Unrelated toxin-antitoxin systems cooperate to induce persistence.

Persisters are drug-tolerant bacteria that account for the majority of bacterial infections. They are not mutants, rather, they are slow-growing cells in an otherwise normally growing population. It is known that the frequency of persisters in a population is correlated with the number of toxin-antitoxin systems in the organism. Our previous work provided a mechanistic link between the two by showing how multiple toxin-antitoxin systems, which are present in nearly all bacteria, can cooperate to induce bistable toxin concentrations that result in a heterogeneous population of slow- and fast-growing cells. As such, the slow-growing persisters are a bet-hedging subpopulation maintained under normal conditions. For technical reasons, the model assumed that the kinetic parameters of the various toxin-antitoxin systems in the cell are identical, but experimental data indicate that they differ, sometimes dramatically. Thus, a critical question remains: whether toxin-antitoxin systems from the diverse families, often found together in a cell, with significantly different kinetics, can cooperate in a similar manner. Here, we characterize the interaction of toxin-antitoxin systems from many families that are unrelated and kinetically diverse, and identify the essential determinant for their cooperation. The generic architecture of toxin-antitoxin systems provides the potential for bistability, and our results show that even when they do not exhibit bistability alone, unrelated systems can be coupled by the growth rate to create a strongly bistable, hysteretic switch between normal (fast-growing) and persistent (slow-growing) states. Different combinations of kinetic parameters can produce similar toxic switching thresholds, and the proximity of the thresholds is the primary determinant of bistability. Stochastic fluctuations can spontaneously switch all of the toxin-antitoxin systems in a cell at once. The spontaneous switch creates a heterogeneous population of growing and non-growing cells, typical of persisters, that exist under normal conditions, rather than only as an induced response. The frequency of persisters in the population can be tuned for a particular environmental niche by mixing and matching unrelated systems via mutation, horizontal gene transfer and selection

Evolution of a genome-encoded bias in amino acid biosynthetic pathways is a potential indicator of amino acid dynamics in the environment.

Overcoming the stress of starvation is one of an organism's most challenging phenotypic responses. Those organisms that frequently survive the challenge, by virtue of their fitness, will have evolved genomes that are shaped by their specific environments. Understanding this genotype-environment-phenotype relationship at a deep level will require quantitative predictive models of the complex molecular systems that link these aspects of an organism's existence. Here, we treat one of the most fundamental molecular systems, protein synthesis, and the amino acid biosynthetic pathways involved in the stringent response to starvation. These systems face an inherent logical dilemma: Building an amino acid biosynthetic pathway to synthesize its product-the cognate amino acid of the pathway-may require that very amino acid when it is no longer available. To study this potential "catch-22," we have created a generic model of amino acid biosynthesis in response to sudden starvation. Our mathematical analysis and computational results indicate that there are two distinctly different outcomes: Partial recovery to a new steady state, or full system failure. Moreover, the cell's fate is dictated by the cognate bias, the number of cognate amino acids in the corresponding biosynthetic pathway relative to the average number of that amino acid in the proteome. We test these implications by analyzing the proteomes of over 1,800 sequenced microbes, which reveals statistically significant evidence of low cognate bias, a genetic trait that would avoid the biosynthetic quandary. Furthermore, these results suggest that the pattern of cognate bias, which is readily derived by genome sequencing, may provide evolutionary clues to an organism's natural environment

IL-6 controls susceptibility to helminth infection by impeding Th2 responsiveness and altering the Treg phenotype in vivo

IL-6 plays a pivotal role in favoring T-cell commitment toward a Th17 cell rather than Treg-cell phenotype, as established through in vitro model systems. We predicted that in the absence of IL-6, mice infected with the gastrointestinal helminth Heligmosomoides polygyrus would show reduced Th17-cell responses, but also enhanced Treg-cell activity and consequently greater susceptibility. Surprisingly, worm expulsion was markedly potentiated in IL-6-deficient mice, with significantly stronger adaptive Th2 responses in both IL-6−/− mice and BALB/c recipients of neutralizing anti-IL-6 monoclonal Ab. Although IL-6-deficient mice showed lower steady-state Th17-cell levels, IL-6-independent Th17-cell responses occurred during in vivo infection. We excluded the Th17 response as a factor in protection, as Ab neutralization did not modify immunity to H. polygyrus infection in BALB/c mice. Resistance did correlate with significant changes to the associated Treg-cell phenotype however, as IL-6-deficient mice displayed reduced expression of Foxp3, Helios, and GATA-3, and enhanced production of cytokines within the Treg-cell population. Administration of an anti-IL-2:IL-2 complex boosted Treg-cell proportions in vivo, reduced adaptive Th2 responses to WT levels, and fully restored susceptibility to H. polygyrus in IL-6-deficient mice. Thus, in vivo, IL-6 limits the Th2 response, modifies the Treg-cell phenotype, and promotes host susceptibility following helminth infection

THE ART OF WAR: PATTERNS AND MECHANISMS UNDERLYING PREDATOR-INDUCED PLASTICITY OF AMPHIBIANS

Organisms often employ phenotypic plasticity as a strategy to cope with variable environments. This is particularly true of predation threats, wherein prey induce defenses to reduce detection or capture by predators. In order to produce appropriate defenses, prey must be able to discern useful information from environmental cues. Despite the pervasive production of inducible defenses, we understand very little of how much useful information is conveyed to organisms in cues, or how the subsequent plastic responses vary within groups of organisms. To address the need for comparative studies of phenotypic plasticity, we sought to examine morphological and behavioral defenses of five species of Ambystoma salamander larvae in response to larval dragonfly (Anax junius) chemical cues in a common garden environment. Dragonfly cues induced relatively few morphological changes across species. Likewise, salamanders did not vary in their refuge use during the experiment, though several species reduced their activity in the presence of predators early in development. Our results suggest that behavioral and morphological defenses in Ambystoma are highly variable among species and the genus appears to be less plastic than tadpoles and other salamander species. To understand what types of information prey are capable of responding to in their environment, we raised grey treefrog tadpoles (Hyla verisciolor) in the presence of cues isolated from different stages of an attack sequence by larval dragonflies (A. junius) or larval dragonflies THE ART OF WAR: PATTERNS AND MECHANISMS UNDERLYING PREDATOR-INDUCED PLASTICITY OF AMPHIBIANS Heather Michelle Shaffery, M.S. University of Pittsburgh, 2013 iv consuming different combinations of grey treefrog tadpoles and snails (Helisoma trivolvis) across different temporal sequences. When exposed to a predator consuming grey treefrogs, tadpoles reduced their activity, increased their hiding behavior, and induced deeper tails. As we exposed prey to more types of cues from an attack sequence, they also increased tail depth and hiding behavior but did not change their activity. Additionally, treefrog tadpoles generally increased their defense as the biomass of treefrogs consumed increased, regardless of whether heterospecifics were being consumed. Our results suggest that treefrogs can gain cue information from all portions of an attack sequence, and that both temporal patterns of feeding and diet content of predators influence the type and magnitude of induced prey defenses

The U.S. Gulf of Mexico Pink Shrimp, Farfantepenaeus duorarum, Fishery: 50 Years of Commercial Catch Statistics

U.S. Gulf of Mexico, pink shrimp, Farfantepenaeus duorarum, catch statistics have been collected by NOAA’s National Marine Fisheries Service, or its predecessor agency, for over 50 years. Recent events, including hurricanes and oil spills within the ecosystem of the fishery, have shown that documentation of these catch data is of primary importance. Fishing effort for this stock has fluctuated over the 50-year period analyzed, ranging from 3,376 to 31,900 days fished, with the most recent years on record, 2008 and 2009, exhibiting declines up to 90% relative to the high levels recorded in the mid 1990’s. Our quantification of F. duorarum landings and catch rates (CPUE) indicates catch have been below the long-term average of about 12 million lb for all of the last 10 years on record. In contrast to catch and effort, catch rates have increased in recent years, with record CPUE levels measured in 2008 and 2009, of 1,340 and 1,144 lb per day fished, respectively. Our regression results revealed catch was dependent upon fishing effort (F=98.48df=1, 48, p<0.001, r2=0.67), (Catch=1,623,378 + (520) × (effort)). High CPUE’s measured indicate stocks were not in decline prior to 2009, despite the decline in catch. The decrease in catch is attributed in large part to low effort levels caused by economical and not biological or habitat related conditions. Future stock assessments using these baseline data will provide further insights and management advice concerning the Gulf of Mexi

The design and evolution of the beta two-stage-to-orbit horizontal takeoff and landing launch system

The Beta launch system was originally conceived in 1986 as a horizontal takeoff and landing, fully reusable, two-stage-to-orbit, manned launch vehicle to replace the Shuttle. It was to be capable of delivering a 50,000 lb. payload to low polar orbit. The booster propulsion system consisted of JP fueled turbojets and LH fueled ramjets mounted in pods in an over/under arrangement, and a single LOX/LH fueled SSME rocket. The second stage orbiter, which staged at Mach 8, was powered by an SSME rocket. A major goal was to develop a vehicle design consistent with near term technology. The vehicle design was completed with a GLOW of approximately 2,000,000 lbs. All design goals were met. Since then, interest has shifted to the 10,000 lbs. to low polar orbit payload class. The original Beta was down-sized to meet this payload class. The GLOW of the down-sized vehicle was approximately 1,000,000 lbs. The booster was converted to exclusively air-breathing operation. Because the booster depends on conventional air-breathing propulsion only, the staging Mach number was reduced to 5.5. The orbiter remains an SSME rocket-powered stage

The Role of Tacit Routines in Coordinating Activity

We explore the influence of tacit routines in obtaining coordination. Our experiment uses simple laboratory "firms," in which we interfere with one kind of firm's ability to develop tacit routines. Thus, our firms vary in the degree to which they rely on this kind of knowledge – instead of other, explicit, mechanisms – for obtaining coordination. We find that interfering with the development of tacit routines harms firms’ ability to coordinate. We then explore the extent to which firms are able to transfer their ability to coordinate activity, either to a new domain or to new members. Our results indicate that tacit routines transfer more easily than other mechanisms to a new, but closely related, domain. However, routine-based firms perform slightly worse in their ability to incorporate new members

Accessing Rydberg-dressed interactions using many-body Ramsey dynamics

We demonstrate that Ramsey spectroscopy can be used to observe Rydberg-dressed interactions. In contrast to many prior proposals, our scheme operates comfortably within experimentally measured lifetimes, and accesses a regime where quantum superpositions are crucial. The key idea is to build a spin-1/2 from one level that is Rydberg-dressed and another that is not. These levels may be hyperfine or long-lived electronic states. An Ising spin model governs the Ramsey dynamics, for which we derive an exact solution. Due to the structure of Rydberg interactions, the dynamics differs significantly from that in other spin systems. As one example, spin echo can increase the rate at which coherence decays. The results also apply to bare (undressed) Rydberg states as a special case, for which we quantitatively reproduce recent ultrafast experiments without fitting

Simulation of Tail Weight Distributions in Biological Year 1986–2006 Landings of Brown Shrimp, Farfantepenaeus aztecus, from the Northern Gulf of Mexico Fishery

Size distribution within re- ported landings is an important aspect of northern Gulf of Mexico penaeid shrimp stock assessments. It reflects shrimp population characteristics such as numerical abundance of various sizes, age structure, and vital rates (e.g. recruitment, growth, and mortality), as well as effects of fishing, fishing power, fishing practices, sampling, size-grading, etc. The usual measure of shrimp size in archived landings data is count (C) the number of shrimp tails (abdomen or edible portion) per pound (0.4536 kg). Shrimp are marketed and landings reported in pounds within tail count categories. Statistically, these count categories are count class intervals or bins with upper and lower limits expressed in C. Count categories vary in width, overlap, and frequency of occurrence within the landings. The upper and lower limits of most count class intervals can be transformed to lower and upper limits (respectively) of class intervals expressed in pounds per shrimp tail, w, the reciprocal of C (i.e. w = 1/C). Age based stock assessments have relied on various algorithms to estimate numbers of shrimp from pounds landed within count categories. These algorithms required un- derlying explicit or implicit assumptions about the distribution of C or w. However, no attempts were made to assess the actual distribution of C or w. Therefore, validity of the algorithms and assumptions could not be determined. When different algorithms were applied to landings within the same size categories, they produced different estimates of numbers of shrimp. This paper demonstrates a method of simulating the distribution of w in reported biological year landings of shrimp. We used, as examples, landings of brown shrimp, Farfantepenaeus aztecus, from the northern Gulf of Mexico fishery in biological years 1986–2006. Brown shrimp biological year, Ti, is defined as beginning on 1 May of the same calendar year as Ti and ending on 30 April of the next calendar year, where subscript i is the place marker for biological year. Biological year landings encompass most if not all of the brown shrimp life cycle and life span. Simulated distributions of w reflect all factors influencing sizes of brown shrimp in the landings within a given biological year. Our method does not require a priori assumptions about the parent distributions of w or C, and it takes into account the variability in width, overlap, and frequency of occurrence of count categories within the landings. Simulated biological year distributions of w can be transformed to equivalent distributions of C. Our method may be useful in future testing of previously applied algorithms and development of new estimators based on statistical estimation theory and the underlying distribution of w or C. We also examine some applications of biological year distributions of w, and additional variables derived from them