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6,383 results for “isolates”
Optimization of nuclei isolation for high-molecular weight DNA extraction of wild plants
<p><strong>Optimization of nuclei isolation for high-molecular weight DNA extraction from wild plants</strong></p> <p><strong>Authors</strong></p> <p>Irene Martínez-García<sup>1</sup>; Martina Degli Alberti<sup>2</sup>; Aureliano, Bombarely<sup>2</sup>; Mario Xavier Ruiz-González<sup>1</sup>; Santiago Vilanova<sup>1</sup>; Silvia Manrique<sup>1</sup></p> <p> </p> <p><strong>Affiliations</strong></p> <p>1 Instituto Universitario para la Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia (UPV), Camino de Vera s/n 46022, Valencia, Spain) 2 Instituto de Biología Molecular y Celular de Plantas (IBMCP) Primo-Yufera, Consejo Superior de Investigaciones Científicas (CSIC)- Universidad Politécnica de Valencia (UPV), Camino de Vera s/n 46022, Valencia, Spain)</p> <p> </p> <p><strong>Abstract</strong></p> <p>Obtaining high-quality, high-molecular-weight (HMW) DNA is mandatory for constructing reference genomes, yet it remains a significant challenge, particularly for non-model plant species. Many plants contain polysaccharides and secondary metabolites such as polyphenols and tannins, which hinder DNA extraction. Exposure to multiple environmental stresses along their lives exacerbate this issue in wild plants collected from nature, as they may synthesize additional compounds that impair DNA extraction.</p> <p>This study investigates the efficacy of various DNA extraction protocols on four recalcitrant plant species—<em>Pistacia lentiscus</em>, <em>Phyllirea angustifolia</em>, <em>Sarcocornia fruticosa</em>, and <em>Limbarda crithmoides</em>—each possessing unique traits complicating DNA extraction (e.g., succulence, lignification, coloration). Samples were collected from El Saler (Valencia), and multiple protocols for nuclei isolation and DNA extraction were tested. The results were systematically evaluated to compile a comprehensive best practices guide, aiding researchers in selecting optimal methods tailored to their species of interest. This guide serves as a valuable resource for future endeavours in genome research, facilitating advancements in understanding and conservation efforts for diverse plant species.</p> <p>Funding: </p> <p>This work was supported by Erasmus+ Program (to MD), Programa María Zambrano 2021 (to SM and MXRG, UPV Ministerio de Universidades, Plan de Recuperación, Transformación y Resiliencia - Financiado por la Unión Europea – NextGenerationEU) and Catalan Initiative For the Earth Biogenome Project (Call1A-2023 to SM and call 2-2023 to AB and SM) and Primeros Proyectos UPV (PAID-06-22 to MXRG).</p>
Linked collectors and determiners for: Revision of the Old World species of the genus Tephritis (Diptera, Tephritidae) with a pair of isolated apical spots.
Natural history specimen data linked to collectors and determiners held within, "Revision of the Old World species of the genus Tephritis (Diptera, Tephritidae) with a pair of isolated apical spots". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/23c131dd-5ac6-4ce7-ba1b-7baf3c4e5e34">https://bionomia.net/dataset/23c131dd-5ac6-4ce7-ba1b-7baf3c4e5e34</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/23c131dd-5ac6-4ce7-ba1b-7baf3c4e5e34">https://gbif.org/dataset/23c131dd-5ac6-4ce7-ba1b-7baf3c4e5e34</a>. Formatted as a Frictionless Data package.
Integrated Omics-Based Discovery of Novel Genes, Secondary Metabolites Clusters, and Small Molecules in Penicillium spp. with Disparate Fungal Isolates
<p><em><span>Penicillium expansum</span></em><span> is a ubiquitous postharvest pathogen of pome fruit that causes blue mold decay of apple fruit while another member of the genus, <em>P. chrysogenum</em><span>,</span><em> </em>is a well-studied saprophyte used for antibiotic and small molecule production. While these two fungi have been investigated individually, the recent discovery of <em>P. chrysogenum </em>hindering <em>P. expansum</em> apple fruit infection has not been well studied. To shed light on this interaction between the two species, we conducted a comparative transcriptomic, metabolomic, and genomic study. Global transcriptional and metabolomic outputs were disparate between the species, nearly identical for the <em>P. chrysogenum </em>isolates, and different between <em>P. expansum </em>isolates. Further, the two <em>P. chrysogenum</em> genomes revealed secondary metabolite gene clusters that differed from <em>P. expansum</em>. This included the absence of an intact patulin gene cluster in <em>P. chrysogenum</em>, which corroborates the metabolomic data regarding the species’ inability to produce patulin. Additionally, <em>P. expansum </em>virulence gene homologues were identified in <em>P. chrysogenum </em>and were similarly transcriptionally regulated <em>in vitro</em>. Molecules with potential antimicrobial activity, and phytohormones like indole-3-acetic acid (IAA), were detected for the first time in <em>P. expansum</em> while pharmacological compounds like the well-studied antibiotic penicillin G were identified in <em>P. chrysogenum</em> culture supernatants. Our findings provide new omics-based resources that enable the study of small molecule production of interest, the potential of <em>Penicillium</em>-derived antimicrobials for postharvest decay control, and <em>P.</em> <em>expansum’s</em> metabolites roles in host-pathogen interactions. </span></p>
Fig. 19. Isolated p4 in A Possible Heptaxodontine and Other Caviidan Rodents from the Quaternary of Jamaica
Fig. 19. Isolated p4 (AMNHP 140816) of capromyid Isolobodon portoricensis from Salt River Bay, St. Croix (?Amerindian site), SEMs at low and high magnification. (A) Transverse section at low magnification, showing distribution of enamel (en), dentine (de), and cementum (ce). (B) Closeup of large boxed area in A, showing cementum and enamel. (C) Closeup of small boxed
Fig. 18. Isolated p4 in A Possible Heptaxodontine and Other Caviidan Rodents from the Quaternary of Jamaica
Fig. 18. Isolated p4 (AMNHP 140817) of Antillean heptaxodontine Elasmodontomys obliquus from Toraño Cave, near Utuado, Puerto Rico, SEMs at low and higher magnification. While this specimen was being cut, the apical end broke off, apparently along an undetected developmental boundary (feature 1 in A). The boundary as seen on the crown end is in contact with the tape (feature 2) used to position the specimen for SEM. (A) Longitudinal section through crown end at low magnification, showing distribution of enamel, dentine and cementum (occlusal surface faces left). (B) Closeup of boxed area in A, showing characteristic histological differences between cementum (ce), enamel (en), and dentine (de). (C) Transverse section through apical end at low magnification; pc, pulp chamber. (D) Closeup of boxed area in C, showing secondary dentine on wall of pulp chamber. Secondary dentine is less irregular in this taxon than in Amblyrhiza (fig. 17).
Magnetic-Free Silicon Nitride Integrated Optical Isolator (Original Data)
<p>This is the raw dataset for the paper titled "Magnetic-Free Silicon Nitride Integrated Optical Isolator", which includes the original data and theoretical code. </p>
P-elements strengthen reproductive isolation within the Drosophila simulans species complex
Determining mechanisms that underlie reproductive isolation is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of reproductive isolation between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause reproductive isolation between PE-containing (P) and PE-lacking (M) lineages of the same species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P-D. simulans father and an M-mother from a sister species exhibit lower F1 female fecundity than crosses involving an M-D. simulans father and an M-sister-species mother. We also find that another TE, I-element, might play a minor role on determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in isolation. --
Original Data for Manuscript "Energy and Momentum Distribution of Surface Plasmon-induced Hot Carriers Isolated via Spatiotemporal Separation"
<p>Raw data of the time-dependent energy density calculation and time-resolved photoemission electron microscopy (TR-PEEM) measurements used in the manuscript.</p> <p>A preprint of the manuscript is available on arXiv: <a href="https://arxiv.org/abs/2107.14277">2107.14277</a></p> <p>The manuscript was published in <em>ACS Nano</em> 2021, 15, 12, 19559-19569 <a href="https://doi.org/10.1021/acsnano.1c06586">10.1021/acsnano.1c06586</a></p> <p>The data is provided in hdf5 files, which were produced using the snomtools python package (<a href="https://github.com/hartelt/snomtools">availale on github</a>) and can be read with any <a href="https://support.hdfgroup.org/HDF5/tools5desc.html">hdf5 compatible software</a>. The calculated data was produced as described in Ref.1 with the parameters given in the manuscript. For the experimental data, each zip file contains the raw data (hdf5 Files) as well as the PEEM settings used (sav Files as output from the experiment control software) for the respective measurement.</p> <p>Parts of the manuscript that are generated from the calculated data [calculation_energy_density.zip]:</p> <ul> <li>Figure 2 A</li> <li>Figure S2</li> </ul> <p>Parts of the manuscript that are evaluated from the PEEM real space dataset [PEEM_realspace.zip]:</p> <ul> <li>Figure 2 B</li> <li>Figure 3</li> <li>Figure S1</li> <li>Figure S3</li> <li>Figure S4</li> <li>Movie S2 [timeseries_binned_fermi.avi] in the supplementary material</li> </ul> <p>Parts of the manuscript that are evaluated from the PEEM momentum space (momentum microscopy) SPP dataset [PEEM_k-space_timesteps_SPP.zip]:</p> <ul> <li>Figure 4 (in combination with the pump pulse reference dataset)</li> <li>Figure S5 B</li> <li>Figure S6 B</li> <li>Figure S7 B</li> </ul> <p>Parts of the manuscript that are evaluated from the PEEM momentum space (momentum microscopy) pump pulse reference dataset [PEEM_k-space_timesteps_pump.zip]:</p> <ul> <li>Figure 4 (in combination with the SPP dataset)</li> <li>Figure S5 A</li> <li>Figure S6 A</li> <li>Figure S7 A</li> </ul> <p>Parts of the manuscript that are evaluated from the PEEM momentum space (momentum microscopy) data of the full timetrace, combining SPP dataset [PEEM_k-space_full-timetrace_SPP.zip] and pump pulse reference dataset [PEEM_k-space_full-timetrace_pump.zip]:</p> <ul> <li>Figure S8</li> </ul>
Data for: The genetic basis of floral mechanical isolation between two hummingbird-pollinated Neotropical understory herbs
<p>Floral divergence can contribute to reproductive isolation among plant lineages, and thus provides an opportunity to study the genetics of speciation, including the number, effect size, mode of action, and interactions of quantitative trait loci (QTL). Moreover, flowers represent suites of functionally interrelated traits, but it is unclear to what extent the phenotypic integration of the flower is underlain by a shared genetic architecture, which could facilitate or constrain correlated evolution of floral traits. Here, we examine the genetic architecture of floral morphological traits involved in an evolutionary switch from bill to forehead pollen placement between two species of hummingbird-pollinated Neotropical understory herbs that are reproductively isolated by these floral differences. For the majority of traits, we find multiple QTL of relatively small effect spread throughout the genome. We also find substantial colocalization and alignment of effects of QTL underlying different floral traits that function together to promote outcrossing and reduce heterospecific pollen transfer. Our results are consistent with adaptive pleiotropy or linkage of many coadapted genes, either of which could have facilitated a response to correlated selection and helped to stabilize divergent phenotypes in the face of low levels of hybridization. Moreover, our results indicate that floral mechanical isolation can be consistent with an infinitesimal model of adaptation.</p>
Recombination and In-silico protein modelling and functional characterization of copLAB genes from Trinidadian Xanthomonas campestris and melonis isolates
<p>RDP, GARD, RaptorX and InterProScan outputs relating to the publication tentatively titled "Heavy metal resistance islands associated with a putative Tn in Trinidadian copper resistant <em>Xanthomonas campestris </em>and <em>melonis </em>strains are strongly linked to homologs from the <em>Stenotrophomonas </em>genus"</p>
Fig. 4 in Mammal Diversity And Conservation In A Small Isolated Forest Of Southern Thailand
Fig. 4. Activity periods of photo-captured animals (N>10) in the Hala-Bala Wildlife Sanctuary, Thailand, from Nov.2004 to Oct.2007. Species are listed in order of decreasing frequency of diurnal activity. Numbers in parentheses indicate sample size.
Fig. 3 in Mammal Diversity And Conservation In A Small Isolated Forest Of Southern Thailand
Fig. 3. Rarefaction curves for photo-captured animal assemblages in primary and logged forests over 3 years (thick line: first year; open circles: second year; solid circles: third year) in the Hala-Bala Wildlife Sanctuary, Thailand. The dotted line represents the 95% CI for the first year. For clarity, the 95% CI for the second and third years are not presented.
Fig. 1 in Mammal Diversity And Conservation In A Small Isolated Forest Of Southern Thailand
Fig. 1. Hala-Bala Wildlife Sanctuary (Bala forest) in southern Thailand, and the road cutting through the forest and associated trails on either side, as used by Gale and Thong-Aree (2006).
Fig. 2 in Mammal Diversity And Conservation In A Small Isolated Forest Of Southern Thailand
Fig. 2. Rarefaction curves for photo-captured animal assemblages in three forest types (thick line: primary forest; open circles: logged forest; solid circles: hill forest) in the Hala-Bala Wildlife Sanctuary, Thailand, from Nov.2004 to Oct.2007. The dotted line represents the 95% CI for the primary forest. For clarity, the 95% CI for the logged and hill forests are not presented.
Figure 1 in Distribution of microarthropods across altitude and aspect in the sub-Antarctic: climate change implications for an isolated oceanic island
Figure 1 Interaction plots of mite and springtail species richness (S) and abundance (N) at low, middle and high altitudes on the eastern and western aspect of Marion Island (weighted means ± 95 % confidence intervals). Groups not sharing letters differ significantly (p <0.05). Model results provided in Table 2 and Appendix 2.
Text-fig. 2. A – First small excavation trench in the newly discovered fossiliferous outcrop area of the Ploužnice lake horizon, locality "Small Ravine" south of the village Ploužnice on the slope of road No. 286. Typical are the red, violet and varicoloured tuffaceous siltstones. Semily Formation, Late Stephanian, Krkonoše Piedmont Basin. B – Basal part of fossiliferous 12 cm to14 cm thick reddish to purple-red tuffaceous siltstone bed from the trench in Text-fig. 2A. Internal bedding is expressed as horizontal but with diffuse changes in grain size from fine silt to coarse, fine sandy silt. Intercalated in places are 3 to 5 mm thick layers (indicated by arrows) with patchy concentrations of isolated fish remains, especially in the first 3 centimetres of this siltstone layer. The large white spot at 2.5 cm is a coprolite fragment. in Fossil Fauna And Flora Of A Re-Discovered Locality In The Late Carboniferous Ploužnice Horizon Of The Krkonoše Piedmont Basin, Bohemian Massif
Text-fig. 2. A – First small excavation trench in the newly discovered fossiliferous outcrop area of the Ploužnice lake horizon, locality "Small Ravine" south of the village Ploužnice on the slope of road No. 286. Typical are the red, violet and varicoloured tuffaceous siltstones. Semily Formation, Late Stephanian, Krkonoše Piedmont Basin. B – Basal part of fossiliferous 12 cm to14 cm thick reddish to purple-red tuffaceous siltstone bed from the trench in Text-fig. 2A. Internal bedding is expressed as horizontal but with diffuse changes in grain size from fine silt to coarse, fine sandy silt. Intercalated in places are 3 to 5 mm thick layers (indicated by arrows) with patchy concentrations of isolated fish remains, especially in the first 3 centimetres of this siltstone layer. The large white spot at 2.5 cm is a coprolite fragment.
Text-fig. 5. Tumidopteris astra sp. nov., holotype GIN 4851/343h, morphology of sori. a, b: line tracing of the sorus; c: an isolated spore preserved on the sporangium. Scale 500 Μm (a, b), 20 Μm (c). in A New Species Of The Genus Tumidopteris Naugolnykh From The Permian Of The Pechora Cis-Urals, Russia
Text-fig. 5. Tumidopteris astra sp. nov., holotype GIN 4851/343h, morphology of sori. a, b: line tracing of the sorus; c: an isolated spore preserved on the sporangium. Scale 500 Μm (a, b), 20 Μm (c).
Text-fig. 42. Scanning electron microscope (SEM) images of monocolpate pollen of Piercipollis sp. 1 (a–c) from an isolated anther and Piercipollis sp. 2 (d–f) from a coprolite (not shown); Torres Vedras locality, Portugal. a) Narrow elongate anther that yielded the pollen in (b) and (c); b) Distal view of pollen grain showing well-developed reticulum that is only loosely attached to the foot layer; note the smooth foot layer (arrowhead) of a grain from which the reticulum has become detached; c) Reticulum showing the smooth muri and long columellae that are mostly detached from the foot layer; d–f) Pollen grains in distal (d, e), and lateral views (f) showing the very long colpus and the well-developed reticulum only loosely attached to the smooth surface of the foot layer; note the main body of the grains (foot layer) does not fill out the whole space of the reticulum (f). Specimens, TV44-S148218 (a–c), TV142-S170216 (d–f). Scale bars 300 Μm (a), 6 Μm (b, d–f), 3 Μm (c). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 42. Scanning electron microscope (SEM) images of monocolpate pollen of Piercipollis sp. 1 (a–c) from an isolated anther and Piercipollis sp. 2 (d–f) from a coprolite (not shown); Torres Vedras locality, Portugal. a) Narrow elongate anther that yielded the pollen in (b) and (c); b) Distal view of pollen grain showing well-developed reticulum that is only loosely attached to the foot layer; note the smooth foot layer (arrowhead) of a grain from which the reticulum has become detached; c) Reticulum showing the smooth muri and long columellae that are mostly detached from the foot layer; d–f) Pollen grains in distal (d, e), and lateral views (f) showing the very long colpus and the well-developed reticulum only loosely attached to the smooth surface of the foot layer; note the main body of the grains (foot layer) does not fill out the whole space of the reticulum (f). Specimens, TV44-S148218 (a–c), TV142-S170216 (d–f). Scale bars 300 Μm (a), 6 Μm (b, d–f), 3 Μm (c).
Text-fig. 19. Scanning electron microscope (SEM; d, e) and synchrotron radiation X-ray tomographic microscopy (SRXTM; a–c) images of a seed of Kvacekispermum costatum sp. nov. (a–c) and Kvacekispermum sp. (d, e); Torres Vedras locality, Portugal. a, b) Isolated, abraded seeds showing densely spaced longitudinal ridges; c) Detail of abraded seed in (b) showing surface of endotesta with imprints of crystals; d) Isolated, abraded seed showing longitudinal ridges; e) Abraded seed surface showing surface of endotesta with imprints of crystals. Specimens, TV44-S174098 (holotype; a), TV38-S174099 (b, c), TV43-S174612 (d, e). Scale bars 300 Μm (a, b, d), 50 Μm (c, e). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 19. Scanning electron microscope (SEM; d, e) and synchrotron radiation X-ray tomographic microscopy (SRXTM; a–c) images of a seed of Kvacekispermum costatum sp. nov. (a–c) and Kvacekispermum sp. (d, e); Torres Vedras locality, Portugal. a, b) Isolated, abraded seeds showing densely spaced longitudinal ridges; c) Detail of abraded seed in (b) showing surface of endotesta with imprints of crystals; d) Isolated, abraded seed showing longitudinal ridges; e) Abraded seed surface showing surface of endotesta with imprints of crystals. Specimens, TV44-S174098 (holotype; a), TV38-S174099 (b, c), TV43-S174612 (d, e). Scale bars 300 Μm (a, b, d), 50 Μm (c, e).
Text-fig. 17. Scanning electron microscope (SEM) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images of a fruit of Canrightia elongata sp. nov. (a–g) and isolated Canrightia-like seeds (h–j); Torres Vedras locality, Portugal. a–c) Holotype; fruit in lateral view showing four fused tepals at the base (c, upper arrowheads) and prominent cavities in the fruit wall formed by scattered oil bodies and possible subtending bract (c, lower arrowhead); d) Transverse section (SRXTM orthoslice xy1510) through the fruit showing three locules, one with the remains of the endothelium (top left, 1), the other two (2, 3) with remains of presumed endosperm tissue; note that the locule to the right (3) is crushed; e, f) Radial longitudinal (e; SRXTM orthoslice xz1212) in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 17. Scanning electron microscope (SEM) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images of a fruit of Canrightia elongata sp. nov. (a–g) and isolated Canrightia-like seeds (h–j); Torres Vedras locality, Portugal. a–c) Holotype; fruit in lateral view showing four fused tepals at the base (c, upper arrowheads) and prominent cavities in the fruit wall formed by scattered oil bodies and possible subtending bract (c, lower arrowhead); d) Transverse section (SRXTM orthoslice xy1510) through the fruit showing three locules, one with the remains of the endothelium (top left, 1), the other two (2, 3) with remains of presumed endosperm tissue; note that the locule to the right (3) is crushed; e, f) Radial longitudinal (e; SRXTM orthoslice xz1212)
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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
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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
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