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389 results for “Herbs”
An unexpected genetic diversity pattern and a complex demographic history of a rare medicinal herb, Chinese asparagus (Asparagus cochinchinensis) in Korea
Range-wide population studies of wide spread species are often associated with complex diversity patterns resulting from genetically divergent evolutionary significant units (ESUs). The compound evolutionary history creating such a pattern of diversity can be inferred through molecular analyses. Asparagus cochinchinensis, a medicinally important perennial herb, is in decline due to overharvesting in Korea. Eight A. cochinchinensis populations in Korea and three neighboring countries (China, Japan and Taiwan) were examined using nine nuclear microsatellite loci and three chloroplast microsatellite loci to characterize molecular diversity patterns. The average within-population diversity was limited likely due to long-term bottlenecks observed in all eight populations. High pairwise FST values indicated that the populations have largely diverged, but the divergences were not correlated with geographic distances. Clustering analyses revealed a highly complex spatial structure pattern associated with two ESUs. Approximate Bayesian Computation (ABC) suggest that the two ESUs split about 21,000 BP, were independently introduced to Korea approximately 1,800 years ago, and admixed in secondary contact zones. The two ESUs found in our study may have different habitat preferences and growth conditions, implying that the two genetically divergent groups should be considered not only for conservation and management but also for breeding programs in agricultural areas.
Data from: Sensitivity to habitat fragmentation across European landscapes in three temperate forest herbs
<p>Context. Evidence for effects of habitat loss and fragmentation on the viability of temperate forest herb populations in agricultural landscapes is so far based on population genetic studies of single species in single landscapes. However, forest herbs differ in their life histories, and landscapes have different environments, structures and histories, making generalizations difficult.</p> <p>Objectives. We compare the response of three slow-colonizing forest herbs to habitat loss and fragmentation and set this in relation to differences in life-history traits, in particular their mating system and associated pollinators.</p> <p>Methods. We analysed the herbs' landscape-scale population genetic structure based on microsatellite markers from forest fragments across seven European agricultural landscapes.</p> <p>Results. All species responded to reductions in population size with a decrease in allelic richness and an increase in genetic differentiation among populations. Genetic differentiation also increased with enhanced spatial isolation. In addition, each species showed unique responses. Heterozygosity in the self-compatible <i>Oxalis acetosella</i> was reduced in smaller populations. The genetic diversity of <i>Anemone nemorosa</i>, whose main pollinators are less mobile, decreased with increasing spatial isolation, but not that of the bumblebee-pollinated <i>Polygonatum multiflorum</i>.</p> <p>Conclusions. Our study indicates that habitat loss and fragmentation compromises the long-term viability of slow-colonizing forest herbs despite their ability to persist for many decades by clonal propagation. The distinct responses of the three species studied within the same landscapes confirm the need of multi-species approaches. The mobility of associated pollinators should be considered an important determinant of forest herbs' sensitivity to habitat loss and fragmentation.</p>
FIGURE 4. Isocolus beheni n in New species of herb gallwasps from the Middle East (Hymenoptera, Cynipidae, Aylacini)
FIGURE 4. Isocolus beheni n. sp.: a, head (front view); b, head (dorsal view); c, antenna, female; d, pronotum (dorsal view); e, mesosoma (lateral view); f, mesoscutum and mesoscutellum (dorsal view); g, propodeum (postero-dorsal view); h, forewing; i, metasoma (lateral view).
FIGURE 3. Isocolus freidbergi n in New species of herb gallwasps from the Middle East (Hymenoptera, Cynipidae, Aylacini)
FIGURE 3. Isocolus freidbergi n. sp.: a, head (front view); b, head (dorsal view); c, antenna, female; d, antenna, male; e, pronotum (dorsal view); f, mesoscutum and mesoscutellum (dorsal view); g, mesosoma (lateral view); h, propodeum (postero-dorsal view); i, forewing; j, metasoma (lateral view).
FIGURE 7. Isocolus karimpouri n in New species of herb gallwasps from the Middle East (Hymenoptera, Cynipidae, Aylacini)
FIGURE 7. Isocolus karimpouri n. sp., galls: a, larval chamber, close–up; b, last instar gallwasp larva (photo by Y. Karimpour); c, larval chamber with emerging hole (longitudinal dissection of the stem) (photos by G. Melika).
FIGURE 2. Aulacidea tavakolii n in New species of herb gallwasps from the Middle East (Hymenoptera, Cynipidae, Aylacini)
FIGURE 2. Aulacidea tavakolii n. sp., galls: a–b, young growing galls; c–d, mature galls; e, dissected gall, showing the multilocular structure (photos by M. Tavakoli).
FIGURE 1. Aulacidea tavakolii n in New species of herb gallwasps from the Middle East (Hymenoptera, Cynipidae, Aylacini)
FIGURE 1. Aulacidea tavakolii n. sp.: a, head (front view); b, head (dorsal view); c, antenna, female; d, antenna, male; e, pronotum (dorsal view); f, mesoscutum and mesoscutellum (dorsal view); g, mesosoma (lateral view); h, propodeum (postero-dorsal view); i, forewing, lrc, length of radial cell, wrc, width of radial cell; j, metasoma (lateral view).
FIGURE 6. Isocolus karimpouri n in New species of herb gallwasps from the Middle East (Hymenoptera, Cynipidae, Aylacini)
FIGURE 6. Isocolus karimpouri n. sp.: a, head (front view); b, head (dorsal view); c, antenna, female; d: antenna, male; e: pronotum (dorsal view); f, mesoscutum and mesoscutellum (dorsal view); g, mesosoma (lateral view); h, propodeum (postero-dorsal view); i, forewing; j, metasoma (lateral view).
Data set of 1) plant abundance in the herb layer and 2) Shrub and tree composition and structure following forest management along a chronosequence
<p>In each site (1200 m²), three circular plots (400 m²) were established (total of 198 plots). Data presented here for 1) plant of the herb layer and 2) shrub and tree are grouped by site (addition of three plots). </p> <p>In the herb layer, total plant species identity and abundance (percentage cover) were sampled in each plot using eight circular micro-plots of 4 m². Data were collected in 2016 and 2017, between June and August. To minimize seasonal variability and allow detection of early spring species, plants (identity and abundance) in the herb layer were measured twice (once in June to early-July, and once in late-July to August).</p> <p>For tree, in each plot, species identity, diameter at breast height (DBH, 1.3 m) and locations of each tree > 9.1 cm DBH were determined. In each plot, species identity and DBH of shrubs and small trees (DBH range: 1.1 to 9.1 cm) were measured in three circular micro-plots of 25 m². Data that were related to the shrub-canopy layer included all trees and shrubs with DBH > 1.1 cm. Here, in each site, forest composition and structure is represented by different combinations of DBH classes (1.1-4 cm, 4-9.1 cm, 9.1-20 cm, 20-35 cm, >35 cm) and species.</p> <p>Plant community composition and abundance were assessed in unmanaged forests (sites of old-growth forest > 100 years, with dominant and co-dominant trees older than 200 years, and no obvious sign of past harvesting), and in even-aged and uneven-aged managed forests along a chronosequence (< 5 years, 15 years, 30 years after forest harvesting).</p>
Staying in situ or shifting range under ongoing climate change: A case of an endemic herb in the Himalaya-Hengduan Mountains across elevational gradients
<p><span><strong>Aim</strong>:</span><span> How species respond to ongoing climate change has been a hot research topic, especially with the controversy in shifting range (movement) or persisting in local habitat (<em>in situ</em>) as the primary response. Assessing the relative roles of range shifts, phenotypic plasticity and genetic adaptation helps us predict the evolutionary fate of species. We aim to explore the evolutionary strategies of plants under climate change from a keystone herb in alpine ecosystems, <em>Mirabilis</em> <em>himalaica</em>, along its elevational gradient.</span></p> <p><span><strong>Location</strong>:</span><span> Himalaya-Hengduan Mountains, China.</span></p> <p><span><strong>Methods</strong>: </span><span>We combined evidence from population genomics and ecological data in both space and time to investigate the state of "staying" or "moving". We identified migration events by assessing historical and contemporary gene flow, and changes in species distribution. Morphological variation was compared by measuring five traits using specimen data. Moreover, we explored climate-driven genetic variation and local selection regimes acting on populations in the alpine landscape along an elevational gradient.</span></p> <p><span><strong>Results</strong>: </span><span>Our results argue that staying <em>in situ</em> by morphological variation and local genetic evolution rather than range shifting plays an important role in <em>M</em>. <em>himalaica</em> response to climate change. We first found trace evidence of upward or climatic-driven shifting along an elevational gradient, although asymmetric gene flow was restricted within microenvironments of mid-elevational populations. Furthermore, morphological variation comparisons revealed clinal variation, as resource allocation showed a declining pattern in vegetative growth but increased reproductive growth with increasing elevation. Outlier tests and environment association analyses indicated adaptative loci primarily related to thermal-driven selection and continuous adaptations to high elevation in the Himalaya-Hengduan Mountains. </span></p> <p><span><strong>Main conclusions</strong>:</span><span> Our findings show <em>M</em>. <em>himalaica</em> may persist in local habitats rather than shifting range under climate change, exhibiting a low risk of genomic vulnerability in current habitats. This study has important implications for improving our understanding of the evolutionary response in alpine </span><span>plants to climate change.</span></p>
Altitude-mediated soil properties, not geography or climatic distance, explain the distribution of a tropical endemic herb
<p><span><span><span><span><span><span><span><span><span><span><span>Understanding the ecological processes that govern species' range margins is a fundamental question in ecology with practical implications in conservation biology. The centre-periphery hypothesis (CPH) predicts that organisms have higher abundance at the centre of their geographic range. However, most tests of the CPH often used raster data, assuming that climatic conditions are consistent across one square km. This assumption is not always justified, particularly for species that live in mountainous regions where climatic conditions often vary widely across a small special scale. When using occurrence data, most previous studies do not evenly sample across the species' distribution. We sampled 54 plots of an endemic perennial herb, <i>Thunbergia atacorensis</i> (Acanthanceae), throughout its range in West-Africa to collect biotic and abiotic variables including, <i>Thunbergia</i> density, leaf mass per area, and basal diameter. The basal diameter was used to estimate population demographic structure (skewness). We used these data to build a structural equation model testing the direct and indirect effects of distance from geographic and climatic niche centres, and altitude on density of <i>Thunbergia atacorensis </i>as mediated by abiotic and biotic factors, population skewness, and individual size. Contrary to the prediction of the CPH, plant density did not vary with distance from geographic or climatic niche centre, indicating that even the climatic centre does not necessarily have optimal ecological conditions. However, soil nitrogen and soil potassium mediated the relationship between altitude and plant density. Further, plant size increased with soil nitrogen and soil potassium. We found no direct or mediating effect of interspecific competition on plant density. Our study highlights the relative role that abiotic factors play in shaping species range limits, and the critical role of altitudinal gradient.</span></span></span></span></span></span></span></span></span></span></span></p>
TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis
<p><strong>ABSTRACT: </strong>Traditional Chinese Medicines Integrated Database and the description about Chinese herbs, including English and Latin names, properties, meridians, medicinal parts, herbal effect and indication. Traditional Chinese Medicine (TCM) is a system of healthcare and healing that has been practiced for thousands of years in China. It is based on a holistic approach that views the human body and its various systems as interconnected. TCM encompasses a wide range of practices, including herbal medicine, acupuncture, massage (tui na), exercise (qigong), and dietary therapy.</p> <p><strong>Instruction: </strong></p> <p>Data was cleaned and duplicates were removed.</p> <p><strong>Inspiration: </strong>The dataset was uploaded to UBRITE for "DGR_DEPOT" summer 2023 team project</p> <p><strong>Acknowledgements: </strong>Ruichao Xue 1, Zhao Fang, Meixia Zhang, Zhenghui Yi, Chengping Wen, Tieliu Shi</p> <p>TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2013 Jan;41(Database issue):D1089-95. doi: 10.1093/nar/gks1100. Epub 2012 Nov 29. PMID: 23203875; PMCID: PMC3531123.</p> <p><strong>U-BRITE LAST UPDATED June 19, 2023</strong></p>
Amplified drought induced by climate change reduces seedling emergence and increases seedling mortality for two Mediterranean perennial herbs
<div>Seedling recruitment is a bottleneck for population dynamics and range shift. The vital rates linked to recruitment by seed are impacted by amplified drought induced by climate change. In the Mediterranean region, autumn and winter seedling emergence and mortality may have strong impact on the overall seedling recruitment. However, studies focussing on the temporal dynamic of recruitment during these seasons are rare.</div> <div> </div> <div>This study was performed in a deciduous Mediterranean oak forest located in southern France and quantifies the impact of amplified drought conditions on autumn and winter seedling emergence and seedling mortality rates of two herbaceous plant species with meso-Mediterranean and supra-Mediterranean distribution (respectively, <em>Silene italica</em> and <em>S. nutans</em>). Seedlings were followed from October 2019 to May 2020 in both undisturbed and disturbed plots where the litter and the aboveground biomass has been removed to create open microsites.</div> <div> </div> <div>Amplified drought conditions reduced seedling emergence and increased seedling mortality for both <em>Silene </em>species but these negative effects were dependent on soil disturbance conditions. Emergence of <em>S. italica</em> decreased only in undisturbed plots (-7%) whereas emergence of <em>S. nutans </em>decreased only in disturbed plots (-10%) under amplified drought conditions. The seedling mortality rate of <em>S. italica </em>was 51% higher under amplified drought conditions in undisturbed plots while that of <em>S. nutans</em> was 38% higher in disturbed plots.</div> <div> </div> <div>Aridification due to lower precipitation in the Mediterranean region will negatively impact the seedling recruitment of these two <em>Silene </em>species. Climate change effects on early vital rates may likely have major negative impacts on the overall population dynamic.</div>
Fig. 7 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins
Fig. 7. Antibacterial effects of a series of purified McDef1 concentration against S. aureus (A), E. coli (B), S. pullorum (C) and A. hydrophila (D). 1: 30 μg/ml, 2: 40 μg/ ml, 3: 50 μg/ml, 4: 60 μg/ml, 5: 80 μg/ml, 6: 100 μg/ml, 7: Negative control, empty vector expression supernatant; 8: Positive control, for A̢B̢C: 0.2 mg/mL Ampicillin, for D: 0.5 mg/mL Kanamycin.
Fig. 6 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins
Fig. 6. Antibacterial effects of recombinant yeasts with McDef1 or McDef2 fermentation supernatant on S. aureus (A), S. pullorum (B), E. coli (C) and A. hydrophila (D). 1: Fermentation supernatant of the recombinant McDef1; 2: Fermentation supernatant of the recombinant McDef2; 3: Negative control, empty vector expression supernatant; 4: Positive control, A̢B̢C: 0.2 mg/mL Ampicillin; D: 0.5 mg/mL Kanamycin.
Fig. 4 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins
Fig. 4. Multiple sequence alignments of the mature peptides of McLTP1 homologs from different plants with ClustalW2. The target proteins McLTP1 of this study are highlighted with yellow fluorescent background. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins
Fig. 2. Multiple sequence alignments of the McDef1 (A) and McDef2-5 (B) homologs from different plants with ClustalW2. The conserved domains α-core and γ-core are marked under the homologous sequences respectively. The target proteins McDef1 in (A) and McDef2-5 in (B) of this study are highlighted with yellow fluorescent background. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins
Fig. 1. The alignment analysis of McDef1-5. The underlined amino acids represent the signal sequence predicted with SignalP. The cysteines are marked in yellow background and the putative disulfide bonds are also shown. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 8 in Preliminary investigations on the pathogenesis-related protein expression profile of the medicinal herb Macleaya cordata and anti-bacterial properties of recombinant proteins
Fig. 8. Antibacterial effects of a series of purified McDef2 concentration against S. aureus (A), E. coli (B), S. pullorum (C) and A. hydrophila (D). 1: 30 μg/ml, 2: 40 μg/ ml, 3: 50 μg/ml, 4: 60 μg/ml, 5: 80 μg/ml, 6: 100 μg/ml, 7: Negative control, empty vector expression supernatant; 8: Positive control, for A̢B̢C: 0.2 mg/mL Ampicillin, for D: 0.5 mg/mL Kanamycin.
Fig. 2 in Comparative transcriptome analysis infers bulb derived in vitro cultures as a promising source for sipeimine biosynthesis in Fritillaria cirrhosa D. Don (Liliaceae, syn. Fritillaria roylei Hook.) - High value Himalayan medicinal herb
Fig. 2. (A–E) Differential gene expression analysis in comparative F. roylei transcriptome: (A) Heat-map showing differential gene expression in the bulb (PKW) vs callus (PK2); bulb (PKW) vs in vitro regenerated plantlets (PK1) and callus (PK2) vs in vitro regenerated plantlets (PK1); (B) Venn diagram represents the differential gene expression in PKW vs PK1; PKW vs PK2; PK2 vs PK1, (C–E) Volcano plots represents the differential gene expression in PKW vs PK1; PKW vs PK2; PK2 vs PK1 as colour description image, where p-value & log2 fold-change in red colour represents genes with log2 fold-change cut off 2 and p-value <=0.05; p-value in blue colour represents genes with no cut off on log2 fold-change and p-value <=0.05. Whereas, log2 fold-change in green colour represents genes with fold-change cut off 2 but no p-value cut off and non-significant (NS) in grey colour represents genes with no filter on log2 fold-change and p-value, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
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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.