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Your search keyword '"Dudley, Aimée M."' showing total 143 results
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143 results on '"Dudley, Aimée M."'

1. Quantifying yeast colony morphologies with feature engineering from time-lapse photography

Author

Goldschmidt, Andy, Kunert-Graf, James, Scott, Adrian C., Tan, Zhihao, Dudley, Aimée M., and Kutz, J. Nathan

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Baker's yeast (Saccharomyces cerevisiae) is a model organism for studying the morphology that emerges at the scale of multi-cell colonies. To look at how morphology develops, we collect a dataset of time-lapse photographs of the growth of different strains of S. cerevisiae. We discuss the general statistical challenges that arise when using time-lapse photographs to extract time-dependent features. In particular, we show how texture-based feature engineering and representative clustering can be successfully applied to categorize the development of yeast colony morphology using our dataset. The local binary pattern (LBP) from image processing is used to score the surface texture of colonies. This texture score develops along a smooth trajectory during growth. The path taken depends on how the morphology emerges. A hierarchical clustering of the colonies is performed according to their texture development trajectories. The clustering method is designed for practical interpretability; it obtains the best representative colony image for any hierarchical sub-cluster., Comment: 15 pages; 7 pages text, 8 pages tables and figures; 4 figures, 4 tables

Published
2022
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3. Rapid Phenotypic and Genotypic Diversification After Exposure to the Oral Host Niche in Candida albicans

Author

Forche, Anja, Cromie, Gareth, Gerstein, Aleeza C, Solis, Norma V, Pisithkul, Tippapha, Srifa, Waracharee, Jeffery, Eric, Abbey, Darren, Filler, Scott G, Dudley, Aimée M, and Berman, Judith

Subjects
Microbiology, Biological Sciences, Dental/Oral and Craniofacial Disease, Genetics, Human Genome, Aetiology, 2.2 Factors relating to the physical environment, Aneuploidy, Animals, Candida albicans, Candidiasis, DNA, Fungal, Fungal Proteins, Galactokinase, Gene Frequency, Genetic Variation, Genotype, Host-Pathogen Interactions, Loss of Heterozygosity, Male, Mice, Mouth, Phenotype, Sequence Analysis, DNA, aneuploidy, loss of heterozygosity, oropharyngeal candidiasis, hyper-variability, colony phenotype, Developmental Biology, Biochemistry and cell biology
Abstract

In vitro studies suggest that stress may generate random standing variation and that different cellular and ploidy states may evolve more rapidly under stress. Yet this idea has not been tested with pathogenic fungi growing within their host niche in vivo Here, we analyzed the generation of both genotypic and phenotypic diversity during exposure of Candida albicans to the mouse oral cavity. Ploidy, aneuploidy, loss of heterozygosity (LOH), and recombination were determined using flow cytometry and double digest restriction site-associated DNA sequencing. Colony phenotypic changes in size and filamentous growth were evident without selection and were enriched among colonies selected for LOH of the GAL1 marker. Aneuploidy and LOH occurred on all chromosomes (Chrs), with aneuploidy more frequent for smaller Chrs and whole Chr LOH more frequent for larger Chrs. Large genome shifts in ploidy to haploidy often maintained one or more heterozygous disomic Chrs, consistent with random Chr missegregation events. Most isolates displayed several different types of genomic changes, suggesting that the oral environment rapidly generates diversity de novo In sharp contrast, following in vitro propagation, isolates were not enriched for multiple LOH events, except in those that underwent haploidization and/or had high levels of Chr loss. The frequency of events was overall 100 times higher for C. albicans populations following in vivo passage compared with in vitro These hyper-diverse in vivo isolates likely provide C. albicans with the ability to adapt rapidly to the diversity of stress environments it encounters inside the host.

Published
2018

5. Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq

Author

Cromie, Gareth A., Hyma, Katie E., Ludlow, Catherine L., Garmendia-Torres, Cecilia, Gilbert, Teresa L., May, Patrick, Huang, Angela A., Dudley, Aimée M., and Fay, Justin C.

Subjects
Quantitative Biology - Populations and Evolution
Abstract

The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (known as RAD-seq) to genotype a large collection of S. cerevisiae strains, isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and mixtures of alleles from European and Asian populations, indicating an admixed origin for this group. In the context of this global diversity, we demonstrate that a collection of seven strains commonly used in the laboratory encompasses only one quarter of the genetic diversity present in the full collection of strains, underscoring the relatively limited genetic diversity captured by the current set of lab strains. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers.

Published
2013

10. The functional impact of 1,570 SNP-accessible missense variants in humanOTC

Author

Lo, Russell S., primary, Cromie, Gareth A., additional, Tang, Michelle, additional, Teng, Kevin, additional, Owens, Katherine, additional, Sirr, Amy, additional, Kutz, J. Nathan, additional, McLaughlin, Richard N., additional, Morizono, Hiroki, additional, Caldovic, Ljubica, additional, Mew, Nicholas Ah, additional, Gropman, Andrea, additional, and Dudley, Aimée M., additional

Published
2022
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17. Exploiting the Autozygome to Support Previously Published Mendelian Gene-Disease Associations: An Update

Author

Maddirevula, Sateesh, primary, Shamseldin, Hanan E., additional, Sirr, Amy, additional, AlAbdi, Lama, additional, Lo, Russell S., additional, Ewida, Nour, additional, Al-Qahtani, Mashael, additional, Hashem, Mais, additional, Abdulwahab, Firdous, additional, Aboyousef, Omar, additional, Kaya, Namik, additional, Monies, Dorota, additional, Salem, May H., additional, Al Harbi, Naffaa, additional, Aldhalaan, Hesham M., additional, Alzaidan, Hamad, additional, Almanea, Hadeel M., additional, Alsalamah, Abrar K., additional, Al Mutairi, Fuad, additional, Ismail, Samira, additional, Abdel-Salam, Ghada M. H., additional, Alhashem, Amal, additional, Asery, Ali, additional, Faqeih, Eissa, additional, AlQassmi, Amal, additional, Al-Hamoudi, Waleed, additional, Algoufi, Talal, additional, Shagrani, Mohammad, additional, Dudley, Aimée M., additional, and Alkuraya, Fowzan S., additional

Published
2020
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18. Meeting Report on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems

Author

Jarosz, Daniel F. and Dudley, Aimée M.

Subjects
0301 basic medicine, Tel aviv, Ecology, Ecology (disciplines), Model system, Meeting Report, Biology, yeast, QH426-470, 03 medical and health sciences, 030104 developmental biology, Eukaryotic genome, evolution, Genetics, ecology, Molecular Biology, Genetics (clinical)
Abstract

The fourth EMBO-sponsored conference on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems (https://www.embl.de/training/events/2016/EAE16-01/), was held at the EMBL in Heidelberg, Germany, October 19–23, 2016. The conference was organized by Judith Berman (Tel Aviv University), Maitreya Dunham (University of Washington), Jun-Yi Leu (Academia Sinica), and Lars Steinmetz (EMBL Heidelberg and Stanford University). The meeting attracted ∼120 researchers from 28 countries and covered a wide range of topics in the fields of genetics, evolutionary biology, and ecology, with a unifying focus on yeast as a model system. Attendees enjoyed the Keith Haring-inspired yeast florescence microscopy artwork (Figure 1), a unique feature of the meeting since its inception, and the 1 min flash talks that catalyzed discussions at two vibrant poster sessions. The meeting coincided with the 20th anniversary of the publication describing the sequence of the first eukaryotic genome, Saccharomyces cerevisiae. Many of the conference talks focused on important questions about what is contained in the genome, how genomes evolve, and the architecture and behavior of communities of phenotypically and genotypically diverse microorganisms. Here, we summarize highlights of the research talks around these themes. Nearly all presentations focused on novel findings, and we refer the reader to relevant manuscripts that have subsequently been published.

Published
2017

25. Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images

Author

Dudley Aimée M, Birbaumer Mirko, Selinummi Jyrki, Garmendia-Torres Cecilia, Chowdhury Sharif, Äijö Tarmo, Ruusuvuori Pekka, Pelkmans Lucas, and Yli-Harja Olli

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Several algorithms have been proposed for detecting fluorescently labeled subcellular objects in microscope images. Many of these algorithms have been designed for specific tasks and validated with limited image data. But despite the potential of using extensive comparisons between algorithms to provide useful information to guide method selection and thus more accurate results, relatively few studies have been performed. Results To better understand algorithm performance under different conditions, we have carried out a comparative study including eleven spot detection or segmentation algorithms from various application fields. We used microscope images from well plate experiments with a human osteosarcoma cell line and frames from image stacks of yeast cells in different focal planes. These experimentally derived images permit a comparison of method performance in realistic situations where the number of objects varies within image set. We also used simulated microscope images in order to compare the methods and validate them against a ground truth reference result. Our study finds major differences in the performance of different algorithms, in terms of both object counts and segmentation accuracies. Conclusions These results suggest that the selection of detection algorithms for image based screens should be done carefully and take into account different conditions, such as the possibility of acquiring empty images or images with very few spots. Our inclusion of methods that have not been used before in this context broadens the set of available detection methods and compares them against the current state-of-the-art methods for subcellular particle detection.

Published
2010
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29. The State of Systems Genetics in 2017

Author

Baliga, Nitin S., primary, Björkegren, Johan L.M., additional, Boeke, Jef D., additional, Boutros, Michael, additional, Crawford, Nigel P.S., additional, Dudley, Aimée M., additional, Farber, Charles R., additional, Jones, Allan, additional, Levey, Allan I., additional, Lusis, Aldons J., additional, Mak, H. Craig, additional, Nadeau, Joseph H., additional, Noyes, Marcus B., additional, Petretto, Enrico, additional, Seyfried, Nicholas T., additional, Steinmetz, Lars M., additional, and Vonesch, Sibylle C., additional

Published
2017
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34. Research article Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images

Author

Ruusuvuori, Pekka, Äijö, Tarmo, Chowdhury, Sharif, Garmendia-Torres, Cecilia, Selinummi, Jyrki, Birbaumer, Mirko, Dudley, Aimée M., Pelkmans, Lucas, and Yli-Harja, Olli

Subjects
Human Osteosarcoma Cell Line, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, Reference Result, Kernel Density Estimation, Simulated Image, Spot Detection
Abstract

Background Several algorithms have been proposed for detecting fluorescently labeled subcellular objects in microscope images. Many of these algorithms have been designed for specific tasks and validated with limited image data. But despite the potential of using extensive comparisons between algorithms to provide useful information to guide method selection and thus more accurate results, relatively few studies have been performed. Results To better understand algorithm performance under different conditions, we have carried out a comparative study including eleven spot detection or segmentation algorithms from various application fields. We used microscope images from well plate experiments with a human osteosarcoma cell line and frames from image stacks of yeast cells in different focal planes. These experimentally derived images permit a comparison of method performance in realistic situations where the number of objects varies within image set. We also used simulated microscope images in order to compare the methods and validate them against a ground truth reference result. Our study finds major differences in the performance of different algorithms, in terms of both object counts and segmentation accuracies. Conclusions These results suggest that the selection of detection algorithms for image based screens should be done carefully and take into account different conditions, such as the possibility of acquiring empty images or images with very few spots. Our inclusion of methods that have not been used before in this context broadens the set of available detection methods and compares them against the current state-of-the-art methods for subcellular particle detection., BMC Bioinformatics, 11, ISSN:1471-2105

Published
2010

36. Unidirectional P-Body Transport during the Yeast Cell Cycle

Author

Garmendia-Torres, Cecilia, primary, Skupin, Alexander, additional, Michael, Sean A., additional, Ruusuvuori, Pekka, additional, Kuwada, Nathan J., additional, Falconnet, Didier, additional, Cary, Gregory A., additional, Hansen, Carl, additional, Wiggins, Paul A., additional, and Dudley, Aimée M., additional

Published
2014
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39. Quantitative analysis of colony morphology in yeast

Author

Ruusuvuori, Pekka, primary, Lin, Jake, additional, Scott, Adrian C., additional, Tan, Zhihao, additional, Sorsa, Saija, additional, Kallio, Aleksi, additional, Nykter, Matti, additional, Yli-Harja, Olli, additional, Shmulevich, Ilya, additional, and Dudley, Aimée M., additional

Published
2014
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41. High-throughput tetrad analysis

Author

Ludlow, Catherine L, primary, Scott, Adrian C, additional, Cromie, Gareth A, additional, Jeffery, Eric W, additional, Sirr, Amy, additional, May, Patrick, additional, Lin, Jake, additional, Gilbert, Teresa L, additional, Hays, Michelle, additional, and Dudley, Aimée M, additional

Published
2013
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47. Identification and characterization of a drug-sensitive strain enables puromycin-based translational assays in Saccharomyces cerevisiae.

Author

Cary, Gregory A., Yoon, Sung Hwan, Garmendia Torres, Cecilia, Wang, Kathie, Hays, Michelle, Ludlow, Catherine, Goodlett, David R., and Dudley, Aimée M.

Abstract

Puromycin is an aminonucleoside antibiotic with structural similarity to aminoacyl tRNA. This structure allows the drug to bind the ribosomal A site and incorporate into nascent polypeptides, causing chain termination, ribosomal subunit dissociation and widespread translational arrest at high concentrations. In contrast, at sufficiently low concentrations, puromycin incorporates primarily at the C-terminus of proteins. While a number of techniques utilize puromycin incorporation as a tool for probing translational activity in vivo, these methods cannot be applied in yeasts that are insensitive to puromycin. Here, we describe a mutant strain of the yeast Saccharomyces cerevisiae that is sensitive to puromycin and characterize the cellular response to the drug. Puromycin inhibits the growth of yeast cells mutant for erg6∆, pdr1∆ and pdr3∆ (EPP) on both solid and liquid media. Puromycin also induces the aggregation of the cytoplasmic processing body component Edc3 in the mutant strain. We establish that puromycin is rapidly incorporated into yeast proteins and test the effects of puromycin on translation in vivo. This study establishes the EPP strain as a valuable tool for implementing puromycin-based assays in yeast, which will enable new avenues of inquiry into protein production and maturation. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Published
2014
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50. Aneuploidy underlies a multicellular phenotypic switch.

Author

Zhihao Tan, Hays, Michelle, Cromie, Gareth A., Jeffery, Eric W., Scott, Adrian C., Ahyong, Vida, Sirr, Amy, Skupin, Alexander, and Dudley, Aimée M.

Subjects
ANEUPLOIDY, PHENOTYPES, CELLS, DNA, CHROMOSOMES
Abstract

Although microorganisms are traditionally used to investigate unicellular processes, the yeast Saccharomyces cerevisiae has the ability to form colonies with highly complex, multicellular structures. Colonies with the "fluffy" morphology have properties reminiscent of bacterial biofilms and are easily distinguished from the "smooth" colonies typically formed by laboratory strains. We have identified strains that are able to reversibly toggle between the fluffy and smooth colony-forming states. Using a combination of flow cytometry and high-throughput restriction-site associated DNA tag sequencing, we show that this switch is correlated with a change in chromosomal copy number. Furthermore, the gain of a single chromosome is sufficient to switch a strain from the fluffy to the smooth state, and its subsequent loss to revert the strain back to the fluffy state. Because copy number imbalance of six of the 16 5. cerevisiae chromosomes and even a single gene can modulate the switch, our results support the hypothesis that the state switch is produced by dosage-sensitive genes, rather than a general response to altered DNA content. These findings add a complex, multicellular phenotype to the list of molecular and cellular traits known to be altered by aneuploidy and suggest that chromosome missegregation can provide a quick, heritable, and reversible mechanism by which organisms can toggle between phenotypes. [ABSTRACT FROM AUTHOR]

Published
2013
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