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Fig. 4 in Ultrastructural and immunocytochemical investigation of paramylon combined with new 18S rDNA-based secondary structure analysis clarifies phylogenetic affiliation of Entosiphon sulcatum (Euglenida: Euglenozoa)
Fig. 4 Schematic phylogram combining molecular and morphological findings corroborating phylogenetic position of Entosiphon as sister group of Helicales within Euglenida. States of key characters are illustrated tabularly: black squares code presence and blanks absence, e.g., paramylon is present only in Entosiphon and Helicales. Unpaired base in 18S rDNA helix 44 is present in primordial petalomonads and kinetoplastids, but absent in more derived taxa within respective groups. White Roman numerals depict heterogeneous dispersal of different types of feeding apparatuses (FA) according to Triemer and Farmer (1991), white Arabic numerals count for number of rods in FA. Heterolobosea and Jakobida represent outgroup taxa
Fig. 2 in Gut-content analysis in four species, combined with comparative analysis of trophic traits, suggests an araneophagous habit for the entire family Palpimanidae (Araneae)
Fig. 2 Comparison of relative 1 conspeccfics spcders cnsects 1 frequency of conspecifics (can- A B nibalism), heterospecific spiders 0.9 0.9 (araneophagy), and insects in 0.8 0.8 the gut of P . gibbulus A, P . 0.7 0.7 potteri B , Diaphorocellus C and frequency Otiothops D . Proportions are 0.6 0.6 estimated per all individuals in e 0.5 0.5 a class (male, female, juvenile). 0.4 0.4 Frequency of cannibalism can be overestimated (see "Discus- Rela 0.3 0.3 sion" for more details), thus 0.2 0.2 should be interpreted with 0.1 0.1 caution 0 0 male female female juvencle adult juvencle adult
Fig. 3 in Gut-content analysis in four species, combined with comparative analysis of trophic traits, suggests an araneophagous habit for the entire family Palpimanidae (Araneae)
Fig. 3 Phylogeny of Palpimanidae plus three other families on the genus level, with estimates of the probabilities of each of five traits at nodes. The fuller the symbol, the higher the probability of a presence of the trait. For trait values at terminals see Table S7
Combined transcriptomics and metabolomics analysis reveals the mechanism behind the pollen abortion in early stage among male sterile lines of alfalfa
<p><span>This study investigates early-stage anther development in cytoplasmic male sterile (CMS) alfalfa lines (MSJN1A) compared to their isotypic maintainer line (MSJN1B). Histological analyses revealed abnormal degradation of tapetal cells post-meiosis in the CMS line. Notably, during the early mononuclear stage, the central vacuole in the microspores was absent, leading to evident pollen abortion. These findings suggest that pollen abortion in the CMS line is associated with the delayed disintegration of the tapetum and structural anomalies in microspore vacuoles.</span><span> </span><span>Non-targeted metabolomic sequencing was employed to analyze the early anther metabolites of alfalfa, identifying four hundred and one and four hundred and five metabolites in the late tetrad and early mononuclear stages, respectively. Among these, thirty-nine metabolites were consistently up-regulated, while eighty-eight were down-regulated. Differential analysis revealed forty-five and thirty-seven unique metabolites in each respective stage. These metabolites primarily featured in pathways related to energy, phenylpropane, sucrose and starch, and fatty acid metabolism. Integrated analysis demonstrated that differentially expressed genes (DEGs) and differential metabolites (DMs) were co-enriched in these pathways. Additionally, quantitative real-time PCR and physiological index analysis confirmed the down-regulation of key genes during anther development, illustrating that changes in gene regulation upstream could significantly impact downstream metabolite levels, ultimately influencing pollen fertility.</span></p>
FIGURE 1 in Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae)
FIGURE 1. Genetic clusters (GC) detected in Santiria samples from western Central Africa. Bayesian clustering analyses were performed on 479 individuals genotyped at 10 microsatellites loci. A. Variation in means of Ln (likelihood) of the data as a function of the number of hypothetical genetic clusters (K), showing a plateau at K=3. B. Histogram of genetic assignment of the 481 individuals at K = 3. C. Distribution of the three genetic clusters in western Central Africa, and delimitation of the distribution of each genetic cluster (dotted line: GC1, solid line: GC2, dashed line: GC3). We extended the distribution ranges of GC2 and GC3 because morphotypes of both genetic clusters were observed in the south of the Republic of the Congo. Note: Interm. GCx and GCy = intermediate individuals between GCx and GCy.
FIGURE 2 in Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae)
FIGURE 2. Extended Principal Component Analysis (the Hill-Smith ordination) of quantitative and qualitative traits assessed in 103 Santiria herbarium samples assigned to GC1 (N = 46, open circles), GC2 (N = 21, stars) and GC3 (N = 36, open triangles). Note: NL = number of leaflets per leaf; LL = length of leaves; LP = length of petiole; WP = width of petiole; LP/WP = ratio between LP and WP; TPeL = terminal petiolule length; TLL = terminal leaflet length; TLW = terminal leaflet width; TLL/TLW = ratio between TLL and TLW; TLWe = terminal leaflet weight dry portion; AL = apex length; GD = glandular dots; Le = lenticels.
FIGURE 2 in Detecting the phylogenetic position of Bovista acuminata (Agaricales, Basidiomycota) by an ITS-LSU combined analysis: the new genus Bryoperdon and revisitation of Lycoperdon subgen. Apioperdon
FIGURE 2. Bryoperdon acuminatum. Fresh basidiomes (TO HG191016). a in field; b in studio; c particular of the exoperidium; d particular of the exoperidium and ellipsoid-lacerate stoma. Scale bars: a, b = 10 mm; c = 5 mm; d = 2 mm. Pictures by A. Vizzini.
FIGURE 1 in Detecting the phylogenetic position of Bovista acuminata (Agaricales, Basidiomycota) by an ITS-LSU combined analysis: the new genus Bryoperdon and revisitation of Lycoperdon subgen. Apioperdon
FIGURE 1. Bayesian phylogenetic analysis based on the combined nrITS/nrLSU dataset of selected Lycoperdaceae. BPP values ≥ 0.7 are shown on the branches. For each sequenced taxon the Genbank number is given. The newly sequenced collections are in bold.
Enhancement of vitamin B6 production driven by omics analysis combined with fermentation optimization
<p>Transcriptome analysis of the mutant strain E. coli in response to PN overproduction from 6 h to 16 h;</p> <p>Metabolic analysis of the mutant strain E. coli in response to PN overproduction between the early and late stages of fermentation</p>
FIGURE 3 in Revision of the genus Reddellomyces (Tuberaceae): a combination of molecular and morphological analysis provides insights into species diversity
FIGURE 3. Phylogeny of Reddellomyces sp. derived from internal transcribed spacers (ITS) rRNA gene sequences rooted with Choiromyces meandriformis. Species with an asterisk are collected from Mediterranean countries Nodes with asterisks (*) are supported with 100 % Bayesian posterior probabilities and>70 % MP, ML bootstrap values.
FIGURE 2 in Revision of the genus Reddellomyces (Tuberaceae): a combination of molecular and morphological analysis provides insights into species diversity
FIGURE 2. Phylogeny of Reddellomyces sp. derived from nuclear large subunit (28S) rRNA gene sequences rooted with Gymnohydnotrya australiana. Nodes with asterisks (*) are supported with 100 % Bayesian posterior probabilities and>70 % MP, ML bootstrap values.
FIGURE 1 in Revision of the genus Reddellomyces (Tuberaceae): a combination of molecular and morphological analysis provides insights into species diversity
FIGURE 1. Light micrographs of MahSb1-3 truffle ascomata: a, overview of the prospected site; b, ascoma; c, cluster of 8 ascomata; d, cross section of the mature and non mature dried ascoma showing the glebal Trama, labyrinthes and peridium (MahSb1 specimens); e, cross section of fresh fruitbodies (MahSb2 specimens); f, cross section of the gleba with sterile veins (arrowheads); g, asci with 5 immature ascospores and paraphyses (MahSb1 specimens); h, mature ascospore (MahSb1 specimens); i, cross section of the gleba showing the hymenium (He) and paraphyses (Pr) (MahSb1 specimens). Scale bars: b = 1 cm; c = 5 cm; d = 3 mm; f = 4 mm; g = 25 μm; h = 15 μm; i = 100 μm.
FIGURE 4. Distinctive RFLP pattern obtained with pDRAW32 in Revision of the genus Reddellomyces (Tuberaceae): a combination of molecular and morphological analysis provides insights into species diversity
FIGURE 4. Distinctive RFLP pattern obtained with pDRAW32 from in silico digestion of ITS rDNA sequences from representative species. In the computer-simulated digestions, the set of seven enzymes AoxI, BtsCI, FatI, GlaI, HaeIII, Hpy1881, HpyCH4V, LmnI, NIaIII, PasI, StyI and TaqI were used. Lanes labelled MW represent Invitrogen 100 kb ladder.
Data from: Combined transcriptome and metabolome analysis identifies defence responses in spider-mite infested pepper
<p>Plants regulate responses towards herbivory through fine-tuning of defence-related hormone production, expression of defence genes and production of secondary metabolites. Jasmonic acid (JA) plays a key role in plant-herbivorous arthropod interactions. To understand how pepper responds to herbivory, leaf transcriptomes and metabolomes of two genotypes different in their susceptibility to spider mites, were studied. Mites induced both JA and salicylic acid (SA) signalling. However, mite infestation and exogenous JA resulted in distinct transcriptome profiles. Compared with JA, mites induced less differentially expressed genes involved in metabolic processes (except for genes involved in the phenylpropanoid pathway) and lipid metabolic processes. Furthermore, pathogen-related defence responses including WRKY transcription factors, were stronger induced upon mite infestation, likely as result of induced SA signalling. Untargeted analysis of secondary metabolites confirmed that JA treatment induced larger changes in metabolism than spider-mite infestation, resulting in a higher terpenoid and flavonoid production. The more resistant genotype exhibited a larger increase in endogenous JA and volatile and non-volatile secondary metabolites upon infestation, which could explain its stronger defence. Reasoning that in JA-SA antagonizing crosstalk, SA-defences are prioritized over JA-defences, we hypothesize that lack of SA-mediated repression of JA-induced defences could result in gain-of-resistance towards spider mites in pepper.</p>
Stability analysis of roadside backfill body at gob-side entry retaining under combined static and dynamic loading
<p>The applications of gob-side entry retaining (GER) techniques tends to increase over time as it can increase the minerals recovery rate and reduce the output of the waste. In the literature, only the performance of the roadside backfill body (RBB) at gob-side entry retaining under static loading has been investigated. However, failure mechanisms of the RBB under dynamic loading with various roof cutting angles have not been addressed. This study presented a numerical simulation of the fracture propagation and distribution in the roadside backfill body along the gob-side under combined static and dynamic loadings using the Trigon model built in UDEC (Discrete element methods) software. The influence of the roof cutting angles on the behavior of the RBB was also discussed. The input parameters were determined by back analysis with the field data. Results of the model show that static loading is a bigger contributor to the failure of the RBB compared to the dynamic loading. Several clear fractures were observed at top left and bottom right of the RBB and the fracture was more intensive at top left. In addition, it was found that if the roof cutting angle is 70°, the influence of the dynamic loading on the RBB is minimum, and the area and severity of the shearing failure in the RBB is minimum as well. As a result, it was determined the optimal roof cutting angle was 70° and a combined support measure of "roof cutting + roof support above RBBs + RBB reinforcement" is proposed. The application of roof cutting in gob-side entry retaining (RCGER) techniques in the Lingzhida coal mine indicates that deformation of the surrounding rocks can be effectively controlled.</p>
Isotope analysis combined with DNA barcoding provide new insights into the dietary niche of khulan in the Mongolian Gobi
<p><span>With increasing livestock numbers, competition and avoidance are increasingly shaping resource availability for wild ungulates. Shifts in the dietary niche of wild ungulates are likely and can be expected to negatively affect their fitness. The Mongolian Gobi constitutes the largest remaining refuge for several threatened ungulates, but unprecedentedly high livestock numbers are sparking growing concerns over rangeland health and impacts on threatened ungulates like the Asiatic wild ass (khulan).</span></p> <p><span>Previous stable isotope analysis of khulan tail hair from the Dzungarian Gobi suggested that they graze in summer but switch to a poorer mixed C3 grass / C4 shrub diet in winter, most likely in reaction to local herders and their livestock. Here we attempt to validate these findings with a different methodology, DNA metabarcoding. Further, we extend the scope of the original study to the South Gobi Region, where we expect higher proportions of low-quality browse in the khulan winter diet due to a higher human and livestock presence.</span></p> <p><span>Barcoding confirmed the assumptions behind the seasonal diet change observed in the Dzungarian Gobi isotope data, and new isotope analysis revealed a strong seasonal pattern and higher C4 plant intake in the South Gobi Region, in line with our expectations. However, DNA barcoding revealed C4 domination of winter diet was due to C4 grasses (rather than shrubs) for the South Gobi Region. Slight climatic differences result in regional shifts in the occurrence of C3 and C4 grasses and shrubs, which do not allow for an isotopic separation along the grazer-browser continuum over the entire Gobi. </span></p> <p><span>Our findings do not allow us to confirm human impacts upon dietary preferences in khulan as we lack seasonal samples from the South Gobi Region. However, these data provide novel insight into khulan diet, raise new questions about plant availability versus preference, and provide a cautionary tale about indirect analysis methods if used in isolation or extrapolated to the landscape level. Good concordance between relative read abundance of C4 genera from barcoding and proportion of C4 plants from isotope analysis adds to a growing body of evidence that barcoding is a promising quantitative tool to understand resource partitioning in ungulates.</span></p>
Competitiveness prediction for nodule colonization in Sinorhizobium meliloti through combined in vitro tagged strain characterization and genome-wide association analysis
<p>Associations between leguminous plants and symbiotic nitrogen-fixing rhizobia are a classic example of mutualism between a eukaryotic host and a specific group of prokaryotic microbes. Although this symbiosis is in part species-specific, different rhizobial strains may colonise the same nodule. Some rhizobial strains are commonly known as better competitors than others, but detailed analyses that aim to predict rhizobial competitive abilities based on genomes are still scarce. Here, we performed a bacterial <em>genome-wide association (GWAS) analysis to define the </em>genomic determinants related to the competitive capabilities in the model rhizobial species <em>Sinorhizobium meliloti.</em> For this, 13 tester strains were GFP-tagged and assayed <i>vs.</i> 3 RFP-tagged reference competitor strains (<em>Rm1021, AK83, and BL225C) in a</em> <i>Medicago sativa</i> nodule occupancy test. Competition data and strain genomic sequences were employed to build a model for GWAS based on <i>k</i>-mers. Among the <i>k</i>-mers with the highest scores, 51 <i>k</i>-mers mapped on the genomes of four strains showing the highest competition phenotypes (> 60% single strain nodule occupancy; GR4, KH35c, KH46 and SM11) <i>vs.</i> BL225C. These <i>k</i>-mers were mainly located on the symbiosis-related megaplasmid pSymA, specifically on genes coding for transporters, proteins involved in the biosynthesis of cofactors and proteins related to metabolism (e.g., fatty acids). The same analysis was performed considering the sum of single and mixed nodules obtained in the competition assays <em>vs. </em>BL225C, retrieving <i>k</i>-mers mapped on the genes previously found and on <i>vir</i> genes. Therefore, the competition abilities seem to be linked to multiple genetic determinants and comprise several cellular components.</p>
FIGURE 3. The strict consensus tree from parsimony analysis for the combined 16S and RAG1-AmpF1 in Maluti Mystery: A systematic review of Amietia vertebralis (Hewitt, 1927) and Strongylopus hymenopus (Boulenger, 1920) (Anura: Pyxicephalidae)
FIGURE 3. The strict consensus tree from parsimony analysis for the combined 16S and RAG1-AmpF1 dataset with Pyxicephalus adspersus as the outgroup. Bootstrap values are shown at the major nodes. Branch lengths are proportional to the number of unambiguous changes in the original sequence data. Abbreviations of localities for sequenced samples are as follows: M = Mohlaka, B = Bafali, D = Senqu, Q = Qabane, S = Tsatsana, T = Tugela, V = Vemvane, J = Sani, * = Genbank sequence. Note that the two Amietia angolensis sequences from Genbank emerge from the tree as divergent lineages. This may indicate cryptic diversity or simply misidentification of these phenotypically diverse and difficult to identify frogs.
FIGURE 2. Most parsimonious combined tree under equal weights, with 17 in Phylogenetic analysis of the Pantomorus-Naupactus complex (Coleoptera: Curculionidae: Entiminae) from North and Central America
FIGURE 2. Most parsimonious combined tree under equal weights, with 17 morphological characters coded as additive. Bootstrap values over 50% below the corresponding branches.
FIGURE 324 in <p><strong>A revision of Afrotropical Quasimodo flies (Diptera: Schizophora; Curtonotidae). Part IV—the continental Afrotropical species of <em>Curtonotum </em>Macquart, with descriptions of thirteen new species and a combined phylogenetic analysis of the Curtonotidae</strong></p>
FIGURE 324. Distribution of continental Afrotropical species of Curtonotum. Major Habitat Types: C. marriott sp. n., C. moffatt sp. n. and C. platyphallum.
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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.