Cytometry and plant sciences: A personal retrospective

Galbraith, David W.

doi:10.1002/cyto.a.10100

Cited by 20 publications

(16 citation statements)

References 102 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This technology can be used to examine many cellular parameters on live or fixed cells, including surface, cytoplasmic, and nuclear proteins, DNA, RNA, reactive-oxygen species, intracellular pH, and calcium flux. Measurement of the expression of cellular-activation markers, intracellular cytokines, immunological signaling, and cytoplasmic and nuclear cell cycle and transcription factors can also be readily performed [9, 11, 12, 27, 28, 33–35]. …”

Section: Introductionmentioning

confidence: 99%

A Survey of Flow Cytometry Data Analysis Methods

Bashashati

Brinkman

2009

Advances in Bioinformatics

112

View full text Add to dashboard Cite

Flow cytometry (FCM) is widely used in health research and in treatment for a variety of tasks, such as in the diagnosis and monitoring of leukemia and lymphoma patients, providing the counts of helper-T lymphocytes needed to monitor the course and treatment of HIV infection, the evaluation of peripheral blood hematopoietic stem cell grafts, and many other diseases. In practice, FCM data analysis is performed manually, a process that requires an inordinate amount of time and is error-prone, nonreproducible, nonstandardized, and not open for re-evaluation, making it the most limiting aspect of this technology. This paper reviews state-of-the-art FCM data analysis approaches using a framework introduced to report each of the components in a data analysis pipeline. Current challenges and possible future directions in developing fully automated FCM data analysis tools are also outlined.

show abstract

Section: Introductionmentioning

confidence: 99%

A Survey of Flow Cytometry Data Analysis Methods

Bashashati

Brinkman

2009

Advances in Bioinformatics

112

View full text Add to dashboard Cite

show abstract

“…Fluorescent in situ hybridization and flow cytometric analyses have been the methods of choice for detection and characterization of aneuploidy in plants (Burton and Husband, 2001; Galbraith, 2004; Henry et al. , 2005; Roux et al.…”

Section: Introductionmentioning

confidence: 99%

Molecular karyotyping and aneuploidy detection in Arabidopsis thaliana using quantitative fluorescent polymerase chain reaction

2006

View full text Add to dashboard Cite

SummaryCertain cellular processes are sensitive to changes in gene dosage. Aneuploidy is deleterious because of an imbalance of gene dosage on a chromosomal scale. Identification, classification and characterization of aneuploidy are therefore important for molecular, population and medical genetics and for a deeper understanding of the mechanisms underlying dosage sensitivity. Notwithstanding recent progress in genomic technologies, limited means are available for detecting and classifying changes in chromosome dose. The development of an inexpensive and scalable karyotyping method would allow rapid detection and characterization of both simple and complex aneuploid types. In addition to the problem of karyotyping, genomic and molecular genetic studies of aneuploids and polyploids are complicated by multiple heterozygous combinations possible at loci present in more than two copies. Quantitative scoring of allele genotypes would enable large-scale population genetic experiments in polyploids, and permit genetic analyses on bulked populations in diploid species. Here, we demonstrate that quantitative fluorescent-polymerase chain reaction (QF-PCR) can be used to simultaneously genotype and karyotype aneuploid and polyploid Arabidopsis thaliana. Comparison of QF-PCR with flow cytometric determination of nuclear DNA content indicated near perfect agreement between the methods, but complete karyotype resolution was only possible using QF-PCR. A complex karyotype, determined by QF-PCR, was validated by comparative genomic hybridization to microarrays. Finally, we screened the progeny of tetraploid individuals and found that more than 25% were aneuploid and that our artificially induced tetraploid strain produced fewer aneuploid individuals than a tetraploid strain isolated from nature.

show abstract

“…FISH and flow cytometric analysis have been the major methods of choice for the characterization of ploidy levels (Burton and Husband. 2001;Galbraith 2004;Henry et al 2005;Roux et al 2003) for genetics studies of polyploid or aneuploid plants. However, flow cytometry is not accurate enough to detect small differences in the genomes of highly polyploid plants and especially in situations where some level of aneuploidy exists because it detects total nuclear DNA content.…”

Section: Discussionmentioning

confidence: 99%

Quantitative real-time PCR to determine allele number for the astringency locus by analysis of a linked marker in Diospyros kaki Thunb

Akagi

Kanzaki

Gao

et al. 2009

Tree Genetics & Genomes

View full text Add to dashboard Cite

Persimmon (Diospyros kaki Thunb.) is a polyploidy fruit tree species of economic importance to East Asia. Natural astringency loss is an important trait in persimmon breeding programs. Quantitative real-time PCR was used to determine the number of AST/ast alleles for fruit astringency in persimmon (D. kaki Thunb.). To this end, the cultivar Jiro was transformed with one or two copies of a gene encoding NADP-dependent sorbitol-6-phosphate dehydrogenase (S6PDH), which was used as a standard for measuring the allele number of a sequenced marker tightly linked to the recessive ast locus for nonastringency. Primers for markers linked to the AST or ast allele were then used to measure the AST to ast ratio directly in the progeny of a full-sib cross. From determination of the AST to ast ratio and the results of the S6PDH copy number, the number of AST and ast alleles at the AST/ast locus was estimated. This research supported the hypothesis that D. kaki is a hexaploid with six AST and/or ast alleles. In addition to the determination of the allelic status of the AST locus, the application of real-time PCR for confirmation of the ploidy level and allelic composition of target genes in autopolyploids or allopolyploids was demonstrated.

show abstract

Cytometry and plant sciences: A personal retrospective

Cited by 20 publications

References 102 publications

A Survey of Flow Cytometry Data Analysis Methods

A Survey of Flow Cytometry Data Analysis Methods

Molecular karyotyping and aneuploidy detection in Arabidopsis thaliana using quantitative fluorescent polymerase chain reaction

Quantitative real-time PCR to determine allele number for the astringency locus by analysis of a linked marker in Diospyros kaki Thunb

Contact Info

Product

Resources

About