Problematic barcoding in flatworms: A case-study on monogeneans and rhabdocoels (Platyhelminthes)

Some taxonomic groups are less amenable to mitochondrial DNA barcoding than others. Due to the paucity of molecular information of understudied groups and the huge molecular diversity within flatworms, primer design has been hampered. Indeed, all attempts to develop universal flatworm-specific COI markers have failed so far. We demonstrate how high molecular variability and contamination problems limit the possibilities for barcoding using standard COI-based protocols in flatworms. As a consequence, molecular identification methods often rely on other widely applicable markers. In the case of Monogenea, a very diverse group of platyhelminth parasites, and Rhabdocoela, representing one-fourth of all free-living flatworm taxa, this has led to a relatively high availability of nuclear ITS and 18S/28S rDNA sequences on GenBank. In a comparison of the effectiveness in species assignment we conclude that mitochondrial and nuclear ribosomal markers perform equally well. In case intraspecific information is needed, rDNA sequences can guide the selection of the appropriate (i.e. taxon-specific) COI primers if available.This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published pdf.NHM Repositor

Biodiversity of Antarctic nematodes: the ‘NEMASLAN’ project

Recent biodiversity research reveals that more than 50% of the free-living marine nematode species found in before unexplored environments, such as Antarctica, are new to science. Too few taxonomists remain to describe them all. Additionally, there are problems with the quality control of the identification of nematode samples since fewer labs possess all the literature (and manpower) required to verify the morphological characteristics of the animals.NEMASLAN, software for a tree-based classification system (Access) is a methodological approach for improving identification, classification and description of specimens in difficult taxonomic groups such as free-living marine nematodes. It seeks to serve as an easy research tool for central management of information of the taxon of the nematodes, and this for people with little training in database technologies.The program consists of four main modules: (see demonstration)1. Module for data- entering: provides possibilities to enter geographic, morphological, ecological, and literature data on species in a record database. An additional connection between these database records and the actual digital sources (e.g. scanned literature from original descriptions and good recent publications) enlarges the scientific value of the system.Personal metadatasets can be created, for example for the use of drawings and/or pictures of undescribed species or not yet published taxonomic papers. 2. Module for document consultation: data sources (PDF documents of original descriptions, text documents, photographs,…) and their references can be consulted. 3. Module for Quick Search: Morphological data from the species identification (e.g. shape and/or position of amphid, cuticle, buccal cavity, tail, oesophagus, caudal glands and spinneret; feeding type; numerical fields of de Man ratios, length, setae, nerve ring, excretory porus, spicule, gubernaculum, male supplements) and other information such as type of biotope and water depth distribution can be consulted; datasheets can be generated.4. Search Module: The output and search within the database can be user configured (i.e. questions like ‘give me all the nematode species so far described from the coastal sites with a spicule longer than 30µm and cuticular punctuations’ get an answer from this database). SQL (Structured Query Language) is the formal language used to query databases. An in-depth knowledge of the fairly complex SQL language is not required.The Windows application functions for multi-users in a local network environment (LAN). The program is distributed free of charge through a website (at present http://allserv.rug.ac.be/~tdeprez: later on through a more specified Antarctic database website) at which demonstration datasets are distributed.NEMASLAN was applied to Antarctic nematodes. The resulting ‘Biodiversity of Antarctic Nematodes’ CD-ROM version includes an archive of all numerical and nominal information for each species ever described in the Southern Ocean. About 350 species have thus been digitized. There is an urgent need to develop appropriate information tools on Antarctic marine biodiversity for scientific, environmental management and conservation purposes. Therefore, the collaboration of three laboratory pioneers in Antarctic biodiversity databases (e.g. Antarctic nematodes, amphipods and echinids, see other presentations) will seek for further developments such as the construction of a common portal, common mapping applications, or links to pertinent information sources of Antarctic benthic biodiversity. The resulting ‘biodiversity information system’ will be made available to the scientific community. This will be done within the framework of the OSTC project on Antarctica - BIANZO (BIodiversity of three representative groups of the ANtarctic ZOobenthos). It will contribute to the DIVERSITAS, SA 2000, CoML-OBIS and GBIF initiatives

Signature of selection on the rhodopsin gene in the marine radiation of American seven-spined gobies (Gobiidae, Gobiosomatini)

In comparison with terrestrial and freshwater ecosystems, information about speciation modes and the role of selection in marine environments is scarce. Recent studies have indicated that spectral adaptation could play an important role in the diversification of marine species flocks. Natural selection influences specific amino acids (AAs) that are involved in the spectral tuning mechanism of visual pigment genes. To study the wider occurrence and the characteristics of spectral adaptation in marine radiations, a reinterpretation of the rhodopsin (RH1) data of American seven-spined gobies (genus Elacatinus; Gobiidae; Teleostei) was carried out. Reanalysis revealed that some AAs, which are well known in the literature as spectral tuning sites, are variable in Elacatinus. Those crucial AA substitutions originated polyphyletically, indicating convergent evolution within the genus Elacatinus. Moreover, statistical tests based on the dN/dS ratio detected selection in several phylogenetic lineages and at specific AAs. Many of these AAs were previously shown to be under selection in other marine radiations. Therefore, the current phylogenetic approach provided an extended list of AAs that are probably involved in spectral tuning, and which should be validated by mutagenic experiments

Tolerability of NGX-4010, a capsaicin 8% patch, in conjunction with three topical anesthetic formulations for the treatment of neuropathic pain

Lynn R Webster1, John F Peppin2, Frederick T Murphy3,4, Jeffrey K Tobias5, Geertrui F Vanhove51Lifetree Clinical Research and Pain Clinic, Lifetree Medical Inc, Salt Lake City, UT, USA; 2Clinical Research Division, The Pain Treatment Center of the Bluegrass, Lexington, KY, USA; 3Altoona Center for Clinical Research, Duncansville, PA, USA; 4University of Pennsylvania, School of Medicine, Philadelphia, PA, USA; 5NeurogesX Inc, San Mateo, CA, USABackground: The objective of this study was to assess the safety, tolerability, and preliminary efficacy of NGX-4010, a capsaicin 8% patch, following pretreatment with three different topical anesthetics in patients with peripheral neuropathic pain.Methods: This open-label, multicenter study enrolled 117 patients with post-herpetic neuralgia, HIV-associated distal sensory polyneuropathy, or painful diabetic neuropathy. Patients received pretreatment with one of three lidocaine 4%-based topical anesthetics (L.M.X.4® [Ferndale Laboratories Inc, Ferndale, MI], Topicaine® Gel [Estela Basso, Jupiter, FL], or Betacaine Enhanced Gel 4 [Tiberius Inc, Tampa, FL]) for 60 minutes followed by a single 60- or 90-minute NGX-4010 application, and were followed for 12 weeks. Tolerability and safety measures included “pain now” Numeric Pain Rating Scale (NPRS) scores, dermal assessments, medication use for treatment-related pain, adverse events (AEs), clinical laboratory parameters, physical examinations, and vital signs. The primary efficacy variable was the percentage change in mean NPRS scores for “average pain for the past 24 hours” from baseline to weeks 2 through 12.Results: Treatment with NGX-4010 following pretreatment with any of the three topical anesthetics was generally safe and well tolerated. Nearly all patients completed ≥90% of the planned NGX-4010 application duration. The most common treatment-related AEs, application-site burning and application-site pain, were transient, mostly mild or moderate, and could be adequately managed by local cooling or short-acting oral opioid analgesics. Although slightly more patients used medication for treatment-related discomfort following pretreatment with Topicaine compared with L.M.X.4 or Betacaine, there were no statistical differences between the topical anesthetics. Neuropathic pain reduction from baseline to weeks 2 through 12 was approximately 30% and was similar among the topical anesthetics; the proportion of responders ranged from 45% to 50%.Conclusion: Treatment with NGX-4010 following pretreatment with any of the three topical anesthetics was generally safe and well tolerated; no significant differences in the parameters measured were noted between the pretreatment groups.Keywords: neuropathic pain, capsaicin patch, tolerability, topical anesthetic

One-loop four-graviton amplitudes in N=4 supergravity models

We evaluate in great detail one-loop four-graviton field theory amplitudes in pure N=4 D=4 supergravity. The expressions are obtained by taking the field theory limits of (4,0) and (2,2) space-time supersymmetric string theory models. For each model we extract the contributions of the spin-1 and spin-2 N=4 supermultiplets running in the loop. We show that all of those constructions lead to the same four-dimensional result for the four-graviton amplitudes in pure supergravity even though they come from different string theory models.Comment: 46 pages. One figure. v2: minor corrections and clarifications. References added. v3: (2,2) analysis corrected, four-graviton amplitudes found to be indentical in all models. Various clarifications and precisions added. References list updated. v4: Assorted spelling and grammar corrections. Version to be publishe

Duality and higher derivative terms in M theory

Dualities of M-theory are used to determine the exact dependence on the coupling constant of the D^6R^4 interaction of the IIA and IIB superstring effective action. Upon lifting to eleven dimensions this determines the coefficient of the D^6R^4 interaction in eleven-dimensional M-theory. These results are obtained by considering the four-graviton two-loop scattering amplitude in eleven-dimensional supergravity compactified on a circle and on a two-torus -- extending earlier results concerning lower-derivative interactions. The torus compactification leads to an interesting SL(2,Z)-invariant function of the complex structure of the torus (the IIB string coupling) that satisfies a Laplace equation with a source term on the fundamental domain of moduli space. The structure of this equation is in accord with general supersymmetry considerations and immediately determines tree-level and one-loop contributions to D^6R^4 in perturbative IIB string theory that agree with explicit string calculations, and two-loop and three-loop contributions that have yet to be obtained in string theory. The complete solution of the Laplace equation contains infinite series' of single D-instanton and double D-instanton contributions, in addition to the perturbative terms. General considerations of the higher loop diagrams of eleven-dimensional supergravity suggest extensions of these results to interactions of higher order in the low energy expansion.Comment: harvmac. 41 pages. 3 figures. v2 typos corrected and reference list updated. v3. Significant new subsection deriving the non-zero coefficient of the IIB string theory three-loop contributio

The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)

Abstract Background Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective. Results Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly ‘primitive’ African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines. Conclusions The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available

Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort

Emerging infections caused by fungi have become a widely recognized global phenomenon and are causing an increasing burden of disease. Genomic techniques are providing new insights into the structure of fungal populations, revealing hitherto undescribed fine-scale adaptations to environments and hosts that govern their emergence as infections. Cryptococcal meningitis is a neglected tropical disease that is responsible for a large proportion of AIDS-related deaths across Africa; however, the ecological determinants that underlie a patient's risk of infection remain largely unexplored. Here, we use genome sequencing and ecological genomics to decipher the evolutionary ecology of the aetiological agents of cryptococcal meningitis, Cryptococcus neoformans and Cryptococcus gattii, across the central African country of Zambia. We show that the occurrence of these two pathogens is differentially associated with biotic (macroecological) and abiotic (physical) factors across two key African ecoregions, Central Miombo woodlands and Zambezi Mopane woodlands. We show that speciation of Cryptococcus has resulted in adaptation to occupy different ecological niches, with C. neoformans found to occupy Zambezi Mopane woodlands and C. gattii primarily recovered from Central Miombo woodlands. Genome sequencing shows that C. neoformans causes 95% of human infections in this region, of which over three-quarters belonged to the globalized lineage VNI. We show that VNI infections are largely associated with urbanized populations in Zambia. Conversely, the majority of C. neoformans isolates recovered in the environment belong to the genetically diverse African-endemic lineage VNB, and we show hitherto unmapped levels of genomic diversity within this lineage. Our results reveal the complex evolutionary ecology that underpins the reservoirs of infection for this, and likely other, deadly pathogenic fungi

D-instantons and Matrix Models

We discuss the Matrix Model aspect of configurations saturating a fixed number of fermionic zero modes. This number is independent of the rank of the gauge group and the instanton number. This will allow us to define a large-$N_c$ limit of the embeddeding of $K$ D-instantons in the Matrix Model and make contact with the leading term (the measure factor) of the supergravity computations of D-instanton effects. We show that the connection between these two approaches is done through the Abelian modes of the Matrix variables.Comment: harvmac (b), 26 pages. v5 : polished final version for publication. Cosmetic changes onl