bluuebunny/crossref_metadata_2025 huggingface dataset:
Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding
Authors: Elbrecht Vasco , Peinert Bianca , Leese Florian
Published: January 2018

1) Environmental bulk samples often contain many taxa with biomass differences of several orders of magnitude. This can be problematic in DNA metabarcoding and metagenomic high throughput sequencing approaches, as large specimens contribute disproportionate amounts of DNA template. Thus a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested.

2) Here we tested the effects of size sorting on taxa detection using freshwater macroinvertebrates. Kick sampling was performed at two locations of a low-mountain stream in West Germany, specimens were morphologically identified and sorted into small, medium and large size classes (< 2.5x5, 5x10 and up to 10x20 mm). Tissue from the 3 size categories was extracted individually, and pooled to simulate samples that were not sorted by biomass and samples that were sorted and then pooled so that each specimen contributed approximately equal amounts of biomass. DNA from all five extractions of samples from both sites was amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene. The library was sequenced on a HiSeq Illumina sequencer.

3) Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately five-fold when sorting the samples into three size classes.

4) Our results demonstrate that even a coarse size sorting can substantially improve detection of taxa using DNA metabarcoding. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.
Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding
Authors: Elbrecht Vasco , Peinert Bianca , Leese Florian
Published: January 2018

Environmental bulk samples often contain many taxa that vary several orders of magnitude in biomass. This can be problematic in DNA metabarcoding and metagenomic high-throughput sequencing approaches, as large specimens contribute disproportionately high amounts of DNA template. Thus, a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples by specimen size and balancing the amounts of tissue used per size fraction should improve detection rates, but this approach has not been systematically tested.

Here we explored the effects of size sorting on taxa detection using two freshwater macroinvertebrate monitoring samples, collected from a low-mountain stream in Germany. Specimens were morphologically identified and sorted into three size classes (body size < 2.5x5, 5x10 and up to 10x20 mm). Tissue from each size category was extracted individually, and pooled to simulate samples that were not sorted by biomass ("Unsorted"). Additionally, size fractions were pooled so that each specimen contributed approximately equal amounts of biomass ("Sorted"). Mock samples were amplified using four different DNA metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene.

Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification of taxa compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased approximately five-fold when sorting the samples into three size classes and pooling by specimen abundance.

Our study demonstrates that even a coarse size sorting can substantially improve taxa detection using DNA metabarcoding. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.
Evolutionary origins of the emergent ST796 clone of vancomycin resistant Enterococcus faecium
Authors: Buultjens Andrew H , Lam Margaret M C , Ballard Susan , Monk Ian R , Mahony Andrew A , Grabsch Elizabeth A , Grayson M Lindsay , Pang Stanley , Coombs Geoffrey W , Robinson J Owen , Seemann Torsten , Johnson Paul D R , Howden Benjamin P , Stinear Timothy P
Published: January 2018

From early 2012, a novel clone of vancomycin resistant Enterococcus faecium (assigned the multi locus sequence type ST796) was simultaneously isolated from geographically separate hospitals in south eastern Australia and New Zealand. Here we describe the complete genome sequence of Ef_aus0233, a representative ST796 E. faecium isolate. We used PacBio single molecule real-time sequencing to establish a high quality, fully assembled genome comprising a circular chromosome of 2,888,087 bp and five plasmids. Comparison of Ef_aus0233 to other E. faecium genomes shows Ef_aus0233 is a member of the epidemic hospital-adapted lineage and has evolved from an ST555-like ancestral progenitor by the accumulation or modification of five mosaic plasmids and five putative prophage, acquisition of two cryptic genomic islands, accrued chromosomal single nucleotide polymorphisms and a 80kb region of recombination, also gaining Tn1549 and Tn916, transposons conferring resistance to vancomycin and tetracycline respectively. The genomic dissection of this new clone presented here underscores the propensity of the hospital E. faecium lineage to change, presumably in response to the specialized conditions of hospital and healthcare environments.
Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods
Authors: Jensen Jan H.
Published: January 2018

Rapid yet accurate pKa prediction for drug-like molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48 drug-like compounds. The approach uses an isodesmic reaction where the pKa value is computed relative to a chemically related reference compound for which the pKa value has been measured experimentally or estimated using a standard empirical approach. The AM1- and PM3-based methods perform best with RMSE values of 1.4 - 1.6 pH units that have uncertainties of ±0.2-0.3 pH units, which make them statistically equivalent. However, for all but PM3/SMD and AM1/SMD the RMSEs are dominated by a single outlier, cefadoxil, caused by proton transfer in the zwitterionic protonation state. If this outlier is removed, the RMSE values for PM3/COSMO and AM1/COSMO drop to 1.0 ± 0.2 and 1.1 ± 0.3, while PM3/SMD and AM1/SMD remain at 1.5 ± 0.3 and 1.6 ± 0.3/0.4 pH units, making the COSMO-based predictions statistically better than the SMD-based predictions. So for pKa calculations where a zwitterionic state is not involved or proton transfer in a zwitterionic state is not observed then PM3/COSMO or AM1/COSMO is the best pKa prediction method, otherwise PM3/SMD or AM1/SMD should be used. Thus, fast and relatively accurate pKa prediction for 100-1000s of drug-line amines is feasible with the current setup and relatively modest computational resources.
Avian community structure and habitat use of Polylepis forests along an elevation gradient
Authors: Sevillano-Rios C Steven , Rodewald Amanda D.
Published: January 2018

Background. As one of the highest and most unique systems in the world, Polylepis forests are recognized both as center of endemism and diversity along the Andes and as a system under serious threat from human activities, fragmentation, and climate change. Effective conservation efforts are limited, in part, by our poor understanding of the habitat needs of the system’s flora and fauna.

Methods. In 2014-2015, we studied bird communities and 19 associated local and landscape attributes within five forested glacial valleys within the Cordillera Blanca and Huascaran National Park, Peru. Birds were surveyed in dry (May-August) and wet (January-April) seasons at 130 points distributed along an elevational gradient (3,300-4,700 masl) and analyzed using Canonical Correspondence Analysis (CCA).

Results. A total of 50 species of birds, including 13 species of high conservation concern, were associated with four basic habitat types: (1) Polylepis sericea forests at low elevations, (2) P. weberbaueri forests at high elevations, (3) Puna grassland and (4) shrublands. Four species of conservation priority (e.g., Poospiza alticola) were strongly associated with large forest patches (~10-ha) dominated by P. sericea at lower elevations (<3,800 masl), whereas another four (e.g., Anairetes alpinus) were associated with less disturbed forests of P. weberbaueri at upper elevations (>4,200 masl).

Discussion. Results suggest that, in addition to conserving large (>10-ha) P. sericea forests at lower elevations as the cornerstone for maintaining bird diversity, any high elevation (>4,200 masl) relicts of P. weberbaueri, irrespective of size, should be prioritized for conservation.
Rosemary: a flexible programming framework to build Science Gateways
Authors: Shahand Shayan , Olabarriaga Sílvia
Published: January 2018

The lessons learned during six years of experience in design, development, and operation of four Science Gateway (SG) generations motivated us to develop yet another generation of platforms coined “Rosemary”. At the core of Rosemary the three fundamental SG functions, namely related to data, computing, and collaboration management, are integrated together. Our earlier studies showed that complete integration between these functions is a feature that is usually overlooked in the existing SG platforms. Rosemary provides a generic data model, RESTful API, and responsive UI that can be customized through programming to build customized SGs. Moreover, Rosemary is designed and implemented to be flexible to changes in e-Infrastructures and user community requirements. The software frameworks, tools and libraries employed in the realization of Rosemary streamline the development, deployment and operation of customized SGs for the users needs. The code of Rosemary is open source, available at https://github.com/AMCeScience/Rosemary-Vanilla. So far the platform has been used to implement prototypes of three SGs for high-throughput analysis and management of neuroimaging data, sharing of data in in-vitro fertilization research, and provenance tracking of DNA sequencing data. This paper presents the design considerations, data model, and system architecture of Rosemary and highlights some of the features that are intrinsic to its design and implementation with examples from the three prototypes.
Interactive web-based visualization of phylogenetic trees using Phylogeny.IO
Authors: Jovanovic Nikola , Mikheyev Alexander S
Published: January 2018

Traditional static publication formats make visualization, exploration and sharing of massive phylogenetic trees difficult. Web-based technologies, such as the Data Driven Document (D3) JavaScript library, exist to overcome such challenges by allowing interactive display of complex data sets. We here we an open-source web-based application that applies the power of D3 to the visualization of phylogenetic trees. Phylogeny.IO (http://phyloeny.io) displays trees together with a range of static (e.g., such as shapes and colors) and dynamic (e.g., pop-up text and images) annotations. Annotated trees can be shared as IFrame HTML objects easily embeddable in any web page.
Derivation of an aquatic benchmark for invertebrates potentially exposed to imidacloprid
Authors: Moore Dwayne RJ , Greer Colleen D , Whitfield-Aslund Melissa , Bowers Lisa M , McGee Sean , Tang Jane
Published: January 2018

Water quality benchmarks are developed by many jurisdictions worldwide with the general goal of identifying concentrations that protect aquatic communities. Imidacloprid is a widely-used neonicotinoid insecticide for which benchmark values vary widely between North America and Europe. For example, the European Food Safety Authority (EFSA) and Dutch National Institute for Public Health and the Environment (RIVM) recently established chronic water quality benchmarks for imidacloprid of 0.009 and 0.0083 µg/L, respectively. In Canada and the United States (US), however, the current chronic water quality benchmarks – termed aquatic life benchmark by the United States Environmental Protection Agency (US EPA) – for freshwater biota are orders of magnitude higher, i.e., 0.23 and 1.05 µg/L, respectively. Historically, aquatic benchmarks for imidacloprid have been derived for invertebrates because they are the most sensitive aquatic receptors. To date, derivation of water quality benchmarks for imidacloprid have relied on the results of laboratory-based toxicity tests on single invertebrate species. Such tests do not account for environmental factors affecting bioavailability and toxicity or species interactions and potential for recovery. Microcosm, mesocosm and field studies are available for aquatic invertebrate communities exposed to imidacloprid. These higher tier studies are more representative of the natural environment and can be used to derive a chronic benchmark for imidacloprid. A water quality benchmark based on the results of higher tier studies is protective of freshwater invertebrate communities without the uncertainty associated with extrapolating from laboratory studies to field conditions. We used the results of higher tier studies to derive a chronic water quality benchmark for imidacloprid as follows: (1) for each taxon (family, subfamily or class depending on the study), we determined the most sensitive 21-day No Observed Effects Concentration (NOEC), (2) we fit the taxon NOECs to five distributions and determined the best-fit distribution, and (3) we determined the HC5 from the best-fit distribution. The higher tier chronic HC5 for imidacloprid is 1.01 µg/L, which is close to the current US EPA chronic aquatic life benchmark of 1.05 µg/L.
Platelets, atherothrombosis, and atherosclerosis
Authors: Egan Karl , Ni Ainle Fionnuala , Kenny Dermot
Published: January 2018

Cardiovascular disease is the leading cause of morbidity and mortality worldwide. In 2008 alone, 17.3 million deaths (representing 30% of all deaths) were attributable to the complications of cardiovascular disease. Of these deaths, 7.3 million were due to coronary artery disease while 6.2 million were attributable to stroke. Cardiovascular disease is expected to remain the leading cause of death globally, with the number of deaths expected to reach 23.6 million annually by 2030 (WHO statistics, 2012). Vascular disease arises through the complications of atherosclerosis, a complex chronic inflammatory condition affecting the arterial circulation. It leads to the development of vascular lesions or atherosclerotic plaques, which manifest as asymmetrical thickenings of the intima of medium to large sized elastic and muscular arteries. Arterial thrombosis on ruptured atherosclerotic plaques can lead to acute events, such as myocardial infarction (MI) and ischemic stroke. Platelets are the key cellular component of arterial thrombi with platelet adhesion under high shear conditions being central to atherothrombosis. In addition, platelets play a role in the progression of atherosclerosis. In this review, we will discuss the evidence for the role of platelets in atherothrombosis, notably the efficacy of antiplatelet agents in the prevention of ischemic events, and finally their role in the progression of atherosclerosis (atherogenesis).
Reconstructing historical egocentric social networks in malacology: can eponyms serve as a proxy for contacts?
Authors: Breure Abraham S
Published: January 2018

During the 19th and 20th century eponyms have been widely used in taxonomy to honour collectors of material on which new taxa have been based. Also have new taxa been dedicated to author-colleagues. Five cases are discussed to trace the extend of overlap between eponyms and known contacts of the author, using different sources of historical data (source publications of the author, provenance data in collections, correspondence archive, reprint administration). Authors have had personal preferences in the extend to which they dedicated eponyms to persons they were in contact, either indirectly (field collectors) or directly (field collectors, cabinet collectors or collegial authors). Eponyms named after a person who is known to have authored malacological papers strongly suggests that there was contact between the two authors (correspondence and/or exchange of material). If eponyms were given in reciprocation their contacts were likely to be relatively strong. Eponyms may be used as a proxy for contacts of the author if the contextual information is taken into account.
Reproducible and reusable research: Are journal data sharing policies meeting the mark?
Authors: Vasilevsky Nicole A , Minnier Jessica , Haendel Melissa A , Champieux Robin E
Published: January 2018

Background. There is wide agreement in the biomedical research community that research data sharing is a primary ingredient for ensuring that science is more transparent and reproducible. Publishers could play an important role in facilitating and enforcing data sharing; however, many journals have not yet implemented data sharing policies and the requirements vary widely across journals. This study set out to analyze the pervasiveness and quality of data sharing policies in the biomedical literature. Methods. The online author's instructions and editorial policies for 318 biomedical journals were manually reviewed to analyze the journal's data sharing requirements and characteristics. The data sharing policies were ranked using a rubric to determine if data sharing was required, recommended, required only for omics data, or not addressed at all. The data sharing method and licensing recommendations were examined, as well any mention of reproducibility or similar concepts. The data was analyzed for patterns relating to publishing volume, Journal Impact Factor, and the publishing model (open access or subscription) of each journal. Results. 11.9% of journals analyzed explicitly stated that data sharing was required as a condition of publication. 9.1% of journals required data sharing, but did not state that it would affect publication decisions. 23.3% of journals had a statement encouraging authors to share their data but did not require it. There was no mention of data sharing in 31.8% of journals. Impact factors were significantly higher for journals with the strongest data sharing policies compared to all other data sharing mark categories. Open access journals were not more likely to require data sharing than subscription journals. Discussion. Our study confirmed earlier investigations which observed that only a minority of biomedical journals require data sharing, and a significant association between higher Impact Factors and journals with a data sharing requirement. Moreover, while 65.7% of the journals in our study that required data sharing addressed the concept of reproducibility, as with earlier investigations, we found that most data sharing policies did not provide specific guidance on the practices that ensure data is maximally available and reusable.
Shallow water sea slugs (Gastropoda: Heterobranchia) from the northwestern coast of the Sea of Japan, north of Peter the Great Bay, Russia
Authors: Chichvarkhin Anton
Published: January 2018

The coast of northern Primorye region, north of Peter the Great Bay has been sparsely studied in regards to its molluscan fauna, with just a few works reviewing the distribution of local mollusks. This work presents a survey of the shallow water heterobranch sea slugs currently occurring around Kievka Bay to Oprichnik Bay, Russia. Thirty-eight species of sea slugs were found in this study and the new species Cadlina olgae sp. nov., described herein. Most (24) of the species occurring in the area have widespread ranges in the northern Pacific Ocean. Eight species are endemic for the Sea of Japan and the adjacent part of the Sea of Okhotsk. Seven others also occur in northern Atlantic and Arctic waters. Thirteen species not known from Peter the Great Bay but known from adjacent northern Pacific waters. The finding of a previously undescribed species emphasizes the need for further surveys, particularly in subtidal and deeper waters, in order to improve the knowledge on this neglected fauna.
Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
Authors: Jungbluth Sean P , Glavina del Rio Tijana , Tringe Susannah G , Stepanauskas Ramunas , Rappé Michael S
Published: January 2018

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling Bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.
SmallOrgan 1 plays an essential role in cell proliferation, cell expansion and cadmium uptake in rice
Authors: Qin Peng , Hu Jiangbo , Chen Weilan , Zhang Guohua , Li Jian , Fan Shijun , Tu Bin , Chen Xuewei , Wang Yuping W , Li Shigui , Ma Bingtian
Published: January 2018

Background: Organ size is determined by the number and size of cells, which are controlled by cell proliferation and cell expansion. Organ size in rice plays a crucial role in determination of rice yield. Cadmium (Cd), one of the major environmental pollutants, is harmful to human health. Cd-polluted rice grains have been a major source of human Cd-intake, thus reducing Cd-uptake into rice grains isimportant. Strigolactone (SL), a hormone, has been well-studied in terms of regulating plant architecture and in its signal perception, but its biological roles in cell proliferation, cell expansion and Cd-uptake have not been uncovered.Methods: We comprehensively investigated agronomic traits and cell size between WT and so1 . We treated WT and so1 with Cd, and analyzed Cd content in rice grain using inductively coupled plasma massspectrometry (ICP-MS). We used bulk segregation analysis for SO1 mapping, and analyzed sequences surrounding SO1 in rufipogo , indica, japonica and intermedia varieties of rice. Results: We identified a spontaneous rice mutant, small organs 1 ( so1) , which exhibited small organs,such as small leaves, panicles and grains. Cytological analysis indicated that the small organs of so1 were due to both impaired cell proliferation and expansion. We found that so1 grains highly accumulated Cd after Cd treatment. In the so1 mutant, an 8bp insertion resulting in a premature stop codon was identified in LOC_Os04g46470 ( High-Tillering Dwarf1 ) which is involved in Strigolactone (SL) synthesis. Because both htd1 and so1 mutants exhibited dwarf and excessive tillers, the 8bp insertion was responsible for the so1 phenotype. SO1/HTD1 was ubiquitously expressed, most highly in stem and sheath. Very few SNP polymorphisms surrounding SO1/HTD1 were identified in japonica group, whereas SNPs were abundant in the rufipogon, indica and intermedia groups.Discussion: Our work showed the novel biological roles of SO1/HTD1 in controlling rice organ size and Cd-uptake, and indicated that the SL signaling pathway is involved in cell proliferation, cell expansion, and Cd-uptake, a role completely different from the previously reported role of HTD1. Therefore, our study is helpful for understanding the molecular functions of SO1/HTD1 and SL during rice development.
Evolution of the patellar sesamoid bone in mammals
Authors: Samuels Mark E , Regnault Sophie , Hutchinson John R
Published: January 2018

The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of the patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella. We infer that patellae most likely evolved between four to six times in crown group Mammalia: in monotremes, in the extinct multituberculates, in one or more stem-mammal genera outside of therian or eutherian mammals, and up to three times in therian mammals. Furthermore, a patella was lost several times in mammals, not including those with absent hindlimbs: once or more in marsupials (with some re-acquisition), and at least once in bats. Our inferences about patellar evolution in mammals are reciprocally informed by the existence of several human genetic conditions in which the patella is either absent or severely reduced. Clearly, development of the patella is under close genomic control, although its responsiveness to its mechanical environment is also important (and perhaps variable among taxa). Where a patella is present it plays an important role in hindlimb function; especially in resisting gravity by providing an enhanced lever system for the knee joint. Yet the evolutionary origins, persistence and modifications of a patella in diverse groups with widely varying habits and habitats -- from digging to running to aquatic, small or large body sizes, bipeds or quadrupeds -- remain complex and perplexing, impeding a conclusive synthesis of form, function, development and genetics across mammalian evolution. This meta-analysis takes an initial step toward such a synthesis by collating available data and elucidating areas of promising future inquiry.
Regression assumptions in clinical psychology research practice - A systematic review of common misconceptions
Authors: Ernst Anja Franziska , Albers Casper J
Published: January 2018

Misconceptions about the assumptions behind the standard linear regression model are widespread and dangerous. These lead to using linear regression when inappropriate, and to employing alternative procedures with less statistical power when unnecessary. Our systematic literature review investigated employment and reporting of assumption checks in twelve clinical psychology journals. The selected journals were representative based on impact factor. Findings indicate that normality of the variables themselves, rather than of the residuals, was wrongfully held for a necessary assumption in 4% of papers that use regression. Furthermore, 92% of all papers using linear regression were unclear about their assumption checks, violating APA-recommendations. This paper appeals for a heightened awareness for and increased transparency in the reporting of statistical assumption checking.
Characterization of the transcriptome and EST-SSR development in Boea clarkeana, a desiccation-tolerant plant endemic to China
Authors: Wang Ying , Liu Kun , Bi De , Zhou Biao Shou , Shao Wen Jian
Published: January 2018

Background. Resurrection plants constitute a unique cadre within angiosperms. Boea clarkeana Hemsl. (Boea, Gesneriaceae) is a desiccation-tolerant dicotyledonous herb that is endemic to China. Although research on angiosperms with DT could be instructive for crops, genomic resources for B. clarkeana remain scarce. In addition, transcriptome sequencing could be an effective way to study desiccation-tolerant plants. Methods. In the present study, we used the platform Illumina HiSeqTM 2000 and de novo assembly technology to obtain leaf transcriptomes of B. clarkeana and conducted a BLASTX alignment of the sequencing data and protein databases for sequence classification and annotation. Then, based on the sequence information obtained, we developed EST-SSR markers by means of EST-SSR mining, primer design and polymorphism identification. Results. A total of 91,449 unigenes were generated from the leaf cDNA library of B. clarkeana in this study. Based on a sequence similarity search with a known protein database, 72,087 unigenes were annotated. Among the annotated unigenes, a total of 71,170 unigenes showed significant similarity to known proteins of 463 popular model species in the Nr database, and 59,962 unigenes and 32,336 unigenes were assigned to GO classifications and COG, respectively. In addition, 44,924 unigenes were mapped in 128 KEGG pathways. Furthermore, a total of 7,610 unigenes with 8,563 microsatellites were found. Seventy-four primer pairs were selected from 436 primer pairs designed for polymorphism validation. SSRs with higher polymorphism rates were concentrated on dinucleotides, pentanucleotides and hexanucleotides. Finally, 17 pairs with highly polymorphic and stable loci were selected for polymorphism screening. There were a total of 65 alleles, with 2–6 alleles at each locus. Mainly due to the unique biological characteristics of plants, the HE, HO and PIC per locus were very low, ranging from 0 to 0.196, 0.082 to 0.14 and 0 to 0.155, respectively. Discussion. A substantial fraction transcriptome sequences of B. clarkeana were generated in this study, which is the first molecular-level analysis of this plant. These sequences are valuable resources for gene annotation and discovery and molecular marker development. These sequences could also provide a valuable basis for the future molecular study of B. clarkeana.
Systmod II: Approaching a real dynamic computer model for fish stock assessment and development of fishery strategies
Authors: Hamre Kristin , Moen Steinar , Hamre Johannes
Published: January 2018

Simulating development of fish stocks may be as complex as calculation of the development of the atmosphere, which is treated in meteorology as an initial value problem in physics. This approach was first proposed by Abbe and Bjerknes in the beginning of the 20 th century and today huge systems of differential equations are used to predict the weather. A similar approach to fisheries biology and ecology requires a real dynamic population model, which calculates the development of fish stocks from an initial state with equations that are independent of time. Here we present Systmod II, which uses a length-based growth function with a parameter for environmental variation and length-based data structure. The model uses monthly time steps to integrate population growth by moving fish to higher length groups as they grow. Since fish growth and maturity correlate more with length than with age, this gives comprehensive and clear results. The model was validated for Norwegian Spring-Spawning herring, using observed data from ICES working groups, and correlations (R2) between simulated and observed stock (total stock, spawning stock and catchable stock, numbers and biomass) were above 0.93. At present, the model makes reliable predictions on the short term (3 year for herring). For long term forecasts, better predictions of recruitment are needed . Since length is the main variable of the growth function, the state of the fish stock, including variability in length per yearclass, can be measured in situ, using hydro-acoustic trawl surveys. Data for modelling of many of the relations are still lacking, but can be filled in from future field studies.
Where do we go from here: Challenges and the future of endocrine disrupting compound screening and testing
Authors: Wilson Vickie S , LeBlanc Gerald A , Kullman Seth , Crofton Kevin , Schmieder Patricia , Jacobs Miriam N
Published: January 2018

Worldwide concern about the impacts of endocrine disrupting compounds on both human and environmental health has led to implementation of multiple screening and testing programs. In most cases these programs have focused on impacts to the estrogen, androgen and thyroid hormone (EAT) signaling pathways. The goal of the presentations in session five of the Society of Environmental Toxicology and Chemistry (SETAC) North America Focused Topic Meeting: Endocrine Disruption (February 4 – 6, 2014) was to discuss moving beyond EAT pathways to address current challenges and identify future approaches for the expansion of screening and testing programs. The session was chaired by Drs. Gerald A. LeBlanc and Vickie S. Wilson and included five presentations. Dr. Gerald A. LeBlanc provided insight on non-EAT endocrine targets that are known to be susceptible to endocrine disrupting compounds. Dr. Seth Kullman gave an overview of emerging technologies that hold promise for the screening of chemicals for interaction with EAT and other endocrine pathways. These were followed by two presentations on the current status and future promise of computational (Dr. Kevin Crofton) and in silico (Dr. Patricia Schmieder) approaches for screening and ranking chemicals for endocrine activity. Dr. Miriam Jacobs culminated the session with an overview of the current understanding of the role of epigenetics in endocrine regulation and approaches for evaluating chemicals for their ability to disrupt the epigenetic regulation of endocrine processes.
Tram tracks as specific anthropogenic habitats for the growth of plants
Authors: Woźnica Paulina , Urbisz Alina , Urbisz Andrzej , Franiel Izabella
Published: January 2018

Although tramway tracks are found in most cities, their flora is not thoroughly researched. Many more studies relate to railway areas as specific anthropogenic habitats for the development of plants. Both railway and tram tracks represent specific ecological migration corridors for plants. The objective of this study was to determine the relationship between the floristic composition and selected soil parameters of tram tracks. In 2014-2015, floristic studies were carried out along tram tracks in the Upper Silesian conurbation (southern Poland). Depending on the dominant species, five groups of sites with varying floristic composition were distinguished. Five plots with an area of 1 m2 were randomly selected in each of the sites. The species composition was determined at each plot together with the cover-abundance of all species occurring at a given plot according to Westhoff’s and van Maarel’s scale. Soil samples were collected from each plot and analysed for pH, the content of biogenic elements and heavy metals. A total of 329 species of vascular plants were identified on the tram tracks of the surveyed area, and 40 species on the plots. The dominant species included: Amaranthus retroflexus, Achillea millefolium, Plantago lanceolata, Hieracium pilosella, Silene vulgaris, Taraxacum sp. and Trifolium repens. Grouping of plots in respect of soil factors largely reflects their species composition. It has been found that the content of nitrate nitrogen, lead and phosphorus has the strongest impact on the floristic diversity of the railway tracks. Based on these parameters, three groups of species were distinguished: nitrophytes, metallophytes and common, i.e. not closely associated with the studied soil properties. Three habitat types of varying plant species composition were distinguished based on the content of nitrate nitrogen and lead: 1) nitrophilous dominated by Amaranthus retroflexus, 2) with increased content of heavy metals, dominated by Silene vulgaris and 3) mesotrophic dominated by meadow species (Achillea millefolium, Plantago lanceolata, Hieracium pilosella, Taraxacum sp., Trifolium repens).
Spatial distribution of environmental DNA in a nearshore marine habitat
Authors: O'Donnell James L , Kelly Ryan P , Shelton Andrew Olaf , Samhouri Jameal F , Lowell Natalie C , Williams Gregory D
Published: January 2018

In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to 4 kilometers from shore. Using massively parallel sequencing of 16S amplicons, we identified a diverse community of metazoans and quantified their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments.
DOC concentrations across a depth gradient on a Caribbean coral reef
Authors: Mueller Benjamin , Meesters Erik H , van Duyl Fleur C
Published: January 2018

The dissolved organic carbon (DOC) pool on tropical coral reefs is mainly fueled by photosynthates released from benthic primary producers (BPP), such as reef algae and scleractinian corals. DOC concentrations near BPP have repeatedly been observed to be elevated compared to those in the surrounding water column. As the DOC release of BPP increases with increasing light availability, elevated DOC concentrations near them will, in part, also depend on light availability. Consequently, DOC concentrations are likely to be higher on the shallow, well-lit reef terrace than in deeper sections on the fore reef slope. We measured in situ DOC concentrations and light intensity in close proximity to the reef alga Dictyota sp. and the scleractinian coral Orbicella faveolata along a depth gradient from 5 to 20 m depth and compared these to background concentrations in the water column. DOC concentrations near Dictyota sp. were significantly higher at 10 m than at 5 and 20 m depth. Furthermore, at 10 m DOC concentrations near Dictyota sp. were elevated by 15 µmol C L-1 compared to background concentrations in the water column, but not at 5 and 20 m. DOC concentrations near O. faveolata and in the water column did not differ between depths and concentrations near O. faveolata were not elevated compared to background concentrations at any of the tested depths. Our results indicate that DOC concentrations near Dictyota sp. can differ along a depth gradient from 5 to 20 m. However, the occurrence of elevated DOC concentrations did not follow a natural light gradient across depth. Instead, a combination of light availability (including a restriction by photoinhibition) and water movement are proposed to interactively determine the DOC concentrations in the close vicinity of BPP across the reef slope.
Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids
Authors: Jungbluth Sean P , Amend Jan P , Rappé Michael S
Published: January 2018

The global deep subsurface biosphere is thought to be one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the subseafloor of the Juan de Fuca Ridge. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs) with completeness > 10%. Of the GFMs, 31 were estimated to be > 90% complete, while an additional 17 were > 70% complete. In most instances, estimated redundancy in the GFMs was < 10%. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs and nearly all were distantly related to known cultivates. In the GFMs, abundant bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria and abundant archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). In this study, we identified the first near-complete genomes from archaeal and bacterial lineages THSCG, MBG-E, and EM3 and, based on the warm, subsurface and hydrothermally-associated from which these groups tend to be found, propose the names, Geothermarchaeota, Hydrothermarchaeota, and Hydrothermae, respectively. The data set presented here are the first description of Juan de Fuca igneous basement microbial GFMs reported and will provide a platform by which one can perform a higher level interrogation of the many uncultivated lineages presented herein.
Tracheophyte phylogeny poster - Vascular plants: systematics and characteristics
Authors: Cole Theodor C H , Bachelier Julien B , Hilger Hartmut H
Published: January 2018

The "Tracheophyte Phylogeny Poster – Vascular Plants: Systematics and Characteristics" is an educational tool presenting an overview of the evolutionary relationships among vascular plants as of 2016. The phylogenetic tree depicts orders and families (incl. genera in gymnosperms), listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical and morphological features. The intuitive color-coding facilitates memorization and teaching. Translations of the poster into various languages are being made available. The recommendations of the Pteridophyte Phylogeny Group (PPG) are followed here. This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
European foulbrood in Czechia after 40 years: application of next-generation sequencing to analyze Melissococcus plutonius transmission and influence on the bacteriome of Apis mellifera
Authors: Erban Tomas , Ledvinka Ondrej , Kamler Martin , Hortova Bronislava , Nesvorna Marta , Tyl Jan , Titera Dalibor , Markovic Martin , Hubert Jan
Published: January 2018

Worker honeybees (Apis mellifera) transmit Melissococcus plutonius between colonies. However, the transmission of M. plutonius, which causes European foulbrood (EFB), is poorly understood. To analyze the first EFB outbreak in 40 years in Czechia, we collected 49 hive worker samples from 18 beehives in two diseased apiaries for bacteriome analysis of the V1-V3 portion of the 16S rRNA gene. When we compared control samples obtained outside of the EFB zone, bees from an EFB apiaries containing colonies without clinical symptoms and bees from colonies with EFB clinical symptoms, there was a 100-fold higher occurrence of M. plutonius in colonies with EFB symptoms. The presence of M. plutonius in controls indicated that this pathogen exists in an enzootic state. EFB influenced the core bacteria in the worker bacteriome because the number of Snodgrassella alvi, Lactobacillus mellis, Lactobacillus melliventris, and Fructobacillus fructosus sequences increased, while Bartonella apis, Frischella perrara, and Commensalibacter intestine sequences decreased. Together, the results of this study suggest worker bees from EFB-diseased apiaries serve as vectors of M. plutonius, and eliminating such colonies is an appropriate method to overcome disease outbreaks. Because M. plutonius exists in honeybee colonies in an enzootic state, there may be similar abundances in control colonies outside the EFB zone to those in asymptomatic colonies from EFB apiaries. High-throughput Illumina next-generation sequencing permitted the quantitative interpretation of M. plutonius within the honeybee worker bacteriome. Future studies focusing on honeybee diseases, colony losses, detection of bacterial pathogens and interactions of bacteriome with pathogenic bacteria will benefit of this study.
A computational technique to estimate within-host productively infected cell lifetimes in emerging viral infections
Authors: Banerjee Soumya
Published: January 2018

Emerging viruses cause a lot of fatalities as they jump to humans from other species. Here we develop a novel technique to computationally estimate an important parameter of within-host viral infection: the lifespan of infected cells. Our approach is general and can be applied to a large class of viruses and leverages experimental data from replicon studies. Current techniques have difficulties reliably estimating infected cell lifetimes due to issues of parameter identifiability and correlation of parameters. The infected cell lifetime is an important parameter that gives an estimate of the how fast virus levels will decline. Our method would also help determine if some infected cells are short-lived or have longer lifespans with the consequence that longer lived cells could be reservoirs of infection. This would give a mechanistic understanding of why particular cell types are reservoirs of infection. We apply our technique to West Nile virus (WNV), an emerging disease of public health relevance related to Zika virus. Our analysis suggests that the most abundant infectible cells are short-lived and could motivate therapy that targets these particular cells. Our approach is very general and can be combined with more traditional methods of using differential equation models to simulate viremia in hosts: the combination of these two techniques will likely yield results that may not be achievable using the models in isolation. This will be of great interest especially in modelling emerging diseases.