title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1771 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Aging and cardiovascular complexity: effect of the length of RR tachograms link: https://peerj.com/articles/2755 last-modified: 2016-12-06 description: As we age, our hearts undergo changes that result in a reduction in complexity of physiological interactions between different control mechanisms. This results in a potential risk of cardiovascular diseases which are the number one cause of death globally. Since cardiac signals are nonstationary and nonlinear in nature, complexity measures are better suited to handle such data. In this study, three complexity measures are used, namely Lempel–Ziv complexity (LZ), Sample Entropy (SampEn) and Effort-To-Compress (ETC). We determined the minimum length of RR tachogram required for characterizing complexity of healthy young and healthy old hearts. All the three measures indicated significantly lower complexity values for older subjects than younger ones. However, the minimum length of heart-beat interval data needed differs for the three measures, with LZ and ETC needing as low as 10 samples, whereas SampEn requires at least 80 samples. Our study indicates that complexity measures such as LZ and ETC are good candidates for the analysis of cardiovascular dynamics since they are able to work with very short RR tachograms. creator: Karthi Balasubramanian creator: Nithin Nagaraj uri: https://doi.org/10.7717/peerj.2755 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Balasubramanian and Nagaraj title: Stress responses of the oil-producing green microalga Botryococcus braunii Race B link: https://peerj.com/articles/2748 last-modified: 2016-12-06 description: Plants react to biotic and abiotic stresses with a variety of responses including the production of reactive oxygen species (ROS), which may result in programmed cell death (PCD). The mechanisms underlying ROS production and PCD have not been well studied in microalgae. Here, we analyzed ROS accumulation, biomass accumulation, and hydrocarbon production in the colony-forming green microalga Botryococcus braunii in response to several stress inducers such as NaCl, NaHCO3, salicylic acid (SA), methyl jasmonate, and acetic acid. We also identified and cloned a single cDNA for the B. braunii ortholog of the Arabidopsis gene defender against cell death 1 (DAD1), a gene that is directly involved in PCD regulation. The function of B. braunii DAD1 was assessed by a complementation assay of the yeast knockout line of the DAD1 ortholog, oligosaccharyl transferase 2. Additionally, we found that DAD1 transcription was induced in response to SA at short times. These results suggest that B. braunii responds to stresses by mechanisms similar to those in land plants and other  organisms. creator: Ivette Cornejo-Corona creator: Hem R. Thapa creator: Daniel R. Browne creator: Timothy P. Devarenne creator: Edmundo Lozoya-Gloria uri: https://doi.org/10.7717/peerj.2748 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cornejo-Corona et al. title: The unique deep sea—land connection: interactive 3D visualization and molecular phylogeny of Bathyhedyle boucheti n. sp. (Bathyhedylidae n. fam.)—the first panpulmonate slug from bathyal zones link: https://peerj.com/articles/2738 last-modified: 2016-12-06 description: The deep sea comprises vast unexplored areas and is expected to conceal significant undescribed invertebrate species diversity. Deep waters may act as a refuge for many relictual groups, including elusive and enigmatic higher taxa, but the evolutionary pathways by which colonization of the deep sea has occurred have scarcely been investigated. Sister group relationships between shallow water and deep sea taxa have been documented in several invertebrate groups, but are unknown between amphibious/terrestrial and deep-sea species. Here we describe in full and interactive 3D morphoanatomical detail the new sea slug species Bathyhedyle boucheti n. sp., dredged from the continental slope off Mozambique. Molecular and morphological analyses reveal that it represents a novel heterobranch gastropod lineage which we establish as the new family Bathyhedylidae. The family is robustly supported as sister to the recently discovered panpulmonate acochlidian family Aitengidae, which comprises amphibious species living along the sea shore as well as fully terrestrial species. This is the first marine-epibenthic representative among hedylopsacean Acochlidiida, the first record of an acochlidian from deep waters and the first documented panpulmonate deep-sea slug. Considering a marine mesopsammic ancestor, the external morphological features of Bathyhedyle n. gen. may be interpreted as independent adaptations to a benthic life style in the deep sea, including the large body size, broad foot and propodial tentacles. Alternatively, the common ancestor of Bathyhedylidae and Aitengidae may have been a macroscopic amphibious or even terrestrial species. We hypothesize that oophagy in the common ancestor of Aitengidae and Bathyhedylidae might explain the impressive ecological and evolutionary flexibility in habitat choice in the Acochlidiida. creator: Timea P. Neusser creator: Katharina M. Jörger creator: Eva Lodde-Bensch creator: Ellen E. Strong creator: Michael Schrödl uri: https://doi.org/10.7717/peerj.2738 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Neusser et al. title: Harmine stimulates proliferation of human neural progenitors link: https://peerj.com/articles/2727 last-modified: 2016-12-06 description: Harmine is the β-carboline alkaloid with the highest concentration in the psychotropic plant decoction Ayahuasca. In rodents, classical antidepressants reverse the symptoms of depression by stimulating neuronal proliferation. It has been shown that Ayahuasca presents antidepressant effects in patients with depressive disorder. In the present study, we investigated the effects of harmine in cell cultures containing human neural progenitor cells (hNPCs, 97% nestin-positive) derived from pluripotent stem cells. After 4 days of treatment, the pool of proliferating hNPCs increased by 71.5%. Harmine has been reported as a potent inhibitor of the dual specificity tyrosine-phosphorylation-regulated kinase (DYRK1A), which regulates cell proliferation and brain development. We tested the effect of analogs of harmine, an inhibitor of DYRK1A (INDY), and an irreversible selective inhibitor of monoamine oxidase (MAO) but not DYRK1A (pargyline). INDY but not pargyline induced proliferation of hNPCs similarly to harmine, suggesting that inhibition of DYRK1A is a possible mechanism to explain harmine effects upon the proliferation of hNPCs. Our findings show that harmine enhances proliferation of hNPCs and suggest that inhibition of DYRK1A may explain its effects upon proliferation in vitro and antidepressant effects in vivo. creator: Vanja Dakic creator: Renata de Moraes Maciel creator: Hannah Drummond creator: Juliana M. Nascimento creator: Pablo Trindade creator: Stevens K. Rehen uri: https://doi.org/10.7717/peerj.2727 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Dakic et al. title: Expression and characterization of thermostable glycogen branching enzyme from Geobacillus mahadia Geo-05 link: https://peerj.com/articles/2714 last-modified: 2016-12-06 description: The glycogen branching enzyme (EC 2.4.1.18), which catalyses the formation of α-1,6-glycosidic branch points in glycogen structure, is often used to enhance the nutritional value and quality of food and beverages. In order to be applicable in industries, enzymes that are stable and active at high temperature are much desired. Using genome mining, the nucleotide sequence of the branching enzyme gene (glgB) was extracted from the Geobacillus mahadia Geo-05 genome sequence provided by the Malaysia Genome Institute. The size of the gene is 2013 bp, and the theoretical molecular weight of the protein is 78.43 kDa. The gene sequence was then used to predict the thermostability, function and the three dimensional structure of the enzyme. The gene was cloned and overexpressed in E. coli to verify the predicted result experimentally. The purified enzyme was used to study the effect of temperature and pH on enzyme activity and stability, and the inhibitory effect by metal ion on enzyme activity. This thermostable glycogen branching enzyme was found to be most active at 55 °C, and the half-life at 60 °C and 70 °C was 24 h and 5 h, respectively. From this research, a thermostable glycogen branching enzyme was successfully isolated from Geobacillus mahadia Geo-05 by genome mining together with molecular biology technique. creator: Nur Syazwani Mohtar creator: Mohd Basyaruddin Abdul Rahman creator: Raja Noor Zaliha Raja Abd Rahman creator: Thean Chor Leow creator: Abu Bakar Salleh creator: Mohd Noor Mat Isa uri: https://doi.org/10.7717/peerj.2714 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Mohtar et al. title: Ten genes and two topologies: an exploration of higher relationships in skipper butterflies (Hesperiidae) link: https://peerj.com/articles/2653 last-modified: 2016-12-06 description: Despite multiple attempts to infer the higher-level phylogenetic relationships of skipper butterflies (Family Hesperiidae), uncertainties in the deep clade relationships persist. The most recent phylogenetic analysis included fewer than 30% of known genera and data from three gene markers. Here we reconstruct the higher-level relationships with a rich sampling of ten nuclear and mitochondrial markers (7,726 bp) from 270 genera and find two distinct but equally plausible topologies among subfamilies at the base of the tree. In one set of analyses, the nuclear markers suggest two contrasting topologies, one of which is supported by the mitochondrial dataset. However, another set of analyses suggests mito-nuclear conflict as the reason for topological incongruence. Neither topology is strongly supported, and we conclude that there is insufficient phylogenetic evidence in the molecular dataset to resolve these relationships. Nevertheless, taking morphological characters into consideration, we suggest that one of the topologies is more likely. creator: Ranjit Kumar Sahoo creator: Andrew D. Warren creator: Niklas Wahlberg creator: Andrew V. Z. Brower creator: Vladimir A. Lukhtanov creator: Ullasa Kodandaramaiah uri: https://doi.org/10.7717/peerj.2653 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sahoo et al. title: Eurasian jays do not copy the choices of conspecifics, but they do show evidence of stimulus enhancement link: https://peerj.com/articles/2746 last-modified: 2016-12-01 description: Corvids (birds in the crow family) are hypothesised to have a general cognitive tool-kit because they show a wide range of transferrable skills across social, physical and temporal tasks, despite differences in socioecology. However, it is unknown whether relatively asocial corvids differ from social corvids in their use of social information in the context of copying the choices of others, because only one such test has been conducted in a relatively asocial corvid. We investigated whether relatively asocial Eurasian jays (Garrulus glandarius) use social information (i.e., information made available by others). Previous studies have indicated that jays attend to social context in their caching and mate provisioning behaviour; however, it is unknown whether jays copy the choices of others. We tested the jays in two different tasks varying in difficulty, where social corvid species have demonstrated social information use in both tasks. Firstly, an object-dropping task was conducted requiring objects to be dropped down a tube to release a food reward from a collapsible platform, which corvids can learn through explicit training. Only one rook and one New Caledonian crow have learned the task using social information from a demonstrator. Secondly, we tested the birds on a simple colour discrimination task, which should be easy to solve, because it has been shown that corvids can make colour discriminations. Using the same colour discrimination task in a previous study, all common ravens and carrion crows copied the demonstrator. After observing a conspecific demonstrator, none of the jays solved the object-dropping task, though all jays were subsequently able to learn to solve the task in a non-social situation through explicit training, and jays chose the demonstrated colour at chance levels. Our results suggest that social and relatively asocial corvids differ in social information use, indicating that relatively asocial species may have secondarily lost this ability due to lack of selection pressure from an asocial environment. creator: Rachael Miller creator: Corina J. Logan creator: Katherine Lister creator: Nicola S. Clayton uri: https://doi.org/10.7717/peerj.2746 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Miller et al. title: Grassland productivity in response to nutrient additions and herbivory is scale-dependent link: https://peerj.com/articles/2745 last-modified: 2016-12-01 description: Vegetation response to nutrient addition can vary across space, yet studies that explicitly incorporate spatial pattern into experimental approaches are rare. To explore whether there are unique spatial scales (grains) at which grass response to nutrients and herbivory is best expressed, we imposed a large (∼3.75 ha) experiment in a South African coastal grassland ecosystem. In two of six 60 × 60 m grassland plots, we imposed a scaled sampling design in which fertilizer was added in replicated sub-plots (1 × 1 m, 2 × 2 m, and 4 × 4 m). The remaining plots either received no additions or were fertilized evenly across the entire area. Three of the six plots were fenced to exclude herbivory. We calculated empirical semivariograms for all plots one year following nutrient additions to determine whether the scale of grass response (biomass and nutrient concentrations) corresponded to the scale of the sub-plot additions and compared these results to reference plots (unfertilized or unscaled) and to plots with and without herbivory. We compared empirical semivariogram parameters to parameters from semivariograms derived from a set of simulated landscapes (neutral models). Empirical semivariograms showed spatial structure in plots that received multi-scaled nutrient additions, particularly at the 2 × 2 m grain. The level of biomass response was predicted by foliar P concentration and, to a lesser extent, N, with the treatment effect of herbivory having a minimal influence. Neutral models confirmed the length scale of the biomass response and indicated few differences due to herbivory. Overall, we conclude that interpretation of nutrient limitation in grasslands is dependent on the grain used to measure grass response and that herbivory had a secondary effect. creator: Erica A.H. Smithwick creator: Douglas C. Baldwin creator: Kusum J. Naithani uri: https://doi.org/10.7717/peerj.2745 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Smithwick et al. title: PATMA: parser of archival tissue microarray link: https://peerj.com/articles/2741 last-modified: 2016-12-01 description: Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images. creator: Lukasz Roszkowiak creator: Carlos Lopez uri: https://doi.org/10.7717/peerj.2741 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Roszkowiak and Lopez title: Drosophila chem mutations disrupt epithelial polarity in Drosophila embryos link: https://peerj.com/articles/2731 last-modified: 2016-12-01 description: Drosophila embryogenesis has proven to be an extremely powerful system for developmental gene discovery and characterization. We isolated five new EMS-induced alleles that do not complement the l(3R)5G83 lethal line isolated in the Nüsslein-Volhard and Wieschaus screens. We have named this locus chem. Lethality of the new alleles as homozygous zygotic mutants is not completely penetrant, and they have an extended phenocritical period. Like the original allele, a fraction of mutant embryos die with cuticular defects, notably head involution and dorsal closure defects. Embryonic defects are much more extreme in germline clones, where the majority of mutant embryos die during embryogenesis and do not form cuticle, implying a strong chem maternal contribution. chem mutations genetically interact with mutations in cytoskeletal genes (arm) and with mutations in the epithelial polarity genes coracle, crumbs, and yurt. chem mutants dorsal open defects are similar to those present in yurt mutants, and, likewise, they have epithelial polarity defects. chem1 and chem3 mutations suppress yurt3, and chem3 mutants suppress crumbs1 mutations. In contrast, chem1 and coracle2 mutations enhance each other. Compared to controls, in chem mutants in embryonic lateral epithelia Crumbs expression is mislocalized and reduced, Coracle is increased and mislocalized basally at embryonic stages 13–14, then reduced at stage 16. Arm expression has a similar pattern but levels are reduced. creator: José M. Zamudio-Arroyo creator: Juan R. Riesgo-Escovar uri: https://doi.org/10.7717/peerj.2731 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zamudio-Arroyo and Riesgo-Escovar