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Two-dimensional gel electrophoresis (2D-GE) image analysis based on CellProfiler: Pseudomonas aeruginosa AG1 as model

Two-dimensional gel electrophoresis (2D-GE) image analysis based on CellProfiler: Pseudomonas aeruginosa AG1 as model
Posted by Troy

The two-dimensional gel electrophoresis (2D-GE) is a technique that is very necessary for the study of biological system proteomas, providing an assessment of changes in abundance of proteins in various experimental conditions. However, because of the complexity of 2D-GE gel, there is no systematic, automatic, and reproducing protocol for image analysis and specific implementation is needed for each context. In addition, practically all available solutions are commercial, which implies high costs and a little flexibility to modulate algorithm parameters.

Using bacterial strains, pseudomonas aeruginosaag1 as a model, we get pictures of 2D-GE protein protein profiles periplasm when strains are exposed to several conditions, including antibiotics. Then, we proceed to implement and evaluate the image analysis protocol with open source software, CellProfiler. First, step preprocessing includes bunwarpj-image pipes to align 2D-GE images. Then, using CellProfiler, we standed two pipes for place identification. The total introduction of places is achieved by using segmentation with intensity, which performance is evaluated when compared to the reference protocol.

In the second pipe with the same program, the identification of differential spots is handled when comparing pairs of protein profiles. Because the program characteristics used, our workflow can automatically analyze a large number of images and parallel, which is an advantage in connection with other implementations. Finally, we compare six experimental conditions of bacterial pressure in the presence or absence of antibiotics, determine the relationship of protein profiles by applying the PCA clustering algorithm (main component analysis) and hierarchy (clustering).

Electrophoresis gel polyacrylamide

Chains of cross-linked from polyacrylamides can be used as electric neutral gel to separate multiple-double DNA fragments according to the size and DNAS stranded single according to size and conformation. Polyacrylamide gel has three main advantages along with axible glass: (1) the power of resolution is so large that they can separate the DNA molecules that are different in length to only 0.1% (eg) 1000 bp). (2) They can accommodate the amount of DNA which is far greater than agarose gel. Up to 10 μg of DNA can be applied to one slot (1 cm × 1 mm) from a typical polyacrylamide gel without losing resolution. (3) DNA recovers from polyacrylamide gel is very pure and can be used for the most demanding purpose (eg, microinjection embryo mouse).

However, polyacrylamide gel has losses to be more difficult to be prepared and handled than gel agarose. The method is presented here to prepare and run polyacrylamide gels that are not prominent and for DNA detection on this gel with coloring.

Comparative analysis using electrophoresis of pulsating gel-field highlights the transmission of salmonella potential between buffalo and asimptomatic pigs on one agriculture

Buffalo and pigs play an important epidemiological roll in the cycle of salmonella infection, and asymptomatic animals can act as a key component in the spread of this disease with horizontal, vertical, and cross species transmissions. Our research is intended and able to confirm the evidence of transmission of cross-agona salmonella species between buffalo and asimptomatic pigs. Also, we describe salmonella infection in the pork production phase, which involves Serotype Agona, Senftenberg and Schwarzengrund.

 Two-dimensional gel electrophoresis (2D-GE) image analysis based on CellProfiler: Pseudomonas aeruginosa AG1 as model

Rectal samples are collected from buffalo jafarabadi (n = 25) and pig piau (n = 32), located on an agriculture. Salmonella Agona was isolated from the buffalo of breastfeeding, gilt, sowing pregnant, and weaning pigs, Salmonella Schwarzengrund from sowing breastfeeding and Salmonella Senftenberg from Gilt, sowing pregnant, sowing weaning, and weaning pigs. The pulsed gel electrophoresis protocol (PFGE) is done and reveals four different profiles. Profile 1 (Salmonella Agona), isolated from pregnant pigs, gold and two breastfeeding buffalo, revealing the PFGE pattern that cannot be distinguished, confirming proof of cross-species transmission potential. Profile 2 (Salmonella Agona), 3 (Salmonella Senftenberg), and 4 (Salmonella Schwarzengrund), isolated from pigs, revealing pfge patterns that cannot be distinguished, proving salmonella infection in the pork production phase.

Consider the epidemiological relevance of the buffalo and pigs in the cycle of salmonella infection, transmission confirmation of the potential species of salmonella agona and potential salmonella infections in the pork production phase highlight the importance of the formation of preventive health strategies correctly on animal husbandry, in particular the importance of avoiding contact between buffalo and pigs, due to cross transmission Species can occur, increasing the risk of disseminating disease.

Seabeam wild or farming gilead (Sparus Aurata)? How to distinguish between them with two-dimensional gel electrophoresis

Because the shares of world wild fish are limited and market demand increases, fish farming has become an alternative food source and a way to reduce costs for consumers. Agricultural sales as wild fish are fraud practices, because it is important to work to provide new tools and alternatives that can help in combating fraud to protect consumers and to ensure food tracing. Proteomic profiles of farm fish and wildly different from each other. With this study we want to identify the marker of the liver protein through two-dimensional electrophoresis (2DE) which will enable us to distinguish wildly from the Seabream Gilhead farming.

Agarose for DNA electrophoresis

16-0027-500 500 g
EUR 410.4

Acrylamide, suitable for electrophoresis

GK5651-100G 100 g
EUR 64.8

Starch (Smithies), for electrophoresis

GE6857-1KG 1 kg
EUR 370.8

Starch (Smithies), for electrophoresis

GE6857-500G 500 g
EUR 217.2

Chiller for Electrophoresis systems

CSLCHILLER EACH
EUR 6453.54

Horizontal head

BV1000-H15 1 PC
EUR 161.26

Horizontal head

BV1000-H150 1 PC
EUR 161.26

Horizontal head

BV1000-H500 1 PC
EUR 2813.28

Horizontal head, for 12 x 1.5ml

BCM1604 1 pcs, 1 UNIT
EUR 200.68

Horizontal head, for 4 x 15ml

BCM1605 1 pcs, 1 UNIT
EUR 200.68

Horizontal head, for 2 x 50ml

BCM1606 1 pcs, 1 UNIT
EUR 200.68

Horizontal head for 12 x 1.5mL

MIX7018 EACH
EUR 121.98

Horizontal head for 4 x 15mL

MIX7020 EACH
EUR 121.98

Horizontal head for 2 x 50mL

MIX7022 EACH
EUR 121.98

Tube Rack for 7x50mL QuEChERs horizontal

MIX7044 EACH
EUR 47.54

Clear Universal Reload Box for Tower Pack Tips

F167100 EACH
EUR 13.68

Horizontal MicroLoops E

M8-L18SP-15H 20 MOUNTS
EUR 112
Description: Horizontal MicroLoops E; box of 20 each 15x150 um aperture mounted on 18 mm rods

Horizontal MicroLoops E

M8-L18SP-50H 20 MOUNTS
EUR 112
Description: Horizontal MicroLoops E; box of 20 each 50x500 um aperture mounted on 18 mm rods

CometAssay Electrophoresis System

4250-050-ES 1 Kit
EUR 3540.96

electrophoresis power supply

EV245 ea
EUR 574.8

miniONE Electrophoresis System

ELE3400 EACH
EUR 624.72

ES 6 Tooth Gel Comb For ES Electrophoresis

LE1011-A4 Ea
EUR 148.8

Horizontal 50mL Tube Holder

MIX5088 EACH
EUR 144.78

Horizontal orientator 384 wells

DD53423 PK2
EUR 63.84

Midi Horizontal Gel Unit

ELE8120 EACH
EUR 630.42

Pipette Tray PVC Horizontal

PIP5500 EACH
EUR 38.76

CometAssay Electrophoresis Starter Kit

4250-050-ESK 1 Kit
EUR 3749.28

myGel Mini Electrophoresis System

BM0286 System
EUR 741.6

6X6 well Electrophoresis Apparatus

EDK626 1 UNIT
EUR 750.6

myGel Mini Electrophoresis System

E1101 1 each
EUR 623.9

Azlon Bottles HPE Heavy Duty Square Graduated Wide Neck

BGE342P PK5
EUR 62.36

Horizontal shelf for freezer capacity for 16 boxes height 50 mm

DD37581 EACH
EUR 352.26

runVIEW horizontal electrophoresis system 15 x 7cm gel tray 1 set of casting dams 8 double sided combs

ELE2300 EACH
EUR 1448.94

ES 8/10 Double Gel Comb For ES Electrophoresis

LE1011-A3 Ea
EUR 148.8

Tower Pack D10 Refill Of 960 Tips

F167101 PK960
EUR 46.74

Tower Pack DL10 Refill Of 960 Tips

F167102 PK960
EUR 46.74

Tower Pack D200 Refill Of 960 Tips

F167103 PK960
EUR 41.04

Tower Pack D1000 Refill Of 672 Tips

F167104 PK672
EUR 33.06

Tower Pack D300 Refill Of 960 Tips

F167105 PK960
EUR 41.04

maxi horizontal unit 20x10 cm

EHS1401-SYS ea
EUR 686.4

maxi horizontal unit 20x20 cm

EHS1402-SYS ea
EUR 727.2

maxi horizontal unit 20x25 cm

EHS1403-SYS ea
EUR 747.6

maxiplus horizontal unit 26x16 cm

EHS1501-SYS ea
EUR 939.6

maxiplus horizontal unit 26x24 cm

EHS1502-SYS ea
EUR 939.6

maxiplus horizontal unit 26x32 cm

EHS1503-SYS ea
EUR 939.6

mini horizontal unit 9x11 cm

EHS3200-SYS ea
EUR 595.2

mini horizontal unit 12x14 cm

EHS3300-SYS ea
EUR 625.2

midi horizontal unit 15x15 cm

EHS3400-SYS ea
EUR 757.2

midi horizontal unit 15x25 cm

EHS3410-SYS ea
EUR 930

midi horizontal unit 20x25 cm

EHS3500-SYS ea
EUR 980.4

wide horizontal unit 23.5x14 cm

EHS3600-SYS ea
EUR 930

wide horizontal unit 23.5x25 cm

EHS3610-SYS ea
EUR 1030.8

mini horizontal unit 7x7 cm

EHS1101-SYS ea
EUR 381.6

mini horizontal unit 7x10 cm

EHS1102-SYS ea
EUR 381.6

midi horizontal unit 10x7 cm

EHS1201-SYS ea
EUR 422.4

midi horizontal unit 10x10 cm

EHS1202-SYS ea
EUR 422.4

midiplus horizontal unit 15x7 cm

EHS1301-SYS ea
EUR 433.2

midiplus horizontal unit 15x10 cm

EHS1302-SYS ea
EUR 433.2

midiplus horizontal unit 15x15 cm

EHS1303-SYS ea
EUR 433.2

6 x 15ml horizontal rotisserie

R4040-HZ15 1 PC
EUR 127.76

6 x 50ml horizontal rotisserie

R4040-HZ50 1 PC
EUR 197.63

HS 260 Basic Horizontal Shaker

3066602 EACH
EUR 3308.28

Horizontal Plastic Clip Microtube Holder

MIX5096 EACH
EUR 173.28

Genie Horizontal Orbital Shaker Attachments

MIX5321 EACH
EUR 523.26

Axygen Horizontal Gel Box 20Cm

HGB-20 EACH
EUR 776.34

electrophoresis ps 400v, 500ma, 50w

EV1450 ea
EUR 574.8

electrophoresis ps 400v, 500ma, 50w

EV1450-UK ea
EUR 574.8

electrophoresis ps 400v, 500ma, 50w

EV1450-US ea
EUR 574.8

electrophoresis ps 1500v, 300ma, 150w

EV2230 ea
EUR 898.8

electrophoresis ps 1500v, 300ma, 150w

EV2230-UK ea
EUR 898.8

electrophoresis ps 1500v, 300ma, 150w

EV2230-US ea
EUR 898.8

electrophoresis ps 300v, 1000ma, 150w

EV2310 ea
EUR 686.4

electrophoresis ps 300v, 1000ma, 150w

EV2310-UK ea
EUR 686.4

electrophoresis ps 300v, 1000ma, 150w

EV2310-US ea
EUR 686.4

electrophoresis ps 3000v, 150ma, 150w

EV2320 ea
EUR 898.8

electrophoresis ps 3000v, 150ma, 150w

EV2320-UK ea
EUR 898.8

electrophoresis ps 3000v, 150ma, 150w

EV2320-US ea
EUR 898.8

electrophoresis power supply uk plug

EV245-UK ea
EUR 574.8

electrophoresis power supply 120 vac

EV245-US ea
EUR 574.8

electrophoresis ps 600v, 500ma, 150w

EV2650 ea
EUR 686.4

electrophoresis ps 600v, 500ma, 150w

EV2650-UK ea
EUR 686.4

electrophoresis ps 600v, 500ma, 150w

EV2650-US ea
EUR 686.4

electrophoresis ps 300v, 2000ma, 300w

EV3020 ea
EUR 960

electrophoresis ps 300v, 2000ma, 300w

EV3020-UK ea
EUR 960

electrophoresis ps 300v, 2000ma, 300w

EV3020-US ea
EUR 960

electrophoresis ps 1200v, 500ma, 300w

EV3150 ea
EUR 960

electrophoresis ps 1200v, 500ma, 300w

EV3150-UK ea
EUR 960

electrophoresis ps 1200v, 500ma, 300w

EV3150-US ea
EUR 960

electrophoresis ps 3000v, 300ma, 300w

EV3330 ea
EUR 1456.8

electrophoresis ps 3000v, 300ma, 300w

EV3330-UK ea
EUR 1456.8

electrophoresis ps 3000v, 300ma, 300w

EV3330-US ea
EUR 1456.8

electrophoresis ps 600v, 1000ma, 300w

EV3610 ea
EUR 960

electrophoresis ps 600v, 1000ma, 300w

EV3610-UK ea
EUR 960

electrophoresis ps 600v, 1000ma, 300w

EV3610-US ea
EUR 960

electrophoresis ps 6000v, 150ma, 300w

EV3620 ea
EUR 1456.8

electrophoresis ps 6000v, 150ma, 300w

EV3620-UK ea
EUR 1456.8

electrophoresis ps 6000v, 150ma, 300w

EV3620-US ea
EUR 1456.8

5 x SDS Electrophoresis Buffer

GR103039 1 L
EUR 128.4

runVIEW horizontal electrophoresis system with 15 x 10cm gel tray 1 set of casting dams and 8 double sided combs

ELE2302 EACH
EUR 1520.76

Tower Pack Sterile D10ST Refill Of 960 Tips

F167201 PK960
EUR 59.28

Tower Pack Sterile DL10ST Refill Of 960 Tips

F167202 PK960
EUR 59.28

Tower Pack Sterile D200ST Refill Of 960 Tips

F167203 PK960
EUR 53.58

Tower Pack Sterile D1000ST Refill Of 960 Tips

F167204 PK672
EUR 41.04

Tower Pack Sterile D300ST Refill Of 960 Tips

F167205 PK960
EUR 53.58

maxi horizontal unit 20x10 & 20x20 cm

EHS1400-SYS ea
EUR 727.2

maxiplus horizontal unit 26x16-24-32cm

EHS1500-SYS ea
EUR 1132.8

mini horizontal unit 7x7 & 7x10 cm

EHS1100-SYS ea
EUR 422.4

midi horizontal unit 10x7 & 10x10 cm

EHS1200-SYS ea
EUR 453.6

CometAssay Single Cell Gel Electrophoresis Assay

4250-050-K 50 tests
EUR 513.6

Electrophoresis Apparatus - 7x10cm (6-10-well)

EDK611 1 UNIT
EUR 383.11

Electrophoresis Apparatus - 7x14cm (6-10-well)

EDK613 1 UNIT
EUR 487.51

10-well protein Vertical Electrophoresis Apparatus

EDK692 1 UNIT
EUR 487.51

4 x Phosphate/SDS Electrophoresis Buffer

GR103033 1 L
EUR 139.2

Holder for Plasmid Midi, Maxi and Maxi plus, Ion Exchange column

FAPDE-holder-for-ion-exchange 1 prep
EUR 189.6

wide horizontal unit 23.5x40 cm ex. port

EHS3620-SYS ea
EUR 1132.8

midiplus horizontal unit 15x7-10-15 cm

EHS1300-SYS ea
EUR 496.8

AXYGEN® HORIZONTAL GEL BOX, 10 CM

HGB-10 1/pk
EUR 399.6
Description: Lab Equipment; Axygen Branded EQ

AXYGEN® HORIZONTAL GEL BOX, 15 CM

HGB-15 1/pk
EUR 583.2
Description: Lab Equipment; Axygen Branded EQ

AXYGEN® HORIZONTAL GEL BOX, 7 CM

HGB-7 1/pk
EUR 343.2
Description: Lab Equipment; Axygen Branded EQ

6 x 15mL horizontal rotisserie 1 ea

MIX7080 EACH
EUR 76.38

6 x 50mL horizontal rotisserie 1 ea

MIX7082 EACH
EUR 76.38

CometAssay Single Cell Gel Electrophoresis Assay-Silver

4251-050-K 1 kit
EUR 684.96

Heart samples of 32 Gilead Seabream, wild and farming, stored at -80 ° C Previous extraction of protein. Samples are subject to 2DE to detect qualitative and quantitative differences. Proteom analysis shows a protein point (molecular weight ~ 34 kDa and isoelectric point ~ 6.9) only in the sample of the Seabread Wild Gilead; Liquid chromatography Tandem mass spectrometry identifies the place as ubiquitin. Ubiquitin can be a valid marker to distinguish wildly from the Seabread of Gilead farming, thus ensuring sustainable monitoring throughout the commercial chain and fighting commercial fraud.

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