for Journals by Title or ISSN
for Articles by Keywords
help
Followed Journals
Journal you Follow: 0
 
Sign Up to follow journals, search in your chosen journals and, optionally, receive Email Alerts when new issues of your Followed Journals are published.
Already have an account? Sign In to see the journals you follow.
Journal Cover PLoS ONE
  [SJR: 1.395]   [H-I: 181]   [715 followers]  Follow
    
  This is an Open Access Journal Open Access journal
   ISSN (Online) 1932-6203
   Published by PLoS Homepage  [13 journals]
  • Correction: Measuring 3D Hand and Finger Kinematics—A Comparison between
           Inertial Sensing and an Opto-Electronic Marker System

    • Authors: Josien C. van den Noort Henk G. Kortier Nathalie van Beek DirkJan H. E. J. Veeger Peter H. Veltink
      Abstract: by Josien C. van den Noort, Henk G. Kortier, Nathalie van Beek, DirkJan H. E. J. Veeger, Peter H. Veltink
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193329
       
  • Correction: Effects of Low Dose Metformin on Metabolic Traits in
           Clozapine-Treated Schizophrenia Patients: An Exploratory Twelve-Week
           Randomized, Double-Blind, Placebo-Controlled Study

    • Authors: Chih-Chiang Chiu Mong-Liang Lu Ming-Chyi Huang Po-Yu Chen Yen-Kuang Lin Shih-Ku Lin Chun-Hsin Chen
      Abstract: by Chih-Chiang Chiu, Mong-Liang Lu, Ming-Chyi Huang, Po-Yu Chen, Yen-Kuang Lin, Shih-Ku Lin, Chun-Hsin Chen
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193315
       
  • Phytoforensics: Trees as bioindicators of potential indoor exposure via
           vapor intrusion

    • Authors: Jordan L. Wilson V. A. Samaranayake Matt A. Limmer Joel G. Burken
      Abstract: by Jordan L. Wilson, V. A. Samaranayake, Matt A. Limmer, Joel G. BurkenHuman exposure to volatile organic compounds (VOCs) via vapor intrusion (VI) is an emerging public health concern with notable detrimental impacts on public health. Phytoforensics, plant sampling to semi-quantitatively delineate subsurface contamination, provides a potential non-invasive screening approach to detect VI potential, and plant sampling is effective and also time- and cost-efficient. Existing VI assessment methods are time- and resource-intensive, invasive, and require access into residential and commercial buildings to drill holes through basement slabs to install sampling ports or require substantial equipment to install groundwater or soil vapor sampling outside the home. Tree-core samples collected in 2 days at the PCE Southeast Contamination Site in York, Nebraska were analyzed for tetrachloroethene (PCE) and results demonstrated positive correlations with groundwater, soil, soil-gas, sub-slab, and indoor-air samples collected over a 2-year period. Because tree-core samples were not collocated with other samples, interpolated surfaces of PCE concentrations were estimated so that comparisons could be made between pairs of data. Results indicate moderate to high correlation with average indoor-air and sub-slab PCE concentrations over long periods of time (months to years) to an interpolated tree-core PCE concentration surface, with Spearman’s correlation coefficients (ρ) ranging from 0.31 to 0.53 that are comparable to the pairwise correlation between sub-slab and indoor-air PCE concentrations (ρ = 0.55, n = 89). Strong correlations between soil-gas, sub-slab, and indoor-air PCE concentrations and an interpolated tree-core PCE concentration surface indicate that trees are valid indicators of potential VI and human exposure to subsurface environment pollutants. The rapid and non-invasive nature of tree sampling are notable advantages: even with less than 60 trees in the vicinity of the source area, roughly 12 hours of tree-core sampling with minimal equipment at the PCE Southeast Contamination Site was sufficient to delineate vapor intrusion potential in the study area and offered comparable delineation to traditional sub-slab sampling performed at 140 properties over a period of approximately 2 years.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193247
       
  • Cooperation enhanced by the coevolution of teaching activity in
           evolutionary prisoner's dilemma games with voluntary participation

    • Authors: Chen Shen Chen Chu Yini Geng Jiahua Jin Fei Chen Lei Shi
      Abstract: by Chen Shen, Chen Chu, Yini Geng, Jiahua Jin, Fei Chen, Lei ShiVoluntary participation, as an additional strategy involved in repeated games, has been proved to be an efficient way to promote the evolution of cooperation theoretically and empirically. Besides, current studies show that the coevolution of teaching activity can promote cooperation. Thus, inspired by aforementioned above, we investigate the effect of coevolution of teaching activity on the evolution of cooperation for prisoner’s dilemma game with voluntary participation: when the focal player successfully enforces its strategy on the opponent, his teaching ability will get an increase. Through numerical simulation, we have shown that voluntary participation could effectively promote the fraction of cooperation, which is also affected by the value of increment. Furthermore, we investigate the influence of the increment value on the density of different strategies and find that there exists an optimal increment value that plays an utmost role on the evolutionary dynamics. With regard to this observation, we unveil that an optimal value of increment can lead to strongest heterogeneity in agents’ teaching ability, further promoting the evolution of cooperation.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193151
       
  • Late effects awareness website for pediatric survivors of acute
           lymphocytic leukemia

    • Authors: Hillary Klonoff-Cohen Ana Navarro Elizabeth A. Klonoff
      Abstract: by Hillary Klonoff-Cohen, Ana Navarro, Elizabeth A. KlonoffObjectives Every day 43 children are newly diagnosed with cancer. Fortunately, almost 90% of these childhood cancer patients will survive. However, 60–90% of these survivors will experience late effects, health problems that occur months or years after treatment has ended. Late effects could occur as a result of the disease, its treatment, and patient-related factors. The two main objectives of this research are to: 1) Examine the existence of all web-based resources for childhood cancer survivors with acute lymphocytic leukemia which focus on medical and psychological aspects of late effects, and 2) Create an innovative website specifically designed to fill this void. Materials and methods A systematic literature review, followed by input from >20 different organizations, resulted in the creation of LEAP3 AHEAD (Late Effects Awareness for Patients, Physicians and the Public; Advancing Health and Eliminating All Disparities), a multi-dimensional website centering on late effects. Results An extensive review revealed 14 pediatric cancer websites, none of which focused exclusively on late effects. LEAP3 AHEAD is the first interactive website for acute lympocytic leukemia childhood cancer survivors and families, as well as physicians, and the public to: a) increase awareness about risks, detection, diagnosis, treatment, and prevention of medical and psychological late effects, b) provide suggestions to successfully reintegrate into schools, careers, and socially, and c) present opportunities including camps, scholarships, and pet therapy programs. Conclusion LEAP3 AHEAD is the first national website to provide a comprehensive, accessible, affordable, and multi-dimensional resource for pediatricians, internists, nurse practitioners, psychologists, survivors and their families, as well as the public about late effects.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193141
       
  • Cas9-mediated excision of proximal DNaseI/H3K4me3 signatures confers
           robust silencing of microRNA and long non-coding RNA genes

    • Authors: Harshavardhan Janga Marina Aznaourova Fabian Boldt Katrin Damm Arnold Grünweller Leon N. Schulte
      Abstract: by Harshavardhan Janga, Marina Aznaourova, Fabian Boldt, Katrin Damm, Arnold Grünweller, Leon N. SchulteCRISPR/Cas9-based approaches have greatly facilitated targeted genomic deletions. Contrary to coding genes however, which can be functionally knocked out by frame-shift mutagenesis, non-coding RNA (ncRNA) gene knockouts have remained challenging. Here we present a universal ncRNA knockout approach guided by epigenetic hallmarks, which enables robust gene silencing even in provisionally annotated gene loci. We build on previous work reporting the presence of overlapping histone H3 lysine 4 tri-methylation (H3K4me3) and DNaseI hypersensitivity sites around the transcriptional start sites of most genes. We demonstrate that excision of this gene-proximal signature leads to loss of microRNA and lincRNA transcription and reveals ncRNA phenotypes. Exemplarily we demonstrate silencing of the constitutively transcribed MALAT1 lincRNA gene as well as of the inducible miR-146a and miR-155 genes in human monocytes. Our results validate a role of miR-146a and miR-155 in negative feedback control of the activity of inflammation master-regulator NFκB and suggest that cell-cycle control is a unique feature of miR-155. We suggest that our epigenetically guided CRISPR approach may improve existing ncRNA knockout strategies and contribute to the development of high-confidence ncRNA phenotyping applications.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193066
       
  • An upstream sequence modulates phenazine production at the level of
           transcription and translation in the biological control strain Pseudomonas
           chlororaphis 30-84

    • Authors: Jun Myoung Yu Dongping Wang Tessa R. Ries Leland S. Pierson III Elizabeth A. Pierson
      Abstract: by Jun Myoung Yu, Dongping Wang, Tessa R. Ries, Leland S. Pierson III, Elizabeth A. PiersonPhenazines are bacterial secondary metabolites and play important roles in the antagonistic activity of the biological control strain P. chlororaphis 30–84 against take-all disease of wheat. The expression of the P. chlororaphis 30–84 phenazine biosynthetic operon (phzXYFABCD) is dependent on the PhzR/PhzI quorum sensing system located immediately upstream of the biosynthetic operon as well as other regulatory systems including Gac/Rsm. Bioinformatic analysis of the sequence between the divergently oriented phzR and phzX promoters identified features within the 5’-untranslated region (5’-UTR) of phzX that are conserved only among 2OHPCA producing Pseudomonas. The conserved sequence features are potentially capable of producing secondary structures that negatively modulate one or both promoters. Transcriptional and translational fusion assays revealed that deletion of 90-bp of sequence at the 5’-UTR of phzX led to up to 4-fold greater expression of the reporters with the deletion compared to the controls, which indicated this sequence negatively modulates phenazine gene expression both transcriptionally and translationally. This 90-bp sequence was deleted from the P. chlororaphis 30–84 chromosome, resulting in 30-84Enh, which produces significantly more phenazine than the wild-type while retaining quorum sensing control. The transcriptional expression of phzR/phzI and amount of AHL signal produced by 30-84Enh also were significantly greater than for the wild-type, suggesting this 90-bp sequence also negatively affects expression of the quorum sensing genes. In addition, deletion of the 90-bp partially relieved RsmE-mediated translational repression, indicating a role for Gac/RsmE interaction. Compared to the wild-type, enhanced phenazine production by 30-84Enh resulted in improvement in fungal inhibition, biofilm formation, extracellular DNA release and suppression of take-all disease of wheat in soil without negative consequences on growth or rhizosphere persistence. This work provides greater insight into the regulation of phenazine biosynthesis with potential applications for improved biological control.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193063
       
  • Brain changes due to hypoxia during light anaesthesia can be prevented by
           deepening anaesthesia; a study in rats

    • Authors: Setayesh R. Tasbihgou Mina Netkova Alain F. Kalmar Janine Doorduin Michel M. R. F. Struys Regien G. Schoemaker Anthony R. Absalom
      Abstract: by Setayesh R. Tasbihgou, Mina Netkova, Alain F. Kalmar, Janine Doorduin, Michel M. R. F. Struys, Regien G. Schoemaker, Anthony R. AbsalomIn anaesthetic practice the risk of cerebral ischemic/hypoxic damage is thought to be attenuated by deep anaesthesia. The rationale is that deeper anaesthesia reduces cerebral oxygen demand more than light anaesthesia, thereby increasing the tolerance to ischemia or hypoxia. However, evidence to support this is scarce. We thus investigated the influence of light versus deep anaesthesia on the responses of rat brains to a period of hypoxia. In the first experiment we exposed adult male Wistar rats to deep or light propofol anaesthesia and then performed [18F]- Fludeoxyglucose (FDG) Positron Emission Tomography (PET) scans to verify the extent of cerebral metabolic suppression. In subsequent experiments, rats were subjected to light/deep propofol anaesthesia and then exposed to a period of hypoxia or ongoing normoxia (n = 9–11 per group). A further 5 rats, not exposed to anaesthesia or hypoxia, served as controls. Four days later a Novel Object Recognition (NOR) test was performed to assess mood and cognition. After another 4 days, the animals were sacrificed for later immunohistochemical analyses of neurogenesis/neuroplasticity (Doublecortin; DCX), Brain Derived Neurotrophic Factor (BDNF) expression and neuroinflammation (Ionized calcium-binding adaptor protein-1; Iba-1) in hippocampal and piriform cortex slices. The hippocampi of rats subjected to hypoxia during light anaesthesia showed lower DCX positivity, and therefore lower neurogenesis, but higher BDNF levels and microglia hyper-ramification. Exploration was reduced, but no significant effect on NOR was observed. In the piriform cortex, higher DCX positivity was observed, associated with neuroplasticity. All these effects were attenuated by deep anaesthesia. Deepening anaesthesia attenuated the brain changes associated with hypoxia. Hypoxia during light anaesthesia had a prolonged effect on the brain, but no impairment in cognitive function was observed. Although reduced hippocampal neurogenesis may be considered unfavourable, higher BDNF expression, associated with microglia hyper-ramification may suggest activation of repair mechanisms. Increased neuroplasticity observed in the piriform cortex supports this, and might reflect a prolonged state of alertness rather than damage.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193062
       
  • The effectiveness of non-surgical intervention (Foot Orthoses) for
           paediatric flexible pes planus: A systematic review: Update

    • Authors: Sindhrani Dars Hayley Uden Helen A. Banwell Saravana Kumar
      Abstract: by Sindhrani Dars, Hayley Uden, Helen A. Banwell, Saravana KumarBackground Flexible pes planus (flat feet) in children is a common presenting condition in clinical practice due to concerns amongst parents and caregivers. While Foot Orthoses (FOs) are a popular intervention, their effectiveness remains unclear. Thus, the aim of this systematic review was to update the current evidence base for the effectiveness of FOs for paediatric flexible pes planus. Methods A systematic search of electronic databases (Cochrane, Medline, AMED, EMBASE, CINHAL, SportDiscus, Scopus and PEDro) was conducted from January 2011 to July 2017. Studies of children (0–18 years) diagnosed with flexible pes planus and intervention to be any type of Foot Orthoses (FOs) were included. This review was conducted and reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. McMaster critical review form for quantitative studies, was used to assess the methodological quality of the included studies. Given the heterogeneity of the included studies, a descriptive synthesis of the included studies was undertaken. Results Out of 606 articles identified, 11 studies (three RCTs; two case-controls; five case-series and one single case study) met the inclusion criteria. A diverse range of pre-fabricated and customised FOs were utilised and effectiveness measured through a plethora of outcomes. Summarised findings from the heterogeneous evidence base indicated that FOs may have a positive impact across a range of outcomes including pain, foot posture, gait, function and structural and kinetic measures. Despite these consistent positive outcomes reported in several studies, the current evidence base lacks clarity and uniformity in terms of diagnostic criteria, interventions delivered and outcomes measured for paediatric flexible pes planus. Conclusion There continues to remain uncertainty on the effectiveness of FOs for paediatric flexible pes planus. Despite a number of methodological limitations, FOs show potential as a treatment method for children with flexible pes planus. PROSPERO registration number CRD42017057310.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193060
       
  • Expression of cell cycle regulators and frequency of TP53 mutations in
           high risk gastrointestinal stromal tumors prior to adjuvant imatinib
           treatment

    • Authors: Michaela Angelika Ihle Sebastian Huss Wiebke Jeske Wolfgang Hartmann Sabine Merkelbach-Bruse Hans-Ulrich Schildhaus Reinhard Büttner Harri Sihto Kirsten Sundby Hall Mikael Eriksson Peter Reichardt Heikki Joensuu Eva Wardelmann
      Abstract: by Michaela Angelika Ihle, Sebastian Huss, Wiebke Jeske, Wolfgang Hartmann, Sabine Merkelbach-Bruse, Hans-Ulrich Schildhaus, Reinhard Büttner, Harri Sihto, Kirsten Sundby Hall, Mikael Eriksson, Peter Reichardt, Heikki Joensuu, Eva WardelmannDespite of multitude investigations no reliable prognostic immunohistochemical biomarkers in GIST have been established so far with added value to predict the recurrence risk of high risk GIST besides mitotic count, primary location and size. In this study, we analyzed the prognostic relevance of eight cell cycle and apoptosis modulators and of TP53 mutations for prognosis in GIST with high risk of recurrence prior to adjuvant treatment with imatinib. In total, 400 patients with high risk for GIST recurrence were randomly assigned for adjuvant imatinib either for one or for three years following laparotomy. 320 primary tumor samples with available tumor tissue were immunohistochemically analyzed prior to treatment for the expression of cell cycle regulators and apoptosis modulators cyclin D1, p21, p16, CDK4, E2F1, MDM2, p53 and p-RB1. TP53 mutational analysis was possible in 245 cases. A high expression of CDK4 was observed in 32.8% of all cases and was associated with a favorable recurrence free survival (RFS), whereas high expression of MDM2 (12.2%) or p53 (35.3%) was associated with a shorter RFS. These results were independent from the primary KIT or PDGFRA mutation. In GISTs with higher mitotic counts was a significantly increased expression of cyclin D1, p53 and E2F1. The expression of p16 and E2F1 significantly correlated to a non-gastric localization. Furthermore, we observed a significant higher expression of p21 and E2F1 in KIT mutant GISTs compared to PDGFRA mutant and wt GISTs. The overall frequency of TP53 mutations was low (n = 8; 3.5%) and could not be predicted by the immunohistochemical expression of p53. In summary, mutation analysis in TP53 plays a minor role in the subgroup of high-risk GIST before adjuvant treatment with imatinib. Strong expression of MDM2 and p53 correlated with a shorter recurrence free survival, whereas a strong expression of CDK4 correlated to a better recurrence free survival.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193048
       
  • Stability lies in flowers: Plant diversification mediating shifts in
           arthropod food webs

    • Authors: Marcelo Mendes Haro Luís Cláudio Paterno Silveira Andrew Wilby
      Abstract: by Marcelo Mendes Haro, Luís Cláudio Paterno Silveira, Andrew WilbyArthropod community composition in agricultural landscapes is dependent on habitat characteristics, such as plant composition, landscape homogeneity and the presence of key resources, which are usually absent in monocultures. Manipulating agroecosystems through the insertion of in-field floral resources is a useful technique to reduce the deleterious effects of habitat simplification. Food web analysis can clarify how the community reacts to the presence of floral resources which favour ecosystem services such as biological control of pest species. Here, we reported quantitative and qualitative alterations in arthropod food web complexity due to the presence of floral resources from the Mexican marigold (Tagetes erecta L.) in a field scale lettuce community network. The presence of marigold flowers in the field successfully increased richness, body size, and the numerical and biomass abundance of natural enemies in the lettuce arthropod community, which affected the number of links, vulnerability, generality, omnivory rate and food chain length in the community, which are key factors for the stability of relationships between species. Our results reinforce the notion that diversification through insertion of floral resources may assist in preventing pest outbreaks in agroecosystems. This community approach to arthropod interactions in agricultural landscapes can be used in the future to predict the effect of different management practices in the food web to contribute with a more sustainable management of arthropod pest species.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193045
       
  • Carbon stock of Moso bamboo (Phyllostachys pubescens) forests along a
           latitude gradient in the subtropical region of China

    • Authors: Mengjie Xu Haibao Ji Shunyao Zhuang
      Abstract: by Mengjie Xu, Haibao Ji, Shunyao ZhuangLatitude is an important factor that influences the carbon stock of Moso bamboo (Phyllostachys pubescens) forests. Accurate estimation of the carbon stock of Moso bamboo forest can contribute to sufficient evaluation of forests in carbon sequestration worldwide. Nevertheless, the effect of latitude on the carbon stock of Moso bamboo remains unclear. In this study, a field survey with 36 plots of Moso bamboo forests along a latitude gradient was conducted to investigate carbon stock. Results showed that the diameter at breast height (DBH) of Moso bamboo culms increased from 8.37 cm to 10.12 cm that well fitted by Weibull model, whereas the bamboo culm density decreased from 4722 culm ha−1 to 3400 culm ha−1 with increasing latitude. The bamboo biomass carbon decreased from 60.58 Mg C ha−1 to 48.31 Mg C ha−1 from north to south. The total carbon stock of Moso bamboo forests, which comprises soil and biomass carbon, ranged from 87.83 Mg C ha−1 to 119.5 Mg C ha−1 and linearly increased with latitude. As a fast-growing plant, Moso bamboo could be harvested amounts of 6.0 Mg C ha−1 to 7.6 Mg C ha−1 annually, which indicates a high potential of this species for carbon sequestration. Parameters obtained in this study can be used to accurately estimate the carbon stock of Moso bamboo forest to establish models of the global carbon balance.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193024
       
  • Synchronic historical patterns of species diversification in seasonal
           aplocheiloid killifishes of the semi-arid Brazilian Caatinga

    • Authors: Wilson J. E. M. Costa Pedro F. Amorim José Leonardo O. Mattos
      Abstract: by Wilson J. E. M. Costa, Pedro F. Amorim, José Leonardo O. MattosThe Caatinga is the largest nucleus of seasonally dry tropical forests in South America, but little is known about the evolutionary history and biogeography of endemic organisms. Evolutionary diversification and distribution of terrestrial vertebrates endemic to the Caatinga have been explained by palaeogeographical Neogene episodes, mostly related to changes in the course of the São Francisco River, the largest river in the region. Our objective is to estimate the timing of divergence of two endemic groups of short-lived seasonal killifishes inhabiting all ecoregions of the Caatinga, testing the occurrence of synchronic events of spatial diversification in light of available data on regional palaeogeography. We performed independent time-calibrated phylogenetic molecular analyses for two clades of sympatric and geographically widespread seasonal killifishes endemic to the Caatinga, the Hypsolebias antenori group and the Cynolebias alpha-clade. Our results consistently indicate that species diversification took place synchronically in both groups, as well as it is contemporary to diversification of other organisms adapted to life in the semi-arid Caatinga, including lizards and small mammals. Both groups originated during the Miocene, but species diversification started between the Late Miocene and Early Pliocene, when global cooling probably favoured the expansion of semi-arid areas. Synchronic diversification patterns found are chronologically related to Tertiary palaeogeographical reorganizations associated to continental drift and to Quaternary climatic changes, corroborating the recent proposal that South American biodiversity has been continuously shaped between the Late Paleogene and Pleistocene.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0193021
       
  • An artificial miRNA system reveals that relative contribution of
           translational inhibition to miRNA-mediated regulation depends on
           environmental and developmental factors in Arabidopsis thaliana

    • Authors: Patrick von Born Marti Bernardo-Faura Ignacio Rubio-Somoza
      Abstract: by Patrick von Born, Marti Bernardo-Faura, Ignacio Rubio-SomozaDevelopment and fitness of any organism rely on properly controlled gene expression. This is especially true for plants, as their development is determined by both internal and external cues. MicroRNAs (miRNAs) are embedded in the genetic cascades that integrate and translate those cues into developmental programs. miRNAs negatively regulate their target genes mainly post-transcriptionally through two co-existing mechanisms; mRNA cleavage and translational inhibition. Despite our increasing knowledge about the genetic and biochemical processes involved in those concurrent mechanisms, little is known about their relative contributions to the overall miRNA-mediated regulation. Here we show that co-existence of cleavage and translational inhibition is dependent on growth temperature and developmental stage. We found that efficiency of an artificial miRNA-mediated (amiRNA) gene silencing declines with age during vegetative development in a temperature-dependent manner. That decline is mainly due to a reduction on the contribution from translational inhibition. Both, temperature and developmental stage were also found to affect mature amiRNA accumulation and the expression patterns of the core players involved in miRNA biogenesis and action. Therefore, that suggests that each miRNA family specifically regulates their respective targets, while temperature and growth might influence the performance of miRNA-dependent regulation in a more general way.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192984
       
  • Identification of the S-transferase like superfamily bacillithiol
           transferases encoded by Bacillus subtilis

    • Authors: Varahenage R. Perera John D. Lapek Jr. Gerald L. Newton David J. Gonzalez Kit Pogliano
      Abstract: by Varahenage R. Perera, John D. Lapek Jr., Gerald L. Newton, David J. Gonzalez, Kit PoglianoBacillithiol is a low molecular weight thiol found in Firmicutes that is analogous to glutathione, which is absent in these bacteria. Bacillithiol transferases catalyze the transfer of bacillithiol to various substrates. The S-transferase-like (STL) superfamily contains over 30,000 putative members, including bacillithiol transferases. Proteins in this family are extremely divergent and are related by structural rather than sequence similarity, leaving it unclear if all share the same biochemical activity. Bacillus subtilis encodes eight predicted STL superfamily members, only one of which has been shown to be a bacillithiol transferase. Here we find that the seven remaining proteins show varying levels of metal dependent bacillithiol transferase activity. We have renamed the eight enzymes BstA-H. Mass spectrometry and gene expression studies revealed that all of the enzymes are produced to varying levels during growth and sporulation, with BstB and BstE being the most abundant and BstF and BstH being the least abundant. Interestingly, several bacillithiol transferases are induced in the mother cell during sporulation. A strain lacking all eight bacillithiol transferases showed normal growth in the presence of stressors that adversely affect growth of bacillithiol-deficient strains, such as paraquat and CdCl2. Thus, the STL bacillithiol transferases represent a new group of proteins that play currently unknown, but potentially significant roles in bacillithiol-dependent reactions. We conclude that these enzymes are highly divergent, perhaps to cope with an equally diverse array of endogenous or exogenous toxic metabolites and oxidants.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192977
       
  • Rapid purification of giant lipid vesicles by microfiltration

    • Authors: Dimitri Fayolle Michele Fiore Pasquale Stano Peter Strazewski
      Abstract: by Dimitri Fayolle, Michele Fiore, Pasquale Stano, Peter StrazewskiGiant lipid vesicles (GVs) are emerging models for investigating the properties and reactivity of cell-like microcompartments, providing useful information about plausible protocellular structures in primitive times, as well as for the modern synthetic biology goal of constructing the first artificial cell from its reconstituted and partly modified components. Here we explore a novel methodology of GV purification by microfiltration under reduced pressure, operated by a simple apparatus. The method has been characterized in terms of flow rate, amount of lipid loss, quality of recovered GVs, and size distribution. A case study is reported to show the practicability of GV microfiltration. A clickable fluorescent probe was encapsulated inside GVs; more than 99.9% of the non-entrapped probe was easily and rapidly removed by multiple microfiltrations. This novel methodology is briefly discussed as a future tool for selection experiments on GV populations.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192975
       
  • Timber isoscapes. A case study in a mountain area in the Italian Alps

    • Authors: Yuri Gori Ana Stradiotti Federica Camin
      Abstract: by Yuri Gori, Ana Stradiotti, Federica CaminBackground Local timber is still one of the main sources of work and income for mountain communities. However, illegal logging is a major cause of deforestation in many countries and has significant impacts on local communities and biodiversity. Techniques for tracing timber would provide a useful tool to protect local timber industries and contribute to the fight against illegal logging. Although considerable progress has been made in food traceability, timber provenance is still a somewhat neglected research area. Stable isotope ratios in plants are known to reflect geographical variations. This study reports accurate spatial distribution of δ18O and δ2H in timber from north-eastern Italy (Trentino) in order to trace geographical origin. Methodology and principal findings We tested the accuracy of four kriging methods using an annual resolution of δ18O and δ2H measured in Picea abies. Pearson’s correlation coefficients revealed altitude to be the most appropriate covariate for the cokriging model, which has ultimately proved to be the best method due to its low estimation error. Conclusions We present regional maps of interpolated δ18O and δ2H in Picea abies wood together with the 95% confidence intervals. The strong spatial structure of the data demonstrates the potential of multivariate spatial interpolation, even in a highly heterogeneous area such as the Alps. We believe that this geospatial approach can be successfully applied on a wider scale in order to combat illegal logging.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192970
       
  • Manipulation of the rhizosphere microbial community through application of
           a new bio-organic fertilizer improves watermelon quality and health

    • Authors: Jia Zhao Jiang Liu Hong Liang Jing Huang Zhe Chen Yuanjun Nie Changbiao Wang Yuguo Wang
      Abstract: by Jia Zhao, Jiang Liu, Hong Liang, Jing Huang, Zhe Chen, Yuanjun Nie, Changbiao Wang, Yuguo WangBio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community. The microbial communities of soil amended with cow plus chicken manure compost (S+M), soil amended with the BOF (S+BOF), and untreated control soil (S) without plants were analyzed through sequence analysis using the Illumina MiSeq platform. The results showed that a new microbial community was formed in the manure compost after fermentation by the Daqu. Application of the BOF to the soil induced remarkable changes in the rhizosphere microbial communities, with increased bacterial diversity and decreased fungal diversity. Most importantly, S+BOF showed the lowest abundance of Fusarium. Moreover, watermelon quality was higher (P < 0.05) in the S+BOF than in the S+M treatment. Thus, application of the BOF favorably altered the composition of the rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant quality.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192967
       
  • Identifying classifier input signals to predict a cross-slope during
           transtibial amputee walking

    • Authors: Courtney E. Shell Glenn K. Klute Richard R. Neptune
      Abstract: by Courtney E. Shell, Glenn K. Klute, Richard R. NeptuneAdvanced prosthetic foot designs often incorporate mechanisms that adapt to terrain changes in real-time to improve mobility. Early identification of terrain (e.g., cross-slopes) is critical to appropriate adaptation. This study suggests that a simple classifier based on linear discriminant analysis can accurately predict a cross-slope encountered (0°, -15°, 15°) using measurements from the residual limb, primarily from the prosthesis itself. The classifier was trained and tested offline using motion capture and in-pylon sensor data collected during walking trials in mid-swing and early stance. Residual limb kinematics, especially measurements from the foot, shank and ankle, successfully predicted the cross-slope terrain with high accuracy (99%). Although accuracy decreased when predictions were made for test data instead of the training data, the accuracy was still relatively high for one input signal set (>89%) and moderate for three others (>71%). This suggests that classifiers can be designed and generalized to be effective for new conditions and/or subjects. While measurements of shank acceleration and angular velocity from only in-pylon sensors were insufficient to accurately predict the cross-slope terrain, the addition of foot and ankle kinematics from motion capture data allowed accurate terrain prediction. Inversion angular velocity and foot vertical velocity were particularly useful. As in-pylon sensor data and shank kinematics from motion capture appeared interchangeable, combining foot and ankle kinematics from prosthesis-mounted sensors with shank kinematics from in-pylon sensors may provide enough information to accurately predict the terrain.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192950
       
  • To what extent do potential conservation donors value community-aspects of
           conservation projects in low income countries'

    • Authors: Amy R. Lewis Richard P. Young James M. Gibbons Julia P. G. Jones
      Abstract: by Amy R. Lewis, Richard P. Young, James M. Gibbons, Julia P. G. JonesThere is a major gap in funding required for conservation, especially in low income countries. Given the significant contribution of taxpayers in industrialized countries to funding conservation overseas, and donations from membership organisation, understanding the preferences of ordinary people in a high income country for different attributes of conservation projects is valuable for future marketing of conservation. We conducted a discrete choice experiment with visitors to a UK zoo, while simultaneously conducting a revealed preference study through a real donation campaign on the same sample. Respondents showed the highest willingness to pay for projects that have local community involvement in management (95% confidence interval £9.82 to £15.83), and for improvement in threatened species populations (£2.97 - £13.87). Both of these were significantly larger than the willingness to pay for projects involving provision of alternative livelihoods, or improving the condition of conservation sites. Results of the simultaneous donation campaign showed that respondents were very willing to donate the suggested £1 or above donation (88% made a donation, n = 1798); there was no effect of which of the two campaigns they were exposed to (threatened species management or community involvement in management). The small number of people who did not make a donation had a higher stated willingness to pay within the choice experiment, which may suggest hypothetical bias. Conservationists increasingly argue that conservation should include local communities in management (for both pragmatic and moral reasons). It is heartening that potential conservation donors seem to agree.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192935
       
  • Otoacoustic emissions from ears with spontaneous activity behave
           differently to those without: Stronger responses to tone bursts as well as
           to clicks

    • Authors: W. Wiktor Jedrzejczak Krzysztof Kochanek Henryk Skarzynski
      Abstract: by W. Wiktor Jedrzejczak, Krzysztof Kochanek, Henryk SkarzynskiIt has been reported that both click-evoked otoacoustic emissions (CEOAEs) and distortion product otoacoustic emissions (DPOAEs) have higher amplitudes in ears that possess spontaneous otoacoustic emissions (SOAEs). The general aim of the present study was to investigate whether the presence of spontaneous activity in the cochlea affected tone-burst evoked otoacoustic emissions (TBOAEs). As a benchmark, the study also measured growth functions of CEOAEs. Spontaneous activity in the cochlea was measured by the level of synchronized spontaneous otoacoustic emissions (SSOAEs), an emission evoked by a click but closely related to spontaneous otoacoustic emissions (SOAEs, which are detectable without any stimulus). Measurements were made on a group of 15 adults whose ears were categorized as either having recordable SSOAEs or no SSOAEs. In each ear, CEOAEs and TBOAEs were registered at frequencies of 0.5, 1, 2, and 4 kHz, and input/output functions were measured at 40, 50, 60, 70, and 80 dB SPL. Global and half-octave-band values of response level and latency were estimated. Our main finding was that in ears with spontaneous activity, TBOAEs had higher levels than in ears without. The difference was more apparent for global values, but were also seen with half-octave-band analysis. Input/output functions had similar growth rates for ears with and without SSOAEs. There were no significant differences in latencies between TBOAEs from ears with and without SSOAEs, although latencies tended to be longer for lower stimulus levels and lower stimulus frequencies. When TBOAE levels were compared to CEOAE levels, the latter showed greater differences between recordings from ears with and without SSOAEs. Although TBOAEs reflect activity from a more restricted cochlear region than CEOAEs, at all stimulus frequencies their behavior still depends on whether SSOAEs are present or not.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192930
       
  • Perceived behavioral control as a potential precursor of walking three
           times a week: Patient's perspectives

    • Authors: Peter Busse J. Jaime Miranda
      Abstract: by Peter Busse, J. Jaime MirandaBackground Behavior change theories can identify people’s main motivations to engage in recommended health practices and thus provide better tools to design interventions, particularly human centered design interventions. Objectives This study had two objectives: (a) to identify salient beliefs about walking three times a week for 30 minutes nonstop among patients with hypertension in a low-resource setting and, (b) to measure the relationships among intentions, attitudes, perceived social pressure and perceived behavioral control about this behavior. Methods Face-to-face interviews with 34 people living with hypertension were conducted in September-October 2011 in Lima, Peru, and data analysis was performed in 2015. The Reasoned Action Approach was used to study the people’s decisions to walk. We elicited people’s salient beliefs and measured the theoretical constructs associated with this behavior. Results Results pointed at salient key behavioral, normative and control beliefs. In particular, perceived behavioral control appeared as an important determinant of walking and a small set of control beliefs were identified as potential targets of health communication campaigns, including (not) having someone to walk with, having work or responsibilities, or having no time. Conclusions This theory-based study with a focus on end-users provides elements to inform the design of an intervention that would motivate people living with hypertension to walk on a regular basis in low-resource settings.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192915
       
  • The impact of “Option B” on HIV transmission from mother to child in
           Rwanda: An interrupted time series analysis

    • Authors: Monique Abimpaye Catherine M. Kirk Hari S. Iyer Neil Gupta Eric Remera Placidie Mugwaneza Michael R. Law
      Abstract: by Monique Abimpaye, Catherine M. Kirk, Hari S. Iyer, Neil Gupta, Eric Remera, Placidie Mugwaneza, Michael R. LawBackground Nearly a quarter of a million children have acquired HIV, prompting the implementation of new protocols—Option B and B+—for treating HIV+ pregnant women. While efficacy has been demonstrated in randomized trials, there is limited real-world evidence on the impact of these changes. Using longitudinal, routinely collected data we assessed the impact of the adoption of WHO Option B in Rwanda on mother to infant transmission. Methods We used interrupted time series analysis to evaluate the impact of Option B on mother-to-child HIV transmission in Rwanda. Our primary outcome was the proportion of HIV tests in infants with positive results at six weeks of age. We included data for 20 months before and 22 months after the 2010 policy change. Results Of the 15,830 HIV tests conducted during our study period, 392 tested positive. We found a significant decrease in both the level (-2.08 positive tests per 100 tests conducted, 95% CI: -2.71 to -1.45, p < 0.001) and trend (-0.11 positive tests per 100 tests conducted per month, 95% CI: -0.16 to -0.07, p < 0.001) of test positivity. This represents an estimated 297 fewer children born without HIV in the post-policy period or a 46% reduction in HIV transmission from mother to child. Conclusions The adoption of Option B in Rwanda contributed to an immediate decrease in the rate of HIV transmission from mother to child. This suggests other countries may benefit from adopting these WHO guidelines.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192910
       
  • The ARID1A, p53 and ß-Catenin statuses are strong prognosticators in
           clear cell and endometrioid carcinoma of the ovary and the endometrium

    • Authors: Marlene Heckl Elisa Schmoeckel Linda Hertlein Miriam Rottmann Udo Jeschke Doris Mayr
      Abstract: by Marlene Heckl, Elisa Schmoeckel, Linda Hertlein, Miriam Rottmann, Udo Jeschke, Doris MayrAim The objective of this study was to evaluate the prognostic value of ARID1A, p53, p21, p16 and ß-Catenin in endometrioid and clear cell ovarian and endometrial carcinomas. Materials and methods 97 tumors were available for analysis of ARID1A, p53, p21, p16 and ß-Catenin with the techniques of tissue microarray and immunohistochemistry. 32 were ovarian carcinomas and 65 were endometrial carcinomas. Results Endometrioid ovarian carcinomas showed negative staining for ARID1A (a) and p21 (b), aberrant expression of p53 (c) and p16 (d) and ß-Catenin positive nuclear expression (e) respectively in 19% (a), 100% (b), 28.6% (c), 52.4% (d) and 4.8% (e) of all cases. In the group of clear cell ovarian carcinomas it was 63.6% (a), 100% (b), 81.8% (c), 54.5% (d) and 0% (e). For endometrioid uterine carcinomas it was 75.7% (a), 94.9% (b), 30.5% (c), 52.1% (d) and 6.8% (e) and for clear cell uterine carcinomas it was 8.6% (a), 100% (b), 50% (c), 100% (d) and 0% (e). Survival analysis showed that negative expression of ARID1A, p53 aberrant expression and ß-Catenin nuclear positive staining are independent negative prognosticators in both, clear cell and endometrioid carcinoma, regardless of ovarian or uterine origin. Cox-Regression analysis showed them again as negative prognostic factors. Furthermore, we found a significant correlation between ARID1A and ß-Catenin expression in endometrioid uterine tumors. Conclusion The analyzed gynaecological carcinoma showed a distinct expression scheme of proteins that are associated with tumor suppression. We may conclude that ARID1A, p53 and ß-Catenin are the strongest prognostic factors by analyzing a subgroup of tumor suppressor genes in clear cell and endometrioid subtypes of ovarian and endometrial cancer and may be used along with traditional morphological and clinical characteristics for prognosis.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192881
       
  • Awareness and attitude of the public toward personalized medicine in Korea

    • Authors: Iyn-Hyang Lee Hye-Young Kang Hae Sun Suh Sukhyang Lee Eun Sil Oh Hotcherl Jeong
      Abstract: by Iyn-Hyang Lee, Hye-Young Kang, Hae Sun Suh, Sukhyang Lee, Eun Sil Oh, Hotcherl JeongObjectives As personalized medicine (PM) is expected to greatly improve health outcomes, efforts have recently been made for its clinical implementation in Korea. We aimed to evaluate public awareness and attitude regarding PM. Methods We performed a self-administered questionnaire survey to 703 adults, who participated in the survey on a voluntary basis. The primary outcome measures included public knowledge, attitude, and acceptance of PM. We conducted multinomial multivariate logistic analysis for outcome variables with three response categories and performed multivariate logistic regression analyses for dichotomous outcome variables. Results Only 28% of participants had knowledge that genetic factors can contribute to inter-individual variations in drug response and the definition of PM (199 out of 702). Higher family income was correlated with greater knowledge concerning PM (OR = 3.76, p = 0.034). A majority of respondents preferred integrated pharmacogenomic testing over drug-specific testing and agreed to inclusion of pharmacogenomic testing in the national health examination (64% and 77%, respectively), but only 51% were willing to pay for it. Discussion Our results identify the urgent need for public education as well as the potential health disparities in access to PM. This study helps to frame policies for implementing PM in clinical practice.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192856
       
  • Ecogeography of teosinte

    • Authors: José de Jesús Sánchez González José Ariel Ruiz Corral Guillermo Medina García Gabriela Ramírez Ojeda Lino De la Cruz Larios James Brendan Holland Roberto Miranda Medrano Giovanni Emmanuel García Romero
      Abstract: by José de Jesús Sánchez González, José Ariel Ruiz Corral, Guillermo Medina García, Gabriela Ramírez Ojeda, Lino De la Cruz Larios, James Brendan Holland, Roberto Miranda Medrano, Giovanni Emmanuel García RomeroAdaptation of crops to climate change has motivated an increasing interest in the potential value of novel traits from wild species; maize wild relatives, the teosintes, harbor traits that may be useful to maize breeding. To study the ecogeographic distribution of teosinte we constructed a robust database of 2363 teosinte occurrences from published sources for the period 1842–2016. A geographical information system integrating 216 environmental variables was created for Mexico and Central America and was used to characterize the environment of each teosinte occurrence site. The natural geographic distribution of teosinte extends from the Western Sierra Madre of the State of Chihuahua, Mexico to the Pacific coast of Nicaragua and Costa Rica, including practically the entire western part of Mesoamerica. The Mexican annuals Zea mays ssp. parviglumis and Zea mays ssp. mexicana show a wide distribution in Mexico, while Zea diploperennis, Zea luxurians, Zea perennis, Zea mays ssp. huehuetenangensis, Zea vespertilio and Zea nicaraguensis had more restricted and distinct ranges, representing less than 20% of the total occurrences. Only 11.2% of teosinte populations are found in Protected Natural Areas in Mexico and Central America. Ecogeographical analysis showed that teosinte can cope with extreme levels of precipitation and temperatures during growing season. Modelling teosinte geographic distribution demonstrated congruence between actual and potential distributions; however, some areas with no occurrences appear to be within the range of adaptation of teosintes. Field surveys should be prioritized to such regions to accelerate the discovery of unknown populations. Potential areas for teosintes Zea mays ssp. mexicana races Chalco, Nobogame, and Durango, Zea mays ssp. huehuetenangensis, Zea luxurians, Zea diploperennis and Zea nicaraguensis are geographically separated; however, partial overlapping occurs between Zea mays ssp. parviglumis and Zea perennis, between Zea mays ssp. parviglumis and Zea diploperennis, and between Zea mays ssp. mexicana race Chalco and Zea mays ssp. mexicana race Central Plateau. Assessing priority of collecting for conservation showed that permanent monitoring programs and in-situ conservation projects with participation of local farmer communities are critically needed; Zea mays ssp. mexicana (races Durango and Nobogame), Zea luxurians, Zea diploperennis, Zea perennis and Zea vespertilio should be considered as the highest priority taxa.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192676
       
  • Selective identification of somatic mutations in pancreatic cancer cells
           through a combination of next-generation sequencing of plasma DNA using
           molecular barcodes and a bioinformatic variant filter

    • Authors: Yoji Kukita Kazuyoshi Ohkawa Ryoji Takada Hiroyuki Uehara Kazuhiro Katayama Kikuya Kato
      Abstract: by Yoji Kukita, Kazuyoshi Ohkawa, Ryoji Takada, Hiroyuki Uehara, Kazuhiro Katayama, Kikuya KatoThe accuracy of next-generation sequencing (NGS) for detecting tumor-specific mutations in plasma DNA is hindered by errors introduced during PCR/sequencing, base substitutions caused by DNA damage, and pre-existing mutations in normal cells that are present at a low frequency. Here, we performed NGS of genes related to pancreatic cancer (comprising 2.8 kb of genomic DNA) in plasma DNA (average 4.5 ng) using molecular barcodes. The average number of sequenced molecules was 900, and the sequencing depth per molecule was 100 or more. We also developed a bioinformatic variant filter, called CV78, to remove variants that were not considered to be tumor-specific, i.e., those that are either absent or occur at low frequencies in the Catalogue of Somatic Mutations in Cancer database. In a cohort comprising 57 pancreatic cancer patients and 12 healthy individuals, sequencing initially identified variants in 31 (54%) and 5 (42%), respectively, whereas after applying the CV78 filter, 19 (33%) and zero were variant-positive. In a validation cohort consisting of 86 patients with pancreatic cancer and 20 patients with intraductal papillary mucinous neoplasm (IPMN), 62 (72%) with pancreatic cancer patients and 10 (50%) IPMN patients were initially variant positive. After CV78 filtering, these values were reduced to 32 (37%) and 1 (5%), respectively. The variant allele frequency of filtered variants in plasma ranged from 0.25% to 76.1%. Therefore, combining NGS and molecular barcodes with subsequent filtering is likely to eliminate most non-tumor-specific mutations.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192611
       
  • De novo transcriptomic analysis of leaf and fruit tissue of Cornus
           officinalis using Illumina platform

    • Authors: Dian-Yun Hou Lin-Chun Shi Meng-Meng Yang Jiong Li Shuang Zhou Hong-Xiao Zhang Hua-Wei Xu
      Abstract: by Dian-Yun Hou, Lin-Chun Shi, Meng-Meng Yang, Jiong Li, Shuang Zhou, Hong-Xiao Zhang, Hua-Wei XuCornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization. Hence, enriching its genomic data and information is very important. In recent years, the fast-growing technology of next generation sequencing has provided an effective path to gain genomic information from nonmodel species. This study is the first to explore the leaf and fruit tissue transcriptome of C. officinalis using the Illumina HiSeq 4000 platform. A total of 57,954,134 and 60,971,652 clean reads from leaf and fruit were acquired, respectively (GenBank number SRP115440). The pooled reads from all two libraries were assembled into 56,392 unigenes with an average length 856 bp. Among these, 41,146 unigenes matched with sequences in the NCBI nonredundant protein database. The Gene Ontology database assigned 24,336 unigenes with biological process (83.26%), cellular components (53.58%), and molecular function (83.93%). In addition, 10,808 unigenes were assigned a KOG functional classification by the KOG database. Searching against the KEGG pathway database indicated that 18,435 unigenes were mapped to 371 KEGG pathways. Moreover, the edgeR database identified 4,585 significant differentially expressed genes (DEGs), of which 1,392 were up-regulated and 3,193 were down-regulated in fruit tissue compared with leaf tissue. Finally, we explored 581 transcription factors with 50 transcription factor gene families. Most DEGs and transcription factors were related to terpene biosynthesis and secondary metabolic regulation. This study not only represented the first de novo transcriptomic analysis of C. officinalis but also provided fundamental information on its genes and biosynthetic pathway. These findings will help us explore the molecular metabolism mechanism of terpene biosynthesis in C. officinalis.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192610
       
  • Apolipoprotein E genotype does not moderate the associations of depressive
           symptoms, neuroticism and allostatic load with cognitive ability and
           cognitive aging in the Lothian Birth Cohort 1936

    • Authors: Zander Crook Tom Booth Simon R. Cox Janie Corley Dominika Dykiert Paul Redmond Alison Pattie Adele M. Taylor Sarah E. Harris John M. Starr Ian J. Deary
      Abstract: by Zander Crook, Tom Booth, Simon R. Cox, Janie Corley, Dominika Dykiert, Paul Redmond, Alison Pattie, Adele M. Taylor, Sarah E. Harris, John M. Starr, Ian J. DearyObjectives In this replication-and-extension study, we tested whether depressive symptoms, neuroticism, and allostatic load (multisystem physiological dysregulation) were related to lower baseline cognitive ability and greater subsequent cognitive decline in older adults, and whether these relationships were moderated by the E4 allele of the apolipoprotein E (APOE) gene. We also tested whether allostatic load mediated the relationships between neuroticism and cognitive outcomes. Methods We used data from the Lothian Birth Cohort 1936 (n at Waves 1–3: 1,028 [M age = 69.5 y]; 820 [M duration since Wave 1 = 2.98 y]; 659 [M duration since Wave 1 = 6.74 y]). We fitted latent growth curve models of general cognitive ability (modeled using five cognitive tests) with groups of APOE E4 non-carriers and carriers. In separate models, depressive symptoms, neuroticism, and allostatic load predicted baseline cognitive ability and subsequent cognitive decline. In addition, models tested whether allostatic load mediated relationships between neuroticism and cognitive outcomes. Results Baseline cognitive ability had small-to-moderate negative associations with depressive symptoms (β range = -0.20 to -0.17), neuroticism (β range = -0.27 to -0.23), and allostatic load (β range = -0.11 to 0.09). Greater cognitive decline was linked to baseline allostatic load (β range = -0.98 to -0.83) and depressive symptoms (β range = -1.00 to -0.88). However, APOE E4 allele possession did not moderate the relationships of depressive symptoms, neuroticism and allostatic load with cognitive ability and cognitive decline. Additionally, the associations of neuroticism with cognitive ability and cognitive decline were not mediated through allostatic load. Conclusions Our results suggest that APOE E4 status does not moderate the relationships of depressive symptoms, neuroticism, and allostatic load with cognitive ability and cognitive decline in healthy older adults. The most notable positive finding in the current research was the strong association between allostatic load and cognitive decline.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192604
       
  • Differences in neural responses to ipsilateral stimuli in wide-view fields
           between face- and house-selective areas

    • Authors: Bin Wang Ting Li Yan Niu Jie Xiang Junjie Cheng Bo Liu Hui Zhang Tianyi Yan Susumu Kanazawa Jinglong Wu
      Abstract: by Bin Wang, Ting Li, Yan Niu, Jie Xiang, Junjie Cheng, Bo Liu, Hui Zhang, Tianyi Yan, Susumu Kanazawa, Jinglong WuCategory-selective brain areas exhibit varying levels of neural activity to ipsilaterally presented stimuli. However, in face- and house-selective areas, the neural responses evoked by ipsilateral stimuli in the peripheral visual field remain unclear. In this study, we displayed face and house images using a wide-view visual presentation system while performing functional magnetic resonance imaging (fMRI). The face-selective areas (fusiform face area (FFA) and occipital face area (OFA)) exhibited intense neural responses to ipsilaterally presented images, whereas the house-selective areas (parahippocampal place area (PPA) and transverse occipital sulcus (TOS)) exhibited substantially smaller and even negative neural responses to the ipsilaterally presented images. We also found that the category preferences of the contralateral and ipsilateral neural responses were similar. Interestingly, the face- and house-selective areas exhibited neural responses to ipsilateral images that were smaller than the responses to the contralateral images. Multi-voxel pattern analysis (MVPA) was implemented to evaluate the difference between the contralateral and ipsilateral responses. The classification accuracies were much greater than those expected by chance. The classification accuracies in the FFA were smaller than those in the PPA and TOS. The closer eccentricities elicited greater classification accuracies in the PPA and TOS. We propose that these ipsilateral neural responses might be interpreted by interhemispheric communication through intrahemispheric connectivity of white matter connection and interhemispheric connectivity via the corpus callosum and occipital white matter connection. Furthermore, the PPA and TOS likely have weaker interhemispheric communication than the FFA and OFA, particularly in the peripheral visual field.
      PubDate: 2018-02-16T22:00:00Z
      DOI: 10.1371/journal.pone.0192532
       
 
 
JournalTOCs
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Email: journaltocs@hw.ac.uk
Tel: +00 44 (0)131 4513762
Fax: +00 44 (0)131 4513327
 
Home (Search)
Subjects A-Z
Publishers A-Z
Customise
APIs
Your IP address: 54.160.153.233
 
About JournalTOCs
API
Help
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-