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Author

Gretchen L. Kiser

Other affiliations: California Institute of Technology, GE Healthcare, Mayo Clinic  ...read more
Bio: Gretchen L. Kiser is an academic researcher from Amersham plc. The author has contributed to research in topics: Substantia nigra & Gene. The author has an hindex of 15, co-authored 18 publications receiving 1794 citations. Previous affiliations of Gretchen L. Kiser include California Institute of Technology & GE Healthcare.

Papers
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Journal ArticleDOI
TL;DR: It is concluded that the checkpoint in budding yeast consists of overlapping S-phase and G2-phase pathways that respond to incomplete DNA replication and/or DNA damage and cause arret of cells before mitosis.
Abstract: In eukaryotes a cell-cycle control termed a checkpoint causes arrest in the S or G2 phases when chromosomes are incompletely replicated or damaged. Previously, we showed in budding yeast that RAD9 and RAD17 are checkpoint genes required for arrest in the G2 phase after DNA damage. Here, we describe a genetic strategy that identified four additional checkpoint genes that act in two pathways. Both classes of genes are required for arrest in the G2 phase after DNA damage, and one class of genes is also required for arrest in S phase when DNA replication is incomplete. The Gz-specific genes include MEC3 (for mitosis entry checkpoint), RAD9, RAD17, and RAD24. The genes common to both S phase and G2 phase pathways are MECl and MEC2. The MEC2 gene proves to be identical to the RAD53 gene. Checkpoint mutants were identified by their interactions with a temperature-sensitive allele of the cell division cycle gene CDC13-, cdcl3 mutants arrested in G2 and survived at the restrictive temperature, whereas all cdcl3 checkpoint double mutants failed to arrest in G2 and died rapidly at the restrictive temperature. The cell-cycle roles of the RAD and MEC genes were examined by combination of rad and mec mutant alleles with 10 cdc mutant alleles that arrest in different stages of the cell cycle at the restrictive temperature and by the response of rad and mec mutant alleles to DNA damaging agents and to hydroxyurea, a drug that inhibits DNA replication. We conclude that the checkpoint in budding yeast consists of overlapping S-phase and G2-phase pathways that respond to incomplete DNA replication and/or DNA damage and cause arrest of cells before mitosis.

773 citations

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TL;DR: The External RNA Controls Consortium (ERCC) is developing commonly agreed-upon and tested controls for use in expression assays, a true industry-wide standard control.
Abstract: Standard controls and best practice guidelines advance acceptance of data from research, preclinical and clinical laboratories by providing a means for evaluating data quality. The External RNA Controls Consortium (ERCC) is developing commonly agreed-upon and tested controls for use in expression assays, a true industry-wide standard control.

337 citations

Journal ArticleDOI
TL;DR: It is demonstrated that cytosolic domains of human CFTR are sufficient to induce inhibition of rat epithelial Na+ currents (rENaC) when coexpressed in Xenopus oocytes and stimulated with 3‐isobutyl‐1‐methylxanthine (IBMX).

151 citations

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TL;DR: Microarray analysis and integrative data mining were used to uncover pathways implicated in the progression of changes in dopaminergic neurons after MPTP administration and disclosed dysregulation of genes in three main areas related to neuronal function.
Abstract: Parkinson's disease pathogenesis proceeds through several phases, culminating in the loss of dopaminergic neurons of the substantia nigra (SN). Although the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of oxidative SN injury is frequently used to study degeneration of dopaminergic neurons in mice and non-human primates, an understanding of the temporal sequence of molecular events from inhibition of mitochondrial complex 1 to neuronal cell death is limited. Here, microarray analysis and integrative data mining were used to uncover pathways implicated in the progression of changes in dopaminergic neurons after MPTP administration. This approach enabled the identification of small, yet consistently significant, changes in gene expression within the SN of MPTP-treated animals. Such an analysis disclosed dysregulation of genes in three main areas related to neuronal function: cytoskeletal stability and maintenance, synaptic integrity, and cell cycle and apoptosis. The discovery and validation of these alterations provide molecular evidence for an evolving cascade of injury, dysfunction, and cell death.

99 citations

Journal ArticleDOI
TL;DR: It is demonstrated that relatively few genes' expression levels can effectively distinguish between disease and control brains, and several interesting patterns of gene expression are identified that illuminate pathogenic cascades in Parkinson's disease.

98 citations


Cited by
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Journal ArticleDOI
TL;DR: New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments, and the voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline.
Abstract: New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods.

4,475 citations

Journal ArticleDOI
21 May 2015-Cell
TL;DR: This work has developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing, which shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays.

2,894 citations

Journal ArticleDOI
23 Jun 1995-Science
TL;DR: A gene, ATM, that is mutated in the autosomal recessive disorder ataxia telangiectasia was identified by positional cloning on chromosome 11q22-23 and encoded a putative protein that is similar to several yeast and mammalian phosphatidylinositol-3' kinases that are involved in mitogenic signal transduction, meiotic recombination, and cell cycle control.
Abstract: A gene, ATM, that is mutated in the autosomal recessive disorder ataxia telangiectasia (AT) was identified by positional cloning on chromosome 11q22-23. AT is characterized by cerebellar degeneration, immunodeficiency, chromosomal instability, cancer predisposition, radiation sensitivity, and cell cycle abnormalities. The disease is genetically heterogeneous, with four complementation groups that have been suspected to represent different genes. ATM, which has a transcript of 12 kilobases, was found to be mutated in AT patients from all complementation groups, indicating that it is probably the sole gene responsible for this disorder. A partial ATM complementary DNA clone of 5.9 kilobases encoded a putative protein that is similar to several yeast and mammalian phosphatidylinositol-3' kinases that are involved in mitogenic signal transduction, meiotic recombination, and cell cycle control. The discovery of ATM should enhance understanding of AT and related syndromes and may allow the identification of AT heterozygotes, who are at increased risk of cancer.

2,729 citations

Journal ArticleDOI
16 Dec 1994-Science
TL;DR: New insights in understanding of the cell cycle reveal how fidelity is normally achieved by the coordinated activity of cyclin-dependent kinases, checkpoint controls, and repair pathways and how this fidelity can be abrogated by specific genetic changes.
Abstract: Multiple genetic changes occur during the evolution of normal cells into cancer cells. This evolution is facilitated in cancer cells by loss of fidelity in the processes that replicate, repair, and segregate the genome. Recent advances in our understanding of the cell cycle reveal how fidelity is normally achieved by the coordinated activity of cyclin-dependent kinases, checkpoint controls, and repair pathways and how this fidelity can be abrogated by specific genetic changes. These insights suggest molecular mechanisms for cellular transformation and may help to identify potential targets for improved cancer therapies.

2,514 citations

Journal ArticleDOI
TL;DR: This article proposes an elegantly simple multi-seed strategy, called seed-and-vote, for mapping reads to a reference genome, which uses a relatively large number of short seeds extracted from each read and allows all the seeds to vote on the optimal location.
Abstract: Read alignment is an ongoing challenge for the analysis of data from sequencing technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and-vote, for mapping reads to a reference genome. The new strategy chooses the mapped genomic location for the read directly from the seeds. It uses a relatively large number of short seeds (called subreads) extracted from each read and allows all the seeds to vote on the optimal location. When the read length is <160 bp, overlapping subreads are used. More conventional alignment algorithms are then used to fill in detailed mismatch and indel information between the subreads that make up the winning voting block. The strategy is fast because the overall genomic location has already been chosen before the detailed alignment is done. It is sensitive because no individual subread is required to map exactly, nor are individual subreads constrained to map close by other subreads. It is accurate because the final location must be supported by several different subreads. The strategy extends easily to find exon junctions, by locating reads that contain sets of subreads mapping to different exons of the same gene. It scales up efficiently for longer reads.

2,228 citations