Digital evolution in time-dependent fitness landscapes

We study the response of populations of digital organisms that adapt to a time-varying (periodic) fitness landscape of two oscillating peaks. We corroborate in general predictions from quasi-species theory in dynamic landscapes, such as adaptation to the average fitness landscape at small periods (high frequency) and quasistatic adaptation at large periods (low frequency). We also observe adaptive phase shifts (time tags between a change in the fitness landscape and art adaptive change in the population) that indicate a low-pass filter effect, in agreement with existing theory,. Finally, we witness long-term adaptation to fluctuating environments not anticipated in previous theoretical work

Predicting the Future: Parental Progeny Investment in Response to Environmental Stress Cues

Environmental stressors can severely limit the ability of an organism to reproduce as lifespan is decreased and resources are shifted away from reproduction to survival. Although this is often detrimental to the organism’s reproductive fitness, certain other reproductive stress responses may mitigate this effect by increasing the likelihood of progeny survival in the F1 and subsequent generations. Here we review three means by which these progeny may be conferred a competitive edge as a result of stress encountered in the parental generation: heritable epigenetic modifications to nucleotides and histones, simple maternal investments of cytosolic components, and the partially overlapping phenomenon of terminal investment, which can entail extreme parental investment strategies in either cytosolic components or gamete production. We examine instances of these categories and their ability to subsequently impact offspring fitness and reproduction. Ultimately, without impacting nucleotide sequence, these more labile alterations may shape development, evolution, ecology and even human health, necessitating further understanding and research into the specific mechanisms by which environmental stressors are sensed and elicit a corresponding response in the parental germline

Insights into Arbovirus Evolution and Adaptation from Experimental Studies

Arthropod-borne viruses (arboviruses) are maintained in nature by cycling between vertebrate hosts and haematophagous invertebrate vectors. These viruses are responsible for causing a significant public health burden throughout the world, with over 100 species having the capacity to cause human disease. Arbovirus outbreaks in previously naïve environments demonstrate the potential of these pathogens for expansion and emergence, possibly exacerbated more recently by changing climates. These recent outbreaks, together with the continued devastation caused by endemic viruses, such as Dengue virus which persists in many areas, demonstrate the need to better understand the selective pressures that shape arbovirus evolution. Specifically, a comprehensive understanding of host-virus interactions and how they shape both host-specific and virus-specific evolutionary pressures is needed to fully evaluate the factors that govern the potential for host shifts and geographic expansions. One approach to advance our understanding of the factors influencing arbovirus evolution in nature is the use of experimental studies in the laboratory. Here, we review the contributions that laboratory passage and experimental infection studies have made to the field of arbovirus adaptation and evolution, and how these studies contribute to the overall field of arbovirus evolution. In particular, this review focuses on the areas of evolutionary constraints and mutant swarm dynamics; how experimental results compare to theoretical predictions; the importance of arbovirus ecology in shaping viral swarms; and how current knowledge should guide future questions relevant to understanding arbovirus evolution

An Overview of Carbon Fiber Electrodes Used in Neurochemical Monitoring

Neurochemistry has always been a topic that many scientists are interested in researching because the brain is such a fascinating and complex organ. Electrochemical methods have proven to be a successful tool for scientists to use for their brain-researching endeavors. Many types of probes and analytical devices have been invented and used in conjunction with electrochemical methods over the past several decades to investigate the inner workings of the brain. In particular, the carbon fiber electrode has become a popular device among scientists due to its favorable qualities.The carbon fiber electrode has several unique characteristics to give it an advantage over other techniques. Carbon fiber electrodes have the ability to monitor in a subsecond time frame and record in real time. Because they are so small, carbon fiber electrodes are also able to sample very small environments, such as a single cell or vesicular volumes, where other devices cannot because they are too big. Evidence has shown that carbon fiber electrodes appear to cause less disruptive tissue damage when implanted into a brain than other devices, for instance a microdialysis probe. On top of that, carbon fiber electrodes are also excellent devices for those seeking greater sensitivity and selectivity by making electrode modifications tailored for the analyte of interest. In addition, carbon fiber electrodes provide a wider range of detectable species, again by simply making slight modifications. One can clearly see that the future for neurochemical monitoring lies heavily in the hands of the carbon fiber electrode. Its advantages over other devices make it superior in many aspects. Researchers will no doubt continue to use the carbon fiber electrode and keep improving it to make it suitable for countless more experiments

Influence of Micro-mixing on the Size of Liposomes Self-Assembled from Miscible Liquid Phases

Ethanol injection and variations of it are a class of methods where two miscible phases---one of which contains dissolved lipids---are mixed together leading to the self-assembly of lipid molecules to form liposomes. This method has been suggested, among other applications, for in-situ synthesis of liposomes as drug delivery capsules. However, the mechanism that leads to a specific size selection of the liposomes in solution based self-assembly in general, and in flow-focussing microfluidic devices in particular, has so far not been established. Here we report two aspects of this problem. A simple and easily fabricated device for synthesis of monodisperse unilamellar liposomes in a co-axial flow-focussing microfluidic geometry is presented. We also show that the size of liposomes is dependent on the extent of micro-convective mixing of the two miscible phases. Here, a viscosity stratification induced hydrodynamic instability leads to a gentle micro-mixing which results in larger liposome size than when the streams are mixed turbulently. The results are in sharp contrast to a purely diffusive mixing in macroscopic laminar flow that was believed to occur under these conditions. Further precise quantification of the mixing characteristics should provide the insights to develop a general theory for size selection for the class of ethanol injection methods. This will also lay grounds for obtaining empirical evidence that will enable better control of liposome sizes and for designing drug encapsulation and delivery devices.Comment: 11 pages, 14 Figure

Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages

This study provides the proof of principle that probing the host and the microbe transcriptomes simultaneously is a valuable means to accessing unique information on host pathogen interactions. Our results also underline the extraordinary plasticity of host cell and pathogen responses to infection, and provide a solid framework to further understand the complex mechanisms involved in immunity to M. tuberculosis and in mycobacterial adaptation to different intracellular environments

Tradeoff between short-term and long-term adaptation in a changing environment

We investigate the competition dynamics of two microbial or viral strains that live in an environment that switches periodically between two states. One of the strains is adapted to the long-term environment, but pays a short-term cost, while the other is adapted to the short-term environment and pays a cost in the long term. We explore the tradeoff between these alternative strategies in extensive numerical simulations, and present a simple analytic model that can predict the outcome of these competitions as a function of the mutation rate and the time scale of the environmental changes. Our model is relevant for arboviruses, which alternate between different host species on a regular basis.Comment: 9 pages, 3 figures, PRE in pres

Hepatitis C quasispecies adaptation in the setting of a variable fidelity polymerase

Hepatitis C (HCV) is a virus characterized by an RNA-dependent RNA polymerase that lacks a proofreading mechanism and, as a result, generates a quasispecies. There is emerging evidence that this RNA-dependent RNA polymerase may in fact have variable fidelity. Here, we review the relevant concepts, including fitness landscapes, clonal interference, robustness, selection, adaptation, mutation rates, and their optimization, and provide a unique interpretation of a number of relevant theoretical models, evolving the theory of replicative homeostasis in light of their findings. We suggest that a variable fidelity polymerase can find its own optimal mutation rate, which is governed by the sequence itself and certain population dynamics. We propose that this concept can explain features of viral kinetics and clearance, both spontaneously and following treatment of chronic HCV. We point to evidence that supports this theory and explain how it refines replicative homeostasis and conclude by discussing particular areas of potential research that might augment our understanding of viral host interactions at an individual cellular level

Multidisciplinary Research Leading to Utilization of Extraterrestrial Resources Quarterly Status Report, 1 Jul. - 1 Oct. 1966

Multidisciplinary research activities on rock formations in lunar surface simulatio