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1,140 results for “colonial”
A droplet digital polymerase chain reaction assay to detect rare helminth parasites infecting natural host populations (Vancouver Island 2023, University of Wisconsin Madison Laboratory colony 2024)
Helminth infections represent a significant challenge to human, livestock, and wildlife health, yet they remain relatively under-studied, especially in terms of their ecological impacts. Better understanding of how these parasites spread in wildlife populations could improve our ability to predict and manage disease transmission across various species. Traditional detection methods, such as visually identifying parasites in environmental samples or infected hosts, often fall short, especially during the early stages of infection when parasite loads are minimal. In this study, we introduce a highly sensitive and precise droplet digital PCR (ddPCR) assay that quantifies helminth DNA in aquatic habitats, focusing on the 18S rRNA gene as a marker. These data utilize the model host-parasite system between the tapeworm Schistocephalus solidus, and its cyclopoid copepod host, Acanthocyclops robustus. The molecular assays are built around creating an infection standard in the lab, where copepods were singly infected with a single tapeworm parasite. We extracted DNA from 100 infected adults and used this as a standard to translate gene copy numbers from the ddPCR reactions to actual animal values. After creating a known lab standard, we then use the generated probes and primers to detect (and quantify!) infection burdens in field samples, which include both water filter samples (eDNA) and zooplankton tows from several lakes around Vancouver Island, B.C. The data presented here include well-specific data from ddPCR runs (amplitude of individual level oil droplets in the reaction) as well as each ddPCR analysis in its entirety. In order to prove the specificity of probes and probe-primers, we include here ddPCR runs of closely related helminth species, Schistocephalus cotti and Schistocephalus pungitii. We also consider the binding to another genera of copepod, the calanoid Eurytomora. All of the data wrangling, analysis, and data visualization are included as .Rmd files in th
Double-crested Cormorant (Nannopterum auritum) nesting colony and environmental data in Biscayne National Park, Florida, USA (2009-2024)
Double-crested Cormorant (DCCO) nesting data were collected from colonies in Biscayne National Park (BISC) by the South Florida/Caribbean Inventory and Monitoring Network as part of the Colonial Nesting Birds vital sign monitoring program. Nesting data collected from 2010 to 2023 are included in this dataset. Salinity, chlorophyll, and ammonia data were acquired from sites monitored in the Surface Water Quality Monitoring Program managed by the Miami-Dade County Division of Environmental Management’s Department of Regulatory and Economic Resources (RER-DERM). Seagrass data were acquired from sites monitored by RER-DERM as a part of the Biscayne Bay Benthic Habitat Monitoring Program. Mangrove fish and epifauna data were acquired from the U.S. National Oceanic and Atmospheric Administration's (NOAA) Integrated Biscayne Bay Ecological Assessment and Monitoring Project (IBBEAM). Environmental data (salinity, chlorophyll, ammonia, seagrass, mangrove fish, and epifauna) were manipulated in order to examine the relationship between DCCO nesting trends and the BISC ecosystem. This data package is completed. Code included is pertinent to the methods described in "Assessment of ecosystem health in Biscayne National Park, Florida according to Double-crested Cormorant (Nannopterum auritum) nesting trends" by Taylor et al. 2025, currently submitted to and under review by Ecological Indicators.
Pre-Colonial and Modern Tree Data from Nine Northeastern States 1620-2008
The northeastern United States is a predominately-forested region that, like most of the eastern U.S., has undergone a 400-year history of intense logging, land clearance for agriculture, and natural reforestation. This setting affords the opportunity to address a major ecological question: How similar are today’s forests to those existing prior to European colonization? Working throughout a nine-state region spanning Maine to Pennsylvania, we assembled a comprehensive database of archival land-survey records describing the forests at the time of European colonization. We compared these records to modern forest inventory data and described: (1) the magnitude and attributes of forest compositional change, (2) the geography of change and (3) the relationships between change and environmental factors and historical land use. We found that with few exceptions, notably the American chestnut, the same taxa that made up the pre-colonial forest still comprise the forest today, despite ample opportunities for species invasion and loss. Nonetheless, there have been dramatic shifts in the relative abundance of forest taxa. The magnitude of change is spatially clustered at local scales (less than 125-km) but exhibits little evidence of regional-scale gradients. Compositional change is most strongly associated with the historical extent of agricultural clearing. Throughout the region, there has been a broad ecological shift away from late successional taxa, such as beech and hemlock, in favor of early- and mid-successional taxa, such as red maple and poplar. Additionally, the modern forest composition is more homogeneous and less coupled to local climatic controls.
Indicative distribution map for Ecosystem Functional Group MT2.2 Large seabird and pinniped colonies
<p>This archive contains indicative distribution maps and profiles for <strong>MT2.2 Large seabird and pinniped colonies</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.1). Please refer to Keith <em>et al.</em> (2020) and Keith <em>et al.</em> (2022) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Dataset: Does vendor breeding colony influence sign- and goal-tracking in Pavlovian conditioned approach?
<p>Vendor differences are thought to affect Pavlovian conditioning in rats. After observing possible differences in sign-tracking and goal-tracking behaviour with rats from different breeding colonies, we performed an empirical replication of the effect. 40 male Long-Evans rats from Charles River colonies ‘K72’ and ‘R06’ received 11 Pavlovian conditioned approach training sessions (or “autoshaping”), with a lever as the conditioned stimulus (CS) and 10% sucrose as the unconditioned stimulus (US). Each 58-min session consisted of 12 CS-US trials. Paired rats (n = 15/colony) received the US following lever retraction. Unpaired control rats (n = 5/colony) received sucrose during the inter-trial interval. Next, we evaluated the conditioned reinforcing properties of the CS, by determining whether rats would learn to nose-poke into a new, active (vs. inactive) port to receive CS presentations alone (no sucrose). Preregistered confirmatory analyses showed that during autoshaping sessions, Paired rats made significantly more CS-triggered entries into the sucrose port (i.e., goal-tracking) and lever activations (sign-tracking) than Unpaired rats did, demonstrating acquisition of the CS-US association. Confirmatory analyses showed no effects of breeding colony on autoshaping. During conditioned reinforcement testing, analysis of data from Paired rats alone showed significantly more active vs. inactive nosepokes, suggesting that in these rats, the lever CS acquired incentive motivational properties. Analysing Paired rats alone also showed that K72 rats had higher Pavlovian Conditioned Approach scores than R06 rats did. Thus, breeding colony can affect outcome in Pavlovian conditioned approach studies, and animal breeding source should be considered as a covariate in such work.Vendor differences are thought to affect Pavlovian conditioning in rats. After observing possible differences in sign-tracking and goal-tracking behaviour with rats from different breeding colonies, we performed an empirical replication of the effect. 40 male Long-Evans rats from Charles River colonies ‘K72’ and ‘R06’ received 11 Pavlovian conditioned approach training sessions (or “autoshaping”), with a lever as the conditioned stimulus (CS) and 10% sucrose as the unconditioned stimulus (US). Each 58-min session consisted of 12 CS-US trials. Paired rats (n = 15/colony) received the US following lever retraction. Unpaired control rats (n = 5/colony) received sucrose during the inter-trial interval. Next, we evaluated the conditioned reinforcing properties of the CS, by determining whether rats would learn to nose-poke into a new, active (vs. inactive) port to receive CS presentations alone (no sucrose). Preregistered confirmatory analyses showed that during autoshaping sessions, Paired rats made significantly more CS-triggered entries into the sucrose port (i.e., goal-tracking) and lever activations (sign-tracking) than Unpaired rats did, demonstrating acquisition of the CS-US association. Confirmatory analyses showed no effects of breeding colony on autoshaping. During conditioned reinforcement testing, analysis of data from Paired rats alone showed significantly more active vs. inactive nosepokes, suggesting that in these rats, the lever CS acquired incentive motivational properties. Analysing Paired rats alone also showed that K72 rats had higher Pavlovian Conditioned Approach scores than R06 rats did. Thus, breeding colony can affect outcome in Pavlovian conditioned approach studies, and animal breeding source should be considered as a covariate in such work.</p>
MCR LTER: Coral Reef Resilience: Live and Dead Pocillopora and Acropora Coral Colony Time Series from 2006 to 2011
These data describe the abundance, size structure, and morphologies of living and dead corals belonging to the genera Pocillopora and Acropora on the forereef (depth = 10 meters) in 2006, 2009, 2010, and 2011. Data were derived from a randomly chosen subset of photo quadrats associated with knb-lter-mcr.4. For each quadrat, individual coral colonies were identified to genus, scored as living or dead, and the total area of their footprint calculated. In addition, branch morphology was scored on a scale from 1 to 3, with 1 representing very tight spacing, and 3 representing open spacing among adjacent branches. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
Adelie penguin colony-specific chick production, 1991-2024
The fundamental long-term objective of the seabird component of the Palmer LTER (PAL) has been to identify and understand the mechanistic processes that regulate the mean fitness (population growth rate) of regional penguin populations. Since the inception of PAL, Adélie penguin populations have effectively collapsed, gentoo penguin populations have increased dramatically and chinstrap penguin populations have remained relatively stable. These trends are spatially and temporally coherent with regional warming and decreasing sea ice duration. Adélie penguins are an ice-obligate polar species whose life history is intimately linked to the presence of sea ice, while chinstrap and gentoo penguins are ice-intolerant species whose life histories evolved in the sub-Antarctic, where sea ice is a less permanent feature of the marine ecosystem. The PAL study region includes five main islands on which Adélie penguin colonies have historically occurred, with each island containing a different number of spatially segregated sub-colonies. These colonies are censused to determine the total number of nests and chicks produced each year, and breeding success. Diet samples are acquired to understand diet composition (e.g., krill, fish) and krill length-frequencies. In general, krill constitute the most important component of the summer diets by mass of these three penguin species, but changes in PAL krill abundances have exhibited no long-term trends and thus far, have failed to explain the divergent patterns in penguin populations evident in our time series. Chick fledging masses are recorded as a cumulative measure of climate, weather, diet, and parental influences on chick health at the end of the breeding season. These data have provided valuable insights into the marine and terrestrial factors that influence Adélie penguin population fitness. No data were collected during the 2021-2022 season due to the Palmer Station pier rebuild.
ARCA (Arte Colonial Americano)
<p>El proyecto ARCA, Arte colonial americano, es una curaduría visual que contiene veinticinco mil pinturas coloniales producidas en las tres américas: Hispano, Luso y Angloamérica. Además de exponer la riqueza visual americana entre 1550 a 1830, fechas extremas de esta colección, se trata de explorar los datos y metadatos que ofrecen las pinturas de manera digital. Por esta razón es una base de datos relacional, interactiva y con algunas herramientas de análisis que permiten extender la escala de la investigación más allá de los mecanismos tradicionales. Arca parte de las propuestas de las Humanidades Digitales, y particularmente se traza como un proyecto de historia digital, en dos sentidos: primero, históricamente abre la exploración a los problemas de la cultura visual colonial desde sus metadatos. En segundo lugar, convierte esta base de datos en un campo para experimentar con metodologías digitales de minería de datos y lectura distante. </p>
Scan4CFU: Low-cost, open-source bacterial colony tracking over large areas and extended incubation times
<p>A hallmark of bacterial populations cultured <em>in vitro</em> is their homogeneity of growth, where the majority of cells display identical growth rate, cell size and content. Recent insights, however, have revealed that even cells growing in exponential growth phase can be heterogeneous with respect to variables typically used to measure cell growth. Bacterial heterogeneity has important implications for how bacteria respond to environmental stresses, such as antibiotics. The phenomenon of antimicrobial persistence, for example, has been linked to a small subpopulation of cells that have entered into a state of dormancy where antibiotics are no longer effective. While methods have been developed for identifying individual non-growing cells in bacterial cultures, there has been less attention paid to how these cells may influence growth in colonies on a solid surface. In response, we have developed a low-cost, open-source platform to perform automated image capture and image analysis of bacterial colony growth on multiple nutrient agar plates simultaneously. The descriptions of the hardware and software are included, along with details about the temperature-controlled growth chamber, high-resolution scanner, and graphical interface to extract and plot the colony lag time and growth kinetics. Experiments were conducted using a wild type strain of <em>Escherichia coli </em>K12 to demonstrate the feasibility and operation of our setup. By automated tracking of bacterial growth kinetics in colonies, the system holds the potential to reveal new insights into understanding the impact of microbial heterogeneity on antibiotic resistance and persistence. </p>
TARA Pacific CTAX colony morphological annotations release version 1_1
<p>PHOTO dataset (<em>in situ</em> photos) and the colony morphometric analysis using <em>in situ </em>photographs of two scleractinian corals and one hydrozoan coral taken during the TARA Pacific Expedition: <em>Pocillopra </em>spp., <em>Porites </em>spp. and <em>Millepora </em>spp. respectively.</p>
Dataset for: Biohybrid superorganisms - on the design of a robotic system for thermal interactions with honeybee colonies
<p>Dataset containing electronic, mechical, firmware, and software design files associated with the article: </p> <p><br>"Biohybrid superorganisms - on the design of a robotic system for thermal interactions with honeybee colonies"<br>By R. Barmak, D. N. Hofstadler, M. Stefanec, L. Piotet, R. Cherfan, T. Schmickl, F. Mondada, and R. Mills. EPFL, Switzerland and Univeristy of Graz, Austria.<br>IEEE Access, 2024, Vol 12, pp 50849-50871.</p> <p>doi: 10.1109/ACCESS.2024.3385658</p> <p><a href="https://doi.org/10.1109/ACCESS.2024.3385658">https://doi.org/10.1109/ACCESS.2024.3385658</a></p> <p> </p> <table> <tbody> <tr> <td><strong>File name</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>1_hw_pcb_schematics_rev2.pdf</td> <td>Electrical schematic of the robotic frame</td> </tr> <tr> <td>2_hw_pcb_stackup_rev2.pdf </td> <td>Technical specifications for the robotic frame PCB manufacturing</td> </tr> <tr> <td>3_hw_pcb_bom_rev2.pdf </td> <td>Electronics Bill of Materials (BoM)</td> </tr> <tr> <td>4_hw_pcb_gerber_rev2.zip </td> <td>Robotic frame PCB manufacturing files (gerbers)</td> </tr> <tr> <td>5_hw_pcb_altium_rev2.zip</td> <td>Altium Designer project files</td> </tr> <tr> <td>6_hw_mechanical_rev2.zip</td> <td>DXF and STEP files of the mechanical structure of the robotic frame</td> </tr> <tr> <td>7_sw_firmware_rev2.zip</td> <td>Firmware source code and compiled binaries for STM32 microcontroller</td> </tr> <tr> <td>8_sw_handlers-1.0.1.zip</td> <td>Software for high-level interface to robot from a host device </td> </tr> </tbody> </table>
Mass mortality among colony-breeding seabirds in the German Wadden Sea in 2022 due to distinct genotypes of HPAIV H5N1 clade 2.3.4.4b: data sets on phylogeographic analyses
<p>Highly pathogenic avian influenza viruses (HPAIV) of clade 2.3.4.4b of the H5 goose/Guangdong (gs/GD) lineage have repeatedly emerged in Germany since 2016. Both poultry holdings and wild birds have been heavily hit but the 2020-2021 and 2021-2022 HPAI winter seasons exceeded all previously recorded epizootics in Germany in terms of number of wild bird cases recorded, genetic diversity of viruses, and duration of virus activity. In past seasons regional massing of wild bird cases were seen at the German coasts of the Baltic and North Sea, but species mainly affected varied from season to season. In 2022 a new and, in Europe, unprecedented aspect was observed when several cormorant and seabird breeding colonies became affected since May at the Baltic Sea coast and in the Wadden Sea, respectively by HPAI H5N1 viruses.</p> <p> </p>
Phaeocystis globosa colonial gene expression
<p>Data and analysis for the paper: </p> <p><strong>Differential gene expression supports a resource-intensive, defensive role for colony production in the bloom-forming haptophyte, <em>Phaeocystis globosa</em></strong></p> <p>by: Margaret Mars Brisbin and Satoshi Mitarai</p> <p>The <em>Phaeocystis globosa</em> CCMP1528 transcriptome used in the study (phaeocystisglobosa_euk_seqs.fasta or pg_euk_seqs_altnames.fasta) was assembled with trimmed sequencing reads from 8 biological replicates (4 colonial replicates and 4 solitary replicates) with the Trinity software (v2.3.2).</p> <p>Raw sequencing reads are available from the NCBI SRA with accession numbers: SRR7811979–SRR7811986.</p> <p>Before assembling the transcriptome, reads were quality filtered and trimmed with the Trimmomatic software (v3.36) using the command:</p> <pre><code>java -jar $TRIM/trimmomatic-0.36.jar PE -phred33 $DATA2/S${SLURM_ARRAY_TASK_ID}_S*_R1_001.fastq.gz \ $DATA2/S${SLURM_ARRAY_TASK_ID}_S*_R2_001.fastq.gz \ $OUT/S${SLURM_ARRAY_TASK_ID}_1_paired.fq $OUT/S${SLURM_ARRAY_TASK_ID}_1_unpaired.fq \ $OUT/S${SLURM_ARRAY_TASK_ID}_2_paired.fq $OUT/S${SLURM_ARRAY_TASK_ID}_2_unpaired.fq \ ILLUMINACLIP:$TRIM/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36</code></pre> <p>Trimmed reads were mapped to the ERCC reference sequences for Mix1 and mapped reads were filtered using the following commands from bowtie2 (v2.2.6), samtools, and bedtools: </p> <pre><code>bowtie2 -t -x $REF \ -1 $DATA/S${SLURM_ARRAY_TASK_ID}_1_paired.fq \ -2 $DATA/S${SLURM_ARRAY_TASK_ID}_2_paired.fq \ -S $OUT/S${SLURM_ARRAY_TASK_ID}_ercc.sam samtools view -bS $DATA/S${SLURM_ARRAY_TASK_ID}_ercc.sam >$DATA/S${SLURM_ARRAY_TASK_ID}.bam samtools sort $DATA/S${SLURM_ARRAY_TASK_ID}.bam $DATA/S${SLURM_ARRAY_TASK_ID}_sorted samtools view -b -f 13 S${SLURM_ARRAY_TASK_ID}_sorted.bam > S${SLURM_ARRAY_TASK_ID}_unmapped.bam samtools sort -n $DATA/S${SLURM_ARRAY_TASK_ID}_unmapped.bam $DATA/S${SLURM_ARRAY_TASK_ID}.qsort bedtools bamtofastq -i $DATA/S${SLURM_ARRAY_TASK_ID}.qsort.bam -fq $DATA/S${SLURM_ARRAY_TASK_ID}_1_paired.fq -fq2 $DATA/S${SLURM_ARRAY_TASK_ID}_2_paired.fq</code></pre> <p>The resulting Trimmed reads without ERCC sequences were used to make the transcriptome assembly: </p> <pre><code>Trinity --seqType fq --max_memory 475G \ --left $DATA2/C1_1_paired.fq,$DATA2/C2_1_paired.fq,$DATA2/C3_1_paired.fq,$DATA2/C4_1_paired.fq,$DATA2/S1_1_paired.fq,$DATA2/S2_1_paired.fq,$DATA2/S3_1_paired.fq,$DATA2/S4_1_paired.fq \ --right $DATA2/C1_2_paired.fq,$DATA2/C2_1_paired.fq,$DATA2/C3_2_paired.fq,$DATA2/C4_2_paired.fq,$DATA2/S1_2_paired.fq,$DATA2/S2_2_paired.fq,$DATA2/S3_2_paired.fq,$DATA2/S4_2_paired.fq \ --CPU 12</code></pre> <p>The Trinity assembly was dereplicated with CD-HIT-EST (v2016-0304) at 95% : </p> <pre><code>cd-hit-est -i $DATA/Trinity.fasta -o Trinity_Pg_clustered_95 -c 0.95 -n 8 -p 1 -g 1 -M 200000 -T 8 -d 40</code></pre> <p>The Trinity assembly was filtered to remove bacterial contamination by first running a blastn(v2.6.0+) against the nr/nt NCBI database:</p> <pre><code>blastn -query $DATA/Trinity_Pg_clustered_95.fasta -task blastn -db $REF -num_threads 12 -max_target_seqs 1 -outfmt 5 > TrinityBlast.xml</code></pre> <p>and then removing bacterial reads with custom python scripts included here: TrinityBlastXML.ipynb and FIlterTrinityEukNotEuk.ipynb </p> <p>RSEM (v1.2.22) was run with the final transcriptome assembly (phaeocystisglobosa_euk_seqs.fasta or pg_euk_seqs_altnames.fasta): </p> <pre><code>rsem-calculate-expression --bowtie2 --paired-end \ $DATA/C${SLURM_ARRAY_TASK_ID}_1_paired.fq \ $DATA/C${SLURM_ARRAY_TASK_ID}_2_paired.fq \ $REF/rsemref_longISO/pg_euks_RSEMref \ $REF/rsemout_longISO/C${SLURM_ARRAY_TASK_ID} rsem-calculate-expression --bowtie2 --paired-end \ $DATA/S${SLURM_ARRAY_TASK_ID}_1_paired.fq \ $DATA/S${SLURM_ARRAY_TASK_ID}_2_paired.fq \ $REF/rsemref_longISO/pg_euks_RSEMref \ $REF/rsemout_longISO/S${SLURM_ARRAY_TASK_ID} </code></pre> <p>The resulting data files are: C*.genes.results and S*.genes.results which were used with DESeq2 in the R environment to analyze different gene expression. The code for these analyses is available in html and R markdown (PhaeoColSol_DE.html, PhaeoColSol_DE.Rmd). </p> <p>The transcriptome assembly was annotated with the Dammit software (v1.0rc2), which wraps Transdecoder, HMMER, and BUSCO, and by submitting the translated amino acid sequences to GhostKOALA. </p> <p>The raw pfam Dammit annotation results are included: pg_euk_seqs.fasta.x.pfam.gff3. These results were parsed with the script: Pfam_gffParsing.ipynb. The resulting file, pfam_parsed_annotation.csv, is used in the script PhaeoColSol_DE.Rmd with pfam2go4R.txt for GO enrichment analysis. The script shinycolsol.Rmd creates an interactive plot of GO enrichment results. </p> <p>The GhostKOALA results are user_ko.csv, and are used in the script PhaeoColSol_DE.Rmd for KEGG pathway enrichment analysis. </p>
Dataset on the dental morphology and occlusal dental wear of pre-colonial societies of the South and Southeast Coast of Brazil
<p>This dataset compiles information on dental morphology and occlusal dental wear of 431 individuals exhumed from coastal and riverine sites of the South and Southeast Coast of Brazil, dated between approximately 10,000 to 1,000 years before present. Dental traits were scored according to the Arizona State University Dental Anthropology System (ASUDAS) (Scott and Irish, 2017; Turner II et al., 1991). Few additional mandibular traits were added following Hauser and Stefano (1989). Occlusal dental wear was scored according to the method described in Smith (1984).</p> <p>Sex and age at death estimations derive from previous studies (Estevam, 2020; Fischer, 2012; Neves et al., 2005; Silva, 2005; Tognoli, 2016; Wesolowski, 2007). When this information was not available from previous studies, it was assessed by the first author (Fidalgo, 2021) using standard protocol methods (Buikstra and Ubelaker, 1994). Further detailed information and description of each variable can be consulted within the “description” and “dental grades” sheets in the excel file.</p> <p>The dataset is part of a PhD project developed at the Museu de Arqueologia e Etnologia da Universidade de São Paulo, carried by Daniel Fidalgo and advised by Veronica Wesolowski and Mark Hubbe (Fidalgo, 2021). Manuscripts have already been published using this data (Fidalgo et al., 2021a, 2021b). All research was funded by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), grants 17/20637-4 and 19/18289-3. It was also supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) grant 001.</p>
Raw images used for colony classification
<p>Raw images of plates with yeast colonies used in Figure 2 of "Carl et al. A fully automated deep learning pipeline for high-throughput colony segmentation and classification" (Biology Open 2020 : bio.052936 doi: 10.1242/bio.052936 Published 2 June 2020). The paper describes the development of a novel computational pipeline for colony segmentation and classification that achieves accuracy comparable to human performance.</p> <p>The actual data was generated in a project that was published earlier (Duempelmann, L. e<em>t al. </em>Inheritance of a Phenotypically Neutral Epimutation Evokes Gene Silencing in Later Generations. <em>Molecular Cell</em> <strong>74, 3</strong> (2019).) The experiments were testing trans-generational inheritance of <em>ade6<sup>+</sup> </em>silencing in <em>Schizosaccharomyces pombe</em>. <em>ade6<sup>+</sup></em> silencing was first induced by expression of small interfering RNAs (siRNAs) that are complementary to the <em>ade6<sup>+</sup></em> gene in a <em>paf1-Q264Stop</em> nonsense-mutant background, leading to red colonies. Paf1 is a subunit of the Paf1 complex (Paf1C), which represses siRNA-induced heterochromatin formation in <em>S. pombe</em>.</p>
Fig. 8. Proformica nasuta Nylander, 1856, male from colony Tarascon 1, France. A. Lateral view. B in Redescription of Proformica nasuta (Nylander, 1856) (Hymenoptera, Formicidae) using an integrative approach
Fig. 8. Proformica nasuta Nylander, 1856, male from colony Tarascon 1, France. A. Lateral view. B. Head in full face view. C. Genitalia in dorsal view. Scale bars = 1 mm. Automontage: Claude Lebas.
Fig. 7. Proformica nasuta Nylander, 1856, queen from colony Beaucaire 1, France. A. Lateral view. B. Dorsal view. C in Redescription of Proformica nasuta (Nylander, 1856) (Hymenoptera, Formicidae) using an integrative approach
Fig. 7. Proformica nasuta Nylander, 1856, queen from colony Beaucaire 1, France. A. Lateral view. B. Dorsal view. C. Head in full face view. Scale bars = 1 mm. Automontage: Claude Lebas.
Dataset of Chen et al. (2023) "MCount: An automated colony counting tool for high-throughput microbiology"
<p>Folder "96 well colonies" contains 10 microplate images with the original resolution. Folder "results" contains a segmentation and quantification results from the microplate images. Folder "Codes" includes Python source code.</p>
Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity
<p>Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed that predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival, or reproduction. Here, we a priori examined the genomic impact of urbanisation on the Neotropical túngara frog (<em>Engystomops pustulosu</em>s), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared to forest populations, and genomic variation was best explained by geographic distance rather than environmental factors. Adopting an a posteriori approach, we additionally found both urban and forest populations to have undergone population declines. The timing of these declines appears to coincide with extensive human activity around the Panama Canal during the last few centuries rather than recent urbanisation. Our study highlights the long-lasting legacy of past anthropogenic disturbances in the genome and the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact non-urban areas on both recent and older timescales. </p>
Solitary foundation or colony fission in ants: an intraspecific study shows that worker presence and number increase colony foundation success
<p>Datasets for the paper published in Oecologia entitled "Solitary foundation or colony fission in ants: an intraspecific study shows that worker presence and number increase colony foundation success"</p> <p>Script_article.R : R code to analyze the data</p> <p>Data.txt : Growth data</p> <p>donnees_survie.txt : Survival data</p> <p>donnees_presence_nid.txt : Data of the presence of queens in the nest</p>
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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.