bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inherited chromosomally integrated human herpesvirus 6 genomes are ancient, intact and potentially able to reactivate from telomeres
Authors: Zhang Enjie , Bell Adam J , Wilkie Gavin S , Suárez Nicolás M , Batini Chiara , Veal Colin D , Armendáriz-Castillo Isaac , Neumann Rita , Cotton Victoria E , Huang Yan , Porteous David J , Jarrett Ruth F , Davison Andrew J , Royle Nicola J 
Published: July 2017

ABSTRACTHuman herpesviruses 6A and 6B (HHV6-A and HHV-6B; speciesHuman herpesvirus 6AandHuman herpesvirus 6B) have the capacity to integrate into telomeres, the essential capping structures of chromosomes that play roles in cancer and ageing. About 1% of people worldwide are carriers of chromosomally integrated HHV-6 (ciHHV-6), which is inherited as a genetic trait. Understanding the consequences of integration for the evolution of the viral genome, for the telomere and for the risk of disease associated with carrier status is hampered by a lack of knowledge about ciHHV-6 genomes. Here, we report an analysis of 28 ciHHV-6 genomes and show that they are significantly divergent from the few modern non-integrated HHV-6 strains for which complete sequences are currently available. In addition ciHHV-6B genomes in Europeans are more closely related to each other than to ciHHV-6B genomes from China and Pakistan, suggesting regional variation of the trait. Remarkably, at least one group of European ciHHV-6B carriers has inherited the same ciHHV-6B genome, integrated in the same telomere allele, from a common ancestor estimated to have existed 24,500 ±10,600 years ago. Despite the antiquity of some, and possibly most, germline HHV-6 integrations, the majority of ciHHV-6B (95%) and ciHHV-6A (72%) genomes contain a full set of intact viral genes and therefore appear to have the capacity for viral gene expression and full reactivation.IMPORTANCEInheritance of HHV-6A or HHV-6B integrated into a telomere occurs at a low frequency in most populations studied to date but its characteristics are poorly understood. However, stratification of ciHHV-6 carriers in modern populations due to common ancestry is an important consideration for genome-wide association studies that aim to identify disease risks for these people. Here we present full sequence analysis of 28 ciHHV-6 genomes and show that ciHHV-6B in many carriers with European ancestry most likely originated from ancient integration events in a small number of ancestors. We propose that ancient ancestral origins for ciHHV-6A and ciHHV-6B are also likely in other populations. Moreover, despite their antiquity, all of the ciHHV-6 genomes appear to retain the capacity to express viral genes and most are predicted to be capable of full viral reactivation. These discoveries represent potentially important considerations in immune-compromised patients, in particular in organ transplantation and in stem cell therapy.
Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution
Authors: Raghwani Jayna , Thompson Robin , Koelle Katia 
Published: July 2017

ABSTRACTMost studies on seasonal influenza A/H3N2 virus adaptation have focused on the main antigenic gene, haemagglutinin. However, there is increasing evidence that the genome-wide genetic background of novel antigenic variants can influence these variants’ emergence probabilities and impact their patterns of dominance in the population. This suggests that non-antigenic genes may be important in shaping the viral evolutionary dynamics. To better understand the role of selection on non-antigenic genes in the adaptive evolution of seasonal influenza viruses, we here develop a simple population genetic model that considers a virus with one antigenic and one non-antigenic gene segment. By simulating this model under different regimes of selection and reassortment, we find that the empirical patterns of lineage turnover for the antigenic and non-antigenic gene segments are best captured when there is both limited viral coinfection and selection operating on both gene segments. In contrast, under a scenario of only neutral evolution in the non-antigenic gene segment, we see persistence of multiple lineages for long periods of time in that segment, which is not compatible with the observed molecular evolutionary patterns. Further, we find that reassortment, occurring in coinfected individuals, can increase the speed of viral adaptive evolution by primarily reducing selective interference and genetic linkage effects mediated by the non-antigenic gene segment. Together, these findings suggest that, for influenza, with 6 internal or non-antigenic gene segments, the evolutionary dynamics of novel antigenic variants are likely to be influenced by the genome-wide genetic background as a result of linked selection among both beneficial and deleterious mutations.
Multi-modal meta-analysis of 1494 hepatocellular carcinoma samples reveals vast impacts of consensus driver genes on phenotypes
Authors: Chaudhary Kumardeep , Poirion Olivier B , Lu Liangqun , Huang Sijia , Ching Travers , Garmire Lana X 
Published: July 2017

AbstractAlthough driver genes in hepatocellular carcinoma (HCC) have been investigated in various previous genetic studies, prevalence of key driver genes among heterogeneous populations is unknown. Moreover, the phenotypic associations of these driver genes are poorly understood. This report aims to reveal the phenotypic impacts of a group of consensus driver genes in HCC. We used MutSigCV and OncodriveFM modules implemented in the IntOGen pipeline to identify consensus driver genes across six HCC cohorts comprising 1,494 samples in total. To access their global impacts, we used TCGA mutations and copy number variations to predict the transcriptomics data, under generalized linear models. We further investigated the associations of the consensus driver genes to patient survival, age, gender, race and risk factors. We identify 10 consensus driver genes across six HCC cohorts in total. Integrative analysis of driver mutations, copy number variations and transcriptomic data reveals that these consensus driver mutations and their copy number variations are associated with majority (62.5%) of the mRNA transcriptome, but only a small fraction (8.9%) of miRNAs. Genes associated withTP53, CTNNB1, andARID1Amutations contribute to the tripod of most densely connected pathway clusters. These driver genes are significantly associated with patients’ overall survival. Some driver genes are significantly linked to HCC gender (CTNNB1, ALB, TP53andAXIN1), race (TP53andCDKN2A), and age (RB1) disparities. This study prioritizes a group of consensus drivers in HCC, which collectively show vast impacts on the phenotypes. These driver genes may warrant as valuable therapeutic targets of HCC.
The Emergence of Egalitarianism in a Model of Early Human Societies
Authors: Calmettes Guillaume , Weiss James N. 
Published: July 2017

AbstractHow did egalitarianism emerge in early human societies? In contrast to dominance hierarchies in non-human primates, human simple forager bands are typically egalitarian, with male hunters often serving as the collective alpha. Here we present a thermodynamics-inspired simple population model, based on stochastic optimization of dominance relationships, in which a dominance hierarchy of individuals with exclusively self-centered characteristics (the desire to dominate, resentment at being dominated) transitions spontaneously to egalitarianism as their capacity for language develops. Language, specifically gossip, allows resentment against being dominated to promote the formation of antidominance coalitions which destabilize the alpha position for individuals, leading to a phase transition in which a coalition of the full population suddenly becomes dominant. Thus, egalitarianism emerges suddenly as the optimal power sharing arrangement in a population of selfish individuals without any inherently altruistic qualities. We speculate that egalitarianism driven by punishment for exhibiting alpha-like behavior may then set the stage for genuinely altruistic traits to propagate as predicted by game theory models. Based on model simulations, we also predict that egalitarianism is a pre-condition for adaptation of tools as weapons. Potential implications for origins of human moral belief systems are discussed.
Environmental anchoring of grid-like representations minimizes spatial uncertainty during navigation
Authors: Navarro Schröder Tobias , Towse Benjamin W. , Nau Matthias , Burgess Neil , Barry Caswell , Doeller Christian F. 
Published: July 2017

SummaryMinimizing spatial uncertainty is essential for navigation, but the neural mechanisms remain elusive. Here we combine predictions of a simulated grid cell system with behavioural and fMRI measures in humans during virtual navigation. First, we showed that polarising cues produce anisotropy in motion parallax. Secondly, we simulated entorhinal grid cells in an environment with anisotropic information and found that self-location is decoded best when grid-patterns are aligned with the axis of greatest information. Thirdly, when exposing human participants to polarised virtual reality environments, we found that navigation performance is anisotropic, in line with the use of parallax. Eye movements showed that participants preferentially viewed polarising cues, which correlated with navigation performance. Finally, using fMRI we found that the orientation of grid-cell-like representations in entorhinal cortex anchored to the environmental axis of greatest parallax information, orthogonal to the polarisation axis. In sum, we demonstrate a crucial role of the entorhinal grid system in reducing uncertainty in representations of self-location and find evidence for adaptive spatial computations underlying entorhinal representations in service of optimal navigation.
Growth strategies and threshold responses to water deficit modulate effects of warming on tree seedlings from forest to alpine
Authors: Lazarus Brynne E. , Castanha Cristina , Germino Matthew J. , Kueppers Lara M. , Moyes Andrew B. 
Published: July 2017

Abstract

Predictions of upslope range shifts for tree species with warming are based on assumptions of moisture stress at lower elevation limits and low‐temperature stress at high‐elevation limits. However, recent studies have shown that warming can reduce tree seedling establishment across the entire gradient from subalpine forest to alpine via moisture limitation. Warming effects also vary with species, potentially resulting in community shifts in high‐elevation forests.

We examined the growth and physiology underlying effects of warming on seedling demographic patterns. We evaluated dry mass (DM), root length, allocation above‐ and below‐ground, and relative growth rate (RGR) of whole seedlings, and their ability to avoid or endure water stress via water‐use efficiency and resisting turgor loss, for Pinus flexilis, Picea engelmannii and Pinus contorta seeded below, at and above tree line in experimentally warmed, watered and control plots in the Rocky Mountains, USA. We expected that growth and allocation responses to warming would relate to moisture status and that variation in drought tolerance traits would explain species differences in survival rates.

Across treatments and elevations, seedlings of all species had weak turgor‐loss resistance, and growth was marginal with negative RGR in the first growth phase (−0.01 to −0.04 g g−1 day−1). Growth was correlated with soil moisture, particularly in the relatively small‐seeded P. contorta and P. engelmannii. Pinus flexilis, known to have the highest survivorship, attained the greatest DM and longest root but was also the slowest growing and most water‐use efficient. This was likely due to its greater reliance on seed reserves. Seedlings developed 15% less total DM, 25% less root DM and 11% shorter roots in heated compared with unheated plots. Higher temperatures slightly increased DM, root length and RGR where soils were wettest, but more strongly decreased these variables under drier conditions.

Synthesis. The surprising heat inhibition of tree seedling establishment at the cold edge of forests appears to have a physiological basis: newly germinated seedlings have poor moisture stress tolerance, which appears related to marginal initial growth and heavy reliance on seed reserves. Variation in these attributes among tree species at tree line helps explain their different climate responses.
Fatal attraction of non‐vector impairs fitness of manipulating plant virus
Authors: Ángeles‐López Yesenia Ithaí , Rivera‐Bustamante Rafael , Heil Martin 
Published: July 2017

Abstract

Host manipulation refers to the expression of a host phenotype that is partly under the genetic control of a parasite. This phenomenon can enhance parasite transmission rates and is responsible for biological marvels such as “Zombie‐ants” and the “fatal attraction” of Toxoplasma‐infected rodents to their feline predators. Such host manipulation has evolved in all major phylogenetic lineages of parasites and is assumed to enhance the fitness of the parasite.

However, the capacity to manipulate is not ubiquitous; that is, many clades of parasites comprise manipulating and non‐manipulating species. This pattern leads to the prediction of costs that select against the evolution of manipulation, but this has been difficult to show empirically.

In the present study, we used a tripartitate system consisting of chili (Capsicum annuum) plants infected with Pepper golden mosaic virus and colonized by non‐vector whiteflies (Trialeurodes vaporariorum), to study the effects on viral load when a non‐vector herbivore feeds on the infected plants.

We observed that virus‐infected plants emitted odours that attracted adult whiteflies, contained three times more amino acids in the phloem than mock‐inoculated controls and supported higher whitefly reproduction as compared to controls. However, viral load decreased almost 100‐fold in whitefly‐carrying plants, which was associated with a depletion of phloem amino acids.

Synthesis. We show that a plant virus can suffer from a reduced within‐host reproduction rate when virus‐induced alterations of the plant cause a “fatal attraction” of a non‐vector insect that exploits the altered plant phenotype at its own benefits. The resulting fitness costs might represent a force that can select against the evolution of host manipulation by parasites.
Metagenome‐based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments
Authors: Doyle Conor J. , O'Toole Paul W. , Cotter Paul D. 
Published: July 2017

SummaryMetagenomic‐based analyses have the potential to revolutionize our understanding of the microbiology of food production and processing environments. By adopting such approaches, it will be possible to more accurately determine sources of microbial contamination, identify critical control points for such contaminants, and select practices that optimize quality and safety. This mini‐review will discuss the merits of adopting metagenostic‐based approaches, highlight novel insights that they have provided to date and consider how they could be further implemented.
Regulatory roles of introns in fungicide sensitivity of Fusarium graminearum
Authors: Li Yanjun , Luo Shunwen , Jia Xiaojing , Zhu Yuanye , Chen Dongming , Duan Yabing , Hou Yiping , Zhou Mingguo 
Published: July 2017

SummaryAlthough the roles of introns have been much debated in eukaryotic organisms, none of them have been functionally characterized in Fusarium graminearum. In this study, we characterized the roles of introns in regulation of fungicide‐sensitivity of F. graminearum. β2tub, cyp51A and myosin‐5 are important target genes of benzimidazoles, triazoles and cyanoacrylates respectively. To explore the sensitivity regulation functions of introns in target genes, several detailed deletion studies were completed on the intronic regions of β2tub, cyp51A and myosin‐5. Phenotypic analyses showed that deletion of the fourth intron from β2tub gene (designated β2Δi4), the sole intron from cyp51A gene (cyp51A‐Δi) and the second intron from myosin‐5 gene (myo5‐Δi2) exhibited an increased sensitivity to corresponding fungicides. In contrast, deletion of the first or second intron from β2tub gene exhibited a decreased sensitivity to carbendazim. qRT‐PCR showed that the mRNA transcript levels of target genes were significantly downregulated in β2Δi4, cyp51A‐Δi and myo5‐Δi2 respectively. Meanwhile, Western blot assays revealed that the protein expression levels of β2tub was also dramatically reduced in β2Δi4, but accumulated in β2Δi1 and β2Δi2. Overall, our results indicate that introns in target genes significantly regulate the fungicide‐sensitivity by influencing expression of the corresponding resident genes in F. graminearum.
Eyeball Position in Facial Approximation: Accuracy of Methods for Predicting Globe Positioning in Lateral View
Authors: Zednikova Mala Pavla , Veleminska Jana 
Published: July 2017

AbstractThis study measured the accuracy of traditional and validated newly proposed methods for globe positioning in lateral view. Eighty lateral head cephalograms of adult subjects from Central Europe were taken, and the actual and predicted dimensions were compared. The anteroposterior eyeball position was estimated as the most accurate method based on the proportion of the orbital height (SEE = 1.9 mm) and was followed by the “tangent to the iris method” showing SEE = 2.4 mm. The traditional “tangent to the cornea method” underestimated the eyeball projection by SEE = 5.8 mm. Concerning the superoinferior eyeball position, the results showed a deviation from a central to a more superior position by 0.3 mm, on average, and the traditional method of central positioning of the globe could not be rejected as inaccurate (SEE = 0.3 mm). Based on regression analyzes or proportionality of the orbital height, the SEE = 2.1 mm.
The Frontal Sinus Cavity Exhibits Sexual Dimorphism in 3D Cone‐beam CT Images and can be Used for Sex Determination
Authors: Choi Isabela G. G. , Duailibi‐Neto Eduardo F. , Beaini Thiago L. , da Silva Renan L. B. , Chilvarquer Israel 
Published: July 2017

AbstractFew studies have assessed the use of the frontal sinus cavities for sex differentiation. In this study, a new methodology was used to assess the reliability of CBCT images of the frontal sinus cavity for determining sex based on the sexual dimorphism found in this anatomical structure. The survey sample consisted of 130 scans that were reconstructed three‐dimensionally. 3D images of the cavity volume in the frontal, lateral, and basal views were exported in TIFF. The following variables were measured in a second program: area, perimeter, bounding rectangle, ellipse fit, circularity, aspect ratio, roundness, solidity, and Feret's diameter. The methodology demonstrated the existence of sexual dimorphism with an accuracy of 80.0% in the logistic regression model. The basal view had the greatest explanatory power in the final model. This methodology may be used as an alternative way of determining a reliable biological profile during the analysis of skeletal remains.
Plant infection by two different viruses induce contrasting changes of vectors fitness and behavior
Authors: Chesnais Quentin , Couty Aude , Uzest Maryline , Brault Véronique , Ameline Arnaud 
Published: July 2017

AbstractInsect‐vectored plant viruses can induce changes in plant phenotypes, thus influencing plant–vector interactions in a way that may promote their dispersal according to their mode of transmission (i.e., circulative vs. noncirculative). This indirect vector manipulation requires host–virus–vector coevolution and would thus be effective solely in very specific plant–virus–vector species associations. Some studies suggest this manipulation may depend on multiple factors relative to various intrinsic characteristics of vectors such as transmission efficiency. In anintegrative study, we tested the effects of infection of the Brassicaceae Camelina sativa with the noncirculative Cauliflower mosaic virus (CaMV) or the circulative Turnip yellows virus (TuYV) on the host‐plant colonization of two aphid species differing in their virus transmission efficiency: the polyphagous Myzus persicae, efficient vector of both viruses, and the Brassicaceae specialist Brevicoryne brassicae, poor vector of TuYV and efficient vector of CaMV. Results confirmed the important role of virus mode of transmission as plant‐mediated effects of CaMV on the two aphid species induced negative alterations of feeding behavior (i.e., decreased phloem sap ingestion) and performance that were both conducive for virus fitness by promoting dispersion after a rapid acquisition. In addition, virus transmission efficiency may also play a role in vector manipulation by viruses as only the responses of the efficient vector to plant‐mediated effects of TuYV, that is, enhanced feeding behavior and performances, were favorable to their acquisition and further dispersal. Altogether, this work demonstrated that vector transmission efficiency also has to be considered when studying the mechanisms underlying vector manipulation by viruses. Our results also reinforce the idea that vector manipulation requires coevolution between plant, virus and vector.
Identification and functional characterization of an odorant receptor in pea aphid, Acyrthosiphon pisum
Authors: Zhang Rui‐Bin , Liu Yang , Yan Shan‐Chun , Wang Gui‐Rong 
Published: July 2017

AbstractThe sensitive olfactory system is necessary for survival of insects. Odorant receptors (ORs) are located on the dendrites of olfactory receptor neurons and play a critical role in odor detection. Insect ORs are functionally analyzed via heterologous expression in a Xenopus oocyte system using a two‐electrode voltage‐clamp (TEVC) electrophysiological recording. Here, we have identified a novel OR in the pea aphid, Acyrthosiphon pisum, then we cloned and named it ApisOR4. We analyzed the ApisOR4 tissue expression patterns and found expression only in antennae tissues. Further functional analysis using TEVC revealed that ApisOR4 is broadly tuned to eight volatiles, which elicit electrophysiological response in pea aphid antennae. This study provides an initial functional analysis of aphid ORs and identifies candidate volatiles to be used in developing new strategies for aphid control.
Attempt to Harvest a Sufficient Number of Mononuclear Cells in an Appropriate Blood Product Volume By Modification of the Default Apheresis Setting
Authors: Tanaka Yumi , Ohishi Kohshi , Sawai Toshiki , Iwasaki Hitoshi , Kageyama Shinichi , Masuya Masahiro , Matsumoto Takeshi , Tanigawa Takashi , Wada Hideo , Shiku Hiroshi , Ito Masaaki , Katayama Naoyuki 
Published: July 2017

AbstractTo harvest for T cell therapy, a 1.6‐fold higher number of CD3+ T cells was collected with MNC mode (N = 10) compared with Auto PBSC mode (N = 5) in COBE Spectra cell separator, but the blood product volume was increased by 3.5‐fold. For therapeutic angiogenesis therapy, apheresis was initially performed using Auto PBSC mode (N = 4) to fine tune the blood product volume to omit cell concentration, but the collected number of mononuclear cells was lower than expected. However, an increase of the harvest cycle number from 3.8 ± 0.5 to 7.4 ± 2.0 cycles (N = 19) resulted in a 2.1‐fold higher number of collected mononuclear cells (8.7 ± 4.1 × 109 vs. 4.1 ± 1.0 × 109 cells, P < 0.05). The increase in blood product volume by this modification appeared to be lower than that expected with MNC mode. These data show that optimal harvesting can be achieved by modification of default collection settings.