Biomedical and Obesity Research Core

NOW OFFERING SERVICES IN THE CORE'S NEW FACILITY IN THE LOWER LEVEL OF LEVERTON HALL.  

The Biomedical and Obesity Research Core (BORC) is now providing services in the newly renovated laboratory in the lower level of Leverton Hall as of December 14, 2015.  Contact the core at BORC@unl.edu.

BORC Interaction Space and Conference Room
















BORC Laboratory Benches and Equipment









BORC Laboratory Freezers and Hoods











Leverton HallAbout the BORC

The Biomedical and Obesity Research Core (BORC) is a one-stop shop core facility in the Nebraska Center for Prevention of Obesity Diseases (NPOD).  The BORC provides cutting-edge biomedical research services for investigators in the University of Nebraska system and also external users in its newly renovated facility in the lower level of Leverton Hall, the NPOD headquarters building (shown at left). The BORC’s new facility includes approximately 2,000 square feet of laboratory space, a state-of-the-art conference room and a collaboration zone for informal discussions. The BORC also maintains a live mouse imaging and phenotyping facility in the Life Science Annex on the University of Nebraska-Lincoln’s East Campus. In addition, to meet our users' need for large capacity, high-speed computational solutions, the BORC is networked with the Holland Computing Center.

BORC’s Goal

1)      To provide facilities, equipment, and resources that enable researchers to discover new signaling mechanisms while receiving valuable guidance regarding experimental design, data analysis, and data interpretation.

2)      To provide training for researchers on services provided through the BORC.

3)      To develop unique and innovative research tools in BORC that will benefit research community at large by contributing to their research discovery and external funding.

4)      To expand the scope of techniques available to investigators, standardize key methodologies, and expedite the research in biomedical fields.

Contact information for any inquiries:

THE SCIENTISTS AND STAFF
Two Ph.D. level scientists, Drs. Kathy Hanford and Steve Kachman serve as the Bioinformatics and Biostatistics Coordinators for the core.  They have extensive experience in statistics, bioinformatics, and genetics. The founder and director of the Holland Computing Center, Dr. David Swanson, serves as the core’s liaison and can create customized solutions to researchers' computational needs.

The core is also staffed with two M.S. level technologists, Emily Barber and Mengna Xia (pictured below left to right), Xiawith more than seven years total of expertise in molecular biology and cell biology research.Barber
 

FEES
The core is supported by funding provided by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number P20GM104320.  Therefore, at this time the user is not charged for the core services.  Available subsidies are reassessed periodically and are dependent upon grant funding.

OFFERED SERVICES

  • Training sessions
  • Molecular and cell biology services
  • Small animal imaging, phenotyping, and metabolism
  • Research tool development program
  • Bioinformatics & biostatistics, experimental design
  • Computational Services

Please inquire with any questions and check back frequently to find out about newly added services.
 
Training Sessions                                                                                                                                                                                                      
The core offers customized training sessions (individual or small groups) and all inquiries are welcome.  Inquiries for more information or to request training can be emailed to Mengna Xia, mxia2@unl.edu .

Graduate students can receive formal training in some of the BORC’s molecular and cell biology protocols through enrolling in class NUTR821 Molecular Nutrition Techniques (3 cr).

Prior training by the BORC staff is required for unsupervised use of select equipment and protocols and will be at the discretion of the core director.

 
Molecular and Cell Biology Services                                                                                                                                                              

  • ChIP assays
  • qRT-PCR
  • Electrophoretic mobility shift assays
  • Antibody development and testing
  • Genotyping
  • Western blotting
  • Site-directed mutagenesis
  • Reporter gene analysis
  • Plasmid development
  • Protein lyophilization
  • DNA and RNA gel electrophoresis
  • Fluorescent plate reader

 

Small Animal Imaging, Phenotyping, and Metabolism                                                                                                                          

  • Metabolic chemistries (clinical analyzer)
  • Infrared imaging in live mice by Pearl Impulse imager
  • Fluorescent protein imaging in live animals by iBox
  • Dual X-ray absorptiometry in humans and mice (collaborative arrangement)
  • Metabolic cages for pigs and mice
  • Proteomics and metabolomics services (collaborative arrangement)
  • Behavioral neuroscience, motor and sensory phenotyping in mice:
  • Rotor-rod
  • Animal grip strength system
  • SR-LAB startle response
  • Radial arm maze
  • Water maze
  • Barnes maze
  • Place preference enclosure


Research Tool Development Program                                                                                                                                                       

The enhancement of research discovery depends on accurate tools and measurements. The core offers an exciting program which supports the development of novel research tools and protocols in our facilities that would benefit the research community at large. There is no cost to the investigator for this program.  All investigators are invited to participate in this program and should contact the NPOD director, Dr. Janos Zempleni, at jzempleni2@unl.edu, to submit proposals and to inquire about the possibility of the core’s developing tools for your research.

 The most important areas are (but not limited to):

  • Biomarkers
  • Molecular biology
  • Bioinformatics
  • Translational research
  • Metabolism
  • Phenotyping
  • Imaging analysis



Bioinformatics & Biostatistics, Experimental Design                                                                                                                              

The BORC bioinformatics and biostatistics coordinators strongly encourage researchers to seek advice early during the planning stages of a project to optimize the experimental design. Please contact our coordinators and identify yourself as a BORC user to receive a free consultation. Collaborative arrangements are a possibility.

Biostatistics Coordinators:

Steve Kachman
Office:  354B Hardin Hall
Email:  steve.kachman@unl.edu
Phone:  (402) 472-7209

Kathy Hanford
Office:  343A Hardin Hall
Email:  kathy.hanford@unl.edu
Phone:  (402) 472-7209


Background:

  • Quantitative genetics (Steve and Kathy)
  • Clinical trials (Kathy
  • Mixed models and their various derivatives (Steve and Kathy)
  • Bayesian models (Steve)
  • Meta-analysis (Kathy)


Services:

  • Design
    • Treatment and experimental designs
    • Sample size and power calculations
  • Analysis
    • Development of analysis plans
    • Development of statistical tools
    • Implementation (R and SAS)


Computational Services                                                                                                                                                                                         

Should your project require large-capacity, high-speed computation, please reach out to the BORC director or Dr. Swanson and identify yourself as a BORC user to receive a free consultation. 


Coordinator:


Dr. David Swanson
Office:  118K Schor Center
Email:  david.swanson@unl.edu
Phone:  (402) 472-5006


ONLINE CORE MANAGEMENT SYSTEM (iLab Solutions)

The BORC services are initiated, tracked, and invoiced using iLab for maximum convenience. To begin using the core services, please reach out to the core technologist to set up an iLab account for you (https://my.ilabsolutions.com/account/login).


THE CORE'S EQUIPMENT

Branson S-450D digital ultrasonic Sonifier®

Branson Sonifier® ultrasonic cell disruptor / homogenizers are versatile laboratory units suitable for a broad range of liquid processing applications such as:

  • Cell disruption
  • Nano particles
  • Chip assay
  • Emulsification
  • Homogenization
  • Cell Lysing
  • Processing DNA & Proteins
  • Acceleration of reactions
  • Leaching & extraction
  • Fine mixing
  • Degassing



FreeZone® 4.5 Liter Freeze Dry Systems

Freeze drying is an important process in sample preparation and for the preservation and storage of biologicals, pharmaceuticals and foods.  In this lyophilizing process, water or other solvent is removed from frozen material by converting the frozen water directly into vapor without the intermediate formation of liquid water. The lyophilizer 10 port chambers can hold simultaneously upto 4.5L frozen samples and can dry upto 2L samples in a day (24h). 



New BrunswickTM Innova® 40











Precise control, automated operation, and high temperature capabilities for culturing a wide variety of organisms. 

  • Programmable Innova controls—automatically changes temperature and speed at programmed and timed intervals
  • Versatile accessory platform accommodates a variety of flasks and conical tubes


Bio-Rad CFX Connect Real-time PCR

 The computer controlled CFX Connect Real-Time PCR Detection System offers:

  • Easy startup — obtain great results right away with factory-calibrated dyes, quick setup, and intuitive software
  • Effortless optimization — optimizing assays in a single run using the thermal gradient
  • Powerful data analysis tools — quickly and accurately validate and analyze data with the advanced analysis modules of CFX Manager™ Software
  • Accelerated publication submission — include MIQE annotations and generate RDML files using Biogazelle's qbase+ Software


QX200™ Droplet Digital™ PCR System

QX200™ Droplet Digital™ PCR System provides absolute quantification of target DNA or RNA molecules using EvaGreen fluorescence or TaqMan hydrolysis probes. The system has C1000 Touch Thermal Cycler – performed on partitioned droplets, PX1 Plate Sealer, Droplet generator and Droplet reader – droplets are sipped and run single file past a two-color detector # of positive and negative droplets is counted to give discrete quantitative data. There is no need any standard curves for analysis.

Application:

  • Cancer biomarker studies
  • Pathogen detection
  • Next generation sequencing
  • Gene expression analysis
  • Environmental monitoring
  • Food Testing












C1000 thermocycler                                                              ddPCR Reader                                      Droplets generator


Malvern NanoSight NS300

The NanoSight NS300 provides rapid and automated analysis of the size distribution and concentration of all types of nanoparticles in suspension in the size range 10-2000nm (depending on material) and addresses the needs of a wide variety of applications including protein aggregation, exosome and macrovesicle research, drug delivery systems and characterization of materials.

This latest NanoSight instrument provides multi-faceted analysis that now includes a motorized filter wheel, as well as a rheology feature that can measure viscosity in the range 0-5 centipoise. With a footprint measuring just 40cm long by 25cm wide, the NS300 is packed with NanoSight’s latest developments. It comes complete with a high sensitivity CMOS camera, temperature control, a choice of laser block.
 
A new top plate and laser module block are removable to enable easy cleaning and assembly. The top plate comes with a replaceable sample chamber designed with a special stem to enable removal without having to handle the sensitive sample area. It has very easy and sophisticated Nanoparticle Tracking Analysis (NTA) software.

XFe-24 Extracellular Flux Analyzer (Seahorse Bioscience)

The XFe-24 flux analyzer measures real time kinetic of the media flux (oxygen consumption rate (OCR) and extracellular acidification rate (ECAR)) in live cellular environment to determine in vitro oxygen consumption rate (OCR), and extracellular acidification rate (ECAR), in order to assess cellular metabolic functions such as oxidative phosphorylation, glycolysis, and fatty acid oxidation. XFe-24 assays apply to all fields of biomedical research. The plate accommodates 24 individual wells, and up to 4 different test compounds (for example, Oligomycin, 2-DG, FCCP, Rotenone) can be injected separately into each well of real time kinetic experiment.



Typical data of XF analysis
















Vitros-250 Chemistry Analyzer

We are incorporating Vitors-250 to our facility very soon. We have already ordered this unique clinical chemistry analyzer which uses dry-slide (micro-slide) technology. Vitros is a computer controlled automated robotic machine hugely used for diagnosis or preclinical and biomedical research, particularly for metabolic diseases. The analyzer is capable of accurately and quantitatively measuring 36 analytes in a single serum, plasma, urine, or other biological fluid with the capacity to run 40 samples simultaneously. It can generate 250 test per hour.

List of Vitros Analytes: 

  • Albumin
  • Carbon Dioxide
  • Alcohol
  • Iron
  • ALKP
  • GGT
  • ALT
  • Glucose
  • Ammonia
  • Potassium
  • Amylase
  • Lactate
  • AST
  • LDH
  • BuBc
  • Lipase
  • BUN
  • Magnesium
  • Calcium
  • Sodium
  • Cholinesterase
  • Phosphorus
  • CHOL
  • CSF Protein
  • CK
  • Total Bilirubin
  • CKMB
  • Total Protein
  • Chloride
  • TRIG
  • Creatinine
  • Urine Protein
  • CRP
  • Uric Acid
  • dHDL






















































Bio Tech Synergy™ H1m


Synergy™ H1m is a flexible monochromator-based multi-mode microplate.
The monochromator optics use a third generation quadruple grating design that works at any excitation or emission wavelength with a 1 nm step. This system supports top and bottom fluorescence intensity, UV-visible absorbance and high performance luminescence detection. It is the ideal system for all the standard microplate applications found in life science research laboratories.

  • A dual reagent injection system is available to automate inject/read assays such as ion channels assays or flash luminescence assays (e.g. luciferase or ATP assays).
  • User-adjustable orbital shaking and advanced 4-Zone™ temperature control
  • Compatible with Take3™ Micro-Volume Plates: Samples down to 2 μL volume can be measured. Especially useful when working with precious samples, for fast and accurate DNA/RNA quantification at 260 nm




LICOR ODYSSEY® CLx

The Odyssey CLx is the next generation multifunctional imaging platform that can provide a wide range of applications. It has a large surface that can accommodate up to six microtiter plates.

Odyssey CLx Applications:

  • Western Blots: Two-Color Infrared and In-Gel
  • Cell-Based Assays: In-Cell Western™ and On-Cell Western
  • Protein Detection: Coomassie-Stained Gels, Membrane and Slide Arrays
  • Small Animal Imaging: In Vivo, Whole Organ, and Tissue Section
  • Nucleic Acid Detection: Mobility Shift Assays,
  • DNA Gel Staining (Syto®60), and Arrays
  • Microwell Assays: ELISA/FLISA, Protein Arrays, and RNAi Analysis



iBox® Scientia™ Small Animal Imaging System

iBox® Scientia is an in vivo fluorescence protein imaging tool for small animals (mice).  It is an easy one touch automated computer (touch screen) controlled system which has highest accuracy and precision. It captures images with the high resolution and high sensitive CCD camera and optics.

 The Main Features of iBox

  • Completely networkable, stand-alone system for fluorescence in vivo imaging
  • Color CCD camera for high resolution, quick image capture of fluorescence in vivo images
  • Darkroom with integrated touch screen technology and easy to use software interface for live preview, capture and saving images
  • BioLite MultiSpectral Light Source for directed, filtered illumination
  • Roll-out tray inside the darkroom providing easy access for placement of mice on the warming plate
  • Easy useable VisionWorksLS Image Acquisition and Analysis Software

 iBox Application
iBox is a very useful tool for cancer research. There is nothing comparable with iBox for identification and measuring the tumor dimension, volume, and growth in vivo animals with a quick one touch computer screen. iBox is also used for heart disease and gene therapy research.

Cat #

EX/EM

WL max

WL

DYE

Ex

38-0358-04

EX

450sp

38-0340-04

EX

475

455-495

GFP

38-0344-04

EX

525

502-547

Td Tomato

38-0341-04

EX

560

533-587

38-0359-04

EX

630

600-645

38-0360-04

EX

715

687-748

iRFP

38-0371-04

EX

720

700-740

Dir,Dilc

Em

38-0361-01

Em

465-495

480

38-0352-01

Em

502-523

513

GFP

38-0340-01

Em

513-557

535

38-0220-01

Em

580-630

605

Td Tomato

38-0369-01

Em

700-740

720

iRFP

38-0362-01

Em

767-807

787

Dir,Dilc

http://www.imb.sinica.edu.tw/core/publicfacilities/pdf/UVP600FilterSelectionChart.pdf

Pearl® Impulse Small Animal Imaging System

  • Pearl® Impulse is the near-infrared imaging system for in vivo animals (mice and rats).
  • Impulse is optimized for tracking disease progression in live animals.
  • Using different IRDye® reagents, impulse has a wide range of imaging applications, including:
Receptor targeting
Transporter targeting
Vasculature structure imaging
Lymphatic imaging
Bone structural imaging




 

Metabolic cages (TSE Systems)

The TSE Systems- Metabolic cages are computer controlled monitoring systems to investigate full metabolic profile on live animals (mice). The TSE system cages simultaneously and non-destructively measure the heat production, energy expenditure, respiratory rate, calorimetry, activity, drinking/feeding intake, and movements of live mice. Mice are acclimated in acclimation cages that are similar to the experimental cages, one mouse per cage. Acclimation starts the Wednesday before the experiment, with the experiment running Monday-Friday.



Phenotyping Equipment for Animal Behavioral Study