Curator Dashboard

Operated by Institute of Marine Sciences with support from UCSC Division of Physical and Biological Sciences. Available to UCSC and University of California marine and coastal research community.Provides equipment including Shimadzu TOC-VCPH TC/TN analyzer,Dionex ICS-2000 Ion Chromatograph,UIC Carbon Coulometer Analyzer, Perkin-Elmer AAnalyst 100 Atomic Absorption Spectrophotometer, Thermo Genesys 10S UV-Visible Spectrophotometer, Turner Designs 10-AU Field Fluorometer, Turner Designs TD-700 Lab Fluorometer, Turner Designs TD-20/20 Luminometer,Lachat QuikChem 8000 Flow Injection Analyzer, Guildline 8410 PortaSal Salinometer, Labconco Freeze Dryer.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Provides advanced imaging technologies and image analysis tools including vital imaging of cellular processes within cells, tissue explants, and organoids.Supports services for transmission electron microscopy of biological samples.Imaging capabilities include fluorescence imaging of samples;Transmitted light imaging; Live cell imaging;FRAP, FLIP, Photoactivation/conversion;FRET, FLIM; Image processing, analysis, quantification; Transmission electron microscopy.Microscopes and Equipment include:Zeiss Axio Imager M2 Motorized Upright Microscope;Zeiss Cell Discoverer 7; Zeiss ELYRA S.1 Superresolution Microscope; Zeiss LSM 780 NLO Multiphoton Microscope;Zeiss TIRF3;Zeiss Stallion Digital Imaging Workstation;FEI Morgagni Transmission Electron Microscope;Leica UC6 Ultramicrotome;ImageXpress Pico & BioTek Cytation 7;Cryostar NX70 Cryostat.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core provides intravital imaging equipment to acquire advanced descriptive and quantitative data for imaging studies. Includes Olympus FVMPE-RS advanced multiphoton microscope, multichannel, multiphoton excitation system specifically tailored for intravital and deep tissue imaging.System is additionally equipped with 458 and 588 nm stimulation laser lines for photobleaching, light stimulation and/or photoactivation of various fluorescent or caged constructs. Uses Spectra-Physics InSight X3 dual-line, tunable multiphoton laser for ultrafast, multichannel imaging.Available Neurotar Mobile Home Cage allows researchers to integrate real-time imaging with behavioral/locomotion tracking. Offers training and access to imaging system, support in design of experimental procedures, acquisition of image data, and analysis of acquired images.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP.

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• RRID
• 4 years ago - submitted by Samantha White

Provides integration and analysis of publicly available resources as well as newly collected transcriptomic data following deubiquitinating enzyme (DUB) knockout or inhibition to facilitate exploration of DUB function in oncology.

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• RRID
• 4 years ago - submitted by Charles Hoyt

Standard for health care data exchange, published by HL7. Platform provides healthcare information exchange standard that makes use of HL7-defined set of “resources” to support information sharing by variety of means, including documents, messages, services and RESTful interfaces. FHIR defines resources for clinical and administrative content (e.g. Observation, Patient, etc.) as well as resources for “infrastructure” purposes. Some of these infrastructure resources are used to define standard itself – i.e. what the characteristics of resources are, what codes can be used in them, etc.

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• dkNET
• 4 years ago - submitted by Maryann Martone

Software tool for identification and classification of phage virion proteins using deep learning.

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• RRID
• 4 years ago - submitted by Zhencheng Fang

Protein synthesis can be controlled with the bacterial translation machinery. Control of invasion is necessary to carry the produced proteins into cells. Invasion requires both flagella and the type III secretion system-1 (T3SS-1). Flagella are essential for cell invasion because they sense the cell surface and determine the optimal location for invasion32. T3SS-1 is a needle apparatus that initiates invasion by injecting effector proteins into cells. These proteins rearrange the actin cytoskeleton and induce endocytosis of the bacteria. Production of these two bacterial structures is controlled by the factors fliZ and hilD, which are, in turn, controlled by the master regulator flhDC. Protein release requires the activation of bacterial genes specifically inside cells. In Salmonella, this can be controlled with the promoters of SPI2 genes.

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• RRID
• 4 years ago - submitted by Jon Matthews

The fast development of genome sequencing technologies and the power of advanced computational analyses of the DNA sequences dramatically increased the potential for natural product discovery. Our knowledge on the biosynthesis of secondary metabolites by bacteria is constantly expanding, thereby adding new information that connects biosynthetic genes with metabolites of particular chemical classes. With the cost-effective and rapid increase in the number of bacterial genomes sequenced, one challenge encountered in current drug discovery efforts is how to effectively prioritize those strains with the greatest ability to produce new compounds and understand the extent of biosynthetic potential that exists in nature. Genomes mining approaches, which often involve identifying the genes involved in secondary metabolite production, have revealed an unprecedented biosynthetic potential in many microbial species. Associated techniques include molecular biology techniques, chemical analysis, cellular biology techniques, and bioinformatic analysis, etc. The genomes mining approaches can be applied in different ways based upon: (i) phenotype of the producer (e.g. bioactivity and biosynthesis of specific compounds or enzymes); (ii) targeted chemical class of natural products (e.g. terpenes, lasso peptides and aromatic polyketides); (iii) the potential uniqueness of the bacterial isolate that may yield novel compounds (e.g. novel or taxonomically divergent species, and isolates from unique environmental sources).

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• RRID
• 4 years ago - submitted by Jon Matthews

Chemotaxonomy, also called chemosystematics, is the attempt to classify and identify organisms according to confirmable differences and similarities in their biochemical compositions. The chemical diversity and the resources of natural products are immense and nowhere near fully exploited. Chemotaxonomy-based strain selection is a prerequisite for successful natural product research. Combined with the fact that fungi, and probably also other types of microorganisms, produce very species-specific profiles of natural products that can be used as efficient tools to select one or a few representative strain(s) for biological testing, and with the revolution in molecular genomics several new strategies for natural products based drug discovery programs are being developed: Knowing the biodiversity and ecology; Using a metabolite profiling approach; Targeting certain ecological niches; Using a genome-based approach.

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• RRID
• 4 years ago - submitted by Jon Matthews

Microorganisms and in particular actinomycetes and microfungi are known to produce a vast number of bioactive secondary metabolites. Natural product research needs to continually improve the efficiency of the selection, screening, dereplication, isolation, and structure elucidation processes, in order for natural product chemistry to continue to be competitive with purely synthetic-based discovery methods. For industrially important fungal genera such as Penicillium and Aspergillus, the production of these compounds has been demonstrated to be very consistent at the species level. This means that direct metabolite profiling techniques such as direct injection mass spectrometry or NMR can easily be used for metabolomics of strains from both culture collections and natural samples using modern informatics tools. Metabolomics can be used for the identification and classification of filamentous fungi and for the discovery of novel compounds when used in combination with modern methods for dereplication. Such approaches will be important for future effective drug discovery strategies, especially for the dereplication of culture collections in order to avoid redundancy in the selection of species. This will maximize the chemical diversity of the microbial natural product libraries that can be generated from fungal collections. Metabolomics aims to detect all small metabolites in a cell or organism. Rapid profiling techniques may determine all metabolites produced by a microorganism. These techniques are generally segregated into fingerprinting, footprinting, profiling, or target analysis.

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• RRID
• 4 years ago - submitted by Jon Matthews

Drugs of natural origin have been classified as (i) original natural products, (ii) products derived or chemically synthesized from natural products or (iii) synthetic products based on natural product structures. Microbes have made a phenomenal contribution to the health and well-being of people throughout the world. In addition to producing many primary metabolites, such as amino acids, vitamins and nucleotides, they are capable of making secondary metabolites, which constitute half of the pharmaceuticals on the market today and provide agriculture with many essential products. For example, immunosuppressants have revolutionized medicine by facilitating organ transplantation. Other applications include antitumor drugs, enzyme inhibitors, gastrointestinal motor stimulator agents, hypocholesterolemic drugs, and other pharmacological activities.

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• RRID
• 4 years ago - submitted by Jon Matthews

Provides research MRI capabilities for investigators at UNMC and across greater Omaha area. Housed in Hixson-Lied Center, CAMRI operates Siemens 3T Prisma MRI instrument that can collect high quality data of any MR modality using advanced gradients and research grade pulse sequences. Variety of head coils (20-, 32-, and 64-channel) are available to optimize data collection for needs of specific studies. Studies incorporating functional MRI can take advantage of CAMRI�s suite of MRI-compatible response devices, mirrored 32-inch LCD screen, and integrated stimulus display computer.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core of University of Ottawa and Ottawa Hospital Research Institute. Provides advice on bioinformatics research design, conduct bioinformatics analysis, and provide support for grant proposals that involve bioinformatics (including conducting pilot studies, support/collaboration letters and methodological text). Areas of expertise include:Analysis of high throughput sequencing data; single cell (Chromium 10x), RNA-seq (including small RNA), ChIP-seq, ATAC-seq, Hi-C.Large scale analysis integrating multiple data types.Helps to arrange for analysis of your biological samples with local core facilities such as StemCore, Proteomics Resource Center, or OHRI Mass Spectrometry Core Facility. Provides yearly training courses in RNA-seq analysis and Bioinformatics analysis using R as well as individual training and analysis support on request.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software tool as amplicon sequence processing workflow using QIIME 2 and Snakemake management system.Enables rapid analysis of environmental and biomedical amplicon data, decreasing time from data generation to actionable results.

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• SciCrunch
• 4 years ago - submitted by Luke Thompson

Software tool for meta analysis. Facilitates integration and synthesis of effect sizes from different studies. Consists of set of workbooks designed for Microsoft Excel that automatically produces all required statistics, tables, figures, and more.

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• RRID
• 4 years ago - by Anonymous

Software Python GUI for graphing measures of liquid ingestion in rodents from Sippers. Python GUI for visualizing Sipper data.

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• RRID
• 4 years ago - submitted by Samantha White

Creative Biogene provides global customers with ROS determination, using electron spin resonance (ESR), DCFH-DA fluorescent probe, NBT staining, DAB staining, and quantitative determination of hydrogen peroxide.

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• RRID
• 4 years ago - submitted by Joe Cohen

Creative Biogene uses Seahorse XF real-time ATP rate measurement platform to efficiently and accurately detect mitochondrial aerobic respiration oxygen consumption rate (OCR) and glycolysis extracellular acidification rate (ECAR), and then convert into mitochondrial respiration ATP, glycolysis ATP, and total ATP production rate.

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• RRID
• 4 years ago - submitted by Joe Cohen