Concurrent Scientific Sessions

Subversion of the Host Epithelial Barrier by Pseudomonas aeruginosa

Joanne Engel, University of California, San Francisco

Dr. Joanne Engel will explore the dynamic interactions between the important human opportunistic pathogen Pseudomonas aeruginosa and the host epithelial barrier.  While normal hosts are constantly exposed to this environmental pathogen, in the setting of epithelial barrier damage and immunocompromise, this bacteria unleashes its armamentarium of virulence factors to cause devastating infections that lead to it being the fourth leading cause of hospital-acquired infections. While we have learned about the interactions of pathogens with host cells using in vitro cell culture systems, we are increasingly recognizing the importance of studying these interactions in the context of polarized epithelial cells in 2 dimensional and 3 dimensional contexts.  In this talk, Dr. Engel will describe how using cutting edge microscopy and cell biology (including cool movies and micrographs), her lab has gained unexpected insights into how these systems allow for the study of bacterial biofilms on the surface of epithelial cells, how pathogens subvert and manipulate host cell polarity, and how the host cell utilize these cues to mount an innate immune response.

Emerging Pathogens: How Do We Detect and Track Them?

Peter Gilligan, University of North Carolina and Chair, ASM Professional Practices Committee

Over the past thirty years, dozens of new pathogens have been discovered.  One of them, HIV, has literally changed the world.  In this presentation, we will discuss how new pathogens emerge, how we first recognize them, and then how we track them so we can learn how they move through a population.  We will use 3 specific examples of emerging pathogens, Burkholderia cepacia complex, enterohaemorrhagic Escherichia coli, and community associated Methicillin resistant Staphylococcus aureus to illustrate these issues.  At the end of presentation, the participant we have an enhanced understanding of:

• How new pathogens emerge
• The molecular tools that can be used to track these organisms spread
• How understanding how these organism spread allow for interventions to control these infection

Specific tools that will be discussed will include PCR for detection, nucleic acid sequencing for identification, and pulse field gel electrophoresis and multi-locus sequence typing for understanding their epidemiology.    

Discoveries in Phylogenetically-Driven Genomic Sequencing Projects and its Potential for Your Students

Cheryl Kerfeld, Joint Genome Institute and 2011 American Society for Biochemistry and Molecular Biology Education Awardee

The Joint Genome Institute (JGI) has undertaken a large-scale, phylogenetically driven approach to microbial genome sequencing.  The results, the Genomic Encyclopedia of Bacteria and Archaea (GEBA), are a treasure trove of new insights into bacterial metabolism.  For example, bacterial microcompartments, which were only known from transmission electron micrographs of a few microbial species, are surprisingly widespread; the potential to form microcompartments can be found in more than 20% of all bacterial genomes and in almost every phyla.  Likewise, deep sequencing within a phylum also provides tremendous insight into the genetic basis of ecophysiology.  The cyanobacteria, arguably one of the most diverse groups in terms of lifestyle and morphology, were until GEBA-Cyano poorly sampled in terms of sequencing.  I’ll present results of these comparative genomic analyses and describe ways in which undergraduates and faculty can get involved in analyzing this exciting data using the IMG-ACT system.    

American Academy of Microbiology Presents: E. coli: The Good, the Bad, and the Ugly

Stanley Maloy, San Diego State University, Past-President, ASM and Moderator, AAM FAQ Series

News headlines in the summer of 2011 painted E. coli as vicious bacteria, capable of causing disease and death. But this is only one small part of the story of E. coli; its relationship to human health and the food we eat is much more complex. Not all E. coli are bad - in fact most are not - and some are even beneficial! Despite last year’s outbreak, most experts agree that food safety is better than ever, but we must remain vigilant to protect our food. E. coli has not been domesticated. There are still “wild” strains that have the capacity to cause illness and death and we should expect new strains to emerge that will continue to threaten our health and the safety of our food. But it is important to remember that these are not new challenges - E. coli has accompanied humans and larger animals for millennia. It has become an important part of our gut and, much more recently, a remarkable tool for scientific study. This session will focus on the larger story of E. coli: its role in human health, in food, and even in our understanding of our own biology.

American Academy of Microbiology Presents: Microbes and Oil Spills

Stanley Maloy, San Diego State University, Past-President, ASM and Moderator, AAM FAQ Series

The Deepwater Horizon oil spill, while tragic, shoved microbiology into the limelight. Speckled throughout the media coverage of the spill was references to microbes’ amazing ability to help “clean up” oil spills, but with little to no explanation of exactly what this meant. Can microbes really “eat” oil? How does this work? And what are the possibilities for microorganisms to be used for bioremediation? This session examines the extreme ecosystem of an oil spill and the oil-munching microorganisms that have evolved the tools to degrade one of the most environmentally pernicious compounds, crude oil. It highlights how environmental factors can help, or hinder, this natural microbial remediation process, and describes how environmental microbiologists and microbes can team up to limit the damage of oil spills to the environment. The interactions between marine microorganisms and oil spills offer a remarkable opportunity to illustrate the diversity of microbial metabolism and a chance to highlight microbes’ powerful impact on the environment. 

The Hosthogen Genome in 4D

JJ Miranda, University of California, San Francisco

The idea that genomes intertwine in the three-dimensional space of the nucleus is reshaping our previously linear concepts of gene regulation. Ubiquitous long-range interactions fold genomes into defined conformations. The CCCTC-binding factor (CTCF) has repeatedly emerged as a necessary component for the formation of loops that bridge distal DNA elements on the same and even different chromosomes to regulate transcription. CTCF-binding sites localize mostly to intergenic regions, but also to introns, promoters, and exons. Indeed, these sequences are enriched at chromatin loops genome-wide. This dynamic and regulated genome organization is one of the large-scale cellular phenomena now becoming amenable to high-resolution mechanistic understanding through the concerted efforts of genetics, biochemistry, and structural biology. I will describe our laboratory's efforts at defining the structure and function of CTCF when bound to human host and viral pathogen genomes.

Resolving Community and Metabolic Dynamics in Colorado Plateau Biological Soil Crusts

Aindrila Mukhopadhyay, Lawrence Berkeley National Laboratory

Desert biological soil crusts are simple cyanobacteria-dominated surface soil microbial communities found on all continents in areas with infrequent wetting, often extreme temperatures, and low coverage of vascular plants. They exist for extended periods in a desiccated dormant state, yet rapidly re-boot metabolism within minutes of wetting. They inhabit “the fringe” of habitability with respect to aridity, constituting the world’s largest biofilm. The scale and potential sensitivity of these crusts to alterations in temperature and precipitation frequency/duration make them particularly relevant to understanding the impact of climate change on soil microbial communities and the pathways through which fixed carbon flows. This talk will describe results from an integrated biogeochemical, microbiological, genomic and metabolomic analysis following a pulsed activity event (precipitation). Here, crust samples from the Colorado Plateau were re-wetted under controlled conditions, maintained in a saturated state for 3 diel cycles before a return to dormancy induced by desiccation.   During this process real-time monitoring of CO₂, O₂, H₂, CH₄ and pH was performed with periodic sampling for dissolved anions and cations. Selected time points were analyzed for community gene expression and metabolism to define the synchronization of microbial physiology, biogeochemistry and such pulsed activity events. Integration of these results provides mechanistic insights into the bioenergetics, stress responses, and community adaptations that occur during a wetting cycle with the eventual goal of predicting environmental ‘tipping-points’ for the crust community.

Innate Immune Detection of Pathogenic Bacteria

Victoria Stone, University of Calfornia, Santa Cruz

The mammalian innate immune system must distinguish between pathogenic and nonpathogenic bacteria. Mutations in the innate immune receptors that mediate this specific recognition cause susceptibility to infectious diseases or inflammatory disorders. Many bacterial pathogens use a specialized apparatus called a type III secretion system (T3SS) to attack mammalian host cells by injecting them with toxins. Mammalian cells defend themselves against this attack by recognizing the T3SS and launching an inflammatory response aimed at eliminating the T3SS-expressing pathogen. How T3SS recognition is achieved remains incompletely understood and is a very active area of research, both in
our lab and others. We will discuss what is currently known about T3SS recognition, using the human pathogen Yersinia pseudotuberculosis as a model system. We will end with a discussion of how Y. pseudotuberculosis T3SS components may have evolved to maximize toxin delivery while limiting inflammation.

The Science of the Microbiome: A Renaissance for Microbiology

James Versalovic, Baylor College of Medicine

The NIH-supported Human Microbiome Project and the International Human Microbiome Consortium highlight the enormous potential of human and animal microbiomes for advancing the life sciences. The human microbiome provides many opportunities for discoveries of nutrients, metabolites, diagnostic targets, and new therapies that may have a major impact collectively in medicine. Medical microbiology is being transformed from an area focused on infectious agents and diseases to the awareness of the much broader roles of microbes in mammalian development, physiology, pathophysiology, immunity and metabolism.  New discoveries and applications of these findings by “mining” the microbiome are already creating a renaissance of microbiology and how we harness the functional capacities of microbes to refine approaches to health maintenance, disease prevention, and molecular medicine. We will review major topics and questions in metagenomics and microbiome research and some examples of how the microbiome may shed light on mammalian physiology.