/deacetylation is critical for
Salmonella enterica
serovar Typhimurium to survive in an acidic environment. We used RNA sequencing to analyze the transcriptome patterns under acid stress and found that the transcriptional levels of genes involved in NAD
+
/NADH metabolism were significantly changed, leading to an increase in the intracellular NAD
+
/NADH ratio. Moreover, acid stress downregulated the transcriptional level of
pat
, encoding acetyltransferase, and genes
cyaA
and
crp
, encoding adenylate cyclase and cyclic AMP receptor protein, respectively, which are positive regulators of
pat
. It was found that the acid signal alerts the tricarboxylic acid cycle to promote the consumption of acetyl coenzyme A (Ac-CoA), an acetyl group donor for the acetylation reaction. A lowered acetylation level not only was the bacterial response to acid stress but also increased the survival rate of
S
. Typhimurium under acid stress. The
pat
deletion mutant had a more stable intracellular pH, which paralleled the higher survival rate after acid treatment compared with that of both the wild-type strain and the
cobB
(encoding deacetylase) deletion mutant. Our data indicate that bacteria can downregulate the protein acetylation level to prevent the intracellular pH from further falling under acid stress, and this work may provide a new perspective to understand the bacterial acid resistance mechanism.
Protozoan Cysts Act as a Survival Niche and Protective Shelter for Foodborne Pathogenic Bacteria
Authors: Lambrecht Ellen , Baré Julie , Chavatte Natascha , Bert Wim , Sabbe Koen , Houf Kurt 
Published: June 2015

ABSTRACT

The production of cysts, an integral part of the life cycle of many free-living protozoa, allows these organisms to survive adverse environmental conditions. Given the prevalence of free-living protozoa in food-related environments, it is hypothesized that these organisms play an important yet currently underinvestigated role in the epidemiology of foodborne pathogenic bacteria. Intracystic bacterial survival is highly relevant, as this would allow bacteria to survive the stringent cleaning and disinfection measures applied in food-related environments. The present study shows that strains of widespread and important foodborne bacteria (
Salmonella enterica
,
Escherichia coli
,
Yersinia enterocolitica
, and
Listeria monocytogenes
) survive inside cysts of the ubiquitous amoeba
Acanthamoeba castellanii
, even when exposed to either antibiotic treatment (100 μg/ml gentamicin) or highly acidic conditions (pH 0.2) and resume active growth in broth media following excystment. Strain- and species-specific differences in survival periods were observed, with
Salmonella enterica
surviving up to 3 weeks inside amoebal cysts. Up to 53% of the cysts were infected with pathogenic bacteria, which were located in the cyst cytosol. Our study suggests that the role of free-living protozoa and especially their cysts in the persistence and epidemiology of foodborne bacterial pathogens in food-related environments may be much more important than hitherto assumed.
World Health Organization International Standard To Harmonize Assays for Detection of Mycoplasma DNA
Authors: Nübling C. Micha , Baylis Sally A. , Hanschmann Kay-Martin , Montag-Lessing Thomas , Chudy Michael , Kreß Julia , Ulrych Ursula , Czurda Stefan , Rosengarten Renate ,   the Mycoplasma Collaborative Study Group
Published: June 2015

ABSTRACT

Nucleic acid amplification technique (NAT)-based assays (referred to here as NAT assays) are increasingly used as an alternative to culture-based approaches for the detection of mycoplasma contamination of cell cultures. Assay features, like the limit of detection or quantification, vary widely between different mycoplasma NAT assays. Biological reference materials may be useful for harmonization of mycoplasma NAT assays. An international feasibility study included lyophilized preparations of four distantly related mycoplasma species (
Acholeplasma laidlawii
,
Mycoplasma fermentans
,
M. orale
,
M. pneumoniae
) at different concentrations which were analyzed by 21 laboratories using 26 NAT assays with a qualitative, semiquantitative, or quantitative design. An
M. fermentans
preparation was shown to decrease the interassay variation when used as a common reference material. The preparation was remanufactured and characterized in a comparability study, and its potency (in NAT-detectable units) across different NATs was determined. The World Health Organization (WHO) Expert Committee on Biological Standardization (ECBS) established this preparation to be the “1st World Health Organization international standard for mycoplasma DNA for nucleic acid amplification technique-based assays designed for generic mycoplasma detection” (WHO Tech Rep Ser 987:42, 2014) with a potency of 200,000 IU/ml. This WHO international standard is now available as a reference preparation for characterization of NAT assays, e.g., for determination of analytic sensitivity, for calibration of quantitative assays in a common unitage, and for defining regulatory requirements in the field of mycoplasma testing.
Microbial Diversity and Putative Diazotrophy in High- and Low-Microbial-Abundance Mediterranean Sponges
Authors: Ribes Marta , Dziallas Claudia , Coma Rafel , Riemann Lasse 
Published: June 2015

ABSTRACT

Microbial communities associated with marine sponges carry out nutrient transformations essential for benthic-pelagic coupling; however, knowledge about their composition and function is still sparse. We evaluated the richness and diversity of prokaryotic assemblages associated with three high-microbial-abundance (HMA) and three low-microbial-abundance (LMA) sympatric Mediterranean sponges to address their stability and uniqueness. Moreover, to examine functionality and because an imbalance between nitrogen ingestion and excretion has been observed for some of these species, we sequenced nitrogenase genes (
nifH
) and measured N
2
fixation. The prokaryotic communities in the two sponge types did not differ in terms of richness, but the highest diversity was found in HMA sponges. Moreover, the discrete composition of the communities in the two sponge types relative to that in the surrounding seawater indicated that horizontal transmission and vertical transmission affect the microbiomes associated with the two sponge categories.
nifH
genes were found in all LMA species and sporadically in one HMA species, and about half of the
nifH
gene sequences were common between the different sponge species and were also found in the surrounding water, suggesting horizontal transmission.
15
N
2
-enriched incubations showed that N
2
fixation was measurable in the water but was not associated with the sponges. Also, the analysis of the isotopic ratio of
15
N to
14
N in sponge tissue indicated that N
2
fixation is not an important source of nitrogen in these Mediterranean sponges. Overall, our results suggest that compositional and functional features differ between the prokaryotic communities associated with HMA and LMA sponges, which may affect sponge ecology.
Relationship between the Presence of Bartonella Species and Bacterial Loads in Cats and Cat Fleas (Ctenocephalides felis) under Natural Conditions
Authors: Gutiérrez Ricardo , Nachum-Biala Yaarit , Harrus Shimon 
Published: June 2015

ABSTRACT

Cats are considered the main reservoir of three zoonotic
Bartonella
species:
Bartonella henselae
,
Bartonella
clarridgeiae
, and
Bartonella
koehlerae
. Cat fleas (
Ctenocephalides felis
) have been experimentally demonstrated to be a competent vector of
B. henselae
and have been proposed as the potential vector of the two other
Bartonella
species. Previous studies have reported a lack of association between the
Bartonella
species infection status (infected or uninfected) and/or bacteremia levels of cats and the infection status of the fleas they host. Nevertheless, to date, no study has compared the quantitative distributions of these bacteria in both cats and their fleas under natural conditions. Thus, the present study explored these relationships by identifying and quantifying the different
Bartonella
species in both cats and their fleas. Therefore, EDTA-blood samples and fleas collected from stray cats were screened for
Bartonella
bacteria. Bacterial loads were quantified by high-resolution melt real-time quantitative PCR assays. The results indicated a moderate correlation between the
Bartonella
bacterial loads in the cats and their fleas when both were infected with the same
Bartonella
species. Moreover, a positive effect of the host infection status on the
Bartonella
bacterial loads of the fleas was observed. Conversely, the cat bacterial loads were not affected by the infection status of their fleas. Our results suggest that the
Bartonella
bacterial loads of fleas are positively affected by the presence of the bacteria in their feline host, probably by multiple acquisitions/accumulation and/or multiplication events.
Sharply Tuned pH Response of Genetic Competence Regulation in Streptococcus mutans: a Microfluidic Study of the Environmental Sensitivity of
comX
Authors: Son Minjun , Ghoreishi Delaram , Ahn Sang-Joon , Burne Robert A. , Hagen Stephen J. 
Published: June 2015

ABSTRACT

Genetic competence in
Streptococcus mutans
is a transient state that is regulated in response to multiple environmental inputs. These include extracellular pH and the concentrations of two secreted peptides, designated CSP (competence-stimulating peptide) and XIP (
comX
-inducing peptide). The role of environmental cues in regulating competence can be difficult to disentangle from the effects of the organism's physiological state and its chemical modification of its environment. We used microfluidics to control the extracellular environment and study the activation of the key competence gene
comX
. We find that the
comX
promoter (P

comX

) responds to XIP or CSP only when the extracellular pH lies within a narrow window, about 1 pH unit wide, near pH 7. Within this pH range, CSP elicits a strong P

comX

response from a subpopulation of cells, whereas outside this range the proportion of cells expressing
comX
declines sharply. Likewise, P

comX

is most sensitive to XIP only within a narrow pH window. While previous work suggested that
comX
may become refractory to CSP or XIP stimulus as cells exit early exponential phase, our microfluidic data show that extracellular pH dominates in determining sensitivity to XIP and CSP. The data are most consistent with an effect of pH on the ComR/ComS system, which has direct control over transcription of
comX
in
S. mutans
.
Targeting Importin-α7 as a Therapeutic Approach against Pandemic Influenza Viruses
Authors: Resa-Infante Patricia , Paterson Duncan , Bonet Jaume , Otte Anna , Oliva Baldo , Fodor Ervin , Gabriel Gülsah 
Published: June 2015

ABSTRACT

Viral drug resistance is believed to be less likely to occur if compounds are directed against cellular rather than viral proteins. In this study, we analyzed the feasibility of a crucial viral replication factor, namely, importin-α7, as a cellular drug target to combat pandemic influenza viruses. Surprisingly, only five viral lung-to-lung passages were required to achieve 100% lethality in importin-α7
−/−
mice that otherwise are resistant. Viral escape from importin-α7 requirement was mediated by five mutations in the viral ribonucleoprotein complex and the surface glycoproteins. Moreover, the importin-α7
−/−
mouse-adapted strain became even more virulent for wild-type mice than the parental strain. These studies show that targeting host proteins may still result in viral escape by alternative pathways, eventually giving rise to even more virulent virus strains. Thus, therapeutic intervention strategies should consider a multitarget approach to reduce viral drug resistance.

IMPORTANCE
Here, we investigated the long-standing hypothesis based on
in vitro
studies that viral drug resistance occurrence is less likely if compounds are directed against cellular rather than viral proteins. Here, we challenged this hypothesis by analyzing, in an
in vivo
animal model, the feasibility of targeting the cellular factor importin-α7, which is crucial for human influenza virus replication and pathogenesis, as an efficient antiviral strategy against pandemic influenza viruses. In summary, our studies suggest that resistance against cellular factors is possible
in vivo
, and the emergence of even more virulent viral escape variants calls for particular caution. Thus, therapeutic intervention strategies should consider a multitarget approach using compounds against viral as well as cellular factors to reduce the risk of viral drug resistance and potentially increased virulence.
Preliminary Evaluation of a Bunyavirus Vector for Cancer Immunotherapy
Authors: Oreshkova N. , Spel L. , Vloet R. P. M. , Wichgers Schreur P. J. , Moormann R. J. M. , Boes M. , Kortekaas J. 
Published: June 2015

ABSTRACT

Replicon particles of Rift Valley fever virus, referred to as nonspreading Rift Valley fever virus (NSR), are intrinsically safe and highly immunogenic. Here, we demonstrate that NSR-infected human dendritic cells can activate CD8
+
T cells
in vitro
and that prophylactic and therapeutic vaccinations of mice with NSR encoding a tumor-associated CD8 peptide can control the outgrowth of lymphoma cells
in vivo
. These results suggest that the NSR system holds promise for cancer immunotherapy.
Epilepsy emergency rescue training
Authors: Shankar Rohit , Jory Caryn , ashton juliet , McLean Brendan , Walker Matthew 
Published: June 2015

AbstractThe NICE audit of epilepsy related deaths revealed that 1200 epilepsy deaths occur every year in the UK, with 42% potentially avoidable.[1] Convulsive status epilepticus (SE) is a life-threatening condition with over 20% mortality rate, especially if early treatment is not initiated .[2] Ten percent of all UK emergency department (ED) admissions are due to epilepsy, usually over represented by cases of SE.[3] Six out of seven epilepsy cases seen in the ED are admitted into medical care.[4]Patients with chronic and/or treatment resistant epilepsy carry a higher risk of premature death. When a seizure lasts for five minutes or more then the patient is at high risk of continuing to SE and this may result in causing brain damage or death.[2]Buccal midazolam is an emergency rescue medication prescribed on a special named patient license to reduce the duration of an epileptic seizure and prevent SE.[2,5] It should be administered by a trained person and is widely used due to its effectiveness and social acceptability. In the UK, epilepsy education and training courses are expected to be conducted by epilepsy professionals in line with the agreed training guidelines of Joint Epilepsy Council (JEC) backed up by evidence from NICE.[6,7] Training should provide an overview of epilepsy to facilitate safe care and appropriate administration of rescue medication for people with epilepsy (PWE) when experiencing a prolonged seizure. The medication is prescribed on specialist advice by the GP or specialists directly.Unfortunately the JEC guidelines are not robust enough to provide assurances of safe care. This problem had a myriad of complexities and an appropriate solution using web based resource was piloted, tested, and applied successfully using quality improvement methodology.
Cost and impoverishment 1 year after hospitalisation due to injuries: a cohort study in Thái Bình, Vietnam
Authors: Nguyen Ha , Ivers Rebecca , Jan Stephen , Martiniuk Alexandra , Segal Leonie , Pham Cuong 
Published: June 2015

BackgroundEvidence on the economic impact on individuals and their families following an injury in Vietnam is limited. This study examines the costs and the risk of impoverishment due to hospitalised injuries at 12 months following hospital discharge and associated factors.MethodEmploying a prospective cohort design, 892 people hospitalised for injury were recruited from Thái Bình General Hospital in Vietnam in 2010 and followed up for 12 months. All out-of-pocket costs incurred and income lost by injured persons and their caregivers associated with care and treatment of their injuries were reported. To examine associated factors, we used generalised estimating equation models for costs and modified Poisson regression for the risk of impoverishment.ResultsThe mean total costs by 12 months postdischarge were US$804, nearly 1.2 times the annual average income. Injuries that incurred highest costs were falls (US$950) and road traffic injuries (RTIs) (US$794). At 12-month follow-up, 181 persons (26.9%) became impoverished, with those injured in RTIs and falls at highest risk (26.1% and 35.4%, respectively). Factors associated with higher costs were also those associated with higher risk of impoverishment. These include those injured in RTIs or falls; having higher severity level; principal injured region as upper extremities, lower extremities or head; physical nature of injuries as fracture or concussion injuries; and longer hospitalisation.ConclusionsInjuries impose significant economic burden on injured persons and their families during and beyond hospitalisation. In addition to prevention, there is a need to reform health financing system to protect injured persons from significant out-of-pocket expense for healthcare services.
Plasma Autoantibodies Associated with Basal-like Breast Cancers
Authors: Wang Jie , Figueroa Jonine D. , Wallstrom Garrick , Barker Kristi , Park Jin G. , Demirkan Gokhan , Lissowska Jolanta , Anderson Karen S. , Qiu Ji , LaBaer Joshua 
Published: June 2015

AbstractBackground: Basal-like breast cancer (BLBC) is a rare aggressive subtype that is less likely to be detected through mammographic screening. Identification of circulating markers associated with BLBC could have promise in detecting and managing this deadly disease.Methods: Using samples from the Polish Breast Cancer study, a high-quality population-based case–control study of breast cancer, we screened 10,000 antigens on protein arrays using 45 BLBC patients and 45 controls, and identified 748 promising plasma autoantibodies (AAbs) associated with BLBC. ELISA assays of promising markers were performed on a total of 145 BLBC cases and 145 age-matched controls. Sensitivities at 98% specificity were calculated and a BLBC classifier was constructed.Results: We identified 13 AAbs (CTAG1B, CTAG2, TP53, RNF216, PPHLN1, PIP4K2C, ZBTB16, TAS2R8, WBP2NL, DOK2, PSRC1, MN1, TRIM21) that distinguished BLBC from controls with 33% sensitivity and 98% specificity. We also discovered a strong association of TP53 AAb with its protein expression (P = 0.009) in BLBC patients. In addition, MN1 and TP53 AAbs were associated with worse survival [MN1 AAb marker HR = 2.25, 95% confidence interval (CI), 1.03–4.91; P = 0.04; TP53, HR = 2.02, 95% CI, 1.06–3.85; P = 0.03]. We found limited evidence that AAb levels differed by demographic characteristics.Conclusions: These AAbs warrant further investigation in clinical studies to determine their value for further understanding the biology of BLBC and possible detection.Impact: Our study identifies 13 AAb markers associated specifically with BLBC and may improve detection or management of this deadly disease. Cancer Epidemiol Biomarkers Prev; 24(9); 1332–40. ©2015 AACR.
Molecular Pathways: Sensitivity and Resistance to Anti-EGFR Antibodies
Authors: Bertotti Andrea , Sassi Francesco 
Published: June 2015

Abstract
Monoclonal antibodies targeting the EGF receptor (EGFR) tyrosine kinase, such as cetuximab and panitumumab, achieve clinically meaningful responses in patients affected by head and neck and colorectal cancers. Despite this evidence of efficacy, no genomic abnormalities that robustly predict sensitivity to EGFR blockade have been yet identified. This suggests that, in some tumor contexts, EGFR dependency is not acquired during neoplastic transformation and rather reflects an aberrant declination of physiologic traits typical of normal tissue counterparts. Indeed, EGFR signals are crucial for the reconstitution of damaged mucosa in the context of acute inflammation, and their sustained activation is likely to turn into a pro-oncogenic cue during chronic inflammation. Although positive predictors of response to anti-EGFR antibodies remain unknown, multiple determinants of resistance have been described, including alterations interfering with antibody–receptor interaction, deregulation of parallel signaling pathways, and mutations in downstream transducers. These findings provide new opportunities for the optimization of therapeutic strategies based on drug combinations. However, the emerging notion that genetic interactions and compensatory mechanisms may affect—both positively and negatively—the efficacy of targeted therapies complicates the rational design of combinatorial approaches and implies a rethinking of the criteria required to prioritize laboratory findings for clinical validation in investigational trials. Clin Cancer Res; 21(15); 3377–83. ©2015 AACR.