Beckman Coulter JCF-Z User manual

PN JCFZ-IM-12AB
June 2019
Instructions For Use
JCF-Z
Zonal and Continuous Flow Rotor
Beckman Coulter, Inc.
250 S. Kraemer Blvd.
Brea, CA 92821 U.S.A.

JCF-Z
Zonal and Continuous Flow Rotor
PN JCFZ-IM-12AB (June 2019)
© 2019 Beckman Coulter, Inc.
All rights reserved.
Beckman Coulter, the stylized logo, and the Beckman
Coulter product and service marks mentioned herein are
trademarks or registered trademarks of Beckman Coulter,
Inc. in the United States and other countries.
All other trademarks, service marks, products, or services
are trademarks or registered trademarks of their
respective holders.
Contact Us
If you have any questions, contact our Customer Support
Center.
• Worldwide, find us via our website at
www.beckman.com/support/technical.
• In the USA and Canada, call us at 1-800-369-0333.
• Outside of the USA and Canada, contact your local
Beckman Coulter Representative.
Find us on the World Wide Web at: www.beckman.com
Beckman Coulter Eurocenter S.A.
22, rue Juste-Olivier
Case Postale 1044
CH - 1260 Nyon 1, Switzerland
Tel: [phone]
May be covered by one or more pat. - see
www.beckman.com/patents
Glossary of Symbols is available at beckman.com/
techdocs (PN C24689).

PN JCFZ-IM-12AB iii
Revision History
This document applies to the latest software listed and higher versions. When a subsequent software
version changes the information in this document, a new issue will be released.
Initial Issue, 02/08
Issue AA, 03/14
Updates were made to the document format. Changes were made to Specifications, Installing the
Zonal Interlock Accessory, Run Procedure For Pelleting Sample (Continuous Flow Cores), Standard Zonal
Core, and Zonal Bracket Kit Contents.
Issue AB, 06/19
Changes were made to CHAPTER 3, J2 and J6 Series Centrifuges, CHAPTER 6, Supply List.

PN JCFZ-IM-12AB
iv
Revision History

PN JCFZ-IM-12AB v
Safety Notice
Read all product manuals and consult with Beckman Coulter-trained personnel before attempting
to operate instrument. Do not attempt to perform any procedure before carefully reading all
instructions. Always follow product labeling and manufacturer’s recommendations. If in doubt as
to how to proceed in any situation, contact your Beckman Coulter Representative.
Alerts for Danger, Warning, Caution, Important, and Note
WARNING
WARNING indicates a potentially hazardous situation which, if not avoided, could
result in death or serious injury. May be used to indicate the possibility of
erroneous data that could result in an incorrect diagnosis.
CAUTION
CAUTION indicates a potentially hazardous situation, which, if not avoided, may
result in minor or moderate injury. It may also be used to alert against unsafe
practices. May be used to indicate the possibility of erroneous data that could
result in an incorrect diagnosis.
IMPORTANT IMPORTANT is used for comments that add value to the step or procedure being performed.
Following the advice in the Important adds benefit to the performance of a piece of equipment or to a
process.
NOTE NOTE is used to call attention to notable information that should be followed during installation, use,
or servicing of this equipment.
This safety notice summarizes information basic to the safe operation of the rotor described in this
manual. The international symbol displayed above is a reminder to the user that all safety
instructions should be read and understood before installation, operation, maintenance, or repair
of this equipment is attempted. When you see the symbol on other pages of this manual, pay special
attention to the specific safety information presented. Observance of safety precautions will also
help to avoid actions that could damage or adversely affect the performance of the rotor. This rotor
was developed, manufactured, and tested for safety and reliability as part of a Beckman Coulter
centrifuge/rotor system. Its safety or reliability cannot be assured if used in a centrifuge not
of Beckman Coulter’s manufacture or in a Beckman Coulter centrifuge that has been modified
without Beckman Coulter’s approval.

PN JCFZ-IM-12AB
vi
Safety Notice
Alerts for Danger, Warning, Caution, Important, and Note
Handle body fluids with care because they can transmit disease. No known test offers complete
assurance that such fluids are free of micro-organisms. Some of the most virulent—Hepatitis (B and
C)) viruses, HIV (I–V, atypical mycobacteria, and certain systemic fungi—further emphasize the
need for aerosol protection. Handle other infectious samples according to good laboratory
procedures and methods to prevent spread of disease. Because spills may generate aerosols,
observe proper safety precautions for aerosol containment. Do not run toxic, pathogenic, or
radioactive materials in a rotor without taking appropriate safety precautions. Biosafe containment
should be used when Risk Group II materials (as identified in the World Health Organization
Laboratory Biosafety Manual) are handled; materials of a higher group require more than one level
of protection.
The rotor and accessories are not designed for use with materials capable of developing flammable
or explosive vapors. Such materials (such as chloroform or ethyl alcohol) should not be centrifuged
in or handled near the centrifuge.
Always connect a pressure gauge between the pump and the rotor. If pressure exceeds 25 psi during
acceleration or rises gradually during centrifugation, there is an air block in the system.
Always turn the pump off before clamping a line.
Always keep two lines to the rotor unclamped when the pump is on.

PN JCFZ-IM-12AB vii
Safety Notice
Alerts for Danger, Warning, Caution, Important, and Note
WARNING
The processing of large volumes of pathogenic materials in the JCF-Z rotors can
produce extremely potent concentrations. Agents that are relatively harmless in
their naturally occurring dilute state may become infectious when concentrated.
Biological hazards must be carefully assessed and precautions taken.
Consideration must be given to the air flow in the room; consult your laboratory
safety officer.
WARNING
Protect your hands when handling bowl and lid threads, which become very sharp
with prolonged use. Do not touch the rotor while the centrifuge is operating.
WARNING
Never attempt to block the open end of any pressurized tubing or coupling with
the figures or hand, as injection of liquid under the skin could occur.
CAUTION
The rotor lid is designed to have liquid support. Never run an empty or partially
empty rotor to full speed. Do not run the rotor above 10 000 rpm unless it is
completely full of liquid.
CAUTION
The seal assembly (used with the standard zonal and all continuous flow cores)
requires liquid lubrication for cooling. Do not stop liquid flow into the rotor for
longer than 2 minutes during centrifugation. Do not run the seal assembly above
3000 rpm without fluid.

PN JCFZ-IM-12AB
viii
Safety Notice
Alerts for Danger, Warning, Caution, Important, and Note

ix
Contents
Revision History,iii
Safety Notice,v
Alerts for Danger, Warning, Caution, Important, and Note,v
CHAPTER 1: The Process of Continuous Flow and Zonal Centrifugation,1-1
Continuous Flow Centrifugation,1-1
ZONAL CENTRIFUGATION,1-3
CHAPTER 2: Description,2-1
Rotor Components,2-1
Specifications,2-6
CHAPTER 3: Assembly and Installation,3-1
Installing the Zonal Bracket (Avanti J Series Centrifuges Only),3-1
Installing the Zonal Interlock Accessory,3-1
Tools and Supplies,3-1
Tools Provided,3-1
Supplies Required But Not Provided,3-2
Assembling the Rotor,3-3
Step 1,3-3
Step 1a,3-3
Step 1b,3-4
Step 1c,3-4
Step 1d,3-5
Step 2,3-6
Step 3,3-7
Step 4,3-8
Step 5,3-9
Step 6,3-10
Step 6a,3-10
Step 6b,3-12
Step 7,3-13
Standard zonal and continuous flow rotors.,3-13
Standard Seal Housing,3-13
High Flow Seal Housing,3-14
Step 8,3-14
Standard zonal and continuous flow rotors,3-14

x
Contents
Step 9,3-15
Step 9a,3-15
Step 9b,3-16
Step 10,3-17
Step 11,3-18
Step 12,3-18
Step 13,3-19
CHAPTER 4: Preparing for Operation,4-1
Determining the Rotor Speed,4-1
Determining The Flow Rate: Large And Standard Pellet Cores,4-2
Setting The Temperature,4-5
Avanti Series Centrifuges,4-5
Microprocessor-controlled J2 And J6 Series Centrifuges (Models J2-
MI, J6-MI, J2-21M, J2-MC, J6-MC, and J2-21 M/E),4-5
Analog J2 And J6 Series Centrifuges (Models J2-HS, J2-21, J2-HC, J6-
HC, and J-6B),4-6
Determining The Liquid Pressure,4-6
Determining Appropriate Gradients,4-6
CHAPTER 5: Operation,5-1
Operating Precautions,5-1
Continuous Flow Operation,5-2
Pelleting Technique,5-2
Run Procedure For Pelleting Sample (Continuous Flow Cores),5-3
Purging Air From The System (Continuous Flow Rotor Only),5-5
Density Gradient Operation (Continuous Flow Cores),5-6
Gradient Or Cushion Separation Techniques,5-6
Forming an Air Block,5-7
Run Procedure for Separating in a Gradient or Cushion
(Continuous Flow Cores),5-9
Zonal Operating Techniques And Run Procedures,5-9
Standard Zonal Core,5-9
Reorienting Gradient (Reograd) Zonal Core,5-13
Ending The Run,5-14
Continuous Flow Core Containing Pellet,5-14
Continuous Flow Core Containing Gradient or Cushion,5-18
Standard Zonal Core,5-19
Reograd Zonal Core,5-20
Flushing The Tubing Lines,5-21
CHAPTER 6: Care and Maintenance,6-1
Maintenance,6-1

xi
Contents
Cleaning,6-1
Decontamination,6-2
Sterilization And Disinfection,6-3
Inspecting The Bearings,6-3
Smoothing (Lapping) The Rotating Seal,6-4
Returning a Rotor,6-4
Supply List,6-5
CHAPTER 7: Troubleshooting,7-1
Leakage,7-1
Rotating Seal/Stationary Seal Interface,7-1
Scavenger Line,7-1
Other Areas,7-1
Mixing of Inlet and Outlet Liquid,7-1
Vibration,7-2
APPENDIX A: Assembling the Rotating Seal,A-1
Assembling the Rotating Seal,A-1
APPENDIX B: Using the JCF-Z Continuous Flow/Zonal
Rotor Bracket (Avanti J Series Centrifuges Only),B-1
Description,B-1
Zonal Bracket Kit Contents,B-2
Assembly Instructions,B-3
Step 1. Install the Rotor,B-3
Step 2. Attach the Zonal Bracket to the Centrifuge Chamber
Wall,B-3
Step 3. Insert the Tubing Through the Door Gasket,B-3
Size 16 Tubing,B-3
Sizes 14 and 15 Tubing,B-4
Step 4. Attach the Tubing to the Zonal Bracket,B-5
Step 5. Attach Tubing to the JCF-Z Seal Assembly Housing,B-6
Step 6. Attach a Scavenger Line (Optional),B-7
JCF-Z Rotor Warranty And Seal Assembly Warranty

xii
Illustrations
Illustrations
1.1 Cross Section of a Continuous Flow Rotor,1-2
1.2 Cross Section of Zonal Rotor with Standard Zonal Core,1-3
2.1 Rotor Components.,2-2
2.2 Seal and Transfer Assemblies,2-3
2.3 Identifying O-Rings. O-rings requiring occasional replacement
are shown, actual size.,2-5
3.1 Tools Provided in Tool Kit 335143.,3-2
4.1 Speed and Flow Rate Nomogram, Standard Pellet Core.,4-4
4.2 Radius Versus Volume for Standard Pellet Core, Standard Zonal
Core, and Reograd Core.,4-7
5.1 Pelleting Technique, Continuous Flow Cores,5-2
5.2 Rotor Installation,5-3
5.3 Line Connections, Continuous Flow Cores. Using this tubing
arrangement for basic pelleting against the rotor wall.,5-4
5.4 Gradient or Cushion Separation Technique, Continuous Flow
Cores.
Technique B, described in Table 5.1, is shown.,5-8
5.5 Sucrose Gradient after One Hour, Monitored by Refractometer.
Diffusion between the discontinuous layers of the step
gradient results in a near-linear gradient.,5-9
5.6 Line Connections, Standard Zonal Core,5-10
5.7 Operating Procedure, Standard Zonal Core,5-11
5.8 Removing and Reinserting Fittings and Liquid Lines,5-12
5.9 Line Connections, Reograd Zonal Core,5-13
5.10 Operating Procedure, Reograd Zonal Core,5-15
5.11 Lowering Rotor onto Plug. Rotor contents will spill out
as soon as the core is removed if the plug and plug O-ring
are not in place.,5-16
5.12 Disassembling the Rotor. Disassemble as shown to remove
sample
(arrows show direction of tool use). See CHAPTER 6, Care and
Maintenance
for instructions on inspecting, cleaning, and replacing the
bearings.,5-17
5.13 Removing Small Pellet. Lift out canoe-shaped pellet container
and
scrape out pellet.,5-18

xiii
Illustrations
A.1 Transfer Tube Assembly Components,A-1
A.2 O-ring (870656) and Silicone Vacuum Grease (335148),A-2
A.3 Fully Assembled Transfer Tube Assembly,A-3
A.4 Transfer Tube Assembly and Rotating Seal
(Ready for Assembly into Rotor),A-3
A.5 Transfer Tube Beveled End,A-4
A.6 Correct Position of the Rotating Seal,A-4
A.7 Incorrect Position of the Rotating Seal (Wrong Spring
Tension),A-5
A.8 Bearing Housing Assembled,A-5
A.9 Stationary Seal Housing Mated to Bearing Housing
(Seal/Bearing Housing),A-6
A.10 Pushing Down on Seal/Bearing Assembly to Tension Spring,A-7
A.11 Finishing Rotor Assembly,A-7
B.1 Avanti J Series Centrifuge Chamber with JCF-Z Rotor and Zonal
Bracket Installed,B-1
B.2 Attaching the Bracket to the Chamber Wall,B-3
B.3 Inserting Size 16 Tubing through the Gasket,B-4
B.4 Attaching Tubing to the Adapter,B-5
B.5 Inserting the Standard-Flow Feed Fitting into the Tubing,B-5
B.6 Attaching the Tubing Clamps to the Bracket,B-6
B.7 Inserting Tubing and Feed Fittings into the JCF-Z Seal
Assembly,B-6
B.8 Attaching a Scavenger Line,B-8

xiv
Tables
Tables
1.1 JCF-Z Continuous Flow Applications,1-2
1.2 JCF-Z Zonal Applications,1-4
2.1 Specifications,2-6
2.2 Different Core Specifications,2-7
4.1 J2 and J6 Series Centrifuge Temperature Settings. All settings
are approximate.,4-6
5.1 Two Techniques for Forming an Air Block During Density
Gradient Operation,5-7
6.1 Supply List,6-5
B.1 Basic Kit 363843 or 366431,B-2
B.2 Kit 363844 Contents (for Size 14 Tubing),B-2
B.3 Kit 363845 Contents (for Size 15 Tubing),B-2

PN JCFZ-IM-12AB 1-1
CHAPTER 1
The Process of Continuous Flow and Zonal
Centrifugation
The JCF-Z rotor, which can be used in Beckman Coulter J2, J6, and Avanti J series centrifuges, has
interchangeable cores that enable it to perform both continuous flow and zonal centrifugation. This
section describes these processes and their applications.
Continuous Flow Centrifugation
In continuous flow centrifugation, solutions are pumped through the rotor continuously while it is
spinning in the centrifuge (Figure 1.1). Particles sediment out of the flowing stream, which then
emerges from the rotor as a particle-depleted effluent. This process continues until the particle-
containing capacity of the rotor is reached, or until the starting material (sample) is completely
processed. Thus the amount of sample that can be processed in one run is determined by the
sample’s volume and concentration of particles.
Continuous flow processing in the JCF-Z rotor allows efficient processing (pelleting, purification, or
concentration) of large sample volumes containing particles with 600 S or higher sedimentation
coefficients*(Table 1.1). Continuous flow processing is suitable for sedimenting bacteria, yeast,
large subcellular particles such as membranes, and mitochondria. It is also frequently used to clear
virus-containing culture media of cellular debris before final isolation of the virus.
* The sedimentation coefficient is usually expressed in Svedberg units (S), where 1 S = 1 ´ 10-13 seconds.

PN JCFZ-IM-12AB
1-2
The Process of Continuous Flow and Zonal Centrifugation
Continuous Flow Centrifugation
Figure 1.1 Cross Section of a Continuous Flow Rotor
Particles may be concentrated in one of three ways: by pelleting onto the wall of the rotor bowl, by
sedimenting onto a cushion of dense liquid such as concentrated sucrose, or by banding in a
gradient. Use of a cushion gradient is appropriate if your solution contains biologically active
particles that could be damaged by pelleting against the rotor wall. Banding in a gradient is
appropriate when it is necessary to separate a certain particle from contaminants of different
sedimentation velocities in the solution.
1. Edgeline Outlet
2. To Center Inlet
3. Rotating Seal Assembly
4. Lid
5. Milled Slot
6. Upper Radial Channel
7. Bowl Wall
8. Core Taper Volume
9. Core
10. Channel Leading to Central Passage
11. Bowl
Table 1.1 JCF-Z Continuous Flow Applications
Core Type Typical Sample Type Resulta
a. Pellet refers to sedimenting particles onto the rotor wall. Concentrate refers to sedimenting particles onto a cushion of dense
solution (e.g., sucrose). Purify refers to sedimenting particles through a step gradient.
Recommended Pellet
Size Range (mL)
Large pellet large viruses (s 600 S),
mitochondria,
tissue homogenates, bacteria
pellet, concentrate 400 to 800
Standard pellet large viruses,
mitochondria,
tissue homogenates, bacteria
pellet, purify, or
concentrate
200 to 400
Small pellet mitochondria, bacteria, algae,
clay
pellet 50 to 200

PN JCFZ-IM-12AB 1-3
The Process of Continuous Flow and Zonal Centrifugation
ZONAL CENTRIFUGATION 1
The amount of pellet anticipated or the necessity to sediment onto a cushion or into a step gradient
determines which of the three available cores is appropriate for your application.
• The standard core rotor configuration has a total capacity of 660 mL. Of this volume, about 400
mL can be occupied by pellet, step gradient, or cushion. This core is suitable if no more than 400
mL of pellet is anticipated.
• The large pellet core rotor configuration has a total capacity of 1250 mL, of which
approximately 800 mL can be occupied by pellet. This core is well suited for centrifuging fluids
with high solid-to-liquid ratios, when a large pellet is expected. Note that when processing a
solution of high solid-to-liquid ratio, the core fills with particles more quickly and must be
unloaded more often than during processing of a less concentrated solution.
• The small pellet core rotor configuration has a total capacity of 240 mL, of which about 200 mL
can be occupied by pellet. It is designed for processing large amounts of material with a low
solid-to-liquid ratio. In order to minimize resuspension of sedimented materials and to
facilitate sample recovery, this core has six individual cavities, each holding removable
containers in which the pellets are collected.
ZONAL CENTRIFUGATION
In density gradient separation, sample capacity is limited by the area in the sample cavity over
which the sample spreads. The only practical way to significantly increase the sample capacity is to
increase the area of the sample cavity. When density gradient separation is performed in a zonal
rotor, gradient and sample are loaded directly into the rotor cavity; no tubes or bottles are used
(Figure 1.2). Cylindrical or bowl-shaped zonal rotors have a capacity 50 to 100 times that of the
typical swinging bucket rotor; thus zonal centrifugation enables large quantities of sample to be
processed in much less time than in other types of rotors.
In the JCF-Z rotor, the zonal technique is useful in separating large particles, such as mammalian
viruses and subcellular organelles, from plant or animal tissue homogenates (see Table 1.2).
Figure 1.2 Cross Section of Zonal Rotor with Standard Zonal Core
1. Rotating Seal Assembly
2. Lid
3. Core
4. Bowl

PN JCFZ-IM-12AB
1-4
The Process of Continuous Flow and Zonal Centrifugation
ZONAL CENTRIFUGATION
Two zonal cores are available with the JCF-Z: standard and reorienting gradient (also known as
reograd). These cores are divided into sector-shaped compartments by vanes attached to the core;
the rotor is enclosed by a threaded lid. A rotating seal assembly allows fluid to be pumped in and
out of the standard zonal core cavity (for loading and unloading only) while the rotor is spinning.
• The standard zonal core has a capacity of 1900 mL. When this core is used, the rotor is loaded
and unloaded at a speed of 2000 rpm. Gradient solution is pumped in at the periphery of the
rotor; the sample and overlay solutions are pumped in through the center. After
centrifugation, the rotor contents are unloaded by introducing heavy displacement fluid at the
periphery and collecting fractions at the center.
• The reograd zonal core has a capacity of 1750 mL. When this core is used, the rotor is loaded and
unloaded at rest. To prevent mixing of the rotor contents, slow acceleration to and deceleration
from 1000 rpm is recommended. This core is recommended for use with long-stranded, fragile
materials that might be damaged by passing through a rotating seal assembly.
Table 1.2 JCF-Z Zonal Applications
Core Type Typical Sample Type Resulta
a. Density gradient may refer either to sedimentation velocity (rate zonal) centrifugation or to equilibrium sedimentation
(isopycnic banding) centrifugation. Concentrate refers to sedimenting particles onto a cushion of dense solution (e.g,
sucrose).
Recommended Sample
Volume (mL)
Standard zonal tissue homogenates, small or
large viruses, chloroplasts,
bacteria, algae, whole cells
density gradient
concentrate
59 to 500
(1400 to 1850 mL
is gradient)
1650 (250 mL
is cushion)
Reorienting gradient
(reograd) zonal
tissue homogenates, small or
large viruses, chloroplasts,
bacteria, algae, whole cells, and
especially fragile material
density gradient
concentrate
50 to 500
(1250 to 1700 mL
is gradient)
1500 (250 mL
is cushion)

PN JCFZ-IM-12AB 2-1
CHAPTER 2
Description
This section describes the JCF-Z rotor components and lists rotor specifications.
Rotor Components
The basic components of the JCF-Z rotor are the rotor bowl and lid, the rotor core, the transfer tube,
and the rotating seal assemblies. The cores are interchangeable. Continuous flow cores are available
in the following sizes: standard pellet, large pellet, and small pellet. Two types of zonal cores are
available: standard and reorienting gradient (also known as reograd). Each core, except the
continuous flow small pellet, has four baffles dividing the rotor interior into four quadrants (the
small pellet core has six cavities). Baffles in continuous flow cores are removable; in zonal cores
they are not. All of the cores have holes drilled through them to enable fluid to flow into or out of
the rotor. The transfer tube separates the sample and effluent channels of fluid flow and transfers
these liquids into and out of the rotor.
The rotor bowl and lid are made of titanium; the rotor cores are made of Noryl plastic. (Components
and materials used in the rotor assemblies are detailed in Figure 2.1 and Figure 2.2) Tygon tubing
feed lines attach to the rotor for fluid introduction and removal. A drive pin in each core seats it
into the centrifuge drive hub to prevent core slippage during acceleration. Depending on which
core is used, the fully loaded JCF-Z rotor weighs 12 to 14 kg (26 to 31 lb). The seal assembly (except
bearings and rotating seal) is warranted for 1 year; other rotor components are warranted for
7 years. See the Warranty for details.

PN JCFZ-IM-12AB
2-2
Description Rotor Components
Figure 2.1 Rotor Components.
The seal and transfer assemblies are described in Figure 2.2. Letters indicate O-rings made
of Buna N or of Viton.
Buna N: (a) 815473, (d) 870315, (e) 870688, (f) 854519 or 870528 (Viton), and (g) 812715.
Viton: (b) 870526 x 4 and (c) 817033. See also Figure 2.3.
1. Seal Assembly
(Standard 335142; high flow
335134)
2. Transfer Assembly (part of 350585)
3. Lid (336282)
4. Small Pellet Core (350601)
5. Standard Core (335130)
6. Large Pellet Core (350641)
7. Standard Zonal Core
(335141)
8. Reorienting Gradient
Core (350585)
9. (354006)
10. (354005)
11. (354005)
12. Continuous Flow
Rotors
13. Zonal Rotors