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Data from: Molecular evolution of the nuclear factor (erythroid-derived 2)-like 2 gene Nrf2 in Old World fruit bats (Chiroptera: Pteropodidae)
Mammals developed antioxidant systems to defend against oxidative damage in their daily life. Enzymatic antioxidants and low molecular weight antioxidants (LMWAs) constitute major parts of the antioxidant systems. Nuclear factor (erythroid-derived 2)-like 2 (Nrf2, encoded by the Nrf2 gene) is a central transcriptional regulator, regulating transcription, of many antioxidant enzymes. Frugivorous bats eat large amounts of fruits that contain high levels of LMWAs such as vitamin C, thus, a reliance on LMWAs might greatly reduce the need for antioxidant enzymes in comparison to insectivorous bats. Therefore, it is possible that frugivorous bats have a reduced need for Nrf2 function due to their substantial intake of diet-antioxidants. To test whether the Nrf2 gene has undergone relaxed evolution in fruit-eating bats, we obtained Nrf2 sequences from 16 species of bats, including four Old World fruit bats (Pteropodidae) and one New World fruit bat (Phyllostomidae). Our molecular evolutionary analyses revealed changes in the selection pressure acting on Nrf2 gene and identified seven specific amino acid substitutions that occurred on the ancestral lineage leading to Old World fruit bats. Biochemical experiments were conducted to examine Nrf2 in Old World fruit bats and showed that the amount of catalase, which is regulated by Nrf2, was significantly lower in the brain, heart and liver of Old World fruit bats despite higher levels of Nrf2 protein in Old World fruit bats. Computational predictions suggest that three of these seven amino acid replacements might be deleterious to Nrf2 function. Therefore, the results suggest that Nrf2 gene might have experienced relaxed constraint in Old World fruit bats, however, we cannot rule out the possibility of positive selection. Our study provides the first data on the molecular adaptation of Nrf2 gene in frugivorous bats in compensation to the increased levels of LWMAs from their fruit-diet.
Data from: Patterns of tree mortality in a temperate deciduous forest derived from a large forest dynamics plot
Tree mortality is one of the most influential drivers of forest dynamics, and characterizing patterns of tree mortality is critical to understanding forest dynamics and ecosystem function in the present era of global change. Here, we use a unique data set of mortality in a temperate deciduous forest to characterize rates and drivers of mortality. At the 25.6-ha Center for Tropical Forest Science—Forest Global Earth Observatory forest dynamics plot at the Smithsonian Conservation Biology Institute (Virginia, USA), we conducted two full tree censuses in 2008 and 2013 and then tracked mortality over the next 2 years (2014 and 2015). Overall, the mortality rate, m, of stems ≥10 cm diameter was 1.3–2.1%/yr. Biomass mortality, M, was 1.9–3.4 Mg·ha−1·yr−1 at the stand level (0.6–1.1%/yr of biomass), less than biomass gains from growth and recruitment, resulting in net live biomass accumulation. Small stems died at the highest rate; however, contributions to M increased toward larger size classes. Most species had m < 2%/yr and M < 0.25 Mg·ha−1·yr−1 (<3%/yr of biomass), whereas two to four species had anomalously high mortality rates during each census period, accounting for 15–24% of m (n = 2, Cercis canadensis, Ulmus species) and 39–75% of M (n = 4 Quercus species). Stems that died, whether or not in association with mechanical damage, tended to grow more slowly in preceding years than surviving stems and, for certain shade-intolerant species, tended to be in neighborhoods with higher basal area. These findings show how relatively fine-scale mortality processes contribute to stand-level compositional change and carbon cycling. The mortality patterns reported here will provide a valuable basis for understanding future disturbance events within eastern deciduous forests and for comparing across forest types.
Data from: Strain identification and quorum sensing inhibition characterization of marine-derived Rhizobium sp. NAO1
A novel strategy for combating pathogens is through the ongoing development and use of anti-quorum sensing (QS) treatments such as therapeutic bacteria or their anti-QS substances. Relatively little is known about the bacteria that inhabit the open ocean and of their potential anti-pathogenic attributes; thus, in an initiative to identify these types of therapeutic bacteria, planktonic microbes from the North Atlantic Ocean were collected, isolated, cultured and screened for anti-QS activity. Screening analysis identified one such strain, Rhizobium sp. NAO1. Extracts of Rhizobium sp. NAO1 were identified via ultra-performance liquid chromatography (UPLC) analysis. They were shown to contain N-acyl homoserine lactone (AHL)-based QS analogues (in particular, the N-butyryl homoserine lactone (C4-AHL) analogue) and could disrupt biofilm formation by Pseudomonas aeruginosa PAO1. QS inhibition was confirmed using confocal scanning laser microscopy and growth curves, and it was shown to occur in a dose-dependent manner without affecting bacterial growth. Secondary metabolites of Rhizobium sp. NAO1 inhibited PAO1 pathogenicity by downregulating AHL-mediated virulence factors such as elastase activity and siderophore production. Furthermore, as a result of biofilm structure damage, the secondary metabolite products of Rhizobium sp. NAO1 significantly increased the sensitivity of PAO1 to aminoglycoside antibiotics. Our results demonstrated that Rhizobium sp. strain NAO1 has the ability to disrupt P. aeruginosa PAO1 biofilm architecture, in addition to attenuating P. aeruginosa PAO1 virulence factor production and pathogenicity. Therefore, the newly identified ocean-derived Rhizobium sp. NAO1 has the potential to serve as a QS inhibitor and may be a new microbial resource for drug development.
Organelle calcium-derived voltage oscillations in pacemaker neurons drive the motor program for food-seeking behavior in Aplysia
<p><span>An atypical neuronal pacemaker mechanism, based on rhythmic intracellular calcium store release in an identified pair of interneurons (B63) and resulting oscillation of the neurons' membrane potential, acts as an autonomous releaser for the irregular occurrences of the <span>motor program for food-seeking behavior</span> in Aplysia. The rhythmic variations of the membrane potential in B63 neurons were analyzed by Fast Fourier Transform (FFT) analysis in a cycle period bandwidth of 512 s to 8 s. The resulting power spectral density periodograms were used to identify oscillation periods of peak magnitude. The periodograms were computed from the FFT frequency spectrograms by converting the frequency band (in Hz) to its reciprocal, period (in secs). These analysis were performed in isolated buccal ganglia preparations bathed in artifical sea water (ASW), in 'Low Ca+Co' saline to block chemical synapses, or in 'Low Ca+Co' saline and after an intracellular injection of organelle membrane calcium channel blocker heparin into either the bilateral B63 or B31 neurons. The oscillations of B63 membrane potential that were recorded in ASW persisted in 'Low Ca+Co', but were suppressed after heparin injection specifically into B63.</span></p>
Derived data for: "Magnetic reconnection near the planet as a possible driver of Jupiter's mysterious polar auroras"
<p>Derived data for "Magnetic reconnection near the planet as a possible driver of Jupiter’s mysterious polar auroras", accepted for publication in the Journal of Geophysical Research: Space Physics.</p>
FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 in Taxonomic identity of the Iranian diploid Triticum as evidenced by nrDNA ITS analysis
FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 sequences inferred by the Neighbor-Joining method using the Kimura 2- parameter model; all bootstrap values over 50% are shown. Sequences obtained from the NCBI are marked with the sequence accession numbers. Aegilops tauschii sequence was defined as an outgroup in the analysis. Clades 1 and 2 are associated with Triticum monococcum s. lat. and T. urartu, respectively.
Primary NMR data: A Facile Approach to the Synthesis of 3-Acylisoxazole Derivatives by the Use of Reusable Solid Acid Catalysts
<p>This dataset is primary NMR data in the paper: A Facile Approach to the Synthesis of 3-Acylisoxazole Derivatives by the Use of Reusable Solid Acid Catalysts.</p>
Figure 1. Haplotype network derived from 704 in Repeated sampling adds to the genetic diversity of Lepidochelys olivacea (Eschscholtz 1829) olive ridley sea turtle
Figure 1. Haplotype network derived from 704 bp mitochondrial D-loop fragment. Circle sizes are proportional to the frequency of each haplotype. The black circles are hypothetical haplotypes not sampled. Each colour represents the ocean basin where the sample was taken: blue is Pacific Ocean, yellow is Indian Ocean, red is Atlantic Ocean, and green is Indo-Pacific Ocean.
Figure 5. Minimum spanning haplotype network derived from a 658 base-pair cytochrome c oxidase subunit I in Six degrees of separation in barnacles? Assessing genetic variability in the sea-turtle epibiont Stomatolepas elegans (Costa) among turtles, beaches and oceans
Figure 5. Minimum spanning haplotype network derived from a 658 base-pair cytochrome c oxidase subunit I (COI) fragment from 57 Stomatolepas elegans collected from nine different Lepidochelys olivacea nesting on Playa Teopa, Jalisco, Mexico, six S. elegans from Caretta caretta from the western Atlantic, and six S. praegustator from C. caretta from the western Atlantic. Circle sizes are proportional to the frequency of each haplotype, with haplotype 1 being most common. Coloured pie slices are also proportional, and represent the number of S. elegans from each turtle characterized by the respective haplotype. Colours represent the nine Mexican turtles randomly sampled for S. elegans populations. Open circles with numbers indicate Atlantic haplotypes. Solid black circles designate hypothetical missing haplotypes. The network includes S. elegans haplotypes 1–21, and S. praegustator haplotypes 19, 26–30. Haplotypes 1–17, shown in colour, represent Jalisco, Mexico specimens collected from nine different turtles in the Pacific, and haplotypes 18–21 and 26–30, shown as unshaded circles, represent southeastern United States Atlantic specimens collected from six different C. caretta (see Table 1).
Figure 1 in Bot flies (Insecta: Oestridae, part) and Glossinidae-Hippoboscidae derive from basal Ephydroidea, not Calyptratae
Figure 1. Male postabdomen, as viewed from the left, of a hypothetical basal ephydroid (see text for sources of information).
Derived Optimal Linear Combination Evapotranspiration (DOLCE)
<p>The Derived Optimal Linear Combination Evapotranspiration (DOLCE) dataset consists of monthly Evapotranspiration (ET) and their associated uncertainty on a global scale. DOLCE is derived at 0.5 spatial resolution and monthly temporal resolution over the period 2000-2009.</p> <p>DOLCE is derived by weighting six existent global ET products based on their ability to match site-level data from 159 globally distributed flux tower sites.</p> <p>The six evapotranspiration products are: GLEAM V2A, GLEAM V2B, GLEAM V3A, MOD16, MPIBGC and PML .</p> <p>DOLCE is a mosaic of three tiers, we derive each tier from a different weighting ensemble and subset of FLUXNET data. The dominant part (i.e. tier1) involves six ET products and data from 138 flux towers, tier2 involves 5 products and 151 flux towers, while tier3 involved 2 products and 159 sites.</p> <p>This dataset was produced by Dr Sanaa Hobeichi as part of her PhD thesis and of the Centre of Excellence for Climate System Science "The role of land surface forcing and feedbacks for regional climate" research program.</p>
FIGURE 10 in Twelve new Demospongiae (Porifera) from Chilean fjords, with remarks upon sponge-derived biogeographic compartments in the SE Pacific
FIGURE 10. Skeletal architecture and spicule complement of Clathria mytilifila sp. nov. (A–I, IZUA-POR 147, holotype), Neopodospongia tupecomareni sp. nov. (J–Q, IZUA-POR 148, holotype; MNRJ 8223 and MNRJ 12927, paratypes), and Myxilla (Burtonanchora) araucana sp. nov. (R–V, MNRJ 8220, holotype). C. mytilifila sp. nov.: A, transverse section showing skeletal architecture near base; B, principal choanosomal subtylostyles; C, detail of base of principal choanosomal subtylostyle; D, ectosomal auxiliary subtylostyle; E, detail of base of ectosomal auxiliary subtylostyle; F, accessory acanthostyles I and II; G, detail of spination of accessory acanthostyle II; H, palmate isochelae; I, toxa. N. tupecomareni sp. nov.: J, transverse section showing skeletal architecture near surface (J', detail of ectosomal region highlighting abundance of spinorhabds); K, megascleres; L, detail of extremities of both megascleres in K; M–P, large spinorhabds; Q, small spinorhabds. M. (B.) araucana sp. nov.: R, transverse section showing choanosomal skeletal architecture; S, choanosomal style; T, ectosomal subtylote; U, details of extremities of ectosomal subtylote; V, anchorate isochelae. Scale bars: A, S, 100 µm; B, D, F, J', T, 50 µm; C, E, G, H, U, 5 µm; L, 10 µm; J, 800 µm; R, 200 µm; M–Q, V, W, X, 20 µm.
FIGURE 9 in Twelve new Demospongiae (Porifera) from Chilean fjords, with remarks upon sponge-derived biogeographic compartments in the SE Pacific
FIGURE 9. Anisodiscorhabds in detail: Latrunculia ciruela sp. nov. (A, IZUA-POR 145, holotype); Latrunculia copihuensis sp. nov. (B, RBINSc-IG 32233-POR 9915, holotype); Latrunculia verenae sp. nov. (C, IZUA-POR 146, holotype); Latrunculia yepayek sp. nov. (D, RBINSc-IG 32233-POR 9940, holotype). Scale bar: 20 µm.
FIGURE 6 in Twelve new Demospongiae (Porifera) from Chilean fjords, with remarks upon sponge-derived biogeographic compartments in the SE Pacific
FIGURE 6. In situ photographs of Latrunculia ciruela sp. nov. (A, IZUA-POR 145, holotype), Latrunculia copihuensis sp. nov. (B, RBINSc-IG 32233-POR 9915, holotype), Latrunculia verenae sp. nov. (C, IZUA-POR 146, holotype), Latrunculia yepayek sp. nov. (D, RBINSc-IG 32233-POR 9940, holotype), Clathria mytilifila sp. nov. (E, MNRJ 8198, holotype), Neopodospongia tupecomareni sp. nov. (F, MNRJ 10787, paratype), and Myxilla araucana sp. nov. (G, MNRJ 8220, holotype). Scale bars: A–D, 5 cm; E–G, 2 cm.
FIGURE 3 in Twelve new Demospongiae (Porifera) from Chilean fjords, with remarks upon sponge-derived biogeographic compartments in the SE Pacific
FIGURE 3. Skeletal architecture and spicule complement of Suberites cranium sp. nov. (A–E) and Tethya melinka sp. nov. (F– P). S. cranium sp. nov.: A, skeletal architecture on transverse view (MNRJ 8944, paratype)—insert, ectosomal brushes of tylostyles-I. B–E, IZUA-POR 140 (holotype); B, tylostyles-I (ectosomal); C, heads of tylostyles-I in detail; D, tylostyle-II (choanosomal); E, heads of tylostyles-II in detail. T. melinka sp. nov. (IZUA-POR 141, holotype): F, ectosomal and subectosomal skeletal architecture on transverse view; G, deeper choanosomal mesohyle with apparent larger strongylasters; H, strongyloxea; I, strongyloxea in detail; J, spheraster; K, oxyaster-like precursor of megasters; L, larger strongylaster; M–O, intermediary sized strongylasters; P, smaller strongylaster (tylaster). Scale bars: A, 500 µm; A', 200 µm; B, D, G, H, 100 µm; C, E, J–P, 20 µm; F, 200 µm; I, 50 µm.
FIGURE 5 in Twelve new Demospongiae (Porifera) from Chilean fjords, with remarks upon sponge-derived biogeographic compartments in the SE Pacific
FIGURE 5. Skeletal architecture and spicule complement of Haliclona (Reniera) caduca sp. nov. (A–B, IZUA-POR 142, holotype), Oceanapia guaiteca sp. nov. (C–E, MNRJ 10927and 10943, paratypes), and Oceanapia spinisphaera sp. nov. (F–I, MHNG 52781, fragment from holotype). H. (R.) caduca sp. nov.: A, skeletal architecture in transverse view; B, spicules. O. guaiteca sp. nov.: C, skeletal architecture in tangential view; D, oxeote and strongylote megascleres; E, sigma microsclere. O. spinisphaera sp. nov.: F, skeletal architecture on tangential view; G, skeletal architecture on transverse view; H, oxeote megascleres; I, sigma microsclere. Scale bars: A, 200 µm; B, D, H, 100 µm; C, F–G, 500 µm; E, I, 10 µm.
FIGURE 8 in Twelve new Demospongiae (Porifera) from Chilean fjords, with remarks upon sponge-derived biogeographic compartments in the SE Pacific
FIGURE 8. Latrunculia ciruela sp. nov. (A–R): A–N, anisodiscorhabds; O, (subtylo)style; P, oxea; Q–R, details of oxeas. Holotype (IZUA-POR 145): F, J. Paratypes: MNRJ 9186, M–N; MNRJ 10811, G, P–R; MNRJ 10844, C, E; MNRJ 10849, K; MNRJ 10855, D, I, O; MNRJ 10861, A, L; MNRJ 10921, H; MNRJ 12928, B. Latrunculia copihuensis sp. nov. (S–AL, RBINSc-IG 32233-POR 9915, holotype): S–AF, anisodiscorhabds; AG–AH, oxeas; AJ–AL, details of (subtylo)styles. Latrunculia verenae sp. nov. (AM–BD, type series): AM–AZ, anisodiscorhabds; BA–BB, acanthostyles; BC–BD, details of acanthostyles. Holotype (IZUA-POR 146): AM–AS, BA. Paratypes: MNRJ 10914, AT–AV; MNRJ 10942, AW–AZ, BB–BD. Latrunculia yepayek sp. nov. (BE–BW, RBINSc-IG 32233-POR 9940, holotype): BE–BR, anisodiscorhabds; BS–BU, styles; BV–BW, details of styles. Scale bars: A–N, Q–AF, AJ–AZ, BE–BR, 10 µm; O–P, AG–AI, BA–BB, BS–BW, 100 µm; BC–BD, BU–BV, 25 µm.
FIGURE 4 in Twelve new Demospongiae (Porifera) from Chilean fjords, with remarks upon sponge-derived biogeographic compartments in the SE Pacific
FIGURE 4. Spicule complement of Suberites puncturatus Thiele, 1905 (A, holotype, ZMB 3275), S. ruber Thiele, 1905 (B, holotype, ZMB 3274), Tethya deformis Thiele, 1898 (C, MHNG 10012), and T. sarai Desqueyroux-Faúndez & van Soest, 1997 (D, MHNG 21024—fragment from holotype). Scale bars: A–B, 200 µm; C–D, 100 µm.
FIGURE 7 in Twelve new Demospongiae (Porifera) from Chilean fjords, with remarks upon sponge-derived biogeographic compartments in the SE Pacific
FIGURE 7. Skeletal architectures in transverse sections of Latrunculia ciruela sp. nov. (A, IZUA-POR 145, holotype), Latrunculia copihuensis sp. nov. (B, RBINSc-IG 32233-POR 9915, holotype), Latrunculia verenae sp. nov. (C, IZUA-POR 146, holotype), and Latrunculia yepayek sp. nov. (D, RBINSc-IG 32233-POR 9940, holotype). Scale bars: A–D, 500 µm.
FIGURE 1. Map illustrating the Chilean coast sectors and the collecting localities which samples studied here originated from. A in Twelve new Demospongiae (Porifera) from Chilean fjords, with remarks upon sponge-derived biogeographic compartments in the SE Pacific
FIGURE 1. Map illustrating the Chilean coast sectors and the collecting localities which samples studied here originated from. A. Chiloé Island and adjacent Gulfs of Ancud and Corcovado (1, Palvitad Fjord). B. Gulf of Ancud, with Fjords Quintupeu (2), Comau (3) and Reñihué (4). C. Gulf of Corcovado with Quellon (5, Piedra Lille), Guaitecas Archipelago (6, Ascension IslandMelinka; 7, channel between Betecoi and Clotilde Islands; 8, Canelo Islet) and Piti Palena Fjord (9). D. Adalberto Channel (10) and Bernardo Fjord (11). E. Copihue Channel (12). Scale bars: large map, 400 km; A, 100 km; B–E, 10 km.
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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.