Anne Rosenwald
Georgetown University, Biology, Faculty Member
Research Interests: Bioinformatics, Biology, Life Sciences, Medicine, Biomedical Research, and 3 moreYeast, Gene, and Homeostasis
Letter to the Editor methods. We describe here our efforts to assemble a network of like-minded bioinformatics educators both to undertake this process and to identify professional development oppor-tunities for today’s life sciences... more
Letter to the Editor methods. We describe here our efforts to assemble a network of like-minded bioinformatics educators both to undertake this process and to identify professional development oppor-tunities for today’s life sciences educators. Our efforts are geared toward first forming, then growing,
The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) has cultivated a collaborative community model to facilitate the development, dissemination, and assessment of bioinformatics learning resources.
Research Interests: Biology and Dissemination
The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) seeks to promote the use of bioinformatics and data science as a way to teach biology.
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The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods in undergraduate education. Initially focused on microarray technology, but with an eye toward diversification, GCAT is a community working to... more
The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods in undergraduate education. Initially focused on microarray technology, but with an eye toward diversification, GCAT is a community working to improve the education of tomor-row’s life science professionals. GCAT participants have access to affordable microarrays, mi-croarray scanners, free software for data analysis, and faculty workshops. Microarrays provided by GCAT have been used by 141 faculty on 134 campuses, including 21 faculty that serve large numbers of underrepresented minority students. An estimated 9480 undergraduates a year will have access to microarrays by 2009 as a direct result of GCAT faculty workshops. Gains for students include significantly improved comprehension of topics in functional genomics and increased interest in research. Faculty reported improved access to new technology and gains in understanding thanks to their involvement with GCAT. GCAT’s network of sup...
Our BIOME Group worked towards developing a set of learning goals for faculty who plan to launch a CURE based on RNA-Seq data. We also developed a workflow for analysis of either prokaryotic or eukaryotic RNA-Seq data with existing tools.
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Since 2006, the Genomics Education Partnership (GEP; http://gep.wustl.edu) has helped faculty bring genomics research experiences into the undergraduate curriculum.
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We reviewed the materials available on Genome Solver (other lessons here) and described our new python pipeline for examining horizontal gene transfer and a new synteny lesson in detail.
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Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. This pre-lesson introduces the BLAST tool.
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The lesson teaches about synteny or the order of genes along a chromosome, which is useful for looking at orthologous genes between two species or strains.
Genome Solver (GS) began in 2011 as an NSF-funded project for faculty training in basic web-based bioinformatics skills.
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Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in... more
Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. Undergraduates can become skilled annotators, and in the process learn both about genes/genomes and about how to utilize large datasets. Data visualizations provided by a genome browser are essential for manual gene annotation, enabling annotators to quickly evaluate multiple lines of evidence (e.g., sequence similarity, RNA-Seq, gene predictions, repeats). However, creating genome browsers requires extensive computational skills; lack of the expertise required remains a major barrier for many biomedical researchers and educators. To address these challenges, the Genomics Education Partnership (GEP; https://gep.wustl.edu...
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To efficiently and effectively integrate bioinformatics instruction into undergraduate life science curricula, educators would benefit from open access, high-quality learning resources (LRs) for use in existing biology classes.
Presentation of poster 464B at TAGC 2020 Online. Files include a PDF of the poster (TAGC 2020 NIBLSE Incubators poster v4.PDF)
Talk on the NIBLSE Resource Collection and Incubators given at ISMB 2018 in Chicago, Illinois
Research Interests: Mathematics and Incubator
Anticipating the specific needs of diverse teaching and learning contexts is impractical. However, we believe that by focusing on the refinement of materials to support particular bioinformatics learning outcomes, and providing teaching... more
Anticipating the specific needs of diverse teaching and learning contexts is impractical. However, we believe that by focusing on the refinement of materials to support particular bioinformatics learning outcomes, and providing teaching notes to make technical topics more accessible, that incubators can broaden access to bioinformatics topics across the undergraduate curriculum. Each incubator establishes a set of goals and tasks that are specific to the development of a particular learning resource. Participants are recruited and take on small tasks that contribute to the development of the revised materials. Incubator groups work synchronously and asynchronously in an online space hosted by QUBESHub. The products of incubators are made available under a creative commons license and the authors are encouraged to pursue publication in outlets like CourseSource. Incubator Structure and Goals
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The Genome Solver Project began as a way to teach faculty some basic skills in bioinformatics - no coding or scripting. These Lessons also work well in the undergraduate classroom, culminating with an authentic community research project.
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This is a collection of posters from members of the Genomics Education Alliance (GEA) that will be presented at the 2020 BIOME Institute.
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Bioinformatics brings together biology, mathematics, statistics, and computer science to analyze biological sequence information. Anyone with a computer, access to the Internet, and basic training in this field can contribute to genomics... more
Bioinformatics brings together biology, mathematics, statistics, and computer science to analyze biological sequence information. Anyone with a computer, access to the Internet, and basic training in this field can contribute to genomics research. Yet many biology faculty feel they lack training in the use of bioinformatics tools and therefore include little bioinformatics content in their courses. To overcome this challenge, the Genome Solver Project was created to empower undergraduate faculty by offering training and resources for creating hands-on bioinformatics course materials. In this study, we show the results of one survey completed directly after the workshop and a further follow-up survey to gain insight into the impact the workshop had on faculty willingness to include bioinformatics content in their courses and what challenges they still faced. We also measured student performance at five different institutions using a 20-question multiple-choice quiz delivered before a...
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Candida glabrata is an important human fungal pathogen whose incidence continues to rise. Because many clinical isolates are resistant to azole drugs, the drugs of choice to treat such infections are members of the echinocandin family,... more
Candida glabrata is an important human fungal pathogen whose incidence continues to rise. Because many clinical isolates are resistant to azole drugs, the drugs of choice to treat such infections are members of the echinocandin family, although there are increasing reports of resistance to these drugs as well. In efforts to better understand the genetic changes that lead to altered responses to echinocandins, we screened a transposon-insertion library of mutants for strains to identify genes that are important for cellular responses to caspofungin, a member of this drug family. We identified 16 genes that when disrupted caused increased tolerance and 48 genes that when disrupted caused increased sensitivity compared to the wild type parental strain. Four of the genes identified as causing sensitivity are orthologs of Saccharomyces cerevisiae genes encoding proteins important for the cell wall integrity (CWI) pathway. In addition, several other genes are orthologs of the high affinit...
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A molecular genetic approach was undertaken in Saccharomyces cerevisiae to examine the functions of ARL1, encoding a G protein of the Ras superfamily. We show here that ARL1 is an important component of the control of intracellular K+.... more
A molecular genetic approach was undertaken in Saccharomyces cerevisiae to examine the functions of ARL1, encoding a G protein of the Ras superfamily. We show here that ARL1 is an important component of the control of intracellular K+. The arl1 mutant was sensitive to toxic cations, including hygromycin B and other aminoglycoside antibiotics, tetramethylammonium ions, methylammonium ions and protons. The hygromycin-B-sensitive phenotype was suppressed by the inclusion of K+ and complemented by wild-type ARL1 and an allele of ARL1 predicted to be unbound to nucleotide in vivo. The arl1 mutant strain internalized ∼25% more [14C]-methylammonium ion than did the wild type, consistent with hyperpolarization of the plasma membrane. The arl1 strain took up 30-40% less 86Rb+ than did the wild type, showing an inability to regulate K+ import properly, contributing to membrane hyperpolarity. By contrast, K+ and H+ efflux were undisturbed. The loss of ARL1 had no effect on the steady-state lev...
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This research explores best-practices in implementation of course-based undergraduate experiences (CUREs). The work is conducted through the Genomics Education Partnership (GEP) a consortium of over 100 faculty conducting biological... more
This research explores best-practices in implementation of course-based undergraduate experiences (CUREs). The work is conducted through the Genomics Education Partnership (GEP) a consortium of over 100 faculty conducting biological research projects in the area of genomics with a diverse range of undergraduate students in laboratory and classroom settings.
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Chlamydia-infecting bacteriophages, members of the Microviridae family, specifically the Gokushovirinae subfamily, are small (4.5-5 kb) single-stranded circles with 8-10 open-reading frames similar to E. coli phage fX174. Using sequence... more
Chlamydia-infecting bacteriophages, members of the Microviridae family, specifically the Gokushovirinae subfamily, are small (4.5-5 kb) single-stranded circles with 8-10 open-reading frames similar to E. coli phage fX174. Using sequence information found in GenBank, we examined related genes in Chlamydophila pneumoniae and Chlamydiainfecting bacteriophages. The 5 completely sequenced C. pneumoniae strains contain a gene orthologous to a phage gene annotated as the putative replication initiation protein (PRIP, also called VP4), which is not found in any other members of the Chlamydiaceae family sequenced to date. The C. pneumoniae strain infecting koalas, LPCoLN, in addition contains another region orthologous to phage sequences derived from the minor capsid protein gene, VP3. Phylogenetically, the phage PRIP sequences are more diverse than the bacterial PRIP sequences; nevertheless, the bacterial sequences and the phage sequences each cluster together in their own clade. Finally, we found evidence for another Microviridae phage-related gene, the major capsid protein gene, VP1 in a number of other bacterial species and 2 eukaryotes, the woodland strawberry and a nematode. Thus, we find considerable evidence for DNA sequences related to genes found in bacteriophages of the Microviridae family not only in a variety of prokaryotic but also eukaryotic species.
Background: The bacterium Helicobacter pylori is associated with ulcers and the development of gastric cancer. Several genes, including cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA), are associated with increased... more
Background: The bacterium Helicobacter pylori is associated with ulcers and the development of gastric cancer. Several genes, including cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA), are associated with increased gastric cancer risk. Some strains of H. pylori also contain sequences related to bacteriophage phiHP33; however, the significance of these phagerelated sequences remains unknown. Materials and Methods: We assessed the extent to which phiHP33-related sequences are present in 335 H. pylori strains using homology searches then mapped shared genes between phiHP33 and H. pylori strains onto an existing phylogeny. Results: One hundred and twenty-one H. pylori strains contain phage orthologous sequences, and the presence of the phage-related sequences correlates with the presence of CagA and VacA. Mapping of the phage orthologs onto a phylogeny of H. pylori is consistent with the hypothesis that these genes were acquired by horizontal gene transfer. Conclusions: phiHP33 phage orthologous sequences might be of significance in understanding virulence of different H. pylori strains.
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metrically modulated by the two categories, respectively (SOM, S5.1). The activation of the precuneus was higher for hard dominance-solvable games than for easy ones (Fig. 4A and table S10). The activation of the insula was higher for the... more
metrically modulated by the two categories, respectively (SOM, S5.1). The activation of the precuneus was higher for hard dominance-solvable games than for easy ones (Fig. 4A and table S10). The activation of the insula was higher for the highly focal coordination games than for less focal ones (Fig. 4B and table S11). Previous studies also found that precuneus activity increased when the number of planned moves increased (40, 41). The higher demand for memory-related imagery and memory retrieval may explain the greater precuneus activation in hard dominance-solvable games. In highly focal coordination games, the participants may have felt quite strongly that the pool students must notice the same salient feature. This may explain why insula activation correlates with NCI. Participants might have disagreed about which games were difficult. We built a third model to investigate whether the frontoparietal activation correlates with how hard a dominance-solvable game is and whether the...
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Developing effective assessments of student learning is a challenging task for faculty and even more difficult for those in emerging disciplines that lack readily available resources and standards.
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As powerful computational tools and ‘big data’ transform the biological sciences, bioinformatics training is becoming necessary to prepare the next generation of life scientists. Furthermore, because the tools and resources employed in... more
As powerful computational tools and ‘big data’ transform the biological sciences, bioinformatics training is becoming necessary to prepare the next generation of life scientists. Furthermore, because the tools and resources employed in bioinformatics are constantly evolving, bioinformatics learning materials must be continuously improved. In addition, these learning materials need to move beyond today’s typical step-by-step guides to promote deeper conceptual understanding by students. One of the goals of the Network for Integrating Bioinformatics into Life Sciences Education (NIBSLE) is to create, curate, disseminate, and assess appropriate open-access bioinformatics learning resources. Here we describe the evolution, integration, and assessment of a learning resource that explores essential concepts of biological sequence similarity. Pre/post student assessment data from diverse life science courses show significant learning gains. These results indicate that the learning resource...
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A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can... more
A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students’ learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our “formative frustration” hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned fru...
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Bioinformatics is becoming increasingly central to research in the life sciences. However, despite its importance, bioinformatics skills and knowledge are not well integrated in undergraduate biology education. This curricular gap... more
Bioinformatics is becoming increasingly central to research in the life sciences. However, despite its importance, bioinformatics skills and knowledge are not well integrated in undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing genomic research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of life sciences faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists, as wel...
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In Saccharomyces cerevisiae, Arl1 and Ypt6, two small GTP-binding proteins that regulate membrane traffic in the secretory and endocytic pathways, are also necessary for autophagy. To gain information about potential partners of Arl1 and... more
In Saccharomyces cerevisiae, Arl1 and Ypt6, two small GTP-binding proteins that regulate membrane traffic in the secretory and endocytic pathways, are also necessary for autophagy. To gain information about potential partners of Arl1 and Ypt6 specifically in autophagy, we carried out a high copy number suppressor screen to identify genes that when overexpressed suppress the rapamycin sensitivity phenotype of arl1Δ and ypt6Δ strains at 37°. From the screen results, we selected COG4, SNX4, TAX4, IVY1, PEP3, SLT2, and ATG5, either membrane traffic or autophagy regulators, to further test whether they can suppress the specific autophagy defects of arl1Δ and ypt6Δ strains. As a result, we identified COG4, SNX4, and TAX4 to be specific suppressors for the arl1Δ strain, and IVY1 and ATG5 for the ypt6Δ strain. Through this screen, we were able to confirm several membrane traffic and autophagy regulators that have novel relationships with Arl1 and Ypt6 during autophagy.
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Global health education has been expanding rapidly and several universities have created an undergraduate major degree (bachelor's degree) in global heath or global health studies. Because there are currently no national guidelines... more
Global health education has been expanding rapidly and several universities have created an undergraduate major degree (bachelor's degree) in global heath or global health studies. Because there are currently no national guidelines for undergraduate degrees in global health, each of these programs was developed along individual lines. To guide the development of future global health majors, we conducted a systematic review of undergraduate majors in global health. We identified eight programs and invited program directors or representatives to a symposium at the Consortium of Universities for Global Health 2016 conference to review their existing undergraduate major in global health and to discuss lessons learned and recommendations for other colleges and universities seeking to develop undergraduate degrees in global health. We noted significant diversity among the existing programs in terms of required courses, international field experiences, and thesis research projects. In ...
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Macroautophagy/autophagy is a cellular degradation process that sequesters organelles or proteins into a double-membrane structure called the phagophore; this transient compartment matures into an autophagosome, which then fuses with the... more
Macroautophagy/autophagy is a cellular degradation process that sequesters organelles or proteins into a double-membrane structure called the phagophore; this transient compartment matures into an autophagosome, which then fuses with the lysosome or vacuole to allow hydrolysis of the cargo. Factors that control membrane traffic are also essential for each step of autophagy. Here we demonstrate that 2 monomeric GTP-binding proteins in Saccharomyces cerevisiae, Arl1 and Ypt6, which belong to the Arf/Arl/Sar protein family and the Rab family, respectively, and control endosome-trans-Golgi traffic, are also necessary for starvation-induced autophagy under high temperature stress. Using established autophagy-specific assays we found that cells lacking either ARL1 or YPT6, which exhibit synthetic lethality with one another, were unable to undergo autophagy at an elevated temperature, although autophagy proceeds normally at normal growth temperature; specifically, strains lacking one or th...
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Macroautophagy/autophagy is a cellular degradation process that sequesters organelles or proteins into a double-membrane structure called the phagophore; this transient compartment matures into an autophagosome, which then fuses with the... more
Macroautophagy/autophagy is a cellular degradation process that sequesters organelles or proteins into a double-membrane structure called the phagophore; this transient compartment matures into an autophagosome, which then fuses with the lysosome or vacuole to allow hydrolysis of the cargo. Factors that control membrane traffic are also essential for each step of autophagy. Here we demonstrate that 2 monomeric GTP-binding proteins in Saccharomyces cerevisiae, Arl1 and Ypt6, which belong to the Arf/Arl/Sar protein family and the Rab family, respectively, and control endosome-trans-Golgi traffic, are also necessary for starvation-induced autophagy under high temperature stress. Using established autophagy-specific assays we found that cells lacking either ARL1 or YPT6, which exhibit synthetic lethality with one another, were unable to undergo autophagy at an elevated temperature, although autophagy proceeds normally at normal growth temperature; specifically, strains lacking one or th...
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We describe a new technique for analysis of proteins located near fluorescent lipid analogs in intact living cells using the membrane-permeant, photoactivatable probe, 5-[125I]iodonaphthyl-1-azide ([125I]INA). [125I] INA can be activated... more
We describe a new technique for analysis of proteins located near fluorescent lipid analogs in intact living cells using the membrane-permeant, photoactivatable probe, 5-[125I]iodonaphthyl-1-azide ([125I]INA). [125I] INA can be activated directly with UV light or indirectly through excitation of adjacent fluorophores (photosensitizers) with visible light to modify nearby proteins covalently with 125I. In this report we demonstrate that fluorescent phospholipids and sphingolipids containing N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-6-aminocaproic acid serve as appropriate photosensitizers for [125I]INA. Using Chinese hamster ovary fibroblasts, we optimized the labeling conditions with respect to lipid concentration and time of irradiation and then examined the profiles of cellular proteins that were labeled when fluorescent analogs of ceramide, sphingomyelin, and phosphatidic acid were used as photosensitizers in living cells. The use of different fluorescent lipids, which label differen...
Research Interests: Metabolism, Fluorescence Microscopy, Localization, Biological Chemistry, Fluorescent Dyes and Reagents, and 13 moreOptimization, Biological Sciences, Lipids, Animals, Method, Analog, Proteins, Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis, CHEMICAL SCIENCES, Fluorescent Labelling, Cricetinae, fluorescent dyes, and Medical and Health Sciences
Biological research has been transformed in recent years by substan-tial advances in efficient data accumulation. The transcription output for every gene in a genome now can be measured in an afternoon; before it might have taken years.... more
Biological research has been transformed in recent years by substan-tial advances in efficient data accumulation. The transcription output for every gene in a genome now can be measured in an afternoon; before it might have taken years. However, the recent advances in ...
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Autophagy is a cellular degradation process that sequesters components into a double-membrane structure called the autophagosome, which then fuses with the lysosome or vacuole for hydrolysis and recycling of building blocks. Bulk phase... more
Autophagy is a cellular degradation process that sequesters components into a double-membrane structure called the autophagosome, which then fuses with the lysosome or vacuole for hydrolysis and recycling of building blocks. Bulk phase autophagy, also known as macroautophagy, controlled by specific Atg proteins, can be triggered by a variety of stresses, including starvation. Because autophagy relies extensively on membrane traffic to form the membranous structures, factors that control membrane traffic are essential for autophagy. Among these factors, the monomeric GTP-binding proteins that cycle between active and inactive conformations form an important group. In this review, we summarize the functions of the monomeric GTP-binding proteins in autophagy, especially with reference to experiments in Saccharomyces cerevisiae.
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Women on the Verge of a Glass-ceiling Breakdown Beyond Bias and Barriers: Fulfilling the Potential of Women in Academic Science and Engineering. Committee on Maximizing the Potential of Women in Academic Science and Engineering; Committee on Science, Engineering, and Public Policy; National Acade...more
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Incubation of vesicular stomatitis virus-infected cells with short-chain, cell-permeable ceramide (Cer) analogs decreased the rate of viral glycoprotein transport through the Golgi complex and reduced the number of infectious virions... more
Incubation of vesicular stomatitis virus-infected cells with short-chain, cell-permeable ceramide (Cer) analogs decreased the rate of viral glycoprotein transport through the Golgi complex and reduced the number of infectious virions released from cells in a concentration-dependent manner. These effects appeared to be caused directly by Cer, rather than by one of its metabolites. Cer treatment also disrupted the Golgi apparatus within 1 h, although cells treated for up to 24 h with Cer remained viable. Our results suggest that endogenous Cer may modulate secretory protein traffic and that exogenously added Cer analogs may be useful as antiviral agents.