ISI Web of Science Journals 2008
Abbreviated Journal Title ISSN 2008 Impact 5-Year 2008
Total Cites Factor Impact Articles
    Factor  
NAT REV MOL CELL BIO 1471-0072 19628 35.423 34.221 84
NATURE 0028-0836 443967 31.434 31.21 899
CELL 0092-8674 142064 31.253 30.149 348
SCIENCE 0036-8075 409290 28.103 30.268 862
NAT MATER 1476-1122 18902 23.132 25.759 129
NAT BIOTECHNOL 1087-0156 28188 22.297 25.329 100
NAT CELL BIOL 1465-7392 22676 17.774 17.637 145
NAT METHODS 1548-7091 5956 13.651 15.011 118
DEV CELL 1534-5807 12421 12.882 13.284 149
PLOS BIOL 1544-9173 12186 12.683 14.662 212
ANNU REV BIOMED ENG 1523-9829 2122 10.789 13.679 15
P NATL ACAD SCI USA 0027-8424 416018 9.38 10.228 3508
ANNU REV FLUID MECH 0066-4189 5239 9.314 13.306 17
ADV MATER 0935-9648 49008 8.191 10.231 772
PHYS REV LETT 0031-9007 310717 7.18 7.134 3905
DEVELOPMENT 0950-1991 46547 6.812 7.218 390
BIOMATERIALS 0142-9612 39782 6.646 7.325 511
SMALL 1613-6810 5016 6.525 7.292 319
LAB CHIP 1473-0197 6369 6.478 7 279
ANAL CHEM 0003-2700 77792 5.712 5.918 1221
LANGMUIR 0743-7463 76864 4.097 4.347 2026
APPL PHYS LETT 0003-6951 179925 3.726 4.096 5449
MICROFLUID NANOFLUID 1613-4982 783 3.314 4.194 133
IEEE CONTR SYST MAG 1066-033X 2245 2.827 2.731 34
J FLUID MECH 0022-1120 30950 2.315 2.714 450
IEEE T CONTR SYST T 1063-6536 3114 2.13 2.566 132
SIAM J CONTROL OPTIM 0363-0129 4356 1.517 1.77 132

 

2008 RANKINGS FOR UNDERGRADUATE SCHOOLS

1. Massachusetts Inst. of Technology 4.9 1- MIT Johns Hopkins University (Whiting) (MD)
2. Stanford University (CA) 4.7 2-Stanford Georgia Institute of Technology
2. University of California–Berkeley * 4.7 3-University of Michigan  University of California–San Diego (Jacobs)
4. California Institute of Technology 4.6 4-University of Illinois at Urbana- Champaign University of Washington
5. Georgia Institute of Technology * 4.5 5-University of California- Berkeley Duke University (NC)
5. U. of Illinois–Urbana-Champaign * 4.5 6-California Institute of Technology Boston University
7. Cornell University (NY) 4.4 7-Princeton University University of Pennsylvania
7. University of Michigan–Ann Arbor * 4.4 8- Cornell Massachusetts Institute of Technology
9. Carnegie Mellon University (PA) 4.2 9-University of Texas at Austin Rice University (Brown) (TX)
9. Purdue Univ.–West Lafayette (IN)* 4.2 10- University of Minnesota  Case Western Reserve University (OH)
9. University of Texas–Austin * 4.2 11-University of California-San Diego University of Michigan–Ann Arbor
12. Princeton University (NJ) 4.1 12-Penn State Northwestern University (McCormick) (IL)
13. Univ. of Wisconsin–Madison * 4.0 13- Northwestern  Stanford University (CA)
14. Johns Hopkins University (MD) 3.9 14-Georgia Institute of Technology University of California–Berkeley 
14. Northwestern University (IL) 3.9 15-University of California- LA Washington University in St. Louis (Sever)
14. Virginia Tech * 3.9 16-Rensselaer Polytechnic Inst University of Pittsburgh
17. Pennsylvania State U.–University Park * 3.8 17- Texas A&M University of Virginia
17. Rice University (TX) 3.8 18-Purdue University University of Texas–Austin
17. Texas A&M Univ.–College Station * 3.8 19-Carnegie Mellon Columbia University (Fu Foundation) (NY)
20. Columbia University (NY) 3.7 20-Brown University of Utah
20. Rensselaer Polytechnic Inst. (NY) 3.7 21-Virginia Polytech Inst & State University  Vanderbilt University (TN)
20. Univ. of California–Los Angeles * 3.7 22-North Carolina State University California Institute of Technology
20. Univ. of Minnesota–Twin Cities * 3.7 23-University of Wisconsin- Madison University of Wisconsin–Madison
20. University of Washington * 3.7 24-University of Pennsylvania Carnegie Mellon University (PA)
25. Duke University (NC) 3.6 25-Ohio State University Cornell University (NY)
25. Ohio State University–Columbus * 3.6 26-Case Western Reserve University Purdue University–West Lafayette (IN)
25. Univ. of California–San Diego * 3.6 27-University of California-Davis University of California–Davis
25. Univ. of Maryland–College Park * 3.6 28-Columbia University University of Minnesota–Twin Cities
29. North Carolina State U.–Raleigh * 3.5 29-Lehigh University Rensselaer Polytechnic Institute (NY)
29. University of Florida * 3.5 30- Michigan State University Arizona State University (Fulton)
29. University of Pennsylvania 3.5 31- Rice Pennsylvania State University–University Park
29. Univ. of Southern California 3.5 32-University of Arizona Texas A&M University–College Station (Look)
33. Harvard University (MA) 3.4 33-University of Maryland College Park University of Southern California (Viterbi)
33. University of California–Davis * 3.4 34-University of Washington CUNY–City College (Grove)
33. University of Colorado–Boulder * 3.4 35-University of Southern California North Carolina State University
33. University of Virginia * 3.4 36- University of Notre Dame University of Iowa
37. Arizona State University * 3.3 37-Rutgers State University- New Brunswick Drexel University (PA)
37. Case Western Reserve Univ. (OH) 3.3 28-Oklahoma State University Harvard University (MA)
37. Iowa State University * 3.3 39-University of Delaware Marquette University (WI)
37. Lehigh University (PA) 3.3 40-Duke Rutgers, the State University of New Jersey–New Brunswick
37. Univ. of California–Santa Barbara * 3.3 41-Johns Hopkins University SUNY–Stony Brook
37. Yale University (CT) 3.3 42-Cuny University of Alabama–Birmingham
43. Brown University (RI) 3.2 43-University of California-Irvine University of California–Irvine (Samueli)
43. Michigan State University * 3.2 44-Clemson University  University of Rochester (NY)
43. University of Notre Dame (IN) 3.2 45-State University of New York-Buffalo Yale University (CT)
43. Vanderbilt University (TN) 3.2 46-University of Cincinnati Brown University (RI)
48. Dartmouth College (NH) 3.1 47-University of Utah Clemson University (SC)
48. University of California–Irvine * 3.1 48-University of Iowa University of California–Los Angeles (Samueli)
49-University of Virginia University of Arizona
  50-University of Colorado  
 

BACKUP of MY sites...July 2009

I am a Ph.D. Candidate in the Department of Mechanical Engineering at Carnegie Mellon University in Pittsburgh, PA. I am advised by Professor Philip R. LeDuc and Professor William C. Messner. I have been working with Professor Lance A. Davidson in the Department of Bioengineering at University of Pittsburgh.

My research has been focusing on Closed-Loop Microfluidic Controls for Cellular Dynamics in Xenopus laevis Embryonic Development. The developing system is based on the control of the laminar flow interface in a microfluidic channel that allows the precise manipulation of the subcellular chemical environments and automated measurements of cellular responses without destruction of cells for long periods of time. This is critical for investigating cell responses in cancer metastasis, embryogenesis, and differentiation, which are often on the order of hours to days.

Before joining in the LeDuc Laboratory as a Ph.D. student, I had worked at Samsung Electronics andHyundai & Kia Motor Company as a Research Engineer. I mainly worked in the field of dynamic system analysis and control device development on real vehicles, living appliances and robot vacuum cleaners. My abilities integrated from these experiences allow the confidence for the challenges to science, cell biology.
 
I'm interested in development of new methodology through integrated engineering technology for the purpose of discovering new transitions in cell biology and developmental biology.
  • Development and instrumentation of the new microfluidic technology with dynamic system and control theory
  • Design and optimization of the new microfluidic device scaling up to milifluidic network for in-vitro tissue environment
  • Using this technology to understand the dynamics of cellular and molecular mechanisms in particularly long-term biological systems including identification of cell motility features in cancer metastasis, and cellular signal pathway and gene expression in Xenopus laevisembryogenesis

Education and Professional Experience  (Further Information : Read Research Experience)

 
Ph.D. Candidate (Aug. 2007 ~ Present)
 
 
Thesis "Closed-Loop Microfluidic Controls for Cellular Dynamics in Xenopus laevis : Embryonic Development Regulated through a Microfluidic Feedback Approach 
 
 
 
Research Engineer (Dec. 2003 ~ Apr. 2007)
 
at Samsung Electronics, Suwon, Korea
 
Project 1 "New robot vacuum cleaner with auto-dischaging device and integrated driving system for novel motion planning and control"
 
Project 2 "Dynamic Regulation of the shaft balance and reduction of noise & vibration in linear and reciprocating compressors"
 
 
 
Assistant Research Engineer (Jan. 2001 ~ Nov. 2003)
 
at Hyundai & Kia Motor Company, Hwasung, Korea 
 
Project "Experimental noise source identification and reduction techniques in real vehicles"
 
 
 
Master of Science (Mar. 1999 ~ Feb. 2001)
 
 
Thesis "Combustion Modeling for Stratified Charge in Direct-Injected Gasoline Engines"
 
     
 
Bachelor of Science (Mar. 1995 ~ Feb. 1999)
 
 
Project title "Robust Design with Active Control of Air Bearing

 

 

 

Journal Publications


 
Y. Kim, W. C. Messner, and P. R. LeDuc, "Three-Dimensional Profile Inversion with Two-Dimensional Fluidic Modules and Autonomous Flow Control at Micrometer to Millimeter Scales", Submitted.

 
C.-M. Cheng, Y. Kim, J. M. Yang, S. H. Leuba, and P. R. LeDuc, "Dynamics of Individual Polymers using Microfluidic based microCurvilinear Flow", Lab Chip, 2009 online DOI:10.1039/b907860f. (Link)
 
Y. Kim, B. Kuczenski, P. R. LeDuc, and W. C. Messner, “Modulation of Fluidic Resistance and Capacitance for Long-Term High-Speed Feedback Control of a Microfluidic Interface”, Lab Chip, 2009 online DOI:10.1039/b822423d. (Link)
 
Y. Kim, S. Pae, and K. Min, “Combustion Modeling for Stratified Charge”, Journal of Korean Society of Automotive Engineers, VOL 9-4, 50-55, 2001.

 

 

Conference Proceedings


Y. Kim, S. D. Joshi, L. A. Davidson, W. C. Messner, and P. R. LeDuc, "Probing Spatiotemporal Dynamics in the Integrated Multi-Cellular Environment of Xenopus laevis: Embryonic Development Regulated through a Microfluidic Feedback Approach", Annual Fall Meeting of Biomedical Engineering Society, 2009. Poster Presentation.

Y. Kim, B. Kuczenski, W. C. Messner, and P. R. LeDuc, "Feedback Approach for Controlling Fluid Interfaces to Probe Cell Responses with Microfluidics", Annual Fall Meeting of BioMedical Engineering Society, 2008. Poster Presentation.

Y. Kim, B. Kuczenski, P. R. LeDuc, and W. C. Messner, "Pressure Modulation using Fluidic Resistance and Capacitance for Fluid Interface Control in Microfluidic Networks", International Conference of Mechanics in Medicine and Biology, 2008. Podium Presentation.
 
Y. Kim, J. Lee, and J. Joo, "Reduction of Radiated Noise in a Reciprocating Compressor",Conference of Korean Society of Noise and Vibration Engineers, 2005. Podium Presentation.

J. Joo, J. Lee, J. Jeong, and Y. Kim, "Development of the Ultra-Silence Refrigerator with Considering Consumer's Hearing", Conference of Korean Society of Noise and Vibration Engineers, 2005.

J. Kang, J. Jeong, and Y. Kim, "Dynamic Analysis of an Inverter Motor Driven Compressor",Conference of Korean Society of Noise and Vibration Engineers, 2004.
 
H. Choi, Y. Kim, and K. Min, "Combustion Modeling for Stratified Charge in GDI Engines", Conference of Korean Society of Automotive Engineers, 2003.

Y. Kim, Y. Kim, O. Ahn and Y. Kang, "Reduction Method of Structural Noise Radiated by Dash Panel of a Passenger Car", Conference of Korean Society of Automotive Engineers, 2002. Podium Presentation.

S. Pae, Y. Kim, J. Lim, and K. Min, "Laminar Flame Velocity of Propane and Isooctane Fuel for Stratified Combustion Modeling", Conference of Korean Society of Mechanical Engineers, 2000. 

 

 

References


Professor Philip R. LeDuc (PhD thesis advisor)
Department of Mechanical Engineering with a courtesy appointment in the Departments of Biomedical Engineering and Biological Sciences
Carnegie Mellon University, Pittsburgh, PA 15213
412-268-2504
 
Professor William C. Messner (PhD thesis advisor)
Department of Mechanical Engineering with a courtesy appointment in the Department of Electrical and Computer Engineering
Carnegie Mellon University, Pittsburgh, PA 15213
412-268-2510
  
Professor Lance A. Davidson (PhD thesis commitee member)
Department of Bioengineering
University of Pittsburgh, Pittsburgh, PA 15260
412-383-5820
 
Professor Kenji Shimada (instructor for whom I served as TA)
Department of Mechanical Engineering with a courtesy appointment in the Departments of Biomedical and Civil and Environmental Engineering, and the Robotics institutes
Carnegie Mellon University, Pittsburgh, PA 15213
412-268-3614
 
Professor KyoungDoug Min (MS thesis advisor)
Department of Mechanical and Aerospace Engineering
Seoul National University, Seoul, South Korea
+82-2-880-1661

 

 

Research Experience


Aug. 2007. ~ Present 
  • Can apply to microfluidic based feedback control device (membrane type) for modulation of fluidic resistance and capacitance. 
  • Will be investigating flow patterns around embryonic tissue explants inside a microfluidic chamber with CFD and flow visualization.
  • Will be creating 3D profile inversion in a gray-scaled microfluidic tube for blood vessel bifurcation simulation. 
  • Investigating cancer cell motility and chemotaxis in microfluidic-based localized chemical gradients. 
  • Developing a spatiotemporal control of the central lane in a three-lane microfluidic network through closed-loop control system. 
  • Probing spatiotemporal dynamics in the integrated multi-cellular environment of Xenopus laevis: embryonic development regulated through a microfluidic feedback approach. (BMES 2009
  • Created three dimensional profile inversion with autonomous flow control in two dimensional microfluidic modules. (Submitted)
  • Developed a novel long-term, high-speed approach that employs modulation of fluidic resistance and fluidic capacitance between a fluid reservoir and a microfluidic network with feedback control to enable long-term dynamic control of a microfluidic interface in time and space.
    (Lab Chip 2009BMES 2008, ICMMB 2008)
  • Probed dynamics of individual polymers using microfluidic based microcurvilinear flow showing that flexible DNA molecules exhibited multimodal responses including distinct conformations and controllable curvatures. (Lab Chip 2009 2nd author)

Dec. 2003. ~ Apr. 2007.
Research Engineer at Samsung Electronics, Suwon, Korea
  • Developed a robot vacuum cleaner.
    • Auto-discharging device and integrated driving system (ADAMS, ReCurDyn)
    • Computational flow path optimization (SC TETRA, FLUENT)
    • Motion planning, coverage, locomotion, new algorithms for efficient cleaning
    • Sensor-based feedback control system for avoiding obstacles
  • Developed a compressor 
    • Dynamic regulation of the shaft balance (ADAMS)
    • Noise and vibration reduction
    • Performance and efficiency improvement
 

Jan. 2001. ~ Nov. 2003.
 
Assistant Research Engineer at Hyundai & Kia Motor Company, Hwasung, Korea 
  • Real vehicle functional development
  • Road noise analysis, intake and exhaust noise contribution and investigation
  • Engine mount system design
  • Experimental source characterization and noise prediction techniques
 

Jan. 1999. ~ Jan. 2001.
  • Combustion modeling for stratified charge
    • Developed novel model for secondary diffusion flame and reaction
  • Simulated flow patterns in engines (CFD, Star-CD, Fluent)
    • CAE - Mesh Generation (ICEM, CD-Adapco Korea)
    • Predicted cavitation in diesel injectors of common-rail system
    • Computed drag coefficients for injected droplets

 

 

Awards and Honors


2008 ~ 2009
Dowd-ICES Fellowship, The Philip and Marsha Dowd Engineering Seed Fund with the Institute for Complex Engineering Systems, Carnegie Mellon University, Pittsburgh, PA. (Four fellowships awarded annually to CMU graduate students.)
2007 ~ 2008
Dean's Fellowship, Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA
2002
Army Commendation Gold Medal (awarded to the best collaborating one for four hundred new recruits), Korean Army Training Center, South Korea
1999 ~ 2000
BrainKorea21 Project Scholarship from Ministry of Education, Seoul National University, Seoul, South Korea

 

 

Teaching Experience


  • Undergraduate Student Research Mentorship
    • Research Mentor, May 2009 - April 2010 (estimated)
    • Participated in the project "Investigating cancer cell motility and chemotaxis in microfluidic-based localized chemical gradients"
    • Microfluidics, Diffusion, Modeling, CFD, Soft lithography, Cell migration and chemotaxis research.
    • Mentored laboratory experimentation and data analysis.

 

  • Undergraduate Mechanical Engineering Design Development and Instruction
    • Teaching Assistance, Engineering Design I (Spring semester 2009)
    • Instructor : professor Kenji Shimada at Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA
    • Participated in the development and solution of design materials.
    • Evaluated design project presentations.
    • Answered design problems and questions on 3D modeling, Finite Element Analysis, and Computational Fluid Dynamics in regular office hours.

 

Patents

 

Wall-following robot cleaner and method to control the same    
US20080249661
 
A robot cleaner that cleans a cleaning region while traveling the cleaning region and a method to control the same are provided. The robot cleaner can uniformly clean a cleaning region based on a wall-following technique which allows the robot cleaner to travel along the outline of the cleaning region. The method selects, as a reference wall, a wall at a left or right side of the robot cleaner at a start position of the robot cleaner based on a left or right-based travel algorithm, which allows the robot cleaner to travel along a left or right wall, and controls the robot cleaner to travel the cleaning region in a zigzag travel pattern in which the robot cleaner moves a predetermined distance in a direction perpendicular to the reference wall at specific intervals along the selected reference wall while following the selected reference wall.
 
 
 
 

Robot cleaner with improved dust collector 
US20080235897

A robot cleaner having a configuration capable of improving an ability to collect dust, etc. is disclosed. The robot cleaner includes a suction hole to suction dust, a dust collector to receive the dust suctioned through the suction hole, and a rotating brush provided at a side of the suction hole. The robot cleaner is configured to sweep up and collect the dust into the dust collector by a drive force of the rotating brush.

 
 
 
 

Robot cleaner system having robot cleaner and docking station
US20080201895
Disclosed is a robot cleaner system having superior functions of sucking dust and exhausting dust to a docking station. The robot cleaner includes a dust suction port to suck dust, a dust collecting chamber to collect dust introduced through the dust suction port, a dust exhaust port to exhaust dust collected in the dust collecting chamber to the docking station, a connection path extending from the dust suction port to the dust exhaust port in adjacent to the dust collecting chamber, and a valve device provided between the connection path and the dust collecting chamber, an opening/closing of the valve device allowing the dust collecting chamber to selectively communicate with the dust suction port or the dust exhaust port according to a pressure difference between the dust collecting chamber and the connection path.
 
 
 

Robot cleaner system and method of controlling the same    
US20080004751

A robot cleaner system and a control method thereof reduce manufacturing costs, expand a detected distance, and precisely control a movement and positioning of a robot cleaner. The robot cleaner system includes a robot cleaner and a station. One of the robot cleaner and the station transmits a signal of a predetermined frequency and the other receives the signal so that a direction toward the transmitting side for transmitting the signal is detected based on a Doppler shift observed by the receiving side that receives the signal.

 
 
 
Apparatus of monitoring rear of vehicle 
US20030202096, EP1356988, JP2003312359
 
Disclosed is an apparatus for monitoring the rear of a vehicle capable of entirely eliminating a blind spot. The apparatus includes a camera for taking a picture of a rear of the vehicle, a liquid crystal display for receiving and displaying the image, and a control section for controlling the camera and the liquid crystal display. The camera is installed in an auxiliary turn indicator mounted on left and right front fenders of the vehicle. The turn indicator includes a partition dividing a chamber into one chamber for accommodating a turn signaling lamp and the other chamber for accommodating the camera.

Ten patents in the Korean Patent Office

  • The dust-box shape with insert pipe in a vacuuming robot (P20060037643)
  • The estimation of a vacuuming robot’s location with three stations (P20060058980)
  • The apparatus of blowing dust with compressed air in a vacuuming robot (P20060049334)
  • The side brush shape in a vacuuming robot (P20060040567)
  • The apparatus of estimating the position of a vacuuming robot (P20060058982)
  • The compressor with hybrid suction mufflers (P20050134800)
  • The exit shape of a suction muffler in a compressor (P20050120029)
  • The absorber in a linear compressor (P20050003875)
  • The shape of suction pipe in a refrigerator (P20040061131)
  • The shape of grommet for insulating vibration in a refrigerator (P20040060326)

 

 

 

 

Cell Fluorescent Imaging

 


Making Ringer's Solution

 

Ringer's Solution is a pH-balanced salt solution that is used for live cell imaging.

From Gerbino, Ruder et al., J Cell Biol. 171 (2), 2005: link to jcb.org

 

 

"Ringer's solution containing 121 mM NaCl, 2.4 mM K2HPO4, 0.4 mM KH2PO4, 1.2 mM CaCl2, 1.2 mM MgCl2, 10 mM glucose, and 10 mM Hepes/NaOH, pH 7.40."

 

Making 10X Stock

Warren generally maintains a bottle of ultra-precise 10x Ringer's stock solution which includes:

 

 

1.21 M NaCl (for 500 mL of solution, use 35.3562 g)

  • 24.0 mM K2HPO4 (500 mL use 2.0902 g)
  • 4.0 mM KH2PO4 (500 mL use 0.27218 g)
  • 100 mM HEPES ( 500 mL use 11.915 g)

     

    Making 1X Solution

    500 mL batch

    You need:

     

     

    Clean Glassware

    1. 1000 mL beaker for preparation
    2. 50 mL precision flask (for measuring 10X stock)
    3. 500 mL precision flask (for final dilution)
    4. magnetic stirrer.
    5. funnel.
    6. A clean container to store the solution in.
  • Also a clean powder scoop, a few transfer pipets, a couple 1 mL or 5 mL pipets.
  •  

     

    pH meter and pH titrating solutions (generally NaOH at 10 M, 1 M, 0.1 M)

     

    Mixing the solution

    1. Wash glassware and rinse 5X with tap water, 5X with distilled water.
    2. Warm the 10X stock in the water bath (it changes density with temperature).
    3. Prepare about 150 mL of DI water in the 1000 mL beaker. Place it on the hot plate / stirrer with a magnetic stirrer inside.
    4. turn on the stirrer (but not the hot plate).
    5. Add 5.5 mM glucose (D-Glucose, anhydrous, 0.496 g or D-glucose monohydrate, 0.545 g).
    6. Measure 50.0 mL of 10X stock in the precision flask. Add it to the beaker. Rinse the flask with DI water and empty into the beaker (you don't want to lose ANY of the 50.0 mL).
    7. Add 1-1.2 mM MgCl2 or MgSO4 (500-600 uL from 1M stock).
    8. If desired, add 1-1.2 mM CaCl2 (500-600 uL from 1M stock).

       

       

      /!\ note: obviously, if you are making Calcium-free Ringer's solution, don't add CaCl2.

    9. Add DI water up to about 300-350 mL.

     

    Balancing the pH

    1. Calibrate the pH meter using the pH 4, pH 7, and pH 10.01 buffers.
      • /!\ Be sure to thoroughly rinse the pH meter with DI water after each stage into a waste container.
    2. Submerge the calibrated probe into the 1000 mL beaker. It should probably be around 6-6.5 pH.
    3. Add drops of NaOH to increase the pH.
      1. One drop of 10M solution will tend to raise it about 0.1-0.5 pH
      2. One drop of 1M solution will tend to raise it about 0.05-0.1 pH
      3. One drop of 0.1M solution will tend to raise it about 0.005-0.01 pH.

       

       

    4. You want a final pH value of 7.4-7.43.
    5. Thoroughly rinse the probe into the beaker and put it away.

     

    Final Dilution

    1. Using the funnel, transfer the contents of the beaker to the 500 mL precision flask.
    2. Rinse the beaker with DI water and pour the runoff into the precision flask as well.
    3. Add DI water until the total volume is 500 mL.

    Pour the contents of the precision flask into the container. Do not rinse the remnants into the container with DI water- this will cause further dilution, which is not desired.

     
    Clean up your glassware.
     

     

     

    Imaging Dye Loaded Cells

    • Turn on the fluorescent lamp and allow it to complete the warm-up cycle.
    • Turn on the microscope and the Insight camera.

     

     

    Finally, turn on the lambda 10.3 controller and choose appropriate shutter setting (see UsingShutterController).

  • Set to the 63x objective, ensure that it is thoroughly cleaned then place two drops of lens immersion oil directly onto the lens to create a bubble. Adjust the objective so that it is slightly under the microscope stage.
  • Place the dye-loaded cells (see additional protocol: LoadingDyeIntoCells) into a stage bracket and clip into the stage manipulator.
  • Using the stage manipulator, ensure that the microscope lens is placed in the coverslip’s center. Afterwards, slowly ascend the objective until it contacts with the coverslip. The surface tension of the oil on the lens will break when it touches the coverslip.
  • Using the halogen lamp locate the cells.
  • On the computer, open the Spot Advance program. Select Live (the fluorescent light should be on- this light should not be on for longer than 5 seconds to avoid photobleaching) and focus the cells quickly until their processes are visible. Press Liveagain to turn fluorescence off.
  • Select a region that contains cells at the desired confluency and morphology.
  • Use Live to focus at best on that region. Following that, select the option below Live, Get an image, to take a picture of the region.
  • Use the picture to determine if additional adjustments are needed. One possible adjustment is the fluorescent intensity (controllable on the lamp power supply). Determine a good range of intensity to first try and focus (the cells should not be too bright and should be focused on the computer). Following the adjustments, take another picture, but ensure that 100% of the light output is directed to the camera
  • Go to the toolbar, and select Camera, and then Get Sequential Images. For the dialog box that appears, select 240 images for the number of images to take with 5 seconds intervals (or the interval most appropriate for your dye). Also adjust the exposure time (also dye-specific). Finally, in fast mode, you must set the TTL lag so that 8ms passes before the camera exposure begins (when the shutter if fully open). Then create a folder with the movie number and in this folder save this procedure as movie number.
  • Select Begin.
  • The shutter and camera will now synchronously take images at the specified intervals and specified exposure time. Make a note of when various stimulants are provided to the cell.
  • In Image J, open the movie file. Circle the region of interest in the cell. On the toolbar select Analyze, then Tools, and thenROI Manager. Using ROI Manager, select the measure option and the mean value of intensities in the ROI selected will be.
  • Select measure for the cell and save results as an excel spreadsheet. Make sure to add .xls extension if you will use Excel for data analysis. Repeat this procedure for all the visible cells.
  • Time traces for each ROI can then be compiled together to plot several cells' ROI responses.
     

    The following is a list of live cell dyes used in the Leduc laboratory and good approaches for their use:

    Fluo-4-AM

    • Prior to the day's experiments, change the medium for the cells.
    • Prepare a aliquots of a 1 mM Fluo-4-AM solution in DMSO. Freeze extra aliquots for future use.
    • Dilute an aliquot to 2 uM in culture media of the cells.
    • Incubate for 20-25 minutes.
    • Arrest the loading by changing the cell bath with either fresh media or Ringer's solution for live cell imaging experiments.
     

     

     

    This protocol describes use of the Lambda 10-3 controller and computer-controlled Smart Shutter. Unless specifically noted, "shutter" refers to the Smart Shutter, and not the built-in Zeiss shutter.

    Before beginning, make sure that the manual (Zeiss) shutter is open. Also, make sure that the fluorescent lamp is already on. You must always turn the shutter controller on after the mercury lamp and turn it off before you turn off the mecury lamp. Turning on the mecury arc lamp power supply produces a surge that can damage the electronics of the shutter controller

    To Enable the Controller for Cell Imaging/Movie Making:

    • Turn on the device with the off/on switch.

     

     

    On the keypad at the right select LOCAL to enable keypad functionality

  • On the keypad at the right select MODE
  • Select option 3-TTL
  • Select 1- Enable shutter (A).
  • Select 1 –Fast, this determines the speed at which the shutter opens.
  • Select 0 – No other options

    The shutter is now controlled by a TTL pulse from the camera controller card. This allows synchronization of image capture by camera and excitation by lamp

    To Disable Controller

     

     

    Select MODE.

  • Choose 3-TTL
  • Select 2-Disable Shutter (A)
  • Choose 0-No other options

    The shutter is now in manual mode.

     

     

    * Press S1 on the keypad until the shutter opens. Ensure the Mercury Arc Light is transmitted through the microscope housing and into the filterblock changer. Turn off the device with the off/ on switch.

    Make sure to leave the shutter open for the next user. This will allow users not familiar with the Lambda Smart Shutter to revert back to the built-in Zeiss shutter.

  • Microfluidics

     

     


    Microfluidics Toolbox

     

    A list of parts and tools we should have readily available to make microfluidic devices.

    • Materials Catalog No.
      Tweezers McMaster-Carr 8384A51
      Scotch tape McMaster-Carr 7636A22
      150 mm Petri Dish Fisher 08-757-14
      Cover glass slips #1 35x50 Fisher 12-545G
      Cover glass slips #1 24x40 Fisher 12-545D
      Cover glass slips # 1-1/2 24x40 Fisher 12-544C
      Wooden sticks ---
      Pipetter Fisher 13-683C
      Small hole punch 75165A552
      Large hole punch ---
      Glass slide ---
      Xacto Knife McMaster-Carr 35435A11
      Xacto Blades McMaster-Carr 35435A82, 35435A14
      PDMS Kit ---

     

     

    Notes for preparing microfluidic devices for Calcium experiments

    • Prepare channels, soak in 70% EtOH for 10 minutes, then pull out and place in the oven overnight to dry.

    Microscopy

     


    How to use the 63X Objective CAREFULLY 

     

     

     


    Microscope Protocol-LeDuc Lab Inserting the Objective (to eliminate objective damage)

     

    1. We will be putting this in a lock-box with personal codes in the future, but we do not have this yet. People need to use this so we are proceeding while we order this box. For now, sign the objective out and remove it from the objective drawer located in the main lab computer desk (not the imaging computer desk).

    2. Remove the microscope shroud.

    3. Place Styrofoam bucket next to the microscope stage (THIS IS TO PROTECT THE OBJECTIVE IN CASE IT FALLS).

    4. Position the 63X objective turret hole to the center turret position. The 63X turret hole is the only hole with a small Wollaston prism underneath it that can be manually adjusted with a thumbscrew. YOU MUST USE THIS HOLE FOR THE 63X. (Hole #1). The 10X Objective should be in Hole #2 and the 20X Objective should be in Hole #6)

    5. Uncap the turret hole (MINIMIZE THE AMOUNT OF TIME THAT ANY TURRET HOLE IS UNCOVERED AS DUST CAN GET INTO THE HOLE WHICH CAN PERMANENTLY APPEAR ON EVERYONE’S IMAGES IN THE FUTURE).

    6. Perform steps 6-11 over the Styrofoam bucket.

    7. Unscrew the objective case cap from the objective case – OVER THE STYROFOAM BUCKET. NOTE: Be careful as there is no guarantee that the previous user screwed the objective into the objective case cap.

    8. Make sure the objective is securely screwed into the objective holder cap.

    9. Using a COTTON TIP APPLICATOR (LIKE A Q-TIP) AND NOT KIM WIPES (WHICH CAN SCRATCH THE OBJECTIVE) to wipe the excessive oil from the objective so that it is not slippery.

    10. Inspect the objective for damage. FOR THE CURRENT DEMO LENS, a small indentation has already been formed at the point where damage occurs. You must ensure that this indentation does not become worse. We will take images so that you will have a comparison point for this. Please inform Phil immediately if you see anything.

    11. Unscrew the objective from the objective cap.

    12. Align the base of the 63X objective with the microscope turret hole (Hole #1, which is marked “1” on the microscope turret)

    13. Gently screw the objective into the turret. Be EXTREMELY CAREFUL not to cross-thread the objective and turret. This will result in irreparable damage of many thousands of dollars. IF IT IS NOT SCREWING IN, DO NOT FORCE IT….UNSCREW IT AND TRY TO SCREW IT BACK IN. IF IT CONTINUES TO NOT WORK, STOP YOUR WORK AND TALK TO PHIL ABOUT IT.

     

    Using the objective:

    1. Apply lens oil to the objective lens. More oil is better than less oil.

    2. Place your glass-bottomed sample in a specimen holder. You must ensure that the specimen glass has been wiped clean of salt crystals using dH2O and a Kim wipe. Salt crystals can scratch the objective lens just like Kim wipes!

    3. Very SLOWLY bring the objective into contact with the specimen.

    4. Look through the specimen to watch when the lens oil surface tension is broken by the specimen.

    5. Use only the FINE FOCUS knob while looking through the eyepieces to focus your specimen. DO NOT USE THE COARSE FOCUS KNOB ONCE THE OIL MAKES CONTACT WITH THE SPECIMEN.

    6. If your experimental protocol requires that you use a 10X, 20X and 63X objective on the same specimen, gently lower the 63X objective and switch to either the 10X or the 20X, then slowly bring the lower magnification focus up to the specimen The 10X Objective should be in Hole #2 and the 20X Objective should be in Hole #6. During this process, your number one task must be to ensure the safety of the 63X objective AS THIS COSTS AROUND $3000 TO REPAIR EVERY TIME IT GETS DAMAGED!!!. Check the location of the 63X objective after every repositioning of the 10X or 20X objective to ensure it is not contacting the stage.

    7. If you wish to use the 5X or the 40X objectives, you must remove the 63X objective entirely.

    8. During the use of the 63X objective, the center turret position must be on the 63X, the 10X or the 20X (the immediate right and left of the 63X turret position).

    9. DO NOT CHANGE THE POSITION OF THE 10X, 20X, OR 63X OBJECTIVES BEFORE TALKING TO PHIL. They will be numbered and labeled to correspond with a specific turret position. The 63X belongs in position #1, the 10X in position #2 and the 20X in position #6

     

     


    Objective removal: Objective removal is the reverse of insertion.

     

    1. Slowly lower the objective and remove the specimen.

    2. Perform steps 3-6 over the Styrofoam box.

    3. Unscrew the objective and screw it securely into the lid of he objective case.

    4. Recap the turret hole immediately.

    5. Using a cotton tip applicator (NOT A KIM WIPE) to remove oil from the objective.

    6. Place the objective into the objective case by screwing the objective case lid into the objective case.

    7. Store the objective in the objective drawer in computer desk located in the main laboratory (not the imaging computer desk).

    8. Sign the objective out
     

    Microscope Maintenance

    The microscope is serviced by WEL Instrument (ph: 724-625-9041; fax: 724-625-9069), which operates out of Mars, PA. The cost of a service call is around $250 (cheap!), so don't hesitate to call if there is a problem. Also, we should make a habit of scheduling an annual optical cleaning and tuneup.

     

    Fluorescent Filters

    The microscope is equipped with fluorescent filters that permit a narrow band of excitation to pass through on its way in and allow out a different band of emitted light. See the drawing below (created with the Wiki!!)

    Our microscope has slots for five filters, but we only have three installed.

    Filter Name Zeiss Filter Number ExcitationFilter BeamSplitter EmissionFilter use for:
    DAPI 01 Bandpass 365 nm Full-transmit 395 nm Lowpass 397 nm CascadeBlue
    FITC 10 Bandpass 450-490 nm Full-transmit 510 nm Bandpass 515-565 nm GreenFluorescentProtein
    TRITC 15 Bandpass 546 nm Full-transmit 580 nm Lowpass 590 nm TexasRed
    Slot #4 is labeled as filter set 25 but is actually all-pass  
    Slot #5 is labeled as filter set 37 but is actually opaque  

     

     

    DAPI Filter Spectrum

    FITC Filter Spectrum

    TRITC Filter Spectrum

    Soft Lithography

     


    Making Wafer Masks

     

    A simple way to make wafer masks is by printing them directly to a transparency on a high-resolution printer.

    Design the mask in a negative sense: portions of the photoresist that are obscured by black ink will not be exposed and will wash away; portions of the photoresist that are exposed to light through a clear mask will be hardened and will form the pattern. Recommended is to use a program capable of generating precise dimensions in its printed output, for example a drafting program.

    I use TeX and PSTricks to print to an encapsulated postscript (EPS) file. Many people in Shelley Ann