bluuebunny/crossref_metadata_2025 huggingface dataset:
Redesign of OGC Symbology Encoding standard for sharing cartography
Authors: Bocher Erwan , Ertz Olivier
Published: January 2018

Despite most Spatial Data Infrastructures are offering service-based visualization of geospatial data, requirements are often at a very basic level leading to poor quality of maps. This is a general observation for any geospatial architecture as soon as open standards as those of the Open Geospatial Consortium (OGC) have to be applied. To improve this situation, this paper does focus on improvements at the (inter)operability side by considering standardization aspects. We propose two major redesign recommendations. First to consolidate the cartographic design knowledge at the core of the OGC Symbology Encoding standard. Secondly to build the standard in a modular way so as to be ready to host upcoming cartographic requirements.

Thus, we start by defining the main portrayal interoperability use cases that frame the concept of sharing cartography. Then we bring to light the strengths and limits of the relevant open standards to consider in this context. Finally we paint a set of recommendations to overcome the limits so as to make these use cases a reality.

Even if the definition of a cartographic-oriented standard is not able to act as a complete cartographic design framework by itself, we argue that pushing forward the standardization work dedicated to cartography is a way to share and disseminate good practices and finally to improve the quality of the visualizations.
A redesign of OGC Symbology Encoding standard for sharing cartography
Authors: Bocher Erwan , Ertz Olivier
Published: January 2018

Despite most Spatial Data Infrastructures are offering service-based visualization of geospatial data, requirements are often at a very basic level leading to poor quality of maps. This is a general observation for any geospatial architecture as soon as open standards as those of the Open Geospatial Consortium (OGC) shall be applied. To improve the situation, this paper does focus on improvements at the portrayal interoperability side by considering standardization aspects. We propose two major redesign recommendations. First to consolidate the cartographic theory at the core of the OGC Symbology Encoding standard. Secondly to build the standard in a modular way so as to be ready to be extended with upcoming future cartographic requirements.

Thus, we start by defining portrayal interoperability by means of typical use cases that frame the concept of sharing cartography. Then we bring to light the strengths and limits of the relevant open standards to consider in this context. Finally we propose a set of recommendations to overcome the limits so as to make these use cases a true reality.

Even if the definition of a cartographic-oriented standard is not able to act as a complete cartographic design framework by itself, we argue that pushing forward the standardization work dedicated to cartography is a way to share and disseminate good practices and finally to improve the quality of the visualizations.
FUCHS - Towards full circular RNA characterization using RNAseq
Authors: Metge Franziska , Czaja-Hasse Lisa F , Reinhardt Richard , Dieterich Chistoph
Published: January 2018

Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5’ splice site is linked to an upstream 3’ splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing. Though functional studies have shown that some circRNAs could act as miRNA-sponges, the function of most circRNAs remains unknown. To expand our understanding of possible roles of circular RNAs, we propose a new pipeline that could fully characterizes candidate circRNA structure from RNAseq data – FUCHS: FUll CHaracterization of circular RNA using RNA- Sequencing.

Currently, most computational prediction pipelines use back-spliced reads to identify circular RNAs. FUCHS extends this concept by considering all RNA-seq information from long reads (typically > 150 bp) to learn more about the exon coverage, the number of double break point fragments, the different circular isoforms arising from one host-gene, and the alternatively spliced exons within the same circRNA boundaries.

This new knowledge will enable the user to carry out differential-motif enrichment and miRNA-seed analysis to determine potential regulators during circRNA biogenesis. FUCHS is an easy-to-use Python based pipeline that contributes a new aspect to the circRNA research.

The pipeline is available as git repository: https://github.com/dieterich-lab/FUCHS
tmod: an R package for general and multivariate enrichment analysis
Authors: Weiner 3rd January , Domaszewska Teresa
Published: January 2018

“Omics” studies generate long lists of genes, proteins, metabolites or other features which can be difficult to decipher. Feature set enrichment analysis utilizing annotated groups/classes of features (such as pathways, gene ontology terms or gene/metabolic modules) can provide a powerful gateway to associate data to phenotypes such as disease process or treatment progression. At the same time, the increasing use of technologies to generate multidimensional omics data sets based on specific cell types or responses to stimuli increases the number and breadth of annotated feature sets available for enrichment analysis, facilitating the ability to draw biologically relevant conclusions. However, existing tools and applications for enrichment analysis are adapted specifically to gene set enrichment and lack functionalities to analyze rapidly growing amounts of metabolomics and other data. Moreover, such tools often provide only a limited range of statistical methods, rely on permutation tests, lack suitable visualization tools to facilitate result interpretation in complex experimental setups, and lack standalone versions usable in semi-automatized workflows. Here, we present tmod, an R package which implements powerful statistical methods for enrichment analysis. Tmod includes definitions of widely used feature sets for transcriptomic and metabolomic profiling and also allows use of custom user-provided feature sets. Moreover, it provides novel and intuitive visualiza- tion methods which facilitate interpretation of complex data sets. The implemented statistical tests allow the significance of enrichment within sorted feature lists to be calculated without randomization tests and thus are suitable for combining functional analysis with multivariate techniques.
Evaluation of reference genes for gene expression in red-tailed phascogale (Phascogale calura) liver, lung, small intestine and spleen
Authors: Ong Oselyne TW , Young Lauren J , Old Julie M
Published: January 2018

Background: Reference genes serve an important role as an endogenous control/standard for data normalisation in gene expression studies. Although reference genes have recently been suggested for marsupials, independent analysis of reference genes on different immune tissues is yet to be tested. Therefore, an assessment of reference genes is needed for the selection of stable, expressed genes across different marsupial tissues.

Methods: The study was conducted on red-tailed phascogales (Phascogale calura) using five juvenile and five adult males. The stability of five reference genes (glyceraldehyde-3-phosphate dehydrogenase, GAPDH; β-Actin, ACTB; 18S rRNA, 18S; 28S rRNA, 28S; and ribosomal protein L13A, RPL13A) was investigated using SYBR Green and analysed with the geNorm application available in qBasePLUS software.

Results: Gene stability for juvenile and adult tissue samples combined show that GAPDH was most stable in liver and lung tissue, and 18S in small intestine and spleen. While all reference genes were suitable for small intestine and spleen tissues, all reference genes except 28S were stable for lung and only 18S and 28S were stable for liver tissue. Separating the two age groups, we found that two different reference genes were considered stable in juveniles (ACTB and GAPDH) and adults (18S and 28S), and RPL13A was not stable for juvenile small intestine tissue. Except for 28S, all reference genes were stable in juvenile and adult lungs, and all five reference genes were stable in spleen tissue.

Discussion: Based on expression stability, ACTB and GAPDH are suitable for all tissues when studying the expression of marsupials in two age groups, except for adult liver tissues. The expression stability between juvenile and adult liver tissue was most unstable, as the stable reference genes for juveniles and adults were different. Juvenile and adult lung, small intestine and spleen share similar stable reference genes, except for small intestine tissues where all reference genes were stable in adults but RPL13A was not suitable in juveniles.
Events recovery under different methods
Authors: Méndez Karen , Miranda-Esquivel Daniel
Published: January 2018

To reconstruct the biogeographic history should be taken into account the processes involved in the current distribution of the biota, for example vicariance, dispersal, sympatry and extinction. Different methods have been created to answer this. From methods to detect only vicariant events to ancestral area analysis under different models where all events are considered to reconstruct the history at individual level and from which analyze if there are congruence with other taxonomic groups, methods based on cells, endemism areas, parsimony, parametric methods, in general there is a great variety of methods. All have a different approach to determine the amount and the location of the event in the phylogeny but all can give a resolution of how have been created this patterns of distribution.
Levels metaphor and building blocks—towards a domain granularity framework for the life sciences
Authors: Vogt Lars
Published: January 2018

Arranging a heterogeneous collection of entities into a hierarchy of linearly ordered levels (layers or strata) is a general ordering scheme that is a widely used notion for organizing knowledge. On the basis of four specific examples, all of which are relevant in the life sciences, I briefly discuss the diversity of different notions of the underlying levels metaphor. Before I turn to ontology research and Keet's formal theory of granularity, I introduce a specific notion of general building blocks, which gives rise to a hierarchy of levels of building blocks that is intended to function as an organizational backbone for integrating various granular perspectives that are relevant in the life sciences. Each such granular perspective employs its own specific application of the levels metaphor, which is integrated with the other perspectives within a general domain granularity framework for the life sciences. The resulting granularity framework is meant to provide the initial basis on which a desperately required overarching and more comprehensive information framework for the life sciences can be developed.
Levels and building blocks—towards a domain granularity framework for the life sciences
Authors: Vogt Lars
Published: January 2018

The use of online data repositories and the establishment of new data standards that require data to be computer-parsable so that algorithms can reason over them have become increasingly important with the emergence of high-throughput technologies, Big Data and eScience. As a consequence, there is an increasing need for new approaches for organizing and structuring data from various sources into integrated hierarchies of levels of entities that facilitate algorithm-based approaches for data exploration, data comparison and analysis. In this paper I contrast various accounts of the level idea and resulting hierarchies published by philosophers and natural scientists with the more formal approaches of theories of granularity published by information scientists and ontology researchers. I discuss the shortcomings of the former and argue that the general theory of granularity proposed by Keet circumvents these problems and allows the integration of various different hierarchies into a domain granularity framework. I introduce the concept of general building blocks, which gives rise to a hierarchy of levels that can be formally characterized by Keet's theory. This hierarchy functions as an organizational backbone for integrating various other hierarchies that I briefly discuss, resulting in a general domain granularity framework for the life sciences. I also discuss the implicit consequences of this granularity framework for the structure of top-level categories of 'material entity' of the Basic Formal Ontology. The here suggested domain granularity framework is meant to provide the basis on which a more comprehensive information framework for the life sciences can be developed.
Hairiness: the missing link between pollinators and pollination
Authors: Stavert Jamie R , Liñán-Cembrano Gustavo , Beggs Jacqueline R , Howlett Brad G , Pattemore David E , Bartomeus Ignasi
Published: January 2018

Functional traits are the primary biotic component driving organism influence on ecosystem functions; in consequence, traits are widely used in ecological research. However, most animal trait-based studies use easy-to-measure characteristics of species that are at best only weakly associated with functions. Animal-mediated pollination is a key ecosystem function and is likely to be influenced by pollinator traits, but to date no one has identified functional traits that are simple to measure and have good predictive power. Here, we show that a simple, easy to measure trait (hairiness) can predict pollinator effectiveness with high accuracy. We used a novel image analysis method to calculate entropy values for insect body surfaces as a measure of hairiness. We evaluated the power of our method for predicting pollinator effectiveness by regressing pollinator hairiness (entropy) against single visit pollen deposition (SVD) and pollen loads on insects. We used linear models and AICC model selection to determine which body regions were the best predictors of SVD and pollen load. We found that hairiness can be used as a robust proxy of SVD. The best models for predicting SVD for the flower species Brassica rapa and Actinidia deliciosa were hairiness on the face and thorax as predictors (R2 = 0.98 and 0.91 respectively). The best model for predicting pollen load for B. rapa was hairiness on the face (R2 = 0.81). Accordingly, we suggest that the match between pollinator body region hairiness and plant reproductive structure morphology is a powerful predictor of pollinator effectiveness. We show that pollinator hairiness is strongly linked to pollination – an important ecosystem function, and provide a rigorous and time-efficient method for measuring hairiness. Identifying and accurately measuring key traits that drive ecosystem processes is critical as global change increasingly alters ecological communities, and subsequently, ecosystem functions worldwide.
Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
Authors: Mishra Priyanka , Kumar Amit , Rodrigues Vereena , Shukla Ashutosh K , Sundaesan Velusamy
Published: January 2018

Premise of the Study. The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae.

Methodology. A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA.

Principal Findings. Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses.

Conclusion. The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1+2 there by concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.
Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)
Authors: Mishra Priyanka , Kumar Amit , Rodrigues Vereena , Shukla Ashutosh K , Sundaesan Velusamy
Published: January 2018

Premise of the Study. The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae.

Methodology. A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA.

Principal Findings. Based on the K2P distance, significant divergences between the inter- and intraspecific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Conclusion. The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1+2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.
An open source device for operant licking in rats
Authors: Longley Matthew , Willis Ethan L , Tay Cindy X , Chen Hao
Published: January 2018

Increasingly complex data sets are needed to fully understand the complexity in behavior. Credit card sized single-board computers with multi-core CPUs are an attractive platform for designing devices capable of collecting multi-dimensional behavioral data. To demonstrate this idea, we created an easy to-use device for operant licking experiments and another device that records environmental variables. These systems collect data obtained from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. http://github.com/chen42/openbehavior.
Physiological, ethological and ecological features of Hermetia illucen
Authors: Marzouk Sammer
Published: January 2018

The Black Soldier Fly [Hermetia illucens] is a true fly in the family Stratiomyidae and subclass Pterygota. H.illucens has been a topic of interest in the ecological research world for many years. H.illucens possesses special physiological, ethological and ecological features that may allow H.illucens to become a model organism. This literature review looks at the physiological, ethological and ecological features of H.illucens. Existing literature about H.illucens has been searched and analyzed for this paper. From the literature search it was discovered that H.illucens is not known to have valuable impacts to the world at large.The purpose of doing this review is so that all information available on H.illucens can be chronicled and so the information can be used in real world applications. It provides a use of H.illucens as a model organism and aims to demonstrate a framework for real-world applications of H.illucens, such as H.illucens becoming a model organism for mosquitoes, Tsetse flies, and houseflies.
Physical features of eight different species with shells
Authors: Marzouk Sammer
Published: January 2018

In this study, eight different shells from different species were examined by looking at the physical features of the shells. The purpose of the study was to identify evolutionary links between species with shells. From these physical features, a morphological phylogeny was compiled. And from the morphological phylogeny, it was shown that their the family of the shells was the first trait defined specific clades and that each synapomorphic trait after this was a physical feature of the shells. From the experiment, the following conclusions were discovered: 1) That Scallops and Cockles are the most morphologic clay similar. 2) For taxa A, trait III is an apomorphy because this trait is a single trait that defines this taxa separately from the other taxa. 3) For taxa A, trait I is a plesiomorphy because it is a trait that is ancestral to trait III which defines taxa A (Fig. 2). From the data, these conclusions could introduce a new topic, new ideas, and new information to existing researches.The influx of new ideas would either become helpful, or build off the research of other researchers. This would help the scientific community in increasing its knowledge of the evolutionary background of more species.
Comparative genomics of Pseudomonas syringae pathovar tomato reveals novel chemotaxis pathways associated with motility and plant pathogenicity
Authors: Clarke Christopher , Hayes Byron W , Runde Brendan J , Markel Eric , Swingle Bryan M , Vinatzer Boris A
Published: January 2018

The majority of bacterial foliar plant pathogens must invade the apoplast of host plants through points of ingress, such as stomata or wounds, to replicate to high population density and cause disease. How pathogens navigate plant surfaces to locate invasion sites remains poorly understood. Many bacteria use chemical-directed regulation of flagellar rotation, a process known as chemotaxis, to move towards favorable environmental conditions. Chemotactic sensing of the plant surface is a potential mechanism through which foliar plant pathogens home in on wounds or stomata, but chemotactic systems in foliar plant pathogens are not well characterized. Comparative genomics of the plant pathogen Pseudomonas syringae pathovar tomato (Pto) implicated annotated chemotaxis genes in the recent adaptations of one Pto lineage. We therefore characterized the chemosensory system of Pto. The Pto genome contains two primary chemotaxis gene clusters, che1 and che2. The che2 cluster is flanked by flagellar biosynthesis genes and similar to the canonical chemotaxis gene clusters of other bacteria based on sequence and synteny. Disruption of the primary phosphorelay kinase gene of the che2 cluster, cheA2, eliminated all swimming and surface motility at 21oC but not 28oC for Pto. The che1 cluster is located next to Type IV pili biosynthesis genes but disruption of cheA1 has no observable effect on twitching motility for Pto. Disruption of cheA2 also alters in planta fitness of the pathogen with strains lacking functional cheA2 being less fit in host plants but more fit in a non-host interaction.
Sensitivity of biogeographic reconstructions to the use of differential extinction rates
Authors: Pinzón Jose Luis
Published: January 2018

Effects of differential extinction rates remain being an issue in biogeographic and evolutionary studies. Here, I use empirical examples and simulated datasets to asses how the specification of different extinction rates influences ancestral range estimation in historical biogeography. The results showed that variations in scale and asymmetry of extinction rates may have notorious effects in the accuracy of biogeographic inferences, specially when the rates of extinction are high. Further work may explore the behavior of current statistical methods of biogeographic inference with different estimates of extinction based on novel developments in this field.
RelocaTE2: a high resolution transposable element polymorphism mapping tool for population resequencing
Authors: Chen Jinfeng , Wrightsman Travis , Wessler Susan R , Stajich Jason E.
Published: January 2018

Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE transposition events or polymorphisms can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools.

Methods We have developed the tool RelocaTE2 ( http://github.com/stajichlab/RelocaTE2 ) for identification of TE polymorphisms at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD) of TE insertions allowing it to report TE polymorphism loci with single base pair precision.

Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrates a higher level of sensitivity and specificity when compared to other tools. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE polymorphisms and can be incorporated into analysis workflows in support of describing the complete genotype from light coverage genome sequencing.
RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing
Authors: Chen Jinfeng , Wrightsman Travis , Wessler Susan R , Stajich Jason E.
Published: January 2018

Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools.

Methods We have developed the tool RelocaTE2 ( http://github.com/stajichlab/RelocaTE2 ) for identification of TE insertion sites at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD) of TE insertions allowing it to report TE polymorphism loci with single base pair precision.

Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrate high level of sensitivity and specificity, particularly when the sequence coverage is not shallow. In comparison to other tools tested, RelocaTE2 achieves the best balance between sensitivity and specificity. In particular, RelocaTE2 performs best in prediction of TSDs for TE insertions. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE insertion sites and can be incorporated into analysis workflows in support of describing the complete genotype from light coverage genome sequencing.
Diversity and mechanisms of arsenic resistance among soil bacteria impacted by the ongoing Centralia coal mine fire
Authors: Dunivin Taylor K , Miller Justine , Shade Ashley
Published: January 2018

We examined diversity and mechanisms of microbial arsenic resistance in Centralia, PA, the site of an underground coal seam fire burning since 1962. From hot soil collected from an active vent, we isolated 25 unique arsenic resistant bacteria spanning six genera. Although arsenic concentrations were measured to be relatively low at the time of soil collection, isolates grew with high concentrations of arsenate and arsenite (>300mM and 20mM respectively). Among these isolates, we found genes for arsenate reduction and arsenite efflux but not methylation or oxidation. Additionally, we observed evidence for horizontal gene transfer of the arsenate reductase gene arsC. Several isolates did not test positive for any of the resistance mechanisms tested, suggesting novelty, untargeted diversity, or nonspecific mechanisms of resistance. Finally, we found that comparisons of isolate growth phenotypes across arsenic concentrations provided insights into cellular responses to arsenic. We suggest that chronic exposures to low arsenic may promote mechanisms that increase environmental solubility and enhance local toxicity (e.g., reduction, arsenite efflux), while intense exposure to arsenic may promote mechanisms that reduce environmental solubility (e.g., oxidation). Thus, disturbance intensity and duration, as well as transferability of the stress response gene(s), together inform microbial community robustness to arsenic and the fate of arsenic in the environment.
Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire
Authors: Dunivin Taylor K , Miller Justine , Shade Ashley
Published: January 2018

Arsenic (As), a toxic element, has impacted life since early Earth. Thus, microorganisms have evolved many As resistance and tolerance mechanisms to improve their survival outcomes given As exposure. We isolated As resistant bacteria from Centralia, PA, the site of an underground coal seam fire that has been burning since 1962. From a 57.4°C soil collected from a vent above the fire, we isolated 25 unique aerobic arsenic resistant bacteria spanning six genera. We examined their diversity, resistance gene content, transformation abilities, inhibitory concentrations, and growth phenotypes. Although As concentrations were low at the time of soil collection (2.58 ppm), isolates had high minimum inhibitory concentrations (MICs) of arsenate and arsenite (>300 mM and 20 mM respectively), and most isolates were capable of arsenate reduction. We screened isolates (PCR and sequencing) using 12 published primer sets for six As resistance genes (AsRG). Genes encoding arsenate reductase (arsC) and arsenite efflux pumps (arsB, ACR3(2)) were present, and phylogenetic incongruence between 16S rRNA genes and AsRG provided evidence for horizontal gene transfer. A detailed investigation of differences in isolate growth phenotypes across As concentrations (lag time to exponential growth, maximum growth rate, and maximum OD590) showed a relationship with taxonomy, providing information that could help to predict an isolate’s performance given arsenic exposure in situ. Our results suggest that considering taxonomically-linked tolerance and potential for resistance transferability from the rare biosphere will inform strategies for microbiological management and remediation of environmental As and contribute to a larger consideration of As-exposed microbial ecology.
Atropos: specific, sensitive, and speedy trimming of sequencing reads
Authors: Didion John P , Collins Francis S
Published: January 2018

A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves a four-fold increase in trimming accuracy and a decrease in execution time of ~50% (using 16 parallel execution threads). Furthermore, Atropos maintains high accuracy even when trimming simulated data with a high rate of error. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of most current-generation sequencing data sets.

Atropos is open source and free software written in Python and available at https://github.com/jdidion/atropos.
Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection
Authors: Rosales Stephanie M , Vega Thurber Rebecca L
Published: January 2018

Diseases of marine mammals can be difficult to diagnose because of the life history and protected status of these animals. Stranded marine mammals have been a particularly useful resource to discover and comprehend the diseases that plague these top predators. Additionally, advancements in high-throughput sequencing (HTS) has contributed to the discovery of novel pathogens in these animals. In this study, we use a combination of HTS and stranded harbor seals (Phoca vitulina) to better understand a known and unknown brain disease. To do this, we used transcriptomics to evaluate brain tissues from seven neonatal harbor seals that expired from an unknown cause of death (UCD) and compared them to four neonatal harbor seals that had confirmed phocine herpesvirus (PhV-1) infections in the brain. Comparing these two disease states we found that UCD animals showed a significant abundance of fatty acid metabolic transcripts in their brain tissue, thus we speculate that a fatty acid metabolic dysregulation contributed to the death of these animals. Furthermore, we were able to describe the response of four young harbor seals with PhV-1 infections in the brain. PhV-1 infected animals showed a significant ability to mount an innate and adaptive immune response, especially to combat viral infections. Our data also suggests that PhV-1 can hijack host pathways for DNA packaging and exocytosis. This is the first study to use transcriptomics in marine mammals to understand host and viral interactions and assess the death of stranded marine mammals with an unknown disease. Furthermore, we show the value of applying transcriptomics on stranded marine mammals for disease characterization.
Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells
Authors: Li Tianyi , Diao Hongying , Zhao Lei , Xing Yue , Zhang Jichang , Liu Ning , Yan Youyou , Tian Xin , Sun Wei , Liu Bin
Published: January 2018

Background. Oxidative stress could induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not cause sufficient attention in related researches. The objective of this study, therefore, was to select a set of stably expressed reference genes for use in qRT-PCR normalization in oxidative stress injuries in human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (H2O2).

Methods. HUVECs were treated with different concentrations of H2O2, geNorm and NormFinder software were conducted to evaluate the expression stabilities of 15 candidate reference genes. The optimal number of reference genes needed for qRT-PCR was determined using geNorm.

Results. Using geNorm analysis, we found that five stably expressed reference genes were sufficient for normalization in qRT-PCR analysis in HUVECs treated with H2O2. Genes with the most stable expression according to geNorm were U6 and TFRC, RPLP0, GAPDH and ACTB, and were ALAS1, TFRC, U6, GAPDH, and ACTB according to NormFinder.

Discussion. Taken together, our study demonstrated that the expression stability of reference genes may differ according to the statistical program used. U6, TFRC, RPLP0, GAPDH, and ACTB was the optimal set of reference genes for studies on gene expression with qRT-PCR assays in HUVECs under oxidative stress study.
Cost hurdles to open access publishing: A citizen scientist perspective
Authors: Ng Wenfa
Published: January 2018

Besides offering fun activities for non-scientists to explore the natural world through experiments, simulations or games, the evolving concept of citizen science is increasingly allowing some serious publication quality science to be published by the practitioners (citizen scientists) themselves. The latter is in contrast to the common perception of citizen science, where most citizen science projects such as Foldit are distribution of piecemeal segments of complex projects suitable for solution by individuals, and where the results are pooled together, or used to inform the design and direction of more complex research initiatives. Usually novices in science publishing but nonetheless aware of the importance of journal articles as the primary medium for communicating new research to the wider community (scientific and general public), citizen scientists do encounter significant challenges in science publication. One challenge is in navigating the lengthy and time-consuming peer review process of most journals. But, as benefactors of open access publishing where most journal articles are within pay walls inaccessible to citizen scientists without any research funding, open access publishing is one platform sought after or exist as an option for citizen scientists. Is the option open? Yes, at the preprint level where figshare, and PeerJ Preprints help provide an avenue for citizen scientists to have a published non peer reviewed article online, but no at the higher end “journal article” level where the manuscript needs to be peer reviewed. Even the biological sciences preprint server, bioRxiv, is closed to citizen scientists as publication on the server requires an institution affiliation with either a university or research institute. Most open access publishers (except eLife) charge a publication fee (in the thousands of dollars per article) to defray the cost of maintaining an online presence for a peer reviewed manuscript as well as those for copyediting during final stages of journal publication. This is a significant barrier to cost constrained citizen scientists who want to contribute to the scientific discourse. For the scientific enterprise, this represent a loss, whose magnitude or severity cannot be quantified since ideas help seed new research or entirely new fields. Thus, can we as a community provide citizen scientists worldwide a chance to publish open access peer reviewed articles without significant cost through a competitive publication fee subsidy scheme where each application is reviewed by the national science funding agency? If the above is possible, it would open up another area where ideas from citizen scientists could percolate into the scientific mainstream, where, as always, vibrancy and diversity of ideas power science forward.
An extension to the spherical metric using polar linear interpolation
Authors: Greenhoe Daniel J
Published: January 2018

The spherical metric d_r operates on the surface of a sphere with radius r centered at the origin in a linear space R^n. Thus, for any pair of points (p,q) on the surface of this sphere, (p,q) is in the domain of d_r and d_r(p,q) is the "distance" between those points. However, if x and y are both in R^n but are not on the surface of a common sphere centered at the origin, then (p,q) is not in the domain of d_r and d_r(p,q) is simply undefined. In certain applications, however, it would be useful to have an extension d of d_r to the entire space R^n (rather than just on a surface in R^n). Real world applications for such an extended metric include calculations involving near earth objects, and for certain distance spaces useful in symbolic sequence processing. This paper introduces an extension to the spherical metric using a polar form of linear interpolation. The extension is herein called the "Lagrange arc distance". It has as its domain the entire space R^n, is homogeneous, and is continuous everywhere in R^n except at the origin. However the extension does come at a cost: The Lagrange arc distance d(p,q), as its name suggests, is a distance function rather than a metric. In particular, the triangle inequality does not in general hold. Moreover, it is not translation invariant, does not induce a norm, and balls in the distance space (R^n,d) are not convex. On the other hand, empirical evidence suggests that the Lagrange arc distance results in structure similar to that of the Euclidean metric in that balls in R^2 and R^3 generated by the two functions are in some regions of R^n very similar in form.
Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica
Authors: Vásquez-Mayorga Marcela , Fuchs Eric J , Hernández Eduardo J , Herrera Franklin , Hernández Jesús , Moreira Ileana María , Arnáez Elizabeth , Barboza Natalia M
Published: January 2018

We estimated the genetic diversity of 50 Jatropha curcas Costa Rican samples using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was also evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable when compared to worldwide values for J. curcas. The PIC (PIC = 0.276) and inbreeding coefficient (f = -0.102) were both low. Clustering was not related to the geographical origin of accessions but Costa Rican J. curcas consistently clustered as a separate group. International accessions clustered independently of collection sites suggesting a lack of genetic structure, probably due to a wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of Jatropha curcas germplasm bank in Costa Rica.