bluuebunny/crossref_metadata_2025 huggingface dataset:
Different regulation of chromatin modification guide cellular reprogramming into a rate-limited step after initiation phase
Authors: Hu Rong , Dai Xianhua , Dai Zhiming , Xiang Qian
Published: January 2018

Background. In the early and late stages of cell reprogramming to induced pluripotent stem cells (iPSCs) ectopic expression of Oct4, Sox2, Klf4 and Myc (OSKM) aroused two peaks of transcriptional and epigenetic change respectively. However, it was relatively quiet in the intermediate stage. In this paper our aim is to gain insight into the molecular events that occur after the initiation phase of pluripotency induction. Methods. GSE42379 containing 28 gene expression profiles and GSE42477 containing 10 genome binding/occupancy profiles of mouse embryonic fibroblasts (MEF) were downloaded from GEO. These datasets included untreated MEFs, OSKM-induced MEFs progressing and refractory to reprogram at 3, 6, 9, 12 day post-transduction, and iPS cell lines. Differentially expressed genes (DEGs) were identified between different cell lines. The Chip-seq peaks and putative target gene were obtained from GeneProf website. Gene ontology analysis was performed on the Ensemble website. Result. Compared with the progressing cells, the refractory cells obtained more than two times DEGs at 6 day post-transduction, in particular, down-regulated DEGs related to cell cycle, cell adhesion and development were over 4 times of that in progressing cells. The expression of the DEGs which could only be detected in refractory cells at 6 day were traced back to day 3, and we found the expression of the up-regulated DEGs at 3 day were higher in refractory cells, whereas the expression of the down-regulated DEGs at 3 day were lower in refractory cells. The analysis of histone modification in genome-wide and in DEGs showed that during the reprogramming process the increase of bivalent sites in genome were mainly attributed to gaining of H3K27me3 and losing of H3K4me3. Different regulation of H3K27me3 in DEGs was the key to regulate the expression differently in progressing and refractory cells. The expression of chromatin modifiers in the two cell populations were checked and found to be differential regulated at different time point during reprogramming process. Conclusion. Genes related to immune response, cell adhesion, DNA replication and cell cycle in the refractory cells responded to the induction factor earlier than in the progressing cells, which led to excessive conversion rate. We supposed that after initiation phase cellular reprogramming required to undergo a rate-limited step guided by different regulation of chromatin modification.
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 region- and/or ecosystem- specific metabarcoding primers are necessary. 2) We developed the R package PrimerMiner, which batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxa and then applies sequence clustering to reduce biases introduced by differed number of available sequences per species. To design primers targeted for freshwater invertebrates, we downloaded COI data for the 15 most important invertebrate groups relevant for stream ecosystem assessment. Four primer sets with high base degeneracy were developed and their performance tested by sequencing ten mock community samples consisting each of 52 freshwater invertebrate taxa. Additionally, we evaluated the developed primers against other metabarcoding primers in silico using PrimerMiner. 3) Amplification and sequencing was successful for all ten mock community samples with the four different primer combinations. The developed primers varied in amplification efficiency and amount of taxa detected, but all primer sets detected more taxa than standard Folmer barcoding primers. Additionally, the BF / BR primers amplified taxa very consistently, the BF2+BR2 and BF2+BR1 primer combination even better than a previously tested ribosomal marker (16S). Except for the BF1+BR1 primer combination, all BF / BR primers detected all 42 insect taxa present in the mock samples. In silico evaluation of the developed primers showed that they are also likely to work very well on other non aquatic invertebrate samples. 4) With PrimerMiner, we here 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 enable us to detect almost 100% of animal taxa present in a sample using the standard COI barcoding gene. Therefore, the PrimerMiner package and primers developed using this tool are useful beyond assessment of biodiversity in aquatic ecosystems.
Validation and development of freshwater invertebrate metabarcoding COI primers for Environmental Impact Assessment
Authors: Elbrecht Vasco , Leese Florian
Published: January 2018

To assess and manage human impacts on freshwater ecosystems is a central challenge in the present era of biodiversity loss. Macroinvertebrates are an ideal group for Environmental Impacts Assessment (EIA). However, generating accurate macroinvertebrate inventories is difficult and error-prone based on larval morphology. Here, DNA metabarcoding provides new opportunities. Its potential to accurately identify bulk invertebrates on species level has been demonstrated in several case studies. However, DNA based identification is often limited by primer bias, potentially leading to taxa in the sample remaining undetected. Thus, the success of DNA metabarcoding as an emerging technique for EIA critically relies on carefully evaluated primers. We used the R package PrimerMiner to obtain and process cytochrome c oxidase I (COI) sequence data for the 15 globally most relevant freshwater invertebrate groups in EIAs. Using these sequence alignments, we developed four primers combinations optimized for freshwater macrozoobenthos. All primers were evaluated by sequencing ten mock community samples each consisting of 52 freshwater invertebrate taxa. Additionally popular metabarcoding primers from the literature and the here developed primers were tested in silico against the 15 relevant invertebrate groups. The developed primers varied in amplification efficiency and the amount of detected taxa, yet all retrieved more taxa than standard ‘Folmer’ barcoding primers. Two new primer combinations showed more consistent amplification than a previously tested ribosomal marker (16S) and detected all 42 insect taxa present in the mock community samples. In silico evaluation revealed critical design flaws in some commonly used primers from the literature. We demonstrate a reliable strategy to develop optimized primers using the tool PrimerMiner. The developed primers detected almost all taxa present in the mock samples, and we argue that high base degeneracy is necessary to decrease primer bias as confirmed by experimental results and in silico primer evaluation. We further demonstrate that not all primers currently used in metabarcoding studies are likely not suitable for amplification of insect and freshwater taxa. Thus careful primer evaluation and more region / ecosystem specific primers might be needed, before DNA metabarcoding can be used for routine EIA of freshwater ecosystems.
Zika virus phosphoproteome through the computational looking-glass and what we found there?
Authors: Basharat Zarrin , Khan Tabeer , Yasmin Azra
Published: January 2018

Computational phospho-mining and related post translational modification analyses using in silico methods is debateable. For some wet lab scientists, it is similar to the twilight zone, where nothing might be quite what it seems. We certainly agree that the wet lab is critical for validation but computational assays rapidly generate preliminary data for assessment and aid wet lab. Zika virus is wrecking a havoc and it is the need of the hour to rapidly assess various phenomenon associated with its pathogenicity and disseminate it to the scientific community for assessment. Phosphorylation assists in viral replication and its association with host receptors. Here, we present a vignette of the phosphorylation potential of Zika virus proteins.
Proline content and varying barometric pressure: an analysis of six genes, across three marine altererythrobacter strains
Authors: Barrie Conor
Published: January 2018

Environmental stresses select for suitably adapted genes. These stresses will promote the propagation of certain mutations, and the loss of others, throughout the evolution of a species. For organisms living two thousand meters below the ocean’s surface, one of these stresses is certainly high barometric pressure. Due to the imino ring structure of proline it was hypothesized that bacteria sampled from greater depths would show a larger proportion of content in their proteins. This hypothesis was examined by analyzing the proline content of 6 proteins common to 3 species from the altereythrobacter speciesl All the selected strains are Gram negative, moderately halophilic marine bacteria with optimum temperatures around 30⁰C. A. marensis strain KCTC22370 (taxonomy ID: 543877) was sampled, and genomically annotated, by Soo and Lee from the surface of the sea near Jeju island in the Republic of North Korea (2010). A. epoxidivorans strain JCS350 (taxonomy ID: 361183) was sampled from cold-seep sediment in the Kagoshima Bay, off the coast of Japan, at an approximate depth of 120m. The strain was isolated and genomically annotated by Kwon et.al. (2007). A. atlanticus strain 26DY36 (taxonomy ID: 1267766) was sampled from a North Atlantic mid ocean range at a depth of 2577m. The strain was isolated and annotated by Wu et. al. (2015). The data showed no significant differences in the proline content of the 3 species examined, however a more expansive study would be required to fully reject the hypothesis.
Geothematic open data in Umbria region
Authors: Motti Andrea , Natali Norman
Published: January 2018

Detailed information about geology, hydrogeology and seismic hazard issues for Umbria region are contained in a spatial database available as open data format (shape file or KMZ) and distributed under the regional open data portal called Open Data Umbria ( http://dati.umbria.it ) where 297 datasets have been produced by Umbria Region until now and most of them are made by Geological Survey. Development of standardized regional geologic database (BDG from now on) took about 20 years since 2010 to manage the huge set of information contained in the 276 geologic maps. As a result of migration to BDG, 231 distinct geologic units were found for Umbria Region territory represented by about 47,000 polygon features. The total land area of Umbria 8,475 km 2 wide is divided in the BDG into 46,982 different geological areas. Analysis of the information contained in the BDG is preliminary to the creation of more geothematic layers and custom maps. The key word is the characteristic index of the single geologic unit. Characteristic index, shown in percentage, calculates the ratio between the surface of the geologic units compared to their thickness. Thickness value for each geologic unit is intended to be based on rank level and calculated as weighted average of the thickness for each geologic unit. Calculations in terms of land area percentage show many differences between portions of the territory capable of storing water and the characteristic index of the geologic units capable of storing water. The situation changes if instead we analyze aquifers within individual geological domains and their characteristic index of the single geologic unit whose charts show significant differences. Moreover, after accurate analysis by the Geological Survey, regional seismic hazard maps were derived from the BDG and available as open data format. Umbria has been divided in thirteen zones where local conditions, i.e. presence of artificial fills or particular surface topography, may affect the shaking levels and amplify the effects of the earthquake. The total land area of Umbria is 8,475 square kilometers, and it has been classified in 69,675 unique zones each one characterized by particular seismic hazard. Statistics also show (in percent) that 48 of Umbria land area is characterized by morphological and stratigraphic conditions affecting the shake while 52 is not subject to amplification. Population living in area with no amplification is 322,987 accounting for 36.5 % of the total while 561,281 accounting for 63.5 % of the total live in area where amplification of the shake is likely to happen. Currently four italian regions, Emilia-Romagna, Marche, Tuscany and Umbria, have planned to cooperate starting from their own BDG and develop, after data generalization and analysis, a shared GIS based geologic database of Northern Appennines, following the European Standard database structure and format.
Geothematic open data in Umbria region
Authors: Motti Andrea , Natali Norman
Published: January 2018

Detailed information about geology, hydrogeology and seismic hazard issues for Umbria region are contained in a spatial database available as open data format (shapefile or KMZ) and distributed under the regional open data portal called Open Data Umbria (http://dati.umbria.it) where 297 datasets have been produced by Umbria Region until now and most of them are made by Geological Survey. Geological Survey of Regione Umbria carried out a 20 years program to produce 276 geological maps at 1:10.000 reference scale with an accurate geological model of the regional surface and providing millions of geological data. The key word is the characteristic index of the single geologic unit. Characteristic index , shown in percentage, calculates the ratio between the surface of the geologic units compared to their thickness. Thickness value for each geologic unit is intended to be based on rank level and calculated as weighted average of the thickness for each geologic unit.
Coupling spatiotemporal community assembly processes to ecosystem function
Authors: Graham Emily , Crump Alex R. , Resch Charles T , Fansler Sarah , Arntzen Evan , Kennedy David , Fredrickson Jim , Stegen James C.
Published: January 2018

Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types (e.g., attached and unattached) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally-explicit multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.
Meta-Barcoding accelerates species discovery and unravel great biodiversity of benthic invertebrates in marine sediments in Campos basin, Brazil
Authors: Schettini Milena Marcela D P , Cardenas Raony G C C L , Detoni Marcella A A , Rebelo Mauro F
Published: January 2018

Biodiversity is currently assessed for environmental characterizations and monitoring through a laborious and time-consuming process of morphological taxonomy. We used rRNA 18S, rRNA 28S and COI, together with NGS and Bioinformatics to identify benthic invertebrate organisms from sediment samples collected in five stations in the Campos Basin in southeast Brazil, an important oil extraction area and one of the best-studied marine biota in Brazil. A total of 3.3 million sequences were clustered in Operational Taxonomic Units and more than 1.6 million sequences (about 50% of all reads) were assigned to 957 prokaryotes and 577 eukaryotes. BLAST identified 23 phyla, 60 classes, 62 orders, 70 families, 67 genus and 46 species of eukaryotes. By meta-barcoding we identified phyla that are traditionally found in samples of marine benthos, such as Annelida, Arthropoda, Mollusca and Chordata, as well as rare phyla like Entoprocta and Gastrotricha. Taxa identified with meta-barcoding were compared to morphology data from previous studies in the area (REVIZEE, Habitats Project) and geo-validated with the database Global Biodiversity Information Facility. For several taxa, this is the first evidence of occurrence in Campos the area and the number of OTU identified suggests an enormous unveiled benthic biodiversity in Campos Basin. Our study supports the application of Meta-Barcoding for environmental characterization and monitoring programs, reducing from years to few months the time currently required for species identification and biodiversity determination.
How barriers shape freshwater fish distributions: a species distribution model approach
Authors: Kuemmerlen Mathias , Stoll Stefan , Haase Peter
Published: January 2018

Barriers, from dams to culverts, continue to be built globally despite their well-known negative effects on freshwater ecosystems. While large barriers strongly influence distribution through habitat fragmentation, the effects of smaller barriers on the distribution patterns of many fish species remains poorly studied. Obstruction metrics were calculated including different types and magnitudes of barriers considering upstream, downstream or barriers within a 10 km stream network distance. These were then included in species distribution models (SDMs) of 20 fish species and compared to predictions without barriers to understand their effects on fish distributions. Barriers were important for the predictions of many fish species with the metric upstream barriers being the most relevant barrier predictor across the fish community. With the inclusion of barriers, most species saw a reduction in their predicted range and habitat suitability decreased, suggesting habitat fragmentation and indicating a higher extirpation risk. Predictions from this SDM application point out how and where barriers influence fish distributions in the studied catchment. This species-specific and spatially-explicit information is highly valuable for target-oriented river restoration measures, biodiversity conservation efforts and catchment management in general.
How barriers shape freshwater fish distributions: a species distribution model approach
Authors: Kuemmerlen Mathias , Stoll Stefan , Haase Peter
Published: January 2018

Aim: Barriers continue to be built globally despite their well-known negative effects on freshwater ecosystems. Fish habitats are disturbed by barriers and the connectivity in the stream network reduced. We implemented and assessed the use of barrier data, including their size and magnitude, in distribution predictions for 20 species of freshwater fish to understand the impacts on freshwater fish distributions. Location: Central Germany. Methods: Obstruction metrics were calculated from barrier data in three different spatial contexts relevant to fish migration and dispersal: upstream, downstream and along 10km of stream network. The metrics were included in a species distribution model and compared to a model without them, to reveal how barriers influence the distribution patterns of fish species. We assess impacts of barriers by estimating species’ specific range gains and losses due to barrier inclusion in the model. Results: Barriers were important for the predictions of many fish species with the metric upstream barriers being the most relevant barrier predictor across the fish community. With the inclusion of barriers, most species saw a reduction in their predicted range and habitat suitability decreased, particularly species with small ranges or considered as threatened. Main conclusions: Predictions from this SDM application point out how and where barriers influence fish distributions in the studied catchment. Our results indicate a reduction in suitable habitat due to barriers and suggest a higher extirpation risk. This species-specific and spatially-explicit information is highly valuable for target-oriented river restoration measures, biodiversity conservation efforts and catchment management in general.
A geoprocessing modelling interoperable framework for AgriGIS using open data and open standards
Authors: Santos Roberto , Huynh Dai , Anand Suchith , Ray Rumiana V , Mayes Sean , Leibovici Didier
Published: January 2018

We retrace the construction of AgriGIS framework between multiple disciplines around a common objective of facilitating research on model simulations for sustainable food security. The geospatial media enabling multidisciplinary research in crop modelling but also supporting new types of hypothesis and analysis, is described with interoperability principles and seamless access and sharing for data, metadata and processing models. Designing the platform achieving this main objective generated a transdisciplinary vision of modelling and forecasting for sustainable agriculture.
Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases
Authors: Silva Pedro J
Published: January 2018

Cofactor-less oxygenases perform challenging catalytic reactions between singlet substrates and triplet oxygen, in spite of apparently violating the spin-conservation rule. In bacterial ring-cleaving 2,4-dioxygenase, the active site has been suggested by quantum chemical computations to fine tune triplet oxygen reactivity, allowing it to interact rapidly with its singlet substrate without the need for spin inversion, and in urate oxidase the reaction is thought to proceed through electron transfer from the deprotonated substrate to an aminoacid sidechain, which then feeds the electron to the oxygen molecule. In this work, we perform additional quantum chemical computations on these two systems to elucidate several intriguing features unaddressed by previous workers. These computations establish that in both enzymes the reaction proceeds through direct electron transfer from substrate to O2 followed by radical recombination, instead of minimum-energy crossing points between singlet and triplet potential energy surfaces without formal electron transfer. The active site does not affect the reactivity of oxygen directly but is crucial for the generation of the deprotonated form of the substrates, which have redox potentials far below those of their protonated forms and therefore may transfer electrons to oxygen without sizeable thermodynamic barriers. This mechanism seems to be shared by most cofactor-less oxidases studied so far.
Mapping irrigated areas using multi-sensor remote sensing data in a Mediterranean environment
Authors: Nino Pasquale , Vanino Silvia , Lupia Flavio , D'Urso Guido , De Michele Carlo , Pulighe Giuseppe , Bonati Guido
Published: January 2018

Water managers need map of irrigated areas (defined as the identification of their location and their areal extent) to plan a rational use of water under limited availability and to prevent the unauthorized withdrawals. Many authors have shown that the Earth Observation techniques are an effective tool for mapping irrigated areas worldwide at different spatial scales (global/regional/and local). This study presents a methodology for mapping irrigated areas in semi-arid environment based on Earth Observation techniques and by fully exploiting datasets freely available processed by open source software and tools. Data acquired with the Landsat 8 Operational Land Imager (OLI) and the new Sentinel 2A MultiSpectral Instrument (MSI) sensors were integrated to obtain cloud free dense time series allowing to monitor the vegetation development throughout the growing seasons. Irrigated areas were identified by analysing the growing patterns under water deficit conditions from NDVI values under the assumption that, in arid and semi-arid environment (like the Mediterranean Region), high trend of vegetation growth are compatible only with irrigation. The method was applied in the Cixerri Consortium Irrigation District located in South of Sardinia (Italy).
The Glass Frogs (Centrolenidae) from the "Río Palenque" Science Center, western Ecuador, with the description of a new species
Authors: Cisneros-Heredia Diego F , McDiarmid Roy W.
Published: January 2018

Ecuador has the biggest number of amphibian species per unit of area in the world (425 species in 276,840 km2). In the last decade, conservative estimates indicate that at least 26 species of Ecuadorian amphibians have declined or gone extinct. The reasons for this crisis are not clear but have been related to habitat destruction, climate change, and/or fungal disease such as the chytridiomycosis. The Río Palenque Science Center (RPSC) was among the last remnants of tropical rainforest in the western lowlands of Ecuador. Twenty years ago, investigations done by R. McDiarmid and others lead to the discovery of an amazing herpetofauna, including several undescribed species. However, the expansion of the agricultural frontier and transformation of the forest remnants into oil palm and banana plantations destroyed this site. Among the species identified from RPSC were five species of glass frogs (Family Centrolenidae): Centrolene prosoblepon, Cochranella spinosai, Hyalinobatrachium fleischmanni, Hyalinobatrachium valerioi, and an undescribed species of the genus Centrolene restricted to the RPSC. This research analyzed the morphological characters and natural history of the five glass frogs of RPSC in order to describe the new species of Centrolene from RPSC, which is critically endangered, if not extinct. The new species is characterized by combination of the following characters: 1) a distinctive coloration with yellow dorsolateral stripes; 2) the presence of an exposed prepollical spine; 3) a humeral spine in the males; and, 4) a unique nuptial pad between the fingers II and I.
A template-based approach to the modification of binding properties of globular proteins I: Background and motivations.
Authors: Jeff-Eke Imadol V
Published: January 2018

Design and production of polypeptide/proteins with desired bind site properties involves utilization of the ligand of interest in selection of those bind sites that yield the desired properties from an assortment bind sites with different structures and properties. Thus, as opposed to an “instructive” role and therefore involvement in determination of these bind site properties, the ligand instead functions in selection of bind sites with preexisting properties. Although there is consensus over this role for ligands, this was not always the case. A debate over the role of cognate ligands dominated discourse during the early- to mid- 20th century. On one hand were proponents of an instructive role (as a direct template), and on the other hand were those in support of “selective” role. Haurowitz and Pauling proposed a role for ligand in determination of bind site properties, whereas Jerne and Burnet proposed selection. Experimental studies and theoretical considerations in immunology –by Nossal and Tonegawa– and in enzymology –by Anfinsen and Haber– provided results in support of the selection theory. Thus, an acceptance of selection- over instruction theory. However, both the uniqueness of antibody production and polyclonality draw questions to the applicability of such generalization of selection theory to other non-immune proteins. It is based on these notions that we advocate reconsideration of the instruction (direct template) theory as [at least] a partial explanation of origins of ligand binding properties of peptide molecules. Such reconsiderations are especially relevant when considering some of the current challenges regarding optimization of catalytic rates of artificially engineered enzymes. In such cases, the instruction theory may stand as part of a solution. In addition, this may create an avenue for optimization of: antibody-based therapeutics; and quantitative and qualitative immunoassays; for all of which binding interactions is a crucial determinant of affinity, specificity as well as sensitivity of agent.
Taxonomy, distribution and conservation of the Glassfrogs (Amphibia, Anura, Centrolenidae) of Ecuador
Authors: Cisneros-Heredia Diego F , McDiarmid Roy W.
Published: January 2018

The Glassfrogs (Centrolenidae) are an apparently monophyletic group of Neotropical anurans that includes 136 described species. The phylogenetic relationships of the family with other clades are still poorly understood and at the moment the family can be defined only by shared apomorphies. The current generic concepts that recognize Centrolene, Cochranella and Hyalinobatrachium do not seem to reflect the true evolutive relationships of the family. Study of ca. 500 specimens from different localities across Central and South America shows the existence of new undescribed species, taxonomic and nomenclatural confusions, and the need to review and reconsider the intra and intergeneric and specific relationships of the Centrolenidae. We restrict the name Hyalinobatrachium petersi for a taxon from the lowlands of the Ecuadorian Choco and report the first records of Centrolene lemniscatum and Hyalinobatrachum ruedai from Ecuador. The discovery of a new species of the group of Centrolene gorzulai on the eastern Andean slopes of Ecuador raises questions about the synapomorphies assigned to each genus and about the biogeography of the family. New data on internal and external morphology and behavior allow reconsidering the classification of intrageneric groups of Centrolene and Cochranella and re-evaluating the taxonomic usefulness of certain characters (e.g., shape/color of liver, humeral spine, color of bones). Our analysis suggests the need to divide the species of southeastern Brazil into a different genus, restricting Hyalionobatrachium to the fleischmanni group; the situation is still confused for the pulveratum group and conservatively is kept within the genus Hyalinobatrachium until additional morphological and phylogenetic analysis. At least five species of glass frogs of Ecuador are critically endangered; some considerations on the state of conservation of Centrolenidae in the country are presented.
Birds of La Plata Island, Machalilla National Park, Ecuador
Authors: Cisneros-Heredia Diego F
Published: January 2018

La Plata Island, Machalilla National Park, is located 30 km off the Ecuadorian coast. In June 2000, I surveyed the avifauna of La Plata Island. In total I observed 57 species of birds (25 families). At least 17 species are known to breed on the island; in fact, for mainland Ecuador, Waved Albatross Phoebastria irrorata, Red-billed Tropicbird Phaethon aethereus, Nazca Booby Sula granti, and Red-footed Booby Sula sula only breed in La Plata. Long-tailed Mockinbird subspecies Mimus longicaudatus platensis is the only endemic bird taxon of the island. House Sparrow Passer domesticus is the only non-native species of the island. Brown Booby Sula leucogaster, Ecuadorian Ground-Dove Columbina buckleyi, Little Woodstar Chaetocercus bombus and Yellow-bellied Elaenia Elaenia flavogaster are reported for the first time on the island. Isla de La Plata maintains an important biodiversity, and it is necessary to implement conservation, management and tourism plans on a sustainable way along with long-term monitoring studies of the fauna and flora.
Optimization of 16S amplicon analysis using mock communities: implications for estimating community diversity
Authors: Krohn Andrew , Stevens Bo , Robbins-Pianka Adam , Belus Matthew , Allan Gerard J , Gehring Catherine
Published: January 2018

Diversity of complex microbial communities can be rapidly assessed by community amplicon sequencing of marker genes (e.g., 16S), often yielding many thousands of DNA sequences per sample. However, analysis of community amplicon sequencing data requires multiple computational steps which affect the outcome of a final data set. Here we use mock communities to describe the effects of parameter adjustments for raw sequence quality filtering, picking operational taxonomic units (OTUs), taxonomic assignment, and OTU table filtering as implemented in QIIME 1.9.1. We demonstrate a workflow optimization based upon this exploration which we also apply to environmental samples. We found that quality filtering of raw data and filtering of OTU tables had large effects on observed OTU diversity. While all taxonomy assigners performed with similar accuracy, an appropriate choice of similarity threshold for defining OTUs depended on the method used for OTU picking. Our “default” analysis in QIIME overestimated mock community diversity by at least a factor of ten, compared to the optimized analysis which correctly characterized the taxonomic composition of the mock communities while still overestimating OTU diversity by about a factor of two. Though observed relative abundances of mock community member taxa were approximately correct, most were still represented by multiple OTUs. Low-frequency OTUs conspecific to constituent mock community taxa were characterized by multiple substitution and indel errors and the presence of a low quality base call resulting in sequence truncation during quality filtering. Low quality base calls were observed at “G” positions most of the time, and were also associated with a preceding “TTT” trinucleotide motif. Environmental diversity estimates were reduced by about 40% from 2508 to 1533 OTUs when comparing output from the default and optimized workflows. We attribute this reduction in observed diversity to the removal of erroneous sequences from the data set. Our results indicate that both strict quality filtering of raw sequencing data and careful filtering of raw OTU tables are important steps for accurate estimation of microbial community diversity.
YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance
Authors: Müller-Moulé Patricia , Nozue Kazunari , Pytlak Melissa L , Palmer Christine M , Covington Michael F , Wallace Andreah D , Harmer Stacey L , Maloof Julin N
Published: January 2018

Plants respond to neighbor shade by increasing stem and petiole elongation. Shade, sensed by phytochrome photoreceptors, causes stabilization of PHYTOCHROME INTERACTING FACTOR (PIF) proteins and subsequent induction of YUCCA auxin biosynthetic genes. To investigate the role of YUCCA genes in shade avoidance we examined auxin signaling kinetics and found that an auxin responsive reporter is rapidly induced within 2 hours of shade exposure. YUCCA2, 5, 8, and 9 are all induced with similar kinetics suggesting that they could act redundantly to control shade-mediated elongation. To test this hypothesis we constructed a yucca2,5,8,9 quadruple mutant and found that the hypocotyl and petiole shade avoidance is completely disrupted. This work shows that YUCCA auxin biosynthetic genes are essential for detectable shade avoidance and that YUCCA genes are important for petiole shade avoidance.
The diversity weighted Living Planet Index: controlling for taxonomic bias in a global biodiversity indicator
Authors: McRae Louise , Deinet Stefanie , Freeman Robin
Published: January 2018

As threats to species continue to increase, precise and unbiased measures of the impact these 14 pressures are having on global biodiversity are urgently needed. Some existing indicators of the 15 status and trends of biodiversity largely rely on publicly available data from the scientific and grey 16 literature, and are therefore prone to biases introduced through over-representation of well-studied 17 groups and regions in monitoring schemes. This can give misleading estimates of biodiversity trends. 18 Here, we report on an approach to tackle taxonomic and geographic bias in one such indicator 19 (Living Planet Index) by accounting for the estimated number of species within biogeographical 20 realms, and the relative diversity of species within them. Based on a proportionally weighted index, 21 we estimate a global population decline in vertebrate species between 1970 and 2012 of 58% rather 22 than 20% from an index with no proportional weighting. From this data set, comprising 14,152 23 populations of 3,706 species from 3,095 data sources, we also find that freshwater populations have 24 declined by 81%, marine populations by 36%, and terrestrial populations by 38% when using 25 proportional weighting (compared to trends of -46%, +12% and +15% respectively). These results not 26 only show starker declines than previously estimated, but suggests that those species for which 27 there is poorer data coverage may be declining more rapidly.
Matlab code for the Discrete Hankel Transform
Authors: Chouinard Ugo , Baddour Natalie
Published: January 2018

Previous definitions of a Discrete Hankel Transform (DHT) have focused on methods to approximate the continuous Hankel integral transform without regard for the properties of the DHT itself. Recently, the theory of a Discrete Hankel Transform was proposed that follows the same path as the Discrete Fourier/Continuous Fourier transform. This DHT possesses orthogonality properties which lead to invertibility and also possesses the standard set of discrete shift, modulation, multiplication and convolution rules. The proposed DHT can be used to approximate the continuous forward and inverse Hankel transform. This paper describes the Matlab code developed for the numerical calculation of this DHT.
Probabilistic graph models for landscape genetics
Authors: Milligan Brook G
Published: January 2018

Progress in landscape genetics depends on a strong conceptual foundation and the means of identifying mechanistic connnections between environmental factors, landscape features, and genetic or genomic variation. Many existing approaches and much of the software commonly in use was developed for population genetics or statistics and is not entirely appropriate for landscape genetics. Probabilistic graph models provide a statistically rigorous and flexible means of constructing models directly applicable to landscape genetics. Sophisticated software also exists for the analysis of graph models. However, much of that software does not handle the types data used by landscape geneticis, model structures involving autoregressive spatial interaction between variables, or the scale of landscape genetics problems. Thus, an important priority for the field is to develop suitably flexible software tools for graph models that overcome these problems and allow landscape geneticists to explore meaningfully mechanistic and flexible models. We are developing such a library and applying it to examples in landscape genetics.
Geospatial Big Data processing in an open source distributed computing environment
Authors: Olasz Angéla , Nguyen Thai Binh
Published: January 2018

In recent years, distributed computing has reached many areas of computer science including geographic and remote sensing information systems. However, distributed data processing solutions have primarily been focused on processing simple structured documents, rather than complex geospatial data. Hence, migrating current algorithms and data management to a distributed processing environment may require a great deal of effort. In data processing, different aspects are to be considered such as speed, precision or timeliness. All depending on data types and processing methods. Available data volume and variety evolving as never before which instantly exceeding the capabilities of traditional algorithm performance and hardware environment in the aspect of data management and computation. Augmented efficiency is required to exploit the available information derived from Geospatial Big Data. Most of the current distributed computing frameworks have important limitations on transparent and flexible control on processing (and/or storage) nodes. Hence, this paper presents a prototype for distribution (“tiling”), aggregation (“stitching”) and processing of Big Geospatial Data focusing the distribution and processing of raster data type. Furthermore, we introduce an own data and metadata catalogue enables to store the “lifecycle” of datasets, accessible for users and processes. The data distribution framework has no limitations on programming environment and can execute scripts (and workflows) written in different language (e.g. Python, R or C#). It is capable of processing raster, vector and point cloud data allowing full control of data distribution and processing. In this paper, the IQLib concept (https://github.com/posseidon/IQLib/) and background of practical realization as a prototype is presented, formulated within the IQmulus EU FP7 research and development project (http://www.iqmulus.eu). Further investigations on algorithmic and implementation details are in focus for the oral presentation.
A GRASS tool for the Sediment Delivery Ratio mapping
Authors: De Rosa Pierluigi , Cencetti Corrado , Fredduzzi Andrea
Published: January 2018

This work involves the implementation of a tool for evaluating Sediment Delivery Ratio (SDR) in a river basin, through GRASS GIS software. The definition of a spatially distributed value of SDR is a very important task as the sediment routing can affect solid transport in stream channels, water quality degradation, and frequency increase of natural disasters such as debris flows and mudflows. For such reason the SDR evaluation, coupled with GIS approach, has been extensively used in scientific literature. Geographic information systems provide a fundamental support for a better prediction of the SDR, since it can consider the space variability of factors influencing the sediment routing processes. Actually a specific GIS module to estimate the spatial variability of SDR does not exist. We implemented a GRASS GIS module (in python language) called r.sdr where the sediment delivery ratio is evaluated by GIS procedure by using several SDR equations available in literature. We applied the tool to the Feo Creek watershed, located in the Apennines area of northeastern Umbria (Italy).
HELP - An Early warning dashboard System, built for the prevention, mitigation and assessment of disasters, with a flexible approach using open data and open source technologies
Authors: Amato Lorenzo , Dello Buono Dimitri , Izzi Francesco , La Scaleia Giuseppe , Maio Donato
Published: January 2018

H.E.L.P is an early warning dashboard system built for the prevention, mitigation and assessment of disasters, be they earthquakes, fires, or meteorological systems. It was built to be easily manageable, customizable and accessible to all users, to facilitate humanitarian and governmental response. In its essence it is an emergency preparedness web tool, which can be used for decision making for a better level of mitigation and response on any level.Risks or disasters are not events in our control, rather, they are situations to which we can better manage with a framework based on preparedness. The earlier and more precise the monitoring of hazards allow for faster response to manage and mitigate a disaster’s impact on a society, economy and environment.This is exactly what HELP offers, it plays a main role in the cycle of early warning and risk (Preparedness, Risk, Mitigation, and Resilience). It provides information in real time on events and hazards, allowing for the possibility to analyze the situation and find a solution whose outcome protects the most lives and has the least economic impact. As a tool it also provides the opportunity to respond to a hazard with resilience in mind, this means that not only does HELP prepare for and mitigate events, it can also be used to implement better organizational methods for future events, thus, minimizing overall risk. Providing people with the means to better be able to take care of themselves, lessening the effects of future hazards each and every time. HELP is a tool in a framework which was created to support governments in their efforts to protect their people, building their response efficiency and resilience. HELP (with the name of E.W.A.R.E. Early Warning and Awareness of Risks and Emergencies) was born as WFP (The World Food Program) and IMAA-CNR (Institute of Methodologies for Environmental Analysis of the National Research Council of Italy) entered into a Cooperation Agreement concerning the development of a Geo-Spatial Data Infrastructure System for the Palestinian Civil Defense with the aim of building an enhanced preparedness capacity in Palestine.HELP has a simple and flexible but very effective logic to perform the early warning: Watch to open data sources on risk themes (NASA satellite data, Weather Forecast, world wide seismic networks, etc); Apply (programmable) “intelligence” to detect critical situations, exceeding of thresholds, population potentially involved by events, etc; Highlight critical elements on the map; Send alerts to emergency managers.
Keys to successful scientific VGI projects
Authors: Ingensand Jens , Composto Sarah , Ertz Olivier , Rappo Daniel , Nappez Marion , Produit Timothée , Oberson Mathias , Widmer Ivo , Joost Stéphane
Published: January 2018

Scientific projects are increasingly using volunteered geographic information (VGI) in order to collect and validate geographic data. This concept relies on the three challenges that first of all users can be found and second be convinced to collaborate and contribute and that scientists finally are able to gather high quality data for their projects. In this paper these three challenges are discussed using the experience with three different research projects: Urbangene, Signalez-nous and BioSentiers.
Exploiting observations and measurement data standard for distributed LTER-Italy freshwater sites. Water quality issues.
Authors: Lanucara Simone , Carrara Paola , Oggioni Alessandro , Rogora Michela , Kamburska Lyudmila , Rossetti Giampaolo
Published: January 2018

Water quality is a multi-source, multi-purpose problem that needs exploiting observations, often taken by a number of heterogeneous bodies. This problem has been tackled within the Italian Long Term Ecological research network (LTER-Italy) in an experiment aimed at testing how ecological observations of mountain lakes water can be shared by OGC (Open Geospatial Consortium) standard services of the Sensor Web Enablement (SWE) initiative. A friendly and easy implementation of these services is fostered by the usage of the open source software Geoinformation Enabling Toolkit StarterKit ® (GET-IT). It has been used in the experiment to create SOS services, upload observations and create SensorML metadata of the involved sensors. This contribution describes the experiment and presents its results.