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3,878 results for “Molecular Data”
Research data supporting "Nanoscale molecular quantification of stem cell-hydrogel interactions"
<p>Raw data supporting: Maynard S. et al., 2020, ACS Nano, DOI: 10.1021/acsnano.0c07428.</p>
Data from: Molecular characterization of resistance to soybean rust (Phakopsora pachyrhizi Syd. & Syd.) in soybean cultivar DT 2000 (PI 635999)
Resistance to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd. & Syd., has been identified in many soybean germplasm accessions and is conferred by either dominant or recessive genes that have been mapped to six independent loci (Rpp1 –Rpp6), but No U.S. cultivars are resistant to SBR. The cultivar DT 2000 (PI 635999) has resistance to P. pachyrhizi isolates and field populations from the United States as well as Vietnam. A F6:7 recombinant inbred line (RIL) population derived from Williams 82 × DT 2000 was used to identify genomic regions associated with resistance to SBR in the field in Ha Noi, Vietnam, and in Quincy, Florida, in 2008. Bulked segregant analysis (BSA) was conducted using the soybean single nucleotide polymorphism (SNP) USLP 1.0 panel along with simple sequence repeat (SSR) markers to detect regions of the genome associated with resistance. BSA identified four BARC_SNP markers near the Rpp3 locus on chromosome (Chr.) 6. Genetic analysis identified an additional genomic region around the Rpp4 locus on Chr. 18 that was significantly associated with variation in the area under disease progress curve (AUDPC) values and sporulation in Vietnam. Molecular markers tightly linked to the DT 2000 resistance alleles on Chrs. 6 and 18 will be useful for marker-assisted selection and backcrossing in order to pyramid these genes with other available SBR resistance genes to develop new varieties with enhanced and durable resistance to SBR.
Data from: Molecular xenomonitoring using mosquitoes to map lymphatic filariasis after mass drug administration in American Samoa
Background: Mass drug administration (MDA) programs have dramatically reduced lymphatic filariasis (LF) incidence in many areas around the globe, including American Samoa. As infection rates decline and MDA programs end, efficient and sensitive methods for detecting infections are needed to monitor for recrudescence. Molecular methods, collectively termed 'molecular xenomonitoring,' can identify parasite DNA or RNA in human blood-feeding mosquitoes. We tested mosquitoes trapped throughout the inhabited islands of American Samoa to identify areas of possible continuing LF transmission after completion of MDA. Methodology/Principle Findings: Mosquitoes were collected using BG Sentinel traps from most of the villages on American Samoa's largest island, Tutuila, and all major villages on the smaller islands of Aunu'u, Ofu, Olosega, and Ta'u. Real-time PCR was used to detect Wuchereria bancrofti DNA in pools of ≤20 mosquitoes, and PoolScreen software was used to infer territory-wide prevalences of W. bancrofti DNA in the mosquitoes. Wuchereria bancrofti DNA was found in mosquitoes from 16 out of the 27 village areas sampled on Tutuila and Aunu'u islands but none of the five villages on the Manu'a islands of Ofu, Olosega, and Ta'u. The overall 95% confidence interval estimate for W. bancrofti DNA prevalence in the LF vector Ae. polynesiensis was 0.20–0.39%, and parasite DNA was also detected in pools of Culex quinquefasciatus, Aedes aegypti, and Aedes (Finlaya) spp. Conclusions/Significance: Our results suggest low but widespread prevalence of LF on Tutuila and Aunu'u where 98% of the population resides, but not Ofu, Olosega, and Ta'u islands. Molecular xenomonitoring can help identify areas of possible LF transmission, but its use in the LF elimination program in American Samoa is limited by the need for more efficient mosquito collection methods and a better understanding of the relationship between prevalence of W. bancrofti DNA in mosquitoes and infection and transmission rates in humans.
Data from: Optical and molecular signatures of dissolved organic matter reflect anthropogenic influence in a coastal river, Northeast China
Sources and molecular composition of dissolved organic matter (DOM) in coastal rivers have been tightly linked with its reactivity and fate, thus influencing element and nutrient cycling. The DOM in coastal rivers is usually sourced from both terrestrial and marine inputs, with further complication by anthropogenic activities, which is less understood in coastal rivers located near populated industrial regions. In this study, DOM in a typical anthropogenically influenced coastal river, Daliao River, was analyzed for optical analyses and for molecular composition via Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to give a better scope of composition and sources of DOM. The DOM was enriched in autochthonous and anthropogenic inputs at upstream sites according to high chlorophyll a concentrations, strong protein-like fluorescence, and nonoxygen heteroatomic CHOS formulae (19–24% by relative peak intensity) detected by FT-ICR MS analysis. A series of surfactant-like formulae, indicative of wastewater inputs, were identified and showed a decreasing trend from upstream to the river mouth. Compared with large world rivers, the DOM of Daliao River is characterized by higher abundances of heteroatomic (excluding O) formulae and molecular lability, which is likely caused by strong autochthonous and anthropogenic inputs. In general, we demonstrate that in addition to optical properties, the molecular composition can assess the specific anthropogenic imprints and molecular lability of DOM, which is essential for constraining sources and identifying processes during the transit of DOM from the river to estuary with increasing urbanization and industrialization.
Data from: An integrative anatomical, morphological, micromorphological and molecular approach to Turkish epidendroid and orchidoid species (Orchidaceae)
We aimed to reveal the morphological, anatomical and micromorphological features of 36 Turkish orchids in detail. UPGMA cluster analysis was based on the presence or absence of anatomical, morphological and micromorphological characters such as root tuber, leaf or flower part structure, pit, sclerenchymatic sheath, vascular bundle shape, crystal and starch, exodermis and endodermis structure, stomata type, bulliform cell in roots, shoots or leaves, and surface structure like papillae, hairs and ornamentation on flower parts, leaves, fruits and seeds. In a phylogenetic framework, nuclear ribosomal ITS were used to investigate diversity in orchid species belonging to 12 genera. The combined evaluation of phylogenetic study, Bayesian Inference analysis obtained from anatomical, morphological and micromorphogical and ITS data confirmed that they can be more effective in assessing orchids having identification problems.
Data from: Convergently evolved toxic secondary metabolites in plants drive the parallel molecular evolution of insect resistance
Natural selection imposed by natural toxins has led to striking levels of convergent evolution at the molecular level. Cardiac glycosides represent a group of plant toxins that block the Na,K-ATPase, a vital membrane protein in animals. Several herbivorous insects have convergently evolved resistant Na,K-ATPases, and in some species, convergent gene duplications have also arisen, likely to cope with pleiotropic costs of resistance. To understand the genetic basis and predictability of these adaptations, we studied five independent lineages of leaf-mining flies (Diptera: Agromyzidae). These flies have colonized host plants in four botanical families that convergently evolved cardiac glycosides of two structural types: cardenolides and bufadienolides. We compared each of six fly species feeding on such plants to a phylogenetically related but nonadapted species. Irrespective of the type of cardiac glycoside in the host plant, five out of six exposed species displayed substitutions in the cardiac glycoside–binding site of the Na,K-ATPase that were previously described in other insect orders; in only one species was the gene duplicated. In vitro assays of nervous tissue extractions confirmed that the substitutions lead to increased resistance of the Na,K-ATPase. Our results demonstrate that target site insensitivity of Na,K-ATPase is a common response to dietary cardiac glycosides leading to highly predictable amino acid changes; nonetheless, convergent evolution of gene duplication for this multifunctional enzyme appears more constrained.
Data from: Taller plants have lower rates of molecular evolution
Rates of molecular evolution have a central role in our understanding of many aspects of species' biology. However, the causes of variation in rates of molecular evolution remain poorly understood, particularly in plants. Here we show that height accounts for about one-fifth of the among-lineage rate variation in the chloroplast and nuclear genomes of plants. This relationship holds across 138 families of flowering plants, and when accounting for variation in species richness, temperature, ultraviolet radiation, latitude and growth form. Our observations can be explained by a link between height and rates of genome copying in plants, and we propose a mechanistic hypothesis to account for this—the 'rate of mitosis' hypothesis. This hypothesis has the potential to explain many disparate observations about rates of molecular evolution across the tree of life. Our results have implications for understanding the evolutionary history and future of plant lineages in a changing world.
Data from: On polyphyly of the former section Ochlopoa Asch. et Graebn. and hybridogenic section Acroleucae Tzvelev et Prob. (Poa L., Poaceae): insights from the molecular phylogenetic analysis
In this study, sequence data of the nuclear region ITS1-5.8S rDNA-ITS2 and the chloroplast region trnL-F as well as few morphological characters were examined trying to elucidate the relationships among known annual bluegrasses. It was shown that all taxa from the aggregate P. annua distinguished by lemma characters and growth form are identical according to ITS and trnL-trnF data wherein all ITS sequences of P. annua aggr. are the same as P. supina and all trnL-trnF sequences are homologous with those of P. infirma. Also we haven't found any differences between unusual samples of P. supina with short spinules on their panicle branches and typical plants according to the sequence data though Siberian samples have minor distinction in trnL-trnF region. Our analysis showed hybrid origin of Asian annual bluegrasses (see also Nosov et al. 2015, Soreng et al. 2017). Their maternal genome is close to the section Homalopoa, but their ITS sequences were different. ITS sequences of some annual Asian bluegrasses group with the section Stenopoa and for other species (close to previous from the morphological traits) they fall into clade with the section Malacanthae. The latter group is distant from the sect. Ochlopoa and is better to be treated as a separate section, Acroleucae. American annual bluegrasses are heterogeneous and also rather distant from the sect. Ochlopoa. P. chapmaniana, species with cleistogamic flowers, is nested with basal Subantarctic sections falling out of its previously described affinity group. It is closer to the sect. Ochlopoa than other annual American bluegrasses. Thus, studied annual species in fact belong to the four independent evolutionary lines (or six including genus Eremopoa and Turkish Poa jubata – Cabi et al. 2017) one of which, Acroleucae, also passed triple reticulation event. As in previous studies our analysis didn't support the generic status of sect. Ochlopoa.
Data from: Molecular determinants of agonist selectivity in glutamate-gated chloride channels which likely explain the agonist selectivity of the vertebrate glycine and GABAA-ρ receptors
Orthologous Cys-loop glutamate-gated chloride channels (GluClR's) have been cloned and described electrophysiologically and pharmacologically in arthropods and nematodes (both members of the invertebrate ecdysozoan superphylum). Recently, GluClR's from Aplysia californica (a mollusc from the lophotrochozoan superphylum) have been cloned and similarly studied. In spite of sharing a common function, the ecdysozoan and lophotrochozoan receptors have been shown by phylogenetic analyses to have evolved independently. The recent crystallization of the GluClR from C. elegans revealed the binding pocket of the nematode receptor. An alignment of the protein sequences of the nematode and molluscan GluClRs showed that the Aplysia receptor does not contain all of the residues defining the binding mode of the ecdysozoan receptor. That the two receptors have slightly different binding modes is not surprising since earlier electrophysiological and pharmacological experiments had suggested that they were differentially responsive to certain agonists. Knowledge of the structure of the C. elegans GluClR has permitted us to generate a homology model of the binding pocket of the Aplysia receptor. We have analyzed the differences between the two binding modes and evaluated the relative significance of their non-common residues. We have compared the GluClRs electrophysiologically and pharmacologically and we have used site-directed mutagenesis on both receptor types to test predictions made from the model. Finally, we propose an explanation derived from the model for why the nematode receptors are gated only by glutamate, whereas the molluscan receptors can also be activated by β-alanine, GABA and taurine. Like the Aplysia receptor, the vertebrate glycine and GABAA-ρ receptors also respond to these other agonists. An alignment of the sequences of the molluscan and vertebrate receptors shows that the reasons we have given for the ability of the other agonists to activate the Aplysia receptor also explain the agonist profile seen in the glycine and GABAA-ρ receptors.
Data from: Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway
Background: Starch is the main source of carbon storage in the Archaeplastida. The Starch Biosynthesis Pathway (SBP) emerged from cytosolic glycogen metabolism shortly after plastid endosymbiosis and was redirected to the plastid stroma during the green lineage divergence. The SBP is a complex network of genes, most of which are members of large multigene families. While some gene duplications occurred in the Archaeplastida ancestor, most were generated during the SBP redirection process, and the remaining few paralogs were generated through compartmentalization or tissue specialization during the evolution of the land plants. In the present study, we tested models of duplicated gene evolution in order to understand the evolutionary forces that have led to the development of SBP in angiosperms. We combined phylogenetic analyses and tests on the rates of evolution along branches emerging from major duplication events in six gene families encoding SBP enzymes. Results: We found evidence of positive selection along branches following cytosolic or plastidial specialization in two starch phosphorylases and identified numerous residues that exhibited changes in volume, polarity or charge. Starch synthases, branching and debranching enzymes functional specializations were also accompanied by accelerated evolution. However, none of the sites targeted by selection corresponded to known functional domains, catalytic or regulatory. Interestingly, among the 13 duplications tested, 7 exhibited evidence of positive selection in both branches emerging from the duplication, 2 in only one branch, and 4 in none of the branches. Conclusions: The majority of duplications were followed by accelerated evolution targeting specific residues along both branches. This pattern was consistent with the optimization of the two sub-functions originally fulfilled by the ancestral gene before duplication. Our results thereby provide strong support to the so-called "Escape from Adaptive Conflict" (EAC) model. Because none of the residues targeted by selection occurred in characterized functional domains, we propose that enzyme specialization has occurred through subtle changes in affinity, activity or interaction with other enzymes in complex formation, while the basic function defined by the catalytic domain has been maintained.
Data from: Multiplex PCR targeting lineage specific SNPs ‐ A highly efficient and simple approach to block out predator sequences in molecular gut content analysis
Background: Food webs form the basis of biological communities, though empirical research has been hindered by difficulties in quantifying interactions. Metabarcoding from predator gut content extractions with universal primers promises to provide simple and rapid insights into food web interactions. However, the highly overabundant predator DNA often completely outcompetes that of the digested prey DNA during PCR, impeding the ability to assess the abundance and diversity of prey items. Methods: Focusing on the issue of overabundance of predator DNA amplified by a commonly used COI primer pair, we use predator lineage-specific SNPs at the 3'-end of PCR primers to selectively block out predators from amplification. While this approach largely prevents predator amplification, it retains high taxonomic versatility for prey lineages. We introduce a novel multilocus assay, targeting four nuclear and mitochondrial rDNA markers and test our approach in a diverse set of spiders from 12 families. We estimate the recovered prey DNA proportions and compare the taxonomic composition of prey communities between markers. Using a feeding experiment, we also explore recovery of prey DNA over time. Results: While commonly used COI primers yield low and very unpredictable amounts of prey DNA, our assay allows for a considerable and consistent prey enrichment across all tested species. The recovered prey's taxonomic composition is comparable between markers and supports results acquired by COI. The new marker set can be amplified in a simple multiplex PCR, considerably reducing the necessary workload. Conclusions: Our multi-locus approach allows the generation of an unprecedented amount of prey data at low cost and effort. Lineage specific PCR is taxonomically versatile and could readily be adapted to any prey-predator interaction, opening up the opportunity for community-wide studies on food web interactions.
Data for manuscripts "Experimental study of the effect of molecular collision frequency and adsorption capacity on gas seepage flux in coal rocks"
<p>Data for manuscripts "Experimental study of the effect of molecular collision frequency and adsorption capacity on gas seepage flux in coal rocks"</p>
Figures 18 from: Xiudan W, Luan L, Yang Z (2024) Discovery of a new species of Synergus (Hymenoptera, Cynipidae, Synergini) based on morphology and molecular data. ZooKeys 1193: 81-94. https://doi.org/10.3897/zookeys.1193.105756
Figures 18 General appearance of Synergus dilatatus sp. nov. galls on twigs of Quercus variabilis.
Figure 4 from: Zhu A-H, Liu Z-B, Li Y, Liu H-G, Yuan Y, He S-H (2024) Molecular and morphological data reveal two new species of Tropicoporus (Hymenochaetaceae, Basidiomycota) from Australia and tropical Asia. MycoKeys 103: 57-70. https://doi.org/10.3897/mycokeys.103.119027
Figure 4 Basidiomata of Tropicoporus zuzaneae (Dai 22171, holotype).
Figure 2 from: Zhu A-H, Liu Z-B, Li Y, Liu H-G, Yuan Y, He S-H (2024) Molecular and morphological data reveal two new species of Tropicoporus (Hymenochaetaceae, Basidiomycota) from Australia and tropical Asia. MycoKeys 103: 57-70. https://doi.org/10.3897/mycokeys.103.119027
Figure 2 Basidiomata of Tropicoporus oceanianus (Dai 18859, holotype).
Data Set_Exploring the Molecular Mechanisms of Endothelial Dysfunction Affecting Myocardial Infarction by Integrating Multiple Datasets with In Vivo Experimental Validation
Open the record for dataset details and reuse information.
Data from: The draft genome of Primula veris yields insights into the molecular basis of heterostyly
[No abstract entered]
Data from: Aster rupestris (Asteraceae, Astereae), a new species from Guizhou, China: Evidence from morphological, molecular and cytological date
[No abstract entered]
Figure 1 from: Esmaeili-Rineh S, Mirghaffari SA, Sharifi M (2017) The description of a new species of Niphargus from Iran based on morphological and molecular data. Subterranean Biology 22: 43-58. https://doi.org/10.3897/subtbiol.22.11286
Figure 1 - Distribution map of the members of genus Niphargus in Iran.
Figure 2 from: Xu K-W, Han Y-T, Dong Y-R, Guo J-Q, Mao L-F, Liao W-B (2024) Asplenium guodanum (Aspleniaceae), a distinct new fern species from northern Guangdong, China, based on morphological data and molecular phylogeny. PhytoKeys 241: 191-200. https://doi.org/10.3897/phytokeys.241.122789
Figure 2 Micromorphology of Asplenium guodanum sp. nov. A–E spore F scale. Scale bar: 1 mm.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.