bluuebunny/crossref_metadata_2025 huggingface dataset:
Label‐Free Quantitative Proteomic Analysis of Differentially Expressed Membrane Proteins of Pulmonary Alveolar Macrophages Infected with Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and Its Attenuated Strain
Authors: Qu Zehui , Gao Fei , Li Liwei , Zhang Yujiao , Jiang Yifeng , Yu Lingxue , Zhou Yanjun , Zheng Hao , Tong Wu , Li Guoxin , Tong Guangzhi
Published: October 2017

Significant differences exist between the highly pathogenic (HP) porcine reproductive and respiratory syndrome virus (PRRSV) and its attenuated pathogenic (AP) strain in the ability to infect host cells. The mechanisms by which different virulent strains invade host cells remain relatively unknown. In this study, pulmonary alveolar macrophages (PAMs) are infected with HP‐PRRSV (HuN4) and AP‐PRRSV (HuN4‐F112) for 24 h, then harvested and subjected to label‐free quantitative MS. A total of 2849 proteins are identified, including 95 that are differentially expressed. Among them, 26 proteins are located on the membrane. The most differentially expressed proteins are involved in response to stimulus, metabolic process, and immune system process, which mainly have the function of binding and catalytic activity. Cluster of differentiation CD163, vimentin (VIM), and nmII as well as detected proteins are assessed together by string analysis, which elucidated a potentially different infection mechanism. According to the function annotations, PRRSV with different virulence may mainly differ in immunology, inflammation, immune evasion as well as cell apoptosis. This is the first attempt to explore the differential characteristics between HP‐PRRSV and its attenuated PRRSV infected PAMs focusing on membrane proteins which will be of great help to further understand the different infective mechanisms of HP‐PRRSV and AP‐PRRSV.
Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily
Authors: Dong Zheng , Zhou Hongyu , Tao Peng
Published: October 2017

PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence‐structure‐dynamics‐function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence‐conserved residues and build phylogenetic tree. Three‐dimensional structure alignment was also applied to obtain structure‐conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics.
Deuterium Markers in CdS and Zn(O,S) Buffer Layers Deposited by Solution Growth for Cu(In,Ga)Se2 Thin‐Film Solar Cells
Authors: Witte Wolfram , De Souza Roger A. , Martin Manfred , Eicke Axel , Hariskos Dimitrios
Published: October 2017

This contribution describes an easy and cheap approach to introduce deuterium (D) as an isotopic marker into the commonly used buffer layer materials CdS and Zn(O,S) for Cu(In,Ga)Se2 (CIGS) thin‐film solar cells. D was successfully incorporated during the growth of Zn(O,S) and CdS buffer layers by chemical bath deposition (CBD) with D2O. CIGS solar cells prepared with D‐containing buffers grown by CBD exhibit power conversion efficiencies above 16%, that is, the D content has no detrimental effect on the performance or other solar cell parameters of the devices. With depth profiles obtained by time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) we clearly detect the intentionally incorporated D within the solution‐grown Zn(O,S) buffer. Assuming that D is present as OD, we compare the amount of OD within the Zn(O,S) layer with the amount of OH on the surface of the subsequent sputtered (Zn,Mg)O layer. Possible applications and future experiments of the method inserting isotopic markers such as D in functional layers of chalcopyrite‐type thin‐film solar cells and beyond are discussed.
Inferior In Vivo Osteogenesis and Superior Angiogeneis of Human Adipose-Derived Stem Cells Compared with Bone Marrow-Derived Stem Cells Cultured in Xeno-Free Conditions
Authors: Brennan Meadhbh A. , Renaud Audrey , Guilloton Fabien , Mebarki Miryam , Trichet Valerie , Sensebé Luc , Deschaseaux Frederic , Chevallier Nathalie , Layrolle Pierre
Published: October 2017

The possibility of using adipose tissue-derived stromal cells (ATSC) as alternatives to bone marrow-derived stromal cells (BMSC) for bone repair has garnered interest due to the accessibility, high cell yield, and rapid in vitro expansion of ATSC. For clinical relevance, their bone forming potential in comparison to BMSC must be proven. Distinct differences between ATSC and BMSC have been observed in vitro and comparison of osteogenic potential in vivo is not clear to date. The aim of the current study was to compare the osteogenesis of human xenofree-expanded ATSC and BMSC in vitro and in an ectopic nude mouse model of bone formation. Human MSC were implanted with biphasic calcium phosphate biomaterials in subcutis pockets for 8 weeks. Implant groups were: BMSC, ATSC, BMSC and ATSC mixed together in different ratios, as well as MSC primed with either osteogenic supplements (250 μM ascorbic acid, 10 mM β-glycerolphosphate, and 10 nM dexamethasone) or 50 ng/ml recombinant bone morphogenetic protein 4 prior to implantation. In vitro results show osteogenic gene expression and differentiation potentials of ATSC. Despite this, ATSC failed to form ectopic bone in vivo, in stark contrast to BMSC, although osteogenic priming did impart minor osteogenesis to ATSC. Neovascularization was enhanced by ATSC compared with BMSC; however, less ATSC engrafted into the implant compared with BMSC. Therefore, in the content of bone regeneration, the advantages of ATSC over BMSC including enhanced angiogenesis, may be negated by their lack of osteogenesis and prerequisite for osteogenic differentiation prior to transplantation.
The Implicit Costs of Motherhood over the Lifecycle: Cross‐Cohort Evidence from Administrative Longitudinal Data
Authors: Neumeier Christian , Sørensen Todd , Webber Douglas
Published: October 2017

It is well known that the explicit costs of raising a child have grown over the past several decades. Less well understood are the implicit costs of having a child, and how they have changed over time. In this article, we are the first to examine the evolution of the implicit costs of motherhood over the lifecycle and across generations using high quality administrative data. We estimate that the lifetime labor market income gap between mothers and women who never have children (never‐mothers) decreases from around $350,000 to $280,000 between women born in the late 1940s and late 1960s. Gaps tend to increase monotonically over the lifecycle, and decrease monotonically between cohorts. Our evidence suggests that changes in the gaps are caused by changing labor force participation rates.
Media Convergence Meets Deconvergence
Authors: Peil Corinna , Sparviero Sergio
Published: October 2017

This introductory chapter explains that there is a widely shared understanding of the imperative nature of media convergence, which is based on different notions connecting positive goals such as efficiency, synergy, simplification, information abundance, participation, availability and multimodality. These social imaginaries of media convergence are powerful concepts that influence political agendas and legitimize policy decisions. In this book, these privileged meanings of media convergence are challenged by presenting alternative and mostly overlooked trends and theories defined under the umbrella term of media deconvergence. The perspective of deconvergence helps to shed light on sites of tension and the simultaneity of competing forces such as coalescence and drifting apart, or linearity and discontinuity. Two of these sites of tension are analyzed more carefully in this chapter: the user’s perspective and the (de)convergence of markets.
Clinical Outcomes of Gastric Cancer Patients Who Underwent Proximal or Total Gastrectomy: A Propensity Score‐Matched Analysis
Authors: Ushimaru Yuki , Fujiwara Yoshiyuki , Shishido Yuji , Yanagimoto Yoshitomo , Moon Jeong‐Ho , Sugimura Keijiro , Omori Takeshi , Miyata Hiroshi , Yano Masahiko
Published: October 2017

Background

Total gastrectomy (TG) and proximal gastrectomy (PG) are used to treat upper‐third early gastric cancer. To date, no consensus has been reached regarding which procedure should be selected. The aim of this study was to validate the usefulness of preserving the stomach in early upper‐third gastric cancer.

Methods

Between 2004 and 2013, 201 patients underwent PG or TG at our institution for treatment of upper‐third early gastric cancer. According to the defined inclusion and exclusion criteria, 192 cases were enrolled in this study. One‐to‐one propensity score matching was performed to compare the outcomes between the two groups.

Results

The operation time was shorter in the PG group. Although no significant difference was observed, the PG group had less bleeding and fewer postoperative complications. R0 resection rate was 100%, and no surgery‐related deaths were observed. The frequencies of reflux symptoms and anastomotic stenosis were significantly higher in the PG group, but could be controlled by balloon dilation and drug therapy. The maintenance rates of body mass index and lean body mass were significantly higher in patients who underwent PG than TG. The total protein and serum albumin values were higher in the PG group than in the TG group and remained statistically superior.

Conclusion

PG group exhibited better perioperative performance. Furthermore, better nutritional results were obtained in the PG group. Although the late stenosis and reflux symptoms must be addressed, the PG is a preferable surgical procedure for the treatment of early proximal gastric cancer.
Glutamine supplementation reduces markers of intestinal permeability during running in the heat in a dose-dependent manner
Authors: Pugh Jamie N. , Sage Stephen , Hutson Mark , Doran Dominic A. , Fleming Simon C. , Highton Jamie , Morton James P. , Close Graeme L.
Published: October 2017

Purpose

To examine the dose–response effects of acute glutamine supplementation on markers of gastrointestinal (GI) permeability, damage and, secondary, subjective symptoms of GI discomfort in response to running in the heat.

Methods

Ten recreationally active males completed a total of four exercise trials; a placebo trial and three glutamine trials at 0.25, 0.5 and 0.9 g kg−1 of fat-free mass (FFM) consumed 2 h before exercise. Each exercise trial consisted of a 60-min treadmill run at 70% of $$\dot {V}{{\text{O}}_{{\text{2max}}}}$$

V
˙

O
2max

in an environmental chamber set at 30 °C. GI permeability was measured using ratio of lactulose to rhamnose (L:R) in serum. Plasma glutamine and intestinal fatty acid binding protein (I-FABP) concentrations were determined pre and post exercise. Subjective GI symptoms were assessed 45 min and 24 h post-exercise.

Results

Relative to placebo, L:R was likely lower following 0.25 g kg−1 (mean difference: − 0.023; ± 0.021) and 0.5 g kg−1 (− 0.019; ± 0.019) and very likely following 0.9 g kg− 1 (− 0.034; ± 0.024). GI symptoms were typically low and there was no effect of supplementation.

Discussion

Acute oral glutamine consumption attenuates GI permeability relative to placebo even at lower doses of 0.25 g kg−1, although larger doses may be more effective. It remains unclear if this will lead to reductions in GI symptoms. Athletes competing in the heat may, therefore, benefit from acute glutamine supplementation prior to exercise in order to maintain gastrointestinal integrity.
Chronic Exercise Reduces CETP and Mesterolone Treatment Counteracts Exercise Benefits on Plasma Lipoproteins Profile: Studies in Transgenic Mice
Authors: Casquero Andrea Camargo , Berti Jairo Augusto , Teixeira Laura Lauand Sampaio , de Oliveira Helena Coutinho Franco
Published: October 2017

Regular exercise and anabolic androgenic steroids have opposing effects on the plasma lipoprotein profile and risk of cardio‐metabolic diseases in humans. Studies in humans and animal models show conflicting results. Here, we used a mice model genetically modified to mimic human lipoprotein profile and metabolism. They under‐express the endogenous LDL receptor gene (R1) and express a human transgene encoding the cholesteryl ester transfer protein (CETP), normally absent in mice. The present study was designed to evaluate the independent and interactive effects of testosterone supplementation, exercise training and CETP expression on the plasma lipoprotein profile and CETP activity. CETP/R1 and R1 mice were submitted to a 6‐week swimming training and mesterolone (MEST) supplementation in the last 3 weeks. MEST treatment increased markedly LDL levels (40%) in sedentary CETP/R1 mice and reduced HDL levels in exercised R1 mice (18%). A multifactorial ANOVA revealed the independent effects of each factor, as follows. CETP expression reduced HDL (21%) and increased non‐HDL (15%) fractions. MEST treatment increased the VLDL concentrations (42%) regardless of other interventions. Exercise training reduced triacylglycerol (25%) and free fatty acids (20%), increased both LDL and HDL (25–33%), and reduced CETP (19%) plasma levels. Significant factor interactions showed that the increase in HDL induced by exercise is explained by reducing CETP activity and that MEST blunted the exercise‐induced elevation of HDL‐cholesterol. These results reinforce the positive metabolic effects of exercise, resolved a controversy about CETP response to exercise and evidenced MEST potency to counteract specific exercise benefits.
A Calabi theorem for solutions to the parabolic Monge–Ampère equation with periodic data
Authors: Zhang Wei , Bao Jiguang
Published: October 2017

We classify all solutions to

−u_{t}\mathrm{\det }⁡D^{2}u = f(x)\:\text{ in }\:\mathbb{R}_{−}^{n + 1},

where

f \in C^{\alpha }(\mathbb{R}^{n})

is a positive periodic function in

x

. More precisely, if

u

is a parabolically convex solution to above equation, then

u

is the sum of a convex quadratic polynomial in

x

, a periodic function in

x

and a linear function of

t

. It can be viewed as a generalization of the work of Gutiérrez and Huang in 1998. And along the line of approach in this paper, we can treat other parabolic Monge–Ampère equations.

Nous classifions toutes les solutions à

−u_{t}\mathrm{\det }⁡D^{2}u = f(x)\:\text{ in }\:\mathbb{R}_{−}^{n + 1},

où

f \in C^{\alpha }(\mathbb{R}^{n})

est une fonction périodique positive en

x

. Plus précisément, si

u

est une solution paraboliquement convexe de l'équation ci-dessus, alors

u

est la somme d'un polynôme quadratique convexe en

x

, une fonction périodique en

x

et une fonction linéaire de

t

. Cela peut être considéré comme une généralisation du travail de Gutiérrez et Huang en 1998. Et le long de la ligne d'approche dans cet article, nous pouvons traiter d'autres équations paraboliques Monge–Ampère.
How Responsive are Political Elites? A Meta-Analysis of Experiments on Public Officials
Authors: Costa Mia
Published: October 2017

In the past decade, the body of research using experimental approaches to investigate the responsiveness of elected officials has grown exponentially. Given this explosion of work, a systematic assessment of these studies is needed not only to take stock of what we have learned so far about democratic responsiveness, but also to inform the design of future studies. In this article, I conduct the first meta-analysis of all experiments that examine elite responsiveness to constituent communication. I find that racial/ethnic minorities and messages sent to elected officials (as opposed to non-elected) are significantly less likely to receive a response. A qualitative review of the literature further suggests that some of these inequalities in responsiveness are driven by personal biases of public officials, rather than strategic, electoral considerations. The findings of this study provide important qualifications and context to prominent individual studies in the field.
The Potential of Fermentation and Contamination of Teff by Soil to Influence Iron Intake and Bioavailability from Injera Flatbread
Authors: Cercamondi Colin I. , Fischer Maren M , Worku Tesfaye G. H. , Wyss Nadine , Herter-Aeberli Isabelle , Zimmermann Michael B. , Egli Ines M. , Hurrell Richard F.
Published: October 2017

Abstract.The high phytic acid (PA) concentration in the diet based on teff injera is a likely contributing cause of iron deficiency in Ethiopia. We monitored PA during teff injera fermentation in 30 households in Debre Zeyit, Ethiopia and evaluated its influence on iron bioavailability, considering contaminant soil iron in teff flour. After fermentation (48h), mean PA concentration in injera batter decreased from 0.87 to 0.58 g/100 g dm (P < 0.001). Low phytase activity in teff flour (0.44 μmol phosphate/min/g) and a rapid drop in pH, indicated that PA degradation was driven by microbial phytases. The iron concentration in injera batter among the households ranged widely from 14.5–160.4 mg/100 g dm (mean: 34.7 mg/100 g dm) principally due to contamination with soil. Estimated intrinsic iron concentration of teff based on the strong correlation between total iron and aluminium concentrations (P < 0.001; aluminium concentrations in injera batter: 28.7–184.9 mg/100 g dm) was 4.4 mg/100 g dm, indicating that 86–97 % is extrinsic iron from soil. The median daily iron intakes from 3-day weighed food records in 10 young children were 18.9 mg/day including soil iron vs. 4.9 mg/day without soil iron (P < 0.01). The PA:iron molar ratios indicated low iron bioavailability from teff injera, particularly when soil iron was excluded. Traditional fermentation thus has a modest influence on PA levels and more complete degradation is needed to improve iron bioavailability. There is an urgent need to better understand the bioavailability of contamination iron from soil before considering national fortification or biofortification strategies in Ethiopia.
Nakajima Receives 2017 Yoram J. Kaufman Unselfish Cooperation in Research Award
Authors:   AGU
Published: October 2017

Teruyuki Nakajima will receive the 2017 Yoram J. Kaufman Unselfish Cooperation in Research Award at the 2017 American Geophysical Union Fall Meeting, to be held 11–15 December in New Orleans, La. The award recognizes “broad influence in atmospheric science through exceptional creativity, inspiration of younger scientists, mentoring, international collaborations, and unselfish cooperation in research.”
Adoptive cell therapy with CD4+ T helper 1 cells and CD8+ cytotoxic T cells enhances complete rejection of an established tumour, leading to generation of endogenous memory responses to non‐targeted tumour epitopes
Authors: Li Kunyu , Donaldson Braeden , Young Vivienne , Ward Vernon , Jackson Christopher , Baird Margaret , Young Sarah
Published: October 2017

The results of adoptive T‐cell therapies (ACTs) are very encouraging and show clinical evidence that ACT can provide a cure for patients with metastatic disease. However, various response rates and long‐term cancer remission have been observed in different ACT trials. The types of T cells, prior treatment with chemotherapy and co‐administration of other immune‐target therapies have been found to influence the efficacy of ACT. In this study, we investigate the ability of ACT using CD4+ T helper 1 (Th1) cells and CD8+ cytotoxic T lymphocytes (CTLs) to reject the growth of established B16‐ovalbumin (OVA) melanoma. CD8+ CTLs were found to be the main effector T cells that mediated tumour regression. However, low tumour‐free survival rates were observed in ACT with CD8+ CTLs only. Co‐transferring CD4+ Th1 cells and CD8+ CTLs has been observed to induce a synergistic antitumour response, resulting in complete regression in 80% of the tumour‐bearing mice. We also examined a prior Dacarbazine (DTIC) and after virus‐like particle (VLP)‐OVA vaccine treatment to enhance ACT, but no therapeutic benefit was observed during primary B16‐OVA tumour growth. Nevertheless, the ACT‐mediated antitumour response was able to generate memory responses to both B16‐OVA and B16‐gp33 tumours. VLP‐OVA vaccination following ACT enhances the memory responses to tumours that express a heterogenic population of both B16‐OVA and B16‐gp33 cells; however, it abolished the memory response to tumours consisting of only gp33‐expressing cells. These findings provide important information for designing therapeutic treatments for patients with metastatic disease and cancer relapse to achieve durable cancer remission.
Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale
Authors: Bernardo Pauline , Charles-Dominique Tristan , Barakat Mohamed , Ortet Philippe , Fernandez Emmanuel , Filloux Denis , Hartnady Penelope , Rebelo Tony A , Cousins Stephen R , Mesleard François , Cohez Damien , Yavercovski Nicole , Varsani Arvind , Harkins Gordon W , Peterschmitt Michel , Malmstrom Carolyn M , Martin Darren P , Roumagnac Philippe
Published: October 2017

Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8–35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.
Recent expansion of heat-activated retrotransposons in the coral symbiont Symbiodinium microadriaticum
Authors: Chen Jit Ern , Cui Guoxin , Wang Xin , Liew Yi Jin , Aranda Manuel
Published: October 2017

Rising sea surface temperature is the main cause of global coral reef decline. Abnormally high temperatures trigger the breakdown of the symbiotic association between corals and their photosynthetic symbionts in the genus Symbiodinium. Higher genetic variation resulting from shorter generation times has previously been proposed to provide increased adaptability to Symbiodinium compared to the host. Retrotransposition is a significant source of genetic variation in eukaryotes and some transposable elements are specifically expressed under adverse environmental conditions. We present transcriptomic and phylogenetic evidence for the existence of heat stress-activated Ty1-copia-type LTR retrotransposons in the coral symbiont Symbiodinium microadriaticum. Genome-wide analyses of emergence patterns of these elements further indicate recent expansion events in the genome of S. microadriaticum. Our findings suggest that acute temperature increases can activate specific retrotransposons in the Symbiodinium genome with potential impacts on the rate of retrotransposition and the generation of genetic variation under heat stress.
Dispersal timing determines the importance of priority effects in bacterial communities
Authors: Svoboda Pavel , Lindström Eva S , Ahmed Osman Omneya , Langenheder Silke
Published: October 2017

The order and timing of species arrival during community assembly can have long term effects on community structure due to priority effects. The importance of such processes in complex bacterial communities where dispersal involves mixing of entire communities is currently not known. Here we used a transplant experiment with two bacterioplankton communities of different origin (freshwater and brackish). Sterile medium of each origin was initially inoculated with a bacterial community of different (‘alien’) origin, followed by dispersal of the respective ‘home’ community at different time points after initial inoculation. We found that the later the dispersal with the ‘home’ community occurred the smaller the effect on the final community composition. This suggests that priority effects by the initially inoculated community reduce the establishment success of taxa from the later arriving community and that this effect depends on dispersal timing.
Correction: Corrigendum: Fatigue in Parkinson’s disease: report from a multidisciplinary symposium
Authors: Friedman Joseph H , Beck James C , Chou Kelvin L , Clark Gracia , Fagundes Christopher P , Goetz Christopher G , Herlofson Karen , Kluger Benzi , Krupp Lauren B , Lang Anthony E , Lou Jao-Shin , Marsh Laura , Newbould Anne , Weintraub Daniel
Published: October 2017

Correction to: npj Parkinson's Disease (2016) 2, 15025. doi: 10.1038/npjparkd.2015.25; published 14 January 2016 The original version of this Article contained an error in the spelling of the title, in which ‘multidisciplinary’ was incorrectly given as ‘mutidisciplinary’. This has now been correctedin both the PDF and HTML versions of the Article.
Correction: Corrigendum: Independent, extensible control of same-frequency superconducting qubits by selective broadcasting
Authors: Asaad Serwan , Dickel Christian , Langford Nathan K , Poletto Stefano , Bruno Alessandro , Rol Michiel Adriaan , Deurloo Duije , DiCarlo Leonardo
Published: October 2017

Correction to: npj Quantum Information (2016) 2, 16029. doi:10.1038/npjqi.2016.29; published online 23 August 2016 The original version of this Article contained an error in one of the calculations within the Results section. Although the authors note that this leakage rate is per Clifford, they actually quote the value per nanosecond:
Burial-induced oxygen-isotope re-equilibration of fossil foraminifera explains ocean paleotemperature paradoxes
Authors: Bernard S. , Daval D. , Ackerer P. , Pont S. , Meibom A.
Published: October 2017

Oxygen-isotope compositions of fossilised planktonic and benthic foraminifera tests are used as proxies for surface- and deep-ocean paleotemperatures, providing a continuous benthic record for the past 115 Ma. However, visually imperceptible processes can alter these proxies during sediment burial. Here, we investigate the diffusion-controlled re-equilibration process with experiments exposing foraminifera tests to elevated pressures and temperatures in isotopically heavy artificial seawater (H218O), followed by scanning electron microscopy and quantitative NanoSIMS imaging: oxygen-isotope compositions changed heterogeneously at submicrometer length scales without any observable modifications of the test ultrastructures. In parallel, numerical modelling of diffusion during burial shows that oxygen-isotope re-equilibration of fossil foraminifera tests can cause significant overestimations of ocean paleotemperatures on a time scale of 107 years under natural conditions. Our results suggest that the late Cretaceous and Paleogene deep-ocean and high-latitude surface-ocean temperatures were significantly lower than is generally accepted, thereby explaining the paradox of the low equator-to-pole surface-ocean thermal gradient inferred for these periods.
Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma
Authors: Sun Yu , Svedberg Jesper , Hiltunen Markus , Corcoran Pádraic , Johannesson Hanna
Published: October 2017

A common feature of eukaryote genomes is large chromosomal regions where recombination is absent or strongly reduced, but the factors that cause this reduction are not well understood. Genomic rearrangements have often been implicated, but they may also be a consequence of recombination suppression rather than a cause. In this study, we generate eight high-quality genomic data sets of the filamentous ascomycete Neurospora tetrasperma, a fungus that lacks recombination over most of its largest chromosome. The genomes surprisingly reveal collinearity of the non-recombining regions and although large inversions are enriched in these regions, we conclude these inversions to be derived and not the cause of the suppression. To our knowledge, this is the first time that non-recombining, genic regions as large as 86% of a full chromosome (or 8 Mbp), are shown to be collinear. These findings are of significant interest for our understanding of the evolution of sex chromosomes and other supergene complexes.
Bisphenol A in eggs causes development-specific liver molecular reprogramming in two generations of rainbow trout
Authors: Sadoul Bastien , Birceanu Oana , Aluru Neel , Thomas Jith K. , Vijayan Mathilakath M.
Published: October 2017

Bisphenol A (BPA) is widely used in the manufacture of plastics and epoxy resins and is prevalent in the aquatic environment. BPA disrupts endocrine pathways in fish, but the long-term developmental implications are unknown. We demonstrate that BPA deposition in the eggs of rainbow trout (Oncorhynchus mykiss), an ecologically and economically important species of fish, reprograms liver metabolism in the offspring and alters the developmental growth trajectory in two generations. Specifically, BPA reduces growth during early development, followed by a catch-up growth post-juveniles. More importantly, we observed a developmental shift in the liver transcriptome, including an increased propensity for protein breakdown during early life stages to lipid and cholesterol synthesis post- juveniles. The liver molecular responses corresponded with the transient growth phenotypes observed in the F1 generation, and this was also evident in the F2 generation. Altogether, maternal and/or ancestral embryonic exposure to BPA affects liver metabolism leading to development-distinct effects on growth, underscoring the need for novel risk assessment strategies for this chemical in the aquatic environment. This is particularly applicable to migratory species, such as salmon, where distinct temporal changes in growth and physiology during development are critical for their spawning success.
Atmospheric Beacons of Life from Exoplanets Around G and K Stars
Authors: Airapetian Vladimir S. , Jackman Charles H. , Mlynczak Martin , Danchi William , Hunt Linda
Published: October 2017

The current explosion in detection and characterization of thousands of extrasolar planets from the Kepler mission, the Hubble Space Telescope, and large ground-based telescopes opens a new era in searches for Earth-analog exoplanets with conditions suitable for sustaining life. As more Earth-sized exoplanets are detected in the near future, we will soon have an opportunity to identify habitale worlds. Which atmospheric biosignature gases from habitable planets can be detected with our current capabilities? The detection of the common biosignatures from nitrogen-oxygen rich terrestrial-type exoplanets including molecular oxygen (O2), ozone (O3), water vapor (H2O), carbon dioxide (CO2), nitrous oxide (N2O), and methane (CH4) requires days of integration time with largest space telescopes, and thus are very challenging for current instruments. In this paper we propose to use the powerful emission from rotational-vibrational bands of nitric oxide, hydroxyl and molecular oxygen as signatures of nitrogen, oxygen, and water rich atmospheres of terrestrial type exoplanets “highlighted” by the magnetic activity from young G and K main-sequence stars. The signals from these fundamental chemical prerequisites of life we call atmospheric “beacons of life” create a unique opportunity to perform direct imaging observations of Earth-sized exoplanets with high signal-to-noise and low spectral resolution with the upcoming NASA missions.
Differentiation of Oligodendrocyte Precursor Cells from Sox10-Venus Mice to Oligodendrocytes and Astrocytes
Authors: Suzuki Nobuharu , Sekimoto Kaori , Hayashi Chikako , Mabuchi Yo , Nakamura Tetsuya , Akazawa Chihiro
Published: October 2017

Oligodendrocytes are well known as myelin-forming cells in the central nervous system (CNS). However, detailed mechanisms of oligodendrocyte differentiation and myelination are poorly understood, particularly due to the difficulty of the purification of murine oligodendrocyte precursor cells (OPCs). We have recently established a transgenic mouse line that expresses a fluorescent protein Venus under the promoter of Sox10, whose expression is restricted to OPCs and oligodendrocytes in the CNS. Here, we have characterized Venus-positive cells from theSox10-Venus mouse brain for analyzing oligodendrocyte differentiation. We first purified Venus-positive cells from the postnatal day 0–2 brain by flow cytometry. Most of the Venus-positive cells expressed NG2, an OPC marker. After induction of differentiation, an increased population of galactocerebroside-positive oligodendrocytes and decrease of OPCs were observed in the Venus-positive culture. Furthermore, a time-lapse analysis showed that Venus-positive oligodendrocytes dynamically changed their morphology with highly branched cell processes during differentiation. In addition, we found that Venus-positive OPCs were able to differentiate to type II astrocytes.In vivo, OPCs and oligodendrocytes express Venus, and some of astrocytes were positive for Venus in the ventral cortex. Taken together, theSox10-Venus mouse system is useful for analyzing differentiation and multipotency of murine OPCs.
High fat diet exacerbates murine psoriatic dermatitis by increasing the number of IL-17-producing γδ T cells
Authors: Nakamizo Satoshi , Honda Tetsuya , Adachi Akimasa , Nagatake Takahiro , Kunisawa Jun , Kitoh Akihiko , Otsuka Atsushi , Dainichi Teruki , Nomura Takashi , Ginhoux Florent , Ikuta Koichi , Egawa Gyohei , Kabashima Kenji
Published: October 2017

Psoriasis is a common, chronic inflammatory skin disease characterized by epidermal hyperplasia via the IL-23/IL-17 axis. Various studies have indicated the association between obesity and psoriasis, however, the underlying mechanisms remains unclarified. To this end, we focused on high-fat diet (HFD) in this study, because HFD is suggested as a contributor to obesity, and HFD-fed mice exhibit exacerbated psoriatic dermatitis. Using murine imiquimod (IMQ)-induced psoriasis and HFD-induced obesity models, we have revealed a novel mechanism of HFD-induced exacerbation of psoriatic dermatitis. HFD-fed mice exhibited aggravated psoriatic dermatitis, which was accompanied with increased accumulation of IL-17A-producing Vγ4+γδ T cells in the skin. HFD also induced the increase of Vγ4+γδ T cells in other organs such as skin draining lymph nodes, which preceded the increase of them in the skin. In addition, HFD-fed mice displayed increased expression of several γδ T cell-recruiting chemokines in the skin. On the other hand,ob/obmice, another model of murine obesity on normal diet, did not exhibit aggravated psoriatic dermatitis nor accumulation of γδ T cells in the dermis. These results indicate that HFD is a key element in exacerbation of IMQ-induced psoriatic dermatitis, and further raise the possibility of HFD as a factor that links obesity and psoriasis.
Methods to Evaluate Cell Growth, Viability, and Response to Treatment in a Tissue Engineered Breast Cancer Model
Authors: Goliwas Kayla F. , Richter Jillian R. , Pruitt Hawley C. , Araysi Lita M. , Anderson Nicholas R. , Samant Rajeev S. , Lobo-Ruppert Susan M. , Berry Joel L. , Frost Andra R.
Published: October 2017

The use of in vitro, engineered surrogates in the field of cancer research is of interest for studies involving mechanisms of growth and metastasis, and response to therapeutic intervention. While biomimetic surrogates better model human disease, their complex composition and dimensionality make them challenging to evaluate in a real-time manner. This feature has hindered the broad implementation of these models, particularly in drug discovery. Herein, several methods and approaches for the real-time, non-invasive analysis of cell growth and response to treatment in tissue-engineered, three-dimensional models of breast cancer are presented. The tissue-engineered surrogates used to demonstrate these methods consist of breast cancer epithelial cells and fibroblasts within a three dimensional volume of extracellular matrix and are continuously perfused with nutrients via a bioreactor system. Growth of the surrogates over time was measured using optical in vivo (IVIS) imaging. Morphologic changes in specific cell populations were evaluated by multi-photon confocal microscopy. Response of the surrogates to treatment with paclitaxel was measured by optical imaging and by analysis of lactate dehydrogenase and caspase-cleaved cytokeratin 18 in the perfused medium. Each method described can be repeatedly performed during culture, allowing for real-time, longitudinal analysis of cell populations within engineered tumor models.
Tuning a sign of magnetoelectric coupling in paramagnetic NH2(CH3)2Al1−xCrx(SO4)2 × 6H2O crystals by metal ion substitution
Authors: Kapustianyk V. , Eliyashevskyy Yu. , Czapla Z. , Rudyk V. , Serkiz R. , Ostapenko N. , Hirnyk I. , Dayen J.-F. , Bobnar M. , Gumeniuk R. , Kundys B.
Published: October 2017

Hybrid organometallic systems offer a wide range of functionalities, including magnetoelectric (ME) interactions. However, the ability to design on-demand ME coupling remains challenging despite a variety of host-guest configurations and ME phases coexistence possibilities. Here, we report the effect of metal-ion substitution on the magnetic and electric properties in the paramagnetic ferroelectric NH2(CH3)2Al1−x
Cr
x
(SO4)2 × 6H2O. Doing so we are able to induce and even tune a sign of the ME interactions, in the paramagnetic ferroelectric (FE) state. Both studied samples with x = 0.065 and x = 0.2 become paramagnetic, contrary to the initial diamagnetic compound. Due to the isomorphous substitution with Cr the ferroelectric phase transition temperature (T
c
) increases nonlinearly, with the shift being larger for the 6.5% of Cr. A magnetic field applied along the polar c axis increases ferroelectricity for the x = 0.065 sample and shifts T
c
to higher values, while inverse effects are observed for x = 0.2. The ME coupling coefficient αME = 1.7 ns/m found for a crystal with Cr content of x = 0.2 is among the highest reported up to now. The observed sign change of αME with a small change in Cr content paves the way for ME coupling engineering.
The Role of Autophagy in Critical Illness-induced Liver Damage
Authors: Thiessen Steven E. , Derese Inge , Derde Sarah , Dufour Thomas , Pauwels Lies , Bekhuis Youri , Pintelon Isabel , Martinet Wim , Van den Berghe Greet , Vanhorebeek Ilse
Published: October 2017

Mitochondrial dysfunction and endoplasmic reticulum (ER) stress, which activates the unfolded protein response (UPR), mediate critical illness-induced organ failure, often affecting the liver. Autophagy is known to alleviate both and suppressed or insufficiently activated autophagy in prolonged illness has shown to associate with organ failure. Whether insufficient autophagy contributes to organ failure during critical illness by affecting these underlying mechanisms is incompletely understood. In this study, we investigated whether the inability to acutely activate hepatic autophagy during critical illness aggravates liver damage by increasing hepatic mitochondrial dysfunction and affecting the UPR. In a mouse model of critical illness, induced by surgery and sepsis, we investigated the impact of inactivating hepatic autophagy on markers of hepatic mitochondrial function, the UPR and liver damage in acute (1 day) and prolonged (3 days) critical illness. Hepatic autophagy inactivation during critical illness acutely worsened mitochondrial dysfunction and time-dependently modulated the hepatic UPR. Furthermore, autophagy inactivation aggravated markers of liver damage on both time points. In conclusion, the inability to acutely activate autophagy in liver during critical illness worsened hepatic mitochondrial damage and dysfunction, partially prohibited acute UPR activation and aggravated liver damage, indicating that autophagy is crucial in alleviating critical illness-induced organ failure.
Bacteria-inspired nanorobots with flagellar polymorphic transformations and bundling
Authors: Ali Jamel , Cheang U Kei , Martindale James D. , Jabbarzadeh Mehdi , Fu Henry C. , Jun Kim Min
Published: October 2017

Wirelessly controlled nanoscale robots have the potential to be used for both in vitro and in vivo biomedical applications. So far, the vast majority of reported micro- and nanoscale swimmers have taken the approach of mimicking the rotary motion of helical bacterial flagella for propulsion, and are often composed of monolithic inorganic materials or photoactive polymers. However, currently no man-made soft nanohelix has the ability to rapidly reconfigure its geometry in response to multiple forms of environmental stimuli, which has the potential to enhance motility in tortuous heterogeneous biological environments. Here, we report magnetic actuation of self-assembled bacterial flagellar nanorobotic swimmers. Bacterial flagella change their helical form in response to environmental stimuli, leading to a difference in propulsion before and after the change in flagellar form. We experimentally and numerically characterize this response by studying the swimming of three flagellar forms. Also, we demonstrate the ability to steer these devices and induce flagellar bundling in multi-flagellated nanoswimmers.
Rancher-reported efficacy of lethal and non-lethal livestock predation mitigation strategies for a suite of carnivores
Authors: Scasta J. D. , Stam B. , Windh J. L.
Published: October 2017

Pastoralists have dealt with livestock losses from predators for millennia, yet effective mitigation strategies that balance wildlife conservation and sustainable agriculture are still needed today. In Wyoming, USA, 274 ranchers responded to a retrospective survey, and rated the efficacy of predation mitigation strategies for foxes, dogs, coyotes, wolves, bobcats, mountain lions, bears, and birds (buzzards, eagles, hawks, ravens). Rancher reported efficacy of mitigation varied by predator species, mitigation strategy, and lethality of strategies, but not livestock type. Ranchers perceive they were most effective at mitigating predation by foxes and coyotes, moderately effective at mitigating large carnivores, and the least effective at mitigating birds. Ranchers also reported that avian predators seem to be the most challenging predator type. The general perception was lethal mitigation strategies were more effective than non-lethal strategies, with guard animals showing the most potential among the non-lethal options. In general, ranchers did not perceive non-lethal strategies as a proxy for lethal strategies. However, a few ranchers reported being successful with non-lethal options such as herding, fencing, and stalling at night but more details about such successful applications are needed. Innovation in current or novel non-lethal mitigation strategies, and examples of efficacy, are needed to justify producer adoption.
ALF: a strategy for identification of unauthorized GMOs in complex mixtures by a GW-NGS method and dedicated bioinformatics analysis
Authors: Košir Alexandra Bogožalec , Arulandhu Alfred J. , Voorhuijzen Marleen M. , Xiao Hongmei , Hagelaar Rico , Staats Martijn , Costessi Adalberto , Žel Jana , Kok Esther J. , Dijk Jeroen P. van
Published: October 2017

The majority of feed products in industrialised countries contains materials derived from genetically modified organisms (GMOs). In parallel, the number of reports of unauthorised GMOs (UGMOs) is gradually increasing. There is a lack of specific detection methods for UGMOs, due to the absence of detailed sequence information and reference materials. In this research, an adapted genome walking approach was developed, called ALF: Amplification of Linearly-enriched Fragments. Coupling of ALF to NGS aims for simultaneous detection and identification of all GMOs, including UGMOs, in one sample, in a single analysis. The ALF approach was assessed on a mixture made of DNA extracts from four reference materials, in an uneven distribution, mimicking a real life situation. The complete insert and genomic flanking regions were known for three of the included GMO events, while for MON15985 only partial sequence information was available. Combined with a known organisation of elements, this GMO served as a model for a UGMO. We successfully identified sequences matching with this organisation of elements serving as proof of principle for ALF as new UGMO detection strategy. Additionally, this study provides a first outline of an automated, web-based analysis pipeline for identification of UGMOs containing known GM elements.
Lateralized occipito-temporal N1 responses to images of salient distorted finger postures
Authors: Espírito Santo Miguel G. , Chen Hsin-Yuan , Schürmann Martin
Published: October 2017

For humans as social beings, other people’s hands are highly visually conspicuous. Exceptionally striking are hands in other than natural configuration which have been found to elicit distinct brain activation. Here we studied response strength and lateralization of this activation using event-related potentials (ERPs), in particular, occipito-temporal N1 responses as correlates of activation in extrastriate body area. Participants viewed computer-generated images of hands, half of them showing distorted fingers, the other half showing natural fingers. As control stimuli of similar geometric complexity, images of chairs were shown, half of them with distorted legs, half with standard legs. The contrast of interest was between distorted and natural/standard stimuli. For hands, stronger N1 responses were observed for distorted (vs natural) stimuli from 170 ms post stimulus. Such stronger N1 responses were found for distorted hands and absent for distorted chairs, therefore likely unrelated to visuospatial processing of the unusual distorted shapes. Rather, N1 modulation over both hemispheres – but robustly right-lateralized – could reflect distorted hands as emotionally laden stimuli. The results are in line with privileged visual processing of hands as highly salient body parts, with distortions engaging neural resources that are especially activated for biological stimuli in social perception.