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New insights into the identity of Discolaimium dubium Das, Khan and Loof, 1969 (Dorylaimida) as derived from its morphological and molecular characterization, with the proposal of its transference to Aporcella Andrassy, 2002.

ABSTRACT: Three Iranian populations of Discolaimium dubium are studied, including their morphological and morphometric characterization, molecular analysis (LSU-rDNA) and the description of the male for the first time. For comparative purposes, this species is distinguished by its 1.10 to 1.40 mm long body, lip region offset by constriction and 8 to 10 µm wide, odontostyle 7.5 to 10.5 µm long with aperture occupying 59 to 76% of total length, neck 300 to 362 µm, pharyngeal expansion 127 to 181 µm long or 44 to 46% of the total neck length, uterus simple and 38 to 53 µm or 1.2 to 1.5 times the body diameter long, V = 52 to 58, tail conical (32-38 µm, c = 32-43, c' = 1.6-2.0) with rounded tip and a hyaline portion occupying 14 to 15% of tail length, spicules 30 to 32 µm long, and two or three widely space ventromedian supplements with hiatus. Both morphological and molecular data support its belonging to the genus Aporcella, whose monophyly is confirmed and to which the species is formally transferred as A. dubia (Das et al., 1969) comb. n.

SUBMITTER: Vazifeh N

PROVIDER: S-EPMC8040145 | biostudies-literature |

REPOSITORIES: biostudies-literature

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New data on two remarkable Antarctic species Amblydorylaimusisokaryon (Loof, 1975) Andrassy, 1998 and Pararhyssocolpusparadoxus (Loof, 1975), gen. n., comb. n. (Nematoda, Dorylaimida).

Project description:The taxonomic position of two antarctic dorylaimid species Amblydorylaimusisokaryon (Loof, 1975) Andrássy, 1998 and Pararhyssocolpusparadoxus (Loof, 1975), gen. n., comb. n. are discussed on the basis of morphological, including SEM study, morphometric, postembryonic and sequence data of 18S rDNA and the D2-D3 expansion fragments of large subunit rDNA. The evolutionary trees inferred from 18S sequences show insufficient resolution to determine the assignment of the two species to particular families, moreover Pararhyssocolpusparadoxus gen. n., comb. n. (=Rhyssocolpusparadoxus) previously regarded as a member of Nordiidae or Qudsianematidae, showed distant relationship both to Rhyssocolpusvinciguerrae and Eudorylaimus spp. The phylogram inferred from 28S sequences revealed that Amblydorylaimusisokaryon is a member of a well-supported group comprised of several Aporcelaimellus spp., while, no close relationships could be revealed for the Pararhyssocolpusparadoxus gen. n., comb. n. to any nematode genus. On the basis of molecular data and morphological characteristics, some taxonomic changes are proposed. Amblydorylaimusisokaryon is transferred from family Qudsianematidae to family Aporcelaimidae, and a new monotypic genus Pararhyssocolpus gen. n. is proposed, attributed to Pararhyssocolpidaefam. n. The diagnosis of the new family is provided together with emended diagnosis of the genera Amblydorylaimus and Pararhyssocolpus gen. n. Data concerning distribution of these endemic genera in the Antarctic region are also given.

| S-EPMC4523744 | biostudies-literature

Trifolium dubium

Project description:Trifolium dubium overview

| PRJNA980357 | ENA

Plagiorhegma dubium

Project description:Plagiorhegma dubium Raw sequence reads

| PRJNA472226 | ENA

Plagiorhegma dubium

Project description:Plagiorhegma dubium overview

| PRJNA552145 | ENA

Assessment of new sequencing information for genetically modified cotton DAS-24236-5 × DAS-21O23-5.

Project description:The GMO Panel has previously assessed genetically modified (GM) cotton DAS-24236-5 × DAS-21Ø23-5 and concluded that it is as safe as its conventional counterpart and other appropriate comparators with respect to potential effects on human and animal health and the environment in the context of its intended uses. On 17 November 2020, the European Commission requested EFSA to evaluate new DNA sequence information and updated bioinformatics data for cotton DAS-24236-5 × DAS-21Ø23-5 and to indicate whether the conclusions of the GMO Panel on the previously assessed cotton DAS-24236-5 × DAS-21Ø23-5 remain valid. The new sequence data of DAS-24236-5 showed the change of one nucleotide that results in one amino acid substitution, in the newly expressed Cry1F (synpro_L620Q) compared to the sequence originally reported. The GMO Panel concludes that this amino acid substitution in the protein is a mutation. Nonetheless with the exception of the bioinformatics analysis, the studies performed for the risk assessment of Cry1F in cotton DAS-24236-5 × DAS-21Ø23-5 remain valid. In addition, the new sequencing data showed a change in one nucleotide in the 5' flanking region of DAS-21Ø23-5 compared to the original sequence reported on the stack cotton DAS-24236-5 × DAS-21Ø23-5. The bioinformatic analyses of the newly sequenced DAS-21Ø23-5 event in the stack DAS-24236-5 × DAS-21Ø23-5 shows that the nucleotide difference is in the 5' flanking region outside the ORFs that span the 5' junction and is therefore not considered further in the safety assessment. Based on the information provided, the GMO Panel concludes that the corrected sequence does not give rise to any safety concerns, and therefore, the original risk assessment of cotton DAS-24236-5 × DAS-21Ø23-5 remains valid.

| S-EPMC9234918 | biostudies-literature

Oostenbrinkia pedrami n. sp. (Dorylaimida: Aulolaimoididae) from Iran, with molecular phylogenetic relationships to some other Dorylaimida Pearse, 1942.

Project description:A population of the rarely collected aulolaimoidid genus, Oostenbrinkia, was recovered from the rhizosphere soil of Fagus orientalis in Mazandaran province, north Iran. Oostenbrinkia pedrami n. sp. is mainly characterized by long females, 920 µm with a 6 to 8 µm long odontostyle, 18 to 21 µm long odontophore with well-developed basal ﬂanges, 124 to 187 µm long neck, vulva post equatorial (V = 58.5-61.0), and tail short (10-18 µm long, c = 42.5-65.2, c' = 0.6-0.9) and rounded. Compared to the generotype species, O. oostenbrinki, the new species has a longer odontostyle, total stylet, a posteriorly located vulva, and shorter rounded tail, and compared to the only one other representative, O. parva, longer females with longer odontostyle and total stylet. In molecular phylogenetic analyses using a near-full-length sequence of the small subunit ribosomal DNA (SSU rDNA), the new species appeared as an independent basal lineage to the included ingroup species. This is the first molecular data of this family.

| S-EPMC8015307 | biostudies-literature

Dasty3, a WEB framework for DAS.

Project description:MotivationDasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification.AvailabilityDasty3 is an open-source tool freely available at http://www.ebi.ac.uk/dasty/ under the terms of the GNU General public license. Source and documentation can be found at http://code.google.com/p/dasty/.Contacthhe@ebi.ac.uk.

| S-EPMC3167052 | biostudies-literature

MyDas, an extensible Java DAS server.

Project description:A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.

| S-EPMC3441562 | biostudies-literature

Confidence interval estimation in R-DAS.

Project description:BackgroundRoughly 25 years ago, the United States National Institute on Drug Abuse (US NIDA) initiated the creation of public use datasets for its National Household Survey on Drug Abuse, since re-named the National Survey on Drug Use and Health (NSDUH). The Substance Abuse and Mental Health Services Administration (SAMHSA), which assumed responsibility for the survey in 1992, has continued and expanded this effort to make the survey data available to researchers. During 2012, SAMHSA created a "Restricted-Use Data Analysis System" (R-DAS) to provide researchers with the capability to create tabulations using restricted NSDUH variables not otherwise available on the public-use files.MethodsThis methods focused article is intended to help potential users of R-DAS-like online data analysis systems by (i) clarifying statistical issues involving approximation of confidence intervals (CI), (ii) providing a way to estimate CI when tabular output is suppressed with an 'error message' based on confidentiality restrictions, and (iii) showing how to make pairwise comparisons of estimates not otherwise allowed.ResultsFor illustration purposes, some empirical estimates are presented on a topic of continuing of public health concern in the US namely, extra-medical use of pain relievers (generally opioids), where the drugs are being used to get high and otherwise outside the boundaries intended by prescribing clinicians.ConclusionThe R-DAS makes it possible to derive state-level estimates of male-female and age-related differences in incidence of extra-medical prescription pain reliever (EMPPR) use, not previously reported in peer-reviewed articles, and not available without research approaches described here.

| S-EPMC6003776 | biostudies-literature

Variovorax sp. 2002 isolate:DPS 2002

Project description:Variovorax sp. 2002 isolate:DPS 2002 Genome sequencing

| PRJNA695729 | ENA