bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosomal Aneuploidy Improves the Brewing Characteristics of Sake Yeast
Authors: Kadowaki Masafumi , Fujimaru Yuki , Taguchi Seiga , Ferdouse Jannatul , Sawada Kazutaka , Kimura Yuta , Terasawa Yohei , Agrimi Gennaro , Anai Toyoaki , Noguchi Hideki , Toyoda Atsushi , Fujiyama Asao , Akao Takeshi , Kitagaki Hiroshi 
Published: October 2017

ABSTRACT

The effect of chromosomal aneuploidy on the brewing characteristics of brewery yeasts has not been studied. Here we report that chromosomal aneuploidy in sake brewery yeast (
Saccharomyces cerevisiae
) leads to the development of favorable brewing characteristics. We found that pyruvate-underproducing sake yeast, which produces less off-flavor diacetyl, is aneuploid and trisomic for chromosomes XI and XIV. To confirm that this phenotype is due to aneuploidy, we obtained 45 haploids with various chromosomal additions and investigated their brewing profiles. A greater number of chromosomes correlated with a decrease in pyruvate production. Especially, sake yeast haploids with extra chromosomes in addition to chromosome XI produced less pyruvate than euploids. Mitochondrion-related metabolites and intracellular oxygen species in chromosome XI aneuploids were higher than those in euploids, and this effect was canceled in their “petite” strains, suggesting that an increase in chromosomes upregulated mitochondrial activity and decreased pyruvate levels. These findings suggested that an increase in chromosome number, including chromosome XI, in sake yeast haploids leads to pyruvate underproduction through the augmentation of mitochondrial activity. This is the first report proposing that aneuploidy in brewery yeasts improves their brewing profile.

IMPORTANCE
Chromosomal aneuploidy has not been evaluated in development of sake brewing yeast strains. This study shows the relationship between chromosomal aneuploidy and brewing characteristics of brewery yeast strains. High concentrations of pyruvate during sake storage give rise to α-acetolactate and, in turn, to high concentrations of diacetyl, which is considered an off-flavor. It was demonstrated that pyruvate-underproducing sake yeast is trisomic for chromosome XI and XIV. Furthermore, sake yeast haploids with extra chromosomes produced reduced levels of pyruvate and showed metabolic processes characteristic of increased mitochondrial activity. This novel discovery will enable the selection of favorable brewery yeasts by monitoring the copy numbers of specific chromosomes through a process that does not involve generation/use of genetically modified organisms.
Stringent Response Regulators Contribute to Recovery from Glucose Phosphate Stress in Escherichia coli
Authors: Kessler Julie R. , Cobe Brandi L. , Richards Gregory R. 
Published: October 2017

ABSTRACT

In enteric bacteria such as
Escherichia coli
, the transcription factor SgrR and the small RNA SgrS regulate the response to glucose phosphate stress, a metabolic dysfunction that results in growth inhibition and stems from the intracellular accumulation of sugar phosphates. SgrR activates the transcription of
sgrS
, and SgrS helps to rescue cells from stress in part by inhibiting the uptake of stressor sugar phosphates. While the regulatory targets of this stress response are well described, less is known about how the SgrR-SgrS response itself is regulated. To further characterize the regulation of the glucose phosphate stress response, we screened global regulator gene mutants for growth changes during glucose phosphate stress. We found that deleting
dksA
, which encodes a regulator of the stringent response to nutrient starvation, decreases growth under glucose phosphate stress conditions. The stringent response alarmone regulator ppGpp (synthesized by RelA and SpoT) also contributes to recovery from glucose phosphate stress: as with
dksA
, mutating
relA
and
spoT
worsens the growth defect of an
sgrS
mutant during stress, although the
sgrS relA spoT
mutant defect was only detectable under lower stress levels. In addition, mutating
dksA
or
relA
and
spoT
lowers
sgrS
expression (as measured with a P

sgrS

-
lacZ
fusion), suggesting that the observed growth defects may be due to decreased induction of the glucose phosphate stress response or related targets. This regulatory effect could occur through altered
sgrR
transcription, as
dksA
and
relA spoT
mutants also exhibit decreased expression of a P

sgrR

-
lacZ
fusion. Taken together, this work supports a role for stringent response regulators in aiding the recovery from glucose phosphate stress.

IMPORTANCE
Glucose phosphate stress leads to growth inhibition in bacteria such as
Escherichia coli
when certain sugar phosphates accumulate in the cell. The transcription factor SgrR and the small RNA SgrS alleviate this stress in part by preventing further sugar phosphate transport. While the regulatory mechanisms of this response have been characterized, the regulation of the SgrR-SgrS response itself is not as well understood. Here, we describe a role for stringent response regulators DksA and ppGpp in the response to glucose phosphate stress.
sgrS dksA
and
sgrS relA spoT
mutants exhibit growth defects under glucose phosphate stress conditions. These defects may be due to a decrease in stress response induction, as deleting
dksA
or
relA
and
spoT
also results in decreased expression of
sgrS
and
sgrR
. This research presents one of the first regulatory effects on the glucose phosphate stress response outside SgrR and SgrS and depicts a novel connection between these two metabolic stress responses.
Genotypic and Phenotypic Characteristics Associated with Biofilm Formation by Human Clinical Escherichia coli Isolates of Different Pathotypes
Authors: Schiebel Juliane , Böhm Alexander , Nitschke Jörg , Burdukiewicz Michał , Weinreich Jörg , Ali Aamir , Roggenbuck Dirk , Rödiger Stefan , Schierack Peter 
Published: October 2017

ABSTRACT

Bacterial biofilm formation is a widespread phenomenon and a complex process requiring a set of genes facilitating the initial adhesion, maturation, and production of the extracellular polymeric matrix and subsequent dispersal of bacteria. Most studies on
Escherichia coli
biofilm formation have investigated nonpathogenic
E. coli
K-12 strains. Due to the extensive focus on laboratory strains in most studies, there is poor information regarding biofilm formation by pathogenic
E. coli
isolates. In this study, we genotypically and phenotypically characterized 187 human clinical
E. coli
isolates representing various pathotypes (e.g., uropathogenic, enteropathogenic, and enteroaggregative
E. coli
). We investigated the presence of biofilm-associated genes (“genotype”) and phenotypically analyzed the isolates for motility and curli and cellulose production (“phenotype”). We developed a new screening method to examine the
in vitro
biofilm formation ability. In summary, we found a high prevalence of biofilm-associated genes. However, we could not detect a biofilm-associated gene or specific phenotype correlating with the biofilm formation ability. In contrast, we did identify an association of increased biofilm formation with a specific
E. coli
pathotype. Enteroaggregative
E. coli
(EAEC) was found to exhibit the highest capacity for biofilm formation. Using our image-based technology for the screening of biofilm formation, we demonstrated the characteristic biofilm formation pattern of EAEC, consisting of thick bacterial aggregates. In summary, our results highlight the fact that biofilm-promoting factors shown to be critical for biofilm formation in nonpathogenic strains do not reflect their impact in clinical isolates and that the ability of biofilm formation is a defined characteristic of EAEC.

IMPORTANCE
Bacterial biofilms are ubiquitous and consist of sessile bacterial cells surrounded by a self-produced extracellular polymeric matrix. They cause chronic and device-related infections due to their high resistance to antibiotics and the host immune system. In nonpathogenic
Escherichia coli
, cell surface components playing a pivotal role in biofilm formation are well known. In contrast, there is poor information for their role in biofilm formation of pathogenic isolates. Our study provides insights into the correlation of biofilm-associated genes or specific phenotypes with the biofilm formation ability of commensal and pathogenic
E. coli
. Additionally, we describe a newly developed method enabling qualitative biofilm analysis by automated image analysis, which is beneficial for high-throughput screenings. Our results help to establish a better understanding of
E. coli
biofilm formation.
Murein Hydrolase LytF of Streptococcus sanguinis and the Ecological Consequences of Competence Development
Authors: Cullin Nyssa , Redanz Sylvio , Lampi Kirsten J. , Merritt Justin , Kreth Jens 
Published: October 2017

ABSTRACT

The overall health of the oral cavity is dependent on proper homeostasis between health-associated bacterial colonizers and bacteria known to promote dental caries.
Streptococcus sanguinis
is a health-associated commensal organism, a known early colonizer of the acquired tooth pellicle, and is naturally competent. We have shown that LytF, a competence-controlled murein hydrolase, is capable of inducing the release of extracellular DNA (eDNA) from oral bacteria. Precipitated LytF and purified LytF were used as treatments against planktonic cultures and biofilms. Larger amounts of eDNA were released from cultures treated with protein samples containing LytF. Additionally, LytF could affect biofilm formation and cellular morphology. Biofilm formation was significantly decreased in the
lytF
-complemented strain, in which increased amounts of LytF are present. The same strain also exhibited cell morphology defects in both planktonic cultures and biofilms. Furthermore, the LytF cell morphology phenotype was reproducible in wild-type cells using purified LytF protein. In sum, our findings demonstrate that LytF can induce the release of eDNA from oral bacteria, and they suggest that, without proper regulation of LytF, cells display morphological abnormalities that contribute to biofilm malformation. In the context of the oral biofilm, LytF may play important roles as part of the competence and biofilm development programs, as well as increasing the availability of eDNA.

IMPORTANCE
Streptococcus sanguinis
, a commensal organism in the oral cavity and one of the pioneer colonizers of the tooth surface, is associated with the overall health of the oral environment. Our laboratory showed previously that, under aerobic conditions,
S. sanguinis
can produce H
2
O
2
to inhibit the growth of bacterial species that promote dental caries. This production of H
2
O
2
by
S. sanguinis
also induces the release of eDNA, which is essential for proper biofilm formation. Under anaerobic conditions,
S. sanguinis
does not produce H
2
O
2
but DNA is still released. Determining how
S. sanguinis
releases DNA is thus essential to understand biofilm formation in the oral cavity.
Differential MS2 Interaction with Food Contact Surfaces Determined by Atomic Force Microscopy and Virus Recovery
Authors: Shim J. , Stewart D. S. , Nikolov A. D. , Wasan D. T. , Wang R. , Yan R. , Shieh Y. C. 
Published: October 2017

ABSTRACT

Enteric viruses are recognized as major etiologies of U.S. foodborne infections. These viruses are easily transmitted via food contact surfaces. Understanding virus interactions with surfaces may facilitate the development of improved means for their removal, thus reducing transmission. Using MS2 coliphage as a virus surrogate, the strength of virus adhesion to common food processing and preparation surfaces of polyvinyl chloride (PVC) and glass was assessed by atomic force microscopy (AFM) and virus recovery assays. The interaction forces of MS2 with various surfaces were measured from adhesion peaks in force-distance curves registered using a spherical bead probe preconjugated with MS2 particles. MS2 in phosphate-buffered saline (PBS) demonstrated approximately 5 times less adhesion force to glass (0.54 nN) than to PVC (2.87 nN) (
P
< 0.0001). This was consistent with the virus recovery data, which showed 1.4-fold fewer virus PFU recovered from PVC than from glass after identical inoculations and 24 h of cold storage. The difference in adhesion was ascribed to both intrinsic chemical characteristics and the substrate surface porosity (smooth glass versus porous PVC). Incorporating a surfactant micellar solution of sodium dodecyl sulfate (SDS) into the PBS reduced the adhesion force for PVC (∼0 nN) and consistently increased virus recovery by 19%. With direct and indirect evidence of virus adhesion, this study illustrated a two-way assessment of virus adhesion for the initial evaluation of potential means to mitigate virus adhesion to food contact surfaces.

IMPORTANCE
The spread of foodborne viruses is likely associated with their adhesive nature. Virus attachment on food contact surfaces has been evaluated by quantitating virus recoveries from inoculated surfaces. This study aimed to evaluate the microenvironment in which nanometer-sized viruses interact with food contact surfaces and to compare the virus adhesion differences using AFM. The virus surrogate MS2 demonstrated less adhesion force to glass than to PVC via AFM, with the force-contributing factors including the intrinsic nature and the topography of the contact surfaces. This adhesion finding is consistent with the virus recoveries, which were determined indirectly. Greater numbers of viruses were recovered from glass than from PVC, after application at the same levels. The stronger MS2 adhesion onto PVC could be interrupted by incorporating a surfactant during the interaction between the virus and the contact surface. This study increases our understanding of the virus adhesion microenvironment and indicates ways to mitigate virus adhesion onto contact surfaces.
Draft Genome Sequences of a Novel Lineage of
Armatimonadetes
Recovered from Japanese Hot Springs
Authors: Ward Lewis M. , McGlynn Shawn E. , Fischer Woodward W. 
Published: October 2017

ABSTRACT

Here, we report two draft genome sequences from a novel lineage within the
Armatimonadetes
phylum recovered from metagenomes sequenced from Japanese hot spring microbial mats. These organisms are aerobic and represent a new lineage related to the characterized
Chthonomonas
and
Fimbriimonas
groups, and they expand the diversity of this enigmatic phylum.
Draft Genome Sequence of
Romboutsia weinsteinii
sp. nov. Strain CCRI-19649
T
Isolated from Surface Water
Authors: Maheux Andrée F. , Boudreau Dominique K. , Bérubé Ève , Boissinot Maurice , Cantin Philippe , Raymond Frédéric , Corbeil Jacques , Omar Rabeea F. , Bergeron Michel G. 
Published: October 2017

ABSTRACT

Romboutsia weinsteinii
sp. nov. CCRI-19649
T
belongs to the genus
Romboutsia
. The strain was isolated from a water sample harvested in Québec City, Québec, Canada. The genome assembly comprised 4,134,593 bp with a 29.3% GC content. This is the first documentation that reports the genome sequence of
R. weinsteinii
.
Metagenomic Sequencing of Bronchoalveolar Lavage Samples from Feedlot Cattle Mortalities Associated with Bovine Respiratory Disease
Authors: Holman Devin B. , Klima Cassidy L. , Ralston Brenda J. , Niu Yan D. , Stanford Kim , Alexander Trevor W. , McAllister Tim A. 
Published: October 2017

ABSTRACT
Bovine respiratory disease (BRD) is a significant and costly illness in feedlot cattle. Metagenomic analysis was performed on bronchoalveolar lavage samples obtained from 18 feedlot cattle that died of BRD.
Prevalence of positive coeliac disease serology and HLA risk genotypes in a multiethnic population of adults in Canada: a cross-sectional study
Authors: Jamnik Joseph , Villa Christopher R , Dhir Sirbarinder Bryn , Jenkins David J A , El-Sohemy Ahmed 
Published: October 2017

ObjectivesCoeliac disease (CD) is a complex autoimmune disorder with known genetic risk factors. Approximately 1% of individuals of European ancestry have CD, but the prevalence among different ethnicities living in Canada remains unknown. The objective of the present study was to determine the prevalence of positive CD serology in a population of Canadian adults living in Toronto, and to determine whether the prevalence of CD seropositivity and predisposing human leucocyte antigen (HLA)-DQ2/DQ8 risk genotypes differ between major ethnocultural groups.DesignCross-sectional screening study of participants from the Toronto Nutrigenomics and Health and the Toronto Healthy Diet studies.SettingUniversity campus and households across Toronto, Canada.Participants: free-livingAdults (n=2832) of diverse ethnocultural backgrounds.Main outcome measuresPrevalence of positive CD serology was determined by screening for antitissue transglutaminase antibodies in individuals with predisposing HLA-DQ2/DQ8 genotypes. HLA genotypes were determined using six single nucleotide polymorphisms in the HLA gene region.ResultsOf the 2832 individuals screened, a total of 25 (0.88%; 95% CI 0.57% to 1.30%) were determined to have positive CD serology. The majority of seropositive CD cases were undiagnosed (87%). Prevalence was highest among Caucasians (1.48%; 95% CI 0.93% to 2.23%), and similar in those of ‘Other’ (0.74%; 95% CI 0.09% to 2.63%) or ‘Unknown’ (0.43; 95% CI 0.01% to 2.36%) ethnicity. No cases of positive CD serology were identified among East Asian or South Asian individuals. East Asians had a lower prevalence of HLA risk genotypes than Caucasians and South Asians (p<0.005).ConclusionsThe prevalence of positive CD serology among Canadian adults living in Toronto is likely ~1%, with 87% of cases being undiagnosed. These findings suggest the need for better screening in high genetic risk groups.Trial registration numberNCT00516620; Post-results.
Improving admission medication reconciliation with pharmacists or pharmacy technicians in the emergency department: a randomised controlled trial
Authors: Pevnick Joshua M , Nguyen Caroline , Jackevicius Cynthia A , Palmer Katherine A , Shane Rita , Cook-Wiens Galen , Rogatko Andre , Bear Mackenzie , Rosen Olga , Seki David , Doyle Brian , Desai Anish , Bell Douglas S 
Published: October 2017

BackgroundAdmission medication history (AMH) errors frequently cause medication order errors and patient harm.ObjectiveTo quantify AMH error reduction achieved when pharmacy staff obtain AMHs before admission medication orders (AMO) are placed.MethodsThis was a three-arm randomised controlled trial of 306 inpatients. In one intervention arm, pharmacists, and in the second intervention arm, pharmacy technicians, obtained initial AMHs prior to admission. They obtained and reconciled medication information from multiple sources. All arms, including the control arm, received usual AMH care, which included variation in several common processes. The primary outcome was severity-weighted mean AMH error score. To detect AMH errors, all patients received reference standard AMHs, which were compared with intervention and control group AMHs. AMH errors and resultant AMO errors were independently identified and rated by ≥2 investigators as significant, serious or life threatening. Each error was assigned 1, 4 or 9 points, respectively, to calculate severity-weighted AMH and AMO error scores for each patient.ResultsPatient characteristics were similar across arms (mean±SD age 72±16 years, number of medications 15±7). Analysis was limited to 278 patients (91%) with reference standard AMHs. Mean±SD AMH errors per patient in the usual care, pharmacist and technician arms were 8.0±5.6, 1.4±1.9 and 1.5±2.1, respectively (p<0.0001). Mean±SD severity-weighted AMH error scores were 23.0±16.1, 4.1±6.8 and 4.1±7.0 per patient, respectively (p<0.0001). These AMH errors led to a mean±SD of 3.2±2.9, 0.6±1.1 and 0.6±1.1 AMO errors per patient, and mean severity-weighted AMO error scores of 6.9±7.2, 1.5±2.9 and 1.2±2.5 per patient, respectively (both p<0.0001).ConclusionsPharmacists and technicians reduced AMH errors and resultant AMO errors by over 80%. Future research should examine other sites and patient-centred outcomes.Trial registration numberNCT02026453.
Mortality, readmission and length of stay have different relationships using hospital-level versus patient-level data: an example of the ecological fallacy affecting hospital performance indicators
Authors: Hofstede Stefanie N , van Bodegom-Vos Leti , Kringos Dionne S , Steyerberg Ewout , Marang-van de Mheen Perla J 
Published: October 2017

BackgroundEcological fallacy refers to an erroneous inference about individuals on the basis of findings for the group to which those individuals belong. Suppose analysis of a large database shows that hospitals with a high proportion of long length of stay (LOS) patients also have higher than average in-hospital mortality. This may prompt efforts to reduce mortality among patients with long LOS. But patients with long LOS may not be the ones at higher risk of death. It may be that hospitals with higher mortality (regardless of LOS) also have more long LOS patients—either because of quality problems on both counts or because of unaccounted differences in case mix. To provide more insight how the ecological fallacy influences the evaluation of hospital performance indicators, we assessed whether hospital-level associations between in-hospital mortality, readmission and long LOS reflect patient-level associations.MethodsPatient admissions from the Dutch National Medical Registration (2007–2012) for specific diseases (stroke, colorectal carcinoma, heart failure, acute myocardial infarction and hip/knee replacements in patients with osteoarthritis) were analysed, as well as all admissions. Logistic regression analysis was used to assess patient-level associations. Pearson correlation coefficients were used to quantify hospital-level associations.ResultsOverall, we observed 2.2% in-hospital mortality, 8.1% readmissions and a mean LOS of 5.9 days among 8 478 884 admissions in 95 hospitals. Of the 10 disease-specific associations tested, 2 were reversed at hospital-level, 3 were consistent and 5 were only significant at either hospital-level or patient-level. A reversed association was found for stroke: patients with long LOS had 58% lower in-hospital mortality (OR 0.42 (95% CI 0.40 to 0.44)), whereas the hospital-level association was reversed (r=0.30, p<0.01). Similar negative patient-level associations were found for each hospital, but LOS varied across hospitals, thereby resulting in a positive hospital-level association. A similar effect was found for long LOS and readmission in patients with heart failure.ConclusionsHospital-level associations did not reflect the same patient-level associations in 7 of 10 associations, and were even reversed in 2 associations. Ecological fallacy thus potentially influences interpretation of hospital performance when patient-level associations are not taken into account.