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13,621 results for “Biologics”
Testing TOMRES rootstocks and their efficiency to utilize biologically fixed nitrogen coming from legumes green manure
<p>This experiment was established to test a promising TOMRES variety cultivated under organic and conventional crop system and test different rootstocks coming from the TOMRES collection. In the organic treatment, legumes were pre-cultivated before the tomato crop and were incorporated in soil as green manure. Worms were also applied in the crop to test their ability to increase yield and wue in tomato crop.</p>
Additional climate information for research paper «Ecological and Geographical Analysis of Distribution of Heracleum persicum, H. mantegazzianum and H. sosnowskyi on The Northern Limit of Its Invaded Range in Europe» submitted to Russian Journal of Biological Invasions
<p><strong>Additional climate information for research paper «Ecological and Geographical Analysis of Distribution of Heracleum persicum, H. mantegazzianum and H. sosnowskyi on The Northern Limit of Its Invaded Range in Europe» submitted to Russian Journal of Biological Invasions </strong></p>
The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
<p>Modern proteomics approaches can explore whole proteomes within a single mass spectrometry (MS) run. However, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and expertise needed from a diverse array of fields. In particular, in the field of microbiology, efforts to combine large-scale proteomic datasets have so far largely been missing. Thus, despite their relatively small genomes, the proteomes of most archaea remain incompletely characterized. This in turn undermines our ability to gain a greater understanding of archaeal cell biology.</p> <p>Therefore, we have initiated the Archaeal Proteome Project (ArcPP), a community effort that works towards a comprehensive analysis of archaeal proteomes. Starting with the model archaeon <em>Haloferax volcanii</em>, using state-of-the-art bioinformatic tools, we have:</p> <ul> <li>reanalyzed more than 26 Mio. spectra</li> <li>optimized the analysis using parameter sweeps, multiple search engines implemented in Ursgal, and the combination of results through the combined PEP approach</li> <li>thoroughly controlled false discovery rates for high confidence protein identifications using the picked protein FDR approach and limiting FDR to 0.5%</li> <li>identified more than 45k peptides, corresponding to 3069 proteins (>75% of the proteome) with a median sequence coverage of 55%.</li> <li>analyzed N-terminal protein processing, including N-terminal acetylation and signal peptide cleavage</li> <li>performed a detailed glycoproteomic analysis, identifying >230 glycopeptides corresponding to 45 glycoproteins</li> </ul> <p>Benefiting from the established bioinformatic infrastructure, we will follow up on this analysis focusing on <em>H. volcanii</em> proteogenomics as well as the characterization of additional post-translational modifications. Furthermore, ArcPP will integrate quantitative results obtained from the individual datasets in order to identify common regulatory mechanisms. These studies on the <em>H. volcanii</em> proteome can serve as a blueprint for comprehensive proteomic analyses performed on a diverse range of archaea and bacteria.</p> <p> </p> <p>For further details, please refer to the following publications. Please also cite this work if you use these results for further analyses:</p> <p>Schulze, S., Adams, Z., Cerletti, M. <em>et al.</em> The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. <em>Nat Commun</em> <strong>11, </strong>3145 (2020). <a href="https://doi.org/10.1038/s41467-020-16784-7">https://doi.org/10.1038/s41467-020-16784-7</a></p> <p>Schulze, S.; Pfeiffer, F.; Garcia, B.A.; Pohlschroder, M. (2021). Comprehensive glycoproteomics shines new light on the complexity and extent of glycosylation in archaea. <em>PLOS Biol</em>. https://doi.org/10.1371/journal.pbio.3001277</p> <p> </p> <p>An interactive website to explore the combined results can be found at <a href="https://archaealproteomeproject.org/">https://archaealproteomeproject.org/</a></p> <p>Scripts and metadata used for the analysis can be found at <a href="https://github.com/arcpp/ArcPP">https://github.com/arcpp/ArcPP</a></p> <p> </p> <p><strong>Updates version 1.3.0:</strong></p> <p>- includes dataset PXD021827</p> <p><strong>Updates version 1.2.0:</strong></p> <p>- Includes dataset PXD021874<br> - Includes results from a comprehensive glycoproteomic analysis of ArcPP datasets</p> <p><strong>Updates version 1.1.0:</strong><br> - <em>Natrialba magadii</em> results are included in PXD009116.zip</p>
Two decades of annual landscape-scale tree growth and dynamics in old-growth tropical rainforest in the CARBONO Project, La Selva Biological Station, 1997-2018
<p>Here we present the complete data series from a 21-yr study of the annual growth and dynamics of trees, palms and lianas in the old-growth tropical rainforest at the La Selva Biological Station in Costa Rica. These observations were part of the CARBONO Project, a multidisciplinary team study of forest carbon cycling. The project was designed to assess forest processes at the landscape scale by sampling with replication across the within-landscape edaphic heterogeneity typical of tropical forests. Through more than two decades, forest growth and dynamics were assessed annually. The annual time-step used in the CARBONO Project effectively captured forest responses to major disturbances and to interannual and climatic variation. Annual measurements also enhanced the accuracy and long-term consistency of the data. To our knowledge, the resulting records are unique for tropical forests, where the dominant approach to studying the dynamics of a given forest has been to use a single plot and multi-year inter-census intervals. To date these CARBONO Project data have revealed: multi-decadal forest stability in spite of the short-term changes in forest structure resulting from major natural disturbances (e.g., the 1997-1998 Strong El Niño, and the extreme windstorm of May 2018); the dynamics and importance of large trees; and the responses of a major component of ecosystem productivity, aboveground wood production, to interannual and long-term climatic and atmospheric change. These data have also contributed to many remote-sensing studies.</p> <p>The data set consists of annual observations through the period 1997–2018 of the floristics, survival, recruitment, and growth of all woody stems (diameter <u>></u> 10 cm) in a landscape-scale plot network. At completion of the study, the data spanned 6705 individuals and 21 years. The data set is complete and has been through extensive internal checks for quality assurance. Detailed data documentation and an emphasis on measurement repeatability were prioritized through the study. The metadata include an extensive README file describing the data files and the methods, a document detailing the data management and qa/qc, and the scanned original field data-sheets for the 22 annual censuses.</p> <p>We gratefully acknowledge the careful long-term field work and data entry and checking by paraforesters Leonel Campos Otoya and William Miranda Conejo. Logistical support and the long-term protection of the La Selva reserve were provided by the Organization for Tropical Studies. The Ministerio de Ambiente y Energía of Costa Rica granted permits to carry out this study through the years of the study (most recently: Resolución No. 037-2018-ACCVC-PI).</p>
The burden of size and growth for the juveniles of large mammalian herbivores: structural and functional constraints in the feeding biology of juveniles relative to adults in red kangaroos, Osphranter rufus
<p>Juvenile mammals in their post weaning developmental stages face many challenges in transitioning to adulthood. Among large grazing species such as ruminant bovids and cervids an overarching challenge is acquiring and processing sufficient nutrients to survive and grow, with a gut that may not yet be fully developed. Marsupial kangaroos of Australia face similar challenges; they also digest vegetation by fermentation in a large foregut. In red kangaroos, Osphranter rufus (= Macropus rufus), the dominant species of Australia's arid interior, females may breed continuously; however, juvenile recruitment to the adult population is irregular and coincident with sporadic rainfall. As compared with adult females the nutritional requirements of juvenile O. rufus are high in relation to their body mass (BM), largely due to the cost of their rapid growth. We examined processes that juveniles have in their morphology, physiology and behaviours to meet their elevated nutritional needs, by comparing recently weaned juveniles of both sexes and adult female O. rufus in their desert habitat. Features studied include relative body sizes, relative dimensions and capacities of principal gut regions, the foregut, small intestine, caecum and large intestine with rectum. Also examined were digesta attributes and rates of digesta excretion. Additionally, the rates of change in skull parameters and dental characteristics to maturity were assessed. Field determinations of diet choice were made for both age classes. In juveniles the content masses of major gut structures were related to body mass (BM), as were those of adult females, i. e. ~BM1.0. In both age classes the digesta mass of the foreguts exceeded 75 % of the total digesta mass. Diets of both juvenile and adult O. rufus largely focused on grasses. Juveniles had higher rates of digesta excretion while foraging than adults. In addition, the foregut contents in juveniles occupies proportionally less of the total gut than in adult females. Together, the higher excretion rate and smaller relative foregut of juveniles suggests that they necessarily focus on forage that can be rapidly digested, such as young, green grasses or herbage. Comparison of the skulls of juveniles and adults revealed how this harvest can occur. Relative to BM juveniles had skulls of larger volume than adults. Additionally, during growth the skull lengthens proportionally faster than increasing. By weaning the dimensions of the incisor bite of juveniles neared those of adult females. The area of wear on premolars/molars increased only slowly relative to the development of incisors, further pointing to juveniles selecting more digestible forage than adults. The intermittent availability of such forage, principally young grasses, appears key to the significant recruitment into the O. rufus population in their arid habitat.</p>
Data from: Chemical novelty facilitates herbivore resistance and biological invasions in some introduced plant species
Ecological release from herbivory due to chemical novelty is commonly predicted to facilitate biological invasions by plants, but has not been tested on a community scale. We used metabolomics based on mass spectrometry molecular networks to assess the novelty of foliar secondary chemistry of 15 invasive plant species compared to 46 native species at a site in eastern North America. Locally, invasive species were more chemically distinctive than natives. Among the 15 invasive species, the more chemically distinct were less preferred by insect herbivores and less browsed by deer. Finally, an assessment of invasion frequency in 2,505 forest plots in the Atlantic coastal plain revealed that, regionally, invasive species that were less preferred by insect herbivores, less browsed by white-tailed deer, and chemically distinct relative to the native plant community occurred more frequently in survey plots. Our results suggest that chemically-mediated release from herbivores contributes to many successful invasions.
Data from: Processing citizen science- and machine-annotated time-lapse imagery for biologically meaningful metrics
Time-lapse cameras facilitate remote and high-resolution monitoring of wild animal and plant communities, but the image data produced require further processing to be useful. Here we publish pipelines to process raw time-lapse imagery, resulting in count data (number of penguins per image) and 'nearest neighbour distance' measurements. The latter provide useful summaries of colony spatial structure (which can indicate phenological stage) and can be used to detect movement – metrics which could be valuable for a number of different monitoring scenarios, including image capture during aerial surveys. We present two alternative pathways for producing counts: 1) via the Zooniverse citizen science project Penguin Watch and 2) via a computer vision algorithm (Pengbot), and share a comparison of citizen science-, machine learning-, and expert- derived counts. We provide example files for 14 Penguin Watch cameras, generated from 63,070 raw images annotated by 50,445 volunteers. We encourage the use of this large open-source dataset, and the associated processing methodologies, for both ecological studies and continued machine learning and computer vision development.
Data of the effects of temperature and dissolved oxygen on thermal biology and aerobic metabolism of tropical Callinectes sapidus crabs
<p>This file contains raw data on the effects of temperature and dissolved oxygen on several aspects of the physiology of the Callinectes sapidus tropical population. </p> <p>I. Data on thermal biology includes the effects of acclimation temperatures on 1) Preferred temperature; 2) Critical thermal minima and maxima; 3) Thermal safety margin (TSM); Thermal metabolic scope (TMS).</p> <p>II. Data on the combined effects of temperature and dissolved oxygen on routine oxygen consumption of C. sapidus. </p> <p>Those data was sent as a scientific paper to the Journal of Thermal Biology. </p> <p> </p>
Dataset for manuscript entitled "The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm"
<p>The following datasets were used for the 16s rRNA analysis in the manuscript entitled " The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm". BZ2 files were obtained from next generation sequencing with the Illumina Mi-Seq. Mothur was used to analyze the BZ2 files, creating the listed excel documents.</p>
Figure 19. Distribution map for Revena plaumanni Bondar, 1943 in Biological aspects and redescription of the weevil Revena plaumanni Bondar (Coleoptera: Curculionidae)
Figure 19. Distribution map for Revena plaumanni Bondar, 1943.
Figure 3 in Biological aspects and redescription of the weevil Revena plaumanni Bondar (Coleoptera: Curculionidae)
Figure 3. Adult of Revena plaumanni, lateral view. Scale line = 1 mm.
Figure 43 in Eucnemid larvae of the Nearctic region. Part V: Fifth instar larval descriptions for eight species of Microrhagus Dejean, 1833 (Coleoptera: Eucnemidae: Melasinae: Dirhagini), with descriptions of four new species and notes on their biology
Figure 43. Microrhagus brunneus, fifth instar, dorsal habitus. Scale line = 2.0 mm.
Figures 1–2. Rearing method. 1 in Eucnemid larvae of the Nearctic region. Part V: Fifth instar larval descriptions for eight species of Microrhagus Dejean, 1833 (Coleoptera: Eucnemidae: Melasinae: Dirhagini), with descriptions of four new species and notes on their biology
Figures 1–2. Rearing method. 1) Storage bag with rotten wood and data. 2) Examined rotten wood.
Figure 38 in Eucnemid larvae of the Nearctic region. Part V: Fifth instar larval descriptions for eight species of Microrhagus Dejean, 1833 (Coleoptera: Eucnemidae: Melasinae: Dirhagini), with descriptions of four new species and notes on their biology
Figure 38. Microrhagus breviangularis, fifth instar, dorsal habitus of paratype.
Figure 61 in Eucnemid larvae of the Nearctic region. Part V: Fifth instar larval descriptions for eight species of Microrhagus Dejean, 1833 (Coleoptera: Eucnemidae: Melasinae: Dirhagini), with descriptions of four new species and notes on their biology
Figure 61. Microrhagus lecontei, fifth instar, dorsal habitus of paratype. Scale line = 2.0 mm.
Resource competition shapes biological rhythms and promotes temporal niche differentiation in a community simulation
<p>This is the code and dataset for the article entitled "Resource competition shapes biological rhythms and promotes temporal niche differentiation in a community simulation," in the journal Ecology and Evolution.</p> <ul> <li>Competition for resources often contributes strongly to defining an organism's ecological niche. Endogenous biological rhythms are important adaptations to the temporal dimension of niches, but how other organisms influence such temporal niches have not been much studied, and the role of competition in particular has been even less examined. We investigated how interspecific and intraspecific competition for resources shape an organism's activity rhythms.</li> <li>To do this, we simulated communities of one or two species in an agent-based model. Individuals in the simulation move according to a circadian activity rhythm and compete for limited resources. Probability of reproduction is proportional to an individual's success in obtaining resources. Offspring may have variance in rhythm parameters, which allow for the population to evolve over time.</li> <li>We demonstrate that when organisms are arrhythmic, one species will always be competitively excluded from the environment, but the existence of activity rhythms allows niche differentiation and indefinite coexistence of the two species. Two species which are initially active at the same phase will differentiate their phase angle of entrainment over time to avoid each other. When only one species is present in an environment, competition within the species strongly selects for niche expansion through arrhythmicity, but the addition of an interspecific competitor facilitates evolution of increased rhythmic amplitude when combined with additional adaptations for temporal specialization. Finally, if individuals preferentially mate with others who are active at similar times of day, then disruptive selection by intraspecific competition can split one population into two reproductively isolated groups separated in activity time.</li> <li>These simulations suggest that biological rhythms are an effective method to temporally differentiate ecological niches, and that competition is an important ecological pressure promoting the evolution of rhythms and sleep. This is the first study to use ecological modeling to examine biological rhythms.</li> </ul>
Figure 4 in Comparative population biology of Uca rapax (Smith, 1870) (Brachyura, Ocypodidae) from two subtropical mangrove habitats on the Brazilian coast
Figure 4. Uca rapax. Monthly size–frequency distributions for the Ubatumirim population.
Figure 3 in Comparative population biology of Uca rapax (Smith, 1870) (Brachyura, Ocypodidae) from two subtropical mangrove habitats on the Brazilian coast
Figure 3. Uca rapax. Monthly size–frequency distributions for the Itamambuca population.
Figure 3 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 3. Pupae containing the exoskeletons of adults. (a) Female; (b) male.
Figure 7 in Biology and life cycle of Tmetonyx similis (G. O. Sars, 1891) (Amphipoda, Lysianassidae), a scavenging amphipod from the continental slope of the Mediterranean
Figure 7. Development of the various male and female generations.
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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.