bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical and Functional Interplay between MazF
1
Bif
and Its Noncognate Antitoxins from Bifidobacterium longum
Authors: Wei Yanxia , Li Yang , Yang Fan , Wu Qiong , Liu Dianbin , Li Xiangyang , Hua Hui , Liu Xiaomei , Wang Yugang , Zheng Kuiyang , Tang Renxian 
Published: February 2017

ABSTRACT

Bifidobacterium longum
strain JDM301, a widely used commercial strain in China, encodes at least two MazEF-like modules and one RelBE-like toxin-antitoxin (TA) system in its chromosome, designated MazE
1
F
1
Bif
, MazE
2
F
2
Bif
, and RelBE
Bif
, respectively. Bacterial TA systems play an important role in several stress responses, but the relationship between these TA systems is largely unknown. In this study, the interactions between MazF
1
Bif
and MazE
2
Bif
or RelB
Bif
were assessed in
B. longum
strain JDM301. MazF
1
Bif
caused the degradation of
tufA
Bif
mRNA, and its toxicity was inhibited by forming a protein complex with its cognate antitoxin, MazE
1
Bif
. Notably, MazF
1
Bif
toxicity was also partially neutralized when jointly expressed with noncognate antitoxin MazE
2
Bif
or RelB
Bif
. Our results show that the two noncognate antitoxins also inhibited mRNA degradation caused by MazF
1
Bif
toxin. Furthermore, the physical interplay between MazF
1
Bif
and its noncognate antitoxins was confirmed by immunoprecipitation. These results suggest that MazF
1
Bif
can arrest cell growth and that MazF
1
Bif
toxicity can be neutralized by its cognate and noncognate antitoxins. These results imply that JDM301 uses a sophisticated toxin-antitoxin interaction network to alter its physiology when coping with environmental stress.

IMPORTANCE
Although toxin-antitoxin (TA) systems play an important role in several stress responses, the regulatory mechanisms of multiple TA system homologs in the bacterial genome remain largely unclear. In this study, the relationships between MazE
1
F
1
Bif
and the other two TA systems of
Bifidobacterium longum
strain JDM301 were explored, and the interactions between MazF
1
Bif
and MazE
2
Bif
or RelB
Bif
were characterized. In addition, the mRNA degradation activity of MazF
1
Bif
was demonstrated. In particular, the interaction of the toxin with noncognate antitoxins was shown, even between different TA families (MazF
1
Bif
toxin and RelB
Bif
antitoxin) in JDM301. This work provides insight into the regulatory mechanisms of TA systems implicated in the stress responses of bifidobacteria.
Accurate Quantification of Laminarin in Marine Organic Matter with Enzymes from Marine Microbes
Authors: Becker Stefan , Scheffel André , Polz Martin F. , Hehemann Jan-Hendrik 
Published: February 2017

ABSTRACT

Marine algae produce a variety of glycans, which fulfill diverse biological functions and fuel the carbon and energy demands of heterotrophic microbes. A common approach to analysis of marine organic matter uses acid to hydrolyze the glycans into measurable monosaccharides. The monosaccharides may be derived from different glycans that are built with the same monosaccharides, however, and this approach does not distinguish between glycans in natural samples. Here we use enzymes to digest selectively and thereby quantify laminarin in particulate organic matter. Environmental metaproteome data revealed carbohydrate-active enzymes from marine flavobacteria as tools for selective hydrolysis of the algal β-glucan laminarin. The enzymes digested laminarin into glucose and oligosaccharides, which we measured with standard methods to establish the amounts of laminarin in the samples. We cloned, expressed, purified, and characterized three new glycoside hydrolases (GHs) of
Formosa
bacteria: two are endo-β-1,3-glucanases, of the GH16 and GH17 families, and the other is a GH30 exo-β-1,6-glucanase.
Formosa
sp. nov strain Hel1_33_131 GH30 (FbGH30) removed the β-1,6-glucose side chains, and
Formosa agariphila
GH17A (FaGH17A) and FaGH16A hydrolyzed the β-1,3-glucose backbone of laminarin. Specificity profiling with a library of glucan oligosaccharides and polysaccharides revealed that FaGH17A and FbGH30 were highly specific enzymes, while FaGH16A also hydrolyzed mixed-linked glucans with β-1,4-glucose. Therefore, we chose the more specific FaGH17A and FbGH30 to quantify laminarin in two cultured diatoms, namely,
Thalassiosira weissflogii
and
Thalassiosira pseudonana
, and in seawater samples from the North Sea and the Arctic Ocean. Combined, these results demonstrate the potential of enzymes for faster, stereospecific, and sequence-specific analysis of select glycans in marine organic matter.

IMPORTANCE
Marine algae synthesize substantial amounts of the glucose polymer laminarin for energy and carbon storage. Its concentrations, rates of production by autotrophic organisms, and rates of digestion by heterotrophic organisms remain unknown. Here we present a method based on enzymes that hydrolyze laminarin and enable its quantification even in crude substrate mixtures, without purification. Compared to the commonly used acid hydrolysis, the enzymatic method presented here is faster and stereospecific and selectively cleaves laminarin in mixtures of glycans, releasing only glucose and oligosaccharides, which can be easily quantified with reducing sugar assays.
Environmental Surveillance of Norovirus Genogroups I and II for Sensitive Detection of Epidemic Variants
Authors: Kazama Shinobu , Miura Takayuki , Masago Yoshifumi , Konta Yoshimitsu , Tohma Kentaro , Manaka Takafumi , Liu Xiaofang , Nakayama Daisuke , Tanno Takashi , Saito Mayuko , Oshitani Hitoshi , Omura Tatsuo 
Published: February 2017

ABSTRACT

Sewage samples have been investigated to study the norovirus concentrations in sewage or the genotypes of noroviruses circulating in human populations. However, the statistical relationship between the concentration of the virus and the number of infected individuals and the clinical importance of genotypes or strains detected in sewage are unclear. In this study, we carried out both environmental and clinical surveillance of noroviruses for 3 years, 2013 to 2016. We performed cross-correlation analysis of the concentrations of norovirus GI or GII in sewage samples collected weekly and the reported number of gastroenteritis cases. Norovirus genotypes in sewage were also analyzed by pyrosequencing and compared with those identified in stool samples. The cross-correlation analysis found the peak coefficient (
R
= 0.51) at a lag of zero, indicating that the variation in the GII concentration, expressed as the log
10
number of copies per milliliter, was coincident with that in the gastroenteritis cases. A total of 15 norovirus genotypes and up to 8 genotypes per sample were detected in sewage, which included all of the 13 genotypes identified in the stool samples except 2. GII.4 was most frequently detected in both sample types, followed by GII.17. Phylogenetic analysis revealed that a strain belonging to the GII.17 Kawasaki 2014 lineage had been introduced into the study area in the 2012-2013 season. An increase in GI.3 cases was observed in the 2015-2016 season, and sewage monitoring identified the presence of GI.3 in the previous season (2014-2015). Our results demonstrated that monitoring of noroviruses in sewage is useful for sensitive detection of epidemic variants in human populations.

IMPORTANCE
We obtained statistical evidence of the relationship between the variation in the norovirus GII concentration in sewage and that of gastroenteritis cases during the 3-year study period. Sewage sample analysis by a pyrosequencing approach enabled us to understand the temporal variation in the norovirus genotypes circulating in human populations. We found that a strain closely related to the GII.17 Kawasaki 2014 lineage had been introduced into the study area at least 1 year before its appearance and identification in clinical cases. A similar pattern was observed for GI.3; cases were reported in the 2015-2016 season, and closely related strains were found in sewage in the previous season. Our observation indicates that monitoring of noroviruses in sewage is useful for the rapid detection of an epidemic and is also sensitive enough to study the molecular epidemiology of noroviruses. Applying this approach to other enteric pathogens in sewage will enhance our understanding of their ecology.
Unique Strain of Rickettsia parkeri Associated with the Hard Tick Dermacentor parumapertus Neumann in the Western United States
Authors: Paddock Christopher D. , Allerdice Michelle E. J. , Karpathy Sandor E. , Nicholson William L. , Levin Michael L. , Smith Travis C. , Becker Tom , Delph Robert J. , Knight Robert N. , Ritter Jana M. , Sanders Jeanine H. , Goddard Jerome 
Published: February 2017

ABSTRACTIn 1953, investigators at the Rocky Mountain Laboratories in Hamilton, MT, described the isolation of a spotted fever groupRickettsia(SFGR) species fromDermacentor parumapertusticks collected from black-tailed jackrabbits (Lepus californicus) in northern Nevada. Several decades later, investigators characterized this SFGR (designated the parumapertus agent) by using mouse serotyping methods and determined that it represented a distinct rickettsial serotype closely related toRickettsia parkeri; nonetheless, the parumapertus agent was not further characterized or studied. To our knowledge, no isolates of the parumapertus agent remain in any rickettsial culture collection, which precludes contemporary phylogenetic placement of this enigmatic SFGR. To rediscover the parumapertus agent, adult-stageD. parumapertusticks were collected from black-tailed jackrabbits shot or encountered as roadkills in Arizona, Utah, or Texas from 2011 to 2016. A total of 339 ticks were collected and evaluated for infection withRickettsiaspecies. Of 112D. parumapertusticks collected in south Texas, 16 (14.3%) contained partialompAsequences with the closest identity (99.6%) toRickettsiasp. strain Atlantic rainforest Aa46, an SFGR that is closely related or identical to an SFGR species that causes a mild rickettsiosis in several states of Brazil. A pure isolate, designated strain Black Gap, was cultivated in Vero E6 cells, and sequence analysis of therrs,gltA,sca0,sca5, andsca4genes also revealed the closest genetic identity toRickettsiasp. Atlantic rainforest Aa46. Phylogenetic analysis of the five concatenated rickettsial genes placeRickettsiasp. strain Black Gap andRickettsiasp. Atlantic rainforest Aa46 withR. parkeriin a distinct and well-supported clade.IMPORTANCEWe suggest thatRickettsiasp. Black Gap andRickettsiasp. Atlantic rainforest Aa46 represent nearly identical strains ofR. parkeriand thatRickettsiasp. Black Gap or a very similar strain ofR. parkerirepresents the parumapertus agent. The close genetic relatedness among these taxa, as well as the response of guinea pigs infected with the Black Gap strain, suggests thatR. parkeriBlack Gap could cause disease in humans. The identification of this organism could also account, at least in part, for the remarkable differences in severity ascribed to Rocky Mountain spotted fever (RMSF) among various regions of the American West during the early 20th century. We suggest that the wide variation in case fatality rates attributed to RMSF could have occurred by the inadvertent inclusion of cases of milder disease caused byR. parkeriBlack Gap.
Critical Concentration of Lecithin Enhances the Antimicrobial Activity of Eugenol against Escherichia coli
Authors: Zhang Haoshu , Dudley Edward G. , Davidson P. Michael , Harte Federico 
Published: February 2017

ABSTRACT

Lecithin is a natural emulsifier used in a wide range of food and nonfood applications to improve physical stability, with no known bioactive effects. In this study, the effect of lecithin on the antimicrobial performance of a constant eugenol concentration was tested against three
Escherichia coli
strains (C600, 0.1229, and O157:H7 strain ATCC 700728). This is the first study, to our knowledge, focusing on lecithin at concentrations below those commonly used in foods to improve the stability of oil in water emulsions (≤10 mg/100 ml). For all three cultures, significant synergistic antimicrobial effects were observed when
E. coli
cultures were exposed to a constant eugenol concentration (ranging from 0.043 to 0.050% [wt/wt]) together with critical lecithin concentrations ranging from 0.5 to 1 mg/100 ml. Increasing the concentration of lecithin above 1 mg/100 ml (up to 10 mg/100 ml lecithin) diminished the antibacterial effect to values similar to those with eugenol-only treatments. The formation of aggregates (<100 nm) at the critical lecithin concentration was observed using cryo-transmission electron microscopy (cryo-TEM), together with a reduction in light absorbance at 284 nm. At critically low concentrations of lecithin, the formation of nanoscale aggregates is responsible for improving eugenol antimicrobial effects.

IMPORTANCE
Essential oils (EOs) are effective natural antimicrobials. However, their hydrophobicity and strong aromatic character limit the use of essential oils in food systems. Emulsifiers (e.g., lecithin) increase the stability of EOs in water-based systems but fail to consistently improve antimicrobial effects. We demonstrate that lecithin, within a narrow critical concentration window, can enhance the antimicrobial properties of eugenol. This study highlights the potential bioactivity of lecithin when utilized to effectively control foodborne pathogens.
Bacillus thuringiensis Vip3Aa Toxin Resistance in Heliothis virescens (Lepidoptera: Noctuidae)
Authors: Pickett Brian R. , Gulzar Asim , Ferré Juan , Wright Denis J. 
Published: February 2017

ABSTRACT

Laboratory selection with Vip3Aa of a field-derived population of
Heliothis virescens
produced >2,040-fold resistance in 12 generations of selection. The Vip3Aa-selected (Vip-Sel)-resistant population showed little cross-resistance to Cry1Ab and no cross-resistance to Cry1Ac. Resistance was unstable after 15 generations without exposure to the toxin. F
1
reciprocal crosses between Vip3Aa-unselected (Vip-Unsel) and Vip-Sel insects indicated a strong paternal influence on the inheritance of resistance. Resistance ranged from almost completely recessive (mean degree of dominance [
h
] = 0.04 if the resistant parent was female) to incompletely dominant (mean
h
= 0.53 if the resistant parent was male). Results from bioassays on the offspring from backcrosses of the F
1
progeny with Vip-Sel insects indicated that resistance was due to more than one locus. The results described in this article provide useful information for the insecticide resistance management strategies designed to overcome the evolution of resistance to Vip3Aa in insect pests.

IMPORTANCE
Heliothis virescens
is an important pest that has the ability to feed on many plant species. The extensive use of
Bacillus thuringiensis
(Bt) crops or spray has already led to the evolution of insect resistance in the field for some species of Lepidoptera and Coleoptera. The development of resistance in insect pests is the main threat to Bt crops. The effective resistance management strategies are very important to prolong the life of Bt plants. Lab selection is the key step to test the assumption and predictions of management strategies prior to field evaluation. Resistant insects offer useful information to determine the inheritance of resistance and the frequency of resistance alleles and to study the mechanism of resistance to insecticides.
Performance of the FreeStyle Libre Flash glucose monitoring system in patients with type 1 and 2 diabetes mellitus
Authors: Fokkert M J , van Dijk P R , Edens M A , Abbes S , de Jong D , Slingerland R J , Bilo H J G 
Published: February 2017

ObjectiveTo evaluate the performance of the FreeStyle Libre Flash continuous glucose monitoring (FSL-CGM) system against established central laboratory methods.Research design and methods20 subjects (8 type 1 diabetes mellitus, 12 type 2 diabetes mellitus) were analyzed. FSL-CGM sensor measurements (inserted in arm and abdomen) were compared with capillary blood glucose results analyzed with StatStrip as semigold standard. The glucose response after a standardized oral glucose load was measured by FSL-CGM and capillary samples analyzed by perchloric acid hexokinase (PCA-HK) method, StatStrip and FSL test strip (FSLC), and a commonly used CGM system (iPro2).ResultsFSL-CGM arm sensor readings showed 85.5% of paired readings falling within Clarke Error Grid (ISO 15197:2013) zone A when compared with StatStrip. For FSL-CGM abdomen and FSLC, these percentages were 64% and 98%, respectively. The overall correlation of FSL-CGM in the arm and the StatStrip indicates a performance with lower results with the FSL-CGM in the arm than expected based on the StatStrip in the lower glucose ranges, and higher results than expected in the higher ranges. Following a standardized glucose load, a slower rise in glucose level was observed for FSL-CGM arm as compared with PCA-HK, StatStrip, FSLC, and iPro2 during the first 45–60 min after glucose load ingestion.ConclusionsCertain matters need attention while using the FSL-CGM in daily life including the observed lower values in the lower ranges, and the underestimation of the effect of a meal on glucose response. These effects of such deviations can partly be overcome by optimizing the available user instructions.Trial registration numberTC5348; results.
Brighter children? The association between seasonality of birth and child IQ in a population-based birth cohort
Authors: Grootendorst-van Mil Nina H , Steegers-Theunissen Régine P M , Hofman Albert , Jaddoe Vincent W V , Verhulst Frank C , Tiemeier Henning 
Published: February 2017

ObjectiveSeason of birth has repeatedly been found to be a risk indicator for adverse neurodevelopmental outcomes. Several explanations for this finding have been put forward but no conclusion has been reached. In the current study, we explored the role of sociodemographic and biological factors in the association between season of birth and child IQ.DesignIn a prenatally recruited birth cohort (born in 2002–2006), we examined the association between season of birth and non-verbal IQ at age 6 years among 6034 children. We explored how adjusting for socioeconomic status and maternal IQ, childbirth outcomes, pregnancy vitamin D status, nutritional intake, exposure to infections, and child age relative to peers in class changed the relation between season of birth and child IQ.ResultsWe found that spring birth was associated with lower non-verbal IQ (estimate: more than 1 point; β−1.24 (95% CI −2.31 to −0.17), p=0.02; seasonal trend β−0.40 (95% CI −0.74 to −0.07), p=0.02) than birth in summer. Adjustment for different covariates led to a substantial reduction (−65.0% change, in a seasonal trend analysis) of this association. In particular, sociodemographic factors and maternal IQ (−10.0% and −22.5% change, respectively) contributed.ConclusionsSeason of birth is an indicator of many underlying factors related to child IQ. The observed effects on IQ were small and therefore not of clinical significance.
Qualitative study of the BREATHER trial (Short Cycle antiretroviral therapy): is it acceptable to young people living with HIV?
Authors: Bernays Sarah , Paparini Sara , Seeley Janet , Namukwaya Kihika Stella , Gibb Diana , Rhodes Tim 
Published: February 2017

ObjectivesA qualitative study of the BREATHER (PENTA 16) randomised clinical trial, which compared virological control of Short Cycle Therapy (SCT) (5 days on: 2 days off) with continuous efavirenz (EFV)-based antiretroviral therapy (CT) in children and young people (aged 8–24) living with HIV with viral load <50 c/mL to examine adaptation, acceptability and experience of SCT to inform intervention development.SettingPaediatric HIV clinics in the UK (2), Ireland (1), the USA (1) and Uganda (1).ParticipantsAll BREATHER trial participants who were over the age of 10 and aware of their HIV diagnosis were invited to participate. 49 young people from both arms of the BREATHER trial (31 females and 18 males; 40% of the total trial population in the respective sites; age range 11–24) gave additional consent to participate in the qualitative study.ResultsYoung people from both trial arms had initial concerns about the impact of SCT on their health and adherence, but these decreased over the early months in the trial. Young people randomised to SCT reported preference for SCT compared with CT pre-trial. Attitudes to SCT did not vary greatly by gender or country. Once short-term adaptation challenges were overcome, SCT was positively described as reducing impact of side effects, easing the pressure to carry and remember medication and enabling more weekend social activities. Young people on both arms reported frequent medication side effects and occasional missed doses that they had rarely voiced to clinical staff. Participants liked SCT by trial end but were concerned that peers who had most problems adhering could find SCT disruptive and difficult to manage.ConclusionsTo realise the potential of SCT (and mitigate possible risks of longer interruptions), careful dissemination and communication post-trial is needed. SCT should be provided alongside a package of monitoring, support and education over 3 months to allow adaptation.Trial registration numberNCT 01641016
White cell count in the normal range and short-term and long-term mortality: international comparisons of electronic health record cohorts in England and New Zealand
Authors: Shah Anoop Dinesh , Thornley Simon , Chung Sheng-Chia , Denaxas Spiros , Jackson Rod , Hemingway Harry 
Published: February 2017

ObjectivesElectronic health records offer the opportunity to discover new clinical implications for established blood tests, but international comparisons have been lacking. We tested the association of total white cell count (WBC) with all-cause mortality in England and New Zealand.SettingPrimary care practices in England (ClinicAl research using LInked Bespoke studies and Electronic health Records (CALIBER)) and New Zealand (PREDICT).DesignAnalysis of linked electronic health record data sets: CALIBER (primary care, hospitalisation, mortality and acute coronary syndrome registry) and PREDICT (cardiovascular risk assessments in primary care, hospitalisations, mortality, dispensed medication and laboratory results).ParticipantsPeople aged 30–75 years with no prior cardiovascular disease (CALIBER: N=686 475, 92.0% white; PREDICT: N=194 513, 53.5% European, 14.7% Pacific, 13.4% Maori), followed until death, transfer out of practice (in CALIBER) or study end.Primary outcome measureHRs for mortality were estimated using Cox models adjusted for age, sex, smoking, diabetes, systolic blood pressure, ethnicity and total:high-density lipoprotein (HDL) cholesterol ratio.ResultsWe found ‘J’-shaped associations between WBC and mortality; the second quintile was associated with lowest risk in both cohorts. High WBC within the reference range (8.65–10.05×109/L) was associated with significantly increased mortality compared to the middle quintile (6.25–7.25×109/L); adjusted HR 1.51 (95% CI 1.43 to 1.59) in CALIBER and 1.33 (95% CI 1.06 to 1.65) in PREDICT. WBC outside the reference range was associated with even greater mortality. The association was stronger over the first 6 months of follow-up, but similar across ethnic groups.ConclusionsClinically recorded WBC within the range considered ‘normal’ is associated with mortality in ethnically different populations from two countries, particularly within the first 6 months. Large-scale international comparisons of electronic health record cohorts might yield new insights from widely performed clinical tests.Trial registration numberNCT02014610.