bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel technologies in doubled haploid line development
Authors: Ren Jiaojiao , Wu Penghao , Trampe Benjamin , Tian Xiaolong , Lübberstedt Thomas , Chen Shaojiang
Published: August 2017

haploid inducer line can be transferred (DH) technology can not only shorten the breeding process but also increase genetic gain. Haploid induction and subsequent genome doubling are the two main steps required for DH technology. Haploids have been generated through the culture of immature male and female gametophytes, and through inter‐ and intraspecific via chromosome elimination. Here, we focus on haploidization via chromosome elimination, especially the recent advances in centromere‐mediated haploidization. Once haploids have been induced, genome doubling is needed to produce DH lines. This study has proposed a new strategy to improve haploid genome doubling by combing haploids and minichromosome technology. With the progress in haploid induction and genome doubling methods, DH technology can facilitate reverse breeding, cytoplasmic male sterile (CMS) line production, gene stacking and a variety of other genetic analysis.
Kierkegaard, Repetition and Ethical Constancy
Authors: Watts Daniel
Published: August 2017

How can a person forge a stable ethical identity over time? On one view, ethical constancy means reapplying the same moral rules. On a rival view, it means continually adapting to one's ethical context in a way that allows one to be recognized as the same practical agent. Focusing on his thinking about repetition, I show how Kierkegaard offers a critical perspective on both these views. From this perspective, neither view can do justice to our vulnerability to certain kinds of crisis, in which our ethical self‐understanding is radically undermined. I further examine his alternative account of ethical constancy, by clarifying Kierkegaard's idea of a ‘second ethics’, as addressed to those who feel ethically powerless and as requiring an ongoing process of self‐transformation.
Effect of image‐matching parameters and local morphology on the geomorphological quality of SPOT DEMs
Authors: El Hage Mhamad , Simonetto Elisabeth , Faour Ghaleb , Polidori Laurent
Published: August 2017

Digital elevation models (DEMs) are used for many applications, including geomorphological feature identification. This study assesses, for selected regions of Lebanon, the impact of matching parameters on the geomorphic indices extracted from photogrammetrically derived DEMs. Three parameters are shown to have a significant effect on the geomorphic indices: the template size and the correlation and curvature thresholds. The most influential parameter is the template size, an increase in which decreases the proportion of interpolated points and leads to more reliable matching, but it also tends to smooth the morphology of the DEM. A small template size tends to preserve the details of the terrain, especially for steep slopes, but it also increases noise in the DEM. For the present study, the optimal value for this parameter is about 13 × 13 pixels. High threshold values lead to more reliable matches but also increase the proportion of interpolated points, which has a significant effect on the resulting geomorphology.
Is nitrogen accumulation in grain legumes responsive to growth or ontogeny?
Authors: Marrou Hélène , Ricaurte Jaumer J. , Ghanem Michel E. , Clavijo Michelangeli José A. , Ghaouti Lamiae , Rao Idupulapati M. , Sinclair Thomas R.
Published: August 2017

Nitrogen (N) accumulation in legumes is one of the main determinants of crop yield. Although N accumulation from symbiotic nitrogen fixation or N absorption from the soil has been widely investigated, there is no clear consensus on timing of the beginning of N accumulation and the termination of N accumulation and the physiological events that may be associated with these two events. The analyses conducted in this study aimed at identifying the determinant of N accumulation in two grain legume species. Nitrogen accumulation dynamics and mass accumulation and development stages were recorded in the field for several genotypes of common bean (Phaseolus vulgaris) and faba bean (Vicia faba) under different growing conditions. This study showed that during the vegetative stages, N accumulation rate was correlated with mass accumulation rate. However, the maximum accumulation of N did not correspond to the time of the maximum mass accumulation. In fact, for both species, N accumulation was found to persist in seed growth. This challenges a common hypothesis that seed growth causes a decrease in N accumulation because of a shift of the photosynthate supply to support the seed growth. Even more surprising was the shift of the active accumulation of N in faba bean to late in the growing season as compared with common bean. N accumulation by faba bean only was initiated at high rates very late in vegetative growth and persisted at high rates well into seed fill.
When Trumps Clash: Dworkin and the Doctrine of Proportionality
Authors: Weinrib Jacob
Published: August 2017

If there is one point on which defenders and critics of the doctrine of proportionality agree, it is that Dworkin's rights as trumps model stands as a radical alternative to the doctrine. Those who are sympathetic to proportionality reject the rights as trumps model for failing to acknowledge that there are conditions under which a right may be justifiably infringed. In turn, those who regard rights as trumps reject the doctrine of proportionality for failing to take rights seriously. This paper argues that each of these views is mistaken. On the one hand, Dworkin's rights as trumps model elides with a prominent version of the proportionality doctrine. On the other, this version takes rights seriously.
Regulatory inspection and the changing legitimacy of health and safety
Authors: Almond Paul , Esbester Mike
Published: August 2017

The regulation of conduct via law is a key mechanism through which broader social meanings are negotiated and expressed. The use of regulatory tools to bring about desired outcomes reflects existing social and political understandings of institutional legitimacy, the meanings attached to regulation, and the values it seeks to advance. But these contextual understandings are not static, and their evolution poses challenges for regulators, particularly when they reflect political framing processes. This paper shows how inspection has been reshaped as a tool within the United Kingdom's health and safety system by changes in the meanings attached to the concept of “risk‐based regulation.” While rates of inspection have fallen dramatically in recent years, the nature and quality of inspection have also been fundamentally reshaped via an increasingly procedural and economically rational “risk‐based” policy context. This has had consequences for the transformative and symbolic value of inspection as a tool of regulatory practice.
Should all dialysis patients with hepatitis C be treated? If so, before or after kidney transplantation?
Authors: Jadoul Michel , Martin Paul
Published: August 2017

HCV infection by genotype 1 and 4 can now be cured in close to 100% of patients with stage 4 or 5 CKD, including dialysis patients. Several regimens are available, all interferon‐free and given for only 12 weeks. Thus unless life expectancy is short, HCV infection should be treated. The optimal timing of antiviral treatment will be dependent on several parameters: the possibility of being transplanted rapidly (either with a HCV+ graft or from a living donor) calls for treatment after transplantation. On the contrary, severe liver fibrosis, especially with portal hypertension calls for immediate treatment of HCV. Finally specific HCV genotype also impacts the treatment decision as genotypes 2,3,5 and 6 currently can be treated more easily after restoration of kidney function rather than in the presence of severe CKD, although this is anticipated to change soon once newer pangenotypic regimens are licensed.
Arabidopsis Chromatin Assembly Factor 1 is required for occupancy and position of a subset of nucleosomes
Authors: Muñoz‐Viana Rafael , Wildhaber Thomas , Trejo‐Arellano Minerva S. , Mozgová Iva , Hennig Lars
Published: August 2017

Chromatin Assembly Factor 1 (CAF‐1) is a major nucleosome assembly complex which functions particularly during DNA replication and repair. Here we studied how the nucleosome landscape changes in a CAF‐1 mutant in the model plant Arabidopsis thaliana. Globally, most nucleosomes were not affected by loss of CAF‐1, indicating the presence of efficient alternative nucleosome assemblers. Nucleosomes that we found depleted in the CAF‐1 mutant were enriched in non‐transcribed regions, consistent with the notion that CAF‐1‐independent nucleosome assembly can compensate for loss of CAF‐1 mainly in transcribed regions. Depleted nucleosomes were particularly enriched in proximal promoters, suggesting that CAF‐1‐independent nucleosome assembly mechanisms are often not efficient upstream of transcription start sites. Genes related to plant defense were particularly prone to lose nucleosomes in their promoters upon CAF‐1 depletion. Reduced nucleosome occupancy at promoters of many defense‐related genes is associated with a primed gene expression state that may considerably increase plant fitness by facilitating plant defense. Together, our results establish that the nucleosome landscape in Arabidopsis is surprisingly robust even in the absence of the dedicated nucleosome assembly machinery CAF‐1 and that CAF‐1‐independent nucleosome assembly mechanisms are less efficient in particular genome regions.
The economic implications of sylvatic rabies eradication in Italy
Authors: Sartore S. , Mulatti P. , Trestini S. , Lorenzetto M. , Gagliazzo L. , Marangon S. , Bonfanti L.
Published: August 2017

After more than 10 years of absence, sylvatic rabies re‐appeared in Italy in 2008. To prevent disease spread, three oral rabies vaccination (ORV) campaigns targeting red foxes were performed through manual distribution of vaccine baits between January and September 2009. As these campaigns proved unsuccessful, at the end of December 2009, baits started being distributed using helicopters, allowing uniform coverage of larger areas in a shorter time period. From winter 2009 to autumn 2016, a total of 15 ORV campaigns (four emergency, four regular and seven preventive ORV) were implemented through aerial distribution of baits. In this study, we assessed the costs of the aerial ORV campaigns, which were aimed at eradicating the disease and reobtaining the rabies‐free status. Cumulative costs per km2 were estimated at €59.45 during emergency campaigns and ranged between €51.94 and €65.67 in the regular vaccinations. The main portion of costs for ORV programmes were related to baits supply and distribution: €49.24 (82.83%) in emergency campaigns and from €40.33 to € 43.35 in regular ORVs (71.97% and 66.02%, respectively). At the end of each ORV campaign, the efficacy of vaccination activities was estimated by assessing the proportion of foxes testing positive for tetracycline biomarker in jawbone, indicating bait intake. Results revealed that the proportion of foxes that ingested baits varied between 70.97% and 95.51%. Statistical analysis indicated that reducing the density of dropped baits could potentially lead to a cost‐saving of 22.81%, still maintaining a satisfactory level of bait intake by the fox population.
5‐Aminoimidazole‐4‐carboxamide ribonucleotide prevents fat gain following the cessation of voluntary physical activity
Authors: Ruegsegger Gregory N. , Sevage Joseph A. , Childs Thomas E. , Grigsby Kolter B. , Booth Frank W.
Published: August 2017

New Findings

What is the central question of this study?

We investigated whether 5‐aminoimidazole‐4‐carboxamide‐1‐beta‐D‐ribofuranoside (AICAR) could prevent acute increases in body fat and changes in omental and subcutaneous adipose tissue following the sudden transition from physical activity to physical inactivity.

What is the main finding and its importance?

AICAR prevented fat gains following the transition from physical activity to inactivity to levels comparable to rats that remained physically active. AICAR and continuous physical activity produced depot‐specific changes in cyclin A1 mRNA and protein that were associated with the prevention of fat gain. These findings suggest that targeting AMP‐activated protein kinase signalling could oppose rapid adipose mass growth.

The transition from physical activity to inactivity is associated with drastic increases in ‘catch‐up’ fat that in turn foster the development of many obesity‐associated maladies. We tested whether 5‐aminoimidazole‐4‐carboxamide‐1‐beta‐D‐ribofuranoside (AICAR) treatment would prevent gains in body fat following the sudden transition from a physically active state to an inactive state by locking a voluntary running wheel. Male Wistar rats were either sedentary (SED) or given wheel access for 4 weeks, at which time rats with wheels continued running (RUN), had their wheel locked (WL) or had WL with daily AICAR injection (WL + AICAR) for 1 week. RUN and WL + AICAR prevented gains in body fat compared with SED and WL (P < 0.001). Cyclin A1 mRNA, a marker of cell proliferation, was decreased in omental, but not subcutaneous adipose tissue, in RUN and WL + AICAR compared with SED and WL groups (P < 0.05). Both cyclin A1 mRNA and protein were positively associated with gains in fat mass (P < 0.05). Cyclin A1 mRNA in omental, but not subcutaneous, adipose tissue was negatively correlated with p‐AMPK levels (P < 0.05). Differences in fat gain and omental mRNA and protein levels were independent of changes in food intake and in differences in select hypothalamic mRNAs. These findings suggest that AICAR treatment prevents acute gains in adipose tissue following physical inactivity to levels of rats that continuously run, and that together, continuous physical activity and AICAR could, at least initially in these conditions, exert similar inhibitory effects on adipogenesis in a depot‐specific manner.
Experimental Study on the Deformation and Failure of the Bellows Structure Beyond the Designed Internal Pressure
Authors: Ando Masanori , Yada Hiroki , Tsukimori Kazuyuki , Ichimiya Masakazu , Anoda Yoshinari
Published: August 2017

Bellows structure is used to absorb the thermal expansion maintaining the boundary of the inside to outside, and it is applied to constitute the containment vessel (CV) boundary of the nuclear power plant. In this study, in order to develop the evaluation method of the ultimate strength of the bellows structure subject to internal pressure beyond the specified limit, the failure test and finite element analysis (FEA) of the bellows structure were performed. Several types of the bellows structure made of SUS304 were tested using pressurized water. The failure modes were demonstrated through the test of five and six specimens with six and five convolutions, respectively. Water leakage was caused by contact of the expanded convolution and the neighbor structure in the specimens with the shipping rod mounts. On the other hand, local failure as leakage in the deformation concentrated location and ductile failure as burst in the expanded convolution were observed in the specimen without shipping rod mounts. The maximum pressures in the test observed local and ductile failure were over ten times larger than the estimated values of the limited design pressure for in-plane instability by the EJMA standard. To simulate the buckling and deformation behavior during the test, the implicit and explicit FEA were performed. Because the inversion of the convolution accompanied by convolution contact observed in the test was too difficult a problem for implicit analysis, the maximum pressures in the step of solution converged were compared to the maximum pressures in the tests. On the other hand, explicit analysis enabled to simulate the complex deformation during the test, and the results were evaluated considering ductile failure to compare the test results.
A Linear Multiport Network Approach for Elastically Coupled Underactuated Grippers
Authors: Martell Michael J. , Díaz J. C. , Schultz Joshua A.
Published: August 2017

This paper presents a framework based on multiport network theory for modeling underactuated grippers where the actuators produce finger motion by deforming an elastic transmission mechanism. If the transmission is synthesized from compliant components joined together with series (equal force) or parallel (equal displacement) connections, the resulting multiport immittance (stiffness) matrix for the entire transmission can be used to deduce how the object will behave in the grasp. To illustrate this, a three-fingered gripper is presented in which each finger is driven by one of two linear two-port spring networks. The multiport approach predicts contact force distribution with good fidelity even with asymmetric objects. The parallel-connected configuration exhibited object rotation and was more prone to object ejection than the series-connected case, which balanced the contact forces evenly.
Complementary empirical data on minimum bow force
Authors: Mores Robert
Published: August 2017

The minimum bow force Fmin necessary to maintain Helmholtz motion on stringed instruments was widely believed to be proportional to the bow velocity vB, to the reciprocal of the bridge resistance R, and to the reciprocal of the relative bow-bridge distance β squared [Schelleng, J. Acoust. Soc. Am. 53, 26–41 (1973)]. More recently, a study reported independence from vB and an overproportional reciprocal effect of R while confirming the 1/β2 proportionality [Schoonderwaldt, Acta Acust. Acust. 94, 604–622 (2008)]. Here, a bowing pendulum is used which facilitates precise control and measurement of related parameters. The string excitation at the contact point is recorded to instantly classify Helmholtz motion (HM) versus non-Helmholtz motion with one (nHM-1) or more additional slips during the stick phase. Monitoring of the classification supports the control of bowing parameters during measurement. These are directed towards the regions of transition between HM and nHM-1 to reveal the parameters related to Fmin. The empirical data gained from cello strings suggest that HM requires a baseline force Fmin,0 even for very low vB. Fmin,0 depends on R and ß.
Time-of-flight dependency on transducer separation distance in a reflective-path guided-wave ultrasonic flow meter at zero flow conditions
Authors: Aanes Magne , Kippersund Remi Andre , Lohne Kjetil Daae , Frøysa Kjell-Eivind , Lunde Per
Published: August 2017

Transit-time flow meters based on guided ultrasonic wave propagation in the pipe spool have several advantages compared to traditional inline ultrasonic flow metering. The extended interrogation field, obtained by continuous leakage from guided waves traveling in the pipe wall, increases robustness toward entrained particles or gas in the flow. In reflective-path guided-wave ultrasonic flow meters (GW-UFMs), the flow equations are derived from signals propagating solely in the pipe wall and from signals passing twice through the fluid. In addition to the time-of-flight (TOF) through the fluid, the fluid path experiences an additional time delay upon reflection at the opposite pipe wall due to specular and non-specular reflections. The present work investigates the influence of these reflections on the TOF in a reflective-path GW-UFM as a function of transducer separation distance at zero flow conditions. Two models are used to describe the signal propagation through the system: (i) a transient full-wave finite element model, and (ii) a combined plane-wave and ray-tracing model. The study shows that a range-dependent time delay is associated with the reflection of the fluid path, introducing transmitter-receiver distance dependence. Based on these results, the applicability of the flow equations derived using model (ii) is discussed.
Analytical model of mechanically excited piezoelectric unimorph beams
Authors: Pillai Minu A. , Ebenezer D. D. , Deenadayalan Ezhilarasi
Published: August 2017

A model is presented of a composite beam with one elastic and one piezoelectric layer. A reduced set of piezoelectric equations of state that has only the longitudinal components of stress and strain and the transverse components of electric field and charge density is consistently used to include the effect of piezoelectric coupling in all the equations. The equi-potential boundary conditions on the electrodes, the open-circuit condition, and the Gauss condition are satisfied. The position of the neutral axis and the dynamic equilibrium equation are derived after including the effect of piezoelectric coupling. All equations are combined to derive an equation of motion that contains only the displacement and the mechanical excitation. The solution to the equation is expressed in terms of a complete set of functions and an auxiliary function that contains the electric potential. The latter is needed to satisfy piezoelectric boundary conditions at the ends of the beam. The electric potential varies along the length of the beam and has a quadratic variation between the electrodes. Analytical expressions for displacement and potential, and numerical results at low frequencies and in the neighborhood of resonance, are presented for certain sets of boundary conditions.
Effect of Body Composition on Physiological Responses to Cold-Water Immersion and the Recovery of Exercise Performance
Authors: Stephens Jessica M. , Halson Shona L. , Miller Joanna , Slater Gary J. , Chapman Dale W. , Askew Christopher D.
Published: August 2017

Purpose: To explore the influence of body composition on thermal responses to cold-water immersion (CWI) and the recovery of exercise performance. Methods: Male subjects were stratified into 2 groups: low fat (LF; n = 10) or high fat (HF; n = 10). Subjects completed a high-intensity interval test (HIIT) on a cycle ergometer followed by a 15-min recovery intervention (control [CON] or CWI). Core temperature (Tc), skin temperature, and heart rate were recorded continuously. Performance was assessed at baseline, immediately post-HIIT, and 40 min postrecovery using a 4-min cycling time trial (TT), countermovement jump (CMJ), and isometric midthigh pull (IMTP). Perceptual measures (thermal sensation [TS], total quality of recovery [TQR], soreness, and fatigue) were also assessed. Results: Tc and TS were significantly lower in LF than in HF from 10 min (Tc, LF 36.5°C ± 0.5°C, HF 37.2°C ± 0.6°C; TS, LF 2.3 ± 0.5 arbitrary units [a.u.], HF 3.0 ± 0.7 a.u.) to 40 min (Tc, LF 36.1°C ± 0.6°C, HF 36.8°C ±0.7°C; TS, LF 2.3 ± 0.6 a.u., HF 3.2 ± 0.7 a.u.) after CWI (P < .05). Recovery of TT performance was significantly enhanced after CWI in HF (10.3 ± 6.1%) compared with LF (3.1 ± 5.6%, P = .01); however, no differences were observed between HF (6.9% ±5.7%) and LF (5.4% ± 5.2%) with CON. No significant differences were observed between groups for CMJ, IMTP, TQR, soreness, or fatigue in either condition. Conclusion: Body composition influences the magnitude of Tc change during and after CWI. In addition, CWI enhanced performance recovery in the HF group only. Therefore, body composition should be considered when planning CWI protocols to avoid overcooling and maximize performance recovery.
Energy Cost Expression for a Youth Compendium of Physical Activities: Rationale for Using Age Groups
Authors: Pfeiffer Karin A. , Watson Kathleen B. , McMurray Robert G. , Bassett David R. , Butte Nancy F. , Crouter Scott E. , Herrmann Stephen D. , Trost Stewart G. , Ainsworth Barbara E. , Fulton Janet E. , Berrigan David , _ _
Published: August 2017

Purpose: This study compared the accuracy of physical activity energy expenditure (PAEE) prediction using 2 methods of accounting for age dependency versus 1 standard (single) value across all ages. Methods: PAEE estimates were derived by pooling data from 5 studies. Participants, 6–18 years (n = 929), engaged in 14 activities while in a room calorimeter or wearing a portable metabolic analyzer. Linear regression was used to estimate the measurement error in PAEE (expressed as youth metabolic equivalent) associated with using age groups (6–9, 10–12, 13–15, and 16–18 y) and age-in-years [each year of chronological age (eg, 12 = 12.0–12.99 y)] versus the standard (a single value across all ages). Results: Age groups and age-in-years showed similar error, and both showed less error than the standard method for cycling, skilled, and moderate- to vigorous-intensity activities. For sedentary and light activities, the standard had similar error to the other 2 methods. Mean values for root mean square error ranged from 0.2 to 1.7 youth metabolic equivalent across all activities. Error reduction ranged from −0.2% to 21.7% for age groups and −0.23% to 18.2% for age-in-years compared with the standard. Conclusions: Accounting for age showed lower errors than a standard (single) value; using an age-dependent model in the Youth Compendium is recommended.
Interest in STEM is contagious for students in biology, chemistry, and physics classes
Authors: Hazari Zahra , Potvin Geoff , Cribbs Jennifer D. , Godwin Allison , Scott Tyler D. , Klotz Leidy
Published: August 2017

Students who perceive a high level of interest among classmates in science classes are more likely to intend pursuing STEM.
Effects of population dispersal on regional signaling networks: An example from northern Iroquoia
Authors: Hart John P. , Birch Jennifer , Gates St-Pierre Christian
Published: August 2017

Social network analyses show St. Lawrence Iroquoians as brokers between nascent Iroquois and Huron confederacies before A.D. 1500.
Papers of note in
Science
357
(6350)
Authors: Ferrarelli Leslie K.
Published: August 2017

This week’s articles uncover mechanisms of drug action, a way bacteria can help defend against the flu, and a ubiquitin ligase that facilitates the maturation of red blood cells.
Impact of Exposure of Methicillin-Resistant Staphylococcus aureus to Polyhexanide
In Vitro
and
In Vivo
Authors: Renzoni A. , Von Dach E. , Landelle C. , Diene S. M. , Manzano C. , Gonzales R. , Abdelhady W. , Randall C. P. , Bonetti E. J. , Baud D. , O'Neill A. J. , Bayer A. , Cherkaoui A. , Schrenzel J. , Harbarth S. , François P.
Published: August 2017

Methicillin-resistant
Staphylococcus aureus
(MRSA) resistant to decolonization agents such as mupirocin and chlorhexidine increases the need for development of alternative decolonization molecules. The absence of reported severe adverse reactions and bacterial resistance to polyhexanide makes it an excellent choice as a topical antiseptic. In the present study, we evaluated the
in vitro
and
in vivo
capacity to generate strains with reduced polyhexanide susceptibility and cross-resistance with chlorhexidine and/or antibiotics currently used in clinic. Here we report the
in vitro
emergence of reduced susceptibility to polyhexanide by prolonged stepwise exposure to low concentrations in broth culture. Reduced susceptibility to polyhexanide was associated with genomic changes in the
mprF
and
purR
genes and with concomitant decreased susceptibility to daptomycin and other cell wall-active antibiotics. However, the
in vitro
emergence of reduced susceptibility to polyhexanide did not result in cross-resistance to chlorhexidine. During
in vivo
polyhexanide clinical decolonization treatment, neither reduced polyhexanide susceptibility nor chlorhexidine cross-resistance was observed. Together, these observations suggest that polyhexanide could be used safely for decolonization of carriers of chlorhexidine-resistant
S. aureus
strains; they also highlight the need for careful use of polyhexanide at low antiseptic concentrations.
Pharmacokinetics of Intravenous Finafloxacin in Healthy Volunteers
Authors: Taubert Max , Chiesa Joseph , Lückermann Mark , Fischer Carsten , Dalhoff Axel , Fuhr Uwe
Published: August 2017

Finafloxacin is a novel fluoroquinolone exhibiting enhanced activity under acidic conditions and a broad-spectrum antibacterial profile. The present study assessed the pharmacokinetic properties and the safety and tolerability of finafloxacin following intravenous infusions. In this mixed-parallel-group, crossover study, healthy male and female volunteers received single ascending doses (18 volunteers, 200 to 1,000 mg) or multiple ascending doses (40 volunteers, 600 to 1,000 mg) of finafloxacin or placebo. Plasma and urine samples were collected by a dense sampling scheme to determine the pharmacokinetics of finafloxacin using a noncompartmental approach. Standard safety and tolerability data were documented. Finafloxacin had a volume of distribution of 90 to 127 liters (range) at steady state and 446 to 550 liters at pseudoequilibrium, indicating the elimination of a large fraction before pseudoequilibrium was reached. Areas under the concentration-time curves and maximum plasma concentrations (geometric means) increased slightly more than proportionally (6.73 to 45.9 μg · h/ml and 2.56 to 20.2 μg/ml, respectively), the terminal elimination half-life increased (10.6 to 17.1 h), and the urinary recovery decreased (44.2% to 31.7%) with increasing finafloxacin doses (single doses of 200 to 1,000 mg). The pharmacokinetic profiles suggested multiphasic elimination by both glomerular filtration and saturable tubular secretion. The values of the parameters were similar for single and multiple administrations. The coefficient of variation for the between-subject variability of exposure ranged from 10% (≤600 mg) to 38% (>600 mg). Adverse events were mild and nonspecific, with no dependence of adverse events on dose or treatment (including placebo) being detected. Despite a relatively high interindividual variability at higher doses, the level of exposure following intravenous administration of finafloxacin appears to be predictable. Individual elimination processes should be evaluated in more detail. Finafloxacin exhibited a favorable safety and tolerability profile. (This study has been registered at ClinicalTrials.gov under registration no. NCT01910883.)
Impairment of Hematopoietic Precursor Cell Activation during the Granulopoietic Response to Bacteremia in Mice with Chronic-Plus-Binge Alcohol Administration
Authors: Shi Xin , Lin Yuan-Ping , Gao Bin , Zhang Ping
Published: August 2017

Alcohol abuse impairs immune defense. To study the effect of chronic-plus-binge alcohol exposure on the granulopoietic response, acute alcohol intoxication (intraperitoneal injection of 5 g alcohol/kg body weight) was introduced to mice chronically fed on the Lieber-DeCarli low-fat liquid alcohol diet for 5 weeks. Bacteremia was induced by intravenous injection of
Escherichia coli
. Bacteremia caused a remarkable increase in marrow lin
−
c-kit
+
Sca-1
+
cells. Activation of cell proliferation supported the increase in marrow lin
−
c-kit
+
Sca-1
+
cells. Alcohol administration inhibited this activation of lin
−
c-kit
+
Sca-1
+
cells. The bone marrow of pair-fed control mice receiving intraperitoneal saline stored a large number of mature granulocytes expressing a high level of Gr1 (Gr1
hi
cells). The proportion of Gr1
hi
cells and the total number of Gr1
+
cells were markedly reduced in the bone marrow, along with an increase in the ratio of Gr1
+
granulocytes in peripheral white blood cells following bacteremia.
E. coli
infection stimulated proliferation of granulopoietic precursor cells, resulting in a marked increase in the ratio of immature Gr1
lo
cells in the bone marrow. Alcohol administration itself triggered marrow release of Gr1
+
cells, resulting in reduction of the marrow granulocyte reserve with an elevation of granulocytes in the circulation. Alcohol also impaired activation of granulopoietic precursor proliferation following bacteremia. Alcohol disrupted lipopolysaccharide (LPS)-TLR4-ERK1/2-cyclin D1 signaling and inhibited upregulation of Sca-1 and C/EBPβ expression by lineage-negative marrow cells in response to bacteremia. These results indicate that chronic-plus-binge alcohol exposure inhibits the granulopoietic response by disrupting key cell signaling for hematopoietic precursor cell activation and commitment to granulocyte lineage development.
Opsin-Mediated Inhibition of Bacterioruberin Synthesis in Halophilic Archaea
Authors: Peck Ronald F. , Pleşa Alexandru M. , Graham Serena M. , Angelini David R. , Shaw Emily L.
Published: August 2017

Halophilic archaea often inhabit environments with limited oxygen, and many produce ion-pumping rhodopsin complexes that allow them to maintain electrochemical gradients when aerobic respiration is inhibited. Rhodopsins require a protein, an opsin, and an organic cofactor, retinal. We previously demonstrated that inHalobacterium salinarum, bacterioopsin (BO), when not bound by retinal, inhibits the production of bacterioruberin, a biochemical pathway that shares intermediates with retinal biosynthesis. In this work, we used heterologous expression in a related halophilic archaeon,Haloferax volcanii, to demonstrate that BO is sufficient to inhibit bacterioruberin synthesis catalyzed by theH. salinarumlycopene elongase (Lye) enzyme. This inhibition was observed both in liquid culture and in a novel colorimetric assay to quantify bacterioruberin abundance based on the colony color. Addition of retinal to convert BO to the bacteriorhodopsin complex resulted in a partial rescue of bacterioruberin production. To explore if this regulatory mechanism occurs in other organisms, we expressed a Lye homolog and an opsin fromHaloarcula vallismortisinH. volcanii.H. vallismortiscruxopsin-3 expression inhibited bacterioruberin synthesis catalyzed byH. vallismortisLye but had no effect when bacterioruberin synthesis was catalyzed byH. salinarumorH. volcaniiLye. Conversely,H. salinarumBO did not inhibitH. vallismortisLye activity. Together, our data suggest that opsin-mediated inhibition of Lye is potentially widespread and represents an elegant regulatory mechanism that allows organisms to efficiently utilize ion-pumping rhodopsins obtained through lateral gene transfer.

IMPORTANCEMany enzymes are complexes of proteins and nonprotein organic molecules called cofactors. To ensure efficient formation of functional complexes, organisms must regulate the production of proteins and cofactors. To study this regulation, we used bacteriorhodopsin from the archaeonHalobacterium salinarum. Bacteriorhodopsin consists of the bacterioopsin protein and a retinal cofactor. In this article, we further characterize a novel regulatory mechanism in which bacterioopsin promotes retinal production by inhibiting a reaction that consumes lycopene, a retinal precursor. By expressingH. salinarumgenes in a different organism,Haloferax volcanii, we demonstrated that bacterioopsin alone is sufficient for this inhibition. We also found that an opsin fromHaloarcula vallismortishas inhibitory activity, suggesting that this regulatory mechanism might be found in other organisms.
Reverse Genetics System Demonstrates that Rotavirus Nonstructural Protein NSP6 Is Not Essential for Viral Replication in Cell Culture
Authors: Komoto Satoshi , Kanai Yuta , Fukuda Saori , Kugita Masanori , Kawagishi Takahiro , Ito Naoto , Sugiyama Makoto , Matsuura Yoshiharu , Kobayashi Takeshi , Taniguchi Koki
Published: August 2017

The use of overlapping open reading frames (ORFs) to synthesize more than one unique protein from a single mRNA has been described for several viruses. Segment 11 of the rotavirus genome encodes two nonstructural proteins, NSP5 and NSP6. The NSP6 ORF is present in the vast majority of rotavirus strains, and therefore the NSP6 protein would be expected to have a function in viral replication. However, there is no direct evidence of its function or requirement in the viral replication cycle yet. Here, taking advantage of a recently established plasmid-only-based reverse genetics system that allows rescue of recombinant rotaviruses entirely from cloned cDNAs, we generated NSP6-deficient viruses to directly address its significance in the viral replication cycle. Viable recombinant NSP6-deficient viruses could be engineered. Single-step growth curves and plaque formation of the NSP6-deficient viruses confirmed that NSP6 expression is of limited significance for RVA replication in cell culture, although the NSP6 protein seemed to promote efficient virus growth.

IMPORTANCERotavirus is one of the most important pathogens of severe diarrhea in young children worldwide. The rotavirus genome, consisting of 11 segments of double-stranded RNA, encodes six structural proteins (VP1 to VP4, VP6, and VP7) and six nonstructural proteins (NSP1 to NSP6). Although specific functions have been ascribed to each of the 12 viral proteins, the role of NSP6 in the viral replication cycle remains unknown. In this study, we demonstrated that the NSP6 protein is not essential for viral replication in cell culture by using a recently developed plasmid-only-based reverse genetics system. This reverse genetics approach will be successfully applied to answer questions of great interest regarding the roles of rotaviral proteins in replication and pathogenicity, which can hardly be addressed by conventional approaches.
Coordinate Regulation of TET2 and EBNA2 Controls the DNA Methylation State of Latent Epstein-Barr Virus
Authors: Lu Fang , Wiedmer Andreas , Martin Kayla A. , Wickramasinghe Priyankara J. M. S. , Kossenkov Andrew V. , Lieberman Paul M.
Published: August 2017

Epstein-Barr virus (EBV) latency and its associated carcinogenesis are regulated by dynamic changes in DNA methylation of both virus and host genomes. We show here that the ten-eleven translocation 2 (TET2) gene, implicated in hydroxymethylation and active DNA demethylation, is a key regulator of EBV latency type DNA methylation patterning. EBV latency types are defined by DNA methylation patterns that restrict expression of viral latency genes. We show that TET2 mRNA and protein expression correlate with the highly demethylated EBV type III latency program permissive for expression of EBNA2, EBNA3s, and LMP transcripts. We show that short hairpin RNA (shRNA) depletion of TET2 results in a decrease in latency gene expression but can also trigger a switch to lytic gene expression. TET2 depletion results in the loss of hydroxymethylated cytosine and a corresponding increase in cytosine methylation at key regulatory regions on the viral and host genomes. This also corresponded to a loss of RBP-jκ binding and decreased histone H3K4 trimethylation at these sites. Furthermore, we show that the TET2 gene itself is regulated in a fashion similar to that of the EBV genome. Chromatin immunoprecipitation high-throughput sequencing (ChIP-seq) revealed that the TET2 gene contains EBNA2-dependent RBP-jκ and EBF1 binding sites and is subject to DNA methylation-associated transcriptional silencing similar to what is seen in EBV latency type III genomes. Finally, we provide evidence that TET2 colocalizes with EBNA2-EBF1-RBP-jκ binding sites and can interact with EBNA2 by coimmunoprecipitation. Taken together, these findings indicate that TET2 gene transcripts are regulated similarly to EBV type III latency genes and that TET2 protein is a cofactor of EBNA2 and coregulator of the EBV type III latency program and DNA methylation state.

IMPORTANCE
Epstein-Barr virus (EBV) latency and carcinogenesis involve the selective epigenetic modification of viral and cellular genes. Here, we show that TET2, a cellular tumor suppressor involved in active DNA demethylation, plays a central role in regulating the DNA methylation state during EBV latency. TET2 is coordinately regulated and functionally interacts with the viral oncogene EBNA2. TET2 and EBNA2 function cooperatively to demethylate genes important for EBV-driven B-cell growth transformation.
Palmitoylation Contributes to Membrane Curvature in Influenza A Virus Assembly and Hemagglutinin-Mediated Membrane Fusion
Authors: Chlanda Petr , Mekhedov Elena , Waters Hang , Sodt Alexander , Schwartz Cindi , Nair Vinod , Blank Paul S. , Zimmerberg Joshua
Published: August 2017

The highly conserved cytoplasmic tail of influenza virus glycoprotein hemagglutinin (HA) contains three cysteines, posttranslationally modified by covalently bound fatty acids. While viral HA acylation is crucial in virus replication, its physico-chemical role is unknown. We used virus-like particles (VLP) to study the effect of acylation on morphology, protein incorporation, lipid composition, and membrane fusion. Deacylation interrupted HA-M1 interactions since deacylated mutant HA failed to incorporate an M1 layer within spheroidal VLP, and filamentous particles incorporated increased numbers of neuraminidase (NA). While HA acylation did not influence VLP shape, lipid composition, or HA lateral spacing, acylation significantly affected envelope curvature. Compared to wild-type HA, deacylated HA is correlated with released particles with flat envelope curvature in the absence of the matrix (M1) protein layer. The spontaneous curvature of palmitate was calculated by molecular dynamic simulations and was found to be comparable to the curvature values derived from VLP size distributions. Cell-cell fusion assays show a strain-independent failure of fusion pore enlargement among H2 (A/Japan/305/57), H3 (A/Aichi/2/68), and H3 (A/Udorn/72) viruses. In contradistinction, acylation made no difference in the low-pH-dependent fusion of isolated VLPs to liposomes: fusion pores formed and expanded, as demonstrated by the presence of complete fusion products observed using cryo-electron tomography (cryo-ET). We propose that the primary mechanism of action of acylation is to control membrane curvature and to modify HA's interaction with M1 protein, while the stunting of fusion by deacylated HA acting in isolation may be balanced by other viral proteins which help lower the energetic barrier to pore expansion.

IMPORTANCEInfluenza A virus is an airborne pathogen causing seasonal epidemics and occasional pandemics. Hemagglutinin (HA), a glycoprotein abundant on the virion surface, is important in both influenza A virus assembly and entry. HA is modified by acylation whose removal abrogates viral replication. Here, we used cryo-electron tomography to obtain three-dimensional images to elucidate a role for HA acylation in VLP assembly. Our data indicate that HA acylation contributes to the capability of HA to bend membranes and to HA's interaction with the M1 scaffold protein during virus assembly. Furthermore, our data on VLP and, by hypothesis, virus suggests that HA acylation, while not critical to fusion pore formation, contributes to pore expansion in a target-dependent fashion.
Highly Pathogenic New World Arenavirus Infection Activates the Pattern Recognition Receptor Protein Kinase R without Attenuating Virus Replication in Human Cells
Authors: Huang Cheng , Kolokoltsova Olga A. , Mateer Elizabeth J. , Koma Takaaki , Paessler Slobodan
Published: August 2017

The arenavirus family consists of several highly pathogenic viruses, including the Old World (OW) arenavirus Lassa fever virus (LASV) and the New World (NW) Junin virus (JUNV) and Machupo virus (MACV). Host response to infection by these pathogenic arenaviruses is distinct in many aspects. JUNV and MACV infections readily induce an interferon (IFN) response in human cells, while LASV infection usually triggers an undetectable or weak IFN response. JUNV induces an IFN response through RIG-I, suggesting that the host non-self RNA sensor readily detects JUNV viral RNAs (vRNAs) during infection and activates IFN response. Double-stranded-RNA (dsRNA)-activated protein kinase R (PKR) is another host non-self RNA sensor classically known for its vRNA recognition activity. Here we report that infection with NW arenaviruses JUNV and MACV, but not OW LASV, activated PKR, concomitant with elevated phosphorylation of the translation initiation factor α subunit of eukaryotic initiation factor 2 (eIF2α). Host protein synthesis was substantially suppressed in MACV- and JUNV-infected cells but was only marginally reduced in LASV-infected cells. Despite the antiviral activity known for PKR against many other viruses, the replication of JUNV and MACV was not impaired but was slightly augmented in wild-type (wt) cells compared to that in PKR-deficient cells, suggesting that PKR or PKR activation did not negatively affect JUNV and MACV infection. Additionally, we found an enhanced IFN response in JUNV- or MACV-infected PKR-deficient cells, which was inversely correlated with virus replication.

IMPORTANCE
The detection of viral RNA by host non-self RNA sensors, including RIG-I and MDA5, is critical to the initiation of the innate immune response to RNA virus infection. Among pathogenic arenaviruses, the OW LASV usually does not elicit an interferon response. However, the NW arenaviruses JUNV and MACV readily trigger an IFN response in a RIG-I-dependent manner. Here, we demonstrate for the first time that pathogenic NW arenaviruses JUNV and MACV, but not the OW arenavirus LASV, activated the dsRNA-dependent PKR, another host non-self RNA sensor, during infection. Interestingly, the replication of JUNV and MACV was not restricted but was rather slightly augmented in the presence of PKR. Our data provide new evidence for a distinct interplay between host non-self RNA sensors and pathogenic arenaviruses, which also provides insights into the pathogenesis of arenaviruses and may facilitate the design of vaccines and treatments against arenavirus-caused diseases.
Hepatitis C Virus Core Protein Modulates Endoglin (CD105) Signaling Pathway for Liver Pathogenesis
Authors: Kwon Young-Chan , Sasaki Reina , Meyer Keith , Ray Ranjit
Published: August 2017

Endoglin is part of the TGF-β receptor complex and has a crucial role in fibrogenesis and angiogenesis. It is also an important protein for tumor growth, survival, and cancer cell metastasis. In a previous study, we have shown that hepatitis C virus (HCV) infection induces epithelial-mesenchymal transition (EMT) state and cancer stem-like cell (CSC) properties in human hepatocytes. Our array data suggested that endoglin (CD105) mRNA is significantly upregulated in HCV-associated CSCs. In this study, we have observed increased endoglin expression on the cell surface of an HCV core-expressing hepatocellular carcinoma (HepG2) cell line or immortalized human hepatocytes (IHH) and activation of its downstream signaling molecules. The status of phospho-SMAD1/5 and the expression of inhibitor of DNA binding protein 1 (ID1) were upregulated in HCV-infected cells or viral core gene-transfected cells. Additionally, we observed upregulation of endoglin/ID1 mRNA expression in chronic HCV patient liver biopsy samples. CSC generation by HCV core protein was dependent on the endoglin signaling pathway using activin receptor-like kinase 1 (ALK1) Fc blocking peptide and endoglin small interfering RNA (siRNA). Further, follow-up from
in vitro
analysis suggested that the antiapoptosis Bcl2 protein, proliferation-related cyclin D1 protein, and CSC-associated Hes1, Notch1, Nanog, and Sox2 proteins are enhanced during infection or ectopic expression of HCV core protein.

IMPORTANCE
Endoglin plays a crucial role in fibrogenesis and angiogenesis and is an important protein for tumor growth, survival, and cancer cell metastasis. Endoglin enhances ALK1-SMAD1/5 signaling in different cell types, leading to increased proliferation and migration responses. We have observed endoglin expression on the HCV core-expressing cell surface of human hepatocyte origin and activation of phospho-SMAD1/5 and ID1 downstream signaling molecules. ID1 protein plays a role in CSC properties, and we found that this pathway is important for antiapoptotic and cell proliferation signaling. Blocking of endoglin-ALK1-SMAD1/5 might be a good candidate for therapy for liver cancer stem cells together with liver cirrhosis.