Biocomp GRADIENT STATION 153 User manual

MODEL 153
GRADIENT STATION
Manual version 3.3
SD Card Memory System
Fractionator software version 8.03
Gradient forming software version 5.3
OPERATOR'S MANUAL
© 2013 BioComp Instruments, Inc.
650 Churchill Row, Fredericton
New Brunswick, Canada E3B 1P6
Ph: [phone]; [phone];
Fx: [phone]; Email: [email protected]
Home Page: <http://www.biocompinstruments.com>

TABLE OF CONTENTS
PART 1. SPECIFICATIONS AND SETUP.
SECTION 1. INTRODUCTION
1.1. Warranty and service 4
1.2. Maintenance 4
1.3. Electrical surge protection 4
1.4. Goods damaged in transit 5
1.5. Instrument overview 5
SECTION 2. SPECIFICATIONS
2.1. Physical measurements 6
2.2. Commercially available parts 6
2.3. Performance characteristics 6
SECTION 3. PARTS DIAGRAMS
3.1. The Gradient Station 7
3.2. Gradient Forming attachment 8
SECTION 4. ORDERING INFORMATION
4.1. The Gradient Station Base unit 8
4.2 Gradient Forming 8
4.2.1 Tube holders 8
4.3 Gradient Fractionation 8
4.3.1 Tube holders 9
4.3.2 Centrifuge tubes 9
4.3.3 Spares 9
SECTION 5. INSTRUMENT SETUP
5.1. Inspect the shipping box 9
5.2. Assemble the left wing 10
5.3. Assemble the Gradient Forming attachment 10
5.4. Attach the Reservoir: 11
5.5. Assemble the computer panel 12
5.6. Install the power cord 13
SECTION 6. GRADIENT FORMING - STATION 15
1.1 Levelling the plate: a critical first step 15
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PART 2. GRADIENT MASTER MANUAL
PART 3. GRADIENT FRACTIONATOR MANUAL
PART 4. GRADIENT PROFILER MANUAL
(where applicable)
PART 5. GRADIENT RUN PARAMETERS
(last pages)

May 22, 2013 GRADIENT STATION
BIOCOMP Model 153
Gradient forming software Version 5.3
Fractionation software Version 8.03
OPERATOR’S MANUAL
SECTION 1. INTRODUCTION
1.1 WARRANTY AND SERVICE
BioComp has a policy of complete customer satisfaction. If, during the first thirty (30) days, you are
unhappy with the GRADIENT STATION, you may return it for a full refund.
BioComp warrants this instrument to be free of defects in workmanship for a period of one year from
the date of receipt for all electronic and mechanical parts. Liability is limited to repairs or replacement
of the unit at BioComp's discretion. This warranty is in lieu of all other warranties either express or
implied.
Claims against this warranty must be made by first contacting BioComp (phone [phone]). At
this time the remedy will be determined. Units returned to BioComp without our knowledge and
permission will not be accepted.
Claims for shortages or damage in transit must be reported to BioComp within ten (10) working days of
the date of receipt. Such claims made after this period cannot be honored.
1.2 MAINTENANCE
Other than the tightening of loose screws and the removal of spilled gradient solutions, no user service
is required. The instrument contains a computer which should not be tampered with. In the unlikely
event of computer failure, contact BioComp and we will ship you a new printed circuit board and
simple instructions for its installation.
1.3 ELECTRICAL SURGE PROTECTION
As with any computer, voltage spikes and power surges can severely damage the sensitive chips in this
instrument. You are strongly encouraged to purchase a surge protector from your local computer or
hardware store and plug the instrument into it. Since surges and spikes can occur at any time, it is also
wise to turn the unit off when not in use to reduce your instrument's exposure to them.
1.4 GOODS DAMAGED IN TRANSIT
If the instrument or any of the accessories are damaged when you receive them, it is critical that you
save the shipping carton(s) and contact us immediately. We will inform you of the return procedure
and shipping addresses to put on the box. If the box is damaged to such an extent that returning the
instrument in it would risk further damage, save the box for inspection by the shipper who will be
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notified to come and inspect it. Failure to adhere to these instructions will void any insurance claims
we might seek and result in BioComp absorbing unnecessary expenses.
1.5 INSTRUMENT OVERVIEW
The Gradient Station combines the best of BioComp’s two premier gradient instruments in one.
The Gradient Master is embodied by a tilting and rotating disk on the right wing of the Piston Gradient
Fractionator.
Gradient forming is accomplished the the patented “tilted tube rotation” method invented by Dr.
David Coombs, the founder of BioComp. This remarkably simple and reproducible system involves
layering the 2 end point solutions in the tube, capping the tube and rotating it for short time at a
predetermined angle. The rotation of the wall of the tube smears the interface between the light and
heavy solutions, forming the desired gradient.
The Piston Gradient Fractionator (PGF) was also invented by Dr. Coombs (Coombs, 1974, Anal.
Biochem. 68:95-1011) and offers a new dimension in fractionation. A piston is forced into the centrifuge
tube from above and it seals against the inside wall of the tube, forcing the gradient out of the tube
layer by layer. The size of the fraction taken is determined by the length of the piston stroke. A key part
of the evolution of the device has been in the shape of the piston face in contact with the gradient. It
converts horizontal bands of particles into vertical tubes traveling up the outlet tubing. The current
Trumpet Tip™ design doubles the peak height and halves the peak width compared with standard
needle puncture devices (see the web page for the actual data).
Dr. Coombs’ work with the purification of viruses led him to develop an exquisitely sensitive
band visualization system. T4 phage at >108phage/ml can be visualized with the naked eye.
Ribosomal subunits are visible. This is possible for two reasons: light scattered by the particles from
the bright spot light shining underneath the tube is seen against the black background of the tube
holder. In addition, when the holder is filled with water before the tube is inserted, the outer surface of
the tube essentially disappears since the refractive index of the solution and the tube are nearly the
same. This lowers the background light scattering to such low levels that the faintest bands are visible.
In the future, we will provide UV sensitivity for particles that do not scatter visible light.
Another key to sensitive fractionation is the ability to clean out the tubing between fractions with
air or buffer. Often the top of a gradient contains large amounts of proteins, lipids or radioactivity that
smear into lower fractions if the tubing is not rinsed. This problem has been eliminated by injecting air
and/or buffer directly into the system at the point of gradient capture in the tip of the piston.
The software has been designed to be as simple as possible, but it will still take getting used to.
The piston’s downward movement at the start of the run is controlled by a dial. The further your turn
the dial, the faster the piston moves downward. As you manually bring the tip of the piston into the
tube, you will be asked to keep an eye on the outlet tubing to spot the first drop to leave the tubing.
This will become the “TOP” of every gradient, and fractionation can proceed accurately below this
point if you press the RESET key to zero the device at this position. The rest is described below.
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SECTION 2. SPECIFICATIONS
2.1 Physical Measurements
Shipping Weight: 52 lbs.
Dimensions: 19.25”W x 16.5”D x 20”H (piston down), X 27"(piston up)
Operating temperatures: Ambient (Cold room only if left turned on in the cold room and for 1 hr after
return to room temperature to prevent condensation)
Input Power: 90-240VAC, 0.4A, 50-60Hz.
2.2 Commercially available parts:
Stepper Motors: All Hurst (Princeton, Indiana) Fractionator; TS -20 reduction cat no. SP3885; Tilt PBS -
150 reduction, 3208-002; Rotate PBS - 20 reduction 3208-009.
Power Supply: 12VDC, 5A ASTEC LPS63
Air Pump: GAST (Benton Harbor, MI) #10D1-101-KGB
Water Pump: Greylor (Cape Coral, FL): #PQ-12DC
Liquid Crystal Display: Excel Technologies (Belle Meade, NJ) # LCM 2420 SFBL
2.3 Performance Characteristics:
Gradient Forming:
Tilt Angle: 0-90° in 0.1° increments.
Rotate speed: 0-60RPM
Fractionation:
Piston Speed: 0.1-6.5 mm/sec down, 6.5 mm/sec upward
Fraction Size: 0.01 mm - full tube length
Number of Fractions: 1-99 in each of 10 sections per gradient
Band Illumination System: 20W halogen spot with dichroic reflector
Rinse Capability (programmable in any order, up to 9 events between each fraction):
•Continuous air to section outflow with air bubbles during fractionation
•Air on demand or automatically between fractions: 15 msec to 9 sec
•Water/Buffer on demand or automatically: 15 msec to 9 sec
•Delay (a programmed interval between fractions): 15 msec to 9 sec
•Pause (an indefinite pause between fractions, broken by pressing START)
•Fraction Advance (a contact closure that signals a connected fraction
collector to advance one fraction): 15 msec to 9 sec pulse
User Memories: 20. Each memory performs automatic fractionation of a specific
gradient and contains up to 10 different segments with each segment
containing user entered values of piston speed, distance per fraction,
number of fractions and rinse.
Macro Record: The device will reproduce a manual run if it is recorded using this
feature. The memory becomes one of the 20 memories listed above and can
be edited and saved.
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SECTION 3. PARTS DIAGRAMS
3.1 THE GRADIENT STATION
!
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3.2 GRADIENT FORMING ATTACHMENT
!
SECTION 4. ORDERING INFORMATION
The Gradient Station™ gradient forming and fractionation system.
4.1 Base Unit: Cat No. 153-001 90-120VAC input;
153-002 220-240VAC input
4.2 Gradient Forming Accessories
2 cannula 1 bubble level
4.2.1 Tube Holders: (each tube holder is shipped with a marker block and 6 or 12 caps, I, R or IR)
105-925-I, R or IR: 25 mm SW28 tube holder
105-916-I, R or IR: 25 mm SW28.1 tube holder
105-914A-I, R or IR: 25 mm SW41 tube holder
105-914B-I, R or IR: 25 mm SW40 tube holder
105-913-I, R or IR: 25 mm SW50 tube holder
105-911A-I, R or IR: 25 mm SW60 tube holder
105-911B-I, R or IR: 25 mm TLS55 tube holder
(8-place tube holders are available for quick seal vertical rotor tubes,but they cannot be fractionated with this device)
4.3 Gradient Fractionation
Includes the following accessories:
1 Manual 1 Left wing for extended working area
1 60 cc syringe rinse reservoir 1 Front panel keypad/LCD display/computer
4 feet 1 Fraction collector advance cable
1 Set of 6 Allen Wrenches, 1 Phillips screw driver
8 Spare check balls and 2 sizes of orings 1 Tubing terminator
1 Cursor for each tube holder 2 sets of assembly screws for computer panel and wings
1 Spare light bulb 1 Water level adjust cannula w/stop
1 Spare valve assembly 1 power cord
1 valve cleaning needle 1 12VDC 6.6A transformer
1 m of spare Teflon tubing 1 SD card with pdf manual and backup files
1 fine marker 1 SD card reader with USB cable
1 fine marker 1 SD LEXAR card reader with USB cable
Tilt
motor
Rotate
plate
Rotate
motor
Bearing
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4.3.1 Tube Holders: (each set includes 4 piston tips and disposable piston tip seals, tube holder, tube locking cap and cursor,
box of 50 Seton centrifuge tubes)
151-125 25 mm dia. tubes for SW28 and like rotors.
151-116 16 mm dia. tubes for SW28.1 and like rotors
151-114A 14 mm tubes for SW41 and like rotors
151-114B 14 mm tubes for SW40 and like rotors
151-113 13 mm tubes for SW55 and like rotors.
151-111A 11 mm tubes for SW60 and like rotors (comes with a different narrow piston/valve assembly and spare)
151-111B 11 mm tubes for TLS-55 and like rotors
4.3.2 Tubes: (Seton PolyClear™ required for use with the fractionator)
151-525 25 x 89 mm tubes for SW28 and like rotors.
151-516 16 x 102 mm tubes for SW28.1 and like rotors
151-514A 14 x 89 mm tubes for SW41 and like rotors
151-514B 14 x 95 mm tubes for SW40 and like rotors
151-513 13 x 51 mm tubes for SW55 and like rotors
151-511A 11 x 60 mm tubes for SW60 and like rotors
151-511B 11 x 34 mm tubes for TLS-55 and like rotors
4.3.3 Spares:
151-2XX-4 (XX is the mm diameter of the tube) 4 Piston tips with seals
151-902 12V 20W Spot light with dichroic reflector
151-905 check valve assembly for piston air/rinse/sample
151-905-11 check valve assembly for piston air/rinse/sample for 11 mm tip
151-931 Bag of 50 mist filter discs
151-919 2 each 1/16” ø stainless ball and 002/003 silicone Orings for check valve assembly
151-925 1 m of replacement tubing for piston 1/16”ø Teflon
151-926 1 m of replacement tubing for rinse system 1/8”ø polyester
SECTION 5. INSTRUMENT SET-UP
5.1 INSPECT THE SHIPPING BOX. If there is any damage to the outside that corresponds to
damage to the instrument, CALL BIOCOMP IMMEDIATELY.
To unpack the instrument, first open the top of the box and remove all the small parts and loose
foam. Then pull out the 4 pieces of foam from the sides of the carton. Pushing down on the box and
pulling up on the sides of the top plate, remove the instrument from the carton. It is attached to a piece
of plywood at the bottom that will pull out with the instrument. Use an adjustable wrench to remove
the 4 bolts holding the plywood to the base of the fractionator.
Locate the 4 feet in the accessory pack and screw them into the holes left by the bolts. Level the
instrument on the bench where it will be used by screwing the feet in or out as needed. Be sure that all
the parts listed on the shipping papers are present.
!
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SAVE THE SHIPPING BOX FOR POSSIBLE RETURN OF THE INSTRUMENT.
5.2 Assemble the Left Wing:
There is a D-shaped black plate in the box. Use the flat head screws and the 1/8” hex wrench to
assemble it to the top plate in the position shown. It extends the working area for tube racks.
!
5.3 Assemble the Gradient Forming attachment:
Carefully remove the Gradient Forming attachment from its box and attach it to the right wing
position. While supporting it, screw in one of the same flat head screws you used for the left wing, then
apply all three screws.
!
When the wing is secure, apply the two motor plugs to the sockets on the right side of the instrument as
shown. Be sure that the plugs are all the way on, touching the white plastic on the socket.
!
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5.4 Attach the Reservoir:
There is a 60 cc syringe in the accessory kit. Pull the plunger out and connect it to the luer-loc
connector at the end of the blue tubing on the right side of the box (pull the tubing out first). Slide the
flanges on the top of the syringe barrel under the screw heads on either side of the notch in the right
wing. Fill the reservoir with FILTERED water or buffer, depending on your needs. Small particles of
dust and debris can clog the valve in the piston tip. The salt in buffer will reduce the carryover between
fractions and keep your samples isotonic. However, it will also put more load on your scintillation
cocktail if you are counting your rinses.
!
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5.5 Assemble the computer panel.
Find the green multi-wire plug and the 2 smaller, white 4-wire motor plugs inside the main unit and
expose them as shown below. Note that the wires on the plugs are labelled “tilt” or “rotate”.
Bring the front panel close to the instrument with its open end up. Observe a green socket along the
front edge of the circuit board and two 6-pin sockets labelled “tilt” and “rotate”. Insert the motor plugs
onto their 6-pin sockets. Note that the motor plugs have red stripes on one side. The must face OUT,
away from the white plastic back on the socket for the plug to fit. Be sure to align the plug directly over
the socket so all the pins are covered.
! !
Next, plug the green connector into the green socket on the back edge of the circuit board. Push it all
the way in very hard. The plug can only be inserted with the scalloped edge up so there is no
danger of inserting it incorrectly.
! !
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Find the Phillips screw driver and 2 of the 8-32 screws in the Accessory Pack. Attach the front panel to
the main unit by inserting its leading edge under the bent edge of the front panel and resting the two
flanges on the screw heads already installed on the side panels of the main unit as shown. Next screw
the computer to the bent edge of the front panel using 3 more 8-32 screws as shown:
!
5.6 Install the power plug.
You are now ready to power up the unit.
Find the external power supply (12VDC Powergate transformer) and insert its plug into the socket on
the right rear corner of the instrument. Non-Euro and North American users must supply the power
cord between the transformer and the wall socket. Be sure the switch above the plug on the back of
the unit is off (0) and plug the power cord into the wall receptacle.
!
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Turn the power switch on. After a brief delay, the display will light up a pale green and a bit later the
display will read:
!!
The instrument is preprogrammed and is now ready to use
The row of 5 blank keys directly below the display are the “smart” keys whose values are determined
by the words above; in this case, for example, the left-most key has the value “FRAC” for fractionate.
When an Xappears beneath a word, it means that its smart key has been pressed.
The dedicated keys in the second row are used only for fractionation and have self-explanatory labels;
AIR turns on the air pump, forcing air into the collection tubing,
RINSE does the same for the water pump,
PROG. RINSE produces whatever series of rinse events is currently saved in
the automatic rinse register,
FRAC. ADV. closes a contact to the fraction collector if connected by a cable and
causes the collector to advance one fraction,
START/STOP key starts, stops or pauses any programmed activity,
depending on the cycle the device is operating in.
This is the “PANIC BUTTON”.
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Section 6. GRADIENT FORMING - STATION
1.1 LEVELLING THE PLATE: A CRITICAL FIRST STEP
1. When you power up the device, the display reads:
GRADIENT STATION v1.03
FRAC GMST
X
Press GMST. After the Gradient Master software has loaded, the display will read:
Reset KNOB to 0 position
Position = 29
Turning the knob until the indicator line is up center (12 o’clock) changes the display to read:
LEVELLING, TURN KNOB
DONE
Find the bubble level in the accessory kit and place it on the center of the plate. Level the unit in two
stages. First, place the level so it runs front-to-back as shown in (A). Adjust the feet under the
corners of the instrument until the level is centered. Next, turn the level so it runs side-to-side as
shown (B).
!
Turn the knob clockwise or counter clockwise to level the plate. For slight adjustments, use slight turns
of the knob; for course adjustments, turn further. There is no harm to the motor if the round plate
contacts the top plate. When the round plate is level, press DONE. This is an essential step in
forming gradients because the device uses the levelled plate (0°) to calculate all the tilt angles.
2. Levelling the plate during use. Press the EXIT key until the display shows the Main Menu;
GRADIENT MASTER ver5.3
GRAD SYST
X
Refer to the Gradient Master Manual that follows for the complete directions on gradient forming:
A
B
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