bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary significance of the embryological development of the daphniid cladocerans Ceriodaphnia Dana, 1853 and Scapholeberis Schoedler, 1858 (Branchiopoda: Cladocera: Daphniidae)
Authors: Uhlik Marcin Edward
Published: October 2019

The embryological development of Ceriodaphnia reticulataDumont & Pensaert, 1983 and Scapholeberis rammneriJurine, 1820 were investigated using scanning electron microscopy. A carapace spine did not develop and there was no fusion of the first antennae. These are apparent apomorphies of DaphniaMüller, 1785, which suggests that the common ancestor of Daphniidae Straus, 1820 did not have a carapace spine during its embryological development, and its first antennae were short and separated during embryogenesis. Morphological evidence thus appears congruent with molecular interpretations showing that ScapholeberisSchoedler, 1858 is basal to other genera of Daphniidae, Ceriodaphnia being a sister taxon to Daphnia.
Recovering Decimation-Based Cryptographic Sequences by Means of Linear CAs
Authors: Cardell Sara D , Aranha Diego F , Fúster-Sabater Amparo
Published: October 2019

The sequences produced by the cryptographic sequence generator known as the shrinking generator can be modelled as the output sequences of linear elementary cellular automata (CA). These sequences are composed of interleaved m-sequences produced by linear structures based on feedback shifts. This profitable characteristic can be used in the cryptanalysis of this generator. In this work we propose an algorithm that takes advantage of the inherent linearity of these CA and the interleaved m-sequences. Although irregularly decimated generators have been conceived and designed as non-linear ones, in practice they can be easily analysed in terms of simple linear structures.
Proteoglycan (Keratan Sulfate) Barrier in Developing Human Forebrain Isolates Cortical Epileptic Networks From Deep Heterotopia, Insulates Axonal Fascicles, and Explains Why Axosomatic Synapses Are Inhibitory
Authors: Sarnat Harvey B
Published: October 2019

Axons from deep heterotopia do not extend through U-fibers, except transmantle dysplasias. Keratan sulfate (KS) in fetal spinal cord/brainstem median septum selectively repels glutamatergic axons while enabling GABAergic commissural axons. Immunocytochemical demonstration of KS in neocortical resections and forebrain at autopsy was studied in 12 fetuses and neonates 9–41 weeks gestational age (GA), 9 infants, children, and adolescents and 5 patients with focal cortical dysplasias (FCD1a). From 9 to 15 weeks GA, no KS is seen in the cortical plate; 19-week GA reactivity is detected in the molecular zone. By 28 weeks GA, patchy granulofilamentous reactivity appears in extracellular matrix and adheres to neuronal somata with increasing intensity in deep cortex and U-fibers at term. Perifascicular KS surrounds axonal bundles of both limbs of the internal capsule and within basal ganglia from 9 weeks GA. Thalamus and globus pallidus exhibit intense astrocytic reactivity from 9 weeks GA. In FCD1a, U-fiber reactivity is normal, discontinuous or radial. Ultrastructural correlates were not demonstrated; KS is not electron-dense. Proteoglycan barrier of the U-fiber layer impedes participation of deep heterotopia in cortical epileptic networks. Perifascicular KS prevents aberrant axonal exit from or entry into long and short tracts. KS adhesion to neuronal somatic membranes may explain inhibitory axosomatic synapses.
Differences in seed properties and germination between native and introduced populations of Triadica sebifera
Authors: Zhang Jialiang , Siemann Evan , Tian Baoliang , Huang Wei , Ding Jianqing
Published: October 2019

Aims

Seeds of many invasive plants germinate more quickly than those of native species, likely facilitating invasion success. Assessing the germination traits and seed properties simultaneously for introduced and native populations of an invasive plant is essential to understanding biological invasions. Here, we used Triadica sebifera as a study organism to examine intraspecific differences in seed germination together with seed characteristics.

Methods

We measured physical (volume, mass, coat hardness and coat thickness of seeds) and chemical (crude fat, soluble protein, sugar, gibberellins [GA] and abscisic acid [ABA] of kernels) properties of T. sebifera seeds collected in 2017 from 12 introduced (United States) populations and 12 native (China) populations and tested their germination rates and timing in a greenhouse experiment in China. Furthermore, we conducted an extra experiment in the United States using seeds collected in 2016 and 2017 to compare the effects of study sites (China vs. United States) and seed collection time (2016 vs. 2017) on seed germination.

Important Findings

Seeds from the introduced range germinated faster than those from the native range. Physical and chemical measurements showed that seeds from the introduced range were larger, had higher GA concentrations and GA:ABA ratio, but lower crude fat concentrations compared to those from the native range. There were no significant differences in seed mass, coat hardness and coat thickness or kernel ABA, soluble protein or sugar concentrations between seeds from introduced vs. native ranges. Germination rates were correlated between United States and China greenhouses but germination rates for populations varied between collection years. Our results suggest that larger seeds and higher GA likely contribute to faster germination, potentially facilitating T. sebifera invasion in the introduced range.
Root cap size and shape influence responses to the physical strength of the growth medium in Arabidopsis thaliana primary roots
Authors: Roué J , Chauvet H , Brunel-Michac N , Bizet F , Moulia B , Badel E , Legué V
Published: October 2019

Analysis of the growth and orientation of roots of Arabidopsis mutants with differing root cap sizes and shapes indicates that the form of the cap affects root responses to variations in the strength of the growth medium.
Sigma factor 1 in chloroplast gene transcription and photosynthetic light acclimation
Authors: Macadlo Lauren A , Ibrahim Iskander M , Puthiyaveetil Sujith
Published: October 2019

Sigma factors are dissociable subunits of bacterial RNA polymerase that ensure efficient transcription initiation from gene promoters. Owing to their prokaryotic origin, chloroplasts possess a typical bacterial RNA polymerase together with its sigma factor subunit. The higher plant Arabidopsis thaliana contain as many as six sigma factors for the hundred or so of its chloroplast genes. The role of this relatively large number of transcription initiation factors for the miniature chloroplast genome, however, is not fully understood. Using two Arabidopsis T-DNA insertion mutants, we show that sigma factor 1 (SIG1) initiates transcription of a specific subset of chloroplast genes. We further show that the photosynthetic control of PSI reaction center gene transcription requires complementary regulation of the nuclear SIG1 gene at the transcriptional level. This SIG1 gene regulation is dependent on both a plastid redox signal and a light signal transduced by the phytochrome photoreceptor.
Arabidopsis thaliana SEED DORMANCY 4-LIKE regulates dormancy and germination by mediating the gibberellin pathway
Authors: Cao Hong , Han Yi , Li Jingyi , Ding Meng , Li Yu , Li Xiaoying , Chen Fengying , Soppe Wim Jj , Liu Yongxiu
Published: October 2019

The molecular mechanisms underlying seed dormancy and germination are not fully understood. Here, we show that Arabidopsis thaliana SEED DORMANCY 4-LIKE (AtSdr4L) is a novel specific regulator of dormancy and germination. AtSdr4L encodes a protein with an unknown biochemical function that is localized in the nucleus and is expressed specifically in seeds. Loss of function of AtSdr4L results in increased seed dormancy. The germination of freshly harvested seeds of the Atsdr4l mutant is insensitive to gibberellin (GA). After-ripened mutant seeds are hypersensitive to the GA biosynthesis-inhibitor paclobutrazol but show unaltered sensitivity to abscisic acid. Several GA biosynthesis genes and GA-regulated cell wall remodeling genes are down-regulated in the mutant in both dormant and after-ripened seeds. These results suggest that the Atsdr4l mutation causes both decreased GA biosynthesis and reduced responses. In addition, a genetic analysis indicated that AtSdr4L is epistatic to DELAY OF GERMINATION1 (DOG1) for dormancy and acts upstream of RGA-LIKE 2 (RGL2) in the GA pathway. We propose that AtSdr4L regulates seed dormancy and germination by mediating both the DOG1 and GA pathways.
Xylem embolism in leaves does not occur with open stomata: evidence from direct observations using the optical visualization technique
Authors: Creek Danielle , Lamarque Laurent J , Torres-Ruiz José M , Parise Camille , Burlett Regis , Tissue David T , Delzon Sylvain
Published: October 2019

Drought represents a major abiotic constraint to plant growth and survival. On the one hand, plants keep stomata open for efficient carbon assimilation while, on the other hand, they close them to prevent permanent hydraulic impairment from xylem embolism. The order of occurrence of these two processes (stomatal closure and the onset of leaf embolism) during plant dehydration has remained controversial, largely due to methodological limitations. However, the newly developed optical visualization method now allows concurrent monitoring of stomatal behaviour and leaf embolism formation in intact plants. We used this new approach directly by dehydrating intact saplings of three contrasting tree species and indirectly by conducting a literature survey across a greater range of plant taxa. Our results indicate that increasing water stress generates the onset of leaf embolism consistently after stomatal closure, and that the lag time between these processes (i.e. the safety margin) rises with increasing embolism resistance. This suggests that during water stress, embolism-mediated declines in leaf hydraulic conductivity are unlikely to act as a signal for stomatal down-regulation. Instead, these species converge towards a strategy of closing stomata early to prevent water loss and delay catastrophic xylem dysfunction.
From antagonist to protagonist: ‘Democracy’ and ‘people’ in British parliamentary debates, 1775–1885
Authors: Bonin Hugo
Published: October 2019

‘Democracy’ is a central word of our current political lexicon, often defined as ‘the power of the people’. However, in 19th century Britain, ‘democracy’ was not characterized by the rule of the ‘people’ but by the power of lower classes, of the ‘populace’ and the ‘mob’. In political discourse, and especially in parliamentary debates, the ‘people’ were an antagonist of ‘democracy’, not its protagonist. To support these statements, this article analyses British parliamentary debates between 1775 and 1885, through both a ‘distant reading’ with the help of corpus linguistics tools and a closer examination of certain key debates and actors. After a brief overview of the methodology, three crucial periods of British political history are analysed. (1) The end of the 18th century, where the impact of the French Revolution on democratic vocabulary is measured. (2) The debates surrounding the 1832 Reform Act, in which the explicit differentiation between the constitutional ‘people’ and the democratic ‘mob’ is drawn out by Whigs and Tories alike. (3) The Second Reform Act (1867), also presented as a ‘popular’ measure, and not a step towards ‘democracy’. In conclusion, the adoption of the democratic vocabulary by British Members of Parliament is traced to the 1880s, notably with the emergence of the idea of ‘Tory democracy’.
Orbital dynamics of circumbinary planets
Authors: Chen Cheng , Franchini Alessia , Lubow Stephen H , Martin Rebecca G
Published: October 2019

We investigate the dynamics of a non-zero mass, circular orbit planet around an eccentric orbit binary for various values of the binary eccentricity, binary mass fraction, planet mass, and planet semimajor axis by means of numerical simulations. Previous studies investigated the secular dynamics mainly by approximate analytic methods. In the stationary inclination state, the planet and binary precess together with no change in relative tilt. For both prograde and retrograde planetary orbits, we explore the conditions for planetary orbital libration versus circulation and the conditions for stationary inclination. As was predicted by analytic models, for sufficiently high initial inclination, a prograde planet’s orbit librates about the stationary tilted state. For a fixed binary eccentricity, the stationary angle is a monotonically decreasing function of the ratio of the planet-to-binary angular momentum j. The larger j, the stronger the evolutionary changes in the binary eccentricity and inclination. We also calculate the critical tilt angle that separates the circulating from the librating orbits for both prograde and retrograde planet orbits. The properties of the librating orbits and stationary angles are quite different for prograde versus retrograde orbits. The results of the numerical simulations are in very good quantitative agreement with the analytic models. Our results have implications for circumbinary planet formation and evolution.
JexoSim: a time-domain simulator of exoplanet transit spectroscopy with JWST
Authors: Sarkar Subhajit , Madhusudhan Nikku , Papageorgiou Andreas
Published: October 2019

The James Webb Space Telescope (JWST) will perform exoplanet transit spectroscopy in the coming decade, promising transformative science results. All four instruments onboard can be used for this technique that reconstructs the atmospheric transmission or emission spectrum of an exoplanet from wavelength-dependent light-curve measurements. Astrophysical and instrumental noise and systematics can affect the precision and accuracy of the final spectrum, and hence, the atmospheric properties derived from the spectrum. Correlated noise and time-dependent systematics that can bias the measured signal must be accounted for in the final uncertainties. However, quantifying these effects can be difficult with real data or simple analytic tools. Existing publicly available simulators for JWST do not adequately simulate complex time-domain processes on exoplanetary transit observations. We report JexoSim, a dedicated time-domain simulator for JWST including all the four instruments for exoplanet transit spectroscopy. JexoSim models both the astrophysics and the instrument, generating 2D images in simulated time akin to a real observation. JexoSim can capture correlated noise and systematic biases on the light curve, giving it great versatility. Potential applications of JexoSim include performance testing of JWST instruments, assessing science return, and testing data reduction pipelines. We describe JexoSim, validate it against other simulators, and present examples of its utility.
Reliable Confidence Intervals for RelTime Estimates of Evolutionary Divergence Times
Authors: Tao Qiqing , Tamura Koichiro , Mello Beatriz , Kumar Sudhir
Published: October 2019

Confidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in dating analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, that is, the actual time is contained within the CIs with a 94% probability. These developments will encourage broader use of computationally efficient RelTime approaches in molecular dating analyses and biological hypothesis testing.
Molecular Biology and Evolution of Cancer: From Discovery to Action
Authors: Somarelli Jason A , Gardner Heather , Cannataro Vincent L , Gunady Ella F , Boddy Amy M , Johnson Norman A , Fisk Jeffrey Nicholas , Gaffney Stephen G , Chuang Jeffrey H , Li Sheng , Ciccarelli Francesca D , Panchenko Anna R , Megquier Kate , Kumar Sudhir , Dornburg Alex , DeGregori James , Townsend Jeffrey P
Published: October 2019

Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution—and progression—require a deep understanding of the underlying molecular evolutionary processes. Herein we discuss a suite of concepts and tools from evolutionary and ecological theory that can inform cancer biology in new and meaningful ways. We also highlight current challenges to applying these concepts, and propose ways in which incorporating these concepts could identify new therapeutic modes and vulnerabilities in cancer.
Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping
Authors: Slyvka Anton , Zagorskaitė Evelina , Czapinska Honorata , Sasnauskas Giedrius , Bochtler Matthias
Published: October 2019

EcoKMcrA from Escherichia coli restricts CpG methylated or hydroxymethylated DNA, and may act as a barrier against host DNA. The enzyme consists of a novel N-terminal specificity domain that we term NEco, and a C-terminal catalytic HNH domain. Here, we report that NEco and full-length EcoKMcrA specificities are consistent. NEco affinity to DNA increases more from hemi- to full-methylation than from non- to hemi-methylation, indicating cooperative binding of the methyl groups. We determined the crystal structures of NEco in complex with fully modified DNA containing three variants of the Y5mCGR EcoKMcrA target sequence: C5mCGG, T5mCGA and T5hmCGA. The structures explain the specificity for the two central base pairs and one of the flanking pairs. As predicted based on earlier biochemical experiments, NEco does not flip any DNA bases. The proximal and distal methyl groups are accommodated in separate pockets. Changes to either pocket reduce DNA binding by NEco and restriction by EcoKMcrA, confirming the relevance of the crystallographically observed binding mode in solution.
PlantRegMap: charting functional regulatory maps in plants
Authors: Tian Feng , Yang De-Chang , Meng Yu-Qi , Jin Jinpu , Gao Ge
Published: October 2019

With the goal of charting plant transcriptional regulatory maps (i.e. transcription factors (TFs), cis-elements and interactions between them), we have upgraded the TF-centred database PlantTFDB (http://planttfdb.cbi.pku.edu.cn/) to a plant regulatory data and analysis platform PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) over the past three years. In this version, we updated the annotations for the previously collected TFs and set up a new section, ‘extended TF repertoires’ (TFext), to allow users prompt access to the TF repertoires of newly sequenced species. In addition to our regular TF updates, we are dedicated to updating the data on cis-elements and functional interactions between TFs and cis-elements. We established genome-wide conservation landscapes for 63 representative plants and then developed an algorithm, FunTFBS, to screen for functional regulatory elements and interactions by coupling the base-varied binding affinities of TFs with the evolutionary footprints on their binding sites. Using the FunTFBS algorithm and the conservation landscapes, we further identified over 20 million functional TF binding sites (TFBSs) and two million functional interactions for 21 346 TFs, charting the functional regulatory maps of these 63 plants. These resources are publicly available at PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) and a cloud-based mirror (http://plantregmap.gao-lab.org/), providing the plant research community with valuable resources for decoding plant transcriptional regulatory systems.
The reactome pathway knowledgebase
Authors: Jassal Bijay , Matthews Lisa , Viteri Guilherme , Gong Chuqiao , Lorente Pascual , Fabregat Antonio , Sidiropoulos Konstantinos , Cook Justin , Gillespie Marc , Haw Robin , Loney Fred , May Bruce , Milacic Marija , Rothfels Karen , Sevilla Cristoffer , Shamovsky Veronica , Shorser Solomon , Varusai Thawfeek , Weiser Joel , Wu Guanming , Stein Lincoln , Hermjakob Henning , D’Eustachio Peter
Published: October 2019

The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data model, an extended version of a classic metabolic map. Reactome functions both as an archive of biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To extend our ability to annotate human disease processes, we have implemented a new drug class and have used it initially to annotate drugs relevant to cardiovascular disease. Our annotation model depends on external domain experts to identify new areas for annotation and to review new content. New web pages facilitate recruitment of community experts and allow those who have contributed to Reactome to identify their contributions and link them to their ORCID records. To improve visualization of our content, we have implemented a new tool to automatically lay out the components of individual reactions with multiple options for downloading the reaction diagrams and associated data, and a new display of our event hierarchy that will facilitate visual interpretation of pathway analysis results.
Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data
Authors: Bogue Molly A , Philip Vivek M , Walton David O , Grubb Stephen C , Dunn Matthew H , Kolishovski Georgi , Emerson Jake , Mukherjee Gaurab , Stearns Timothy , He Hao , Sinha Vinita , Kadakkuzha Beena , Kunde-Ramamoorthy Govindarajan , Chesler Elissa J
Published: October 2019

The Mouse Phenome Database (MPD; https://phenome.jax.org) is a widely accessed and highly functional data repository housing primary phenotype data for the laboratory mouse accessible via APIs and providing tools to analyze and visualize those data. Data come from investigators around the world and represent a broad scope of phenotyping endpoints and disease-related traits in naïve mice and those exposed to drugs, environmental agents or other treatments. MPD houses rigorously curated per-animal data with detailed protocols. Public ontologies and controlled vocabularies are used for annotation. In addition to phenotype tools, genetic analysis tools enable users to integrate and interpret genome–phenome relations across the database. Strain types and populations include inbred, recombinant inbred, F1 hybrid, transgenic, targeted mutants, chromosome substitution, Collaborative Cross, Diversity Outbred and other mapping populations. Our new analysis tools allow users to apply selected data in an integrated fashion to address problems in trait associations, reproducibility, polygenic syndrome model selection and multi-trait modeling. As we refine these tools and approaches, we will continue to provide users a means to identify consistent, quality studies that have high translational relevance.
DDBJ Database updates and computational infrastructure enhancement
Authors: Ogasawara Osamu , Kodama Yuichi , Mashima Jun , Kosuge Takehide , Fujisawa Takatomo
Published: October 2019

The Bioinformation and DDBJ Center (https://www.ddbj.nig.ac.jp) in the National Institute of Genetics (NIG) maintains a primary nucleotide sequence database as a member of the International Nucleotide Sequence Database Collaboration (INSDC) in partnership with the US National Center for Biotechnology Information and the European Bioinformatics Institute. The NIG operates the NIG supercomputer as a computational basis for the construction of DDBJ databases and as a large-scale computational resource for Japanese biologists and medical researchers. In order to accommodate the rapidly growing amount of deoxyribonucleic acid (DNA) nucleotide sequence data, NIG replaced its supercomputer system, which is designed for big data analysis of genome data, in early 2019. The new system is equipped with 30 PB of DNA data archiving storage; large-scale parallel distributed file systems (13.8 PB in total) and 1.1 PFLOPS computation nodes and graphics processing units (GPUs). Moreover, as a starting point of developing multi-cloud infrastructure of bioinformatics, we have also installed an automatic file transfer system that allows users to prevent data lock-in and to achieve cost/performance balance by exploiting the most suitable environment from among the supercomputer and public clouds for different workloads.
TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration
Authors: Urán Landaburu Lionel , Berenstein Ariel J , Videla Santiago , Maru Parag , Shanmugam Dhanasekaran , Chernomoretz Ariel , Agüero Fernán
Published: October 2019

The volume of biological, chemical and functional data deposited in the public domain is growing rapidly, thanks to next generation sequencing and highly-automated screening technologies. These datasets represent invaluable resources for drug discovery, particularly for less studied neglected disease pathogens. To leverage these datasets, smart and intensive data integration is required to guide computational inferences across diverse organisms. The TDR Targets chemogenomics resource integrates genomic data from human pathogens and model organisms along with information on bioactive compounds and their annotated activities. This report highlights the latest updates on the available data and functionality in TDR Targets 6. Based on chemogenomic network models providing links between inhibitors and targets, the database now incorporates network-driven target prioritizations, and novel visualizations of network subgraphs displaying chemical- and target-similarity neighborhoods along with associated target-compound bioactivity links. Available data can be browsed and queried through a new user interface, that allow users to perform prioritizations of protein targets and chemical inhibitors. As such, TDR Targets now facilitates the investigation of drug repurposing against pathogen targets, which can potentially help in identifying candidate targets for bioactive compounds with previously unknown targets. TDR Targets is available at https://tdrtargets.org.
Rethinking the economics of rural water in Africa
Authors: Hope Rob , Thomson Patrick , Koehler Johanna , Foster Tim
Published: October 2019

Rural Africa lags behind global progress to provide safe drinking water to everyone. Decades of effort and billions of dollars of investment have yielded modest gains, with high but avoidable health and economic costs borne by over 300m people lacking basic water access. We explore why rural water is different for communities, schools, and healthcare facilities across characteristics of scale, institutions, demand, and finance. The findings conclude with policy recommendations to (i) network rural services at scale, (ii) unlock rural payments by creating value, and (iii) design and test performance-based funding models at national and regional scales, with an ambition to eliminate the need for future, sustainable development goals.
Reproductive performance of the Antarctic tardigrades, Acutuncus antarcticus (Eutardigrada: Hypsibiidae), revived after being frozen for over 30 years and of their offspring
Authors: Tsujimoto Megumu , Kagoshima Hiroshi , Kanda Hiroshi , Watanabe Kenichi , Imura Satoshi
Published: October 2019

Studies on the long-term survival of animals often focus on the specific instance of survival of animals only, and descriptions of subsequent reproduction are generally not reported. In this study, we recorded the reproductive performance of the first-generation offspring of the resuscitated individual (SB-1) and the hatchling of the resuscitated egg (SB-3) of the Antarctic tardigrade, Acutuncus antarcticus, after being frozen for 30.5 years. By providing further detailed description of the reproduction of SB-1 and SB-3 after revival, and then comparing the reproductive performance with that of their first-generation offspring, the possible indications of the damage accrued during the long-term preservation in SB-1 and SB-3 were more specifically detected. Additionally, the DNA analysis revealed two distinctively different mitochondrial genetic sequences of A. antarcticus between the SB strains and the LSW strain. The observed differences in some of the reproductive parameters between the two genetic types suggested a possible relationship between the life-history traits and genetic type in the species A. antarcticus. Further experiments using the SB-1 and SB-3 strains reared for a long period to exclude the instant effect of preservation are expected to improve our understanding of the mechanisms underlying the long-term survival of animals.
Genome-Wide Associations and Transcriptional Profiling Reveal ROS Regulation as One Underlying Mechanism of Sheath Blight Resistance in Rice
Authors: Oreiro Eula Gems , Grimares Earlyn Kate , Atienza-Grande Genelou , Quibod Ian Lorenzo , Roman-Reyna Veronica , Oliva Ricardo
Published: October 2019

Rice sheath blight, caused by the necrotrophic fungus Rhizoctonia solani Kühn, continues to be an important and challenging rice disease worldwide. Here, we used genome-wide association studies over a high-density rice array to facilitate the identification of potential novel genes and quantitative trait loci related to sheath blight resistance. We identified multiple regions that significantly associated with independent disease components in chromosomes 1, 4, and 11 under controlled condition. In particular, we investigated qLN1128, a quantitative trait locus enriched with defense-related genes that reduce disease lesions in a near-isogenic line. RNA profiling of the line carrying qLN1128 showed a number of differentially expressed genes related to the reactive oxygen species (ROS)-redox pathway. Histochemical staining revealed less ROS accumulation on the resistant line, suggesting efficient ROS deregulation that delays pathogen colonization. The detection of genomic regions controlling multiple mechanisms of resistance to sheath blight will provide tools to design effective breeding interventions in rice.
Hydrogen Peroxide Metabolism in Interkingdom Interaction Between Bacteria and Wheat Seeds and Seedlings
Authors: Gerna Davide , Roach Thomas , Mitter Birgit , Stöggl Wolfgang , Kranner Ilse
Published: October 2019

In endophytes, the abundance of genes coding for enzymes processing reactive oxygen species (ROS), including hydrogen peroxide (H2O2), argues for a crucial role of ROS metabolism in plant-microbe interaction for plant colonization. Here, we studied H2O2 metabolism of bread wheat (Triticum aestivum L.) seeds and their microbiota during germination and early seedling growth, the most vulnerable stages in the plant life cycle. Treatment with hot steam diminished the seed microbiota, and these seeds produced less extracellular H2O2 than untreated seeds. Using a culture-dependent approach, Pantoea and Pseudomonas genera were the most abundant epiphytes of dry untreated seeds. Incubating intact seedlings from hot steam–treated seeds with Pantoea strains triggered H2O2 production, whereas Pseudomonas strains dampened H2O2 levels, attributable to higher catalase activities. The genus Pantoea was much less represented among seedling endophytes than genus Pseudomonas, with other endophytic genera, including Bacillus and Paenibacillus, also possessing high catalase activities. Overall, our results show that certain bacteria of the seed microbiota are able to modulate the extracellular redox environment during germination and early seedling growth, and high catalase activity is proposed as a key trait of seed endophytes.
Deepening understanding of language through synaesthesia: a call to reform and expand
Authors: Mankin Jennifer L.
Published: October 2019

In this paper, I present arguments and suggestions for the improvement of the scientific study of synaesthesia, and particularly grapheme-colour synaesthesia in relation to psycholinguistic research, although the principles I advocate can be easily adapted to any subfield of synaesthesia study. I postulate that the current state of research on synaesthesia in general, and on grapheme-colour synaesthesia in particular, suffers from a lack of exploratory evidence and essential groundwork upon which to build hypothesis-testing studies. In particular, I argue that synaesthesia research has been artificially bounded by assumptions about the nature of synaesthetic experiences, which constrain both the questions that researchers ask and the way in which they go about answering those questions. As a specific example, I detail how much of the current research on grapheme-colour synaesthesia is built to accommodate two major assumptions about the nature of colours for letters and for words—assumptions which I will contend are not universally true, and the exceptions to which point to a much richer and heterogeneous understanding of synaesthetic experience than current research practices capture. The top-down predetermination of what is important or meaningful to measure, and what is not, has subsequently impeded a full understanding of what synaesthesia is and how it works. I argue that these assumptions must be carefully addressed and evaluated, both for the particular case of grapheme-colour synaesthesia and for the field as a whole, to move towards a holistic and fruitful understanding of synaesthesia as a phenomenon and as a tool to study language, thought and perception. To that end, I propose specific recommendations for synaesthesia researchers to solidify and expand their understanding and to capture the actual experience of synaesthetes.

This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
Synaesthesia: a distinct entity that is an emergent feature of adaptive neurocognitive differences
Authors: Ward Jamie
Published: October 2019

In this article, I argue that synaesthesia is not on a continuum with neurotypical cognition. Synaesthesia is special: its phenomenology is different; it has distinct causal mechanisms; and is likely to be associated with a distinct neurocognitive profile. However, not all synaesthetes are the same, and there are quantifiable differences between them. In particular, the number of types of synaesthesia that a person possesses is a hitherto underappreciated variable that predicts cognitive differences along a number of dimensions (mental imagery, sensory sensitivity, attention to detail). Together with enhanced memory, this may constitute a common core of abilities that may go some way to explaining why synaesthesia might have evolved. I argue that the direct benefits of synaesthesia are generally limited (i.e. the synaesthetic associations do not convey novel information about the world) but, nevertheless, synaesthesia may develop due to other adaptive functions (e.g. perceptual ability, memory) that necessitate changes to design features of the brain. The article concludes by suggesting that synaesthesia forces us to reconsider what we mean by a ‘normal’ mind/brain. There may be multiple ‘normal’ neurodevelopmental trajectories that can sculpt very different ways of experiencing the world, of which synaesthesia is but one.

This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
Do synaesthesia and mental imagery tap into similar cross-modal processes?
Authors: O'Dowd Alan , Cooney Sarah M. , McGovern David P. , Newell Fiona N.
Published: October 2019

Synaesthesia has previously been linked with imagery abilities, although an understanding of a causal role for mental imagery in broader synaesthetic experiences remains elusive. This can be partly attributed to our relatively poor understanding of imagery in sensory domains beyond vision. Investigations into the neural and behavioural underpinnings of mental imagery have nevertheless identified an important role for imagery in perception, particularly in mediating cross-modal interactions. However, the phenomenology of synaesthesia gives rise to the assumption that associated cross-modal interactions may be encapsulated and specific to synaesthesia. As such, evidence for a link between imagery and perception may not generalize to synaesthesia. Here, we present results that challenge this idea: first, we found enhanced somatosensory imagery evoked by visual stimuli of body parts in mirror-touch synaesthetes, relative to other synaesthetes or controls. Moreover, this enhanced imagery generalized to tactile object properties not directly linked to their synaesthetic associations. Second, we report evidence that concurrent experience evoked in grapheme—colour synaesthesia was sufficient to trigger visual-to-tactile correspondences that are common to all. Together, these findings show that enhanced mental imagery is a consistent hallmark of synaesthesia, and suggest the intriguing possibility that imagery may facilitate the cross-modal interactions that underpin synaesthesic experiences.

This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
How non-veridical perception drives actions in healthy humans: evidence from synaesthesia
Authors: Schreiter Marie Luise , Chmielewski Witold X. , Ward Jamie , Beste Christian
Published: October 2019

We continually perform actions that are driven by our perception and it is a commonly held view that only objectively perceived changes within the ‘real’ world affect behaviour. Exceptions are generally only made for mental health disorders associated with delusions and hallucinations where behaviour may be triggered by the experience of objectively non-existent percepts. Here, we demonstrate, using synaesthesia as a model condition (inN= 19 grapheme-colour synaesthetes), how objectively non-existent (i.e. non-veridical) but still non-pathological perceptions affect actions in healthy humans. Using electroencephalography, we determine whether early-stage perceptual processes (reflected by P1 and N1 event-related potential (ERP) components), or late-stage-integration processes (reflected by N2 component), underlie the effects of non-veridical perceptions on action control. ERP analysis suggests that even though the examined peculiarities and experimental variations are perceptual in nature, it is not early-stage perceptual processes, but rather higher-order executive control processes linking perceptions to the appropriate motor response underlying this effect. Source localization analysis implicates activation within medial frontal cortices in the effect of how irrelevant non-veridical perceptions modulate behaviour. Our results challenge common conceptions about the determinants of human behaviour but can be explained by well-established theoretical frameworks detailing the link between perception and action.

This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
Autistic traits in synaesthesia: atypical sensory sensitivity and enhanced perception of details
Authors: van Leeuwen Tessa M. , van Petersen Eline , Burghoorn Floor , Dingemanse Mark , van Lier Rob
Published: October 2019

In synaesthetes, specific sensory stimuli (e.g. black letters) elicit additional experiences (e.g. colour). Synaesthesia is highly prevalent among individuals with autism spectrum disorder (ASD), but the mechanisms of this co-occurrence are not clear. We hypothesized autism and synaesthesia share atypical sensory sensitivity and perception. We assessed autistic traits, sensory sensitivity and visual perception in two synaesthete populations. In Study 1, synaesthetes (
N
= 79, of different types) scored higher than non-synaesthetes (
N
= 76) on the Attention-to-detail and Social skills subscales of the autism spectrum quotient indexing autistic traits, and on the Glasgow Sensory Questionnaire indexing sensory hypersensitivity and hyposensitivity which frequently occur in autism. Synaesthetes performed two local/global visual tasks because individuals with autism typically show a bias towards detail processing. In synaesthetes, elevated motion coherence thresholds (MCTs) suggested reduced global motion perception, and higher accuracy on an embedded figures task suggested enhanced local perception. In Study 2, sequence-space synaesthetes (
N
= 18) completed the same tasks. Questionnaire and embedded figures results qualitatively resembled Study 1 results, but no significant group differences with non-synaesthetes (
N
= 20) were obtained. Unexpectedly, sequence-space synaesthetes had reduced MCTs. Altogether, our studies suggest atypical sensory sensitivity and a bias towards detail processing are shared features of synaesthesia and ASD.

This article is part of the discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
Stochastic resonance model of synaesthesia
Authors: Lalwani Poortata , Brang David
Published: October 2019

In synaesthesia, stimulation of one sensory modality evokes additional experiences in another modality (e.g. sounds evoking colours). Along with these cross-sensory experiences, there are several cognitive and perceptual differences between synaesthetes and non-synaesthetes. For example, synaesthetes demonstrate enhanced imagery, increased cortical excitability and greater perceptual sensitivity in the concurrent modality. Previous models suggest that synaesthesia results from increased connectivity between corresponding sensory regions or disinhibited feedback from higher cortical areas. While these models explain how one sense can evoke qualitative experiences in another, they fail to predict the broader phenotype of differences observed in synaesthetes. Here, we propose a novel model of synaesthesia based on the principles of stochastic resonance. Specifically, we hypothesize that synaesthetes have greater neural noise in sensory regions, which allows pre-existing multisensory pathways to elicit supra-threshold activation (i.e. synaesthetic experiences). The strengths of this model are (a) it predicts the broader cognitive and perceptual differences in synaesthetes, (b) it provides a unified framework linking developmental and induced synaesthesias, and (c) it explains why synaesthetic associations are inconsistent at onset but stabilize over time. We review research consistent with this model and propose future studies to test its limits.

This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
Neurophenomenology of induced and natural synaesthesia
Authors: Schwartzman David J. , Bor Daniel , Rothen Nicolas , Seth Anil K.
Published: October 2019

People with synaesthesia have additional perceptual experiences, which are automatically and consistently triggered by specific inducing stimuli. Synaesthesia therefore offers a unique window into the neurocognitive mechanisms underlying conscious perception. A long-standing question in synaesthesia research is whether it is possible to artificially induce non-synaesthetic individuals to have synaesthesia-like experiences. Although synaesthesia is widely considered a congenital condition, increasing evidence points to the potential of a variety of approaches to induce synaesthesia-like experiences, even in adulthood. Here, we summarize a range of methods for artificially inducing synaesthesia-like experiences, comparing the resulting experiences to the key hallmarks of natural synaesthesia which include consistency, automaticity and a lack of ‘perceptual presence’. We conclude that a number of aspects of synaesthesia can be artificially induced in non-synaesthetes. These data suggest the involvement of developmental and/or learning components in the acquisition of synaesthesia, and they extend previous reports of perceptual plasticity leading to dramatic changes in perceptual phenomenology in adults.

This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
A cost-effective colourimetric assay for quantifying hydrogen peroxide in honey
Authors: Lehmann D. M. , Krishnakumar K. , Batres M. A. , Hakola-Parry A. , Cokcetin N. , Harry E. , Carter D. A.
Published: October 2019

Honey is a natural product with many beneficial properties including antimicrobial action. Production of hydrogen peroxide (H2O2) in diluted honey is central to this action. Here, we describe an optimized method for measuring levels of H2O2 in honey. This method is based on established methods, with the level of dilution, the time between dilution and reading the assay, and aeration of the samples during the assay identified as critical points for ensuring reliability and reproducibility. The method is cost-effective and easy to perform using common laboratory equipment. Using this method, we quantified the hydrogen peroxide content of five different, unprocessed polyfloral honeys collected in NC, USA. Our results show that H2O2 production by these honeys varies greatly, with some samples producing negligible levels of H2O2. We assessed the effect of colour on the assay by measuring the recovery of spiked H2O2 from light and dark honey and from serially diluted dark corn syrup, and found the amount of H2O2 that could be detected was lower in dark corn syrup and darker honey samples.
Exploring the overlap between rheumatoid arthritis susceptibility loci and long non-coding RNA annotations
Authors: Ding James , Shi Chenfu , Bowes John , Eyre Stephen , Orozco Gisela
Published: October 2019

Whilst susceptibility variants for many complex diseases, such as rheumatoid arthritis (RA), have been well characterised, the mechanism by which risk is mediated is still unclear for many loci. This is especially true for the majority of variants that do not affect protein-coding regions. lncRNA represent a group of molecules that have been shown to be enriched amongst variants associated with RA and other complex diseases, compared to random variants. In order to establish to what degree direct disruption of lncRNA may represent a potential mechanism for mediating RA susceptibility, we chose to further explore this overlap. By testing the ability of annotated features to improve a model of disease susceptibility, we were able to demonstrate a local enrichment of enhancers from immune-relevant cell types amongst RA susceptibility variants (log2 enrichment 3.40). This was not possible for lncRNA annotations in general, however a small, but significant enrichment was observed for immune-enriched lncRNA (log2 enrichment 0.867002). This enrichment was no longer apparent when the model was conditioned on immune-relevant enhancers (log2 enrichment -0.372734), suggesting that direct disruption of lncRNA sequence, independent of enhancer disruption, does not represent a major mechanism by which susceptibility to complex diseases is mediated. Furthermore, we demonstrated that, in keeping with general lncRNA characteristics, immune-enriched lncRNA are expressed at low levels that may not be amenable to functional characterisation.