The relevance,biases, and importance of digitising opportunistic non-standardised collections: A case study in Iberian harvestmen fauna with BOS Arthropod Collection datasets (Arachnida,Opiliones)

In this study, we analyse the relevance of harvestmen distribution data derived from opportunistic, unplanned, and non-standardised collection events in an area in the north of the Iberian Peninsula. Using specimens deposited in the BOS Arthropod Collection at the University of Oviedo, we compared these data with data from planned, standardised, and periodic collections with pitfall traps in several locations in the same area. The Arthropod Collection, begun in 1977, includes specimens derived from both sampling types, and its recent digitisation allows for this type of comparative analysis. Therefore, this is the first data-paper employing a hybrid approach, wherein subset metadata are described alongside a comparative analysis. The full dataset can be accessed through Spanish GBIF IPT at http://www.gbif.es:8080/ipt/archive.do?r=Bos-Opi, and the metadata of the unplanned collection events at http://www.gbif.es:8080/ipt/resource.do?r=bos-opi_unplanned_collection_events. We have mapped the data on the 18 harvestmen species included in the unplanned collections and provided records for some species in six provinces for the first time. We have also provided the locations of Phalangium opilio in eight provinces without published records. These results highlight the importance of digitising data from unplanned biodiversity collections, as well as those derived from planned collections, especially in scarcely studied groups and areas.     

Online database for mosquito (Diptera,Culicidae) occurrence records in French Guiana

A database providing information on mosquito specimens (Arthropoda: Diptera: Culicidae) collected in French Guiana is presented. Field collections were initiated in 2013 under the auspices of the CEnter for the study of Biodiversity in Amazonia (CEBA: http://www.labexceba.fr/en/). This study is part of an ongoing process aiming to understand the distribution of mosquitoes, including vector species, across French Guiana. Occurrences are recorded after each collecting trip in a database managed by the laboratory Evolution et Diversité Biologique (EDB), Toulouse, France. The dataset is updated monthly and is available online. Voucher specimens and their associated DNA are stored at the laboratory Ecologie des Forêts de Guyane (Ecofog), Kourou, French Guiana. The latest version of the dataset is accessible through EDB’s Integrated Publication Toolkit at http://130.120.204.55:8080/ipt/resource.do?r=mosquitoes_of_french_guiana or through the Global Biodiversity Information Facility data portal at http://www.gbif.org/dataset/5a8aa2ad-261c-4f61-a98e-26dd752fe1c5 It can also be viewed through the Guyanensis platform at http://guyanensis.ups-tlse.fr     

FORMIDABEL: The Belgian Ants Database

FORMIDABEL is a database of Belgian Ants containing more than 27.000 occurrence records. These records originate from collections, field sampling and literature. The database gives information on 76 native and 9 introduced ant species found in Belgium. The collection records originated mainly from the ants collection in Royal Belgian Institute of Natural Sciences (RBINS), the ‘Gaspar’ Ants collection in Gembloux and the zoological collection of the University of Liège (ULG). The oldest occurrences date back from May 1866, the most recent refer to August 2012. FORMIDABEL is a work in progress and the database is updated twice a year.The latest version of the dataset is publicly and freely accessible through this url: http://ipt.biodiversity.be/resource.do?r=formidabel. The dataset is also retrievable via the GBIF data portal through this link: http://data.gbif.org/datasets/resource/14697A dedicated geo-portal, developed by the Belgian Biodiversity Platform is accessible at: http://www.formicidae-atlas.bePurpose: FORMIDABEL is a joint cooperation of the Flemish ants working group “Polyergus” (http://formicidae.be) and the Wallonian ants working group “FourmisWalBru” (http://fourmiswalbru.be). The original database was created in 2002 in the context of the preliminary red data book of Flemish Ants (Dekoninck et al. 2003). Later, in 2005, data from the Southern part of Belgium; Wallonia and Brussels were added. In 2012 this dataset was again updated for the creation of the first Belgian Ants Atlas (Figure 1) (Dekoninck et al. 2012). The main purpose of this atlas was to generate maps for all outdoor-living ant species in Belgium using an overlay of the standard Belgian ecoregions. By using this overlay for most species, we can discern a clear and often restricted distribution pattern in Belgium, mainly based on vegetation and soil types.Open in a separate windowFigure 1.www.formicidae-atlas.be     

Afrotropical Cynipoidea (Hymenoptera)

The Afrotropical Cynipoidea are represented by 306 described species and 54 genera in four families: Cynipidae, Figitidae, Liopteridae and Ibaliidae, the latter represented by a single introduced species. Seven of these genera are only represented by undescribed species in the region. Seven new genus-level synonymies, one genus resurrected from synonymy, 54 new combinations, one combination reinstated, and one new replacement name are presented. We provide identification keys to the families, subfamilies and genera of cynipoid wasps occurring in the Afrotropical region (Africa south of the Sahara, including Madagascar and southern Arabian Peninsula). Online interactive Lucid Phoenix and Lucid matrix keys are available at: http://www.waspweb.org/Cynipoidea/Keys/index.htm. An overview of the biology and checklists of species for each genus are provided. This paper constitutes the first contributory chapter to the book on Afrotropical Hymenoptera.     

Complete genome sequence of Thermovibrio ammonificans HB-1T,a thermophilic,chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent

Thermovibrio ammonificans type strain HB-1^T is a thermophilic (T_opt: 75°C), strictly anaerobic, chemolithoautotrophic bacterium that was isolated from an active, high temperature deep-sea hydrothermal vent on the East Pacific Rise. This organism grows on mineral salts medium in the presence of CO₂/H₂, using NO₃^- or S⁰ as electron acceptors, which are reduced to ammonium or hydrogen sulfide, respectively. T. ammonificans is one of only three species within the genus Thermovibrio, a member of the family Desulfurobacteriaceae, and it forms a deep branch within the phylum Aquificae. Here we report the main features of the genome of T. ammonificans strain HB-1^T (DSM 15698^T).     

Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T)

Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).     

ChiloKey,an interactive identification tool for the geophilomorph centipedes of Europe (Chilopoda,Geophilomorpha)

ChiloKey is a matrix-based, interactive key to all 179 species of Geophilomorpha (Chilopoda) recorded from Europe, including species of uncertain identity and those whose morphology is known partially only. The key is intended to assist in identification of subadult and adult specimens, by means of microscopy and simple dissection techniques whenever necessary. The key is freely available through the web at: http://www.biologia.unipd.it/chilokey/ and at http://www.interactive-keys.eu/chilokey/.     

Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium

Fenollaria massiliensis strain 9401234^T, is the type strain of Fenollaria massiliensis gen. nov., sp. nov., a new species within a new genus Fenollaria. This strain, whose genome is described here, was isolated from an osteoarticular sample. F. massiliensis strain 9401234^T is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1.71 Mbp long genome exhibits a G+C content of 34.46% and contains 1,667 protein-coding and 30 RNA genes, including 3 rRNA genes.     

The Anaphase Promoting Complex Regulates Yeast Lifespan and rDNA Stability by Targeting Fob1 for Degradation

Genomic stability, stress response, and nutrient signaling all play critical, evolutionarily conserved roles in lifespan determination. However, the molecular mechanisms coordinating these processes with longevity remain unresolved. Here we investigate the involvement of the yeast anaphase promoting complex (APC) in longevity. The APC governs passage through M and G1 via ubiquitin-dependent targeting of substrate proteins and is associated with cancer and premature aging when defective. Our two-hybrid screen utilizing Apc5 as bait recovered the lifespan determinant Fob1 as prey. Fob1 is unstable specifically in G1, cycles throughout the cell cycle in a manner similar to Clb2 (an APC target), and is stabilized in APC (apc5^CA) and proteasome (rpn10∆) mutants. Deletion of FOB1 increased replicative lifespan (RLS) in wild type (WT), apc5^CA, and apc10∆ cells, and suppressed apc5^CA cell cycle progression and rDNA recombination defects. Alternatively, increased FOB1 expression decreased RLS in WT cells, but did not reduce the already short apc5^CA RLS, suggesting an epistatic interaction between apc5^CA and fob1∆. Mutation to a putative L-Box (Fob1^E420V), a Destruction Box-like motif, abolished Fob1 modifications, stabilized the protein, and increased rDNA recombination. Our work provides a mechanistic role played by the APC to promote replicative longevity and genomic stability in yeast.     

Genetic Interactions Between UNC-17/VAChT and a Novel Transmembrane Protein in Caenorhabditis elegans

The unc-17 gene encodes the vesicular acetylcholine transporter (VAChT) in Caenorhabditis elegans. unc-17 reduction-of-function mutants are small, slow growing, and uncoordinated. Several independent unc-17 alleles are associated with a glycine-to-arginine substitution (G347R), which introduces a positive charge in the ninth transmembrane domain (TMD) of UNC-17. To identify proteins that interact with UNC-17/VAChT, we screened for mutations that suppress the uncoordinated phenotype of UNC-17(G347R) mutants. We identified several dominant allele-specific suppressors, including mutations in the sup-1 locus. The sup-1 gene encodes a single-pass transmembrane protein that is expressed in a subset of neurons and in body muscles. Two independent suppressor alleles of sup-1 are associated with a glycine-to-glutamic acid substitution (G84E), resulting in a negative charge in the SUP-1 TMD. A sup-1 null mutant has no obvious deficits in cholinergic neurotransmission and does not suppress unc-17 mutant phenotypes. Bimolecular fluorescence complementation (BiFC) analysis demonstrated close association of SUP-1 and UNC-17 in synapse-rich regions of the cholinergic nervous system, including the nerve ring and dorsal nerve cords. These observations suggest that UNC-17 and SUP-1 are in close proximity at synapses. We propose that electrostatic interactions between the UNC-17(G347R) and SUP-1(G84E) TMDs alter the conformation of the mutant UNC-17 protein, thereby restoring UNC-17 function; this is similar to the interaction between UNC-17/VAChT and synaptobrevin.     

Genetics of Lipid-Storage Management in Caenorhabditis elegans Embryos

Lipids play a pivotal role in embryogenesis as structural components of cellular membranes, as a source of energy, and as signaling molecules. On the basis of a collection of temperature-sensitive embryonic lethal mutants, a systematic database search, and a subsequent microscopic analysis of >300 interference RNA (RNAi)–treated/mutant worms, we identified a couple of evolutionary conserved genes associated with lipid storage in Caenorhabditis elegans embryos. The genes include cpl-1 (cathepsin L–like cysteine protease), ccz-1 (guanine nucleotide exchange factor subunit), and asm-3 (acid sphingomyelinase), which is closely related to the human Niemann-Pick disease–causing gene SMPD1. The respective mutant embryos accumulate enlarged droplets of neutral lipids (cpl-1) and yolk-containing lipid droplets (ccz-1) or have larger genuine lipid droplets (asm-3). The asm-3 mutant embryos additionally showed an enhanced resistance against C band ultraviolet (UV-C) light. Herein we propose that cpl-1, ccz-1, and asm-3 are genes required for the processing of lipid-containing droplets in C. elegans embryos. Owing to the high levels of conservation, the identified genes are also useful in studies of embryonic lipid storage in other organisms.     

Circumpolar dataset of sequenced specimens of Promachocrinus kerguelensis (Echinodermata,Crinoidea)

This circumpolar dataset of the comatulid (Echinodermata: Crinoidea) Promachocrinus kerguelensis (Carpenter, 1888) from the Southern Ocean, documents biodiversity associated with the specimens sequenced in Hemery et al. (2012). The aim of Hemery et al. (2012) paper was to use phylogeographic and phylogenetic tools to assess the genetic diversity, demographic history and evolutionary relationships of this very common and abundant comatulid, in the context of the glacial history of the Antarctic and Sub-Antarctic shelves (Thatje et al. 2005, 2008). Over one thousand three hundred specimens (1307) used in this study were collected during seventeen cruises from 1996 to 2010, in eight regions of the Southern Ocean: Kerguelen Plateau, Davis Sea, Dumont d’Urville Sea, Ross Sea, Amundsen Sea, West Antarctic Peninsula, East Weddell Sea and Scotia Arc including the tip of the Antarctic Peninsula and the Bransfield Strait. We give here the metadata of this dataset, which lists sampling sources (cruise ID, ship name, sampling date, sampling gear), sampling sites (station, geographic coordinates, depth) and genetic data (phylogroup, haplotype, sequence ID) for each of the 1307 specimens. The identification of the specimens was controlled by an expert taxonomist specialist of crinoids (Marc Eléaume, Muséum national d’Histoire naturelle, Paris) and all the COI sequences were matched against those available on the Barcode of Life Data System (BOLD: http://www.boldsystems.org/index.php/IDS_OpenIdEngine). This dataset can be used by studies dealing with, among other interests, Antarctic and/or crinoid diversity (species richness, distribution patterns), biogeography or habitat / ecological niche modeling. This dataset is accessible through the GBIF network at http://ipt.biodiversity.aq/resource.do?r=proke.     

The complete genome sequence of Clostridium indolis DSM 755T

Clostridium indolis DSM 755^T is a bacterium commonly found in soils and the feces of birds and mammals. Despite its prevalence, little is known about the ecology or physiology of this species. However, close relatives, C. saccharolyticum and C. hathewayi, have demonstrated interesting metabolic potentials related to plant degradation and human health. The genome of C. indolis DSM 755^T reveals an abundance of genes in functional groups associated with the transport and utilization of carbohydrates, as well as citrate, lactate, and aromatics. Ecologically relevant gene clusters related to nitrogen fixation and a unique type of bacterial microcompartment, the CoAT BMC, are also detected. Our genome analysis suggests hypotheses to be tested in future culture based work to better understand the physiology of this poorly described species.     

A Novel Gene Controlling the Timing of Courtship Initiation in Drosophila melanogaster

Over the past 35 years, developmental geneticists have made impressive progress toward an understanding of how genes specify morphology and function, particularly as they relate to the specification of each physical component of an organism. In the last 20 years, male courtship behavior in Drosophila melanogaster has emerged as a robust model system for the study of genetic specification of behavior. Courtship behavior is both complex and innate, and a single gene, fruitless (fru), is both necessary and sufficient for all aspects of the courtship ritual. Typically, loss of male-specific Fruitless protein function results in male flies that perform the courtship ritual incorrectly, slowly, or not at all. Here we describe a novel requirement for fru: we have identified a group of cells in which male Fru proteins are required to reduce the speed of courtship initiation. In addition, we have identified a gene, Trapped in endoderm 1 (Tre1), which is required in these cells for normal courtship and mating behavior. Tre1 encodes a G-protein-coupled receptor required for establishment of cell polarity and cell migration and has previously not been shown to be involved in courtship behavior. We describe the results of feminization of the Tre1-expressing neurons, as well as the effects on courtship behavior of mutation of Tre1. In addition, we show that Tre1 is expressed in a sexually dimorphic pattern in the central and peripheral nervous systems and investigate the role of the Tre1 cells in mate identification.     

Autophagy Competes for a Common Phosphatidylethanolamine Pool with Major Cellular PE-Consuming Pathways in Saccharomyces cerevisiae

Autophagy is a highly regulated pathway that selectively degrades cellular constituents such as protein aggregates and excessive or damaged organelles. This transport route is characterized by engulfment of the targeted cargo by autophagosomes. The formation of these double-membrane vesicles requires the covalent conjugation of the ubiquitin-like protein Atg8 to phosphatidylethanolamine (PE). However, the origin of PE and the regulation of lipid flux required for autophagy remain poorly understood. Using a genetic screen, we found that the temperature-sensitive growth and intracellular membrane organization defects of mcd4-174 and mcd4-P301L mutants are suppressed by deletion of essential autophagy genes such as ATG1 or ATG7. MCD4 encodes an ethanolamine phosphate transferase that uses PE as a precursor for an essential step in the synthesis of the glycosylphosphatidylinositol (GPI) anchor used to link a subset of plasma membrane proteins to lipid bilayers. Similar to the deletion of CHO2, a gene encoding the enzyme converting PE to phosphatidylcholine (PC), deletion of ATG7 was able to restore lipidation and plasma membrane localization of the GPI-anchored protein Gas1 and normal organization of intracellular membranes. Conversely, overexpression of Cho2 was lethal in mcd4-174 cells grown at restrictive temperature. Quantitative lipid analysis revealed that PE levels are substantially reduced in the mcd4-174 mutant but can be restored by deletion of ATG7 or CHO2. Taken together, these data suggest that autophagy competes for a common PE pool with major cellular PE-consuming pathways such as the GPI anchor and PC synthesis, highlighting the possible interplay between these pathways and the existence of signals that may coordinate PE flux.     

Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov.

Oceanobacillus massiliensis strain N’Diop^T sp. nov. is the type strain of O. massiliensis sp. nov., a new species within the genus Oceanobacillus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. O. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,532,675 bp long genome contains 3,519 protein-coding genes and 72 RNA genes, including between 6 and 8 rRNA operons.     

The Register of Antarctic Marine Species (RAMS): a ten-year appraisal

The Register of Antarctic Marine Species (RAMS) is a marine species database that manages an authoritative taxonomic list of species occurring in the Southern Ocean. RAMS links with several other initiatives managing biogeographic or genomics information. The current paper aims to briefly present RAMS and provides an updated snapshot of its contents, in the form of a DarwinCore checklist (available through http://ipt.biodiversity.aq/resource.do?r=rams) and illustrative barplots. Moreover, this article presents a ten year appraisal (since the creation of RAMS). This appraisal first focuses on RAMS bibliometrics. We observed that RAMS was cited (Google Scholar) in 50 distinct publications among which 32 were peer-reviewed in 18 different journals. Three journals (Antarctic Science, Polar Biology, ZooKeys) represent almost 40% of these peer-review publications. The second appraisal focuses on the evolution of new RAMS records. We observed an important decrease in data additions since 2011. As a case study, we focused on an original dataset for a specific group (Asteroidea, Echinodermata). It appears that around one hundred species of asteroids are lacking in RAMS despite the relatively high availability of these data. This suggests that the users’ community (or collaborative projects such as AquaRES) could be helpful in order to maintain the RAMS database over the long term.     

Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov.

Brevibacillus massiliensis strain phR^T sp. nov. is the type strain of B. massiliensis sp. nov., a new species within the genus Brevibacillus. This strain was isolated from the fecal flora of a woman suffering from morbid obesity. B. massiliensis is a Gram-positive aerobic rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,051,018 bp long genome (1 chromosome but no plasmid) contains 5,051 protein-coding and 84 RNA genes, and exhibits a G+C content of 53.1%.