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111 results for “acorn”
Effects of Acorn Production on White-Footed Mouse Populations at Harvard Forest 1997-1999
Recently several authors have documented fluctuations in the abundance of white-footed mice (Peromyscus leucopus noveboracensis) with fluctuations in acorn production (Elkinton et al. 1996, Ostfeld et al. 1996, Wolff 1996, Jones et al. 1998). Acorns are the major food source of white-footed mice during winter and are extensively cached. They are also food for many other species as well; over 100 species of birds and mammals feed on acorns (Van Dersal 1940). A large mast crop in fall usually correlates with a large mouse population the following summer, whereas a poor crop correlates with low population numbers. One experimental study supplementing acorns on forest plots demonstrated a concomitant increase in white-footed mice populations (Jones et al. 1998). It has been hypothesized that a large mast crop increases overwinter survival and may allow continued reproduction during the winter months, which results in a larger population the following year. We have four objectives in monitoring acorn abundance at Harvard Forest: 1) test for correlation of estimates of acorn production with estimates of overwinter survival probabilities and abundance of white-footed mice using mark-recapture statistical models (HF054), 2) document annual variation in acorn abundance and quality, which compliments a program at Harvard Forest documenting changes in woody plant phenology with climatic variation (HF003), 3) test hypotheses concerning the correlation of acorn production with environmental factors such as temperature, rainfall, and weevil infestation, and 4) provide data for inter-site comparisons, such as to test for synchrony in production at various scales across the landscape. We estimate acorn production with timed visual surveys following methods adapted from Koenig et al. (1994). Individual tagged trees on two small mammal trapping plots are surveyed each year by two observers. Detailed methods are described in the metadata.
Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity
<p>The data present in this repository reflect intermediate and processed data presented in the manuscript, <em>Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity. </em>This manuscript is still under review; as such, this page will be updated upon publication.</p> <p> </p> <p><strong>Manuscript Abstract:</strong></p> <p>Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Though their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, <em>Saccoglossus kowalevskii</em>, and place them in the context of immunity evolution within deuterostomes – the animal clade composed of chordates, hemichordates, and echinoderms. Following acute exposure to the synthetic viral dsRNA analog, poly(I:C), we show that <em>S. kowalevskii </em>responds by regulating the transcription of genes associated with canonical innate immunity signaling pathways (e.g., NF-κB and IRF signaling) and metabolic processes (e.g., lipid metabolism), as well as many genes without clear evidence of orthology with those of model species. Aggregated across all experimental time point contrasts, we identify 423 genes that are differentially expressed in response to poly(I:C). We also identify 147 genes with altered temporal patterns of expression in response to immune challenge. By characterizing the molecular toolkit involved in hemichordate antiviral immunity, our findings provide vital evolutionary context for understanding the origins of immune systems within Deuterostomia.</p> <p> </p> <p><strong>Repository contents:</strong></p> <p>### Processed Data ###</p> <ul> <li><em>Full_DESeq2_matrix.csv </em>--> DESeq2 results for each contrast (e.g., 2hpi treatment vs. control)</li> <li><em>MaSigPro.Clusters.csv</em> --> Mean expression for each gene placed within a pDEG cluster</li> <li><em>MaSigPro.SigGenes.TreatmentvsControl.Robj</em> --> T.fit() R-object output from MaSigPro pipeline. This can be opened in R using the load() function.</li> </ul> <p>### Homology Assessment ###</p> <ul> <li><em>Orthofinder.tar.gz</em> --> OrthoFinder results</li> <li><em>Skowalevskii_Genome_Annotation.SPHuman_and_HOG.csv</em> --> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-Human" and "HOG" output described in the main text of the paper</li> <li><em>Skowalevskii_Genome_Annotation.SPPANTHER.csv </em>--> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-SwissProt" output described in the main text of the paper</li> </ul> <p>### Functional Annotation ###</p> <ul> <li><em>Skow.HMMER_Pfam.domtblout.tsv</em> --> Pfam annotation of the Skow1.1 genome assembly in HMMER's domblout format</li> <li><em>Skow.KofamKOALA.detail.tsv</em> --> KO annotation of the Skow1.1 genome assembly using KofamKOALA (detailed output)</li> <li><em>Skow.KofamKOALA.detail.tsv </em>--> KO annotation of the Skow1.1 genome assembly using KofamKOALA (mapper output)</li> <li><em>SkowAnnotations.GO.tsv</em> --> GO annotation of the Skow1.1 genome assembly</li> <li><em>SkowAnnotations.PF.tsv</em> --> PF annotation of the Skow1.1 genome assembly</li> <li><em>SkowAnnotations.PP.tsv</em> --> PP annotation of the Skow1.1 genome assembly</li> </ul> <p>### Enrichment Data ###</p> <ul> <li><em>DESeqEnrichments.tsv</em> --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by DESeq2.</li> <li><em>MaSigProEnrichments.tsv</em> --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by MaSigPro.</li> </ul>
Acorn mast data (1995-2025), Black Rock Forest, Cornwall, NY
Acorn abundance has been tracked annually since 1995 at Black Rock Forest (BRF), Cornwall, NY between September and October to coincide with peak acorn drop. From 1995 to 2010 all acorns were counted within a circular plot thrown 10 times at 15 to 20 locations throughout BRF. Beginning in 2004 individual oak trees were visited and DBH and number of acorns under the drip line of the tree were counted at the same 15 to 20 locations within BRF. Beginning in 2024 four 1-meter square quadrats were used to count acorns under 10 trees at each location.
HAC features and metadata for the ACORNS Caregiver dataset
<p>Histograms of co-occurence features from the Caregiver dataset.</p> <p>Each files contains the features corresponding to one speaker. The features were extracted using matlab code from the ACORNS project, except for the ones postfixed with "_python" that were extracted with code from http://github.com/omangin/multimodal/features/hac.py.</p> <p>The .json files contains metadata for the the datasets. See http://github.com/omangin/multimodal/db/models/acorns.py for more information on the format.</p> <p>For more information and data, the English part of the ACORNS CAREGIVER corpus is available from the language archive (TLA -MPI for psycholinguistics Nijmegen) for reproducibility and transparency reasons in accordance with the agreements that were obtained from the speakers. Visit the following link for the corpus: https://corpus1.mpi.nl/ds/asv/;jsessionid=0717131F4474EDF6A9002460E8921321?0&openhandle=hdl:1839/00-0000-0000-001A-D60B-1</p> <p>Information on permissions for using the corpus at http://dx.doi.org/10.1371/journal.pone.0132245</p>
Text-fig. 8. a–e: Quercus aff. cerris. a: Cup, Oriolo MSF 984. b: Cup, Oriolo MSF 982. c: Leaf, Oriolo MSF 689. d: Leaf, Oriolo MSF 659. e: Oriolo MSF 657. f: Quercus aff. pubescens Oriolo MSF 688. g: Quercus sect. Quercus acorn, Oriolo MSF 658. h–j: Quercus iberica. h: Oriolo MSF 694. i: Oriolo MSF 639. j: Oriolo MSF 698. Scale bars 10 mm (a, b, g), 50 mm (c–f, h–j). in The Late Early Pleistocene Flora Of Oriolo, Faenza (Italy): Assembly Of The Modern Forest Biome
Text-fig. 8. a–e: Quercus aff. cerris. a: Cup, Oriolo MSF 984. b: Cup, Oriolo MSF 982. c: Leaf, Oriolo MSF 689. d: Leaf, Oriolo MSF 659. e: Oriolo MSF 657. f: Quercus aff. pubescens Oriolo MSF 688. g: Quercus sect. Quercus acorn, Oriolo MSF 658. h–j: Quercus iberica. h: Oriolo MSF 694. i: Oriolo MSF 639. j: Oriolo MSF 698. Scale bars 10 mm (a, b, g), 50 mm (c–f, h–j).
Data from: Does the history of option quality affect nest site choice in the acorn ant?
<p>During decision−making, animals consider not only the current but also the past quality of options. For example, when humans evaluate performance (e.g. sales) of employees, they do not only consider the average performance but also the trend of performance ascending performance is often viewed as more favorable than descending performance. In our study, we test if non-human animals have a similar bias when they are evaluating options using house-hunting by the acorn ant, <em>Temnothorax curvispinosus</em>, as our model system. Our data show that when nest-site quality is static over time, ant colonies tend to prefer the nest site which was better (i.e. darker) between two nest options. However, when the nest quality changes—one improves and the other worsens—over time, more colonies choose the low-quality, but improving, nest than the high-quality, but worsening, nest. These results suggest that a continuous change of option quality may influence evaluation. We discuss alternative explanations for our results, possible mechanisms and potential ecological benefits for keeping track of the nest-site quality.</p>
FIGURE 5 in An early Cambrian pelago-benthic acorn worm and the origin of the hemichordate larva
FIGURE 5. Reconstruction of Cambrobranchus pelagobenthos from the Haiyan Lagerstätte of China: Artistic reconstruction of larvae, juveniles, and an adult specimen by C. McCall.
FIGURE 2 in An early Cambrian pelago-benthic acorn worm and the origin of the hemichordate larva
FIGURE 2. Adult specimens of Cambrobranchus pelagobenthos from the Haiyan Lagerstätte of China. A, U-shaped individual with preserved post-anal organ, YKLP14530. B, Interpretative drawing of A. C, Nearly complete curved specimen, co-occurring with some incomplete specimens, YKLP14531. D, Interpretative drawing of C. Scale bars, 1 mm. A, anus; CO, collar; EBR, epibranchial ridge; GB+TB, gill and tongue bars; In, intestine; KHS, kidney–heart–stomochord complex; P, proboscis; PAO, post-anal organ; PR, parabranchial ridges; T, trunk.
FIGURE 3 in An early Cambrian pelago-benthic acorn worm and the origin of the hemichordate larva
FIGURE 3. Larvae and juvenile specimens of Cambrobranchus pelagobenthos from the Haiyan Lagerstätte of China, and comparison to extant hemichordate and echinoderm larvae. A, Post-hatched early stage tornaria larva, YKLP 14532. B, Interpretive drawing of A. C, Early to middle stage larva, YKLP14540. D, Interpretive drawing of C. E, Juvenile specimen, YKLP14533. F, Juvenile specimen, YKLP14536. G, Juvenile specimen, YKLP14548. H, Juvenile specimen with at least two pairs of preserved oval-shaped gill pores, YKLP14549. I, Interpretive drawing of E. J, Interpretive drawing of F. K, Interpretive drawing of G. L, Interpretive drawing of H. M, Juvenile specimen, YKLP14551. N, SEM micrograph of an extant tornaria larva of Schizocardium sp. from the coast of Texas. O, SEM micrograph of an extant early stage juvenile of Schizocardium sp. from the coast of Texas. P–S, Interpretive drawings of the developing stages of an indirect developing modern enteropneust (modified from Gonzalez et al., 2017). P, Early stage tornaria larva. Q, Middle stage tornaria larva. R, Late stage tornaria larva. S, Post metamorphic juvenile. T, Interpretive drawing of an echinoderm (Holothuroidea) larva (modified from Dyachuk and Odintsova, 2013). Scale bars, 500 μm (A–L, N, O), 1 mm (M). AO, apical organ. CB, ciliary band; CO, collar; D, digestive tract; ES, esophagus; GP, gill pore; In, intestine; KHS, kidney–heart–stomochord complex; M, mouth; P, proboscis; PAO, post-anal organ; PFB, perioral feeding band; PT, post telotroch; T, trunk.; TL, telotroch.
FIGURE 1 in An early Cambrian pelago-benthic acorn worm and the origin of the hemichordate larva
FIGURE 1. Adult specimens of Cambrobranchus pelagobenthos from the Haiyan Lagerstätte of China. A, Part of the holotype, YKLP14443. B, X-ray tomographic image of YKLP14443. C, Interpretative drawing of the anterior part of A. D, A well-preserved individual attached to an uncertain sclerite, YKLP14529. E, Fluorescent microscopy image of the white dashed area in C. F, Interpretative drawing of C. Scale bars, 2 mm (A–C, G), 1 mm (D–F). CO, collar; EBR, epibranchial ridge; GB+TB, gill and tongue bars; GP, gill pore; KHS, kidney–heart–stomochord complex; M, mouth; NS, nuchal skeleton; P, proboscis; PR, parabranchial ridges; T, trunk.
FIGURE 4 in An early Cambrian pelago-benthic acorn worm and the origin of the hemichordate larva
FIGURE 4. SEM and SEM-EDX analyses of Cambrobranchus pelagobenthos from the Haiyan Lagerstätte of China. A–H, Soft-bodied tissue preservation of YKLP14532. A, A SEM micrograph showing the larva. B–H, Individual elemental maps. B, Iron. C, Sulfur. D, Carbon. E, Oxygen. F, Aluminum. G, Silicon. H, Potassium. I–P, Soft-bodied tissue preservation of YKLP14540. I, A SEM micrograph showing the larva. J–P, Individual elemental maps. J, Iron. K, Sulfur. L, Carbon. M, Oxygen. N, Aluminum. O, Silicon. P, Potassium. Scale bars equal 200 μm.
FIGURE 6 in An early Cambrian pelago-benthic acorn worm and the origin of the hemichordate larva
FIGURE 6. Inferred phylogenetic relationships: Phylogenetic position of Cambrobranchus pelagobenthos and other Cambrian ambulacrarians using majority-rules Bayesian analysis of 113 characters and 27 taxa. Numbers at nodes represent posterior probabilities. Pie charts indicate the results of an ancestral state reconstruction.
Fig. 1 in High winter survival rate of acorn ants inside artificial nest sites (Hymenoptera: Formicidae)
Fig. 1 – Changes in temperature recorded near the nest sites with the Temnothorax crassispinus ant colonies localised at ground level, as well as near the nest sites about 5 cm below ground level and 1.5 m above ground level. The experiment lasted from 4 December 2020 to 24 February 2021, but only the temperatures for February are presented. The higher temperatures recorded at ground level and 5 cm below ground level, compared to the temperatures 1.5 above ground level, were probably affected by heating from the sun; the data loggers situated 1.5 m above ground level were attached to trees on the north side, so they were not affected by the sun.
FIG. 7 in A new deep-sea species of epibenthic acorn worm (Hemichordata, Enteropneusta)
FIG. 7. — Bayesian cladogram based on enteropneust 18S and 16S rRNA sequences, rooted using an echinoid echinoderm (Echinocrepis rostrata Mironov, 1973). Numbers at nodes represent posterior probabilities (p). All nodes with p<0.95 were collapsed into polytomies.
FIG. 3. — Tergivelum baldwinae n. gen., n in A new deep-sea species of epibenthic acorn worm (Hemichordata, Enteropneusta)
FIG. 3. — Tergivelum baldwinae n. gen., n. sp. in approximate dorsal view: A, surface details; B, locations of major nerves and muscles associated with proboscis and collar. Abbreviations for structural features: see text.
FIG. 8 in A new deep-sea species of epibenthic acorn worm (Hemichordata, Enteropneusta)
FIG. 8. — Single frame (at 5 min: 37 sec) of 8-min videotape of Tergivelum baldwinae n. gen., n. sp. paratype IV. Filled circles show path of a particle transported unobstructed about 5 cm above the bottom (from 5:47 to 5:53). Open circles show path of particle (small polychaete) drifting about 2 cm above the bottom and evidently getting stuck (at 5:36) in substantial mucus surrounding acorn worm;arrow indicates shadow cast on sea floor by the immobilized particle. Scale bar: 5 cm.
FIG. 6 in A new deep-sea species of epibenthic acorn worm (Hemichordata, Enteropneusta)
FIG. 6. — Cross sections (B-J) of Tergivelum baldwinae n. gen., n. sp. at levels indicated in 4B: A, parasagittal section in region of gill pores showing primary gill bar with skeleton (arrowed) and secondary gill bar with skeleton (arrowheads) and coelomic space (asterisk); B, cross section of trunk near anterior extremity of ventral nerve cord (in rectangle); C, detail from rectangle in 6B with ventral nerve cord underlain by ventral blood vessel (arrowhead); D, cross section of anterior trunk showing dorsal protuberances and back veils (the left one broken off); dark spheres are testes; E-J, intestinal region of trunk; asterisks mark lateroventral folds); dorsal and ventral nerve cords indicated, respectively, by arrows and arrowheads; K, section through three testes; L, detail of testis with spermatozoafilled lumen toward top right; M, medium-sized oocytes; N, large oocyte. Abbreviations for structural features: see text. Scale bars: A, 100 μm; B, D, 1 mm; C, 50 μm; E-J, N, 500 μm; K, M, 200 μm; L, 20 μm.
FIG. 5 in A new deep-sea species of epibenthic acorn worm (Hemichordata, Enteropneusta)
FIG. 5. — Cross sections of Tergivelum baldwinae n. gen., n. sp. at levels indicated in Figure 4B: A, near anterior tip of proboscis, arrow indicates tract of longitudinal muscle fibers; B, enlargement of rectangle in 5A showing epidermis (toward right) underlain by basal concentration (arrowed) of diffuse intraepidermal nervous system; proboscis coelom contains meshwork of connective tissue and muscle cells; C, more posterior section of proboscis; D, section through collar showing anterior end of right buccal muscle; specimen oriented with left side somewhat in advance of right, so left buccal muscle not yet in view; E, detail of the center rectangle in 5D; showing lumen of collar cord separating dorsal non-neural and ventral neural regions; perihaemal coeloms (marked by asterisks) lie on either side of dorsal blood vessel; F, detail of left-hand rectangle in 5D. Collar-trunk septum separates trunk coelom (above) from collar coelom (below); G, section through level of the mouth; lateral lips comprise ventral region of collar; posteroventral extremity of proboscis forms anterior margin of mouth; H, detail in the rectangle in 5G; beneath dorsal nerve cord is dorsal blood vessel with parts of trunk coelom (asterisks) on either side; I, section at level of posterior rim of mouth; buccal muscles approaching each other and will merge a few sections more posteriorly; pharynx comprising ventral digestive region (arrowheads) and dorsal branchial region (obliquely sectioned) penetrated by gill pores. Abbreviations for structural features: see text. Scale bars: A, C, D, G, I, 1 mm; B, 50 μm; E, 100 μm; F, 300 μm; H, 200 μm.
FIG. 4 in A new deep-sea species of epibenthic acorn worm (Hemichordata, Enteropneusta)
FIG. 4. — Fixed specimens of Tergivelum baldwinae n. gen., n. sp.: A, holotype (ventral view) which broke into three parts when fixed – namely the left back veil (lbv), most of intestinal region of trunk (at right), and anterior body (at left, comprising proboscis, collar, and anterior extremity of trunk); B, holotype (dorsal view, excluding left back veil) with numbered letters indicating levels of cross section in Figures 5 and 6; C, enlargement of anterior portion of holotype in ventral view; lateral lips of collar (arrowheads) curl dorsally as a preservation artifact; D, enlargement of anterior portion of the holotype in dorsal view; arrows indicate dorsal protuberances; E, enlargement of anterior portion of holotype in left side view with arrow indicating fossa of left proboscis nerve; F, dorsal view of anterior region of trunk of paratype II (corresponding to area in rectangle in panel 4D); back veils and dorsal protuberances dissected away revealing dorsal nerve cord (arrowed) flanked by slot-shaped gill pores. Abbreviations for structural features: see text. Scale bars: A, B, 1 cm; C-F, 2 mm.
FIG. 2 in A new deep-sea species of epibenthic acorn worm (Hemichordata, Enteropneusta)
FIG. 2. — Single video frames of living Tergivelum baldwinae n. gen., n. sp.: A, anterior of paratype IV, white arrowhead indicates fossa of left proboscis nerve; B, holotype laying down fecal trail; suction sampler in background; C, paratype II laying down fecal trail, 29 cm between red laser dots. Abbreviations: co, collar; lbv, left back veil; pr, proboscis; rlf, right lateroventral fold. Scale bars: A, 2 cm; B, C, 3 cm.
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