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Services and Equipment


  • Fiscal Year 19 (July 1, 2018 – June 30, 2019)

    The BRC has three Service Fee Groups:
    BSU-Boise State University users (faculty, staff student)
    Non-Profit- Other Academic or Federally funded users
    Commercial– Commercial for – profit entity users

    *Current as of July  2018: Cost Schedules for all equipment will be reviewed regularly and rates adjusted

    MASS SPECTROMETRY

    DescriptionService ProvidedBSU UserNon-ProfitCommercial
    Tryptic protein digestion
    Sample Preparation
    $8.85/sample
    $12.43/sample
    $20.00/sample
    LC-MS shotgun Proteomics analysis
    Mass Spec Analysis
    $73.66/sample$103.49/sample$200.00/sample
    MS Analysis by direct infusionMass Spec Analysis
    $37.67/sample
    $52.93/sample
    $120.00/sample
    LC_MS analysis of metabolites or intact proteinsMass Spec Analysis$58.20/sample
    $81.77/sample
    $150.00/sample

    IMAGING

    DescriptionService ProvidedBSU UserNon-ProfitCommercial
    Zeiss LSM 510 Meta Confocal
    Microscope - Operation Rate
    Instrument Usage and Training$16.71/hour
    $23.48/hour
    $150.00/hour
    Skyscan 1172 Scanner MicroCT- Operation RateInstrument Usage and Training$85.30/hour$119.85/hour$200.00/hour

    HISTOLOGY

    DescriptionService ProvidedBSU UserNon-ProfitCommercial
    Tissue Embedding System Leica TP1020/Leica EG1150H
    Paraffin Embedding of Tissues$2.24/sample$3.14/sample$50.00/sample
    Paraffin Sectioning Leica RM 2235Thin Sectioning of Paraffin Embedded Tissues$3.20/block
    $0.21/slide
    $4.50/block
    $0.30/slide
    $35.00/block
    $6.00/slide
    Frozen Tissue Sectioning Leica CM1950
    Thin Sectioning of Frozen Tissues$59.54/hour$83.66/hour$125.00/hour
    Thick Tissue Sectioning Leica VT1000
    Thick Sectioning of Fresh & Fixed Tissues$1.01/hour$1.41/hour$50.00/hour
    Autostaining System Leica AutostainerHistological Staining (H&E)$1.54/slide$2.17/slide$32.00/slide

    BIOMOLECULAR CHARACTERIZATION

    DescriptionService ProvidedBSU UserNon-ProfitCommercial
    Jasco J-810 CD SpectropolarimeterInstrument Usage and Training$25.55/hour$35.90/hour$60.00/hour
    Beckman ProteomeLab XL-1 AUCIn-solution Characterization$147.05/run$206.61/run$250.00/run
    Plasmid Propagation from Cell StockSample Preparation $17.57/sample$24.68/sample$50.00/sample
    Plasmid Propagation from Plasmid Stock Sample Preparation$39.37/sample$55.32/sample$75.00/sample
    Soluble Protein Expression TestSample Preparation$136.78/sample$192.18/sample$200.00/sample
    Plasmid MaxiPrep
    Sample Preparation$58.81/sample
    $78.41/sample
    $185.00/sample
    Isotope N15 Label Prep (500ml)
    Sample Preparation$132.10/sample
    $185.60/sample
    $1100.00/sample
    Isotope N15/C13 Label Prep (500ml)
    Sample Preparation$264.10/sample
    $371.06/sample
    $1200.00/sample
    LB Prep (500ml)
    Sample Preparation$86.22/sample
    $121.13/sample
    $1000.00/sample
    Protein Purification (IMAC)Sample Preparation $66.14/sample$92.92/sample$300.00/sample


  • BRC Mass Spectrometry Banner

    Welcome to the BRC Mass Spectrometry Facility!

    Our mission is to provide a wide range of analytical capabilities through fee-for-service in the areas of protein, biological and small molecule research to Boise State University investigators, external academic and industrial partners. If you have any questions regarding our services or wish to know more about mass spectrometry, its capabilities and applications, please contact us:

    Xinzhu Pu, PhD
    Mass Spec Facility Manager
    1910 University Drive
    Boise, ID 83725-1511
    Phone: (208)4262233
    Email: shinpu@boisestate.edu

    Instrumentation
    Fees
    Services


    Instrumentation

    The Biomolecular Research Center currently has two mass spectrometers; a Bruker Daltonics maXis Quadrupole Time-of-Flight, Thermo Scientific Velos Pro Dual-Pressure Linear Ion Trap.  Both instruments are located in the BRC, room 215 in the Mathematics Building.

    Bruker Daltonics maXis Quadrupole Time-of-Flight (Q-TOF) Mass Spectrometer

    Bruker QTOFThe Bruker Q-TOF Mass Spectrometer is a hybrid tandem mass spectrometer with outstanding performance including fast acquisition rate (up to 30 Hz for small molecules, up to 5Hz dynamic for peptides), high resolution (50,000 Full Sensitivity and Resolution), high resolution EIC (0.5 – 1mDa on typical LC peaks), and  excellent sensitivity (1 pg Reserpine >100:1 S/N RMS). This mass spectrometer is coupled with a Dionex Ultimate 3000 HPLC system and an innovative Captive electrospray source. In combination with software tools, including Bruker Compass Data Analysis, Smartformula, ProteinScape, Mascot protein search engine, and Profile Analysis, we use this LC-MS system in small molecule identification, metabolomics analysis and protein characterization.

    Publications and presentations utilizing data from samples analyzed with the Bruker maXis Q-TOF  Mass Spectrometer should include the following acknowledgement:  “This research  was made possible by the National Science Foundation Grant NO: 0923535.”

    Thermo Scientific Velos Pro Dual-Pressure Linear Ion Trap (LIT) Mass Spectrometer

    Velos LIT_2The Themo Scientific Velos Pro Linear Ion Trap Mass Spectrometer offers Trap-HCD (Higher-Energy Collisional Dissociation) combined with CID (Collision-Induced Dissociation), and PQD (Pulsed-Q Dissociation) to enhance coverage and sensitivity of proteomic analysis. An Easy nLCII nano liquid chromatographic system is coupled to the mass spectrometer through a nanoelectrospray source for protein characterization. In combination with the Thermo Proteome Discoverer 1.3, Sequest and Mascot database search engine, this LC-MS system is our work horse for routine proteomic analysis.

    Publications and presentations utilizing data from samples analyzed with the LTQ Velos Mass Spectrometer should include the following acknowledgement:  “This research  was made possible by the INBRE Program, National Institutes of Health Grant NOs: P20 RR016454 (National Center for Research Resources) and P20 GM103408 (National Institute of General Medical Sciences),  by the Idaho State Board of Education’s Higher Education Research Council (HERC) and the Biomolecular Research Center at Boise State University.


    Fees

    We charge for every sample run, regardless of whether an expected result is obtained. The only exception is if the lack of result is caused by human errors or instrument problems in the mass spec facility.

    Analyses are charged at the rates listed below per sample submitted:

    DescriptionService ProvidedBSU UserNon-ProfitCommercial
    Tryptic protein digestion
    Sample Preparation
    $8.85/sample
    $12.43/sample
    $20.00/sample
    LC-MS shotgun Proteomics analysis
    Mass Spec Analysis
    $73.66/sample$103.49/sample$200.00/sample
    MS Analysis by direct infusionMass Spec Analysis
    $37.67/sample
    $52.93/sample
    $120.00/sample
    LC_MS analysis of metabolites or intact proteinsMass Spec Analysis$58.20/sample
    $81.77/sample
    $150.00/sample

    Services

    We currently provide the mass spectrometry analyses listed below. If you have needs which are not listed below, please contact us to discuss your project with our staff. We will do our best to help you get your research done!

    Mass spectrometry is a powerful tool in protein and metabolite identification and quantification. However, just like many other analytical tools, it has limitations and there are many factors that will affect the results.  We strongly encourage our users to discuss their projects with our facility staff before they submit samples for analysis. We would like to discuss if mass spectrometry is a suitable for your project, the best mass spec workflow for your specific needs, and how to prepare your sample for mass spec analysis. To ensure the success of analysis, samples must be prepared in a way that is compatible with mass spec. Please follow the sample preparation guide to prepare your samples for mass spec analysis.

    Tryptic Digestion and Protein Identification

    Protein identification by tandem MS after protease digestion is a robust tool in proteomics with high successful rates. Samples can be visible bands excised from Coomassie blue or silver-stained gels. Silver staining must be performed with mass-spec compatible reagents,e.g. Pierce Silver Stain Kit for Mass Spectrometry, catalog # 24600. We may refuse submissions stained using MS incompatible methods. We also accept samples in solution which contains purified protein or several proteins. Please contact facility staff before you prepare your sample for in-solution digestion because some of the chemical commonly used in protein extraction are detrimental to mass spec. For complex samples, fractionation is usually required, for example, SDS-PAGE or 2D gel electrophoresis. Protein samples will be digested with protease in gel or in solution and resulted peptides will be analyzed by tandem MS. Trypsin is the most commonly used protease and is the enzyme we routinely use. Some proteins may require other proteases, such as Lys-C, Asp-N, chymotrypsin, etc. If this is case, we can accommodate.

    Guideline for Preparing gel slice/band:

    • Electrophoresis
      • Try to use a 1 mm thick gel.
      • If possible, try using precast gels and pre-made electrophoresis running buffer.
      • We highly recommended to electrophorese a positive control such as BSA or some other known protein that stains to approximately the same level as your unknown protein of interest.
    • Band excision
      • Use a clean scalpel or razor blade (you may wish to first sonicate the blade for 5 min acetonitrile or ethanol in a glass beaker) to excise protein bands/spots of interest from the stained polyacrylamide gel. Excise only the stained part(s) of the band and trim off the non-stained gel as much as possible. Gel band/slice size should be no larger than 5mm in length.
      • Cut each gel slice into small pieces (~1 mm3) and transfer the pieces to a clean, sterile 1.5 mL microcentrifuge tube pre-rinsed with 50% organic solvent, such as methanol and acetonitrile.
      • Also excise and dice a gel piece from a protein-free region of the gel in parallel as a negative control, and your positive control (for example, BSA) if you ran it.
      • Close the tube as soon as your bands are inside. Submit sample to the Mass-Spec facility immediately or store gel slices at -20C for a brief period before submission.
    • Strategies to avoid Keratin contamination

    All humans are constantly shedding skin cells so there is a large amount of keratin in the air of labs, on surfaces, and in gel boxes, glassware etc. that have been left uncovered on benches. Large amounts of keratin in a sample can mask proteins of interest that are less abundant. Although human keratin contamination cannot be completely avoided, it is important to minimize it during each sample preparation step.  Cleanliness is the key. Here are some recommendations:

    • A key factor in avoiding keratin is to avoid contamination with dust particles. Start with a scrupulously clean work surface. If possible, for best dust control during sample prep work such as cutting gel bands or performing in-gel trypsin digestion, try working in a HEPA-filtered laminar-airflow hood. Wipe the inside of the hood and surface of plasticware packs with ethanol.
    • DO NOT handle anything that will come into contact with your protein with your bare hands! Always wear powder-free nitrile gloves (never use latex gloves, as natural rubber contains significant amounts of keratin and other proteinaceous materials). It may be necessary to wear protective clothing during all phases of sample preparation and to cover your head.
    • Try using precast gels, pre-made electrophoresis running buffer.
    • If casting your own gel:
      • Clean the gel plates well with a soapy sponge, rinsing well with ethanol (or bleach overnight).
      • Handle the plates by the edges and wear gloves to avoid transfer of keratin from your hands to the gel plates.
      • Before preparing solutions, wash the glassware well to remove any dust that might have accumulated during storage.
      • When staining gels:
        • Rinse the staining container well before beginning. Also, rinse the gel thoroughly at each stage. Keep the container closed to keep dust out.
        • When cutting gel bands:
          • This is the step where keratin contamination is most likely to occur. If possible, work in a laminar flow hood. Before starting, wipe down the work a wipe down the work area and any tools that will contact the gel band with an ethanol-soaked Kimwipe.

    Prepare sample for in-solution digestion

    Detergents are incompatible with mass-spectrometry and must be avoided. Failure to do so will contaminate the instrument and result in costly and time-consume maintenance and serious down-time for the instruments. Therefore we require users to contact facility staff before preparing in-solution sample for submission to ensure samples are free of mass spec in=compatible reagents.

    • Do not use ANY detergents in ANY step of sample-prep. This includes, but is not limited to: SDS, CHAPS, NP-40, and Triton-X100 (or related).
    • If detergents and other reagents that are not compatible with mass spec must be used to extract protein, precipitation procedure, for example, acetone precipitation can be used to eliminate these interfering reagents.
    • Optimal sample quantity is 20 µg protein in ~20µL solution.

    Protein molecular weight determination

    Molecular weight determination of intact protein can be achieved by direct infusion via a syringe pump or Liquid Chromatographic (LC) – Electro Spray Ionization (ESI) on our Bruker maXis Q-TOF. A concentrated solution of desalted protein is sprayed into the instrument. . Ion signals that correspond to different charge states of the intact protein molecule are recorded. This data is then deconvoluted to obtained protein molecular mass, typically up to 200kDa, depending on the homogeneity of the sample.

    HPLC-MS is the recommended method because it removes salts and other interfering compounds and enhances signal to noise ratio. This is the method we routinely use to determine the molecular weight of intact proteins. However, non-covalent protein complexes cannot be measured with HPLC because they require 100% aqueous conditions at neutral pH value. In this case, direct infusion via a syringe pump is the method of choice.

    Sample preparation guide:

    • Samples should be free of detergents and viscous solvents, including DMSO, DMF, and THF.
    • Trifluoroacetic acid (TFA) suppresses ionization, and should be kept below 0.1%. Commonly used alternatives to high concentrations of TFA are mixtures of either 1% acetic or 0.1% formic acid with 0.025% TFA
    • Because LC cannot be used to desalt samples, non-volatile buffers should be avoided when analyzing non-covalent protein complexes. A recommended solvent for this sample type is 10 mM ammonium acetate solution in water. Other protein sample, the recommended solvent is 1% formic acid and 25-50% acetonitrile in water. Since LC will be used to clean up salts and other contaminants for this type of samples, non-volatile salts can present in the sample. However, concentration should be kept as low as possible.
    • Glycerol should be limited to no greater than 1%.
    • Sample concentration: Good results can be obtained with 2.5 µM at 5 kD, 5 µM at 20 kD, 10 µM at 40 kD, and 25 µM at 60 kD.
    • Sample volume: 20-50 µL for HPLC and 50-100 µL for direct infusion.

    Small molecule identification by direct infusion

    We provide accurate mass analysis of small molecules in relatively pure samples. This analysis will be carried out on our Bruker maXis Q-TOF.

    Sample preparation guide:

    • In general, volatile low MW protic solvents are preferred. Methanol or water-methanol solution is the typical dilution solvent. Isopropanol and acetonitrile-water mixtures are also acceptable solvents. Pure water or pure acetonitrile are not good solvents for electrospray ionization. If water is required for solubility, up to 50% water may be added. Try to use the highest purity solvents including water, preferably MS grade or HPLC grade.
    • High MW or viscous solvents should be avoided, including DMSO, DMF, and THF.
    • Hydrocarbon solvents, such as hexane and benzene, are not amenable to ESI.
    • Acetone may be used but is not preferred, as even high-grade acetone typically contains contaminants which show up as strong peaks in the MS, and may overwhelm the analyte signal.
    • If the sample contains TFA (e.g. from a reverse-phase HPLC run), remove the TFA by lyophilization or by drying down the sample overnight under high vacuum.
    • Please be sure to indicate if the compound is sensitive to acid or basic conditions, as small amounts of acid (formic, acetic) or base (ammonium hydroxide, triethylamine) are often added to samples in order to enhance ionization. This information will also help determine which MS polarity should be used.
    • In general, 50-100 µL of 1mg/ml sample is more than enough for analysis. Largely due to differences in the ionization efficiency, sensitivity for different compounds may vary. Our instruments are capable of detecting down to the 1 µg/mL level. However, it is good practice to submit around 1 mg/mL.
    • All samples must be filtered through 0.22 µM filter as the particles in sample may clog the spray needle.
    • Please specify if compound may become unstable under certain conditions.

    Metabolites analysis by LC-MS Instrumentation

    We provide quantitation of small molecular metabolites. This measurement is carried on our Bruker maXis Q-TOF coupled with a Dionex Ultimate 3000 LC.

    Sample Preparation for L-MS analysis of metabolites

    • Samples should be dissolved in water-miscible solvents. Optimal solvent is the one with similar strength to LC mobile phase at the start of the LC gradient. Try to use the highest purity solvents including water, preferably MS grade or HPLC grade.
    • High MW or viscous solvents should be avoided, including DMSO, DMF, and THF.
    • If the sample contains TFA (e.g. from a reverse-phase HPLC run), remove the TFA by lyophilization or by drying down the sample overnight under high vacuum.
    • Please be sure to indicate if the compound is sensitive to acid or basic conditions, as small amounts of acid (formic, acetic) or base (ammonium hydroxide, triethylamine) are often added to the LC mobile phase in order to enhance ionization. This information will also help determine which MS polarity should be used.
    • Sample volume: In general, 50-100 µL of sample is enough for analysis.
    • All samples must be filtered through 0.22 µM filter as the particles in sample may clog LC autosampler needle and column.
    • Please specify if compound may not be stable under certain conditions.

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  • Skyscan

     Skyscan banner images Jan2013

    BRC Skyscan 1172 Micro-CT Scanner

    The Biomolecular Research Center’s Skyscan 1172 Micro-CT Scanner is located in room 213 in the Mathematics building on the campus of Boise State University.  The Skyscan 1172 scanner, with an X-ray source of 20-100V, 10W, <5 µm spot size or 20-80V, 8W, <8 µm spot size, has a fully distortion-corrected 11Mp X-ray detector that is a 12-bit cooled CCD fiber-optically camera coupled to scintillator.  The detail detectability of the Skyscan 1172 ranges from 0.8/1.0 µm (when operated at the highest resolution) to 25 µm. The Skyscan 1172 currently has two filter choices that can be set into 3 positions to allow for scanning high-density tissues such as bones to low-density softer tissue such as lung. The maximum object size, or field of view, is 50 mm in either diameter or height when scanner is run in offset mode. The Skyscan 1172 with dynamically variable acquisition geometry provides the shortest scan times possible at any magnification and cross-section images are generated in a wide range of formats up to 8000 x 8000 pixels.  2D/3D reconstruction can be performed using a single PC or using the 4-PC cluster in the BRC facility to enhance post-scan reconstructions times.

    Use and Management
    The purpose of this instrument is to support research at Boise State University and surrounding res earch facilities and is operated as a recharge instrument at an hourly rate. Scan times are dependent on specimen size and resolution parameters.

    Contact Information
    Raquel Brown
    BRC Manager/Confocal Microscope System
    (208) 426-2125
    rbrown@boisestate.edu

    Publications and presentations utilizing data from samples imaged with the Skyscan MicroCT should include the following acknowledgement:  “This research was made possible by support from the Idaho State Board of Education’s Higher Education Research Council (HERC) and the Biomolecular Research Center at Boise State University.”

    Zeiss

    Confocal banner images Jan2013

    BRC Zeiss LSM Meta 510

    The Biomolecular Research Center’s Zeiss Microscope, LSM 510 Meta confocal imaging system is located in room 213 of the Mathematics building on the campus of Boise State University.  The Axiovert Observer Z1 inverted microscope has filter sets appropriate for DAPI, FITC and CY3/TRITC to view samples in a conventional widefield microscopy mode as well as the objective lens: 10x, 20x, 40x, 63x and 100x.  The LSM Meta 510 is configured with six excitation lasers lines (405, 458, 488, 514, 543 and 633 nm), two photomultipliers, a detector for bright field image acquisition and a polychromatic META detector capable of detecting many standard fluorophores, including DAPI, FITC, CFP, YFP, Rhodamine, TRITC, Cy3, Cy5, Texas Red  and many AlexaFluor dyes.  Excitation dichroics and emission filters are operated via the LSM software. Added accessories include a heated stage chamber and objective warmer from PECON for live cell experiments and an AxioCam MRm monochrome digital camera.

    Use and Management
    The purpose of this instrument is to support research at Boise State University and surrounding research facilities.  The instrument is managed by Raquel Brown. Users with substantial needs for the confocal microscope will be trained so they can use the system unassisted.  New users will have a 3-4 hour introduction that covers start-up, computer software introduction for basic confocal system operation, basic image manipulation, data storage, and clean-up/shut-down procedures. In a follow-up session, the potential user will demonstrate that he/she can safely and competently operate the instrument. With this, the user will have allowable unsupervised access to the instrument at the confocal system hourly rate. There will be a discounted hourly rate available for long-term experiments that utilize the scope after hours.
    Users, who have simple or solitary studies and who do not want to be formally trained can elect to have the system operated by Raquel while providing investigator feedback for the price of confocal hourly rate plus a consulting fee.

    LabImaging Software on Monitor

    Contact Information
    Raquel Brown
    BRC Manager/Confocal Microscope System
    (208) 426-2125
    rbrown@boisestate.edu

    Publications and presentations utilizing data from samples imaged with the  Zeiss LSM Meta 510 confocal microscope should include the following acknowledgement:  “This research  was made possible by the INBRE Program, National Institutes of Health Grant NOs: P20 RR016454 (National Center for Research Resources) and P20 GM103408 (National Institute of General Medical Sciences) and the National Science Foundation Grant NO: 0619793. “

  • Welcome to the BRC Histology Facility!

    Our mission is to provide access to a wide range of histological services for Boise State investigators, external academic investigators and industrial partners.  We can provide direct services, training and/or access to equipment for embedding, sectioning and staining of various tissue specimens. We are a fee-for-service center, and use of our facility requires users to establish an ilabs account.  To establish an account, or to ask questions regarding our equipment and/or services, please contact:

    Cindy Keller-Peck, PhD
    Histology Facility Manager
    Biomolecular Research Center
    1910 University Drive
    Boise, ID 83725-1511
    Phone: (208) 426-2254
    Email: CKPeck@boisestate.edu

    Instrumentation
    Services
    Sample Submission


    Services

    Paraffin Embedding 

    Leica TP1020 + EG1150 150px

     

    The BRC uses a Leica TP1020 benchtop tissue processor to dehydrate, clear and infiltrate tissues with paraffin.  Embedding is done with the aid of a Leica Tissue Embedding Center.   Completed blocks will fit in most standard microtome specimen clamps.  We currently do not offer training for this equipment.

     

     

    Paraffin Sectioning

    Leica RM2235 150px

    The BRC uses a Leica RM2235 manual rotary microtome to section blocks of paraffin embedded tissues.  Most sections are cut at 8 mm, but the microtome has a sectioning range of 1-60 mm in thickness.  We can section tissue regardless of whether it was embedded in our facilities.  The microtome is available for independent use.  We will train users who wish to learn about the technique or would like to section their own tissues.

    Frozen Sectioning

    Leica CM1950 150px x 150px

    Tissues for frozen sectioning can be prepared according to investigator needs.  Fresh tissues are generally snap frozen in OCT using liquid nitrogen/isopentane.  Fixed, cryoprotected tissues may be frozen using liquid nitrogen or dry ice.  The BRC currently uses a Leica CM1950 clinical cryostat for sectioning frozen tissues.  It has a sectioning range of 1-100 mm.  The cryostat is available for independent use.  If requested, we will train users to freeze and section their own tissues.
    Vibratome Sectioning

    Leica VT1000 150px

    Thick sections of tissues are cut on the Leica VT1000 vibratome.  It has a sectioning range of 10-999 mm.  Additional adjustable parameters include blade clearance angle, frequency, amplitude and sectioning speed.  Tissues with a high degree of structural integrity may be sectioned without a support medium.  In instances where a tissue requires support, tissue may be embedded in low melting point agarose. The vibratome is available for independent use. If requested, we will train users to embed and section their own tissues.

    Staining

    Leica autostainer XL 150px

    The histology facility currently offers staining with the following histological dyes:  Hematoxylin & Eosin, Alcian Blue, and Sirius Red.  New dyes and immunohistochemistry services are being added as needed, please email the facility for special requests.   We are not currently training investigators to use the Leica Autostainer.  However, we will train interested parties in staining techniques to be used back in their individual laboratories.


    Service Equipment Training Available
    Paraffin EmbeddingLecia TP1020/Leica EG1150 embedding equipmentNo*
    Paraffin SectioningLecia RM2235 MicrotomeYes
    Frozen SectioningLeica CM1950 CryostatYes
    Vibratome SectioningLecia Vibratome VT1000Yes
    StainingLeica Autostainer XLNo*

    Sample Submission

    Users who wish to submit samples for processing must first obtain an iLabs account.  A one-time registration is required to place service requests or reserve equipment. Please visit the  iLabs registration page:  https://boisestate.ilabsolutions.com/account/login.  For questions on using iLabs to set up histology services, please contact the Histology Facility Manager.

    Once an iLabs account is established, and a service request or equipment reservation is made, tissue should be delivered to the Histology Lab in room 211 of the Math building.  The tissue should be accompanied by a completed copy of the BRC Histology Request Form. This form may also be filled out and emailed to CKPeck@boisestate.edu.

    Tissue Preparation:  Tissues are most commonly submitted to the BRC in 10% neutral buffered formalin (NBF).  However, tissues are accepted in other fixatives provided the researcher feels it is the most appropriate way to maintain the molecular and macromolecular aspects under investigation.

  • Biomolecular Characterization Facility

    Our mission is to provide access to biomolecular characterization services for Boise State investigators, external academic investigators, and industry partners. We can provide direct services, training and/or access to equipment for plasmid propagation, rapid protein solubility screen, circular dichroism and analytical ultracentrifugation. We are a fee-for-service center and use of our facility requires users to establish an ilabs account for reservations. To establish an account, or to inquire about our services and equipment, please contact:

    Lisa Warner, PhD
    Biomolecular Characterization Manager
    Biomolecular Research Center
    1910 University Drive
    Boise, ID 83725-1511
    Phone: (208) 426-2260
    Email: lisawarner@boisestate.edu


    SERVICES

    Protein Expression and Purification
    The first step in biomolecular characterization usually requires recombinant expression of proteins of interest. At the BRC, we provide services to propagate plasmids as well as a rapid, small scale screen for soluble protein expression in E. coli using up to 4 expression strains including basic BL21(DE3) and derivatives that can increase soluble expression of proteins with cell toxicity (e.g. enzymes), and with disulfide bonds, and from plasmids with rare codon usage.

    Sample requirements

    • Plasmid propagation: Cell stock (e.g. plasmids from Addgene) or plasmid stock.
    • Small scale solubility screen: Expression plasmid with T7 inducible promoter.

    Circular Dichroism
    The BRC houses a Jasco J-810 Spectropolarimeter (163-900 nm). This hybrid instrument consists of a variable wavelength spectropolarimeter and absorption spectrophotometer. It is equipped with a computer-controlled Peltier device (3-90 °C) and a two-syringe titrator, which can be used to assess thermal/chemical stabilities of proteins/polypeptides or to monitor ligand binding.

    CD applications include determining:

    • Optical purity of substance
    • Protein and nucleic acid secondary and tertiary structure
    • Conformational stability at varying temperature, pH, or denaturant concentrations
    • Conformational changes due to molecular interactions
    • Conformation of mutants or proteins expressed in different systems
    • Thermodynamics binding constants
    • Kinetics of folding and unfolding of macromolecules

     Buffer Requirements

    • Buffers that absorb in the spectral region of interest should be avoided.
    • 10 mM sodium or potassium phosphate buffer is generally recommended for CD. Tris or TEA can be used but should be pH’d with sulphuric or phosphoric acid.
    • Many buffers absorb at the shorter wavelengths where most of the structural information of interest is found. AVOID chloride, citrates, MOPS, imidazole and DTT.
    • Record a spectrum of the buffer alone before starting with samples to ensure the buffer absorbance is not a problem.

    Sample Requirements:

    • The sample should be as pure as possible since impurities will contribute to the CD signal. Dialyzing into the buffer of choice is highly recommended.
    • The sample concentration is determined by the pathlength of the cuvette. The BRC has several choices.
      • A starting guideline is the sample should not exceed an absorbance of 0.9 OD over the wavelengths you want to scan. Measure the absorbance of your sample at all of the wavelengths you plan to use in your experiment to ensure your sample does not exceed 0.9 OD.
      • When using a 1 mm cuvette, 0.2 mg/ml for the 190-230nm range is a good starting estimation.
    • A smaller pathlength cuvette will decrease solvent absorbance to allow scanning down to lower wavelengths but will require a more concentrated sample.
    • Bring at least 500uL of sample and at least 10mL of identical buffer, ideally from dialysis.

    Use and Management
    The purpose of this instrument is to support research at Boise State University and surrounding research facilities. First-time users please contact the BRC for information on training and access requirements. Qualified users will be able to book instrument time and use the instrument independently.


    Analytical Ultracentrifugation
    Analytical ultracentrifugation relies on the simple premise that biomolecules in solution will sediment in the presence of the gravitational force applied by the centrifuge. The rate at which the particle sediments will be affected by its molecular weight, size and shape allowing one to determine these parameters experimentally. There are two basic types of experiments performed with the analytical ultracentrifuge, sedimentation velocity and sedimentation equilibrium.

    • Sedimentation velocity experiments rely on a high angular velocity which causes the solute to sediment rapidly leading to a depletion of solute near the meniscus. A boundary forms between the depleted and uniform concentration areas of the solute which can be monitored to determine the sedimentation coefficient which is a measure of the effective size of the solute.
    • Sedimentation equilibrium experiments employ a smaller angular velocity than sedimentation velocity which causes the solute to sediment at a much slower rate. As sedimentation occurs, diffusion opposes the gradual concentration increase in the bottom of the cell. After the two opposing forces reach equilibrium, the diffusional flow exactly balances the sedimentation flow leading to a concentration profile that is constant over time from which the molecular weight of the solute can be determined.

    AUC applications include determining:

    • Sample purity
    • Molecular weight
    • Oligomer formation
    • Conformational changes
    • Ligand binding

    Instrument Information:

    • XL-I (Beckman Coulter, Installed)
    • Rotors:
      • An-60 Ti – 4-place titanium rotor rated for 60,000 rpm
      • An-Ti 50 – 8-place titanium rotor rated for 50,500 rpm

    Sample Requirements:
    Sedimentation Velocity: At least 500uL of sample with an OD of 0.7-0.8 at the absorbance wavelength.
    Sedimentation Equilibrium: At least 500uL of sample with an OD of 0.2-0.3 at the scanning wavelength.
    **Bring at least 10mL of buffer as well.

    Use and Management
    The purpose of this instrument is to support research at Boise State University and surrounding research facilities. First-time users please contact the BRC for information on training and access requirements. Qualified users will be able to book instrument time and use the instrument independently.

    Rate Information

    DescriptionService ProvidedBSU UserNon-ProfitCommercial
    Jasco J-810 CD SpectropolarimeterInstrument Usage and Training$25.55/hour$35.90/hour$60.00/hour
    Beckman ProteomeLab XL-1 AUCIn-solution Characterization$147.05/run$206.61/run$250.00/run
    Plasmid Propagation from Cell StockSample Preparation $17.57/sample$24.68/sample$50.00/sample
    Plasmid Propagation from Plasmid Stock Sample Preparation$39.37/sample$55.32/sample$75.00/sample
    Soluble Protein Expression TestSample Preparation$136.78/sample$192.18/sample$200.00/sample
    Plasmid MaxiPrep
    Sample Preparation$58.81/sample
    $78.41/sample
    $185.00/sample
    Isotope N15 Label Prep (500ml)
    Sample Preparation$132.10/sample
    $185.60/sample
    $1100.00/sample
    Isotope N15/C13 Label Prep (500ml)
    Sample Preparation$264.10/sample
    $371.06/sample
    $1200.00/sample
    LB Prep (500ml)
    Sample Preparation$86.22/sample
    $121.13/sample
    $1000.00/sample
    Protein Purification (IMAC)Sample Preparation $66.14/sample$92.92/sample$300.00/sample

    Please contact Dr. Lisa Warner at (208) 426-2260 or by email at lisawarner@boisestate.edu  for more information.

    Jasco

    JascoImage

     

     

    The Jasco J-810 Spectropolarimeter (163-900 nm) is a hybrid instrument consisting of a variable wavelength polarimeter and absorption spectrophotometer. It is designed to allow secondary structure determination by circular dichroism; specifically measuring the left-and right-handed circularly polarized light of optically active molecules.  It is equipped with an equipped with a computer-controlled Peltier device (3-90 °C) and a two-syringe titrator to assess thermal/chemical stabilities of proteins/ polypeptides or to monitor ligand binding and  is controlled by Jasco’s Spectra Manager software.

    CD applications include:

    • Determination of optical purity
    • Estimation of protein and nucleic acid conformation
    • Determination of the conformational changes of protein and nucleic due to molecular interactions
    • Structural comparison between wild-type and mutant proteins
    • Determination of the thermodynamically dependent folding and unfolding of proteins and nucleic acids
    • Determining the binding constants
    • Kinetics of folding and unfolding of macromolecules
    • Thermodynamic parameters from temperature dependencies of CD signals

    Use and Management
    The purpose of this instrument is to support research at Boise State University and surrounding research facilities.  First-time users please contact the BRC for information on training and access requirements. Qualified users will be able to book instrument time and use the instrument independently.

    Boise State University users – faculty, staff, students
    Non-profit – Other academic or federally funded users
    Commercial – For profit users

    Circular Dichroism References:

    UCI Department of Chemistry Introduction to circular dichroism
    Circular Dichroism_Greenfield 2004
    J-810 Series Hardware Function Manual