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3,878 results for “Molecular Data”
Data from: Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)
Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina's platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.
Data from: Molecular and cytogenetic study of East African Highland Banana
East African highland bananas (EAHB) are staple food crop in Uganda, Tanzania, Burundi and other countries in the African Great Lakes region. Even though several morphologically different types exist, all EAHB are triploid and display minimal genetic variation. To provide more insights into the genetic variation within EAHB, genotyping using simple sequence repeat (SSR) markers, molecular analysis of ITS1-5.8S-ITS2 region of ribosomal DNA locus and the analysis of chromosomal distribution of ribosomal DNA sequences was done. A total of 40 triploid EAHB accessions available in the Musa germplasm collection (International Transit Centre, Leuven, Belgium) were characterized. Six diploid accessions of Musa acuminata ssp. zebrina, ssp. banksii and ssp. malaccensis representing putative parents of EAHB were included in the study. Flow cytometric estimation of 2C nuclear DNA content revealed small differences (max ~ 6.5 %) in genome size among the EAHB clones. While no differences in the number of 45S and 5S rDNA loci were found, genotyping using 19 SSR markers resulted in grouping the EAHB accessions into four clusters. DNA sequence analysis of the ITS region indicated a relation of EAHB clones with M. acuminata and, surprisingly, also with M. schizocarpa. The results suggest that EAHB cultivars originated from a single hybrid clone with M. acuminata ssp. zebrina and ssp. banksii being its most probable parents. However, M. schizocarpa seems to have contributed to the formation of this group of banana.
Data from: Molecular analysis of parasitoid linkages (MAPL): gut contents of adult parasitoid wasps reveal larval host
Metamorphosing insects often have complex and poorly known life-histories. In particular, what they feed on during their larval stages remains unknown for the vast majority of species and its documentation only results from difficult and time-intensive field observations, rearing or dissections. Through the application of a DNA analysis of gut contents in adult parasitoid wasps, we were able to selectively sequence a diagnostic DNA marker that permitted the identification of the host used by these wasps during their larval stages. By reproducing these results in species with different life-histories, we excluded other potential sources of host DNA, confirming that after ingestion by the parasitoid larva the host DNA can persist through metamorphosis in the abdominal contents of the adult wasp. Our discovery considerably extends the applicability of molecular analysis of gut contents by enabling documentation of the food used by insects during their larval stages and thus increasing the accuracy and precision of food web-studies. The 24% success rate of our approach is surprisingly high considering the challenging context for host DNA preservation, and we discuss the factors possibly affecting this rate. We propose Molecular Analysis of Parasitoid Linkages (MAPL) as a new method to document host-parasitoid associations at a faster pace and with unrivalled precision. Because of the key regulatory role of parasitoid wasps in ecosystems, which makes them the most commonly used biological control agents, MAPL will have immediate applications in both basic and applied biological sciences.
Data from: Seasonally varying marine influences on the coastal ecosystem detected through molecular gut analysis
Terrestrial predators on marine shores benefit from the inflow of organisms and matter from the marine ecosystem, often causing very high predator densities and indirectly affecting the abundance of other prey species on shores. This indirect effect may be particularly strong if predators shift diets between seasons. We therefore quantified the seasonal variation in diet of two wolf spider species that dominate the shoreline predator community, using molecular gut content analyses with general primers to detect the full prey range. Across the season, spider diets changed, with predominantly terrestrial prey from May until July and predominantly marine prey (mainly chironomids) from August until October. This pattern coincided with a change in the spider age and size structure, and prey abundance data and resource selection analyses suggest that the higher consumption of chironomids during autumn is due to an ontogenetic diet shift rather than to variation in prey abundance. The analyses suggested that small dipterans with a weak flight capacity, such as Chironomidae, Sphaeroceridae, Scatopsidae and Ephydridae, were overrepresented in the gut of small juvenile spiders during autumn, whereas larger, more robust prey, such as Lepidoptera, Anthomyidae and Dolichopodidae, were overrepresented in the diet of adult spiders during spring. The effect of this inflow may be that the survival and growth of juvenile spiders is higher in areas with high chironomid abundances, leading to higher densities of adult spiders and higher predation rates on the terrestrial prey next spring.
Data from: Phylogeny of the Stachys coccinea (Lamiaceae) complex based on molecular and morphological data
One of the largest genera within the Lamiaceae, Stachys, is in extreme need of taxonomic revision due to its demonstrated phylogenetic polyphyly. Among the New World Stachys, a group of seven species belonging to the Stachys coccinea complex is widely distributed in Mexico, where four of the species in this complex are considered endemic. The members of this complex are characterized by having large and red, orange, or purple corollas. The observed morphological variation, however, may insufficiently circumscribe this number of species, and an assessment combining the use of morphological and molecular data is needed. Here, we evaluated the circumscription of the Stachys coccinea complex and relationships among its members using phylogenetic analyses of chloroplast (cp) DNA sequence data and numerical analysis applied to morphological data. We found that morphological variation in this complex insufficiently circumscribed members of the complex, possibly caused by plasticity of diagnostic morphological characters. In addition, the utilized cpDNA regions, which are commonly used in plant phylogenetic reconstruction (trnL intron, trnL-F spacer, and rps16 intron sequences), render relationships among most of the species in the complex unresolved. We propose that the Stachys coccinea complex be recircumscribed, reducing the number of members to three species: Stachys coccinea, S. lindenii, and S. albotomentosa, keeping the original circumscription of these species and including S. pacifica, S. manantlanensis, S. torresii, and S. jaimehintonii as varieties of S. coccinea.
Data from: Molecular phylogeny, revised higher classification, and implications for conservation of endangered Hawaiian leaf-mining moths (Lepidoptera: Gracillariidae: Philodoria)
The leaf-mining moth genus Philodoria Walsingham (Lepidoptera: Gracillariidae) is composed of 30 described species, all of which are endemic to the Hawaiian Islands. Philodoria is known to feed on 10 families of endemic Hawaiian host plants, with several species recorded only from threatened or endangered hosts. Beyond their dependence on these plants, little is known of their evolutionary history and conservation status. We constructed a molecular phylogeny of Philodoria to assess validity of its current subgeneric classification and to help guide future work on this threatened Hawaiian lineage. Mitochondrial and nuclear DNA sequences from three genes (CO1, CAD, EF-1α) combining for a total of 2,041 base pairs, were collected from 11 Philodoria species, incorporating taxa from both currently recognized subgenera. These data were analyzed using both parsimony and model-based phylogenetic approaches. Contrary to the most recent systematic treatment of Philodoria, our results indicate strongly that the two currently recognized Philodoria subgenera are not monophyletic and that morphological characters used to classify them are homoplasious. Based on our robust results, we revised the higher classification of Philodoria: the subgenus Eophilodoria Zimmerman, 1978 is established as subjective junior synonym of Philodoria Walsingham, 1907. We also present new host plant and distribution data and discuss host range of Philodoria as it pertains to endangered Hawaiian plants.
Data from: Time-calibrated molecular phylogeny of pteropods
Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and examine the evolutionary history of pteropods based on combined analyses of Cytochrome Oxidase I, 28S, and 18S ribosomal rRNA sequences and a molecular clock calibrated using fossils and the estimated timing of the formation of the Isthmus of Panama. Euthecosomes with uncoiled shells were monophyletic with Creseis as the earliest diverging lineage, estimated at 41–38 million years ago (mya). The coiled euthecosomes (Limacina, Heliconoides, Thielea) were not monophyletic contrary to the accepted morphology-based taxonomy; however, due to their high rate heterogeneity no firm conclusions can be drawn. We found strong support for monophyly of most euthecosome genera, but Clio appeared as a polyphyletic group, and Diacavolinia grouped within Cavolinia, making the latter genus paraphyletic. The highest evolutionary rates were observed in Heliconoides inflatus and Limacina bulimoides for both 28S and 18S partitions. Using a fossil-calibrated phylogeny that sets the first occurrence of coiled euthecosomes at 79–66 mya, we estimate that uncoiled euthecosomes evolved 51–42 mya and that most extant uncoiled genera originated 40–15 mya. These findings are congruent with a molecular clock analysis using the Isthmus of Panama formation as an independent calibration. Although not all phylogenetic relationships could be resolved based on three molecular markers, this study provides a useful resource to study pteropod diversity and provides general insight into the processes that generate and maintain their diversity in the open ocean.
Data from: Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)
The cyprinid tribe Labeonini (sensu Rainboth, 1991) is a large group of freshwater fishes containing around 40 genera and 400 species. They are characterized by an amazing diversity of modifications to their lips and associated structures. In this study, a total of 34 genera and 142 species of putative members of this tribe, which represent most of the generic diversity and more than one third of the species diversity of the group, were sampled and sequenced for four nuclear genes and five mitochondrial genes (totalling 9,465 bp). Phylogenetic relationships and subdivision of this tribe were investigated and the placement and status of most genera are discussed. Partitioned maximum likelihood analyses were performed based on the nuclear dataset, mitochondrial dataset, combined dataset, and the dataset for each nuclear gene. Inclusion of the genera Paracrossochilus, Barbichthys, Thynnichthys, and Linichthys in the Labeonini was either confirmed or proposed for the first time. None of the genera Labeo, Garra, Bangana, Cirrhinus, and Crossocheilus are monophyletic. Taxonomic revisions of some genera were made: the generic names Gymnostomus Heckel, 1843, Ageneiogarra Garman, 1912 and Gonorhynchus McClelland, 1839 were revalidated; Akrokolioplax Zhang and Kottelat, 2006 becomes a junior synonym of Gonorhynchus; the species Osteochilus nashii was found to be a member of the barbin genus Osteochilichthys. Five historical hypotheses on the classification of the Labeonini were tested and rejected. We proposed to subdivide the tribe, which is strongly supported as monophyletic, into four subtribes: Labeoina, Garraina, Osteochilina, and Semilabeoina. The taxa included in each subtribe were listed and those taxa that need taxonomic revision were discussed.
Data from: Phylogenetic systematics of Cochlospermaceae (Malvales) based on molecular and morphological evidence
Cochlospermaceae (Malvales) is a small family of two genera, Amoreuxia and Cochlospermum. Cochlospermum has a pantropical distribution with species present in Mexico, Central and South America, the West Indies, Africa, India, Southeast Asia, and northern Australia, whereas Amoreuxia has a more restricted distribution in the Americas. Amoreuxia is comprised of four herbaceous species, and Cochlospermum has seven tree species and five that are suffrutescent subshrubs. The two genera also differ in floral symmetry, corolla coloration patterns, and stamen morphology. The goals of this study were to reconstruct the phylogeny of Cochlospermaceae to evaluate the monophyly of the family and its two genera, to resolve interspecific relationships, and to interpret patterns of morphological evolution. In addition, a minor goal was to examine its relationship to sister families, such as Bixaceae, a family in which Cochlospermaceae has been variously placed. Phylogenetic analyses were carried out using DNA sequences of the following markers: nuclear ribosomal ITS and the chloroplast trnG and trnL-F regions. The data support the monophyly of Cochlospermaceae and its distinctiveness from its sister families. While Amoreuxia is supported as monophyletic, Cochlospermum is paraphyletic with two species (C. orinocense and C. tetraporum) consistently placed outside a clade of all remaining Cochlospermum species. Ancestral character state reconstructions of morphology indicate that the tree habit may be ancestral in Cochlospermaceae with a single shift to an herbaceous growth form in Amoreuxia with the suffrutescent growth form having arisen twice within Cochlospermum, once in South America and once in Africa. There has been a single shift in floral morphology from radial symmetry, solid yellow petals, and uniform stamens to bilateral symmetry, two-toned petals, and dimorphic stamens in Amoreuxia. Anthers with one apical pore found in core Cochlospermum species may be a reduction from anthers with two pores, such as those found in Amoreuxia and in C. orinocense and C. tetraporum. Seed shape supports the sister relationships within Cochlospermaceae, particularly within Amoreuxia.
Supplementary material 1 from: Jordaens K, Goergen G, Skevington JH, Kelso S, De Meyer M (2021) Revision of the Afrotropical species of the hover fly genus Mesembrius Rondani (Diptera, Syrphidae) using morphological and molecular data. ZooKeys 1046: 1-141. https://doi.org/10.3897/zookeys.1046.57052
Table S1. List of specimens, collection information, DNA voucher codes and GenBank/Barcode of Life Datasystems (BOLD) accession numbers used for the DNA barcode and phylogenetic analyses
FIGURES 7-13 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data
FIGURES 7-13. Head in dorsal view. Tubercles (shadow) at antennal base in (7) Rhamphus oxyacanthae; (8) R. bavierai. Vertex of head (shadow) of (9) Rhamphus oxyacanthae (flat); (10) R. bavierai (moderately convex). Uncus of mesotibia of (11) Rhamphus oxyacanthae; (12) R. monzinii; (13) R. pulicarius.
FIGURES 14-21 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data
FIGURES 14-21. Antenna of (14) Rhamphus bavierai (scape included); (15) R. monzinii; arrows indicate the first segment of the funicle. Metafemur and metatarsus of (16) Rhamphus oxyacanthae; (17) R. bavierai; arrows indicate the first tarsomere. Penis of (18) Rhamphus oxyacanthae; (19) R. bavierai; (20) R. hampsicora; (21) R. monzinii.
FIGURE 3. Statistical parsimony haplotype network constructed from 621 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data
FIGURE 3. Statistical parsimony haplotype network constructed from 621 bp of the mtCOI gene of Rhamphus bavierai n. sp. (GenBank accession number MW879286- MW879303). Circle sizes are proportional to haplotype frequency (for details see supplementary Table S1). Numbers in brackets above/beside the solid broken line represent the number of mutations connecting mitochondrial lineages.
FIGURE 2. Statistical parsimony haplotype network constructed from 621 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data
FIGURE 2. Statistical parsimony haplotype network constructed from 621 bp of the mtCOI gene of Rhamphus oxyacanthae in Italy (GenBank accession number MW879276- MW879285). Circles sizes are proportional to haplotype frequency (for details see supplementary S1).
FIGURE 1. Bayesian phylogenetic tree inferred from 621 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data
FIGURE 1. Bayesian phylogenetic tree inferred from 621 bp of the mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COI) gene sampled from the Rhamphus specimens originated from Italy. Bayesian a posteriori probabilities are shown above/below branches (values below 0.7 are omitted). Abbreviation: oxy = R. oxyacanthae; bav = R.bavierai n. sp.; ham = R. hampsicora n. sp.; mon = R. monzinii.
Molecular Dynamics simulation data of Cyt c at pH 7 at the water|TFT interface
<p>Programmed cell death via apoptosis is a natural defence against excessive cell division, crucial for foetal development to maintenance of homeostasis and elimination of precancerous and senescent cells. Here we demonstrate an electrified liquid bio-interface that replicates the molecular machinery of the inner mitochondrial membrane at the onset of apoptosis. By mimicking in vivo cytochrome c (Cyt c) interactions with cell membranes, our platform allows us to modulate the conformational plasticity of the protein by simply varying the electrochemical environment at an aqueous|organic interface. Remarkably, we observe interfacial electron transfer between an organic electron donor decamethylferrocene and O2, electrocatalysed by Cyt c. This interfacial reaction requires partial Cyt c unfolding, mimicking Cyt c in vivo peroxidase activity. As proof-of-concept, we use our electrified liquid bio-interface to identify drug molecules, such as bifonazole, that can potentially downregulate Cyt c and protect against uncontrolled neuronal cell death in neurodegenerative disorders.</p>
Data from: High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine
The lumen of the small intestine (SI) is filled with particulates: microbes, therapeutic particles, and food granules. The structure of this particulate suspension could impact uptake of drugs and nutrients and the function of microorganisms; however, little is understood about how this suspension is re-structured as it transits the gut. Here, we demonstrate that particles spontaneously aggregate in SI luminal fluid ex vivo. We find that mucins and immunoglobulins are not required for aggregation. Instead, aggregation can be controlled using polymers from dietary fiber in a manner that is qualitatively consistent with polymer-induced depletion interactions, which do not require specific chemical interactions. Furthermore, we find that aggregation is tunable; by feeding mice dietary fibers of different molecular weights, we can control aggregation in SI luminal fluid. This work suggests that the molecular weight and concentration of dietary polymers play an underappreciated role in shaping the physicochemical environment of the gut.
FIGURE 4 in Molecular relationships of the Australian Ennominae (Lepidoptera: Geometridae) and implications for the phylogeny of the Geometridae from molecular and morphological data
FIGURE 4. Twodimensional structure of a 28S D2 for the Australian geometrid moth Ciampa arietaria. The subdomains (D2a, D2b and D2c) are labelled following Michot and Bachellerie (1987); numbers correspond to nucleotide positions in Fig. 2.
FIGURE 3. Gap data matrix for 28S D2 in Molecular relationships of the Australian Ennominae (Lepidoptera: Geometridae) and implications for the phylogeny of the Geometridae from molecular and morphological data
FIGURE 3. Gap data matrix for 28S D2 sequences of geometrid species used to create a phylogeny for the Australian Geometridae. (0) gap absent; (1) gap present; () inapplicable.
FIGURE 9 in Molecular relationships of the Australian Ennominae (Lepidoptera: Geometridae) and implications for the phylogeny of the Geometridae from molecular and morphological data
FIGURE 9. Strict consensus cladogram of 3629 equally most parsimonious trees obtained using step matrix unweighted parsimony analysis of the 28S D2 fragment of geometrid species used to create a phylogeny for the Australian Geometridae. A = Archiearinae, Al = Alsophilinae, Am = Amphypyrinae, Az = Azelinini, B = Boarmiini, Ca = Caberini, Ci = Cidariini, C = Colotoini, D = Drepanidae, E = Ennomini, G = Geometrinae, Ha = Hadeninae, H = Hydriomenini, La = Larentiinae, L = Lithinini, M = Macariini, Nac = Nacophorini, N = Noctuinae, O = Oenochrominae, Op = Operophterini, S = Sterrhinae, U = unplaced, X = Xanthorhoini.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.