Download Xpedition 2011 - Zymo Research

Take the Lab to the Field
Portable Cell Lysis & Sample Preservation Technologies
“Take the Lab to the Field”
With Portable Cell Lysis
&
Sample Preservation Technologies
Degradation and contamination of biological samples have been obstacles to scientific study, and may be
particularly problematic in highly sensitive molecular-analysis techniques (e.g., PCR of low copy DNA). Use of
cryogenic freezing methods for environmental/forensic sample preservation may often be too impractical to be
employed. The solution is the Xpedition™ Sample Processor (XSP) and Xpedition™ Sample Prep Technologies
from Zymo Research. The XSP is a portable, hand-held device developed for vigorous cell disruption (bead
beating) that allows the researcher/investigator to “Take the Lab to the Field”.
DNA in samples processed with Xpedition™ DNA Sample Prep Technology is
preserved for subsequent storage/transportation without the requirement for
refrigeration. This is due to a unique lysis/stabilization solution that is featured in
all Xpedition™ DNA Prep kits.
The XSP is ideal for both field and lab use. You can use it here, use it there,
you can use it anywhere!
Workflow (e.g., DNA Purification)
Lyse/stabilize samples during your expedition
using Xpedition™ Sample Processor & Lysis/Stabilization Solution
2
Store/transport lysates
without refrigeration
www.zymoresearch.com
Process later using
Xpedition™ DNA Prep Kits
Intact, inhibitor-free DNA
ready for analysis!
Xpedition™ Overview:
On-Site Sample Processing & Preservation
Sample Collection
6
Soil
Da
M
PC
R
Da
y1
1
Da
y1
4
Da
y1
6
Da
y9
Da
y7
Da
y4
Da
y1
M
Da
y2
y1
4
DNA in lysates is preserved (see
below) for non- refrigerated storage/
transport.
y1
Da
M
PC
R
Da
y1
1
Da
y1
4
Da
y9
Da
y7
Da
y4
Da
y2
Da
y1
Da
y1
Xpedition™
Lysis/Stabilization Solution
Da
y2
TE
Da
y2
M
H 20
Da
y1
Samples are efficiently lysed on-site
using BashingBead™ & Xpedition™
Sample Processor Technologies
Liver
DNA in lysates is effectively stabilized for non-refrigerated storage/transport using the Xpedition™ Lysis/Stabilization Solution. For both
soil and liver samples: lysates were generated using the Xpedition™ Sample Processor and stored at room temperature over the course of two
weeks prior to DNA isolation using the appropriate Xpedition™ kit (back cover). Equal volumes of eluate were subsequently visualized in 0.8%
(w/v) agarose/ethidium bromide gels (shown above). The size marker (M) is a 1 kb ladder (Zymo Research). Also, PCR amplicons generated
from final time points are shown in gel images to the right as indicated.
www.zymoresearch.com
3
Purification of
Inhibitor-Free DNA
Process later in the laboratory using
Xpedition™ DNA Prep Kits
Preserved Sample Lysates
$
Filter Lysate
$
Bind,
Wash,
Elute DNA
$
M
M
PCR-Ready Ultra-pure DNA
Continue with the following step for
Xpedition™ Soil/Fecal & Plant/Seed DNA Kits only.
Polyphenolic Removal
$
PCR-Ready Ultra-pure DNA
Shown in the figures above are the DNA yields from various insect, mouse, marine invertebrate, etc. samples using Xpedition™ Sample
Prep Technology. Two (2) weeks following sample processing with the XSP, DNA was isolated from biological source materials using specific
Xpedition™ DNA Sample Prep Kits (back cover). Equal volumes of eluted DNA analyzed in 0.8% (w/v) agarose/ethidium bromide gels (show in
the images above). M is a 1 kb DNA size maker is from Zymo Research.
Genotyping
Dietary Evaluation
Forensics
Genetic ID
Metagenomic Analysis
Phylogenetics
DNA Bar Coding
Host/Vector Analysis
Epigenetic Analysis
Expedition Recipe:
basic dutch oven cobbler
Ingredients
▪ 1 box of yellow cake mix
▪ 1 can cherry pie filling
▪ 1 can crushed pineapple
▪ 1 stick melted butter or margarine (8 tablespoons)
▪ chopped nuts (optional)
Preparation
Dump in pie filling and pineapple. Pour dry cake mix over the top. Drizzle butter over cake
mix. Add nuts as desired. Put on coals and then put hot coals on top of the lid (8 - 10).
Cook for 25 - 35 minutes. Check occasionally so that spots don’t burn.
4
www.zymoresearch.com
Not on an expedition
... but still need DNA from environmental samples?
For routine use, the BashingBead™ DNA purification kits from Zymo Research are for rapid recovery of inhibitor-free PCR-ready DNA
from a broad range of tough-to-lyse organisms and environmental samples. Kits have been specifically designed for the efficient
recovery of inhibitor-free DNA from plants, seeds, tissues, insects, and microorganisms that inhabit soil, sludge, sediment, and fecal
samples. Products are available in spin column Micro- (5 µg/prep), Mini- (25 µg/prep), Midi- (125 µg/prep) and 96-well (5 µg/well)
formats – Micro- and MiniPrep formats are diagrammed below. Note: Micro & Miniprep versions are compatible with the Xpedition™
Sample Processor.
Samples
ZR Soil Microbe DNA Kits
1 kb
A
 Applications: Soil, Sediment, Sludge, Gram (+) Bacteria, Gram (-)
Bacteria, Yeast, Filamentous Fungi, Unicellular Algae, Filamentous
Algae, Protist
B
2
3
4
5

Zymo Research
Supplier M
Yeast
Yeast
1 kb Spores E. coli Spores E. coli
Fungal and bacterial DNA purification. DNA
isolated from Saccharomyces cerevisiae (spores)
and E. coli using the ZR Fungal/Bacterial DNA
MiniPrep™ is high quality and structurally intact. DNA
were analyzed in a 0.8% (w/v) agarose/ethidium
bromide gel. The size marker is a 1 kb ladder (Zymo
Research).
 Applications: Gram (+) Bacteria, Gram (-) Bacteria, Yeast,
Filamentous Fungi, Unicellular Algae, Filamentous Algae, Protist
Other Suppliers
Zymo
Research
ZR Fecal DNA Kits
M
Q
Comparison of DNA yields from rat feces using
the ZR Fecal DNA MiniPrep™ and kits from
suppliers M and Q. Equivalent amounts of feces
were processed using each kit and then equal
volumes of eluted DNA were analyzed in a 0.8%
(w/v) agarose/ethidium bromide gel. Samples were
processed in triplicate.
20
as
va
te
rl en
B
a
ick
ee
=
10
et
tle rvae
1
la
kb
rv n =
a
20
M
ou
se
Ki
M
dn
ou
ey
se
L
M
ou ive
r
se
Ta
ils
ni
p
=
Plant
1
2
 Applications: Plant Material, Seeds, Fruit
ar
rl
rn
te
og
Cr
rk
lin
g
an
el
Da
te
as
as
og
m
D.
og
an
an
el
an
el
m
m
el
ZR Plant DNA Kits
D.
m
M
D.
kb
D.
1
 Applications: Soft & Solid Tissues (Food), Tough-to-Lyse Tissues,
Tough-to-Lyse Organisms, Insects/Arthropods
og
as
te
rn
=
10
 Applications: Feces, Bacteria Gram (+), Bacteria Gram (-), Yeast,
Filamentous Fungi, Unicellular Algae, Filamentous Algae, Protist
ZR Tissue & Insect DNA Kits
The ZR Soil Microbe MiniPrep Kit™ can be used
to isolate high quality DNA (A) from a variety of
soil types (1-5) which yields robust products
following PCR (B & C). DNA were analyzed in a
0.8% (w/v) agarose/ethidium bromide gel.

C
ZR Fungal/Bacterial DNA Kits
1
DNA yields from various insect and mouse
samples using the ZR Insect & Tissue DNA
MiniPrep™. Various amounts of sample were
processed with equal volumes of eluted DNA
analyzed in a 0.8% (w/v) agarose/ethidium bromide
gel. The 1 kb DNA size marker is from Zymo
Research.
Seed
M
3
4
5
6
Comparison of DNA yields from various plant
and seed samples using the ZR Plant/Seed DNA
MiniPrep™. Equivalent amounts of plant materials
were processed with equal volumes of eluted DNA
analyzed in a 0.8% (w/v) agarose/ethidium bromide
gel. M is a 1 kb DNA size marker (Zymo Research).
Arabidopsis thaliana (1), juniper (2), corn kernel (3,
4), sunflower seed (5, 6).
Expedition Tip:
Map Orientation
First step in orienteering is to properly align the map with the earth’s magnetic azimuth.
▪ Align compass with straight edge of map
▪ Rotate map & compass together until the compass needle is parallel to the declination index on the map
www.zymoresearch.com
5
Environmental RNA Purification Kits
The BashingBead™ RNA purification kits from Zymo Research are designed for quick and efficient isolation of RT-ready total RNA,
including small RNAs, from tough-to-lyse environmental samples. Inhibitor-free RNA can be isolated from a broad range of species,
including plants, insects and diverse microbial populations. Ultra-high density BashingBeads™ can be used with any bead mill, disrupter,
vortex or the convenient and portable Xpedition™ Sample Processor.
RT-PCR
M
ZR Soil/Fecal RNA MicroPrep™
+HRC
Control
-HRC
 Applications: Soil, Sediment, Sludge, Gram (+) Bacteria, Gram (-)
Bacteria, Yeast, Filamentous Fungi, Unicellular Algae, Filamentous
Algae, Protist and Host RNA from Fecal (Mammalian, Avian, etc.)
Samples
RNA
Ladder
ZR Fungal/Bacterial RNA Kits
 Applications: Gram(+) and (-) Bacteria, Yeast, Filamentous Fungi,
Unicellular Algae, Filamentous Algae, Protists, Soft Tissue (limited)
and Food
Zymo
Research
Supplier DNA
Q
Ladder
9.0 6.0 -
- 10.0
- 3.0
3.0 2.0 -
- 1.0
1.0 -
- 0.5
0.5 kb
kb
DNase I * DNase I
M
ZR Tissue Insect RNA Kits
1
2
9.0 -
 Applications: Soft and Solid Tissues (e.g., Food), Tough-to-Lyse
Tissues, Tough-to-Lyse Organisms, Insects/Arthropods
6.0 5.0 4.0 3.0 2.5 2.0 -
PCR amplification of a eukaryotic transcript postRT: Total RNA isolated from sludge with or without
inclusion of the Zymo-Spin™ IV-HRC spin filter
during the ZR Soil/Fecal RNA MicroPrep™ protocol.
RNA was resolved in a 1% (w/v) nondenaturing
agarose gel. M is a ZR 1 kb DNA Marker (Zymo
Research).
Total RNA was isolated from equal amounts of
pelleted E. coli cells containing plasmid DNA
(pGEM®) using the ZR Fungal/Bacterial RNA
MicroPrep™ or the kit from Supplier Q. The
samples were resolved in a 2% (w/v) agarose gel.
RNA Millenium Markers (Ambion) and ZR 1 kb DNA
Marker (Zymo Research) were used.
* = genomic (> 10 kb) and plasmid (> 3 kb) DNA
contamination; DNase I = samples treated with
DNase I.
Analysis of ZR Tissue & Insect RNA MicroPrep™.
Isolation of total RNA from n=2 Drosophila sp.
individuals was performed in duplicate (lanes 1 and
2). Samples were processed (2 x 30 sec at 6 m/s)
using a FastPrep®-24 Instrument (MP Biomedicals)
and resolved alongside (lane M) RNA Millenium™
Markers (Ambion) in a 1% (w/v) non-denaturing
agarose gel.
1.5 1.0 kb
Sample 1 Sample 2
ZR Plant RNA MiniPrep™
 Applications: Leaves, Stems, Buds, Flowers, Seeds, Fruit and
Other Plant Tissues
Isolation of total RNA from 10 mg of a fresh leaf
material (Nicotiana sp.) using the ZR Plant RNA
MiniPrep™. Leaves were minced then processed
using a FastPrep®-24 instrument (MP Biomedicals).
Samples 1 and 2 were loaded in 2x and 1x volume
aliquots, respectively, and resolved in a 1% (w/v)
nondenaturing agarose gel. RNA Millenium™ Markers
(Ambion) were used as size standards.
Expedition Tip:
COMMON Poisonous plant SPECIES
Avoiding some of the most common poisonous plants on your expedition can prevent you from the uncomfort of contact dermatitis.
Poison Ivy
Toxicodendron radicans
6
Poison Sumac
Toxicodendron vernix
Pacific Poison-oak
Toxicodendron diversilobum
www.zymoresearch.com
Atlantic Poison-oak
Toxicodendron pubescens
Unlock Your PCR
With OneStep™ PCR Inhibitor Removal Kits
 Removes PCR inhibitors such as polyphenolics, humic/fulvic acids, tannins,
melanin, etc. from nucleic acid solutions to yield high quality DNA or RNA
OneStep™ PCR Inhibitor Removal Kit Procedure
Spin Column Format
96-Well Format
 Fast, one-step procedure for cleaning impure samples prior to PCR,
sequencing, reverse transcription (RT), etc
 Applications: Polyphenolic PCR Inhibitor Removal from DNA, Polyphenolic RT
Inhibitor Removal from RNA
Add Sample
$
DNA Sample Containing Humic Acid
Ladder
Controls
Non-Treated
Inhibitor-Free DNA (or RNA)
Treated
300 bp -

200 bp -
Product
M
100 bp -
RT-PCR
+
DNA is efficiently amplified by PCR following humic acid removal
with the OneStep™PCR Inhibitor Removal Kit. The figure shows
amplification of a 200 bp product from DNA containing humic acid that
was treated with the kit. Alternatively, PCR amplification was completely
inhibited in the case of the non-treated sample. In each case, equal
amounts of DNA were used for each PCR and equivalent amounts of the
reaction were then analyzed in a 2.0% (w/v) agarose/TAE/EtBr gel. The
ladder is a 100 bp DNA marker (Zymo Research). Hot start PCR was
performed using ZymoTaq™ PreMix (Zymo Research).
Control
-
PCR amplification of an eukaryotic transcript (post-RT): Total RNA
isolated from sludge with (+) or without (-) inclusion of the OneStep™
technology. RNA was resolved in a 1% (w/v) nondenaturing agarose gel.
M is a 1 kb DNA Marker (Zymo Research).
Unparalleled Performance:
BashingBead™ Lysis
ZR BashingBead™ Lysis Tubes
 Each impact resistant 2.0 ml tube contains 0.7 ml (dry volume) of ZR BashingBead™ lysis matrix, available in 0.5 or 2 mm
 These state-of-the-art, ultra-high density beads are fracture resistant and chemically inert and ideal for disrupting tough-tolyse bacteria, yeast, fungi, algae, cells, tissues, organisms, etc
ZR BashingBead™ Lysis Racks
 Each impact resistant 1.1 ml tube contains 0.5 ml dry volume of ZR BashingBead™ lysis matrix, available in 0.5 or 2 mm
 Tubes are in a 96-well rack with caps and a cover
 Perfect for high-throughput processing of tough-to-lyse biological materials
Expedition Tip:
HOW TO tie a bowline
The bowline is well known as a rescue knot for such purposes as rescuing people who might
have fallen down a hole, or off a cliff onto a ledge.
www.zymoresearch.com
7
Xpedition™ Sample Prep Technologies:
The Complete Solution to “TAKE THE LAB TO THE FIELD”
For Portable Sample Lysis...
Xpedition™ Sample Processor
S6020
Xpedition™ Sample Processor
1 unit
D6202
Xpedition™ Soil & Fecal DNA MiniPrep
50 preps.
D6206
Xpedition™ Fungal/Bacterial DNA MiniPrep
50 preps.
D6216
Xpedition™ Tissue & Insect DNA MiniPrep
50 preps.
D6221
Xpedition™ Plant & Seed DNA MiniPrep
50 preps.
D6202-1-40
Xpedition™ Lysis/Stabilization Solution
40 ml
All Xpedition™ DNA MiniPrep Kits feature a unique lysis/stabilization solution. This allows high
quality DNA to be isolated immediately or when convenient for the researcher following storage/
transport of sample lysates.
Other Popular Environmental DNA/RNA Purification Products
Environmental DNA
Environmental RNA
R2040
ZR Soil/Fecal RNA MicroPrep™
50 preps.
50 preps.
R2010
ZR Fungal/Bacterial RNA MicroPrep™
50 preps.
50 preps.
R2014
ZR Fungal/Bacterial RNA MiniPrep™
50 preps.
R2030
ZR Tissue & Insect RNA MicroPrep™
50 preps.
R2024
ZR Plant RNA MiniPrep™
50 preps.
D6003
ZR Soil Microbe DNA MicroPrep™
50 preps.
D6001
ZR Soil Microbe DNA MiniPrep
™
50 preps.
D6101
ZR Soil Microbe DNA MidiPrep™
25 preps.
D6002
ZR-96 Soil Microbe DNA Kit™
2 x 96 preps.
D6007
ZR Fungal/Bacterial DNA MicroPrep™
D6005
ZR Fungal/Bacterial DNA MiniPrep
™
D6105
ZR Fungal/Bacterial DNA MidiPrep™
25 preps.
D6006
ZR-96 Fungal/Bacterial DNA Kit™
2 x 96 preps.
D6012
ZR Fecal DNA MicroPrep™
50 preps.
D6010
ZR Fecal DNA MiniPrep™
50 preps.
D6110
ZR Fecal DNA MidiPrep™
25 preps.
D6011
ZR-96 Fecal DNA Kit
2 x 96 preps.
D6015
ZR Tissue & Insect DNA MicroPrep™
50 preps.
D6016
ZR Tissue & Insect DNA MiniPrep
™
50 preps.
D6115
ZR Tissue & Insect DNA MidiPrep™
25 preps.
D6017
ZR-96 Tissue & Insect DNA Kit™
2 x 96 preps.
D6022
ZR Plant/Seed DNA MicroPrep™
50 preps.
D6020
ZR Plant/Seed DNA MiniPrep™
50 preps.
D6120
ZR Plant/Seed DNA MidiPrep
25 preps.
D6021
ZR-96 Plant/Seed DNA Kit™
™
™
2 x 96 preps.
also available
D6030
OneStep™ PCR Inhibitor Removal Kit
50 preps.
D6035
OneStep-96 PCR Inhibitor Removal Kit
2 x 96 preps.
S6002-50
ZR BashingBead™ Lysis Tubes (0.5 mm)
50 tubes
S6003-50
ZR BashingBead™ Lysis Tubes (2.0 mm)
50 tubes
S6002-96-1
ZR-96 BashingBead™ Lysis Rack (0.5 mm)
1 rack
S6002-96-2
ZR-96 BashingBead™ Lysis Rack (2.0 mm)
1 rack
™
For a complete product listing,
please visit www.zymoresearch.com
www.zymoresearch.com/xpedition
See the Xpedition™ Sample Processor in action!
Find us on Facebook & follow us on Twitter for the latest
product releases, special offers, and more!