bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical relevance of cyclooxygenase 2 and peroxisome proliferator‐activated receptor γ in eyelid sebaceous gland carcinoma
Authors: Jayaraj Perumal , Sen Seema , Bhattacharya Tanaya , Arora Juhi , Yadav Sameeksha , Chhoker Varsha , Kumar Abhishek , Dhanaraj Pakitapillil S , Yadavilli Kameshwar S. , Verma Mansi
Published: January 2016

Aims

Sebaceous gland carcinoma (SGC) is a malignancy associated with the pilosebaceous unit, and occurs at ocular or non‐ocular sites. Cyclooxygenases (COXs) are enzymes that are crucial for lipid metabolism. COX‐2 is overexpressed in various cancers, and its inhibition by non‐steroidal anti‐inflammatory drugs is known to reduce the risk of many cancers. Peroxisome proliferator‐activated receptor (PPAR)‐γ is a transcription factor involved in adipogenesis. PPAR‐γ is a potential therapeutic target for the treatment of malignant tumours, including colon carcinoma. The aim of this study was to explore the status of COX‐2 and PPAR‐γ as prognostic markers in human eyelid SGC.

Methods and results

The immunohistochemical expression of COX‐2 and PPAR‐γ was evaluated in 31 SGC cases. Cytoplasmic expression of COX‐2 was detected in 80% of the SGC cases, and nuclear expression of PPAR‐γ in 87%. There were significant correlations of PPAR‐γ expression with well‐differentiated SGC [19/21 (90%)] and of COX‐2 overexpression with reduced disease‐free survival (P = 0.0441, log rank analysis). COX‐2 expression [odds ratio (OR) 3.82, 95% confidence interval (CI) 1.02–14.33, P = 0.046] and lymph node metastasis (OR 0.17, 95% CI 0.04–0.65, P = 0.009) emerged as significant risk factors in the univariate analysis. However, COX‐2 expression did not emerge as a significant independent prognostic factor in multivariate analysis.

Conclusions

COX‐2 is a potential marker for identifying high‐risk SGC patients. Expression of PPAR‐γ in eyelid SGC cases reflects terminal sebaceous differentiation. Inhibitors of COX‐2 signalling and PPAR‐γ agonists are both prospective novel therapeutic targets in the management of eyelid SGC patients.
Positive selection and high sensitivity test for MYD88 mutations using locked nucleic acid
Authors: Albitar A. , Ma W. , DeDios I. , Estella J. , Agersborg S. , Albitar M.
Published: January 2016

Introduction

Detection of mutations in the myeloid differentiation primary response gene 88 (MYD88) has clinical implications on diagnosis and therapy, especially in patients with Waldenström's macroglobulinemia (WM) and IgM monoclonal gammopathy of unknown significance (IgM‐MGUS). We describe a method that provides greatly increased sensitivity for detecting minority mutations in MYD88.

Methods

We used a locked nucleic acid oligonucleotide to block amplification of wild‐type DNA during polymerase chain reaction (PCR). Sanger sequencing of amplified DNA was used for detecting mutations in MYD88 gene. This approach was used to test samples from patients with WM and IgM‐MGUS.

Results

When compared to traditional PCR followed by Sanger sequencing, our methodology was significantly more sensitive (one mutant allele in a background of 200 wild‐type alleles). Using sequencing allowed us to visualize the PCR product, giving advantages over other methodologies such as allele‐specific PCR. Based on analyzing 36 randomly selected, MYD88 mutated, clinically tested samples, we demonstrate that traditional PCR failed to detect MYD88 mutations in 64% of the samples that were clearly positive by wild‐type blocking PCR.

Conclusion

The new methodology is essential for attaining accurate results in clinical testing.
Combined predictive value of the expanded donor criteria for long‐term graft survival of kidneys from donors after cardiac death: A single‐center experience over three decades
Authors: Kusaka Mamoru , Kubota Yusuke , Sasaki Hitomi , Fukami Naohiko , Fujita Tamio , Hirose Yuichi , Takahashi Hiroshi , Kenmochi Takashi , Shiroki Ryoichi , Hoshinaga Kiyotaka
Published: January 2016

Objectives

Kidneys procured from the deceased hold great potential for expanding the donor pool. The aims of the present study were to investigate the post‐transplant outcomes of renal allografts recovered from donors after cardiac death, to identify risk factors affecting the renal prognosis and to compare the long‐term survival from donors after cardiac death according to the number of risk factors shown by expanded criteria donors.

Methods

A total of 443 grafts recovered using an in situ regional cooling technique from 1983 to 2011 were assessed. To assess the combined predictive value of the significant expanded criteria donor risk criteria, the patients were divided into three groups: those with no expanded criteria donor risk factors (no risk), one expanded criteria donor risk factor (single‐risk) and two or more expanded criteria donor risk factors (multiple‐risk).

Results

Among the donor factors, age ≥50 years, hypertension, maximum serum creatinine level ≥1.5 mg/dL and a warm ischemia time ≥30 min were identified as independent predictors of long‐term graft failure on multivariate analysis. Regarding the expanded criteria donors criteria for marginal donors, cerebrovascular disease, hypertension and maximum serum creatinine level ≥1.5 mg/dL were identified as significant predictors on univariate analysis. The single‐ and multiple‐risk groups showed 2.01‐ and 2.40‐fold higher risks of graft loss, respectively.

Conclusions

Renal grafts recovered from donors after cardiac death donors have a good renal function with an excellent long‐term graft survival. However, an increased number of expanded criteria donors risk factors increase the risk of graft loss.
The curious case of the 1960 Nobel Prize to Burnet and Medawar
Authors: Silverstein Arthur M.
Published: January 2016

The 1960 Nobel Prize was awarded to Macfarlane Burnet and Peter Medawar for immunological tolerance. The Nobel Archives reveal that the two were never nominated together by anyone; Burnet had repeatedly been nominated for his virology studies, and the Medawar group (including Rupert Billingham and Leslie Brent) had been nominated independently for their transplantation work. A review of the 1950s literature suggests that tolerance had not yet, by 1960, reached the level of acceptance and acclaim in the immunological community to appear to justify the award. Burnet probably should have received the Prize for his virus work, and perhaps also for his Clonal Selection Theory, whereas Billingham and Brent should have shared in a Prize with Medawar for transplantation. If a Prize were to be given for tolerance, most agree that Ray Owen should have shared in it, for his work on cattle chimerism. It is suggested that the 1960 Nobel Prize to Burnet and Medawar for immunological tolerance may have been given for the wrong reasons and to the wrong associates.
Inter‐annual variability and long‐term trends in breeding success in a declining population of migratory swans
Authors: Wood Kevin A. , Newth Julia L. , Hilton Geoff M. , Nolet Bart A. , Rees Eileen C.
Published: January 2016

Population declines among migratory Arctic‐breeding birds are a growing concern for conservationists. To inform the conservation of these declining populations, we need to understand how demographic rates such as breeding success are influenced by combinations of extrinsic and intrinsic factors. In this study we examined inter‐annual variation and long‐term trends in two aspects of the breeding success of a migratory herbivore, the Bewick's swanCygnus columbianus bewickii, which is currently undergoing a population decline: 1) the percentage of young within the wintering population and 2) mean brood size. We used an information‐theoretic approach to test how these two measures of productivity were influenced over a 26 yr period by 12 potential explanatory variables, encompassing both environmental (e.g. temperature) and intrinsic (e.g. pair‐bond duration) factors. Swan productivity exhibited sensitivity to both types of explanatory variable. Fewer young were observed on the wintering grounds in years in which the breeding period (May to September) was colder and predator (Arctic fox) abundance was higher. The percentage of young within the wintering population also showed negative density‐dependence. Inter‐annual variance in mean swan brood size was best explained by a model comprised of the negative degree days during the swan breeding period, mean pair‐bond duration of all paired swans (i.e. mean pair duration), and an interaction between these two variables. In particular, mean pair duration had a strong positive effect on mean brood size. However, we found no long‐term directional trend in either measure of breeding success, despite the recent decline in the NW European population. Our results highlight that inter‐annual variability in breeding success is sensitive to the combined effects of both intrinsic and extrinsic factors.
Cost of reproduction: a comparison of survival rates of breeding and non‐breeding male ortolan buntings
Authors: Dale Svein
Published: January 2016

The cost of reproduction is expected to influence survival or future reproduction. Most previous studies have assessed cost of reproduction in relation to natural and experimental variation in number of offspring produced. The ortolan bunting Emberiza hortulana is a passerine bird species with biparental care, and the Norwegian population of the species has an extraordinarily skewed sex ratio with only about half of the males attracting a female, and therefore provides a rare opportunity to compare survival of males that have paired and bred with that of non‐breeders (unpaired males), which have not paid a cost of reproduction. Results showed that survival rates of paired (65.0%) and unpaired (64.2%) males did not differ. However, when comparisons were restricted to paired males that definitely had nestlings, their survival rate (76.8%) was significantly higher than that of unpaired males, and the same was the case when comparisons were further restricted to paired males that had offspring recruiting to the population the next year (76.8% survived). Males breeding successfully are likely to be a biased subset of high quality males. In analyses of a subset of males that had bred successfully when young, there was no difference in survival of paired and unpaired individuals when these males were older. In conclusion, breeding male ortolan buntings did not appear to pay a cost of reproduction in terms of reduced survival to the next year compared to non‐breeding males. These results may be explained by non‐breeding males also incurring extra costs during the breeding season, and that costs of reproduction are not shared equally among sexes in the ortolan bunting and other bird species with biparental care.
Shape Complexity and Process Energy Consumption in Electron Beam Melting: A Case of Something for Nothing in Additive Manufacturing?
Authors: Baumers Martin , Tuck Chris , Wildman Ricky , Ashcroft Ian , Hague Richard
Published: January 2016

Additive manufacturing (AM) technology is capable of building up component geometry in a layer‐by‐layer process, entirely without tools, molds, or dies. One advantage of the approach is that it is capable of efficiently creating complex product geometry. Using experimental data collected during the manufacture of a titanium test part on a variant of AM technology, electron beam melting (EBM), this research studies the effect of a variation in product shape complexity on process energy consumption. This is done by applying a computationally quantifiable convexity‐based characteristic associated with shape complexity to the test part and correlating this quantity with per‐layer process energy consumption on the EBM system. Only a weak correlation is found between the complexity metric and energy consumption (ρ = .35), suggesting that process energy consumption is indeed not driven by shape complexity. This result is discussed in the context of the energy consumption of computer‐controlled machining technology, which forms an important substitute to EBM. This article further discusses the impact of available additional shape complexity at the manufacturing process level on the incentives toward minimization of energy inputs, additional benefits arising later within the product's life cycle, and its implications for value creation possibilities.
Powerful Unit Root Tests Free of Nuisance Parameters
Authors: Hosseinkouchack Mehdi , Hassler Uwe
Published: January 2016

We propose a variance ratio‐type unit root test where the nuisance parameter cancels asymptotically under both the null of a unit root and a local‐to‐unity alternative. Critical values and asymptotic power curves can be computed using standard numerical techniques. Our test exhibits higher power compared with tests that share the virtue of being free of tuning parameters. In fact, the local asymptotic power curves of our procedure get close to the power functions of the point optimal test, where the latter suffers from the drawback of having to correct for a nuisance parameter consistently.
Bats as prey of diurnal birds: a global perspective
Authors: Mikula Peter , Morelli Federico , Lučan Radek K. , Jones Darryl N. , Tryjanowski Piotr
Published: January 2016

Predation is an important selective pressure that can influence prey species in numerous ways. Predator–prey relationships are, however, poorly understood in taxa not typically associated with these interactions; this is especially the case when bats (Chiroptera) are the prey.

The main aim here is to review and synthesise global information on the predation of bats by birds of prey (Accipitriformes and Falconiformes) and other diurnal bird groups.

We compiled data on incidences of predation of bats by diurnal birds, through an extensive multilingual study of bibliographic and Internet‐based sources. Scientific papers were found mainly via the Thomson Reuters (Web of Science and Zoological Record) and Scopus databases, Google Scholar, and Google Books. Additional data were found through Internet searches of trip reports, images and videos carried by Google, Google Images, Flickr, and YouTube.

In total, more than 1500 cases of bats being attacked by diurnal predatory birds were obtained. Reports were documented from every continent (exceptAntarctica) and from 109 countries, and were thus distributed globally between 70°Nand 43°S. Overall, we found evidence for predation of bats by 143 species of diurnal raptors (Accipitriformes 107 spp. and Falconiformes 36 spp.) and by 94 non‐raptor bird species from 28 families. At least 124 and 50 bat species were taken as prey by raptors and by other diurnal bird species, respectively.

Attacks on bats by diurnal raptors were found to be distributed globally and were present in the majority of extant raptor lineages. Attacks on bats by other diurnal birds were also occasionally recorded. Furthermore, the majority of extant bat families featured as prey. These results strongly suggest that predation by birds may act as a major factor affecting the scarcity of daytime activity in bats and as a driver in the evolution of bat nocturnality.
Forest trees filter chronic wind‐signals to acclimate to high winds
Authors: Bonnesoeur Vivien , Constant Thiéry , Moulia Bruno , Fournier Meriem
Published: January 2016

Controlled experiments have shown that trees acclimate thigmomorphogenetically to wind‐loads by sensing their deformation (strain). However, the strain regime in nature is exposed to a full spectrum of winds. We hypothesized that trees avoid overreacting by responding only to winds which bring information on local climate and/or wind exposure. Additionally, competition for light dependent on tree social status also likely affects thigmomorphogenesis.

We monitored and manipulated quantitatively the strain regimes of 15 pairs of beech (Fagus sylvatica) trees of contrasting social status in an acclimated stand, and quantified the effects of these regimes on the radial growth over a vegetative season.

Trees exposed to artificial bending, the intensity of which corresponds to the strongest wind‐induced strains, enhanced their secondary growth by at least 80%. Surprisingly, this reaction was even greater – relatively – for suppressed trees than for dominant ones.

Acclimated trees did not sense the different types of wind events in the same way. Daily wind speed peaks due to thermal winds were filtered out. Thigmomorphogenesis was therefore driven by intense storms. Thigmomorphogenesis is also likely to be involved in determining social status.
Effect of gender and Frankfort mandibular plane angle on orthodontic space closure: a randomized controlled trial
Authors: Ireland A. J. , Songra G. , Clover M. , Atack N. E. , Sherriff M. , Sandy J. R.
Published: January 2016

Structured Abstract

Objectives

To determine the effect of gender and Frankfort mandibular plane angle (FMPA) on extraction space closure.

Setting and Sample Population

A single district general hospital. The sample population were 11‐ to 18‐year‐olds undergoing upper and lower fixed appliance therapy following the loss of a premolar in each quadrant.

Methods

A total of 100 patients undergoing upper and lower fixed appliance therapy following the loss of four premolars were randomized with stratification on two age ranges (11–14 years and 15–18 years) and three FMPAs (high, medium and low). Allocation was to one of three treatment groups: conventional, active or passive self‐ligating brackets, with an allocation ratio of 1:2:2. All subjects were treated using the same archwire sequence and space closing mechanics. Space closure was measured on models taken every 12 weeks throughout treatment. All measurements were taken by one operator, blinded to bracket type.

Results

A total of 98 patients were followed to completion. Data were analysed using linear mixed models and demonstrated no statistically significant difference between bracket types with respect to space closure. Therefore, the data were pooled to determine the effect of gender and FMPA on space closure. At all stages of space closure, there was a significant effect of gender (results are presented as effect size, lower and upper 95% confidence intervals and probability), that is passive [1.064, 0.521, 1.607, 0.001], active [0.825, 0.312, 1.339, 0.002] and total space closure [1.029, 0.527, 1.531, 0.001]. There was no statistically significant effect of FMPA on space closure.

Conclusions

Space closure during fixed appliance therapy is affected by gender but is unaffected by FMPA.
A Rare Case of Atypical Myxoid Cellular Neurothekeoma in a 6‐Year‐Old Girl
Authors: Han Tae Young , Han Byeol , Lee Young Chae , Lee June Hyunkyung , Son Sook‐Ja
Published: January 2016

Neurothekeoma (nerve sheath myxoma)is a benign tumor of probable nerve sheath origin. The atypical cellular variant of this tumor, showing a peculiar histologic pattern, has been very rarely reported in the literature. The atypical variant of cellular neurothekeoma is characterized by features such as large size, deep penetration extending into skeletal muscle and/or subcutaneous fat, diffuse infiltration borders, vascular invasion, high mitotic rate and marked cytologic pleomorphism. We describe a rare form of atypical myxoid cellular neurothekeoma in a 6‐year‐old girl.
Environmental Harm and “the Good Farmer”: Conceptualizing Discourses of Environmental Sustainability in the Beef Industry
Authors: Kessler Anna , Parkins John R. , Huddart Kennedy Emily
Published: January 2016

Maintaining sustainability discourses in the face of evidence to the contrary is a topic of considerable interest in sociology. We approach this topic with a focus on the beef industry in Alberta, Canada. By studying the discourses of cow and calf producers this article addresses the following questions: (1) What are the discourses that producers draw on to support their self‐perceptions as stewards of the land, (2) how are these discourses used by producers to negotiate and reconcile their involvement in a system that contributes to environmental degradation, and (3) what are key elements to interpreting these discourses of sustainability? Methods include semistructured interviews with attention to the potential of genomics for enhanced cattle breeding to ameliorate harmful methane emissions. Our findings indicate that producers draw on narratives of balance between economic and environmental concerns, focus on epistemic nearness, and fragment their understanding of the beef industry to maintain discourses of sustainability. These findings offer insights into the impacts that embodied, material forms of knowledge have on farmers’ perceptions of the land, and demonstrate that these narratives and ways of knowing predicate farmers’ understandings of sustainable development.
Twelve‐point scale grading system of scanning electron microscopic examination to investigate subtle changes in damaged hair surface
Authors: Lee S. Y. , Choi A. R. , Baek J. H. , Kim H. O. , Shin M. K. , Koh J. S.
Published: January 2016

Background

To assess the hair surface condition, scanning electron microscope (SEM) is commonly used and it remains an indispensable hair morphology characterization technique. Yet, the technique is criticized for having subjective viewpoints and limitations in distinguishing the appearance of cuticle layers.

Objectives

The aim of this study is to establish an objective classification system and also to subdivide by detailed description of damaged cuticle layers.

Methods

Hair samples were collected from female subjects (n = 500) who participated in hair efficacy study and Asian hair bunches (n = 180) that were previously collected. Damage to hair was initiated by chemical, heat stress and ultraviolet irradiation. We suggested the grading criterion on a 12‐point scale and compared with a wide range grading system on a 5‐point scale. We evaluated other hair surface‐related parameters such as hair luster‐ring and combing load to verify the validity and efficacy of our new grading system.

Results

The grading criterion on our 12‐point scale revealed an improved discrimination compared to the wide range grading system. Hair surface‐related parameters were significantly improved after hair care product, and these tendencies were likely to be determined to be similarly improved using the 12‐point scale grading system.

Conclusion

The 12‐point scale classification system was demonstrated to be a more precise standardization and appropriate evaluation method to investigate the subtle distinction of the hair shaft after hair care product application.
Component Mode Synthesis Order-Reduction for Dynamic Analysis of Structure Modeled With NURBS Finite Element
Authors: Zhou K. , Liang G. , Tang J.
Published: January 2016

Nonuniform rational B-splines (NURBS) finite element has advantages in analyzing the structure with curved surface geometry. In this research, we develop a component mode synthesis (CMS) based order-reduction technique which can be applied to large-scale NURBS finite element dynamic analysis. In particular, we establish a new substructure division scheme. The underlying idea is to optimally construct interface between adjacent substructures that can maximize the geometry consistency between the original structure and the divided substructures and at the meantime facilitate the compatibility conditions needed in mode synthesis. Case studies are carried out to validate the performance of the order-reduction formulation.
A Preliminary Study on Hybrid Use of Thermal Spray Coating and Ultrasonic Nanocrystalline Surface Modification Technique on the Tribological Properties of Yttria-Stabilized Zirconia Coating
Authors: Amanov Auezhan , Pyun Young-Sik
Published: January 2016

An ultrasonic nanocrystal surface modification (UNSM) technique was applied to a thermally sprayed yttria-stabilized zirconia (YSZ) ceramic coating deposited onto a hot tool steel substrate to improve the mechanical and tribological properties. The friction test results showed that the UNSM-treated coating had a smoother surface, a lower friction, and a higher resistance to wear compared to that of the as-sprayed coating. It was also demonstrated that the UNSM technique improved the adhesion behavior of the coating by about 24%. Hence, it was found that a hybrid use of thermal spray coating (TSC) and UNSM technique is a meaningful way to bring together synergy effect of two emerging surface technologies in terms of tribology.
On motion in a resisting medium: A historical perspective
Authors: Hackborn William W.
Published: January 2016

This paper examines, compares, and contrasts ideas about motion, especially the motion of a body in a resisting medium, proposed by Galileo, Newton, and Tartaglia, the author of the first text on exterior ballistics, within the context of the Aristotelian philosophy prevalent when these scholars developed their ideas. This historical perspective offers insights on the emergence of a scientific paradigm for motion, particularly with respect to the challenge of incorporating into this paradigm the role played by the medium.
Delayed-choice quantum eraser for the undergraduate laboratory
Authors: Ashby James M. , Schwarz Peter D. , Schlosshauer Maximilian
Published: January 2016

In a delayed-choice quantum eraser, interference fringes are obtained by erasing which-way information after the interfering particle has already been irreversibly detected. Following an introductory review of delayed-choice experiments and quantum erasure, we describe the experimental realization of an optical delayed-choice quantum eraser, suitable for advanced undergraduates, based on polarization-entangled pairs of single photons. In our experiment, the delay of the erasure is implemented using two different setups. The first setup employs an arrangement of mirrors to increase the optical path length of the photons carrying which-way information. In the second setup, we use fiber-optic cables to elongate the path of these photons after their passage through the polarization analyzer but prior to their arrival at the detector. We compare our results to data obtained in the absence of a delay and find excellent agreement. This shows that the timing of the erasure is irrelevant, as also predicted by quantum mechanics. The experiment can serve as a valuable pedagogical tool for conveying the fundamentals of quantum mechanics.
Temporal weighting of loudness: Comparison between two different psychophysical tasks
Authors: Ponsot Emmanuel , Susini Patrick , Oberfeld Daniel
Published: January 2016

Psychophysical studies on loudness have so far examined the temporal weighting of loudness solely in level-discrimination tasks. Typically, listeners were asked to discriminate hundreds of level-fluctuating sounds regarding their global loudness. Temporal weights, i.e., the importance of each temporal portion of the stimuli for the loudness judgment, were then estimated from listeners' responses. Consistent non-uniform “u-shaped” temporal weighting patterns were observed, with greater weights assigned to the first and the last temporal portions of the stimuli, revealing significant primacy and recency effects, respectively. In this study, the question was addressed whether the same weighting pattern could be found in a traditional loudness estimation task. Temporal loudness weights were compared between a level-discrimination (LD) task and an absolute magnitude estimation (AME) task. Stimuli were 3-s broadband noises consisting of 250-ms segments randomly varying in level. Listeners were asked to evaluate the global loudness of the stimuli by classifying them as “loud” or “soft” (LD), or by assigning a number representing their loudness (AME). Results showed non-uniform temporal weighting in both tasks, but also significant differences between the two tasks. An explanation based on the difference in complexity between the evaluation processes underlying each task is proposed.
Debate sharpens over U.K. threat to leave Europe
Authors: Rabesandratana Tania , Stokstad Erik
Published: January 2016

Many researchers worry about a loss of funds and influence, but some say the fears are overblown.
Number 9
Authors: Hand Eric
Published: January 2016

A new giant planet, still unseen, appears to be shaping the orbits of objects beyond Neptune.
Oxytocin-dependent consolation behavior in rodents
Authors: Burkett J. P. , Andari E. , Johnson Z. V. , Curry D. C. , de Waal F. B. M. , Young L. J.
Published: January 2016

Let me comfort you

Consolation behavior promotes stress reduction of one by another. We know that consolation occurs in humans and apes. Burkett
et al.
observed that within a pair of monogamous prairie voles, an unstressed partner increased its grooming of a stressed partner. Furthermore, the unstressed partner matched the stressed partner in its stress hormone response. Thus, consolation may be more common than assumed in animals, and prairie voles may prove a useful model for understanding the physical and neural mechanisms underlying consolation behavior.

Science
, this issue p.
375
Cyclic programmed cell death stimulates hormone signaling and root development in
Arabidopsis
Authors: Xuan Wei , Band Leah R. , Kumpf Robert P. , Van Damme Daniël , Parizot Boris , De Rop Gieljan , Opdenacker Davy , Möller Barbara K. , Skorzinski Noemi , Njo Maria F. , De Rybel Bert , Audenaert Dominique , Nowack Moritz K. , Vanneste Steffen , Beeckman Tom
Published: January 2016

Cell death establishes a site for development

As plant roots grow through the soil, lateral roots emerge to reach more resources. Xuan
et al.
now show that programmed cell death sets the course for lateral root development. Cells in a specialized region of the root cap periodically die off as a group, defining a location at which a lateral root will later develop.

Science
, this issue p.
384
The beauty of botanicals
The Cabaret of Plants
Richard Mabey
Norton, 2016. 384 pp.
Authors: Curry Helen Anne
Published: January 2016

A naturalist takes a round-the-world romp through the plants that have helped shape human history
Pneumococcal Colonization Rates in Patients Admitted to a United Kingdom Hospital with Lower Respiratory Tract Infection: a Prospective Case-Control Study
Authors: Collins Andrea M. , Johnstone Catherine M. K. , Gritzfeld Jenna F. , Banyard Antonia , Hancock Carole A. , Wright Angela D. , Macfarlane Laura , Ferreira Daniela M. , Gordon Stephen B.
Published: January 2016

Current diagnostic tests are ineffective for identifying the etiological pathogen in hospitalized adults with lower respiratory tract infections (LRTIs). The association of pneumococcal colonization with disease has been suggested as a means to increase the diagnostic precision. We compared the pneumococcal colonization rates and the densities of nasal pneumococcal colonization by (i) classical culture and (ii) quantitative real-time PCR (qPCR) targeting
lytA
in patients with LRTIs admitted to a hospital in the United Kingdom and control patients. A total of 826 patients were screened for inclusion in this prospective case-control study. Of these, 38 patients were recruited, 19 with confirmed LRTIs and 19 controls with other diagnoses. Nasal wash (NW) samples were collected at the time of recruitment. Pneumococcal colonization was detected in 1 patient with LRTI and 3 controls (
P
= 0.6) by classical culture. By qPCR, pneumococcal colonization was detected in 10 LRTI patients and 8 controls (
P
= 0.5). Antibiotic usage prior to sampling was significantly higher in the LRTI group than in the control group (19 versus 3;
P
< 0.001). With a clinically relevant cutoff of >8,000 copies/ml on qPCR, pneumococcal colonization was found in 3 LRTI patients and 4 controls (
P
> 0.05). We conclude that neither the prevalence nor the density of nasal pneumococcal colonization (by culture and qPCR) can be used as a method of microbiological diagnosis in hospitalized adults with LRTI in the United Kingdom. A community-based study recruiting patients prior to antibiotic therapy may be a useful future step.
Influenza Virus and Chromatin: Role of the CHD1 Chromatin Remodeler in the Virus Life Cycle
Authors: Marcos-Villar Laura , Pazo Alejandra , Nieto Amelia
Published: January 2016

Influenza A virus requires ongoing cellular transcription to carry out the cap-snatching process. Chromatin remodelers modify chromatin structure to produce an active or inactive conformation, which enables or prevents the recruitment of transcriptional complexes to specific genes; viral transcription thus depends on chromatin dynamics. Influenza virus polymerase associates with chromatin components of the infected cell, such as RNA polymerase II (RNAP II) or the CHD6 chromatin remodeler. Here we show that another CHD family member, CHD1 protein, also interacts with the influenza virus polymerase complex. CHD1 recognizes the H3K4me3 (histone 3 with a trimethyl group in lysine 4) histone modification, a hallmark of active chromatin. Downregulation of CHD1 causes a reduction in viral polymerase activity, viral RNA transcription, and the production of infectious particles. Despite the dependence of influenza virus on cellular transcription, RNAP II is degraded when viral transcription is complete, and recombinant viruses unable to degrade RNAP II show decreased pathogenicity in the murine model. We describe the CHD1–RNAP II association, as well as the parallel degradation of both proteins during infection with viruses showing full or reduced induction of degradation. The H3K4me3 histone mark also decreased during influenza virus infection, whereas a histone mark of inactive chromatin, H3K27me3, remained unchanged. Our results indicate that CHD1 is a positive regulator of influenza virus multiplication and suggest a role for chromatin remodeling in the control of the influenza virus life cycle.

IMPORTANCE
Although influenza virus is not integrated into the genome of the infected cell, it needs continuous cellular transcription to synthesize viral mRNA. This mechanism implies functional association with host genome expression and thus depends on chromatin dynamics. Influenza virus polymerase associates with transcription-related factors, such as RNA polymerase II, and with chromatin remodelers, such as CHD6. We identified the association of viral polymerase with another chromatin remodeler, the CHD1 protein, which positively modulated viral polymerase activity, viral RNA transcription, and virus multiplication. Once viral transcription is complete, RNAP II is degraded in infected cells, probably as a virus-induced mechanism to reduce the antiviral response. CHD1 associated with RNAP II and paralleled its degradation during infection with viruses that induce full or reduced degradation. These findings suggest that RNAP II degradation and CHD1 degradation cooperate to reduce the antiviral response.
An Evolutionary View of the Arms Race between Protein Kinase R and Large DNA Viruses
Authors: Carpentier Kathryn S. , Geballe Adam P.
Published: January 2016

To establish productive infections, viruses must counteract numerous cellular defenses that are poised to recognize viruses as nonself and to activate antiviral pathways. The opposing goals of host and viral factors lead to evolutionary arms races that can be illuminated by evolutionary and computational methods and tested in experimental models. Here we illustrate how this perspective has been contributing to our understanding of the interactions of the protein kinase R pathway with large DNA viruses.
Role of Viral RNA and Co-opted Cellular ESCRT-I and ESCRT-III Factors in Formation of Tombusvirus Spherules Harboring the Tombusvirus Replicase
Authors: Kovalev Nikolay , de Castro Martín Isabel Fernández , Pogany Judit , Barajas Daniel , Pathak Kunj , Risco Cristina , Nagy Peter D.
Published: January 2016

Plus-stranded RNA viruses induce membrane deformations in infected cells in order to build viral replication complexes (VRCs).
Tomato bushy stunt virus
(TBSV) co-opts cellular ESCRT (endosomal sorting complexes required for transport) proteins to induce the formation of vesicle (spherule)-like structures in the peroxisomal membrane with tight openings toward the cytosol. In this study, using a yeast (
Saccharomyces cerevisiae
)
vps23
Δ
bro1
Δ double-deletion mutant, we showed that the Vps23p ESCRT-I protein (Tsg101 in mammals) and Bro1p (ALIX) ESCRT-associated protein, both of which bind to the viral p33 replication protein, play partially complementary roles in TBSV replication in cells and in cell extracts. Dual expression of dominant-negative versions of
Arabidopsis
homologs of Vps23p and Bro1p inhibited tombusvirus replication to greater extent than individual expression in
Nicotiana benthamiana
leaves. We also demonstrated the critical role of Snf7p (CHMP4), Vps20p, and Vps24p ESCRT-III proteins in tombusvirus replication in yeast and
in vitro
. Electron microscopic imaging of
vps23
Δ yeast revealed the lack of tombusvirus-induced spherule-like structures, while crescent-like structures are formed in ESCRT-III deletion yeasts replicating TBSV RNA. In addition, we also showed that the length of the viral RNA affects the sizes of spherules formed in
N. benthamiana
cells. The 4.8-kb genomic RNA is needed for the formation of spherules 66 nm in diameter, while spherules formed during the replication of the ∼600-nucleotide (nt)-long defective interfering RNA in the presence of p33 and p92 replication proteins are 42 nm. We propose that the viral RNA serves as a “measuring string” during VRC assembly and spherule formation.

IMPORTANCE
Plant positive-strand RNA viruses, similarly to animal positive-strand RNA viruses, replicate in membrane-bound viral replicase complexes in the cytoplasm of infected cells. Identification of cellular and viral factors affecting the formation of the membrane-bound viral replication complex is a major frontier in current virology research. In this study, we dissected the functions of co-opted cellular ESCRT-I (endosomal sorting complexes required for transport I) and ESCRT-III proteins and the viral RNA in tombusvirus replicase complex formation using
in vitro
, yeast-based, and plant-based approaches. Electron microscopic imaging revealed the lack of tombusvirus-induced spherule-like structures in ESCRT-I or ESCRT-III deletion yeasts replicating TBSV RNA, demonstrating the requirement for these co-opted cellular factors in tombusvirus replicase formation. The work could be of broad interest in virology and beyond.
Hepatocyte Factor JMJD5 Regulates Hepatitis B Virus Replication through Interaction with HBx
Authors: Kouwaki Takahisa , Okamoto Toru , Ito Ayano , Sugiyama Yukari , Yamashita Kazuo , Suzuki Tatsuya , Kusakabe Shinji , Hirano Junki , Fukuhara Takasuke , Yamashita Atsuya , Saito Kazunobu , Okuzaki Daisuke , Watashi Koichi , Sugiyama Masaya , Yoshio Sachiyo , Standley Daron M. , Kanto Tatsuya , Mizokami Masashi , Moriishi Kohji , Matsuura Yoshiharu
Published: January 2016

Hepatitis B virus (HBV) is a causative agent for chronic liver diseases such as hepatitis, cirrhosis, and hepatocellular carcinoma (HCC). HBx protein encoded by the HBV genome plays crucial roles not only in pathogenesis but also in replication of HBV. Although HBx has been shown to bind to a number of host proteins, the molecular mechanisms by which HBx regulates HBV replication are largely unknown. In this study, we identified jumonji C-domain-containing 5 (JMJD5) as a novel binding partner of HBx interacting in the cytoplasm. DNA microarray analysis revealed that JMJD5-knockout (JMJD5KO) Huh7 cells exhibited a significant reduction in the expression of transcriptional factors involved in hepatocyte differentiation, such as HNF4A, CEBPA, and FOXA3. We found that hydroxylase activity of JMJD5 participates in the regulation of these transcriptional factors. Moreover, JMJD5KO Huh7 cells exhibited a severe reduction in HBV replication, and complementation of HBx expression failed to rescue replication of a mutant HBV deficient in HBx, suggesting that JMJD5 participates in HBV replication through an interaction with HBx. We also found that replacing Gly
135
with Glu in JMJD5 abrogates binding with HBx and replication of HBV. Moreover, the hydroxylase activity of JMJD5 was crucial for HBV replication. Collectively, these results suggest that direct interaction of JMJD5 with HBx facilitates HBV replication through the hydroxylase activity of JMJD5.

IMPORTANCE
HBx protein encoded by hepatitis B virus (HBV) plays important roles in pathogenesis and replication of HBV. We identified jumonji C-domain-containing 5 (JMJD5) as a novel binding partner to HBx. JMJD5 was shown to regulate several transcriptional factors to maintain hepatocyte function. Although HBx had been shown to support HBV replication, deficiency of JMJD5 abolished contribution of HBx in HBV replication, suggesting that HBx-mediated HBV replication is largely dependent on JMJD5. We showed that hydroxylase activity of JMJD5 in the C terminus region is crucial for expression of HNF4A and replication of HBV. Furthermore, a mutant JMJD5 with Gly
135
replaced by Glu failed to interact with HBx and to rescue the replication of HBV in JMJD5-knockout cells. Taken together, our data suggest that interaction of JMJD5 with HBx facilitates HBV replication through the hydroxylase activity of JMJD5.
During Infection, Theiler's Virions Are Cleaved by Caspases and Disassembled into Pentamers
Authors: Arslan Sevim Yildiz , Son Kyung-No , Lipton Howard L.
Published: January 2016

Infected macrophages in spinal cords of mice persistently infected with Theiler's murine encephalomyelitis virus (TMEV) undergo apoptosis, resulting in restricted virus yields, as do infected macrophages in culture. Apoptosis of murine macrophages in culture occurs via the intrinsic pathway later in infection (>10 h postinfection [p.i.]) after maximal virus titers (150 to 200 PFU/cell) have been reached, with loss of most infectious virus (<5 PFU/cell) by 20 to 24 h p.i. Here, we show that BeAn virus RNA replication, translation, polyprotein processing into final protein products, and assembly of protomers and pentamers in infected M1-D macrophages did not differ from those processes in TMEV-infected BHK-21 cells, which undergo necroptosis. However, the initial difference from BHK-21 cell infection was seen at 10 to 12 h p.i., where virions from the 160S peak in sucrose gradients had incompletely processed VP0 (compared to that in infected BHK-21 cells). Thereafter, there was a gradual loss of the 160S virion peak in sucrose gradients, with replacement by a 216S peak that was observed to contain pentamers among lipid debris in negatively stained grids by electron microscopy. After infection or incubation of purified virions with activated caspase-3
in vitro
, 13- and 17-kDa capsid peptide fragments were observed and were predicted by algorithms to contain cleavage sites within proteins by cysteine-dependent aspartate-directed proteases. These findings suggest that caspase cleavage of sites in exposed capsid loops of assembled virions occurs contemporaneously with the onset and progression of apoptosis later in the infection.

IMPORTANCE
Theiler's murine encephalomyelitis virus (TMEV) infection in mice results in establishment of virus persistence in the central nervous system and chronic inflammatory demyelinating disease, providing an experimental animal model for multiple sclerosis. Virus persistence takes place primarily in macrophages recruited into the spinal cord that undergo apoptosis and in turn may facilitate viral spread via infected apoptotic blebs. Infection of murine macrophages in culture results in restricted virus yields late in infection. Here it is shown that the early steps of the virus life cycle in infected macrophages
in vitro
do not differ from these processes in TMEV-infected BHK-21 cells, which undergo necroptosis. However, the findings late in infection suggest that caspases cleave sites in exposed capsid loops and possibly internal sites of assembled virions occurring contemporaneously with onset and progression of apoptosis. Mechanistically, this would explain the dramatic loss in virus yields during TMEV-induced apoptosis and attenuate the virus, enabling persistence.
Human Cytomegalovirus-Encoded Human Interleukin-10 (IL-10) Homolog Amplifies Its Immunomodulatory Potential by Upregulating Human IL-10 in Monocytes
Authors: Avdic Selmir , McSharry Brian P. , Steain Megan , Poole Emma , Sinclair John , Abendroth Allison , Slobedman Barry
Published: January 2016

The human cytomegalovirus (HCMV) gene UL111A encodes cytomegalovirus-encoded human interleukin-10 (cmvIL-10), a homolog of the potent immunomodulatory cytokine human interleukin 10 (hIL-10). This viral homolog exhibits a range of immunomodulatory functions, including suppression of proinflammatory cytokine production and dendritic cell (DC) maturation, as well as inhibition of major histocompatibility complex (MHC) class I and class II. Here, we present data showing that cmvIL-10 upregulates hIL-10, and we identify CD14+monocytes and monocyte-derived macrophages and DCs as major sources of hIL-10 secretion in response to cmvIL-10. Monocyte activation was not a prerequisite for cmvIL-10-mediated upregulation of hIL-10, which was dose dependent and controlled at the transcriptional level. Furthermore, cmvIL-10 upregulated expression of tumor progression locus 2 (TPL2), which is a regulator of the positive hIL-10 feedback loop, whereas expression of a negative regulator of the hIL-10 feedback loop, dual-specificity phosphatase 1 (DUSP1), remained unchanged. Engagement of the hIL-10 receptor (hIL-10R) by cmvIL-10 led to upregulation of heme oxygenase 1 (HO-1), an enzyme linked with suppression of inflammatory responses, and this upregulation was required for cmvIL-10-mediated upregulation of hIL-10. We also demonstrate an important role for both phosphatidylinositol 3-kinase (PI3K) and STAT3 in the upregulation of HO-1 and hIL-10 by cmvIL-10. In addition to upregulating hIL-10, cmvIL-10 could exert a direct immunomodulatory function, as demonstrated by its capacity to upregulate expression of cell surface CD163 when hIL-10 was neutralized. This study identifies a mechanistic basis for cmvIL-10 function, including the capacity of this viral cytokine to potentially amplify its immunosuppressive impact by upregulating hIL-10 expression.

IMPORTANCEHuman cytomegalovirus (HCMV) is a large, double-stranded DNA virus that causes significant human disease, particularly in the congenital setting and in solid-organ and hematopoietic stem cell transplant patients. A prominent feature of HCMV is the wide range of viral gene products that it encodes which function to modulate host defenses. One of these is cmvIL-10, which is a homolog of the potent immunomodulatory cytokine human interleukin 10 (hIL-10). In this study, we report that, in addition to exerting a direct biological impact, cmvIL-10 upregulates the expression of hIL-10 by primary blood-derived monocytes and that it does so by modulating existing cellular pathways. This capacity of cmvIL-10 to upregulate hIL-10 represents a mechanism by which HCMV may amplify its immunomodulatory impact during infection.