bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure, dynamics and predicted functional ecology of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico
Authors: Cicala Francesco , Cisterna-Céliz José Alejandro , Moore James Douglas , Rocha-Olivares Axayácatl
Published: January 2018

The gastro-intestinal (GI) microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA 454 pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intra-specific variation. This resulted from differences of the species with most reads in each GI metagenome, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found for the explored metabolic pathways between species despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a deep taxonomic and functional split between the microbiota of HF and HC abalone.
Segmented co-infection of tree bark by different fungus
Authors: Ng Wenfa
Published: January 2018

Co-existence of microbes in a community is the de facto state of microbial lifestyle in almost all niches on Earth. Thus, microbes live with other microbial species in close proximity, and evolution has selected for specific methods of communication between microbes that facilitated chemical cross-talk for understanding the identities of different microbes, and their relative antagonistic behaviour towards each other. Observation of different patches of dark and white on a tree bark highlights possible segmented co-infection of the bark with at least two different species of fungi. Although without clear boundary of separation between patches, antagonistic behaviour between the two species could not be ruled out. Other forms of interactions such as mutualism and symbiosis between the different fungal species could be elucidated with time of flight secondary ion mass spectrometry (TOF-SIMS) profiling of the biomolecules and chemicals mediating the communication highway between the microbes, whose identities could be determined by 16S rRNA sequencing.
Epistasis analysis reveals associations between gene variants and bipolar disorder
Authors: Maj Carlo , Milanesi Elena , Gennarelli Massimo , Milanesi Luciano , Merelli ivan
Published: January 2018

In complex phenotypes (e.g., psychiatric diseases) single locus tests, commonly performed with Genome-Wide Association Studies, have proven to be limited in discovering strong gene associations. A growing body of evidence suggests that epistatic non-linear effects may be responsible for complex phenotypes arising from the interaction of different biological factors. A major issue in epistasis analysis is the computational burden due to the huge number of statistical tests to be performed when considering all the potential genotype combinations. In this work, we developed a computational efficient pipeline to investigate the presence of epistasis at a genome-wide scale in bipolar disorder, which is a typical example of complex phenotype with a relevant but unexplained genetic background. By running our pipeline we were able to identify 13 epistasis interactions between variants located in genes potentially involved in biological processes associated with the analyzed phenotype.
An anterior sauropod caudal from the Peterborough Oxford Clay: Whose tail is it anyway?
Authors: Holwerda Femke M , Liston Jeff J
Published: January 2018

The Callovian Oxford Clay of England has yielded a rich and diverse marine fauna, mainly discovered and described by Alfred Leeds. However, occasionally it also brought forth terrestrial fossils, including four isolated cases of sauropod remains, one of a stegosaurid, and another of a dryosaurid. Thus far, only Cetiosaurus oxoniensis and Cetiosauriscus stewarti are confirmed sauropod taxa from these beds. Here, we describe an isolated sauropod anterior caudal vertebra from the Oxford Clay near Peterborough. Incomplete, it has been immersed in seawater post-mortem, indicated by the adhesion of molluscs, but some characters can nevertheless be used for diagnosis and comparisons. The anterior articular surface is round, whereas the posterior articular surface is heart- shaped, as in many eusauropods, including Cetiosaurus. Interestingly, the ventral surface shows a keel-like structure; a character shared with neosauropods (e.g. Barosaurus) but also with an as yet unnamed Middle Jurassic sauropod caudal from York, UK. The posterior side of the neural canal is teardrop-shaped, a character shared with most basal eusauropods. Below the posterior neural canal, a lip-like structure seems to be present; a character which is shared with Cetiosaurus. However, the anterior caudal transverse process (ACTP) complex is similar to, although more pronounced than Cetiosauriscus, being more similar to more derived sauropods (Neosauropoda). Thus, an incomplete isolated element may help elucidate sauropod species diversity and dispersal in the Middle Jurassic of England.
In-silico prediction and modeling of ApxA exotoxins of Actinobacillus pleuropneumoniae: ApxIA, -IIA, -IIIA and -IVA
Authors: Oh Myung Whan , Yoo Han Sang
Published: January 2018

Background. Actinobacillus pleuropneumonia is a gram-negative bacterium that serves as the major etiological agent for porcine pleuropneumonia, one of critical diseases causing substantial socio-economic losses in swine rearing industry world-wide. Apx exotoxins are the members of RTX-toxin family secreted by gram-negative bacteria that facilitates Type-I Secretion System (T1SS), reported as the major virulence factor in the pathogenesis. This study was conducted to demonstrate successful pre-experimental approach by predicting the tertiary structures of ApxA exotoxins and further characterizing their structural and functional annotations via application of appropriate in silico methods.

Methods. The sequences of ApxA exotoxins were retrieved from the National Centre for Biotechnology Information database (NCBI) for bioinformatics analyses in this study. ApxA exotoxins were subjected to several computational analyses to characterize in different aspects. I-TASSER and Phyre2 servers were used to predict 3-D structures of ApxA toxins which were further validated by ProSA and SAVES servers. Antigenic epitopes of each ApxA exotoxin were predicted using the BepiPred 2.0 program.

Results. Based on predictions on secondary structure compositions, hydropathicity, domain boundaries, tertiary structures and their structural analogs, ApxIA, -IIA and –IIIA shared remarkable resemblance in structural and functional aspects while ApxIVA exhibited distinct and complex characteristics.

Discussion. 3-D modeling of ApxA exotoxins were executed to best interpret the proteins in their structure and functions to gain novel insights of their pathogenesis. The domain-wise interpretation of the proteins indicates the likely roles of each toxin with conjectured antigenic epitopes. The structural and functional annotations suggested in this study via in silico predictive approach may provide insights to prevent and control A. pleuropneumoniae by development of diagnostic methods and vaccine candidates.
The anatomy and relationships of Eucamerotus foxi (Dinosauria, Sauropoda) from the Early Cretaceous of England
Authors: Campbell Amy , Upchurch Paul , Mannion Phillip D
Published: January 2018

Eucamerotus foxi is a macronarian sauropod from the Wessex Formation (Early Cretaceous, Barremian) of the Isle of Wight. It is represented by NHMUK R2522, a partial dorsal neural arch, and differs from other known sauropods by the presence of a stout robust prezygoparapophyseal lamina (PRPL) which bifurcates distally. NHMUK R90 are a pair of dorsal vertebrae also from the Wessex Formation which have been designated as paratypes of E. foxi. Both NHMUK R2522 and NHMUK R90 have traditionally been regarded as either basal titanosauriformes or of brachiosaurid affinities. Here, phylogenetic analysis using the Lusotitan Standard Discrete Matrix recovered NHMUK R90 as a non-titanosaurian somphospondylan nested in a clade made up of ((Tastavinsaurus (Chubutisaurus, Angolatitan, NHMUK R90)) though Bremer support for this group was low. Analyses recovered E. foxi as a neosauropod of uncertain affinities with little resolution throughout the tree. NHMUK R90 is recognised as being distinct from E. foxi based on the lack of a robust distally bifurcated PRPL and is likely representative of a new sauropod taxon. E. foxi is here retained as a valid species of basal macronarian.
Hortense: Horizontal gene transfer detection directly from proteomic MS/MS data
Authors: Trappe Kathrin , Wulf Ben , Doellinger Joerg , Halbedel Sven , Muth Thilo , Renard Bernhard Y
Published: January 2018

Horizontal gene transfer (HGT) is a powerful mechanism that allows bacteria to directly transfer long stretches of genomic sequence from one individual to another. The transfer of antimicrobial resistance genes is a prominent example of HGT events in the context of multi-resistant bacteria which pose a high risk to human health. While several approaches for HGT detection exist on the genomic level, to the best of our knowledge, HGT events have not been investigated in a detailed mass spectrometry (MS)-based proteomic study. However, the mere presence of a gene does not necessarily correlate with its expression at the protein level. Consequently, to draw conclusions with respect to the expression of HGT-mediated genes, MS-based proteomics can be employed. We developed a first computational approach - called Hortense - for automated HGT detection directly from shotgun proteomics experiments. We extend the standard database search by a critical cross-validation to unravel potential HGT proteins. A proteogenomic extension gives information about the genomic origin and enables an integration with existing genome-based methods. We successfully validated our approach on simulated data, and further evaluated it on real data from a transgenic organism and a negative control from an organism not harboring a transferred gene. Our results indicate that our method facilitates MS-based analysis for proteomic evidence of HGT events. Especially as an orthogonal approach to genome-based HGT detection methods, our proposed workflow is a first step toward a systematic and large scale analysis of HGT events in, e.g., antimicrobial resistance context. Hortense is publicly available at https://gitlab.com/rki_bioinformatics/.
Molecular phylogeny of genus Horaglanis (Indian blind catfishes) within Family Clariidae
Authors: Pavan-Kumar Annam
Published: January 2018

Background: India is one of the mega biodiverse countries with a large number of endemic freshwater fishes. Recently, species of genus Horaglanis (family: Clariidae) have been reported from the southern part of India. Due to their unique morphological adaptations, these enigmatic species have been subjected to phylogenetic studies to understand the evolution of adaptive traits. Further, the taxonomic status of these species has not been verified using molecular data.

Methods: In the present study, secondary data i.e. reported sequences of mitochondrial cytochrome c oxidase subunit I gene was used to estimate the genetic divergence values for 14 species of the family Clariidae. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian Inference methods.

Results: The average genetic divergence value among genera Clarias-Clariallabes-Platyallabes-Dolichallabes-Gymnallabes-Tanganikallabes-Channallabes was 0.082 ± 0.01. However, these genera showed an average divergence value of 0.296±0.02 with genus Horaglanis. In all tree topologies, species of the genus Horaglanis formed a basal group to all other clariids.

Discussion : The higher genetic divergence value between genus Horaglanis and other genera of Clariidae family suggested that genus Horaglanis may belong to a separate sub family. Based on phylogenetic trees, it is evident that species of Horaglanis might have originated early in the evolution of Clariids than other species.
Identification of mutational signatures active in individual tumors
Authors: Krüger Sandra , Piro Rosario M
Published: January 2018

The mutational processes responsible for the somatic mutations observed in tumor samples can significantly vary not only between tumor types but also among the individual cancers within a tumor class. Mutational processes can be represented by so called “mutational signatures” which reflect the occurrences of base changes within their sequence contexts (i.e., in dependence on their flanking bases).

We present a user-friendly R package, called decompTumor2Sig, that can be used to evaluate the contribution of Shiraishi signatures to the somatic mutations found in an individual tumor.
Multiplication over Extended Galois Field: A New Approach to Find Monic Irreducible Polynomials over Galois Field GF(p^q).
Authors: Dey Sankhanil , Ghosh Ranjan
Published: January 2018

Searching for Monic Irreducible Polynomials (IPs) over extended Galois Field GF(p^q) for large value of prime moduli p and extension to Galois Field q is a well needed solution in the field of Cryptography. In this paper a new algorithm to obtain Monic IPs over extended Galois Fields GF(p^q) for large value of p and q has been introduced. The algorithm has been based on Multiplication algorithm over Galois Field GF(p^q).Time complexity analysis of the said algorithm has also been executed that ensures the algorithm to be less time consuming.
Melanoma expression analysis with Big Data technologies
Authors: Fernandez-Rovira Alicia , Lavado Rocio , Berciano Guerrero Miguel Ángel , Navas-Delgado Ismael , Aldana-Montes José F
Published: January 2018

Melanoma is a highly immunogenic tumor. Therefore, in recent years physicians have incorporated drugs that alter the immune system into their therapeutic arsenal against this disease, revolutionizing in the treatment of patients in an advanced stage of the disease. This has led us to explore and deepen our knowledge of the immunology surrounding melanoma, in order to optimize its approach. At present, immunotherapy for metastatic melanoma is based on stimulating an individual’s own immune system through the use of specific monoclonal antibodies. The use of immunotherapy has meant that many of patients with melanoma have survived and therefore it constitutes a present and future treatment in this field. At the same time, drugs have been developed targeting specific mutations, specifically BRAF, resulting in large responses in tumor regression (set up in this clinical study to 18 months), as well as a higher percentage of long-term survivors. The analysis of the gene expression changes and their correlation with clinical changes can be developed using the tools provided by those companies which currently provide gene expression platforms. The gene expression platform used in this clinical study is NanoString, which provides nCounter. However, nCounter has some limitations as the type of analysis is restricted to a predefined set, and the introduction of clinical features is a complex task. This paper presents an approach to collect the clinical information using a structured database and a Web user interface to introduce this information, including the results of the gene expression measurements, to go a step further than the nCounter tool. As part of this work, we present an initial analysis of changes in the gene expression of a set of patients before and after targeted therapy. This analysis has been carried out using Big Data technologies (Apache Spark) with the final goal being to scale up to large numbers of patients, even though this initial study has a limited number of enrolled patients (12 in the first analysis). This is not a Big Data problem, but the underlaying study aims at targeting 20 patients per year just in Málaga, and this could be extended to be used to analyze the 3.600 patients diagnosed with melanoma per year.
Relevance of single cell and single molecule studies at different biological and physical length scales
Authors: Ng Wenfa
Published: January 2018

Scale transcends multiple levels of biological and physical organization, and is the critical factor that determines success of any scientific investigation. Specifically, the scale at which a question is posed plays a crucial role in influencing the type of experiments and apparatuses needed. Single cell and single molecule experiments came to the fore of experiment science due to its capability at addressing a fundamental problem in biology and physical science: does the same behavior in cells and molecules transcend different length and population scales? Thus far, single cell experiments could be achieved with trapping of single cell using optical tweezer traps and microfluidic channels. The same, however, is not true for single molecule studies, which remains in the realm of theoretical and simulation studies. Specifically, single molecule experiment remains at the hundreds to thousands of molecules level, where possible skew in the population of molecules sampled could provide a false depiction of molecular reality of a larger population. But, what do scientists learn from single cell and single molecule studies? Is it the uncovering of mysteries of the probabilistic behavior at the single entity level, guided by perhaps quantum mechanics? The answer is no for single cell studies, given that cellular decision making require the input of tens to hundreds of molecular sensors and effectors within a cell. Hence, single cell behavior is not random, but directed at a nutrient or concentration gradient or signaling source. On the other hand, enzymatic catalysis of a single molecule substrate with the active site involves a quantum mechanical crosstalk. Thus, reaction between the substrate molecule and the active site proceeds if suitable energy levels (i.e., quantum mechanical states) are found for both parties. Given that distribution of quantum mechanical states is probabilistic, stochasticity rules single molecule interaction such as a covalent bond formation reaction between reactant A and B. Thus, single cell and single molecule studies do hold relevance in biological and physical sciences research if the correct experiment tool is used for a pertinent question at an appropriate length and population scale. For example, while tremendous amount of basic understanding could be derived from single cell experiments, single cell perspective is not relevant to questions examining the interactions between two large subpopulations of cells. Single molecule experiments, on the other hand, remains in the theoretical and simulation realm for highlighting the effect of quantum mechanics in guiding the behavior of molecules at the nanoscale.
A Dynamic Bayesian Network model for simulation of disease progression in Amyotrophic Lateral Sclerosis patients
Authors: Zandonà Alessandro , Francescon Matilde , Bronfeld Maya , Calvo Andrea , Chiò Adriano , Di Camillo Barbara
Published: January 2018

Background. Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease primarily affecting upper and lower motor neurons in the brain and spinal cord. The heterogeneity in the course of ALS clinical progression and ultimately survival, coupled with the rarity of this disease, make predicting disease outcome at the level of the individual patient very challenging. Besides, stratification of ALS patients has been known for years as a question of great importance to clinical practice, research and drug development.

Methods. In this work, we present a Dynamic Bayesian Network (DBN) model of ALS progression to detect probabilistic relationships among variables included in the Pooled Resource Open-Access ALS Clinical Trials Database (PRO-ACT), which provides records of over 10,700 patients from different clinical trials, and with over 2,869,973 longitudinally collected data measurements.

Results. Our model unravels new dependencies among clinical variables in relation to ALS progression, such as the influence of basophil count and creatine kinase on patients’ clinical status and the respiratory functional state, respectively. Furthermore, it provided an indication of ALS temporal evolution, in terms of the most probable disease trajectories across time at the level of both patient population and individual patient.

Conclusions. The risk factors identified by out DBN model could allow patients' stratification based on velocity of disease progression and a sensitivity analysis on this latter in response to changes in input variables, i.e. variables measured at diagnosis.
Overexpression of VrPDF1 gene confers resistance to weevils in transgenic mung bean plants
Authors: Ngoc Lan Nguyen Thi , Thao Hoang Thi , Son Le Van , Hoang Mau Chu
Published: January 2018

Plant defensins are known for different biological functions such as insect resistance, antibacterial, antifungal and antiviral activities. The role of plant defensins against weevils is based on inhibitor of alpha-amylase activity in weevil gut, therefore, weevils can not digest starch and then die. The low content of Vigna radiata plant defensin 1 (VrPDF1) in mung bean seeds is promted researches to increase the VrPDF1content, in which leads to enhance alpha-amylase inhibition and improve bruchid resistance in mung bean. This article presents the results of overexpression of VrPDF1 gene in transgenic mung bean plants. VrPDF1 gene was successfully transferred into DX22 mung bean cultivar and expressed in T1 generation transgenic mung bean seeds. The extract containing recombinant VrPDF1 protein inhibited alpha-amylase of weevil larvae in its larval stage. The performance of alpha-amylase inhibitor of DX1-3 and DX1-7 transgenic mung bean lines increased by 166.40% and 178.19% respectively, in comparison with non-transgenic plants. The enhancement of alpha-amylase inhibitor ability of rVrPDF1 extracted from transgenic plants is scientifically fundamental to confirm the effectiveness of the application of gene technology in enhancement the ability of mung bean weevil resistance in particular and grain crops in general revenue.
Forward teaching: Recommendations for improving statistical literacy in psychological and behavioral sciences
Authors: Ruggeri Kai
Published: January 2018

To improve outcomes in statistics education - namely the acquisition of statistical literacy - we need a new approach to how the subject is delivered in psychology and behavioral sciences. To do this, key indicators and impacts of barriers to learning statistics can be utilized from existing evidence from recent findings on statistical literacy. Using these, this paper proposes nine elements seen as critical for improving the delivery and associated outcomes for statistics teaching in higher education. Each of the nine elements may be systematically assessed and translated for wider use if effective.
Personalised models for human – gut microbiota interaction
Authors: Gilbert David , Heiner Monika , Ghanbar Leila
Published: January 2018

It is now becoming feasible to determine the composition of an individual gut microbiota (gut microflora), as well as the individual genome. In addition, whole genome scale metabolic models (GEMs) exist for a range of bacteria, and also for human. In principle this enables us to build models for gut microbiota by aggregating strain-specific models and also place this within the human context, and to make predictions on a personalised basis of the influence of gut microbiota on human metabolism, and how the interactions between these microbiota and also the human may evolve. Such aggregation, however, raises several challenges, which we discuss in this paper.

Furthermore, we present techniques and supporting tools which permit the development of personlised models for human – gut microbiota interaction. The construction of such models is supported by a suite of modelling and analysis tools which permit the exploration of the dynamic behaviour of the very large metabolic models, comprising Snoopy, Charlie, Prolog, MC2, and Marcie.

Our tools could be applied to populations of models in the context of human - gut microbiota in- teractions. Our approach that we have developed permits the description of the dynamic behavioural interaction between different bacterial strains and their human host on a personalised level within one aggregated model represented as a coloured Petri net. We use simulative model checking techniques over coloured traces to analyse the huge amounts of data generated by the dynamic simulation of these very large and hierarchically structured models.
Poster abstracts of the 25th German Conference on Bioinformatics
Authors: Nieselt Kay , Pfeifer Nico , Lupas Andrei , Kohlbacher Oliver
Published: January 2018

The annual German Conference on Bioinformatics (GCB) has brought together renowned international scientists in bioinformatics, computational biology, biostatistics, biology and medicine since 1993. The 25th GCB was held in Tübingen from 18th to 21st of September 2017, making its second appearance at the vivid university city with its internationally renowned medical faculty as well as the faculty of science, and several top research institutes like the Max Planck Institute for Developmental Biology. This environment has created and attracted several internationally recognized research groups in bioinformatics, computational biology, and biomedical data science out of which many have contributed in organizing the GCB 2017.

Following are the abstracts of posters accepted for presentation at the conference, showing the wide range of different areas from bioinformatics infrastructure to theoretical approaches in single cell analyses.
Evolution of temporal interaction: A comparative approach to social timing
Authors: Ravignani Andrea , Kotz Sonja
Published: January 2018

Increasing empirical research shows a deep connection between timing processes and neural processing of social information. An integrative theoretical framework for prospective studies in humans was recently proposed, linking timing to sociality. A similar framework guiding research in non-human animals is desirable, ideally encompassing as many taxonomic groups and sensory modalities as possible in order to embrace the diversity of social and timing behaviour across species. Here we expand on a previous theoretical account, introducing this debate to animal behaviour. We suggest adopting an evolutionary perspective on social timing in animals: i.e. a comparative approach to probe the link between temporal and social behaviour across a broad range of animal species. This approach should advance our understanding of animal social timing that is, how social behaviour and timing are mutually affected, and possibly of its evolutionary history in our own lineage. We conclude by identifying outstanding questions and testable hypotheses in animal social timing.
Chronic toxicity of ZnO nanoparticles: effects on survival and reproductive traits of the marine copepod Tigriopus fulvus
Authors: Parlapiano Isabella , Biandolino Francesca , Russo Valentino , Manfra Loredana , Rotini Alice , Migliore Luciana , Prato Ermelinda
Published: January 2018

The use of biological models has been recognized as very important in nanoecotoxicology for the understanding of Nanoparticle (NP) ecotoxicological effects. This study aimed to assess, for the first time, the chronic toxicity of Zinc Oxide NPs (ZnO NPs) on survival and reproductive traits of the marine copepod Tigriopus fulvus. Moults number, sex ratio, developmental time of nauplius and copepodid, fecundity and hatching time were assessed as sublethal endpoints. The results showed significant effects of ZnO NP exposure on all reproductive traits if compared to the control (seawater without ZnO NPs). The mean number of nauplii per brood was significantly reduced already (p<0.05) at 0.10 mg/L and even fecundity (as mean total number of nauplii per female) was significantly reduced at all ZnO NPs concentrations. A reduced number of broods per female were recorded at all nZnO concentrations (0.05-0.1-0.15-0.2-0.25 mg/L), compared to control (6.7±0.2), with the lowest value (2.8±0.3) at the highest concentration (ANOVA, p<0.05). This study evidenced the toxicity of ZnO NPs and the capacity to inhibit the reproductive activity of the marine copepod T. fulvus. These results highlight the intrinsic risk in the use and disposal of manufactured nanomaterials, as well as the importance of the research on the NP toxicity to enhance risk management. Given the lack of reliable information on ecological hazards and consequences of ZnO NPs, and particularly on its chronic toxicity to marine species, a better and relevant understanding of the effects represents a priority.
The most complete ankylosaur skull ever found in the Wessex Sub-basin (Lower Cretaceous) of the Isle of Wight.
Authors: Pond Stuart
Published: January 2018

Ankylosaur remains are frequently recovered from the Lower Cretaceous Wealden deposits of the Isle of Wight, although the vast majority of these fossils represent postcranial elements and osteoderms. The rarity of ankylosaur cranial material means any new specimens are important for understanding the morphology, palaeoecology and evolution of these taxa. Here we describe a well-preserved partial ankylosaur cranium recovered with associated ankylosaur remains from the Wessex Formation at Compton Bay. This is the most complete ankylosaur skull ever recovered from the Wessex Sub-basin and is now held at Dinosaur Isle Museum (DI), Sandown, IOW. A highly water worn specimen held at the Sedgwick Museum of Earth Sciences was found at Chilton Chine in the early 1990s and assigned to cf. Polacanthus, and the two crania are compared here.

The specimen consists of the posterior part of the basicranium and skull roof including the proximal paraoccipital processes, occipital condyle and basal tuberosity. Both skulls share characters including the position of some of the foramina exiting the endocranium and lateral curvature of the skull roof. The DI skull differs from the Sedgwick specimen by the presence of a well-defined, notched border of the supraoccipital, flat rostal-caudal dorsal cranial surface, the occipital condyle being more bulbous and angled more ventrally, a well-defined nuchal shelf and being smaller and less robust. Differences between the specimens may be due to sexual dimorphism, ontogeny or they may represent different taxa.
Introgression between ecologically distinct species following increased salinity in the Colorado Delta- Worldwide implications for impacted estuary diversity
Authors: Lau Clive L.F. , Jacobs David K.
Published: January 2018

We investigate hybridization and introgression between ecologically distinct sister species of silverside fish in the Gulf of California through combined analysis of morphological, sequence, and genotypic data. Water diversions in the past century turned the Colorado River Delta from a normal estuary to a hypersaline inverse estuary, raising concerns for the local fauna, much of which is endangered. Salinity differences are known to generate ecological species pairs and we anticipated that loss of the fresher-water historic salinity regime could alter the adaptive factors maintaining distinction between the broadly distributed Gulf-endemic Colpichthys regis and the narrowly restricted Delta-endemic Colpichthis hubbsi, the species that experienced dramatic environmental change. In this altered environmental context, these long-isolated species (as revealed by Cytochrome b sequences) show genotypic (RAG1, microsatellites) evidence of active hybridization where the species ranges abut, as well as directional introgression from C. regis into the range center of C. hubbsi. Bayesian group assignment (STRUCTURE) on six microsatellite loci and multivariate analyses (DAPC) on both microsatellites and phenotypic data further support substantial recent admixture between the sister species. Although we find no evidence for recent population decline in C. hubbsi based on mitochondrial sequence, introgression may be placing an ancient ecological species at risk of extinction. Such introgressive extinction risk should also pertain to a number of other ecological species historically sustained by the now changing Delta environment. More broadly, salinity gradient associated ecological speciation is evident in silverside species pairs in many estuarine systems around the world. Ecological species pairs among other taxa in such systems are likely poorly understood or cryptic. As water extraction accelerates in river systems worldwide, salinity gradients will necessarily be altered, impacting many more estuary and delta systems. Such alteration of habitats will place biodiversity at risk not only from direct effects of habitat destruction, but also from the potential for the breakdown of ecological species. Thus, evolutionary response to the anthropogenic alteration of salinity gradients in estuaries merits investigation as the number of impacted systems increases around the globe, permitting parallel study of multiple systems, while also permitting a conservation management response to help preserve this little championed component of biodiversity.
Gene expression of settled and metamorphosed Orbicella faveolata during establishment of symbiosis
Authors: O'Rourke Aubrie , Ohdera Aki , Sunagawa Shinichi , Diaz-Almeyda Erika M , DeSalvo Michael K , Coffroth Mary Alice , Voolstra Christian R , Medina Mónica
Published: January 2018

Corals rely on a symbiosis with dinoflagellate algae (Symbiodinium spp.) to thrive in nutrient poor tropical oceans. However, the coral-algal symbiosis can break down during bleaching events, potentially leading to coral death. While genome-wide expression studies have shown the genes associated with the breakdown of this partnership, the full conglomerate of genes responsible for the establishment and maintenance of a healthy symbiosis remains unknown. Results from previous studies suggested little transcriptomic change associated with the establishment of symbiosis. We examined the transcriptomic response of the coral Orbicella faveolata in the presence (symbiotic) and absence (aposymbiotic) of Symbiodinium minutum, one of its associated symbionts. 9 days post-metamorphic aposymbiotic coral polyps of O. faveolata were compared to symbiotic coral polyps and the subsequent differential gene expression between control and treatment was quantified using cDNA microarray technology. Coral polyps exhibited differential expression of genes associated with nutrient metabolism and development, providing insight into control of pathways as a result of symbiosis driving early polyp growth. Furthermore, genes associated with lysosomal fusion were also upregulated, suggesting host regulation of symbiont densities soon after infection.
Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex
Authors: Islam Md Rakeb-Ul , Schmidt Daniel J , Crook David A , Hughes Jane M
Published: January 2018

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinninae: Retropinna semoni) is a facultatively diadromous fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations at the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to potamodromous behaviour. We investigated populations corresponding with two putative cryptic species, the South East Queensland (SEQ), and Central East Queensland (CEQ) lineages. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ FST = 0.13; CEQ FST = 0.30). The two putative cryptic species, formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within clades. Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting potamodromous behaviour does not homogenise populations at the within-river scale. Overall, northern groups in the smelt cryptic species exhibit higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units to guide future conservation management.
Ecosystem distribution profiling of bacteria from a unique hypersaline sediment (sabkha) reveals ecological specialization among communities in the environment
Authors: Wan Abdul-Matiin , Martin-Platero Antonio M. , Alsheikh-Hussain Areej , Kamarul Azman Syafiq , Yousef Lina F. , Henschel Andreas
Published: January 2018

Advances in genomic sequencing technologies resulted in massive microbial diversity data (16S ribosomal gene sequences, rDNA) being generated in every possible environment. However, the majority of microorganisms have never been cultured, and therefore, nor cataloged. This poses a problem for molecular microbial ecologists because a large portion of the marker sequences can not be taxonomically resolved past the phylum taxon level. This tells very little about who or what these microorganisms are doing in relation to their environment. Our study describes an approach to assist in drawing ecological information from a sample when the taxon resolution is poor. We generated 16S rDNA libraries from a hypersaline marine sediment (coastal Sabkha) and saline mangrove soil in Abu Dhabi and then compared the compositional features to a database of 20,470 publicly available microbial community profiles (comprising the entire Earth Microbiome Project, EMP) that were annotated with terms from the Environmental Ontology (EnvO). An accurate taxonomic classification was not possible for 80% of the Sabkha operational taxonomic units (OTUs) beyond phylum level with widely used taxonomy classification tools, but habitat profiling performed on the community revealed strong links to bacterial assemblages of soil and marine origins. To capture the notion of generalist vs. specialist formally, we developed an algorithm to derive empirical probability distributions of OTUs over ecosystems from observed occurrences in the sample database, which then give rise to OTU-specific ecosystem entropies. We observed very low average ecosystem entropy of the Sabkha in contrast to other environmental samples. Based on this concept, the Sabkha community, while of midrange alpha diversity, presented largely specialist characteristics, with most OTUs identified to be unique to the Sabkha habitat. This finding is further corroborated by the observation that the Sabkha sample is unique with respect to the EMP-derived dataset (which contains 74 hypersaline and thousands of marine samples), as a comprehensive UniFrac similarity search did not yield any significant matches. Finally, we show that the ecosystem entropy formalism, which intrinsically accounts for the ability of OTUs to cross ecosystem borders according to a context database, is a novel, informative tool to describe and identify extreme environments in addition to conventional ecological diversity measures.
In silico identification of off-target pesticidal dsRNA binding in honey bees (Apis mellifera)
Authors: Mogren Christina L , Lundgren Jonathan Gary
Published: January 2018

Background. Pesticidal RNAs silencing critical gene function have great potential in pest management, but the benefits of this technology must be weighed against non-target organism risks. Methods. Published studies that developed pesticidal dsRNAs were collated into a database. The target gene sequences for these pesticidal RNAs were determined, and the degree of sequence homology with the honey bee genome were evaluated statistically for each. Results. We identified 101 insecticidal dsRNAs sharing high sequence homology with genomic regions in honey bees. The likelihood of off-target sequence homology increased with the parent dsRNA length. Non-target gene binding was unaffected by taxonomic relatedness of the target insect to honey bees, contrary to previous assertions. Gene groups active during honey bee development had disproportionately high sequence homology with pesticidal RNAs relative to other areas of the genome. Discussion. Although sequence homology does not itself guarantee a significant phenotypic effect in honey bees, in silico screening may help to identify appropriate experimental endpoints within a risk assessment framework for pesticidal RNAi.
Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils
Authors: Anderson Craig , Beare Mike , Buckley Hannah L , Lear Gavin
Published: January 2018

In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ~20 and ~10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.
Implementing a multilayer framework for pathway data integration, analysis and visualization
Authors: Hammoud Zaynab , Kramer Frank
Published: January 2018

Personalized medicine, i.e. a medicine focused on the individual and proactive in nature, promises an improved health care by customizing the treatment according to patient needs. The methods to analyze data, model knowledge and store interpretable results vary widely. A common approach is to use networks for modelling and organizing this information.

Network theory has been used for many years in the modelling and analysis of complex systems, as epidemiology, biology and biomedicine. As the data evolves and becomes more heterogeneous and complex, monoplex networks become an oversimplification of the corresponding systems. This imposes a need to go beyond traditional networks into a richer framework capable of hosting objects and relations of different scales, called Multilayered Network.

These complex networks have contributed in many contexts and fields, and they are very applicable in the investigation of biological networks.

In order to enrich this investigation, we aim to implement a multilayer framework that can be applicable in various domains, especially in the field of pathway modelling.

Our idea is to integrate pathways and their related knowledge into a multilayer model, where each layer represents one of their elements. The model offers a feature we call “Selective Inclusion of Knowledge”, as well as a collection of related knowledge into a single graph, like diseases and drugs. The main layers are mapped to the entities of the pathways and the additional knowledge, for instance, a convenient model would have 3 layers respectively representing proteins, drugs and diseases. The model imports knowledge from multiple sources like the Reactome database, PharmGKB, DrugBank, OMIM and other public sources.

The submitted poster will give an overview of the various models of multilayered networks, then it will describe the model we are building, and the workflow of implementing it into R as well as the future plan. The workflow consists of multiple R packages, of which we present the first implemented package, mully, that provides the multilayer layout. The data import and the integration will be done by another package to be implemented, Multipath.
Reference standards to assess physical fitness of children and adolescents of Brazil: an approach to the students of the lake Itaipú region - Brazil
Authors: Hobold Edilson , Pires-Lopes Vitor , Gomez-Campos Rossana , Arruda Miguel , Andruske Cynthia Lee , Pacheco-Carrillo Jaime , Cossio-Bolaños Marco Antonio
Published: January 2018

Background.The importance of assessing body fat variables and physical fitness tests play an important role in monitoring the level of activity and physical fitness of the general population. The objective of this study was to develop reference norms to evaluate the physical fitness aptitudes of children and adolescents based on age and sex from the lake region of Itaipú, Brazil. Methods.A descriptive cross-sectional study was carried out with 5,962 students (2938 males and 3,024 females) with an age range of 6.0 and 17.9 years. Weight (kg), height (cm), and triceps (mm), and sub-scapular skinfolds (mm) were measured. Body Mass Index (BMI kg/m2) was calculated. To evaluate the 4 physical fitness aptitude dimensions (morphological, muscular strength, flexibility, and cardio-respiratory), the following physical education tests were given to the students: sit-and-reach (cm), push-ups (rep), standing long jump (cm), and 20-m shuttle run (m). Results and Discussion.Females showed greater flexibility in the sit-and-reach test and greater body fat than the males. No differences were found in BMI. Percentiles were created for the 4 components for the physical fitness aptitudes, BMI, and skinfolds by using the LMS method based on age and sex. The proposed reference values may be used for detecting talents and promoting health in children and adolescents.