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Primer3–new capabilities and interfaces.

Posted on April 29, 2021 by Leah

Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets.

Accurate normalization is an absolute prerequisite for correct measurement of gene expression. For quantitative real-time reverse transcription-PCR (RT-PCR), the most commonly used normalization strategy involves standardization to a single constitutively expressed control gene. However, in recent years, it has become clear that no single gene is constitutively expressed in all cell types and under all experimental conditions, implying that the expression stability of the intended control gene has to be verified before each experiment. We outline a novel, innovative, and robust strategy to identify stably expressed genes among a set of candidate normalization genes. The strategy is rooted in a mathematical model of gene expression that enables estimation not only of the overall variation of the candidate normalization genes but also of the variation between sample subgroups of the sample set.
Notably, the strategy provides a direct measure for the estimated expression variation, enabling the user to evaluate the systematic error introduced when using the gene. In a side-by-side comparison with a previously published strategy, our model-based approach performed in a more robust manner and showed less sensitivity toward coregulation of the candidate normalization genes. We used the model-based strategy to identify genes suited to normalize quantitative RT-PCR data from colon cancer and bladder cancer. These genes are UBC, GAPD, and TPT1 for the colon and HSPCB, TEGT, and ATP5B for the bladder. The presented strategy can be applied to evaluate the suitability of any normalization gene candidate in any kind of experimental design and should allow more reliable normalization of RT-PCR data.
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DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates.

We describe “universal” DNA primers for polymerase chain reaction (PCR) amplification of a 710-bp fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) from 11 invertebrate phyla: Echinodermata, Mollusca, Annelida, Pogonophora, Arthropoda, Nemertinea, Echiura, Sipuncula, Platyhelminthes, Tardigrada, and Coelenterata, as well as the putative phylum Vestimentifera. Preliminary comparisons revealed that these COI primers generate informative sequences for phylogenetic analyses at the species and higher taxonomic levels.

Real-time quantification of microRNAs by stem-loop RT-PCR.

A novel microRNA (miRNA) quantification method has been developed using stem-loop RT followed by TaqMan PCR analysis. Stem-loop RT primers are better than conventional ones in terms of RT efficiency and specificity. TaqMan miRNA assays are specific for mature miRNAs and discriminate among related miRNAs that differ by as little as one nucleotide. Furthermore, they are not affected by genomic DNA contamination. Precise quantification is achieved routinely with as little as 25 pg of total RNA for most miRNAs.
In fact, the high sensitivity, specificity and precision of this method allows for direct analysis of a single cell without nucleic acid purification. Like standard TaqMan gene expression assays, TaqMan miRNA assays exhibit a dynamic range of seven orders of magnitude. Quantification of five miRNAs in seven mouse tissues showed variation from less than 10 to more than 30,000 copies per cell. This method enables fast, accurate and sensitive miRNA expression profiling and can identify and monitor potential biomarkers specific to tissues or diseases. Stem-loop RT-PCR can be used for the quantification of other small RNA molecules such as short interfering RNAs (siRNAs). Furthermore, the concept of stem-loop RT primer design could be applied in small RNA cloning and multiplex assays for better specificity and efficiency.
 

Primer3–new capabilities and interfaces.

Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications.
It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers.
Additional enhancements include more precise control of primer placement-a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.

Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands.

Precise mapping of DNA methylation patterns in CpG islands has become essential for understanding diverse biological processes such as the regulation of imprinted genes, X chromosome inactivation, and tumor suppressor gene silencing in human cancer. We describe a new method, MSP (methylation-specific PCR), which can rapidly assess the methylation status of virtually any group of CpG sites within a CpG island, independent of the use of methylation-sensitive restriction enzymes.
This assay entails initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. MSP requires only small quantities of DNA, is sensitive to 0.1% methylated alleles of a given CpG island locus, and can be performed on DNA extracted from paraffin-embedded samples.
MSP eliminates the false positive results inherent to previous PCR-based approaches which relied on differential restriction enzyme cleavage to distinguish methylated from unmethylated DNA. In this study, we demonstrate the use of MSP to identify promoter region hypermethylation changes associated with transcriptional inactivation in four important tumor suppressor genes (p16, p15, E-cadherin, and von Hippel-Lindau) in human cancer.

Flat Replaceable Tips 25 mm Diameter Flat Titanium Tip

0-120-0018 Biologics 25 mm
EUR 100
Description: use with corresponding Tapped Tips and Tapped Extender Tips

Titanium Cup Tip, 250 ml

0-120-0019 Biologics 250 ml
EUR 1377
Description: includes Interface Washers

Microtube Tray, 8 Position (for 250 ml Cup Tip)

0-120-0021 Biologics each
EUR 113
Description: includes Interface Washers

Continuous Flow Chamber

0-120-0026 Biologics each
EUR 774
Description: includes Interface Washers

Interface Washers 1.5” Diameter, 5/Pkg

0-120-003 Biologics 1.5'' Diameter
EUR 31

13 mm Diameter Solid Titanium Extender Tip

0-120-0032 Biologics 13 mm
EUR 301

13 mm Diameter Tapped Titanium Extender Tip

0-120-0033 Biologics 13 mm
EUR 362

19 mm Diameter Solid Titanium Extender Tip

0-120-0034 Biologics 19 mm
EUR 315

19 mm Diameter Tapped Titanium Extender Tip

0-120-0035 Biologics 19 mm
EUR 375

25 mm Diameter Solid Titanium Extender Tip

0-120-0036 Biologics 25 mm
EUR 328

25 mm Diameter Tapped Titanium Extender Tip

0-120-0037 Biologics 25 mm
EUR 389

KoldPod, 1.5ml Micro Tube

0-120-0038 Biologics 1.5 ml
EUR 152
Description: Thermo conductive tube pods

KoldPod, 15ml Conical Tube

0-120-0039 Biologics 15 ml
EUR 275
Description: Thermo conductive tube pods

KoldPod, 50ml Conical Tube

0-120-0040 Biologics 50 ml
EUR 290
Description: Thermo conductive tube pods

Model 150 V/T Ultrasonic Homogenizer

0-121-0002 Biologics 210-240V/50-60Hz
EUR 2920
Description: Delivers up to 150 Watts of ultrasonic power to the Titanium Tip. The Timer and Duty Cycle function increase preciosion in sample processing processing.

Model 300 V/T Ultrasonic Homogenizer

0-122-0002 Biologics 210-240V/50-60Hz
EUR 3520
Description: Delivers up to 300 Watts of ultrasonic power to the Titanium Tip. The Timer and Duty Cycle function increase preciosion in sample.

SONABOZ Sound Abating Chamber

0-125-0001 Biologics each
EUR 1020
Description: Reduces cavitational sound emitted during processing.

Model 3000 Ultrasonic Homogenizer

0-127-0002 Biologics 210-240V/50-60Hz
EUR 4120
Description: Delivers up to 300 Watts of ultrasonic power to the Titanium Tip and includes an intergrated Sound Abating Chmaber to reduce cavitational sound emitted during processing. The Timer and Duty Cycle function increase preciosion in sample.

Model 3000MP Ultrasonic Homogenizer

0-128-0002 Biologics 210-240V/50-60Hz
EUR 4720
Description: Delivers up to 300 Watts of ultrasonic power to the Titanium Tip with preciosion control from a microprocessor and a graphical user interface displayed on a large (145 mm) LCD display. The integrated Sound Abating Chamber reduces cavitational sound emitted during processing.

OMNICON® Zone Reader, 210-240V/50-60Hz

0-131-0002 Biologics 210-240V/50-60Hz
EUR 35200
Description: Designed to Perform multi-plate Assays on round 90/100mm Petri Dishes. The integrated LED illumination system provides transmitted light for brightfield and darkfield illumination of transparent media.

OMNI-Noculator Peni Cylinder Filler, 210-240V/50-60Hz

0-134-0002 Biologics 210-240V/50-60Hz
EUR 32200
Description: A robotic liquid handling system designed to dispense Peni Cylinders and fill Peni Cylinders with the corresponding antibiotic liquid sample.

Peni Cylinder Dispenser with Manual Hopper

0-144-0002 Biologics each
EUR 5406
Description: Dispenser can be configured to dispense 4 or 6 Peni Cylinders onto a petri dish.

Peni Cylinder Dispenser with Motorized Hopper, 100-240V/50-60Hz

0-144-0003 Biologics 100-240V/50-60Hz
EUR 6254
Description: The motorized hopper can be configured to dispense 4 or 6 Peni Cylinders onto a petri Dispenser can be disassembled for disinfection.

Stainless Steel Peni Cylinder with Flat Face

0-144-0005 Biologics 6mm I.D. x 8mm O.D. x 10mm Long
EUR 399
Description: sold in packages of 100 pieces

Stainless Steel Peni Cylinder with Chamfered Face

0-144-0006 Biologics 6mm I.D. x 8mm O.D. x 10mm Long
EUR 412
Description: sold in packages of 100 pieces

Custom development of ELISAs for other species or antibody isotypes not listed in the catalog. Custom testing of samples for IgG/IgM/IgA or total (IgG+IgM+IgA)

000-CUS Alpha Diagnostics Custom
EUR 602

Alpha-Bungarotoxin, CF®405S, 500 ug

00002 Biotium 1UG
EUR 527
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-bungarotoxin, CF405s

00002 Cusabio 500uG
EUR 594
Description: Minimum order quantity: 1 unit of 500uG

Alpha-Bungarotoxin, CF®405S, 500 ug

00002-1 Biotium EA
EUR 527

Alpha-Bungarotoxin, CF®405S 100ug

00002-100ug Biotium 100uG
EUR 132
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®680R, 500 ug

9-00003 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®680R, 500 ug

00003-1 Biotium EA
EUR 527

Alpha-Bungarotoxin, CF®680R 100ug

9-00003 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®640R, 500 ug

9-00004 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®640R, 500 ug

00004-1 Biotium EA
EUR 527

Alpha-Bungarotoxin, CF®640R 100ug

9-00004 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®488A, 500 ug

9-00005 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®488A, 500 ug

00005-1 Biotium EA
EUR 527

Alpha-Bungarotoxin CF®488A 100ug

9-00005 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®568, 500 ug

9-00006 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®568, 500 ug

00006-1 Biotium EA
EUR 527

Alpha-Bungarotoxin, CF®568 100ug

9-00006 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®594, 500 ug

9-00007 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®594, 500 ug

00007-1 Biotium EA
EUR 527

Alpha-Bungarotoxin CF®594 100ug

9-00007 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®633, 500 ug

9-00009 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®633, 500 ug

00009-1 Biotium EA
EUR 527

Alpha-Bungarotoxin, CF®633 100ug

9-00009 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100uG
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

SARS-CoV-2 Indicator Cell Line for RNA Replication - GFP Reporter only

0001-PP-001 IBT Bioservices 1 cell line (can order x amount)
EUR 12000
Description: SARS-CoV-2 GFP reporter cell line using HEK293T (ACE2/TMPRSS2) cells

Alpha-Bungarotoxin, 1 mg

00010-1 Biotium 1MG
EUR 193
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, 1 mg

00010-1-1 Biotium EA
EUR 193

Fluorescein-Alpha-Bungarotoxin, 500 ug

00011 Biotium 500uG
EUR 376
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Fluorescein-Alpha-Bungarotoxin, 500 ug

00011-1 Biotium EA
EUR 376

Tetramethylrhodamine-Alpha-Bungarotoxin, 500 ug

00012 Biotium 500uG
EUR 394
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Tetramethylrhodamine-Alpha-Bungarotoxin, 500 ug

00012-1 Biotium EA
EUR 394

Fluorescein-alpha-bungarotoxin, 10x50ug

00013 Biotium 10ST
EUR 436
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Fluorescein-alpha-bungarotoxin, 10x50ug

00013-1 Biotium EA
EUR 436

Tetramethylrhodamine-A-Bungarotoxin, 10x50 ug

00014 Biotium 10ST
EUR 494
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Tetramethylrhodamine-A-Bungarotoxin, 10x50 ug

00014-1 Biotium EA
EUR 494

Sulforhodamine 101-Alpha-Bungarotoxin, 500 ug

00015 Biotium 500uG
EUR 494
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Sulforhodamine 101-Alpha-Bungarotoxin, 500 ug

00015-1 Biotium EA
EUR 494

Sulforhodamine 101-Alpha-Bungarotoxin, 50 ug

00016 Biotium 10ST
EUR 560
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Sulforhodamine 101-Alpha-Bungarotoxin, 50 ug

00016-1 Biotium EA
EUR 560

Biotin-XX-A-Bungarotoxin, 500 ug

00017 Biotium 500uG
EUR 455
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Biotin-XX-A-Bungarotoxin, 500 ug

00017-1 Biotium EA
EUR 455

Alpha-Bungarotoxin, CF®555, 500 ug

9-00018 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100ug
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®555, 500 ug

00018-1 Biotium EA
EUR 527

Alpha-Bungarotoxin, CF®555 100ug

9-00018 Biotium
  • Ask for price
  • Ask for price
  • 500uG
  • 100ug
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Acrylamide, Chemzymes Ultra Pure®

00019-100 Polysciences Europe GmbH 100g
EUR 101.52
Description: 79-06-1

Acrylamide, Chemzymes Ultra Pure®

00019-500 Polysciences Europe GmbH 500g
EUR 270
Description: 79-06-1

Biotin-cAMP, 1 mg

00020 Biotium 1MG
EUR 298
Description: N/A

Biotin-cAMP, 1 mg

00020-1 Biotium 20ST
EUR 298
Description: N/A

Biotin-cAMP, 50 ug

00020-1-1 Biotium EA
EUR 414

Biotin-cGMP, 1 mg

00021 Biotium 1MG
EUR 331
Description: N/A

Biotin-cGMP, 1 mg

00021-1 Biotium 20ST
EUR 331
Description: N/A

Biotin-cGMP, 20x50 ug

00021-1-1 Biotium EA
EUR 447

Cyanine 644-cAMP, 1 mg

00022 Biotium 1MG
EUR 496
Description: N/A

Cyanine 644-cAMP, 1 mg

00022-1 Biotium 20ST
EUR 496
Description: N/A

Cyanine 644-cAMP, 20x50 ug

00022-1-1 Biotium EA
EUR 647

Fluorescein Methotrexate, Triammonium Salt, 1 mg

00023 Biotium 1MG
EUR 285
Description: N/A

Fluorescein Methotrexate, Triammonium Salt, 1 mg

00023-1 Biotium EA
EUR 285

Staurosporine

00025 Biotium 100uG
EUR 100
Description: N/A

Staurosporine

00025-1 Biotium EA
EUR 100

Alpha-Bungarotoxin, CF®543, 500 ug

00026 Biotium 500uG
EUR 527
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Alpha-Bungarotoxin, CF®543, 500 ug

00026-1 Biotium EA
EUR 527

Alpha-Bungarotoxin, CF®543, 100 ug

00026-100ug Biotium 1UG
EUR 132
Description: Alpha-bungarotoxin from Krait snake venom (Bungarus multicinctus)

Rhodamine Phalloidin 300U

00027 Biotium 300
EUR 364
Description: N/A

Rhodamine Phalloidin 300U

00027-1 Biotium EA
EUR 364

Biotin-XX-Phalloidin

00028 Biotium 100U
EUR 466
Description: N/A

Biotin-XX-Phalloidin

00028-1 Biotium EA
EUR 466

Fluorescein-Phalloidin

00030 Biotium 300U
EUR 364
Description: N/A

Fluorescein-Phalloidin

00030-1 Biotium EA
EUR 364

Rhodamine 110 Phalloidin

00032 Biotium 300ST
EUR 364
Description: N/A

Rhodamine 110 Phalloidin

00032-1 Biotium EA
EUR 364

Sulforhodamine 101 (Texas Red®) Phalloidin

00033 Biotium 300EU
EUR 364
Description: N/A

Sulforhodamine 101 (Texas Red®) Phalloidin

00033-1 Biotium EA
EUR 364

Phalloidin, CF®405M

00034 Biotium 300U
EUR 482
Description: N/A

Phalloidin, CF®405M

00034-1 Biotium EA
EUR 482

Phalloidin, CF®405M

00034-T Biotium 50U
EUR 101
Description: N/A

Phalloidin, CF®405M

00034-T-1 Biotium EA
EUR 101

CF®488A-cAMP

00036 Biotium 100ug
EUR 136
Description: N/A

CF®488A-cAMP

00036-1 Biotium EA
EUR 136

CF®640R-cAMP

00037 Biotium 100ug
EUR 136
Description: N/A

CF®640R-cAMP

00037-1 Biotium EA
EUR 136

Phalloidin, CF555

00040 Biotium 300U
EUR 530.4
Description: Minimum order quantity: 1 unit of 300U

Phalloidin, CF555

00040-T Biotium 50U
EUR 159.6
Description: Minimum order quantity: 1 unit of 50U

Phalloidin, CF®647, 300 U

00041 Biotium 300U
EUR 482
Description: N/A

Phalloidin, CF®647, 300 U

00041-1 Biotium EA
EUR 482

Phalloidin, CF®647, 50 U

00041-T Biotium 50U
EUR 101
Description: N/A

Phalloidin, CF®647, 50 U

00041-T-1 Biotium EA
EUR 101

Phalloidin, CF®488A, 300 U

00042 Biotium 300U
EUR 482
Description: N/A

Phalloidin, CF®488A, 300 U

00042-1 Biotium EA
EUR 482

Phalloidin, CF®488A, 50 U

00042-T Biotium 50U
EUR 101
Description: N/A

Phalloidin, CF®488A, 50 U

00042-T-1 Biotium EA
EUR 101

Phalloidin, CF®543, 300 U

00043 Biotium 300U
EUR 482
Description: N/A

Phalloidin, CF®543, 300 U

00043-1 Biotium EA
EUR 482

Phalloidin, CF®543, 50 U

00043-T Biotium 50U
EUR 101
Description: N/A

Phalloidin, CF®543, 50 U

00043-T-1 Biotium EA
EUR 101

Phalloidin, CF®568, 300 U

00044 Biotium 300U
EUR 482
Description: N/A

Phalloidin, CF®568, 300 U

00044-1 Biotium EA
EUR 482

Phalloidin, CF®568, 50 U

00044-T Biotium 50U
EUR 101
Description: N/A

Phalloidin, CF®568, 50 U

00044-T-1 Biotium EA
EUR 101

Phalloidin, CF®594, 300 U

00045 Biotium 300U
EUR 482
Description: N/A

Phalloidin, CF®594, 300 U

00045-1 Biotium EA
EUR 482

Phalloidin, CF®594, 50 U

00045-T Biotium 50U
EUR 101
Description: N/A

Phalloidin, CF®594, 50 U

00045-T-1 Biotium EA
EUR 101

Phalloidin, CF®633, 300 U

00046 Biotium 300U
EUR 482
Description: N/A

Phalloidin, CF®633, 300 U

00046-1 Biotium EA
EUR 482

Phalloidin, CF®633, 50 U

00046-T Biotium 50U
EUR 101
Description: N/A

Phalloidin, CF®633, 50 U

00046-T-1 Biotium EA
EUR 101

Phalloidin, CF®660R, 300 U

00047 Biotium 300U
EUR 482
Description: N/A

Phalloidin, CF®660R, 300 U

00047-1 Biotium EA
EUR 482

Phalloidin, CF®660R, 50 U

00047-T Biotium 50U
EUR 101
Description: N/A
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