bluuebunny/crossref_metadata_2025 huggingface dataset:
Food safety in Thailand 4: Comparison of pesticide residues found in three commonly consumed vegetables purchased from local markets and supermarkets in Thailand
Authors: Wanwimolruk Sompon , Phopin Kamonrat , Boonpangrak Somchai , Prachayasittikul Virapong
Published: January 2018

Background The wide use of pesticides raises concerns on the health risks associated with pesticide exposure. For developing countries, pesticide residues in vegetables and fruits have not been totally monitored. This study aims at providing comparison data on pesticide residues found in three commonly consumed vegetables (Chinese kale, pakchoi and morning glory) purchased from some local markets and supermarkets in Thailand. Methods These vegetables were randomly bought from local markets and supermarkets. Then they were analyzed for the content of 28 pesticides by using GC-MS/MS. Results Types of pesticides detected in the samples either from local markets or supermarkets were similar. The incidence of detected pesticides was 100% (local markets) and 99% (supermarkets) for the Chinese kale; 98% (local markets) and 100% (supermarkets) for the pakchoi; and 99% (local markets) and 97% (supermarkets) for the morning glory samples. The pesticides were detected exceeding their MRL at a rate of 48% (local markets) and 35% (supermarkets) for the Chinese kale; 71% (local markets) and 55% (supermarkets) for the pakchoi, and 42% (local markets) and 49% (supermarkets) for the morning glory. Discussion These rates are much higher than those seen in developed countries. It should be noted that these findings were assessed on basis of using criteria (such as MRL) obtained from developed countries. Our findings were also confined to these vegetables sold in a few central provinces of Thailand and did not reflect for the whole country as sample sizes were small. Risk assessment due to consuming these pesticide contaminated vegetables, still remains to be evaluated. It is unlikely that this will affect the health of tourists visiting Thailand because they do not consume these vegetables daily and in large amount. However, remarkably high incidence rates of detected pesticides give warning to the Thai authorities to implement proper regulations on pesticide monitoring programme. Similar incidence of pesticide contamination found in the vegetables bought from local markets and supermarkets raises question regarding the quality of organic vegetables domestically sold in Thailand. This conclusion excludes Thai export quality vegetables and fruits routinely monitored for pesticide contamination before exporting.
Future population trends and drivers of change for Alexander Archipelago wolves on and near Prince of Wales Island, Alaska
Authors: Gilbert Sophie L , Haynes Trevor , Lindberg Mark S , Albert David , Kissling Michelle , Person David K
Published: January 2018

Background. The Alexander Archipelago wolf, inhabiting the coastal temperate rainforest of North America, was recently evaluated for protection under the U.S. Endangered Species Act, but ultimately was not listed. Stressors thought to be impacting the population include about habitat alteration from industrial timber harvest and subsequent declines in prey (deer), increased human-caused mortality, and climate change. Methods. To evaluate how these factors likely will affect future abundance of wolves and deer, we constructed a model linking wolf and deer population dynamics to environmental conditions and management regulations. We restricted our model to Prince of Wales and outlying islands, because this area is partially isolated, is the focus of timber harvest in the region, and has the most empirical data available for model parameterization. We examined 6 combinations of future timber harvest, winter severity, wolf harvest regulations, and roads on population dynamics of deer and wolves, developed by a panel of experts. Results. Outcomes across scenarios after 30 years varied, with changes in wolf abundance ranging from a 156% increase to a 41% decline, whereas deer abundance declined from 10−37% after 30 years. Mean percentage of the 31 pack areas that were vacant after 30 years ranged from 0 to 67%, indicating that environmental conditions strongly affected pack success. Variation in wolf abundance was driven primarily by changes in wolf harvest regulations, with smaller contributions from road density, forest succession, and severe-winter frequency. Given current low estimated wolf numbers and continued legal and illegal harvest, this raises conservation concerns for the future of wolves in our study area. In addition, we found that wolf declines could be greater if wolves rely more heavily on deer in the future, for instance if salmon availability declines under future climate change, but also that reduction of deer hunting could increase wolf abundance. Discussion. The potential importance of illegal harvest in wolf population dynamics needs further acknowledgement and treatment. However, changes to harvest regulations, which would not reduce unreported harvest, could still be a powerful tool for management of this small, declining, and insular population. Nevertheless, maximum abundance of wolves appears to be curtailed by the steady decline in carrying capacity forecast across all timber management plans currently under consideration. Although we evaluated factors affecting wolf abundance individually, we encourage a holistic approach to management of this predator-prey system in an altered ecosystem.
Delineating flood prone areas using a statistical approach
Authors: Marchesini Ivan , Rossi Mauro , Salvati Paola , Donnini Marco , Sterlacchini Simone , Guzzetti Fausto
Published: January 2018

Floods are frequent and widespread in Italy and pose a severe risk for the population. Local administrations commonly use flow propagation models to delineate the flood prone areas. These modeling approaches require a detail geo-environmental data knowledge, intensive calculation and long computational times. Conversely, statistical methods can be used to asses flood hazard over large areas, or to extend the flood hazard zonation to the portion of the river networks where hydraulic models have still not been applied or can be applied with difficulties. In this paper, we describe a statistical approach to prepare flood hazard maps for the whole of Italy. The proposed method is based on a multivariate machine learning algorithm calibrated using in input flood hazard maps delineated by the local authorities and terrain elevation data. The preliminary results obtained in several major Italian catchments indicate good performances of the statistical algorithm in matching the training data. Results are promising giving the possibility to obtain reliable delineations of flood prone areas obtained in the rest of the Italian territory.
Predicting trophic discrimination factor using Bayesian inference and phylogenetic, ecological and physiological data. DEsIR: Discrimination Estimation in R.
Authors: Healy Kevin , Kelly Seán B.A , Guillerme Thomas , Inger Richard , Bearhop Stuart , Jackson Andrew L
Published: January 2018

1. Stable isotope analysis is a widely used tool for the reconstruction and interpretation of animal diets and trophic relationships. Analytical tools have improved the robustness of inferring the relative contribution of different prey sources to an animal’s diet by accounting for many of the sources of variation in isotopic data. One major source of uncertainty is Trophic Discrimination Factor (TDF), the change in isotopic signatures between consumers’ tissues and their food sources. This parameter can have a profound impact on model predictions, but often, it is not feasible to estimate a species’ TDF value and so researchers often use aggregated or taxon level estimates, an assumption that in turn has major implications for the interpretation of subsequent analyses.

2. We collected extensive carbon (δ13C) and nitrogen (δ15N) TDF data on mammals and birds from published literature. We then used a Bayesian linear modelling approach to determine if, and to what extent, variation in TDF values can be attributed to a species’ ecology, physiology, phylogenetic relationships and experimental variation. Finally, we developed a Bayesian imputation approach to estimate unknown TDF values and compared the accuracy of this tool using a series of cross-validation tests.

3. Our results show that, for birds and mammals, TDF values are influenced by phylogeny, tissue type sampled, diet of consumer, isotopic signature of food source, and the error associated with the measurement of TDF within a species. Furthermore, our cross-validation tests determined that, our tool can (i) produce accurate estimates of TDF values with a mean distance of 0.2 ‰ from observed TDF values, and (ii) provide an estimate of the precision associated with these estimates, with species presence in the data allowing for a reduced level of uncertainty.

4. By incorporating various sources of variation and reflecting the levels of uncertainty associated with TDF estimates our novel tool will contribute to more accurate and honest reconstructions and interpretations of animal diets and trophic interactions. This tool can be extended readily to include other taxa and sources of variation as data becomes available. To facilitate this, we provide a step-by-step guide and code for this tool: Discrimination Estimation in R (DEsiR)
The ontogenetic transformation of the mesosaurid tarsus: a contribution to the origin of the primitive amniotic astragalus
Authors: Piñeiro Graciela , Núñez Demarco Pablo , Meneghel Melitta D
Published: January 2018

The hypotheses about the origin of the primitive amniotic tarsus are very speculative. Early studies argued that the origin of the astragalus, one of the largest proximal bones in the tarsus of basal amniotes, was produced by either the fusion of two, three, or even four of the original tarsal bones, the intermedium, the tibiale and the proximal centralia (c4 and c3), or that the intermedium alone transforms into the primitive astragalus. More recent studies have shown that the structure of the tarsus in Captorhinus supports the former hypothesis about a fusion of the intermedium, the tibiale, the proximal centrale (c4) and eventually c3, producing a purportedly multipartite structure of the amniotic astragalus, but the issue remained contentious. Very well preserved tarsi of the Early Permian aquatic amniote Mesosaurus tenuidens Gervais, 1864-1865, which represent the most complete ontogenetic succession known for a basal amniote (the other exceptional one is provided by the Late Permian diapsid Hovasaurus boulei Piveteau, 1926), suggest that there is more than one ossification center for the astragalus and that these fuse during late embryonic stages or maybe early after birth. A non-hatched Mesosaurus in an advanced stage of development shows that the tarsus is represented by a single bone, most probably the astragalus, which seems to be formed by the suturing of three bones, which we interpret as being the intermedium, the tibiale, which could have already integrated the c4 in an earlier stage of the development, and the c3. An amniote-like tarsal structure is observed in very basal Carboniferous and Permian tetrapods such as Proterogyrinus, Gephyrostegus, the diadectids Diadectes and Orobates, some microsaurs like Tuditanus and Pantylus, and possibly Westlothiana, taxa that were all considered as true amniotes in their original descriptions. Therefore, the structure of the amniotic tarsus, including the configuration of the proximal series formed by the astragalus and the calcaneum, typically a pair of enlarged bones, could have been established well before the first recognized amniote walked on Earth. Accordingly, the tarsus of these taxa does not constitute specialized convergences that appeared in unrelated groups, they might be instead, part of a transformation series that involves taxa closely related to the early amniotes as some hypotheses have suggested.
Effects of different concentration of Ca (NO 3)2 on quinoa treated with salinity
Authors: Yan Hong , Liu Fulai
Published: January 2018

Salinity has some adverse effects on the morphology and physiology in many crops. To alleviate the damages of salinity, the applications of calcium nitrate on quinoa-treated NaCl (Chenopodium quinoa Willd) were investigated under the supported-hydroponic environment. The plants were exposed to 200mM NaCl with 20mM and 150mM Ca (NO 3 ) 2 (EC 18.61~37.85 ds·m -1 and osmotic potential -0.89~-1.71MPa), and sampled for measurements of osmotic potential, stomatal characteristics, and root characteristics. The presence of 200 mM NaCl alone decreased the relative parameters in different degrees. In all treatments, the indexes on stomatal characteristic were decreased with increasing electrical conductivity (EC) levels except for stomatal density. Stomatal conductance decreased more markedly when osmotic potential reached -0.89Mpa. Increasing in stomatal density observed in higher Ca(NO 3 ) 2 level (150mM) might be caused by the inhibition of cell division in the epidermis , which was also due to reduction of osmotic potential of the solutions.A similar trend was observed for osmotic potentials in the same tissue, which were deceased with increasing EC of the solutions. Although no significant differences in the all treatments were observed for the average diameter of roots, the beneficial effect of Ca(NO 3 ) 2 application at the concentration of 20 mM was significant in projected area, surface area, and volume. The phenomenon showed that moderate reduction in osmotic potential was favorable to cell extension due to maintaining cell turgor pressure. Much lower osmotic potential possibly inhibited cell division of root apical meristem. From the above results, it might be concluded that the effects of Ca(NO 3 ) 2 applications depended on the concentration, while the significant differences between the stomata and root morphology represented the tissue-specific as well.
Temporal variation in wolf predation dynamics in the multi-prey system of northern Yellowstone National Park
Authors: Metz Matthew C , Smith Douglas W , Hebblewhite Mark , Stahler Daniel R
Published: January 2018

Predation is a fundamental ecological process that shapes ecosystem structure and biodiversity. For large carnivores preying on large ungulates, predation dynamics are influenced by many factors, including climatic conditions, prey abundance, and prey body size. Evaluating the factors that influence how large carnivore predation varies among different-sized prey, both among and within prey species, is critical for understanding how large carnivores influence prey species population dynamics. Here, in the wolf (Canis lupus)-multi-prey system of northern Yellowstone National Park, we assess how temporal variation in prey abundance and vulnerability affect seasonal wolf predation patterns. More specifically, we characterize wolf predation patterns during four seasons of the year (early winter [mid-November to mid-December], late winter [March], spring [May], summer [June, July]) and evaluate the influence of inter-annual variation in the abundance of the two, primary, year-round ungulate prey (elk [Cervus elaphus], bison [Bison bison]) from 1995-2015. Our results highlight how the wolf-prey system of northern Yellowstone National Park has shifted from a wolf-elk system to a wolf-elk-bison system. That is, although elk are still the primary prey for wolves, the proportion of wolf kills that are elk has declined over the last twenty years. Now, bison are more commonly preyed on by wolves, and possibly most importantly, are increasingly scavenged. This change has occurred due to the decline in the northern Yellowstone elk population and concurrent increase in the northern Yellowstone bison population. Although wolf predation of bison is minimal and likely has no influence on bison population abundance, increased use of bison by wolves has a potential effect on wolf population abundance, and as a result, elk population abundance. Our results highlight the importance of considering how subsidies provided through preying on and scavenging secondary prey affect predator-primary prey dynamics.
Involvement of the mirror neuron system and the mentalizing system during communicative gesture production: a meta-analysis
Authors: Yang Jie
Published: January 2018

Background. Hand gestures play an important role in face-to-face communication. Although studies have shown that the mirror neuron system and the mentalizing system are involved in gesture comprehension, evidence of how the two systems are activated during gesture production is scattered and the conclusion is unclear. Methods. To address this issue, the current meta-analysis used activation likelihood estimation (ALE) method to quantitatively summarize the results of previous functional magnetic resonance imaging (fMRI) studies on communicative gesture production. Eight studies were selected based on several criteria (e.g., using fMRI technique, involving healthy adults, using gesture production tasks, conducting whole-brain analysis, and reporting activation foci in the MNI or Talairach space). ALE was conducted to calculate the overall brain effects for gesture production, and subsequently the brain effects for gesture execution, planning, and imitation. Results. The meta-analysis results showed that overall both systems (inferior parietal lobule and medial cortical structures) were involved in gesture production. Further analyses indicated that the mirror neuron system and the primary motor cortex were selectively involved in gesture execution, whereas the menalizing system and the premotor cortex were selectively involved in gesture planning. In gesture imitation, significant effects were found in both systems. Discussion. These results suggest that the mirror neuron system and the mentalizing system play different roles during gesture production. The former may be involved in the processes that require the mapping between observed actions and motor representations or the retrieval of motor representations; whereas the later may be involved when the production tasks require understanding others’ mental states.
The health care and life sciences community profile for dataset descriptions
Authors: Dumontier Michel , Gray Alasdair J G , Marshall M. Scott , Alexiev Vladimir , Ansell Peter , Bader Gary D , Baran Joachim , Bolleman Jerven T , Callahan Alison , Cruz-Toledo José , Gaudet Pascale , Gombocz Erich A , Gonzalez Beltran Alejandra N , Groth Paul , Haendel Melissa , Ito Maori , Jupp Simon , Juty Nick , Katayama Toshiaki , Kobayashi Norio , Krishnaswami Kalpana , Laibe Camille , Le Novère Nicolas , Lin Simon , Malone James , Miller Michael , Mungall Chris , Rietveld Laurens , Wimalaratne Sarala M , Yamaguchi Atsuko
Published: January 2018

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.
BioMine: A database for metazoan biomineralization proteins
Authors: Hanna Bishoy S , Voolstra Christian R , Medina Mónica
Published: January 2018

Biomineralization is the process by which living organisms construct hard skeletons creating complex structures that range from specialized tissues such as bone or teeth to ecosystems such as coral reefs. Biominerals are composed of both inorganic minerals and proteins, which give them extra hardness and special attributes. Biomineralization proteins are also known to be associated with multiple bone disorders and are therefore of biomedical importance. Herein we describe BioMine, a biomineralization centric protein database. Availability and implementation: BioMine can be accessed at http://biomine.net, SQL dump, FASTA files and source code are available for download as well.
Mitochondrial DNA suggests recent origins in two coastal avian subspecies in northwestern North America
Authors: Cheek Rebecca , Campbell Kyle K , Dickerman Robert , Wijdeven Berry , Winker Kevin
Published: January 2018

Genetic studies of subspecies endemic to Haida Gwaii (Queen Charlotte Islands), British Columbia and the Alexander Archipelago of southeast Alaska have frequently found genetic corroboration for these phenotypically based taxa. Divergence and speciation are common among island populations of birds, and evidence suggests this region has fostered such divergence during previous glacial maxima. We examined genetic divergence in mitochondrial DNA (mtDNA) of two coastal subspecies endemic to this region: sharp-shinned hawk (Accipiter striatus perobscurus) and great blue heron (Ardea herodias fannini). Genetic diversity in both species was remarkably low, with both coastal subspecies possessing only the most common haplotype found in continental populations. We found low but significant population divergence between A. s. perobscurus and continental populations of sharp-shinned hawks and no significant population divergence in the herons. The refugial history of the region suggests that these subspecies may have arisen relatively recently compared with other regional endemics for which genetic and phenotypic data both show divergence. Alternatively, species-wide selective sweeps of mtDNA prior to divergence may have rendered this genetic marker less useful for tracking that divergence.
Determining factors affecting moose population change in British Columbia: an update
Authors: Marshall Shelley , Kuzyk Gerald , Heard Doug , Procter Chris , Gillingham Michael , Schnwantje Helen , Thiessen Conrad , Cadsand Becky , Klaczek Michael , Batho Adrian , Nelson Cait , Schindler Heidi , Hodder Dexter
Published: January 2018

In response to declining moose numbers in central British Columbia (BC), the BC Ministry of Forests, Lands and Natural Resource Operations initiated a five-year (December 2013–March 2018) provincially coordinated, moose-research project. The primary research objective is to identify the causes and rates of cow moose mortality and examine factors that contributed to their increased vulnerability, with particular reference to the landscape-change hypothesis. Cow moose were instrumented with GPS (Global Positioning System) radio collars and monitored in five study areas that were selected based on their moose population trend and landscape conditions, particularly the degree of mountain pine beetle salvage logging and associated road building. Samples were collected during capture for health testing. Rapid-response, mortality-site investigations were the key technique to determining probable cause of death of the collared cows. As of April 19, 2016, 336 cow moose had been fitted with GPS collars. The majority of cow moose were in good body condition, had pregnancy rates within the normal range, and showed no indication of immediate disease or parasite concerns at the population level. During this study period, the status of radio-collared cow moose was: 243 active, 49 failed (i.e., either stopped collecting location data or slipped from moose), and 44 mortalities. Probable cause of death for the 44 mortalities was predation (20), hunting (9; licensed 1, unlicensed 8), apparent starvation (4), vehicle collision (1), natural (1), unknown natural (1), health-related (1), unknown health-related (4), and unknown (3). The combined annual survival rate of cow moose from all study areas was 92 ± 8% in 2013/14, 92 ± 5% in 2014/15 and 88 ± 4% in 2015/16 (to April 19, 2016) — all within the normal range for stable moose populations. Preliminary results determined predation was responsible for 45% of the collared moose mortalities. Health testing is pending on samples collected from these collared moose mortalities which may provide insight on body condition or pre-existing conditions that may have increased their vulnerability to predation.
Challenges in VGI for scientific projects
Authors: Ingensand Jens , Composto Sarah , Nappez Marion , Produit Timothée , Ertz Olivier , Oberson Mathias , Rappo Daniel
Published: January 2018

Volunteered Geographic Information (VGI) is a recent trend that has been successfully used in order to collect and share geographic information. This method is of interest for scientists who are in need of data and who want to get people involved in their cause. In this paper we discuss the challenges and opportunities that scientists may face when using the concept. An initial challenge is to find users who are willing to contribute. Second, scientist must get these users to interact with the application and with each other. The final goal is to end up with high quality data that can be used for scientific research.
Potential ecosystem service delivery by endemic plants in New Zealand vineyards: successes and prospects
Authors: Shields Morgan , Tompkins Jean-Marie , Saville David J , Meurk Colin D , Wratten Stephen
Published: January 2018

Vineyards worldwide occupy over 7 million hectares and are typically virtual monocultures, with high and costly inputs of water and agro-chemicals. Understanding and enhancing ecosystem services can reduce inputs and their costs and help satisfy market demands for evidence of more sustainable practices. In this New Zealand work, low-growing, endemic plant species were evaluated for their potential benefits as Service Providing Units (SPUs) or Ecosystem Service Providers (ESPs). The services provided were weed suppression, conservation of beneficial invertebrates, soil moisture retention and microbial activity. The potential Ecosystem Dis-services (EDS) from the selected plant species by hosting the larvae of a key vine moth pest, the light-brown apple moth (Epiphyas postvittana), was also quantified. Questionnaires were used to evaluate winegrowers’ perceptions of the value of and problems associated with such endemic plant species in their vineyards. Growth and survival rates of the 14 plant species, in eight families, were evaluated, with Leptinella dioica (Asteraceae) and Acaena inermis ‘purpurea’ (Rosaceae) having the highest growth rates in terms of area covered and the highest survival rate after 12 months. All 14 plant species suppressed weeds, with Leptinella squalida, Geranium sessiliforum (Geraniaceae), Hebe chathamica (Plantaginaceae), Scleranthus uniflorus (Caryophyllaceae) and L. dioica, each reducing weed cover by > 95%. Plant species also differed in the diversity of arthropod taxa that they supported, with the Shannon Wiener diversity index (H') for these arthropods ranging from 0 to 1.3. G. sessiliforum and Muehlenbeckia axillaris (Polygonaceae) had the highest invertebrate diversity. Density of spiders was correlated with arthropod diversity and G. sessiliflorum and H. chathamica had the highest densities of these arthropods. Several plant species led to higher soil moisture content than in control plots. The best performing species in this context were A. inermis ‘purpurea’ and Lobelia angulata (Lobeliaceae). Soil beneath all plant species had a higher microbial activity than in control plots, with L. dioica being highest in this respect. Survival proportion to the adult stage of the moth pest, E. postvittana, on all plant species was poor (<0.3). When judged by a ranking combining multiple criteria, the most promising plant species were (in decreasing order) G. sessiliflorum, A. inermis ‘purpurea’, H. chathamica, M. axillaris, L. dioica, L. angulata, L. squalida and S. uniflorus. Winegrowers surveyed said that they probably would deploy endemic plants around their vines. This research demonstrates that enhancing plant diversity in vineyards can deliver SPUs, harbour ESPs and therefore deliver ES. The data also shows that growers are willing to follow these protocols, with appropriate advice founded on sound research.
Making scientific research accessible: Urban teens conducting field research in the Chicago metropolitan area
Authors: Mulligan Matthew P , Bechtol Ellen , Fidino Mason , Lehrer Elizabeth W , Heintz Matthew , Grant Christina , Magle Seth B , Herget Jamie , Melber Leah , Martell Emma
Published: January 2018

As human populations’ transition to urban and suburban environments, there can be an evident disconnect from the natural world. Interactive programs can introduce youth to scientific methods with the hope of invoking an interest in nature. A majority of these programs, however, are brief and do not revisit key concepts after the data collection process is complete. To address this, the Hurvis Center for Learning Innovation and Collaboration designed programs primarily for underserved Chicago-area high school youth to work as “student field researchers.” The Partners in Fieldwork program contains 9 schools with 577 students collecting wildlife data throughout the school year using camera traps, bird surveys, giving-up density (GUD) studies, and acoustic bat monitors for our Urban Wildlife Institute (UWI) scientists. Cognitive gains and affective impact of participating students were analyzed by administering pre- and post-knowledge questionnaires, post-program surveys (0, 6, and 12 months after the program), and focus group discussions. Another program, the Research Apprenticeship Program (RAP) allows four teen youth to shadow both the UWI and the Davee Center for Epidemiology and Endocrinology at Lincoln Park Zoo. Youth collected data over the course of eight weeks ranging from butterfly and dragonfly surveys to evaluating stress hormones in Bactrian Camels. RAP youth compiled and analyzed their data into scientific posters and a formal presentation. An extension of the RAP program allows youth to continue their experience once a month during the school year by strengthening their career building skills and designing a custom field trip for their peers. Further evaluation of both programs is currently underway.
Finding melanoma drugs through a probabilistic knowledge graph
Authors: McCusker James P , Dumontier Michel , Yan Rui , He Sylvia , Dordick Jonathan S , McGuinness Deborah L
Published: January 2018

Metastatic cutaneous melanoma is an aggressive skin cancer with some progression-slowing treatments but no known cure. The omics data explosion has created many possible drug candidates, however filtering criteria remain challenging, and systems biology approaches have become fragmented with many disconnected databases. Using drug, protein, and disease interactions, we built an evidence-weighted knowledge graph of integrated interactions. Our knowledge graph-based system, ReDrugS, can be used via an API or web interface, and has generated 25 high quality melanoma drug candidates. We show that probabilistic analysis of systems biology graphs increases drug candidate quality compared to non-probabilistic methods. Four of the 25 candidates are novel therapies, three of which have been tested with other cancers. All other candidates have current or completed clinical trials, or have been studied in in vivo or in vitro. This approach can be used to identify candidate therapies for use in research or personalized medicine.
Information theoretic alignment free variant calling
Authors: Bedo Justin , Goudey Benjamin , Wazny Jeremy , Zhou Zeyu
Published: January 2018

While traditional methods for calling variants across whole genome sequence data rely on alignment to an appropriate reference sequence, alternative techniques are needed when a suitable reference does not exist. We present a novel alignment and assembly free variant calling method based on information theoretic principles designed to detect variants have strong statistical evidence for their ability to segregate samples in a given dataset. Our method uses the context surrounding a particular nucleotide to define variants. Given a set of reads, we model the probability of observing a given nucleotide conditioned on the surrounding prefix and suffixes of length k as a multinomial distribution. We then estimate which of these contexts are stable intra-sample and varying inter-sample using a statistic based on the Kullback–Leibler divergence. The utility of the variant calling method was evaluated through analysis of a pair of bacterial datasets and a mouse dataset. We found that our variants are highly informative for supervised learning tasks with performance similar to standard reference based calls and another reference free method (DiscoSNP++). Comparisons against reference based calls showed our method was able to capture very similar population structure on the bacterial dataset. The algorithm’s focus on discriminatory variants makes it suitable for many common analysis tasks for organisms that are too diverse to be mapped back to a single reference sequence.
The Masquerade Game: marine mimicry adaptation between egg-cowries and octocorals
Authors: Sánchez Juan A , Fuentes-Pardo Angela P , Ní Almhain Íde , Ardila-Espitia Néstor E , Cantera-Kintz Jaime , Forero-Shelton Manu
Published: January 2018

Background. Background matching, as a camouflage strategy, is one of the most outstanding examples of adaptation, where little error or mismatch means high vulnerability to predation. It is assumed that the interplay of natural selection and adaptation are the main evolutionary forces shaping the great diversity of phenotypes observed in mimicry, however there may be other significant processes that intervene in the development of mimicry such as phenotypic plasticity. Based on observations of background mismatching during reproduction events of egg-cowries, sea snails of the family Ovulidae that mimic the octocoral where they inhabit, we wondered if they match the host species diversity. Using observations in the field and molecular systematics, we set out to establish whether the different egg-cowrie color/shape polymorphisms correspond to distinct lineages restricted to specific octocoral species. Methods. Collection and observations of egg-cowries and their octocoral hosts were done using SCUBA diving between 2009-2012 at two localities in the Tropical Eastern Pacific (TEP), Malpelo Island and Cabo Corrientes (Colombia). Detailed host preference observations were done bi-annually at Malpelo Island. We analyzed the DNA sequence of the mitochondrial genes COI and 16S rDNA, extensively used in phylogenetic and DNA barcoding studies, to assess the evolutionary relationship among different egg-cowrie colorations and morphologies. Results. No genetic divergence among egg-cowries associated to different species of the same octocoral genus was observed based on the two mitochondrial genes analyzed. For instance, all egg-cowrie individuals from the two sampled localities observed on 8 different Pacifigorgia-Eugorgia species showed negligible mitochondrial divergence yet large morphologic divergence, which suggests that morphologies belonging to at least two sea snail species, Simnia avena (=S. aequalis) and Simnialena rufa, can cross-fertilize. Discussion. Our study system comprised background-matching mimicry, of the masquerade type, between egg-cowries (Simnia/Simnialena) and octocorals (Pacifigorgia/Eugorgia/Leptogorgia). We observed mimicry mismatches related to fitness trade-offs, such as reproductive aggregations vs. vulnerability against predators. Despite the general assumption that coevolution of mimicry involves speciation, egg-cowries with different hosts and colorations comprise the same lineages. Consequently, we infer that there would be significant tradeoffs between mimicry and the pursuit of reproductive aggregations in egg-cowries. The findings of this study not only contribute to the understanding of the evolution of mimicry in egg-cowries, a poorly studied group of marine gastropods, but also to the development of a new biologically meaningful board game that could be implemented as a learning tool.
A novel baculovirus-derived promoter with high activity in the Baculovirus Expression System
Authors: Martínez-Solís María , Gómez-Sebastián Silvia , Escribano José M , Jakubowska Agata K , Herrero Salvador
Published: January 2018

The baculovirus expression vector system (BEVS) has been widely used to produce a large number of recombinant proteins, and is becoming one of the most powerful, robust, and cost-effective systems for the production of eukaryotic proteins. Nevertheless, as in any other protein expression system, it is important to improve the production capabilities of this vector. The orf46 viral gene was identified among the most highly abundant sequences in the transcriptome of Spodoptera exigua larvae infected with its native baculovirus, the S. exigua multiple nucleopolyhedrovirus (SeMNPV). Different sequences upstream of the orf46 gene were cloned, and their promoter activities were tested by the expression of the GFP reporter gene using the Autographa californica nucleopolyhedrovirus (AcMNPV) vector system in different insect cell lines (Sf21, Se301, and Hi5) and in larvae from S. exigua and Trichoplusia ni. The strongest promoter activity was defined by a 120 nt sequence upstream of the ATG start codon for the orf46 gene. On average, GFP expression under this new promoter was more than two fold higher than the expression obtained with the standard polyhedrin (pph) promoter. Additionally, the orf46 promoter was also tested in combination with the pph promoter, revealing an additive effect over the pph promoter activity. In conclusion, this new characterized promoter represents an excellent alternative to the most commonly used baculovirus promoters for the efficient expression of recombinant proteins using the BEVS.
Mapping the functional connectivity of predation by large carnivores in the Canadian Rocky Mountains
Authors: Ford Adam
Published: January 2018

After decades of persecution, large carnivores are returning to human-occupied landscapes in many areas of North America and Europe. To ensure the safety of both people and wildlife, we need to understand how these animals perceive and select habitat as they navigate through developed area. Here, I investigate habitat selection by wolves and cougars in a 20,000 km2 landscape characterized by a marked gradient of urban and industrial development. I used data from over 15,000 km of wolf and cougar movement pathways, and from over 750 kill sites made by these two predators. These data were collected during the past 22 winters in Banff National Park (Alberta, Canada) and environs. Using GIS software, I created habitat selection models by comparing ‘used’ resources (e.g., topography, habitat type) found along movement pathways and at kill sites, with random points located <500 m from used sites. I then incorporated the results of these habitat selection models into a connectivity analysis to quantify the predicted flow of both movement and predation across the landscape. These results illustrate the extent to which ‘connectivity’ depends on species (e.g., cougars vs. wolves), behavior (movement vs. foraging), and proximity to people. These results are being used to inform policy on land-use planning in areas where large carnivores and people co-exist.
Genome editing weds CRISPR: what is in it for phytoremediation?
Authors: Basharat Zarrin , Yasmin Azra
Published: January 2018

CRISPR has transformed the genome editing process. CRISPR could be used to modify and regulate phenomenon of our interest in organisms from all three domains of life. Applications of CRISPR mediated precision genome engineering are immense and we are optimistic that it marks the dawn of a remarkable era of genome reprogrammed achievements. In this perspective piece, we postulate how the scientific breakthrough of CRISPR-Cas9 facilitated genome engineering could help in achieving sustainable environmental cleanup via phytoremediation.
Contrasting molecular and morphological evidence for the identification of an anomalous Buteo: a cautionary tale for hybrid diagnosis
Authors: Clark William S , Galen Spencer C , Hull Joshua M , Mayo Megan A , Engilis Jr Andrew , Witt Christopher C
Published: January 2018

An adult Buteo was found dead as a road-kill south of Sacramento, California, and was thought to represent the first state record of the eastern Red-shouldered Hawk (B. lineatus lineatus; Pyle et al. 2004). It is now a specimen in the Museum of Wildlife and Fish Biology (WFB 4816) at the U. of California, Davis. We examined this specimen and found that many of its plumage characters differed from all other adult Red-shouldered Hawks examined, including nominate adults. Plumage markings and measurements were intermediate between Red-tailed Hawk (Buteo jamaicensis, ssp calurus) and Red-shouldered Hawk (ssp elegans), leading us to hypothesize that the bird was a hybrid. However, mtDNA sequences and nuDNA microsatellites proved definitively that the bird was a Red-shouldered Hawk, most likely of eastern origin. This case illustrates that apparent hybrids or apparent vagrants could be individuals with anomalous phenotypes caused by rare genetic variation or novel epigenetic effects.
Evolutionary plasticity of AmrZ regulation in Pseudomonas
Authors: Baltrus David A , Dougherty Kevin , Dias Beatriz , Murillo Rachel
Published: January 2018

amrZ, a master regulator protein conserved across Pseudomonads, can be either a positive or negative regulator of swimming motility depending on the species examined. To better understand plasticity in the regulatory function of AmrZ, we characterized the mode of regulation for this protein for two different motility related phenotypes in P. stutzeri. As in P. syringae, AmrZ functions as a positive regulator of swimming motility within P. stutzeri, which suggests that the functions of this protein with regards to swimming motility have switched at least twice across Pseudomonads. Shifts in mode of regulation cannot be explained by changes in AmrZ sequence alone. We further show that AmrZ acts as a positive regulator of colony spreading within this strain, and that this regulation is at least partially independent of swimming motility. Closer investigation of mechanistic shifts in dual function regulators like AmrZ could provide unique insights into how transcriptional pathways are rewired between closely related species.
Microsatellite loci in the tiger shark and cross-species ampliﬁcation using pyrosequencing technology
Authors: Mendes Natália J , Cruz Vanessa P , Ashikaga Fernando Y , Camargo Sâmia M , Oliveira Claudio , Piercy Andrew N , Burgess George H , Coelho Rui , Santos Miguel N , Mendonça Fernando F , Foresti Fausto
Published: January 2018

The tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study we identified 9 microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci was assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was assessed in three other species: Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide.
Evolutionary patterns of range size, abundance and species richness in Amazonian trees
Authors: Dexter Kyle , Chave Jérôme
Published: January 2018

Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to analyse evolutionary patterns of range size, abundance, and species richness. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics, i.e. closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species, while mean range size and abundance are significantly, positively correlated. These correlations are stronger in the raw data, but still significant when using phylogenetically independent contrasts. We suggest that tree stature and/or other phylogenetically related biological traits underlie these results. Lineages comprised of small-statured trees show greater species richness and smaller range sizes and abundances. Lastly, the phylogenetic signal that we evidence for range size suggests that should many small ranged species go extinct, greater phylogenetic diversity may be lost than expected if range size were distributed randomly across the phylogeny.
Development and validation of DNA metabarcoding COI primers for aquatic invertebrates using the R package "PrimerMiner"
Authors: Elbrecht Vasco , Leese Florian
Published: January 2018

1) DNA metabarcoding is a powerful tool to assess biodiversity by amplifying and sequencing a standardized gene marker region. However, typically used barcoding genes, such as the cytochrome c oxidase subunit I (COI) region for animals, are highly variable. Thus, different taxa in communities under study are often not amplified equally well and some might even remain undetected due to primer bias. To reduce these problems, optimized metabarcoding primers for the typical communities found in certain geographic regions- and/or ecosystems are necessary.

2) We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering to reduce biases introduced by the different number of available sequences per species. We downloaded COI data for the 15 most relevant freshwater invertebrate groups for stream ecosystem assessment and developed four primer sets with high base degeneracy based on that. Primer performance was tested by sequencing ten mock community samples each consisting of 52 freshwater invertebrate taxa. Additionally, we used PrimerMiner to evaluate the developed primers against other metabarcoding primers in silico.

3) The developed primers varied in amplification efficiency and the amount of detected taxa, yet all retrieved more taxa than standard Folmer barcoding primers. Additionally, the BF/BR primers amplified taxa very consistently, with the BF2+BR2 and BF2+BR1 primer combinations showing better amplification than a previously tested ribosomal marker (16S). Except for the BF1+BR1 primers all BF/BR primers combinations detected all 42 insect taxa present in the mock community samples. In silico evaluation of the developed primers demonstrates their suitability for metabarcoding of non-aquatic insect samples.

4) With PrimerMiner we provide a useful tool to obtain relevant sequence data for targeted primer development and evaluation. Our sequence datasets generated with the newly developed metabarcoding primers demonstrate that the design of optimized primers with high base degeneracy is superior to classical markers and enables us to detect almost 100% of animal taxa present in a sample using the standard COI barcoding gene. Therefore, the PrimerMiner package and the developed primers are useful beyond biodiversity assessment in aquatic ecosystems.