Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing

Background: In the event of biocrimes or infectious disease outbreaks, high-resolution genetic characterization for identifying the agent and attributing it to a specific source can be crucial for an effective response. Until recently, in-depth genetic characterization required expensive and time-consuming Sanger sequencing of a few strains, followed by genotyping of a small number of marker loci in a panel of isolates at or by gel-based approaches such as pulsed field gel electrophoresis, which by necessity ignores most of the genome. Next-generation, massively parallel sequencing (MPS) technology (specifically the Applied Biosystems sequencing by oligonucleotide ligation and detection (SOLiD™) system) is a powerful investigative tool for rapid, cost-effective and parallel microbial whole-genome characterization. Results: To demonstrate the utility of MPS for whole-genome typing of monomorphic pathogens, four Bacillus anthracis and four Yersinia pestis strains were sequenced in parallel. Reads were aligned to complete reference genomes, and genomic variations were identified. Resequencing of the B. anthracis Ames ancestor strain detected no false-positive single-nucleotide polymorphisms (SNPs), and mapping of reads to the Sterne strain correctly identified 98% of the 133 SNPs that are not clustered or associated with repeats. Three geographically distinct B. anthracis strains from the A branch lineage were found to have between 352 and 471 SNPs each, relative to the Ames genome, and one strain harbored a genomic amplification. Sequencing of four Y. pestis strains from the Orientalis lineage identified between 20 and 54 SNPs per strain relative to the CO92 genome, with the single Bolivian isolate having approximately twice as many SNPs as the three more closely related North American strains. Coverage plotting also revealed a common deletion in two strains and an amplification in the Bolivian strain that appear to be due to insertion element-mediated recombination events. Most private SNPs (that is, a, variant found in only one strain in this set) selected for validation by Sanger sequencing were confirmed, although rare falsepositive SNPs were associated with variable nucleotide tandem repeats. Conclusions: The high-throughput, multiplexing capability, and accuracy of this system make it suitable for rapid whole-genome typing of microbial pathogens during a forensic or epidemiological investigation. By interrogating nearly every base of the genome, rare polymorphisms can be reliably discovered, thus facilitating high-resolution strain tracking and strengthening forensic attribution

Phenotypic and Genetic Divergence among Poison Frog Populations in a Mimetic Radiation

The evolution of Müllerian mimicry is, paradoxically, associated with high levels of diversity in color and pattern. In a mimetic radiation, different populations of a species evolve to resemble different models, which can lead to speciation. Yet there are circumstances under which initial selection for divergence under mimicry may be reversed. Here we provide evidence for the evolution of extensive phenotypic divergence in a mimetic radiation in Ranitomeya imitator, the mimic poison frog, in Peru. Analyses of color hue (spectral reflectance) and pattern reveal substantial divergence between morphs. However, we also report that there is a “transition-zone� with mixed phenotypes. Analyses of genetic structure using microsatellite variation reveals some differentiation between populations, but this does not strictly correspond to color pattern divergence. Analyses of gene flow between populations suggest that, while historical levels of gene flow were low, recent levels are high in some cases, including substantial gene flow between some color pattern morphs. We discuss possible explanations for these observations

Adsorptive uptake of water by semisolid secondary organic aerosols

Aerosol climate effects are intimately tied to interactions with water. Here we combine hygroscopicity measurements with direct observations about the phase of secondary organic aerosol (SOA) particles to show that water uptake by slightly oxygenated SOA is an adsorption-dominated process under subsaturated conditions, where low solubility inhibits water uptake until the humidity is high enough for dissolution to occur. This reconciles reported discrepancies in previous hygroscopicity closure studies. We demonstrate that the difference in SOA hygroscopic behavior in subsaturated and supersaturated conditions can lead to an effect up to about 30% in the direct aerosol forcinghighlighting the need to implement correct descriptions of these processes in atmospheric models. Obtaining closure across the water saturation point is therefore a critical issue for accurate climate modeling.Peer reviewe

A private ultraviolet channel in visual communication.

Although private communication is considered an important diversifying force in evolution, there is little direct behavioural evidence to support this notion. Here, we show that ultraviolet (UV) signalling in northern swordtails (Xiphophorus) affords a channel for communication that is not accessible to their major predator, Astyanax mexicanus, the Mexican tetra. Laboratory and field behavioural experiments with swordtails (X. nigrensis) and predators (A. mexicanus) demonstrate that male UV ornamentation significantly increases their attractiveness to females but not to this predator, which is less sensitive to UV. UV reflectance among swordtail species correlates positively with tetra densities across habitats, and visual contrast estimates suggest that UV signals are highly conspicuous to swordtails in their natural environment. Cross-species comparisons also support the hypothesis that natural selection drives the use of UV communication. We compared two species, one with high (X. nigrensis) and one with low (X. malinche) Mexican tetra densities. Xiphophorus nigrensis males reflect significantly more UV than X. malinche, exhibit significant UV sexual dimorphism, and UV is a salient component of the sexual communication system. In X. malinche, however, males reflect minimally in the UV, there is no UV sexual dimorphism, and UV does not play a part in its communication system

Is UV ornamentation an amplifier in swordtails

ABSTRACT 9

CD4(+) T Cells and Toll-Like Receptors Recognize Salmonella Antigens Expressed in Bacterial Surface Organelles

A better understanding of immunity to infection is revealed from the characteristics of microbial ligands recognized by host immune responses. Murine infection with the intracellular bacterium Salmonella generates CD4(+) T cells that specifically recognize Salmonella proteins expressed in bacterial surface organelles such as flagella and membrane vesicles. These natural Salmonella antigens are also ligands for Toll-like receptors (TLRs) or avidly associated with TLR ligands such as lipopolysaccharide (LPS). PhoP/PhoQ, a regulon controlling Salmonella virulence and remodeling of LPS to resist innate immunity, coordinately represses production of surface-exposed antigens recognized by CD4(+) T cells and TLRs. These data suggest that genetically coordinated surface modifications may provide a growth advantage for Salmonella in host tissues by limiting both innate and adaptive immune recognition

Localizing Brain Regions Associated with Female Mate Preference Behavior in a Swordtail

Female mate choice behavior is a critical component of sexual selection, yet identifying the neural basis of this behavior is largely unresolved. Previous studies have implicated sensory processing and hypothalamic brain regions during female mate choice and there is a conserved network of brain regions (Social Behavior Network, SBN) that underlies sexual behaviors. However, we are only beginning to understand the role this network has in pre-copulatory female mate choice. Using in situ hybridization, we identify brain regions associated with mate preference in female Xiphophorus nigrensis, a swordtail species with a female choice mating system. We measure gene expression in 10 brain regions (linked to sexual behavior, reward, sensory integration or other processes) and find significant correlations between female preference behavior and gene expression in two telencephalic areas associated with reward, learning and multi-sensory processing (medial and lateral zones of the dorsal telencephalon) as well as an SBN region traditionally associated with sexual response (preoptic area). Network analysis shows that these brain regions may also be important in mate preference and that correlated patterns of neuroserpin expression between regions co-vary with differential compositions of the mate choice environment. Our results expand the emerging network for female preference from one that focused on sensory processing and midbrain sexual response centers to a more complex coordination involving forebrain areas that integrate primary sensory processing and reward.This work was funded by research fellowships from the University of Texas (UT) Ecology, Evolution and Behavior graduate program (to RYW), along with a Reeder Fellowship, UT SRA, UT StartUp funds, National Science Foundation SGER IOS-0813742 and IOS-0843000 (to MEC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o

Multiple Origins of Aposematism in the Poison Frog Family

To my parents, Ernesto and Sara, for being there every time To Natalia and Ignacio for smiling, completing, and enlightening my life To the Poison Frogs for teaching me about humilityAcknowledgements This dissertation is the result of my interaction with great people at all levels during my career as undergraduate and graduate student. I thank Luis Coloma for his insights in the poison frogs and his uncommon knowledge into the Neotropical natural history of frogs. I thank the David Cannatella and the Cannatella Lab (past and present) for the companionship, support, and criticisms during my years as a graduate student. I thank Art Woods for a complete and clear introduction to experimental physiology; Richard Ree for sharing his insights in historical biogeography; Janalee Caldwell and Kyle Summers for sharing their knowledge on the biology of poison frogs. I thank N. Biani, J. Brown, E. Lemmon, G. Pauly, and B. Symula for suggestions about data analysis and proofreading my texts. I thank to my friends in EEB for their support, camaraderie, and amity during my years in Texas. I thank specially to Catalina, Samraat, Barrett, Naira, Juanita, Carlos