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7,849 results for “Conservancy”
Data and Code for: Landscape-level synergistic and antagonistic effects among conservation measures drive wild bee densities and species richness
<p>Data and R code for 'Landscape-level synergistic and antagonistic effects among conservation measures drive wild bee densities and species richness'.</p> <p>Information about the files can be found in the README file.</p>
Confocal microscopy data associated with "The conserved aphid saliva chemosensory protein effector Mp10 targets plant AMSH deubiquitinases at cellular membranes to suppress pattern-triggered immunity"
<p><strong>Confocal microscopy data as described in "The conserved aphid saliva chemosensory protein effector Mp10 targets plant AMSH deubiquitinases at cellular membranes to suppress pattern-triggered immunity".</strong></p> <p> </p> <p>Data relate to Figure 2 (“Mp10 interacts with AMSH deubiquitinases in yeast and plants”) involving FLIM-FRET imaging data to determine the interaction between eGFP-tagged <em>Myzus persicae </em>Mp10 and mCherry-tagged <em>Nicotiana benthamiana </em>AMSH proteins in plant cells; and Figure 6 (“Mp10 affects the abundance and localisation of cell-surface receptor-like kinases) involving confocal microscopy showing the effect of Mp10-expression on the localisation of the GFP-tagged FLS2 receptor-kinase protein, and it’s colocalization with RFP-tagged markers of the plasma membrane and the tonoplast in plant cells.</p> <p>Constructs encoding fluorescent protein fusions were transformed into <em>Agrobacterium tumefaciens </em>GV3101, and mixed Agrobacterium cultures were infiltrated into mature leaves of <em>N. benthamiana </em>plants to co-express the desired combinations of proteins. All image data was gathered from lower epidermal leaf cells of infiltrated leaves 2-3 days post infiltration.</p> <p> </p> <p><strong>FLIM-FRET assays.</strong></p> <p>eGFP-tagged Mp10, or eGFP-alone, was co-expressed with mCherry-tagged AMSH proteins, or mCherry fused to aquaeorin in <em>N. benthamiana</em> via agroinfiltration as described above. Lower epidermal cells of leaf sections were imaged 2-3 days after infiltration using a Leica Stellaris 8. Images were captured detecting fluorescence from eGFP (WLL laser, ex.488 nm, em 509-534 nm.) mCherry (lWLL aser, ex. 587 nm em 603-625 nm.) and chlorophyll (WLL laser, ex 587 nm. em 687-712 nm.). Regions of cells showing expression of both eGFP- and mCherry- tagged proteins but lacking chlorophyll were selected for FLIM analysis to avoid bleed through of chlorophyll fluorescence into the eGFP chanel. Fluorescence lifetime data of EGFP were collected from these regions in FLIM mode (WLL laser ex. 488nm, em 525-530 nm.), data were collected at 128x128 resolution until 1000 photons per pixel were collected for the most intense regions of the image. Instrument response function was captured using erythrosine on each day of data collection. FLIM data were analysed using Leica LASX FLIM FCS software. Fluorescence lifetime decay curves of free eGFP control samples were modelled as a 2-component exponential function, and all samples from each experimental set were modelled against the fluorescence lifetime from the corresponding control samples to derive values for fluorescent lifetime and %FRET efficiency for each image collected. %FRET efficiency was mapped to the images and phasor plots were generated for regions with the highest and lowest FRET efficiency, showing that the FRET signal was associated with a clockwise shift on the phasor plot consistent with <em>bona-fide </em>FRET. Full experimental metadata for each image set are included within the .lif files.</p> <p> </p> <p><strong>FLS2-GFP localisation experiments.</strong></p> <p>Confocal microscopy analysis was performed on a Leica TCS SP8X confocal DM6 microscope with a 63x water-immersion objective, using Leica Application Suite X (LAS X) software (3.5.7.23225). eGFP and chlorophyll signals were excited by a 488 nm Argon laser with emission, respectively, at 495–545 nm and 690-710 nm. RFP signal was excited by a 590 nm white light laser (WLL) with emission at 605–650 nm. Full experimental metadata for each image set are included within the .lif files.</p> <p> </p> <p>Leica Image Files (.lif) that contain multiple images including metadata associated with image acquisition and processing.</p> <p> </p> <p>FLIM030823.lif</p> <p>FLIM130724.lif</p> <p>FLIM140623.lif</p> <p>FLIM160623.lif</p> <p>FLIM240523.lif</p> <p>FLIM250523.lif</p> <p>Files include FLIM-FRET data as shown in Figure 2 parts D-L.</p> <p>FLIM-data-files.xlsx includes a description of the individual image filenames, and the combinations of fluorophore imaged in each.</p> <p> </p> <p>Fig6cSlFLS2-gfp_Mp10-RFP.lif</p> <p>Fig6c-SlFLS2-GFP_EV-RFP.lif</p> <p>Correspond to Figure 6 C showing co-expression of RFP-tagged Mp10 (or free RFP control) co-expressed with GFP-tagged FLS2</p> <p> </p> <p>20230828_SlFLS2-GFP_Flag-Mp10_Flag-alone_Remorin-RFP-3-3-1x.lif</p> <p>20230828_SlFLS2-GFP_Flag-Mp10_Flag-alone_Remorin-RFP-3-3-3x.lif</p> <p>20230828_SlFLS2-GFP_Flag-Mp10_Flag-alone_Remorin-RFP-4-2-3x.lif</p> <p>0230828_SlFLS2-GFP_Flag-Mp10_Flag-alone_Remorin-RFP4-2-1x.lif</p> <p>Correspond to Figure 6 D showing co-expression of FLAG-tagged Mp10 (or free FLAG control) co-expressed with GFP-tagged FLS2 together with RFP-tagged plasma membrane marker Remorin</p> <p> </p> <p>20230911_SlFLS2-GFP_Flag-Mp10_Flag-alone_StSUC4-RFP-14-5-1x.lif</p> <p>20230911_SlFLS2-GFP_Flag-Mp10_Flag-alone_StSUC4-RFP-14-5-3x.lif</p> <p>20230911_SlFLS2-GFP_Flag-Mp10_Flag-alone_StSUC4-RFP-16-1-1x.lif</p> <p>20230911_SlFLS2-GFP_Flag-Mp10_Flag-alone_StSUC4-RFP-16-1a-3x.lif</p> <p>20230911_SlFLS2-GFP_Flag-Mp10_Flag-alone_StSUC4-RFP-16-1b-1x.lif</p> <p>Correspond to Figure 6 E showing co-expression of FLAG-tagged Mp10 (or free FLAG control) co-expressed with GFP-tagged FLS2 together with RFP-tagged tonoplast marker SUC4.</p> <p> </p> <p>We are grateful to the John Innes Centre (JIC) Bioimaging Platform for training and technical support</p> <p>This work was funded by UK Research and Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) grants to SAH (BB/V008544/1 and BB/N009169/1), Additional Support was provided by the BBSRC Institute Strategy Programmes (BBS/E/J/000PR9797 and BBS/E/JI/230001B) awarded to the John Innes Centre (JIC). The JIC is grant-aided by the John Innes Foundation.</p> <p> </p>
Data from: Assortative mating among animals of captive and wild origin following experimental conservation releases
Captive breeding is a high profile management tool used for conserving threatened species. However, the inevitable consequence of generations in captivity is broad scale and often-rapid phenotypic divergence between captive and wild individuals, through environmental differences and genetic processes. Although poorly understood, mate choice preference is one of the changes that may occur in captivity that could have important implications for the reintroduction success of captive-bred animals. We bred wild-caught house mice for three generations to examine mating patterns and reproductive outcomes when these animals were simultaneously released into multiple outdoor enclosures with wild conspecifics. At release, there were significant differences in phenotypic (e.g. body mass) and genetic measures (e.g. Gst and F) between captive-bred and wild adult mice. Furthermore, 83% of offspring produced post-release were of same source parentage, inferring pronounced assortative mating. Our findings suggest that captive breeding may affect mating preferences, with potentially adverse implications for the success of threatened species reintroduction programmes.
Data from: Highly conserved Z and molecularly diverged W chromosomes in the fish genus Triportheus (Characiformes, Triportheidae)
The main objectives of this study were to test: (1) whether the W-chromosome differentiation matches to species' evolutionary divergence (phylogenetic concordance) and (2) whether sex chromosomes share a common ancestor within a congeneric group. The monophyletic genus Triportheus (Characiformes, Triportheidae) was the model group for this study. All species in this genus so far analyzed have ZW sex chromosome system, where the Z is always the largest chromosome of the karyotype, whereas the W chromosome is highly variable ranging from almost homomorphic to highly heteromorphic. We applied conventional and molecular cytogenetic approaches including C-banding, ribosomal DNA mapping, comparative genomic hybridization (CGH) and cross-species whole chromosome painting (WCP) to test our questions. We developed Z- and W-chromosome paints from T. auritus for cross-species WCP and performed CGH in a representative species (T. signatus) to decipher level of homologies and rates of differentiation of W chromosomes. Our study revealed that the ZW sex chromosome system had a common origin, showing highly conserved Z chromosomes and remarkably divergent W chromosomes. Notably, the W chromosomes have evolved to different shapes and sequence contents within ~15–25 Myr of divergence time. Such differentiation highlights a dynamic process of W-chromosome evolution within congeneric species of Triportheus.
Data from: Evolution and conservation of Characidium sex chromosomes
Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used restriction-site associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heteromorphic ZW/ZZ sex chromosomes. We screened 9863 single-nucleotide polymorphisms (SNPs), corresponding to ~1 marker/100 kb distributed across the genome for sex-linked variation. With this data set, we identified 26 female-specific RAD loci, putatively located on the W chromosome, as well as 148 sex-associated SNPs showing significant differentiation (average FST=0.144) between males and females, and therefore in regions of more recent divergence between the Z and W chromosomes. In addition, we detected 25 RAD loci showing extreme heterozygote deficiency in females but which were in Hardy–Weinberg equilibrium in males, consistent with degeneration of the W chromosome and therefore female hemizygosity. We validated seven female-specific and two sex-associated markers in a larger sample of C. gomesi, of which three localised to the W chromosome, thereby providing useful markers for sexing wild samples. Validated markers were evaluated in other populations and species of the genus Characidium, this exploration suggesting a rapid turnover of W-specific repetitive elements. Together, our analyses point to a complex origin for the sex chromosome of C. gomesi and highlight the utility of RAD-seq for studying the composition and evolution of sex chromosomes systems in wild populations.
Data from: Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes
The free-living (FL) and particle-attached (PA) marine microbial communities have repeatedly been proved to differ in their diversity and composition in the photic ocean and also recently in the bathypelagic ocean at a global scale. However, although high taxonomic ranks have been proved to exhibit preferences for a PA or FL mode of life, it remains poorly understood whether two clear lifestyles do exist and how these are distributed across the prokaryotic phylogeny. We studied the FL and PA prokaryotes in 30 stations distributed worldwide within the bathypelagic oceanic realm using high throughput sequencing of their 16S rDNA. A high proportion of the bathypelagic prokaryotes were mostly found either attached to particles or freely in the surrounding water but rarely in both types of environments. In particular, this trait was deeply conserved through their phylogeny suggesting that the deep-ocean particles and the surrounding water constitute two highly distinct niches and that transitions from one to the other have been rare at an evolutionary time-scale. As a consequence, PA and FL communities had clear alpha- and beta-diversity differences that exceeded the global-scale geographical variation. Our study organizes the bathypelagic prokaryotic diversity into a reasonable number of ecologically coherent taxa regarding their association to particles, a first step for understanding which are the microbes responsible for the processing of the dissolved and particulate pools of organic matter that have a very different biogeochemical role in the deep ocean. --
Figure 3 in Bird diversity and conservation in the southern coast of Santa Catarina state, Brazil
Figure 3. Records of conservation concern birds in the southern coast of Santa Catarina state, Brazil. (A) Larus atlanticus, Balneário Rincão; (B) Thalasseus maximus, Balneário Rincão; (C) Tachuris rubrigastra, Balneário Gaivota; (D) Xanthopsar flavus (yellow bird) and Xolmis dominicanus (black-and-white bird), Balneário Gaivota; (E) Xolmis dominicanus, Balneário Gaivota.
Fig. 16 in A Reassessment of Saltuarius swaini (Lacertilia: Diplodactylidae) in Southeastern Queensland and New South Wales; Two New Taxa, Phylogeny, Biogeography and Conservation
Fig. 16. AM R160423, Saltuarius swaini, Mt. Warning NP (28°24'05"S 153°16'54"E) NSW
Figures 1–5. Polyphylla anivallis. 1–4 in Natural history, ecology, and conservation of the genus Polyphylla Harris, 1841. 1. New species from the southwestern United States and Baja California, Mexico, with notes on distribution and synonymy (Coleoptera: Scarabaeidae: Melolonthinae)
Figures 1–5. Polyphylla anivallis. 1–4) Holotype male. 5) Left elytron of paratype male.
Figures 6–10. Polyphylla koso. 6–9 in Natural history, ecology, and conservation of the genus Polyphylla Harris, 1841. 1. New species from the southwestern United States and Baja California, Mexico, with notes on distribution and synonymy (Coleoptera: Scarabaeidae: Melolonthinae)
Figures 6–10. Polyphylla koso. 6–9) Holotype male. 10) Left elytron of paratype male.
Figures 20–27. Polyphylla socorriana. 20, 22, 24–26 in Natural history, ecology, and conservation of the genus Polyphylla Harris, 1841. 1. New species from the southwestern United States and Baja California, Mexico, with notes on distribution and synonymy (Coleoptera: Scarabaeidae: Melolonthinae)
Figures 20–27. Polyphylla socorriana. 20, 22, 24–26) Holotype male. 21, 23, 27) Allotype female.
Fig 4 from: Ngoute CO, Hunter D, Lecoq M (2021) Perception and knowledge of grasshoppers among indigenous communities in tropical forest areas of southern Cameroon: Ecosystem conservation, food security, and health. Journal of Orthoptera Research 30(2): 117-130. https://doi.org/10.3897/jor.30.64266
Fig 4 Impact of pest activities on the productivity of crops.
Fig 1 from: Ngoute CO, Hunter D, Lecoq M (2021) Perception and knowledge of grasshoppers among indigenous communities in tropical forest areas of southern Cameroon: Ecosystem conservation, food security, and health. Journal of Orthoptera Research 30(2): 117-130. https://doi.org/10.3897/jor.30.64266
Fig 1 Study sites in Cameroon.
Fig 2 from: Ngoute CO, Hunter D, Lecoq M (2021) Perception and knowledge of grasshoppers among indigenous communities in tropical forest areas of southern Cameroon: Ecosystem conservation, food security, and health. Journal of Orthoptera Research 30(2): 117-130. https://doi.org/10.3897/jor.30.64266
Fig 2 Abundance of grasshoppers in different landscapes (A), forests (B), and seasons (C).
Rediscovery of the greater chestnut weevil highlights the power of digital platforms in biodiversity research and conservation
Open the record for dataset details and reuse information.
Figure 5 from: Murphy R, Berry K, Edwards T, Leviton A, Lathrop A, Riedle J (2011) The dazed and confused identity of Agassiz's land tortoise, Gopherus agassizii (Testudines: Testudinidae) with the description of a new species and its consequences for conservation. ZooKeys 113: 39-71. https://doi.org/10.3897/zookeys.113.1353
Figure 5 - Ventral view of the holotype of Gopherus agassizii, USNM 7888. Black bar is 3 cm.
Figure 4 from: Murphy R, Berry K, Edwards T, Leviton A, Lathrop A, Riedle J (2011) The dazed and confused identity of Agassiz's land tortoise, Gopherus agassizii (Testudines: Testudinidae) with the description of a new species and its consequences for conservation. ZooKeys 113: 39-71. https://doi.org/10.3897/zookeys.113.1353
Figure 4 - Dorsal view of the lectotype of Gopherus agassizii, USNM 7888. Black bar is 3 cm.
Figure 14 from: Murphy R, Berry K, Edwards T, Leviton A, Lathrop A, Riedle J (2011) The dazed and confused identity of Agassiz's land tortoise, Gopherus agassizii (Testudines: Testudinidae) with the description of a new species and its consequences for conservation. ZooKeys 113: 39-71. https://doi.org/10.3897/zookeys.113.1353
Figure 14 - Right, lateral view of the head of the holotype of Gopherus morafkai, CAS 33867.
Figure 13 from: Murphy R, Berry K, Edwards T, Leviton A, Lathrop A, Riedle J (2011) The dazed and confused identity of Agassiz's land tortoise, Gopherus agassizii (Testudines: Testudinidae) with the description of a new species and its consequences for conservation. ZooKeys 113: 39-71. https://doi.org/10.3897/zookeys.113.1353
Figure 13 - Detail of head scales of the holotype of Gopherus morafkai, CAS 33867.
Figure 11 from: Murphy R, Berry K, Edwards T, Leviton A, Lathrop A, Riedle J (2011) The dazed and confused identity of Agassiz's land tortoise, Gopherus agassizii (Testudines: Testudinidae) with the description of a new species and its consequences for conservation. ZooKeys 113: 39-71. https://doi.org/10.3897/zookeys.113.1353
Figure 11 - Anterior view of the holotype of Gopherus morafkai, CAS 33867.
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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)
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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.