bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary bottlenecks in brackish water habitats drive the colonization of fresh water by stingrays
Authors: Kirchhoff K. N. , Hauffe T. , Stelbrink B. , Albrecht C. , Wilke T.
Published: June 2017

Species richness in freshwater bony fishes depends on two main processes: the transition into and the diversification within freshwater habitats. In contrast to bony fishes, only few cartilaginous fishes, mostly stingrays (Myliobatoidei), were able to colonize fresh water. Respective transition processes have been mainly assessed from a physiological and morphological perspective, indicating that the freshwater lifestyle is strongly limited by the ability to perform osmoregulatory adaptations. However, the transition history and the effect of physiological constraints on the diversification in stingrays remain poorly understood. Herein, we estimated the geographic pathways of freshwater colonization and inferred the mode of habitat transitions. Further, we assessed habitat‐related speciation rates in a time‐calibrated phylogenetic framework to understand factors driving the transition of stingrays into and the diversification within fresh water. Using South American and Southeast Asian freshwater taxa as model organisms, we found one independent freshwater colonization event by stingrays in South America and at least three in Southeast Asia. We revealed that vicariant processes most likely caused freshwater transition during the time of major marine incursions. The habitat transition rates indicate that brackish water species switch preferably back into marine than forth into freshwater habitats. Moreover, our results showed significantly lower diversification rates in brackish water lineages, whereas freshwater and marine lineages exhibit similar rates. Thus, brackish water habitats may have functioned as evolutionary bottlenecks for the colonization of fresh water by stingrays, probably because of the higher variability of environmental conditions in brackish water.
Adolescents' smokeless tobacco susceptibility by perceived professional baseball players' use
Authors: Chaffee Benjamin W. , Couch Elizabeth T. , Gansky Stuart A.
Published: June 2017

Objective

Measure associations between adolescent baseball players' perceptions of smokeless tobacco (ST) use by professional baseball players and those adolescents' actual ST use and susceptibility.

Methods

Male baseball players (N = 360) at 25 rural California high schools completed tobacco behavior surveys and reported how likely they believed it was their favorite major league baseball player used ST. We compared ST use and, among ST never‐users, willingness and expectations to use ST, according to perceived favorite player's use.

Results

Adolescents responding that their favorite player definitely or probably used ST were significantly more likely to use ST themselves. High school ST never‐users who perceived that their favorite player definitely used ST were 2.5 to 3‐times more likely to be susceptible to ST initiation than participants responding that their favorite player definitely did not use ST.

Conclusions

Adolescents' ST behaviors and intentions were correlated with their perceptions of professional baseball players' ST use.
Phenotypic switching prevention and proliferation/migration inhibition of vascular smooth muscle cells by the ruthenium nitrosyl complex trans-[Ru(NO)Cl(cyclam](PF6)2
Authors: de Oliveira Mariana G , Doro Fabio G , Tfouni Elia , Krieger Marta H
Published: June 2017

Objectives

Vascular smooth muscle cell (VSMC) migration and proliferation at sites of vascular injury are both critical steps in the development of intimal hyperplasia (IH). Local delivery of nitric oxide (NO) largely prevents these events. Among the NO donors, tetraazamacrocyclic nitrosyl complexes, such as trans-[Ru(NO)Cl(cyclam)](PF6)2 (cyclamNO), gained attention for their features, which include the possibility of being embedded in solid matrices, and ability to participate in a nitrite/NO catalytic conversion cycle.

Methods

Methods used to evaluate cyclamNO activity: safety margin by NR and MTT; cell proliferation by 3H-thymidine incorporation and proliferating cell nuclear antigen (PCNA) expression; antimigratory properties by transwell and wound healing; prevention of cell phenotypic switching under platelet-derived growth factor type BB (PDGF-BB) stimuli by analysis of alpha smooth muscle actin (α-SMA) expression.

Key findings

Cell proliferation and migration induced by PDGF-BB were significantly inhibited by cyclamNO. The ~60% reduction on expression of contractile protein α-SMA induced by PDGF-BB revealed VSMC phenotypic switching which is significantly prevented by cyclamNO. Compared to the NO donor sodium nitroprusside, cyclamNO showed to be significantly less cytotoxic.

Conclusions

With great potential to maintain VSMC functionality and prevent IH-associated events, cyclamNO might be a promissory drug for several applications in cardiovascular medicine, as in stents.
Porphyromonas gingivalis lipopolysaccharide regulates ephrin/Eph signalling in human periodontal ligament fibroblasts
Authors: Li M. , Zhang C. , Jin L. , Matsuo K. , Yang Y.
Published: June 2017

Objective

EphrinA2‐EphA2 and ephrinB2‐EphB4 critically engage in bidirectional signalling to modulate alveolar bone remodelling. The present study aimed to investigate the effects of lipopolysaccharides (LPS) derived from Porphyromonas gingivalis on ephrin/Eph signalling in periodontal ligament fibroblasts (PDLFs).

Material and Methods

The primary cultured PDLFs were incubated in the absence (as a control) or presence of P. gingivalisLPS at 0.001‐10 μg/mL for 24 hours. The PDLFs were then stimulated with P. gingivalisLPS at the optimal concentration (0.1 μg/mL) for different periods (6‐48 hours). The expression of ephrinA2, ephrinB2, EphA2 and EphB4 was assessed by quantitative reverse‐transcription real‐time polymerase chain reaction and western blotting. The osteoblastic markers alkaline phosphatase, osteocalcin and Runt‐related transcription factor 2 (Runx2), and the osteoclastogenesis‐related factors receptor activator of nuclear factor kappa‐B ligand (RANKL) and osteoprotegerin were also evaluated.

Results

The ephrinA2 and EphA2 expression was upregulated and EphB4 expression was downregulated by stimulation of P. gingivalisLPS. EphrinA2 mRNA expression in the PDLFs was significantly upregulated from 12 to 48 hours (P<.05), whereas EphA2 exhibited no change for the first 24 hours, after which there was a significant increase at 48 hours (P<.05). EphB4 exhibited lower mRNA expression at 12 and 24 hours than did the control (P<.05), but the change was insignificant at 48 hours. In contrast, the expression of ephrinB2 remained unchanged. The expressions of ephrinA2, EphA2, ephrinB2 and EphB4 at the protein level showed a similar pattern to that at the mRNA level. The expression of Runx2 and osteocalcin significantly decreased, whereas that of RANKL/osteoprotegerin increased.

Conclusion

The present study suggest that P. gingivalisLPS would contribute to a dysregulation of bone remodelling, whereby ephrinA2/EphA2 expression is stimulated and EphB4 expression is inhibited.
R202Q/M694V as novel MEFV gene mutations in chronic periodontitis and familial Mediterranean fever
Authors: Fentoğlu Ö. , Dinç G. , Bağcı Ö. , Doğru A. , İlhan İ. , Kırzıoğlu F. Y. , Orhan H.
Published: June 2017

Background and Objective

Familial Mediterranean fever (FMF) and chronic periodontitis are inflammatory diseases leading to an increase in the number of inflammasomes. To date, no published studies have reported on mutations in the Mediterranean fever (MEFV) gene in patients with chronic periodontitis, although the roles of MEFV gene mutations in FMF and FMF‐associated amyloidosis (FMF‐A) are well known. Therefore, the aim of this study was to evaluate the frequencies of MEFV gene mutations and serum amyloid A (SAA) and high‐sensitivity C‐reactive protein (hs‐CRP) levels in patients with chronic periodontitis, FMF and FMF‐A.

Material and Methods

The study population included 122 patients with FMF and 128 subjects who were systemically healthy. Clinical periodontal parameters, including the plaque index, gingival index, probing pocket depth, clinical attachment level and percentage of bleeding on probing were recorded. Blood samples were obtained from patients with FMF and systemically healthy controls, and all mutations located on exons 2 and 10 of the MEFV gene were analyzed by DNA Sanger Sequencing, which is the gold standard. SAA and high‐sensitive CRP levels were also assessed.

Results

Mean gingival index, percentage of bleeding on probing, probing pocket depth and clinical attachment level, and the levels of SAA and hs‐CRP were higher in the FMF‐A group than those in the FMF and control groups. The two most relevant mutations in patients with FMF were heterozygous M694V (46.2%), and heterozygous R202Q (32.7%). The frequencies of the homozygous M694V and R202Q mutations in the FMF‐A group were 53.8% and 46.1%, respectively. The complex R202Q/M694V homozygous state led to an increased risk of chronic periodontitis (odds ratio: 3.6), and FMF‐A (odds ratio: 7.6).

Conclusion

This is the first study to report the R202Q mutation in patients with periodontitis. Furthermore, the MEFV gene‐mediated inflammatory pathway increased serum acute phase reactants, and the changes in the R202Q and M694V could play a role in inflammatory‐genetic diseases, such as FMF, FMF‐associated amyloidosis and chronic periodontitis.
Development of a cytoplasmic male‐sterile line NJCMS4A for hybrid soybean production
Authors: Nie Zhixing , Zhao Tuanjie , Yang Shouping , Gai Junyi
Published: June 2017

Cytoplasmic male‐sterile (CMS) lines are being used to produce hybrid seeds. Thus far, four CMS sources in soybean [Glycine max (L.) Merr.] have been reported in China. However, they are not sufficient or efficient in meeting the requirements of commercial soybean hybrid seed production. In this study, 33 varieties were tested for CMS using 45 crosses among 37 landraces and 17 annual wild soybean accessions (Glycine soja Sieb. et Zucc.). The cross of N23661 × N23658 showed partial to complete male sterility in backcross generations, while the corresponding reciprocal cross showed normal male fertility. Thus, the cytoplasm of N23661 is male‐sterile, the continuously backcrossed line is a male‐sterile line (designated NJCMS4A), and N23658 is its maintainer (designated NJCM4B). The male fertility of NJCMS4A was restored by another accession, Nansheng9403. Accordingly, NJCMS4A along with its maintainer and restorer composes a complete set of three lines for producing hybrid soybean. Using mitochondrial markers and sequence analyses, NJCMS4A is a CMS line with its cytoplasm not identical to the four previously reported CMS sources in soybean.
Stereotypes, Conceptual Centrality and Gender Bias: An Empirical Investigation
Authors: Del Pinal Guillermo , Madva Alex , Reuter Kevin
Published: June 2017

Discussions in social psychology overlook an important way in which biases can be encoded in conceptual representations. Most accounts of implicit bias focus on ‘mere associations’ between features and representations of social groups. While some have argued that some implicit biases must have a richer conceptual structure, they have said little about what this richer structure might be. To address this lacuna, we build on research in philosophy and cognitive science demonstrating that concepts represent dependency relations between features. These relations, in turn, determine the centrality of a featureffor a conceptC: roughly, the more features ofCdepend onf, the more centralfis forC. In this paper, we argue that the dependency networks that link features can encode significant biases. To support this claim, we present a series of studies that show how a particular brilliance‐gender bias is encoded in the dependency networks which are part of the concepts of female and male academics. We also argue that biases which are encoded in dependency networks have unique implications for social cognition.
Unravelling the impact of early life exposures on lung structure and function in the developmental origins of asthma
Authors: Pascoe Christopher D.
Published: June 2017

See related Article
Cost projections for implementation of safety interventions to prevent transfusion‐transmitted Zika virus infection in the United States
Authors: Ellingson Katherine D. , Sapiano Mathew R.P. , Haass Kathryn A. , Savinkina Alexandra A. , Baker Misha L. , Henry Richard A. , Berger James J. , Kuehnert Matthew J. , Basavaraju Sridhar V.
Published: June 2017

BACKGROUND

In August 2016, the Food and Drug Administration advised US blood centers to screen all whole blood and apheresis donations for Zika virus (ZIKV) with an individual‐donor nucleic acid test (ID‐NAT) or to use approved pathogen reduction technology (PRT). The cost of implementing this guidance nationally has not been assessed.

STUDY DESIGN AND METHODS

Scenarios were constructed to characterize approaches to ZIKV screening, including universal ID‐NAT, risk‐based seasonal allowance of minipool (MP) NAT by state, and universal MP‐NAT. Data from the 2015 National Blood Collection and Utilization Survey (NBCUS) were used to characterize the number of donations nationally and by state. For each scenario, the estimated cost per donor ($3‐$9 for MP‐NAT, $7‐$13 for ID‐NAT) was multiplied by the estimated number of relevant donations from the NBCUS. Cost of PRT was calculated by multiplying the cost per unit ($50‐$125) by the number of units approved for PRT. Prediction intervals for costs were generated using Monte Carlo simulation methods.

RESULTS

Screening all donations in the 50 states and DC for ZIKV by ID‐NAT would cost $137 million (95% confidence interval [CI], $109‐$167) annually. Allowing seasonal MP‐NAT in states with lower ZIKV risk could reduce NAT screening costs by 18% to 25%. Application of PRT to all platelet (PLT) and plasma units would cost $213 million (95% CI, $156‐$304).

CONCLUSION

Universal ID‐NAT screening for ZIKV will cost US blood centers more than $100 million annually. The high cost of PRT for apheresis PLTs and plasma could be mitigated if, once validated, testing for transfusion transmissible pathogens could be eliminated.
Donald Trump and the Republican Party: The Making of a Faustian Bargain
Authors: White John Kenneth
Published: June 2017

Donald Trump’s presidency is likely to become what Stephen Skowronek once labeled as a “disjunctive presidency.”  Trump’s election in 2016 and the issue positions he has taken mark the end of the Reagan Era.  Just as Jimmy Carter’s one-term signaled the end of the New Deal era begun by Franklin D. Roosevelt, so, too, does Trump’s already troubled presidency signify the end of Reagan’s conservatism. Changing demographics have hastened the end of the Reagan era, and the next presidential contest is likely to be one that James David Barber called a “politics as conscience,” not a conflict election to which Trump was well-suited.  Trump’s victory, along with the end of the Reagan era, also signals a moment of significant danger for the Republican Party, despite the present unified GOP control of the federal government and recent gains that the party has made at the state and local levels.
Exergy Destruction Mechanism of Coal Gasification by Combining the Kinetic Method and the Energy Utilization Diagram
Authors: Wu Handong , Li Sheng , Gao Lin
Published: June 2017

Gasification is the core unit of coal-based production systems and is also the site where one of the largest exergy destruction occurs. This paper reveals the exergy destruction mechanism of carbon gasification through a combined analysis of the kinetic method and the energy utilization diagram (EUD). Instead of a lumped exergy destruction using the traditional “black-box” and other models, the role of each reaction in carbon gasification is revealed. The results show that the exergy destruction caused by chemical reactions accounts for 86.3% of the entire carbon gasification process. Furthermore, approximately 90.3% of exergy destruction of chemical reactions is caused by the exothermal carbon partial oxidation reaction (reaction 1), 6.0% is caused by the carbon dioxide gasification reaction (reaction 2), 2.4% is caused by the steam gasification reaction (reaction 3), and 1.3% is caused by other reactions under the base condition. With increasing O2 content α and decreasing steam content β, the proportion of exergy destruction from reaction 1 decreases due to the higher gasification temperature (a higher energy level of energy acceptor in EUD), while the proportions of other reactions increase. This shows that the chemical efficiency is optimal when the extent of reactions 1 and 3 is equal and the shift reaction extent approaches zero at the same time.
Ellipsometric Measurements of the Thermal Stability of Alternative Fuels
Authors: Nash Leigh , Klettlinger Jennifer , Vasu Subith
Published: June 2017

Thermal stability is an important characteristic of alternative fuels that must be evaluated before they can be used in aviation engines. Thermal stability refers to the degree to which a fuel breaks down when it is heated prior to combustion. This characteristic is of great importance to the effectiveness of the fuel as a coolant and to the engine's combustion performance. The thermal stability of Sasol iso-paraffinic kerosene (IPK), a synthetic alternative to Jet-A, with varying levels of naphthalene has been studied on aluminum and stainless steel substrates at 300–400 °C. This was conducted using a spectroscopic ellipsometer to measure the thickness of deposits left on the heated substrates. Ellipsometry is an optical technique that measures the changes in a light beam's polarization and intensity after it reflects from a thin film to determine the film's physical and optical properties. It was observed that, as would be expected, increasing the temperature minimally increased the deposit thickness for a constant concentration of naphthalene on both substrates. The repeatability of these measurements was verified using multiple trials at identical test conditions. Finally, the effect of increasing the naphthalene concentration at a constant temperature was found to also minimally increase the deposit thickness.
Smart Expandable Cement Additive to Achieve Better Wellbore Integrity
Authors: Dahi Taleghani A. , Li G. , Moayeri M.
Published: June 2017

One of the serious challenges encountered in cementing oil and gas wells is the failure of the cement sheaths and its debonding from casing or formation rock. Shrinkage of the cement during setting is identified as one of the driving factors behind these issues. Some expansive cement systems have been developed in the oil and gas industry to compensate for the shrinkage effect. All the expansive additives which have been developed so far have chemical reactions with the cement itself that would significantly impact the mechanical strength of the cement. In this paper, we present a new class of polymer-based expandable cement additive particles which are made of shape memory polymers (SMP). This class of polymers is designed to expand to the required extent when exposed to temperatures above 50–100 °C (122–212 °F) which is below the temperature of the cementing zone. It is notable that expansion occurs after placement of the cement but before its setting. The API RP 10 B-2 and 5 have been followed as standard test methods to evaluate expansion and strength of the cement slurry after utilizing the new additive. The proposed additive does not react with the water or cement content of the slurry. Mechanical evaluation tests confirm the potential benefit of this additive without any deteriorative effect on mechanical properties or setting time of the cement paste and significant impact on its mechanical properties. Hence, this additive would provide a reliable way to prevent cement channeling, debonding, and fluid migration to upper formations.
Pavement type and wear condition classification from tire cavity acoustic measurements with artificial neural networks
Authors: Masino Johannes , Foitzik Michael-Jan , Frey Michael , Gauterin Frank
Published: June 2017

Tire road noise is the major contributor to traffic noise, which leads to general annoyance, speech interference, and sleep disturbances. Standardized methods to measure tire road noise are expensive, sophisticated to use, and they cannot be applied comprehensively. This paper presents a method to automatically classify different types of pavement and the wear condition to identify noisy road surfaces. The methods are based on spectra of time series data of the tire cavity sound, acquired under normal vehicle operation. The classifier, an artificial neural network, correctly predicts three pavement types, whereas there are few bidirectional mis-classifications for two pavements, which have similar physical characteristics. The performance measures of the classifier to predict a new or worn out condition are over 94.6%. One could create a digital map with the output of the presented method. On the basis of these digital maps, road segments with a strong impact on tire road noise could be automatically identified. Furthermore, the method can estimate the road macro-texture, which has an impact on the tire road friction especially on wet conditions. Overall, this digital map would have a great benefit for civil engineering departments, road infrastructure operators, and for advanced driver assistance systems.
Enhancement effects of clear speech and word-initial position in Korean glides
Authors: Chang Seung-Eun
Published: June 2017

The current study investigated the enhancement effect in Korean speakers' clear speech and word-initial position, using acoustic analyses of the Korean glides /w/ and /j/. The results showed that the transitions of glides /w/ and /j/ at onset were enhanced in clear speech with an expanded vowel space. An expanded vowel space was also observed in the word-initial position, but the expansion was not statistically significant. However, the significant interaction between speaking style and word position revealed that the articulatory and global modifications in clear speech were noticeably greater at onset in the word-medial compared to the word-initial position. Also, the mid-front vowel /e/ shifted downward and leftward in clear speech, indicating that mid-front vowels are fronted and lowered in clear speech. As a language-specific issue, no phonetic evidence was found supporting the existence of two Korean glides, /wε/ and /we/, even in clear speech and word-initial position, indicating a diachronic sound merger of these two glides. In addition, the glide /je/ after a consonant was neutralized into /e/ in casual speech. These findings suggest a relationship between speaking style effects, word position effects, and changing phonetic targets due to diachronic sound change.
Nutritional Strategies of Mountain Marathon Competitors—An Observational Study
Authors: Clark Heather R. , Barker Margo E. , Corfe Bernard M.
Published: June 2017

Mountain marathons are 2-d, self-supported adventure races, during which competitors must carry all nutritional requirements to sustain athletic effort. This requires a compromise between the energy required to perform and the weight penalty of carrying it. We have undertaken a nutritional survey of event competitors in the UK using a questionnaire-based approach and have monitored dehydration during the event. We found that competitors in longer-distance classes (> 50 km) carry significantly less mass of food, which is more energy dense, but that the calorific value is lower than that of competitors in shorter classes. Carbohydrate and protein consumption both positively associated with performance. Competitors became progressively dehydrated throughout the event. Counterintuitively, the better-performing subjects became the most dehydrated. Competitors at all distances should make more effort to rehydrate during breaks in the event. Competitors at shorter distances could choose more energy-dense foods to reduce weight penalty.
Dietary Supplement Use by Varsity Athletes at a Canadian University
Authors: Kristiansen Martin , Levy-Milne Ryna , Barr Susan , Flint Anne
Published: June 2017

The purpose of this study was to assess reasons for and prevalence of supplement use among varsity athletes and nonvarsity athlete students (controls) at a Canadian university. A questionnaire, distributed to 247 varsity athletes and 204 controls, included variables regarding sports participation, supplements used, reasons for usage, perceived effects, and areas of interest about supplements. Response rates were 85.5% among varsity athletes and 44.6% among controls. Supplements were used by 98.6% of varsity athletes and 94.3% of controls. Varsity men most often reported using sports drinks, and used these (and carbohydrate gels, protein powder, and creatine) more than varsity women. Caffeine products were most often reported by other groups. Health professionals and the Internet were the most reported information sources, while friends most often recommended supplements. Many subjects indicated knowing little about supplements and wanting to learn more. Results indicate a need for nutrition education among both varsity athletes and university students.
Variability in Exercise Capacity and Metabolic Response During Endurance Exercise After a Low Carbohydrate Diet
Authors: Claassen Amanda , Lambert Estelle V. , Bosch Andrew N. , Rodger Ian M. , Gibson Alan St. Clair , Noakes Timothy D.
Published: June 2017

The impact of altered blood glucose concentrations on exercise metabolism and performance after a low carbohydrate (CHO) diet was investigated. In random order, 1 wk apart, 9 trained men underwent euglycemic (CI) or placebo (PI) clamps, while performing up to 150 min of cycling at 70% VO2max, after 48 h on a low CHO diet. The range in improvement in endurance capacity with glucose infusion was large (28 ± 26%, P < 0.05). Fifty-six percent of subjects in CI failed to complete 150 min of exercise despite maintenance of euglycemia, while only 2 subjects in PI completed 150 min of exercise, despite being hypoglycemic. Total CHO oxidation remained similar between trials. Despite longer exercise times in CI, similar amounts of muscle glycogen were used to PI. Maintenance of euglycemia in the CHO-depleted state might have an ergogenic effect, however, the effect is highly variable between individuals and independent of changes in CHO oxidation.
Coaching Life Skills Development: Best Practices and High School Tennis Coach Exemplar
Authors: Sackett Sarah Carson , Gano-Overway Lori A.
Published: June 2017

Sport has the potential to foster the development of life skills, such as initiative, teamwork, emotion regulation, and goal setting, that transcend the fields and courts on which youth participate (Danish, Forneris, Hodge, & Heke, 2004). However, it is often acknowledged that this growth does not occur on its own. One factor that plays a central role in shaping positive sport experiences is the coach (Hellison & Cutforth, 1997). The purpose of this paper is to review the current literature on coaching strategies considered best practices for life skills development as well as to provide illustrative examples of many of these practices garnered from a case study of a model coach and the strategies he used in his high school tennis program. The paper concludes with additional practical considerations and recommendations for practitioners, coach educators, and scholars who continue to add to the body of knowledge regarding a coach’s role in positive youth development.
Five Perspectives on Pursuing Mastery in Coaching
Authors: Van Mullem Pete , Dahlin Sean
Published: June 2017

The pursuit of mastery in coaching is an ongoing journey, requiring a commitment to life-long learning (Gallimore, Gilbert, & Nater, 2014). The purpose of this paper is to share the insight of five professionals (i.e., educator, sport ethicist, administrator, sport researcher, and a coach), participating in a panel session at the 2016 U.S. National Coaching Conference, on pursuing mastery as a coach. The term mastery is often associated with expertise. To be considered an expert, a coach must also be effective (Côté & Gilbert, 2009). Coaches that have achieved this level of effectiveness are often referred to as master teachers. Across the session the views of the panel members emphasized the pursuit of mastery as an ongoing journey of continuous learning. Insight from the panelists is compared with literature in coaching science and recommendations are provided for coaches and coaching educators on how to deliberately pursue mastery as a coach.
Spatial Distribution and Ribosome-Binding Dynamics of EF-P in Live
Escherichia coli
Authors: Mohapatra Sonisilpa , Choi Heejun , Ge Xueliang , Sanyal Suparna , Weisshaar James C.
Published: June 2017

In vitro
assays find that ribosomes form peptide bonds to proline (Pro) residues more slowly than to other residues. Ribosome profiling shows that stalling at Pro-Pro-X triplets is especially severe but is largely alleviated in
Escherichia coli
by the action of elongation factor EF-P. EF-P and its eukaryotic/archaeal homolog IF5A enhance the peptidyl transfer step of elongation. Here, a superresolution fluorescence localization and tracking study of EF-P–mEos2 in live
E. coli
provides the first
in vivo
information about the spatial distribution and on-off binding kinetics of EF-P. Fast imaging at 2 ms/frame helps to distinguish ribosome-bound (slowly diffusing) EF-P from free (rapidly diffusing) EF-P. Wild-type EF-P exhibits a three-peaked axial spatial distribution similar to that of ribosomes, indicating substantial binding. The mutant EF-P
K34A
exhibits a homogeneous distribution, indicating little or no binding. Some 30% of EF-P copies are bound to ribosomes at a given time. Two-state modeling and copy number estimates indicate that EF-P binds to 70S ribosomes during 25 to 100% of translation cycles. The timescale of the typical diffusive search by free EF-P for a ribosome-binding site is τ
free
≈ 16 ms. The typical residence time of an EF-P on the ribosome is very short, τ
bound
≈ 7 ms. Evidently, EF-P binds to ribosomes during many or most elongation cycles, much more often than the frequency of Pro-Pro motifs. Emptying of the E site during part of the cycle is consistent with recent
in vitro
experiments indicating dissociation of the deacylated tRNA upon translocation.

IMPORTANCE
Ribosomes translate the codon sequence within mRNA into the corresponding sequence of amino acids within the nascent polypeptide chain, which in turn ultimately folds into functional protein. At each codon, bacterial ribosomes are assisted by two well-known elongation factors: EF-Tu, which aids binding of the correct aminoacyl-tRNA to the ribosome, and EF-G, which promotes tRNA translocation after formation of the new peptide bond. A third factor, EF-P, has been shown to alleviate ribosomal pausing at rare Pro-Pro motifs, which are translated very slowly without EF-P. Here, we use superresolution fluorescence imaging to study the spatial distribution and ribosome-binding dynamics of EF-P in live
E. coli
cells. We were surprised to learn that EF-P binds to and unbinds from translating ribosomes during at least 25% of all elongation events; it may bind during every elongation cycle.
Complete Biosynthesis of Anthocyanins Using
E. coli
Polycultures
Authors: Jones J. Andrew , Vernacchio Victoria R. , Collins Shannon M. , Shirke Abhijit N. , Xiu Yu , Englaender Jacob A. , Cress Brady F. , McCutcheon Catherine C. , Linhardt Robert J. , Gross Richard A. , Koffas Mattheos A. G.
Published: June 2017

Fermentation-based chemical production strategies provide a feasible route for the rapid, safe, and sustainable production of a wide variety of important chemical products, ranging from fuels to pharmaceuticals. These strategies have yet to find wide industrial utilization due to their inability to economically compete with traditional extraction and chemical production methods. Here, we engineer for the first time the complex microbial biosynthesis of an anthocyanin plant natural product, starting from sugar. This was accomplished through the development of a synthetic, 4-strain
Escherichia coli
polyculture collectively expressing 15 exogenous or modified pathway enzymes from diverse plants and other microbes. This synthetic consortium-based approach enables the functional expression and connection of lengthy pathways while effectively managing the accompanying metabolic burden. The
de novo
production of specific anthocyanin molecules, such as calistephin, has been an elusive metabolic engineering target for over a decade. The utilization of our polyculture strategy affords milligram-per-liter production titers. This study also lays the groundwork for significant advances in strain and process design toward the development of cost-competitive biochemical production hosts through nontraditional methodologies.

IMPORTANCE
To efficiently express active extensive recombinant pathways with high flux in microbial hosts requires careful balance and allocation of metabolic resources such as ATP, reducing equivalents, and malonyl coenzyme A (malonyl-CoA), as well as various other pathway-dependent cofactors and precursors. To address this issue, we report the design, characterization, and implementation of the first synthetic 4-strain polyculture. Division of the overexpression of 15 enzymes and transcription factors over 4 independent strain modules allowed for the division of metabolic burden and for independent strain optimization for module-specific metabolite needs. This study represents the most complex synthetic consortia constructed to date for metabolic engineering applications and provides a new paradigm in metabolic engineering for the reconstitution of extensive metabolic pathways in nonnative hosts.
Lateral Gene Transfer Dynamics in the Ancient Bacterial GenusStreptomyces
Authors: McDonald Bradon R. , Currie Cameron R.
Published: June 2017

Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genusStreptomyces. Using a molecular clock, we estimate that theStreptomycesbacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span,Streptomycesaccumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.

IMPORTANCETree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genusStreptomyces, with merely one gene acquired inStreptomyceslineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial.
The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions
Authors: Wuchty S. , Rajagopala S. V. , Blazie S. M. , Parrish J. R. , Khuri S. , Finley R. L. , Uetz P.
Published: June 2017

Identification of protein interactions in bacterial species can help define the individual roles that proteins play in cellular pathways and pathogenesis. Very few protein interactions have been identified for the important human pathogenS. pneumoniae. We used an experimental approach to identify over 2,000 new protein interactions forS. pneumoniae, the most extensive interactome data for this bacterium to date. To predict protein function, we used our interactome data augmented with interactions from other closely related bacteria. The combination of the experimental data and meta-interactome data significantly improved the prediction results, allowing us to assign possible functions to a large number of poorly characterized proteins.
Differences in subependymal vein anatomy may predispose preterm infants to GMH–IVH
Authors: Tortora Domenico , Severino Mariasavina , Malova Mariya , Parodi Alessandro , Morana Giovanni , Sedlacik Jan , Govaert Paul , Volpe Joseph J , Rossi Andrea , Ramenghi Luca Antonio
Published: June 2017

Background and purpose

The anatomy of the deep venous system plays an important role in the pathogenesis of brain lesions in the preterm brain as shown by different histological studies. The aims of this study were to compare the subependymal vein anatomy of preterm neonates with germinal matrix haemorrhage–intraventricular haemorrhage (GMH–IVH), as evaluated by susceptibility-weighted imaging (SWI) venography, with a group of age-matched controls with normal brain MRI, and to explore the relationship between the anatomical features of subependymal veins and clinical risk factors for GMH–IVH.

Methods

SWI venographies of 48 neonates with GMH–IVH and 130 neonates with normal brain MRI were retrospectively evaluated. Subependymal vein anatomy was classified into six different patterns: type 1 represented the classic pattern and types 2–6 were considered anatomic variants. A quantitative analysis of the venous curvature index was performed. Variables were analysed by using Mann-Whitney U and χ2 tests, and a multiple logistic regression analysis was performed to evaluate the association between anatomical features, clinical factors and GMH–IVH.

Results

A significant difference was noticed among the six anatomical patterns according to the presence of GMH–IVH (χ2=14.242, p=0.014). Anatomic variants were observed with higher frequency in neonates with GMH–IVH than in controls (62.2% and 49.6%, respectively). Neonates with GMH–IVH presented a narrower curvature of the terminal portion of subependymal veins (p<0.05). These anatomical features were significantly associated with GMH–IVH (p<0.05).

Conclusion

Preterm neonates with GMH–IVH show higher variability of subependymal veins anatomy confirming a potential role as predisposing factor for GMH–IVH.
Staffs’ and managers’ perceptions of how and when discrete event simulation modelling can be used as a decision support in quality improvement: a focus group discussion study at two hospital settings in Sweden
Authors: Hvitfeldt-Forsberg Helena , Mazzocato Pamela , Glaser Daniel , Keller Christina , Unbeck Maria
Published: June 2017

Objective

To explore healthcare staffs’ and managers’ perceptions of how and when discrete event simulation modelling can be used as a decision support in improvement efforts.

Design

Two focus group discussions were performed.

Setting

Two settings were included: a rheumatology department and an orthopaedic section both situated in Sweden.

Participants

Healthcare staff and managers (n=13) from the two settings.

Interventions

Two workshops were performed, one at each setting. Workshops were initiated by a short introduction to simulation modelling. Results from the respective simulation model were then presented and discussed in the following focus group discussion.

Results

Categories from the content analysis are presented according to the following research questions: how and when simulation modelling can assist healthcare improvement? Regarding how, the participants mentioned that simulation modelling could act as a tool for support and a way to visualise problems, potential solutions and their effects. Regarding when, simulation modelling could be used both locally and by management, as well as a pedagogical tool to develop and test innovative ideas and to involve everyone in the improvement work.

Conclusions

Its potential as an information and communication tool and as an instrument for pedagogic work within healthcare improvement render a broader application and value of simulation modelling than previously reported.
Cross-sectional analysis of two social determinants of health in California cities: racial/ethnic and geographic disparities
Authors: Bustamante-Zamora Dulce , Maizlish Neil
Published: June 2017

Objective

To study the magnitude and direction of city-level racial and ethnic differences in poverty and education to characterise health equity and social determinants of health in California cities.

Design

We used data from the American Community Survey, United States Census Bureau, 2006–2010, and calculated differences in the prevalence of poverty and low educational attainment in adults by race/ethnicity and by census tracts within California cities. For race/ethnicity comparisons, when the referent group (p2) to calculate the difference (p1−p2) was the non-Hispanic White population (considered a historically advantaged group), a positive difference was considered a health inequity. Differences with a non-White reference group were considered health disparities.

Setting

Cities of the State of California, USA.

Results

Within-city differences in the prevalence of poverty and low educational attainment disfavoured Black and Latinos compared with Whites in over 78% of the cities. Compared with Whites, the median within-city poverty difference was 7.0% for Latinos and 6.2% for Blacks. For education, median within-city difference was 26.6% for Latinos compared with Whites. In a small, but not negligible proportion of cities, historically disadvantaged race/ethnicity groups had better social determinants of health outcomes than Whites. The median difference between the highest and lowest census tracts within cities was 14.3% for poverty and 15.7% for low educational attainment. Overall city poverty rate was weakly, but positively correlated with within-city racial/ethnic differences.

Conclusions

Disparities and inequities are widespread in California. Local health departments can use these findings to partner with cities in their jurisdiction and design strategies to reduce racial, ethnic and geographic differences in economic and educational outcomes. These analytic methods could be used in an ongoing surveillance system to monitor these determinants of health.
Clinicians’ perspectives of parental decision-making following diagnosis of a severe congenital anomaly: a qualitative study
Authors: Lotto Robyn , Smith Lucy K , Armstrong Natalie
Published: June 2017

Objective

To explore clinicians’ perspectives on supporting parents’ decision-making following diagnosis of a severe congenital anomaly, and how this is shaped by current policy.

Methods

This paper reports data collated as part of a larger project examining parents’ decision-making following antenatal diagnosis. The focus of this paper is the data arising from semistructured interviews conducted with 18 clinicians, with findings further supported by data generated from consultations between clinicians and parents. All interviews and consultations were audio-recorded and transcribed verbatim, with analysis based on the constant comparative approach.

Results

Three key themes emerged which together shape the practice of clinicians working in this area: first, the law governing termination of pregnancy (TOP) and how clinicians believe this influences the context in which decisions about whether to terminate or continue an affected pregnancy are made; second, approaches to the management of cases seen as particularly challenging; and third, how clinicians understand their role when working with parents. These themes combine to create a strong desire on the part of clinicians for parents to engage in a particular ‘rational’ form of decision-making and to be able to demonstrate the enactment of this. This is seen as important in order to ensure the ‘right’ decision has been reached and, particularly when the decision is to terminate, will withstand possible scrutiny.

Conclusions

The policy context in which these decisions are made strongly shapes how clinicians practise and what they want to see from the parents with whom they work. The ways in which they seek to overcome the difficulties in interpreting the law may result in variations in the offer of late TOP, both between and within units. This may inadvertently affect the options available to women least able to engage in this idealised form of decision-making.
Influence of polyphenol-rich diet on exercise-induced immunomodulation in male endurance athletes
Authors: Lackermair Korbinian , Scherr Johannes , Waidhauser Georg , Methe Heiko , Hoster Eva , Nieman David C. , Hanley Alan , Clauss Sebastian , Halle Martin , Nickel Thomas
Published: June 2017

Stress is associated with increased susceptibility to infection. We investigated if the mechanism involves immunomodulation of dendritic cells and whether this can be inhibited by a polyphenol-rich diet. Blood samples were taken from a total of 100 male endurance athletes at 5 time points around a marathon run: 4 weeks before; 1 week before; and immediately, 24 h, and 72 h after. Participants were randomized into 2 double-blinded groups. One group received a polyphenol-rich beverage during a 3-week training phase before marathon while the other group received a placebo beverage. Flow cytometric analysis of dendritic cell (DC) counts and subpopulation counts (myeloid, plasmocytoid DCs) was performed. Levels of viral antigen presenting toll-like receptor (TLR) 7 messenger RNA was measured by real-time polymerase chain reaction. Marathon running induced a significant increase of circulating myeloid DCs (0.2% vs. 0.33% of whole-blood leukocytes (wbl); p < 0.01) and a significant decrease of plasmozytoid DCs (0.12% vs. 0.03% of wbl; p < 0.01) and TLR7 expression (decline of 60%; p < 0.01). Polyphenol supplementation did not significantly affect mobilization of dendritic cells but showed beneficial effects on regeneration of TLR7 expression in wbl at 3 days postmarathon (decline of 40% vs. increase of 1000%; p < 0.05). In conclusion, physical stress affects circulating DCs, with an increase of myeloid and a decrease of plasmozytoid DCs. This may partially explain the susceptibility to viral infections after strenuous exercise. These detrimental effects are not attenuated by polyphenol supplementation. However, polyphenols support regeneration of viral antigen presenting TLR7 after strenuous exercise.