bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolution of growth patterns in mammalian versus nonmammalian cynodonts
Authors: O’Meara Rachel N. , Asher Robert J.
Published: April 2016

One of the major evolutionary transitions of the mammaliaform lineage was the origin of a typically mammalian pattern of growth. This is characterized by rapid juvenile growth followed by abrupt cessation of growth at adult size and may be linked with other important mammaliaform apomorphies of dental replacement and morphology. Investigation of growth patterns in the tritylodontid cynodontOligokyphusand the basal mammaliaformMorganucodonprovides insight into this crucial transition. We collected mandibular depth measurements from large samples ofMorganucodonandOligokyphusand constructed distributions of mandibular depth versus frequency for each species. These were compared with distributions from species from three different growth classes of extant amniote: testudines + crocodilians, mammals + birds, and lepidosaurs. Discriminant function analysis was used to differentiate between known growth classes by using different combinations of three measures of mandibular depth distribution shape (skew, kurtosis, and coefficient of variation) as proxies for different juvenile and adult growth patterns. Classification of the fossil species showed thatMorganucodonclosely resembled extant placental mammals in having rapid juvenile growth followed by truncated, determinate adult growth.Oligokyphusshowed intermediate growth patterns, with more extended adult growth patterns thanMorganucodonand slightly slower juvenile growth. This suggests a gradual evolution of mammalian growth patterns across the cynodont to mammaliaform transition, possibly with the origin of rapid juvenile growth preceding that of truncated, determinate adult growth. In turn, acquisition of both these aspects of mammalian growth was likely necessary for the evolution of diphyodont tooth replacement in the mammaliaform lineage.
Electronic Dietary Intake Assessment (e-DIA): relative validity of a mobile phone application to measure intake of food groups
Authors: Rangan Anna M. , Tieleman Laurissa , Louie Jimmy C. Y. , Tang Lie Ming , Hebden Lana , Roy Rajshri , Kay Judy , Allman-Farinelli Margaret
Published: April 2016

Automation of dietary assessment can reduce limitations of established methodologies, by alleviating participant and researcher burden. Designed as a research tool, the electronic Dietary Intake Assessment (e-DIA) is a food record in mobile phone application format. The present study aimed to examine the relative validity of the e-DIA with the 24-h recall method to estimate intake of food groups. A sample of eighty university students aged 19–24 years recorded 5 d of e-DIA and 3 d of recall within this 5-d period. The three matching days of dietary data were used for analysis. Food intake data were disaggregated and apportioned to one of eight food groups. Median intakes of food groups were similar between the methods, and strong correlations were found (mean: 0·79, range: 0·69–0·88). Cross-classification by tertiles produced a high level of exact agreement (mean: 71 %, range: 65–75 %), and weightedκvalues were moderate to good (range: 0·54–0·71). Although mean differences (e-DIA–recall) were small (range: –13 to 23 g), limits of agreement (LOA) were relatively large (e.g. for vegetables, mean difference: –4 g, LOA: –159 to 151 g). The Bland–Altman plots showed robust agreement, with minimum bias. This analysis supports the use of e-DIA as an alternative to the repeated 24-h recall method for ranking individuals’ food group intake.
Predictors of folate status among pregnant Japanese women: the Hokkaido Study on Environment and Children’s Health, 2002–2012
Authors: Yila Thamar A. , Araki Atsuko , Sasaki Seiko , Miyashita Chihiro , Itoh Kumiko , Ikeno Tamiko , Yoshioka Eiji , Kobayashi Sumitaka , Goudarzi Houman , Baba Toshiaki , Braimoh Titilola , Minakami Hisanori , Endo Toshiaki , Sengoku Kazuo , Kishi Reiko
Published: April 2016

The International Clearinghouse for Birth Defects, Surveillance and Research reports a rise in the prevalence rate of spina bifida in Japan. We determined first-trimester folate status of Hokkaido women and identified potential predictors. Participants were 15 266 pregnant women of the Hokkaido Study on Environment and Children’s Health Cohort. Data were extracted from self-reported questionnaires and biochemical assay results. Demographic determinants of low folate status were younger maternal age (adjusted OR (AOR) 1·48; 95 % CI 1·32, 1·66), lower educational level (AOR 1·27; 95 % CI 1·17, 1·39) and lower annual income (AOR 1·11; 95 % CI 1·01, 1·22). Plasma cotinine concentrations of 1·19–65·21 nmol/l increased the risk of low folate status (AOR 1·20; 95 % CI 1·10, 1·31) and concentrations >65·21 nmol/l further increased the risk (AOR 1·91; 95 % CI 1·70, 2·14). The most favourable predictor was use of folic acid (FA) supplements (AOR 0·19; 95 % CI 0·17, 0·22). Certain socio-demographic factors influence folate status among pregnant Japanese women. Modifiable negative and positive predictors were active and passive tobacco smoking and use of FA supplements. Avoiding both active and passive tobacco smoking and using FA supplements could improve the folate status of Japanese women.
Detrital zircon U–Pb ages and Hf isotopic composition of the Ordovician Duguer quartz schist, central Tibetan Plateau: constraints on tectonic affinity and sedimentary source regions
Authors: LIU YIMING , LI CAI , XIE CHAOMING , FAN JIANJUN , WU HAO
Published: April 2016

Many previous studies have investigated the late Palaeozoic ophiolites, migmatites and high-pressure metamorphic belts of the Tibetan Plateau, whereas the early Palaeozoic evolution of the regions is relatively poorly understood. Lower Palaeozoic strata, including the Duguer quartz schist, occur in the Himalaya, Lhasa and South Qiangtang terranes of the Tibetan Plateau. In this study, we report the depositional age and sedimentary provenance of the Duguer quartz schist of the central South Qiangtang terrane, which enables us to interpret the tectonic affinity of the terrane. We obtained U–Pb ages, trace-element compositions and Hf isotopic data from zircons from the Duguer quartz schist. A total of 162 U–Pb analyses of detrital zircons from the schist yielded two pronounced age peaks at c. 600 Ma and c. 960 Ma. These results indicate that the provenance of the Duguer quartz schist is India Gondwana or the terranes that share an affinity with India Gondwana in the Tibetan Plateau, which include the South Qiangtang and Himalaya terranes. Detrital zircon crystals show large variations in Hf isotope compositions, with εHf(t), TDM and TDMC values of −52.5 to 13.2, 900–3300 Ma and 1010–4240 Ma, respectively. This suggests that the source area for the Duguer quartz schist included Precambrian rocks and, more specifically, Pan-African and Grenville–Jinning crustal material. During Pan-African and Grenville–Jinning events, crustal recycling and the addition of mantle material occurred in the source regions of the quartz schist, when the South Qiangtang, Lhasa and Himalaya terranes were all part of the northern margin of Gondwana.
Influence of temporal variation and host condition on helminth abundance in the lizard Tropidurus hispidus from north-eastern Brazil
Authors: Filho J.A. Araujo , Brito S.V. , Lima V.F. , Pereira A.M.A. , Mesquita D.O. , Albuquerque R.L. , Almeida W.O.
Published: April 2016

Ecological characteristics and environmental variation influence both host species composition and parasite abundance. Abiotic factors such as rainfall and temperature can improve parasite development and increase its reproduction rate. The comparison of these assemblages between different environments may give us a more refined analysis of how environment affects the variation of helminth parasite abundance. The aim of the present study was to evaluate how temporal variation, host size, sex and reproduction affect helminth abundance in the Tropidurus hispidus lizard in Caatinga, Restinga and Atlantic Forest environments. Overall, larger-sized lizards showed higher helminth abundance. We found a monthly variation in the helminth species abundance in all studied areas. In the Caatinga area, monoxenic and heteroxenic parasites were related to the rainy season and to the reproductive period of lizards. In Restinga, monoxenic and heteroxenic helminth species were more abundant during the driest months. In the Atlantic Forest, the rainy and host reproductive season occurred continuously throughout the year, so parasite abundance was relatively constant. Nevertheless, heteroxenic species were more abundant in this area. The present results showed that the temporal variation, body size, sex, reproductive period and habitat type influence the abundance and composition of helminth species in T. hispidus.
The Unexpected Power of Informal Workers in the Public Square: A Comparison of Mexican and US Organizing Models
Authors: Sarmiento Hugo , Tilly Chris , de la Garza Toledo Enrique , Gayosso Ramírez José Luis
Published: April 2016

Street vendors in Mexico and day laborers in the United States, both groups of informal workers who labor in public space, face formidable structural obstacles to securing their rights as workers. Despite their apparent vulnerability, these informal workers have built perhaps the most powerful informal worker organizations in their countries. In this article, we explore and explain to the extent possible the sources, forms, and limits of this unexpected power. We explore organizational and strategic commonalities as well as differences and seek to explain both.
Robert Castel's Les métamorphoses de la question sociale (1995)
Authors: van der Linden Marcel
Published: April 2016

In the scholarly debate about the increasingly flexible, informal, and precarious nature of employment relations, it is often suggested that these trends are new. This is especially true for the advanced capitalist countries. “Previously,” employees had permanent jobs, with good social benefits and a vast array of rights, whereas “nowadays” they are losing these forms of security and are more vulnerable to market whims. These observations do not take into account that standard employment relationships in fact came about relatively recently. In the past, insecurity and absence of rights were at least as prevalent as they are today. Standard employment appears to have been generalized rather briefly in a small part of the world. The crucial question is not why the old lack of security is returning, but why it was possible to reduce such insecurity for a small share of the world population for a few decades. While the answer to this crucial question remains unclear; studies reconstructing the course of events over several centuries will clearly be necessary to solve this problem.
The TUC and the Failure of Labour's Postwar Social Agenda
Authors: Oude Nijhuis Dennie
Published: April 2016

This article illustrates the crucial role played by the Trades Union Congress and its occupationally organized union affiliates in the failure of Labour's postwar social agenda. It has been widely recognized that Labour's inability to improve the social insurance system and construct an effective floor under wages during the first decades of the postwar period was of crucial importance to the continual underdevelopment of the British welfare state and the emergence of a dual welfare system in the United Kingdom. Yet that Labour's inability to do so was to a large extent the result of union opposition has largely been neglected. This article shows that Labour's postwar social agenda had strong consequences for the distribution of earnings among different groups of workers and that these consequences were fiercely resisted by unions representing privileged workers. In doing so, this article illustrates the limited political feasibility of government measures to provide adequate earnings and security against labor market risks for all workers in countries where privileged workers largely organize along occupational lines.
Precarious Labor, South and North: An Introduction
Authors: Mosoetsa Sarah , Stillerman Joel , Tilly Chris
Published: April 2016

This special issue on precarious labor in global perspective includes analyses of precarious work in South Africa, Mexico, the United States, China and India. The key strengths of the contributions to this issue are that they demonstrate precarious workers’ capacity for collective action, the hidden forms of work that are not tracked by states, long-term historical continuities of precarious work, and differences between precarious work in the Global North and South. This introduction explores the challenges of conceptualizing precarious work; the history of precarious labor; its variations in the Global North and South; possible differences across sectors of precarious work; and the intersections between precarious work and categories of gender, race, and citizenship status. We conclude with a summary of the articles included in the issue.
Naadmaagewin … The Art of Working Together in Our Communities
Authors: Mumford Marrie
Published: April 2016

During her tenure as Trent University's Canada Research Chair, Marrie Mumford created the Indigenous Performance Studies program and redefined her research goals as “Naadmaagewin … The Art of Working Together in Our Communities.” Anishinaabeg grandmothers in the United States who participate in the Mother Earth Water Walks around the Great Lakes requested the creation of a work about water. The journey began in 2011 at Trent, with Rulan Tangen working with student investigations that led to the creation and production of a work-in-progress. This new work developed into a site-specific work in 2012 and intergenerational workshops that resulted in the creation of a major new work that has since been performed in Santa Fe, New York City, and New Zealand. This article charts the journey of this original work on behalf of the act of clean water.
Slow Scrape (2012–2015)
Authors: Linklater Tanya Lukin
Published: April 2016

How to describe my experience? Some Indigenous peoples have prescribed, specific protocols around introductions, but this is not the case where I'm from. Or, if it was this way in the past, we've lost the knowledge of those introductory protocols. I respect that we should give space to those who have Indigenous ways of introducing themselves. As an Alutiiq woman who lives in a kind of diaspora from my island home of Kodiak in Alaska— and my villages of Port Lions and Afognak—I don't always know how to describe my experience. I am an artist. I live in Canada. I make dance, video, photos, texts.
Catalyst
Authors: Johnson Emily
Published: April 2016

I'm a choreographer and I make performance installation. I am from a very small town on the Kenai Peninsula of Alaska. I'm Yup'ik on my father's side, and my Alaska family is from the Yukon-Kuskokwim Delta. I share this because it's where I'm from, and it's also where my work is from: the physical place of Alaska, and the confluence of my heritage and performance work.
Synthesis, crystal structure, and thermal stability of new borates Na3REB2O6(RE = Pr, Sm, Eu)
Authors: Wang Zhixun , Li Hangkong , Cai Gemei , Jin Zhanpeng
Published: April 2016

Subsolidus phase equilibrium of Na2O–Sm2O3–B2O3system has been investigated mainly by solid-state reaction and powder X-ray diffraction method. There are nine definite three-phase regions and three ternary compounds determined under present experimental conditions. A novel compound Na3SmB2O6was found and confirmed in this system, along with its two homogeneous compounds Na3REB2O6(RE = Pr, Eu) synthesized for the first time. The indexing results showed that all three compounds crystallize in the monoclinic space groupP21/c(No.14) with the same structure type as both Na3NdB2O6and Na3GdB2O6. The lattice parameters (a, b, andc) of new borates Na3REB2O6(RE = Pr, Sm, Eu) decrease linearly with a decreasing radius of RE ion, which obeys the Lanthanide-contraction rule. The existence of a trigonal BO3group in the Na3REB2O6(RE = Pr, Sm) compounds was confirmed by analysis of their infrared absorption spectra. Thermal stabilities of the three new borates have been investigated.
Mathematical modelling of crime and security: Special Issue of EJAM
Authors: Bertozzi Andrea L. , Johnson Shane D. , Ward Michael J.
Published: April 2016

This special issue of the European journal of applied mathematics features research articles that involve the application of mathematical methodologies to the modelling of a broad range of problems related to crime and security. Some specific topics in this issue include recent developments in mathematical models of residential burglary, a dynamical model for the spatial spread of riots initiated by some triggering event, the analysis and development of game-theoretic models of crime and conflict, the study of statistically based models of insurgent activity and terrorism using real-world data sets, models for the optimal strategy of police deployment under realistic constraints, and a model of cyber crime as related to the study of spiking behaviour in social network cyberspace communications. Overall, the mathematical and computational methodologies employed in these studies are as diverse as the specific applications themselves and the scales (spatial or otherwise) to which they are applied. These methodologies range from statistical and stochastic methods based on maximum likelihood methods, Bayesian equilibria, regression analysis, self-excited Hawkes point processes, agent-based random walk models on networks, to more traditional applied mathematical methods such as dynamical systems and stability theory, the theory of Nash equilibria, rigorous methods in partial differential equations and travelling wave theory, and asymptotic methods that exploit disparate space and time scales.
Sibling eating behaviours and parental feeding practices with siblings: similar or different?
Authors: Berge Jerica M , Tate Allan D , Trofholz Amanda , Conger Katherine , Neumark-Sztainer Dianne
Published: April 2016

Objective

Little is known about whether siblings have similar or different eating behaviours or whether parents tailor their feeding practices to different siblings. The main objectives of the present study were to examine similarities and differences in child eating behaviours and parental feeding practices with siblings and to determine whether child eating behaviours and parental feeding practices differ depending on sibling concordant (i.e. both siblings overweight or healthy weight) or discordant (i.e. one sibling overweight and one sibling healthy weight) weight status.

Design

Cross-sectional, mixed-methods study.

Setting

In-home visits were conducted by research staff. Surveys were conducted with parents and anthropometry was collected on parents and siblings.

Subjects

Children (n 88) aged 6–12 years (mean age 9 (sd 2) years), their parents (mean age 34 (sd 7) years) and near-age siblings (mean age 9 (sd 4) years) from diverse racial/ethnic and low-income households participated.

Results

Results indicated that siblings with higher BMI engaged in higher levels of emotional eating compared with siblings with lower BMI. Additionally, results indicated that when families had sibling dyads discordant on weight status, the sibling who was overweight had higher food enjoyment and lower levels of food satiety. Additionally, within siblings with discordant weight status, parents were more likely to use restrictive feeding practices with the overweight sibling and pressure-to-eat and encouragement-to-eat feeding practices with the healthy-weight sibling.

Conclusions

Family-based childhood obesity interventions may need to assess for sibling weight status when researching the home environment and intervene with parents to avoid using restriction or pressure-to-eat feeding practices when siblings are discordant on weight status.
Geschlechtsbezogene Analyse des Tabakkonsums bei Auszubildenden in Pflegeberufen
Authors: Bühler Anneke , Schulze Katrin , Rustler Christa , Scheifhacken Sabine , Schweizer Ines , Bonse-Rohmann Mathias
Published: April 2016

Zusammenfassung. Fragestellung: Raucher- und Frauenanteil sind in der Gruppe der Pflegeberufe überproportional hoch. Es wird überprüft, ob sich Pflegeschüler und Pflegeschülerinnen in Rauchverhalten, rauchbezogenen Risikofaktoren und Einstellung gegenüber verhältnis- und verhaltensbezogenen Maßnahmen voneinander unterscheiden. Zudem interessiert, ob der Raucheranteil bereits zu Beginn der Ausbildung erhöht ist. Methode: Querschnittliche Daten von 357 Auszubildenden aus bundesweit zehn Pflegeschulen wurden ausgewertet. Ergebnisse: Es zeigten sich Geschlechtsunterschiede in einigen Risikofaktoren, weniger im Rauchverhalten oder der Veränderungsbereitschaft. In der Widerstandsgewissheit wiesen Frauen höhere Werte auf als Männer. Rauchende Männer hatten eine weniger riskante deskriptive aber tendenziell riskantere injunktive Normerwartung und äußerten sich eher bereit zur Teilnahme an einem Rauchstoppgruppenkurs. Der hohe Raucheranteil war unter Auszubildenden mit 52,8 % etwa 1,5 Mal so hoch als unter bereits beschäftigten Pflegekräften. Schlussfolgerungen: Eine vorsichtige Interpretation ist angesichts der anfallenden Stichprobe angezeigt. Es besteht ein Bedarf für Tabakentwöhnung sowohl unter Pflegeschülern als auch Pflegeschülerinnen, da viele schon zu Ausbildungsbeginn rauchen. Eine Intervention muss sowohl verhaltens- als auch verhältnisbezogene Elemente beinhalten. Ihre Implementation steht vor der Herausforderung eines Ausbildungskontextes, dessen soziale Norm als rauchfreundlich zu bezeichnen ist.
Lernen mit Texten und Bildern
Authors: Scheiter Katharina , Eitel Alexander , Schüler Anne
Published: April 2016

Zusammenfassung. Das Lernen mit Texten und Bildern (Multimedia) bildet einen wesentlichen Gegenstandsbereich der empirischen Lehr-Lernforschung. Kognitive Theorien des Lernens mit Multimedia fokussieren vor dem Hintergrund des Dreispeichermodells des Gedächtnisses auf die beim Lernen mit Multimedia ablaufenden Informationsverarbeitungsprozesse, von denen angenommen wird, dass diese zunächst in für Text und Bild spezifischen Gedächtnisrepräsentationen resultieren. Dabei wird das Wechselspiel bei der Verarbeitung von Text und Bild und dessen zentrale Rolle für den Aufbau einer Verständnis-basierten mentalen Repräsentation eher vernachlässigt. Im vorliegenden Beitrag skizzieren wir zunächst Befunde unserer Arbeitsgruppe, die für eine stärkere Abhängigkeit von Text- und Bildverarbeitung beim Aufbau eines mentalen Modells sprechen. Darauf aufbauend werden pädagogisch-psychologische Implikationen dieser Forschung beschrieben und mit weiteren empirischen Befunden untermauert. Abschließend wird eine theoretische Perspektive, die stärker durch Modelle des Textverstehens als durch Gedächtnistheorien geprägt ist, für das Lernen mit Multimedia diskutiert.
Climate Modeling with Decision Makers in Mind
Authors: Jones Andrew , Calvin Katherine , Lamarque Jean-François
Published: April 2016

Impact Relevance and Usability of High Resolution Climate Modeling and Datasets; Aspen, Colorado, 2–7 August 2015
Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance
Authors: Brooun Alexei , Gajiwala Ketan S. , Deng Ya-Li , Liu Wei , Bolaños Ben , Bingham Patrick , He You-Ai , Diehl Wade , Grable Nicole , Kung Pei-Pei , Sutton Scott , Maegley Karen A. , Yu Xiu , Stewart Al E.
Published: April 2016

Polycomb repressive complex 2 (PRC2) mediates gene silencing through chromatin reorganization by methylation of histone H3 lysine 27 (H3K27). Overexpression of the complex and point mutations in the individual subunits of PRC2 have been shown to contribute to tumorigenesis. Several inhibitors of the PRC2 activity have shown efficacy in EZH2-mutated lymphomas and are currently in clinical development, although the molecular basis of inhibitor recognition remains unknown. Here we report the crystal structures of the inhibitor-bound wild-type and Y641N PRC2. The structures illuminate an important role played by a stretch of 17 residues in the N-terminal region of EZH2, we call the activation loop, in the stimulation of the enzyme activity, inhibitor recognition and the potential development of the mutation-mediated drug resistance. The work presented here provides new avenues for the design and development of next-generation PRC2 inhibitors through establishment of a structure-based drug design platform.
Trapping mammalian protein complexes in viral particles
Authors: Eyckerman Sven , Titeca Kevin , Van Quickelberghe Emmy , Cloots Eva , Verhee Annick , Samyn Noortje , De Ceuninck Leentje , Timmerman Evy , De Sutter Delphine , Lievens Sam , Van Calenbergh Serge , Gevaert Kris , Tavernier Jan
Published: April 2016

Cell lysis is an inevitable step in classical mass spectrometry–based strategies to analyse protein complexes. Complementary lysis conditions, in situ cross-linking strategies and proximal labelling techniques are currently used to reduce lysis effects on the protein complex. We have developed Virotrap, a viral particle sorting approach that obviates the need for cell homogenization and preserves the protein complexes during purification. By fusing a bait protein to the HIV-1 GAG protein, we show that interaction partners become trapped within virus-like particles (VLPs) that bud from mammalian cells. Using an efficient VLP enrichment protocol, Virotrap allows the detection of known binary interactions and MS-based identification of novel protein partners as well. In addition, we show the identification of stimulus-dependent interactions and demonstrate trapping of protein partners for small molecules. Virotrap constitutes an elegant complementary approach to the arsenal of methods to study protein complexes.
An essential malaria protein defines the architecture of blood-stage and transmission-stage parasites
Authors: Absalon Sabrina , Robbins Jonathan A. , Dvorin Jeffrey D.
Published: April 2016

Blood-stage replication of the human malaria parasite Plasmodium falciparum occurs via schizogony, wherein daughter parasites are formed by a specialized cytokinesis known as segmentation. Here we identify a parasite protein, which we name P. falciparum Merozoite Organizing Protein (PfMOP), as essential for cytokinesis of blood-stage parasites. We show that, following PfMOP knockdown, parasites undergo incomplete segmentation resulting in a residual agglomerate of partially divided cells. While organelles develop normally, the structural scaffold of daughter parasites, the inner membrane complex (IMC), fails to form in this agglomerate causing flawed segmentation. In PfMOP-deficient gametocytes, the IMC formation defect causes maturation arrest with aberrant morphology and death. Our results provide insight into the mechanisms of replication and maturation of malaria parasites.
Imaging large-scale cellular activity in spinal cord of freely behaving mice
Authors: Sekiguchi Kohei J. , Shekhtmeyster Pavel , Merten Katharina , Arena Alexander , Cook Daniela , Hoffman Elizabeth , Ngo Alexander , Nimmerjahn Axel
Published: April 2016

Sensory information from mechanoreceptors and nociceptors in the skin plays key roles in adaptive and protective motor behaviours. To date, very little is known about how this information is encoded by spinal cord cell types and their activity patterns, particularly under freely behaving conditions. To enable stable measurement of neuronal and glial cell activity in behaving mice, we have developed fluorescence imaging approaches based on two- and miniaturized one-photon microscopy. We show that distinct cutaneous stimuli activate overlapping ensembles of dorsal horn neurons, and that stimulus type and intensity is encoded at the single-cell level. In contrast, astrocytes show large-scale coordinated calcium responses to intense but not weak sensory inputs. Sensory-evoked activity is potently suppressed by anaesthesia. By revealing the cellular and computational logic of spinal cord networks under behaving conditions, our approach holds promise for better understanding of healthy and aberrant spinal cord processes.
The structural basis of chicken, swine and bovine CD8αα dimers provides insight into the co-evolution with MHC I in endotherm species
Authors: Liu Yanjie , Li Xin , Qi Jianxun , Zhang Nianzhi , Xia Chun
Published: April 2016

It is unclear how the pivotal molecules of the adaptive immune system (AIS) maintain their inherent characteristics and relationships with their co-receptors over the course of co-evolution. CD8α, a fundamental but simple AIS component with only one immunoglobulin variable (IgV) domain, is a good example with which to explore this question because it can fold correctly to form homodimers (CD8αα) and interact with peptide-MHC I (p/MHC I) with low sequence identities between different species. Hereby, we resolved the crystal structures of chicken, swine and bovine CD8αα. They are typical homodimers consisting of two symmetric IgV domains with distinct species specificities. The CD8αα structures indicated that a few highly conserved residues are important in CD8 dimerization and in interacting with p/MHC I. The dimerization of CD8αα mainly depends on the pivotal residues on the dimer interface; in particular, four aromatic residues provide many intermolecular forces and contact areas. Three residues on the surface of CD8α connecting cavities that formed most of the hydrogen bonds with p/MHC I were also completely conserved. Our data propose that a few key conserved residues are able to ensure the CD8α own structural characteristics despite the great sequence variation that occurs during evolution in endotherms.
Complete genomes of Hairstreak butterflies, their speciation and nucleo-mitochondrial incongruence
Authors: Cong Qian , Shen Jinhui , Borek Dominika , Robbins Robert K. , Otwinowski Zbyszek , Grishin Nick V.
Published: April 2016

Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729 Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30 years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies.
High-resolution analytical imaging and electron holography of magnetite particles in amyloid cores of Alzheimer’s disease
Authors: Plascencia-Villa Germán , Ponce Arturo , Collingwood Joanna F. , Arellano-Jiménez M. Josefina , Zhu Xiongwei , Rogers Jack T. , Betancourt Israel , José-Yacamán Miguel , Perry George
Published: April 2016

Abnormal accumulation of brain metals is a key feature of Alzheimer’s disease (AD). Formation of amyloid-β plaque cores (APC) is related to interactions with biometals, especially Fe, Cu and Zn, but their particular structural associations and roles remain unclear. Using an integrative set of advanced transmission electron microscopy (TEM) techniques, including spherical aberration-corrected scanning transmission electron microscopy (Cs-STEM), nano-beam electron diffraction, electron holography and analytical spectroscopy techniques (EDX and EELS), we demonstrate that Fe in APC is present as iron oxide (Fe3O4) magnetite nanoparticles. Here we show that Fe was accumulated primarily as nanostructured particles within APC, whereas Cu and Zn were distributed through the amyloid fibers. Remarkably, these highly organized crystalline magnetite nanostructures directly bound into fibrillar Aβ showed characteristic superparamagnetic responses with saturated magnetization with circular contours, as observed for the first time by off-axis electron holography of nanometer scale particles.
PTIR: Predicted Tomato Interactome Resource
Authors: Yue Junyang , Xu Wei , Ban Rongjun , Huang Shengxiong , Miao Min , Tang Xiaofeng , Liu Guoqing , Liu Yongsheng
Published: April 2016

Protein-protein interactions (PPIs) are involved in almost all biological processes and form the basis of the entire interactomics systems of living organisms. Identification and characterization of these interactions are fundamental to elucidating the molecular mechanisms of signal transduction and metabolic pathways at both the cellular and systemic levels. Although a number of experimental and computational studies have been performed on model organisms, the studies exploring and investigating PPIs in tomatoes remain lacking. Here, we developed a Predicted Tomato Interactome Resource (PTIR), based on experimentally determined orthologous interactions in six model organisms. The reliability of individual PPIs was also evaluated by shared gene ontology (GO) terms, co-evolution, co-expression, co-localization and available domain-domain interactions (DDIs). Currently, the PTIR covers 357,946 non-redundant PPIs among 10,626 proteins, including 12,291 high-confidence, 226,553 medium-confidence and 119,102 low-confidence interactions. These interactions are expected to cover 30.6% of the entire tomato proteome and possess a reasonable distribution. In addition, ten randomly selected PPIs were verified using yeast two-hybrid (Y2H) screening or a bimolecular fluorescence complementation (BiFC) assay. The PTIR was constructed and implemented as a dedicated database and is available at http://bdg.hfut.edu.cn/ptir/index.html without registration.
Screening of efficient siRNA carriers in a library of surface-engineered dendrimers
Authors: Liu Hongmei , Chang Hong , Lv Jia , Jiang Cong , Li Zhenxi , Wang Fei , Wang Hui , Wang Mingming , Liu Chongyi , Wang Xinyu , Shao Naimin , He Bingwei , Shen Wanwan , Zhang Qiang , Cheng Yiyun
Published: April 2016

Polymers are widely used as non-viral carriers for siRNA delivery, but concern has also arisen in their limited efficacy and inherent toxicity. Whilst many of previous efforts have been documented towards improving the performance of polymers via chemical modifications, the structure-activity relationships (SAR) of these ligand-modified polymers are not well understood. To address this issue, we systemically prepared a library of surface-engineered dendrimers (>300) as the screening pool to discover efficient siRNA carriers. The modified ligands include alkyls and fluoroalkyls, amino acids, benzene derivatives and heterocyclic compounds. Gene silencing results showed that the lead material shows excellent efficacy even in hard-to-transfect cells such as mesenchymal stem cells. The SAR studies revealed that ligands containing appropriate hydrophobicity, or ligands with both hydrophobic and functional atoms/groups are essential for polymers to achive efficient knockdown efficacy. A second-generation library designed based on the above principles further confirms the proposed design criteria. The results enable the future rational design of potent siRNA carriers.
Self-assembled Biodegradable Nanoparticles and Polysaccharides as Biomimetic ECM Nanostructures for the Synergistic effect of RGD and BMP-2 on Bone Formation
Authors: Wang Zhenming , Dong Li , Han Lu , Wang Kefeng , Lu Xiong , Fang Liming , Qu Shuxin , Chan Chun Wai
Published: April 2016

Producing biomimetic extracellular matrix (ECM) is an effective approach to improve biocompatibility of medical devices. In this study, biomimetic ECM nanostructures are constructed through layer-by-layer self-assembling positively charged chitosan (Chi), negatively charged oxidized sodium alginate (OAlg), and positively charged bovine serum albumin (BSA)-based nanoparticles. The BSA-based nanoparticles in the self-assembled films not only result in porous nanostructures similar to natural ECM, but also preserve the activity and realize the sustained release of Bone morphogenetic protein-2 (BMP-2). The results of bone marrow stem cells (BMSCs) culture demonstrate that the penta-peptide glycine-arginine-glycine-aspartate-serine (GRGDS) grafted Chi/OAlg films favor cell adhesion and proliferation. GRGDS and BMP-2 in biomimetic ECM nanostructures synergistically promote BMSC functions and new bone formation. The RGD and BMP incorporated biomimetic ECM coatings could be applied on a variety of biomedical devices to improve the bioactivity and biocompatibility.
Discovery of a novel glucose metabolism in cancer: The role of endoplasmic reticulum beyond glycolysis and pentose phosphate shunt
Authors: Marini Cecilia , Ravera Silvia , Buschiazzo Ambra , Bianchi Giovanna , Orengo Anna Maria , Bruno Silvia , Bottoni Gianluca , Emionite Laura , Pastorino Fabio , Monteverde Elena , Garaboldi Lucia , Martella Roberto , Salani Barbara , Maggi Davide , Ponzoni Mirco , Fais Franco , Raffaghello Lizzia , Sambuceti Gianmario
Published: April 2016

Cancer metabolism is characterized by an accelerated glycolytic rate facing reduced activity of oxidative phosphorylation. This “Warburg effect” represents a standard to diagnose and monitor tumor aggressiveness with 18F-fluorodeoxyglucose whose uptake is currently regarded as an accurate index of total glucose consumption. Studying cancer metabolic response to respiratory chain inhibition by metformin, we repeatedly observed a reduction of tracer uptake facing a marked increase in glucose consumption. This puzzling discordance brought us to discover that 18F-fluorodeoxyglucose preferentially accumulates within endoplasmic reticulum by exploiting the catalytic function of hexose-6-phosphate-dehydrogenase. Silencing enzyme expression and activity decreased both tracer uptake and glucose consumption, caused severe energy depletion and decreased NADPH content without altering mitochondrial function. These data document the existence of an unknown glucose metabolism triggered by hexose-6-phosphate-dehydrogenase within endoplasmic reticulum of cancer cells. Besides its basic relevance, this finding can improve clinical cancer diagnosis and might represent potential target for therapy.
Plet1 is an epigenetically regulated cell surface protein that provides essential cues to direct trophoblast stem cell differentiation
Authors: Murray Alexander , Sienerth Arnold R. , Hemberger Myriam
Published: April 2016

Gene loci that are hypermethylated and repressed in embryonic (ESCs) but hypomethylated and expressed in trophoblast (TSCs) stem cells are very rare and may have particularly important roles in early developmental cell fate decisions, as previously shown for Elf5. Here, we assessed another member of this small group of genes, Placenta Expressed Transcript 1 (Plet1), for its function in establishing trophoblast lineage identity and modulating trophoblast differentiation. We find that Plet1 is tightly repressed by DNA methylation in ESCs but expressed on the cell surface of TSCs and trophoblast giant cells. In hypomethylated ESCs that are prone to acquire some trophoblast characteristics, Plet1 is required to confer a trophoblast-specific gene expression pattern, including up-regulation of Elf5. Plet1 displays an unusual biphasic expression profile during TSC differentiation and thus may be pivotal in balancing trophoblast self-renewal and differentiation. Furthermore, overexpression and CRISPR/Cas9-mediated knockout in TSCs showed that high Plet1 levels favour differentiation towards the trophoblast giant cell lineage, whereas lack of Plet1 preferentially induces syncytiotrophoblast formation. Thus, the endogenous dynamics of Plet1 expression establish important patterning cues within the trophoblast compartment by promoting differentiation towards the syncytiotrophoblast or giant cell pathway in Plet1-low and Plet1-high cells, respectively.
Histone Modifications in a Mouse Model of Early Adversities and Panic Disorder: Role for Asic1 and Neurodevelopmental Genes
Authors: Cittaro Davide , Lampis Valentina , Luchetti Alessandra , Coccurello Roberto , Guffanti Alessandro , Felsani Armando , Moles Anna , Stupka Elia , D’ Amato Francesca R. , Battaglia Marco
Published: April 2016

Hyperventilation following transient, CO2-induced acidosis is ubiquitous in mammals and heritable. In humans, respiratory and emotional hypersensitivity to CO2 marks separation anxiety and panic disorders and is enhanced by early-life adversities. Mice exposed to the repeated cross-fostering paradigm (RCF) of interference with maternal environment show heightened separation anxiety and hyperventilation to 6% CO2-enriched air. Gene-environment interactions affect CO2 hypersensitivity in both humans and mice. We therefore hypothesised that epigenetic modifications and increased expression of genes involved in pH-detection could explain these relationships. Medullae oblongata of RCF- and normally-reared female outbred mice were assessed by ChIP-seq for H3Ac, H3K4me3, H3K27me3 histone modifications and by SAGE for differential gene expression. Integration of multiple experiments by network analysis revealed an active component of 148 genes pointing to the mTOR signalling pathway and nociception. Among these genes, Asic1 showed heightened mRNA expression, coherent with RCF-mice’s respiratory hypersensitivity to CO2 and altered nociception. Functional enrichment and mRNA transcript analyses yielded a consistent picture of enhancement for several genes affecting chemoception, neurodevelopment and emotionality. Particularly, results with Asic1 support recent human findings with panic and CO2 responses and provide new perspectives on how early adversities and genes interplay to affect key components of panic and related disorders.
Saffron with resistance exercise improves diabetic parameters through the GLUT4/AMPK pathway in-vitro and in-vivo
Authors: Dehghan Firouzeh , Hajiaghaalipour Fatemeh , Yusof Ashril , Muniandy Sekaran , Hosseini Seyed Ali , Heydari Sedigheh , Salim Landa Zeenelabdin Ali , Azarbayjani Mohammad Ali
Published: April 2016

Saffron is consumed as food and medicine to treat several illnesses. This study elucidates the saffron effectiveness on diabetic parameters in-vitro and combined with resistance exercise in-vivo. The antioxidant properties of saffron was examined. Insulin secretion and glucose uptake were examined by cultured RIN-5F and L6 myotubes cells. The expressions of GLUT2, GLUT4 and AMPKα were determined by Western blot. Diabetic and non-diabetic male rats were divided into: control, training, extract treatment, training + extract treatment and metformin. The exercise and 40 mg/kg/day saffron treatments were carried out for six weeks. The antioxidant capacity of saffron was higher compare to positive control (P < 0.01). High dose of saffron stimulated insulin release in RIN-5F cells and improved glucose uptake in L6 myotubes. GLUT4 and AMPKα expressions increased in both doses of saffron (P < 0.01), whereas GLUT2 not changed (p > 0.05). Serum glucose, cholesterol, triglyceride, low-density lipoprotein, very low-density lipoprotein, insulin resistance and glycated hemoglobin levels decreased in treated rats compared to untreated (p < 0.01). However, no significant differences were observed in the high-density lipoprotein, insulin, adiponectin and leptin concentration levels in all groups (p > 0.05). The findings suggest that saffron consuming alongside exercise could improve diabetic parameters through redox-mediated mechanisms and GLUT4/AMPK pathway to entrap glucose uptake.
Epitaxial growth and magnetic properties of ultraviolet transparent Ga2O3/(Ga1−xFex)2O3 multilayer thin films
Authors: Guo Daoyou , An Yuehua , Cui Wei , Zhi Yusong , Zhao Xiaolong , Lei Ming , Li Linghong , Li Peigang , Wu Zhenping , Tang Weihua
Published: April 2016

Multilayer thin films based on the ferromagnetic and ultraviolet transparent semiconductors may be interesting because their magnetic/electronic/photonic properties can be manipulated by the high energy photons. Herein, the Ga2O3/(Ga1−xFex)2O3 multilayer epitaxial thin films were obtained by alternating depositing of wide band gap Ga2O3 layer and Fe ultrathin layer due to inter diffusion between two layers at high temperature using the laser molecular beam epitaxy technique. The multilayer films exhibits a preferred growth orientation of "Equation missing" crystal plane and the crystal lattice expands as Fe replaces Ga site. Fe ions with a mixed valence of Fe2+ and Fe3+ are stratified distributed in the film and exhibit obvious agglomerated areas. The multilayer films only show a sharp absorption edge at about 250 nm, indicating a high transparency for ultraviolet light. What’s more, the Ga2O3/(Ga1−xFex)2O3 multilayer epitaxial thin films also exhibits room temperature ferromagnetism deriving from the Fe doping Ga2O3.
Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions
Authors: Belmonte Frances R. , Martin James L. , Frescura Kristin , Damas Joana , Pereira Filipe , Tarnopolsky Mark A. , Kaufman Brett A.
Published: April 2016

Mitochondrial DNA (mtDNA) mutations are a common cause of primary mitochondrial disorders and have also been implicated in a broad collection of conditions, including aging, neurodegeneration and cancer. Prevalent among these pathogenic variants are mtDNA deletions, which show a strong bias for the loss of sequence in the major arc between, but not including, the heavy and light strand origins of replication. Because individual mtDNA deletions can accumulate focally, occur with multiple mixed breakpoints and in the presence of normal mtDNA sequences, methods that detect broad-spectrum mutations with enhanced sensitivity and limited costs have both research and clinical applications. In this study, we evaluated semi-quantitative and digital PCR-based methods of mtDNA deletion detection using double-stranded reference templates or biological samples. Our aim was to describe key experimental assay parameters that will enable the analysis of low levels or small differences in mtDNA deletion load during disease progression, with limited false-positive detection. We determined that the digital PCR method significantly improved mtDNA deletion detection sensitivity through absolute quantitation, improved precision and reduced assay standard error.
Effect of electrode position on azo dye removal in an up-flow hybrid anaerobic digestion reactor with built-in bioelectrochemical system
Authors: Cui Min-Hua , Cui Dan , Lee Hyung-Sool , Liang Bin , Wang Ai-Jie , Cheng Hao-Yi
Published: April 2016

In this study, two modes of hybrid anaerobic digestion (AD) bioreactor with built-in BESs (electrodes installed in liquid phase (R1) and sludge phase (R2)) were tested for identifying the effect of electrodes position on azo dye wastewater treatment. Alizarin yellow R (AYR) was used as a model dye. Decolorization efficiency of R1 was 90.41 ± 6.20% at influent loading rate of 800 g-AYR/ m3·d, which was 39% higher than that of R2. The contribution of bioelectrochemical reduction to AYR decolorization (16.23 ± 1.86% for R1 versus 22.24 ± 2.14% for R2) implied that although azo dye was mainly removed in sludge zone, BES further improved the effluent quality, especially for R1 where electrodes were installed in liquid phase. The microbial communities in the electrode biofilms (dominant by Enterobacter) and sludge (dominant by Enterococcus) were well distinguished in R1, but they were similar in R2. These results suggest that electrodes installed in liquid phase in the anaerobic hybrid system are more efficient than that in sludge phase for azo dye removal, which give great inspirations for the application of AD-BES hybrid process for various refractory wastewaters treatment.