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253 results for “functional organization”
Data for: Cover crop functional types differentially alter the content and composition of soil organic carbon in particulate and mineral-associated fractions
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Soil organic matter responses to nutrient enrichment in the Nutrient Network:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function.
This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
Soil organic matter, total nitrogen and pH:Microbial composition and function across an old-field chronosequence
As mediators of biogeochemical cycles, understanding the ecological forces structuring soil microbial communities is of ecosystem-level significance. Due to gradual shifts in plant species composition and litter addition through time, succession can be used as a model to understand how plant communities shape microbial community composition and function in soil. Numerous studies have investigated microbial biomass and diversity along successional gradients, yet few have quantified changes in microbial communities. Using the established successional dynamics experiment at Cedar Creek, principal investigators Lauren C. Cline and Donald R. Zak investigated the influence of plant community composition in structuring microbial community composition and function. Specifically, their research addressed the following questions: 1. Do shifts in saprotrophic microbial communities correlate to changes in plant community composition through successional time? 2. What is the relative influence of soil properties and plant community characteristics in determining microbial community dynamics? Cline and Zak sampled soils from 8 established abandoned agricultural fields (e054), as well as three adjacent forests representing potential late-successional ecosystems, to investigate microbial dynamics using three complementary approaches: targeted sequencing of fungal and bacterial communities, quantitative PCR, and shotgun metagenomics. Further, the characterization of soil properties across the chronosequence will enable us to disentangle the impact of abiotic factors in structuring microbial communities.
Data from: System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of Soybean (Glycine max)
Cellular interactome, in which genes and/or their products interact on several levels, forming transcriptional regulatory-, protein interaction-, metabolic-, signal transduction networks, etc., has attracted decades of research focuses. However, such a specific type of network alone can hardly explain the various interactive activities among genes. These networks characterize different interaction relationships, implying their unique intrinsic properties and defects, and covering different slices of biological information. Functional gene network (FGN), a consolidated interaction network that models fuzzy and more generalized notion of gene-gene relations, have been proposed to combine heterogeneous networks with the goal of identifying functional modules supported by multiple interaction types. There are yet no successful precedents of FGNs on sparsely studied non-model organisms, such as soybean (Glycine max), due to the absence of sufficient heterogeneous interaction data. We present an alternative solution for inferring the FGNs of soybean (SoyFGNs), in a pioneering study on the soybean interactome, which is also applicable to other organisms. SoyFGNs exhibit the typical characteristics of biological networks: scale-free, small-world architecture and modularization. Verified by co-expression and KEGG pathways, SoyFGNs are more extensive and accurate than an orthology network derived from Arabidopsis. As a case study, network-guided disease-resistance gene discovery indicates that SoyFGNs can provide system-level studies on gene functions and interactions. This work suggests that inferring and modelling the interactome of a non-model plant are feasible. It will speed up the discovery and definition of the functions and interactions of other genes that control important functions, such as nitrogen fixation and protein or lipid synthesis. The efforts of the study are the basis of our further comprehensive studies on the soybean functional interactome at the genome and microRNome levels. Additionally, a web tool for information retrieval and analysis of SoyFGNs can be accessed at SoyFN: http://nclab.hit.edu.cn/SoyFN.
Data from: Hydrogen sulfide regulates cardiovascular function by influencing the excitability of subfornical organ neurons
Hydrogen sulfide (H2S), a gasotransmitter endogenously found in the central nervous system, has recently been suggested to act as a signalling molecule in the brain having beneficial effects on cardiovascular function. This study was thus undertaken to investigate the effect of NaHS (an H2S donor) in the subfornical organ (SFO), a central nervous system site important to blood pressure regulation. We used male Sprague-Dawley rats for both in vivo and in vitro experiments. We first used RT-PCR to confirm our previous microarray analyses showing that mRNAs for the enzymes required to produce H2S are expressed in the SFO. We then used microinjection techniques to investigate the physiological effects of NaHS in SFO, and found that NaHS microinjection (5 nmol) significantly increased blood pressure (mean AUC = 853.5±105.7 mmHg*s, n = 5). Further, we used patch-clamp electrophysiology and found that 97.8% (88 of 90) of neurons depolarized in response to NaHS. This response was found to be concentration dependent with an EC50 of 35.6 µM. Coupled with the depolarized membrane potential, we observed an overall increase in neuronal excitability using an analysis of rheobase and action potential firing patterns. This study has provided the first evidence of NaHS and thus H2S actions and their cellular correlates in SFO, implicating this brain area as a site where H2S may act to control blood pressure.
Original data and code for Kang, Mooshagian, and Snyder (2024) Functional organization of posterior parietal cortex circuitry based on inferred information flow
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Fig. 1 in Histochemistry and functional organization of the dorsal skin of Ancistrus dolichopterus (Siluriformes: Loricariidae)
Fig. 1. Skin of Ancistrus dolichopterus. A) Epidermis (Ep) and thick dermis (De) of A. dolichopterus showing stratum laxum (SL) and stratum compactum (SC), note also the hollow osteoderm and the denticle (HE). Scale bar = 100 mm. B) Denticle at higher magnification. (PAS) Scale bar = 10 mm. C) Denticles with pointed crown and broad basal parts. The narrow pedestal basal part fit in the cup shaped structure of dermal osteoderm (arrows). The dentine surrounds the pulp cavity, filled with cells and connective tissue, and covered by a thin enamel layer. The osteoderm is connected with the denticles with attachment fibers (small arrows). (HE) Scale bar = 20 mm. D) Epidermis showing epithelial cells distributed in different layers, low columnar cells in basal, polygonal in the middle and flat cells in the superficial layer. Spherical eosinophilic granular cells (arrows) with granular cytoplasmic contents and eccentric nucleus. Note the pigment cells with dark brown coarse granules (*) in a continuous layer below the basement membrane (HE). Scale bar = 10 mm. E) General glycoproteins in the epidermis. The mucous cell (*) and EGCs (arrows) stain very strong while epithelial cells located in superficial and outer middle layers stain moderately (AB/PAS). Scale bar = 10 mm. F) A pear shaped taste bud (arrow) (AB/PAS) Scale bar = 10 mm.
Figure 5 from: Schmitt M, Uhl G (2015) Functional morphology of the copulatory organs of a reed beetle and a shining leaf beetle (Coleoptera: Chrysomelidae: Donaciinae, Criocerinae) using X-ray micro-computed tomography. In: Jolivet P, Santiago-Blay J, Schmitt M (Eds) Research on Chrysomelidae 5. ZooKeys 547: 193–203. https://doi.org/10.3897/zookeys.547.7143
Figure 5 - Donacia semicuprea. Volume rendering of the virtual sections – sagittal, right to the median – through the abdomina of a mating pair. The opening of the bursa copulatrix (circle) is armed with a conspicuous ring muscle. C: the compound muscle inserting at the manubrium and extending to the lateral rims of the basal orifice of the median lobe; M: median lobe; P: paramere.
Figure 1 from: Schmitt M, Uhl G (2015) Functional morphology of the copulatory organs of a reed beetle and a shining leaf beetle (Coleoptera: Chrysomelidae: Donaciinae, Criocerinae) using X-ray micro-computed tomography. In: Jolivet P, Santiago-Blay J, Schmitt M (Eds) Research on Chrysomelidae 5. ZooKeys 547: 193–203. https://doi.org/10.3897/zookeys.547.7143
Figure 1 - Schematic drawing of the sclerotised part of a Donaciinae aedeagus. The given terms of orientation do not refer to the position within the male abdomen nor within the female during copulation since these structures are rotated during mating. The median lobe is shaded grey. Paramere, tegminal ring and manubrium compose the tegmen.
Figure 6 from: Schmitt M, Uhl G (2015) Functional morphology of the copulatory organs of a reed beetle and a shining leaf beetle (Coleoptera: Chrysomelidae: Donaciinae, Criocerinae) using X-ray micro-computed tomography. In: Jolivet P, Santiago-Blay J, Schmitt M (Eds) Research on Chrysomelidae 5. ZooKeys 547: 193–203. https://doi.org/10.3897/zookeys.547.7143
Figure 6 - Donacia semicuprea, Volume rendering of ca. 390 virtual sections – sagittal, paramedian, tilted to the right – through the abdomina of a mating pair. The bursa is elongate, as seen from the proximal wall (arrow). The yellow shining areas inside the female abdomen are parts of the left ovary. P: paramere.
Figure 3 from: Schmitt M, Uhl G (2015) Functional morphology of the copulatory organs of a reed beetle and a shining leaf beetle (Coleoptera: Chrysomelidae: Donaciinae, Criocerinae) using X-ray micro-computed tomography. In: Jolivet P, Santiago-Blay J, Schmitt M (Eds) Research on Chrysomelidae 5. ZooKeys 547: 193–203. https://doi.org/10.3897/zookeys.547.7143
Figure 3 - Lilioceris lilii, copulating pair. Volume rendering of the virtual sections right to the median, digitally stained. The terminal part of the spermathecal duct can be seen immediately left to the bursa wall. The shape of the bursa is nearly globular. B: bursa copulatrix; C: the compound muscle inserting at the manubrium and extending to the lateral rims of the basal orifice of the median lobe; E: endophallus; M: median lobe.
Figure 2 from: Schmitt M, Uhl G (2015) Functional morphology of the copulatory organs of a reed beetle and a shining leaf beetle (Coleoptera: Chrysomelidae: Donaciinae, Criocerinae) using X-ray micro-computed tomography. In: Jolivet P, Santiago-Blay J, Schmitt M (Eds) Research on Chrysomelidae 5. ZooKeys 547: 193–203. https://doi.org/10.3897/zookeys.547.7143
Figure 2 - Lilioceris lilii. Virtual section – sagittal, median - through the abdomina of a mating pair. The endophallus is fully inflated (2a), the flagellum is positioned over the opening of the spermathecal duct (2b).
Figure 4 from: Schmitt M, Uhl G (2015) Functional morphology of the copulatory organs of a reed beetle and a shining leaf beetle (Coleoptera: Chrysomelidae: Donaciinae, Criocerinae) using X-ray micro-computed tomography. In: Jolivet P, Santiago-Blay J, Schmitt M (Eds) Research on Chrysomelidae 5. ZooKeys 547: 193–203. https://doi.org/10.3897/zookeys.547.7143
Figure 4 - Lilioceris lilii, as Fig. 3, the opening of the bursa copulatrix and the adjacent part of the bursa wall (circle) do not show significant muscle layers but are mere membranes. B: bursa copulatrix; M: median lobe.
Supplementary material 1 from: Balestrini R, Delconte C, Buffagni A, Fumagalli A, Freppaz M, Calvo E, Buzzetti I (2019) Dynamic of nitrogen and dissolved organic carbon in an alpine forested catchment: atmospheric deposition and soil solution trends. In: Mazzocchi MG, Capotondi L, Freppaz M, Lugliè A, Campanaro A (Eds) Italian Long-Term Ecological Research for understanding ecosystem diversity and functioning. Case studies from aquatic, terrestrial and transitional domains. Nature Conservation 34: 41-66. https://doi.org/10.3897/natureconservation.34.30738
: Data type: statistical data
Assessment of Algorithm-Based Hydroxyurea Dosing on Fetal Hemoglobin Response, Acute Complications, and Organ Function in People With Sickle Cell Disease
ClinicalTrials.gov study NCT02225132. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Non-myeloablative Haploidentical HCT Study for Patients With Sickle Cell Disease, Including Compromised Organ Function
ClinicalTrials.gov study NCT06145282. IPD Sharing: NO. Countries: 1. Publications: 0.
CD34+ Cell Enriched and T Cell Depleted Allogeneic Stem Cell Transplantation for Patients With Mismatched Related Donors or Borderline Organ Function
ClinicalTrials.gov study NCT02162511. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of Soybean (Glycine max)
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The functional organization of excitation and inhibition in the dendritic arbors of retinal direction-selective ganglion cells
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Data from: Hydrogen sulfide regulates cardiovascular function by influencing the excitability of subfornical organ neurons
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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.