scholarly journals High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae

2019 ◽  
Author(s):  
Vincent J. Fasanello ◽  
Ping Liu ◽  
Carlos A. Botero ◽  
Justin C. Fay
Keyword(s):  
Saccharomyces Cerevisiae ◽  
High Throughput ◽  
Experimental Evolution ◽  
Evolutionary Dynamics ◽  
Central Component ◽  
Evolution System ◽  
High Throughput Analysis ◽  
Wide Range ◽  
Asexual Populations ◽  
Complex Phenomena

AbstractBackgroundExperimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in Saccharomyces cerevisiae that utilizes genetic barcoding to overcome this challenge.ResultsWe first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics.ConclusionsOur experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.

scholarly journals High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10118
Author(s):  
Vincent J. Fasanello ◽  
Ping Liu ◽  
Carlos A. Botero ◽  
Justin C. Fay
Keyword(s):  
Saccharomyces Cerevisiae ◽  
High Throughput ◽  
Experimental Evolution ◽  
Evolutionary Dynamics ◽  
Central Component ◽  
Evolution System ◽  
High Throughput Analysis ◽  
Wide Range ◽  
Asexual Populations ◽  
Complex Phenomena

Background Experimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in Saccharomyces cerevisiae that utilizes genetic barcoding to overcome this challenge. Results We first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics. Conclusions Our experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.

scholarly journals Dung beetles as vertebrate samplers – a test of high throughput analysis of dung beetle iDNA

2021 ◽  
Author(s):  
Rosie Drinkwater ◽  
Elizabeth L. Clare ◽  
Arthur Y. C. Chung ◽  
Stephen J. Rossiter ◽  
Eleanor M. Slade
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Dung Beetle ◽  
Blood Feeding ◽  
Preliminary Evidence ◽  
Dung Beetles ◽  
High Throughput Analysis ◽  
Humid Forest ◽  
Terrestrial Vertebrates ◽  
Wide Range

AbstractThe application of environmental DNA (eDNA) sampling in biodiversity surveys has gained widespread acceptance, especially in aquatic systems where free eDNA can be readily collected by filtering water. In terrestrial systems, eDNA-based approaches for assaying vertebrate biodiversity have tended to rely on blood-feeding invertebrates, including leeches and mosquitoes (termed invertebrate-derived DNA or iDNA). However, a key limitation of using blood-feeding taxa as samplers is that they are difficult to trap, and, in the case of leeches, are highly restricted to humid forest ecosystems. Dung beetles (superfamily Scarabaeoidea) feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps; are globally distributed; and also occur in a wide range of biomes, allowing mammal diversity to be compared across habitats. In this exploratory study, we test the potential utility of dung beetles as vertebrate samplers by sequencing the mammal DNA contained within their guts. First, using a controlled feeding experiment, we show that mammalian DNA can be retrieved from the guts of large dung beetles (Catharsius renaudpauliani) for up to 10 hours after feeding. Second, by combining high-throughput sequencing of a multi-species assemblage of dung beetles with PCR replicates, we show that multiple mammal taxa can be identified with high confidence. By providing preliminary evidence that dung beetles can be used as a source of mammal DNA, our study highlights the potential for this widespread group to be used in future biodiversity monitoring surveys.

scholarly journals High-throughput analysis of endogenous fruit glycosyl hydrolases using a novel chromogenic hydrogel substrate assay

2017 ◽  
Vol 9 (8) ◽  
pp. 1242-1247 ◽  
Author(s):  
Julia Schückel ◽  
Stjepan Krešimir Kračun ◽  
Thomas Frederik Lausen ◽  
William George Tycho Willats ◽  
Bodil Jørgensen
Keyword(s):  
High Throughput ◽  
Enzyme Activities ◽  
Glycosyl Hydrolases ◽  
Fruiting Bodies ◽  
High Throughput Analysis ◽  
Efficient Manner ◽  
Throughput Analysis ◽  
Wide Range

A broad range of enzyme activities can be found in a wide range of different fruits and fruiting bodies and we demonstrate how many samples and diverse activities can be handled in a high-throughput and efficient manner.

scholarly journals High-Throughput Analysis of Gene Function in the Bacterial PredatorBdellovibrio bacteriovorus

mBio ◽  
2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Miles C. Duncan ◽  
Rebecca K. Gillette ◽  
Micah A. Maglasang ◽  
Elizabeth A. Corn ◽  
Albert K. Tai ◽  
...  
Keyword(s):  
High Throughput ◽  
Gram Negative Bacteria ◽  
Human Pathogens ◽  
High Throughput Analysis ◽  
Bdellovibrio Bacteriovorus ◽  
Gram Negative ◽  
Content Type ◽  
Genetically Engineer ◽  
Wide Range ◽  
Specific Species

ABSTRACTBdellovibrio bacteriovorusis a bacterial predator capable of killing and replicating inside most Gram-negative bacteria, including antibiotic-resistant pathogens. Despite growing interest in this organism as a potential therapeutic, many of its genes remain uncharacterized. Here, we perform a high-throughput genetic screen withB. bacteriovorususing transposon sequencing (Tn-seq) to explore the genetic requirements of predation. Two hundred one genes were deemed essential for growth in the absence of prey, whereas over 100 genes were found to be specifically required for predative growth on the human pathogensVibrio choleraeandEscherichia coliin both planktonic and biofilm states. To further this work, we created an ordered-knockout library inB. bacteriovorusand developed new high-throughput techniques to characterize the mutants by their stage of deficiency in the predator life cycle. Using microscopy and flow cytometry, we confirmed 10 mutants defective in prey attachment and eight mutants defective in prey rounding. The majority of these genes are hypothetical and previously uncharacterized. Finally, we propose new nomenclature to groupB. bacteriovorusmutants into classes based on their stage of predation defect. These results contribute to our basic understanding of bacterial predation and may be useful for harnessingB. bacteriovorusto kill harmful pathogens in the clinical setting.IMPORTANCEBdellovibrio bacteriovorusis a predatory bacterium that can kill a wide range of Gram-negative bacteria, including many human pathogens. Given the global rise of antibiotic resistance and dearth of new antibiotics discovered in the past 30 years, this predator has potential as an alternative to traditional antibiotics. For many years,B. bacteriovorusresearch was hampered by a lack of genetic tools, and the genetic mechanisms of predation have only recently begun to be established. Here, we comprehensively identify and characterize predator genes required for killing bacterial prey, as well as genes that interfere in this process, which may allow us to design better therapeutic predators. Based on our study, we and other researchers may ultimately be able to genetically engineer strains that have improved killing rates, target specific species of prey, or preferentially target prey in the planktonic or biofilm state.

scholarly journals When sinks become sources: adaptive colonization in asexuals

2018 ◽  
Author(s):  
Florian Lavigne ◽  
Guillaume Martin ◽  
Yoann Anciaux ◽  
Julien Papaϯx ◽  
Lionel Roques
Keyword(s):  
Mutation Rate ◽  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Management Strategies ◽  
Geometrical Model ◽  
Immigration Rate ◽  
Lethal Mutagenesis ◽  
Wide Range ◽  
Asexual Populations ◽  
Rate Threshold

AbstractThe successful establishment of a population into a new empty habitat outside of its initial niche is a phenomenon akin to evolutionary rescue in the presence of immigration. It underlies a wide range of processes, such as biological invasions by alien organisms, host shifts in pathogens or the emergence of resistance to pesticides or antibiotics from untreated areas.In this study, we derive an analytically tractable framework to describe the coupled evolutionary and demographic dynamics of asexual populations in a source-sink system. In particular, we analyze the influence of several factors — immigration rate, mutational parameters, and harshness of the stress induced by the change of environment — on the establishment success in the sink (i.e. the formation of a self-sufficient population in the sink), and on the time until establishment. To this aim, we use a classic phenotype-fitness landscape (Fisher’s geometrical model in n dimensions) where source and sink habitats determine distinct phenotypic optima. The harshness of stress, in the sink, is determined by the distance between the fitness optimum in the sink and that of the source. The dynamics of the full distribution of fitness and of population size in the sink are analytically predicted under a strong mutation strong immigration limit where the population is always polymorphic.The resulting eco-evolutionary dynamics depend on mutation and immigration rates in a non straightforward way. Below some mutation rate threshold, establishment always occurs in the sink, following a typical four-phases trajectory of the mean fitness. The waiting time to this establishment is independent of the immigration rate and decreases with the mutation rate. Beyond the mutation rate threshold, lethal mutagenesis impedes establishment and the sink population remains so, albeit with an equilibrium state that depends on the details of the fitness landscape. We use these results to get some insight into possible effects of several management strategies.

High-Throughput Analysis of Materials for Chemical Looping Processes

2020 ◽  
Author(s):  
Nicholas Singstock ◽  
Christopher Bartel ◽  
Aaron M. Holder ◽  
Charles B. Musgrave
Keyword(s):  
High Throughput ◽  
Process Design ◽  
Experimental Studies ◽  
Chemical Processes ◽  
Chemical Looping Combustion ◽  
Chemical Looping ◽  
Active Materials ◽  
High Throughput Analysis ◽  
Wide Range ◽  
Modern Chemical

Chemical looping is a promising approach for improving the energy efficiency of many industrial chemical processes. However, a major limitation of modern chemical looping technologies is the lack of suitable active materials to mediate the involved subreactions. Identification of suitable materials has been historically limited by the scarcity of high-temperature (> 600 °C) thermochemical data to evaluate candidate materials. An accurate thermodynamic approach is demonstrated here to rapidly identify active materials which is applicable to a wide variety of chemical looping chemistries. Application of this analysis to chemical looping combustion correctly classifies 17/17 experimentally studied redox materials by their viability and identifies over 1,300 promising yet previously unstudied active materials. This approach is further demonstrated by analyzing redox pairs for mediating a novel chemical looping process for producing pure SO2 from raw sulfur and air which could provide a more efficient and lower emission route to sulfuric acid. 12 promising redox materials for this process are identified, two of which are supported by previous experimental studies of their individual oxidation and reduction reactions. This approach provides the necessary foundation for connecting process design with high-throughput materials discovery to accelerate the innovation and development of a wide-range of chemical looping technologies.

High-Throughput Analysis of Materials for Chemical Looping Processes

2020 ◽  
Author(s):  
Nicholas Singstock ◽  
Christopher Bartel ◽  
Aaron M. Holder ◽  
Charles B. Musgrave
Keyword(s):  
High Throughput ◽  
Process Design ◽  
Experimental Studies ◽  
Chemical Processes ◽  
Chemical Looping Combustion ◽  
Chemical Looping ◽  
Active Materials ◽  
High Throughput Analysis ◽  
Wide Range ◽  
Modern Chemical

Chemical looping is a promising approach for improving the energy efficiency of many industrial chemical processes. However, a major limitation of modern chemical looping technologies is the lack of suitable active materials to mediate the involved subreactions. Identification of suitable materials has been historically limited by the scarcity of high-temperature (> 600 °C) thermochemical data to evaluate candidate materials. An accurate thermodynamic approach is demonstrated here to rapidly identify active materials which is applicable to a wide variety of chemical looping chemistries. Application of this analysis to chemical looping combustion correctly classifies 17/17 experimentally studied redox materials by their viability and identifies over 1,300 promising yet previously unstudied active materials. This approach is further demonstrated by analyzing redox pairs for mediating a novel chemical looping process for producing pure SO2 from raw sulfur and air which could provide a more efficient and lower emission route to sulfuric acid. 12 promising redox materials for this process are identified, two of which are supported by previous experimental studies of their individual oxidation and reduction reactions. This approach provides the necessary foundation for connecting process design with high-throughput materials discovery to accelerate the innovation and development of a wide-range of chemical looping technologies.

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