Find research datasets worth reusing

opencc-zeroJun 2024View details →

Data from: More evolvable bacteriophages better suppress their host

The number of multidrug-resistant strains of bacteria is increasing rapidly, while the number of new antibiotic discoveries has stagnated. This trend has caused a surge in interest in bacteriophages as anti-bacterial therapeutics, in part because there is near limitless diversity of phages to harness. While this diversity provides an opportunity, it also creates the dilemma of having to decide which criteria to use to select phages. Here we test whether a phage's ability to coevolve with its host (evolvability) should be considered and how this property compares to two previously proposed criteria: fast reproduction and thermostability. To do this, we compared the suppressiveness of three phages that vary by a single amino acid yet differ in these traits such that each strain maximized two of three characteristics. Our studies revealed that both evolvability and reproductive rate are independently important. The phage most able to suppress bacterial populations was the strain with high evolvability and reproductive rate, yet this phage was unstable. Phages varied due to differences in the types of resistance evolved against them and their ability to counteract resistance. When conditions were shifted to exaggerate the importance of thermostability, one of the stable phages was most suppressive in the short-term, but not over the long-term. Our results demonstrate the utility of biological therapeutics' capacities to evolve and adjust in action to resolve complications like resistance evolution. Furthermore, evolvability is a property that can be engineered into phage therapeutics to enhance their effectiveness.

opencc-by-4.0Apr 2018View details →

Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria

Code and data for Frenoy & Bonhoeffer 2018 (Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria, in PLoS Biology) See README for details and steps to reproduce the full analysis from the raw data

opencc-by-4.0Jul 2019View details →

Data and Analysis Artifacts for Service-Based Evolvability Patterns (Experiment and Metrics)

Two functionally equivalent service-based web-shop systems (one version with selected service-based patterns, one without) were analyzed with a controlled experiment as well as with structural maintainability metrics. This repo contains all analysis artifacts.

opencc-by-4.0Jul 2024View details →

An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway

Data underlying the figures/tables of the publication "An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway" Nat. Chem. (2024). https://doi.org/10.1038/s41557-024-01562-5

opencc-zeroJul 2021View details →

Cooperative communication with humans evolved to emerge early in domestic dogs

While we know that dogs evolved from wolves, it remains unclear how domestication affected dog cognition. One hypothesis suggests dog domestication altered social maturation by a process of selecting for an attraction to humans. Under this account, dogs became more flexible in using inherited skills to cooperatively-communicate with a new social partner that was previously feared and expressed these unusual social skills early in development. Here we tested dog (N=44) and wolf (N=37) puppies, 5-18 weeks old, on a battery of temperament and cognition tasks. We found that dog puppies were more attracted to humans, read human gestures more skillfully, and made more eye contact with humans than wolf puppies. The two species were similarly attracted to objects and performed similarly on nonsocial measures of memory and inhibitory control. These results are consistent with the idea that domestication enhanced the cooperative-communicative abilities of dogs as selection for attraction to humans altered social maturation.

opencc-zeroJul 2021View details →

Male reproductive effort might be evolving in the face of devastating disease in a threatened amphibian

The devastating infectious disease chytridiomycosis has caused declines of amphibians across the globe, yet some populations are persisting and even recovering. One understudied effect of wildlife disease is changes in reproductive effort. Here we aimed to understand if disease has plastic effects on reproduction and if reproductive effort could evolve with disease endemism. We compared the effects of experimental pathogen exposure (trait plasticity) and population-level disease history (evolution in trait baseline) on reproductive effort using gametogenesis as a proxy in the declining and endangered frog Litoria verreauxii alpina. We found that unexposed males from disease-endemic populations had higher reproductive effort, which is consistent with an evolutionary response to chytridiomycosis. We also found evidence of trait plasticity, where males and females were affected differently by infection: pathogen exposed males had higher reproductive effort (larger testes), whereas females had reduced reproductive effort (smaller and fewer developed eggs) regardless of the population of origin. Infectious disease can cause plastic changes in reproductive effort at an individual level, and population-level disease exposure can result in changes to baseline reproductive effort; therefore, individual- and population-level effects of disease should be considered when designing management and conservation programs for threatened and declining species. --

opencc-zeroJul 2021View details →

Macroevolutionary foundations of a recently-evolved innate immune defense (data)

Antagonistic interactions between hosts and parasites may drive the evolution of novel host defenses, or new parasite strategies. Host immunity is therefore one of the fastest evolving traits. But where do the novel immune traits come from? Here, we test for phylogenetic conservation in a rapidly evolving immune trait – peritoneal fibrosis. Peritoneal fibrosis is a costly defense against a specialist tapeworm, Schistocephalus solidus (Cestoda), expressed in some freshwater populations of threespine stickleback fish (Gasterosteus aculeatus, Perciformes). We asked whether stickleback fibrosis is a derived species-specific trait or an ancestral immune response that was widely distributed across ray-finned fish (Actinopterygii) only to be employed by threespine stickleback against the specialist parasite. We combined literature review on peritoneal fibrosis with a comparative experiment using either parasite-specific, or non-specific, immune challenge in deliberately selected species across fish tree of life. We show that ray-finned fish are broadly, but not universally, able to induce peritoneal fibrosis when challenged with a generic stimulus (Alum adjuvant). The experimental species were, however, largely indifferent to the tapeworm antigen homogenate. Peritoneal fibrosis, thus, appears to be a common and deeply conserved fish immune response that was co-opted by stickleback to adapt to a new selective challenge.

opencc-by-4.0Dec 2022View details →

Dataset for "Evolving scattering networks for engineering disorder"

The design of stealthy hyperuniform materials has been a critical topic in realizing bandgap materials without crystalline order. Most previous approaches to constructing SHU materials, such as the collective coordinate method, have assumed the closed system, maintaining the number of particles inside a system during the design process. Here, I upload the dataset for the concept of evolving wave networks. The datasets are applied to introduce the concept of evolving wave networks (dataset for Fig. 2), classify material states according to network parameters (dataset for Fig. 3), generate the stealthy hyperuniformity (SHU) shielding of existing materials (dataset for Fig. 4), realize preferential attachment in evolving wave networks (dataset for Fig. 5), and obtain the following phase diagram of disordered materials (dataset for Fig. 6).  raw_data_FigXabc: the file represents the data for the figure X and abc denotes the sub-figure number. raw_data_Fig6_alpha_MMM: the file represents the data for figure 6: SHU states, and MMM denotes the value of alpha that determines the preference / anti-preference. raw_data_Fig6_Crystal_NNN: the file represents the data for figure 6: Crystal states, and NNN denotes the particle number. raw_data_Fig6_Poisson: the file represents the data for figure 6: Poisson state. Each file is composed of two-column data, representing (x,y) positions of particles. While each realization possesses 500 particles (500 row data), [raw_data_Fig3adgj], [raw_data_Fig3behk], [raw_data_Fig4a], [raw_data_Fig4b], [raw_data_Fig4c], [raw_data_Fig4d], [raw_data_Fig4e], [raw_data_Fig4f], [raw_data_Fig5abc], [raw_data_Fig5def], and [raw_data_Fig5ghi] include the data for 100 realizations: 50000 row data. In the data for Fig. 6, the SHU and Poisson states also possess 50000 row data with 100 realizations, while the crystal states have 500 row data with 1 realization.

opencc-zeroDec 2022View details →

Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose

Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also <a>constrain</a> sequence divergence over evolutionary time scales.

opencc-zeroMar 2023View details →

Sexually antagonistic selection maintains genetic variance when sexual dimorphism evolves

Breeding design data for body size in seed beetles (a sexually antagonistic trait) after 10 generations under different artificial selection conditions to test the effects of selection on the genetic variance of body size. The breeding design and sample size of the study allow us to partition genetic variances into additive autosomal, additive sex-linked, autosomal dominance and X-linked dominance variance. See related dataset for body size data of the ancestral population before selection.

opencc-by-4.0Apr 2023View details →

Data and code: Plants cultivated for ecosystem restoration can evolve towards a domestication syndrome

Data and code to the publication Conrady et al (2023): Plants cultivated for ecosystem restoration can evolve towards a domestication syndrome, PNAS.

opencc-zeroApr 2023View details →

A rapidly evolving cricket produces percussive vibrations: how, who, when, and why

Sexual signals are often transmitted through multiple modalities (e.g., visual and chemical), and under selection from both intended and unintended receivers. A nuanced understanding of sexual signal evolution is important since they play a critical role in diversification. We recently documented percussive substrate-borne vibrations in the Pacific field cricket (Teleogryllus oceanicus), a species that uses airborne acoustic and chemical signals to attract and secure mates. The airborne signals of Hawaiian T. oceanicus are currently undergoing rapid evolution; at least five novel male morphs have arisen in the past 20 years. Nothing is yet known about the newly discovered percussive substrate-borne vibrations, so we ask 'how' they are produced, 'who' produces them (e.g., population, morph), 'when' they produce them (e.g., whether they are plastic), and 'why' (e.g., do they play a role in mating). We show that the vibrations are produced exclusively by males and during courtship via foreleg drumming. One novel morph, purring, produces quieter airborne songs and is more likely to drum than the ancestral morph. However, drumming behavior is also contextually plastic for some males; when we removed the ability of males to produce airborne song, ancestral males became more likely to drum, whereas two novel morphs were equally likely to drum regardless of their ability to produce song. Opposite our prediction, females were less likely to mate with males who drummed. We discuss why that might be and describe what we can learn about complex signal evolution from this newly discovered behavior.

Datasets for "Time-evolving effective dispersion (TED) model for1 transport in porous media"

Temporal evolution of \(D^{\mathrm{eff}}_{\mathrm L}(t)\) simulated by particle tracking. Ensemble of 100 realisations. var: \(\sigma^2_f\).

opencc-zeroSep 2023View details →

Contaminated sediment in the Detroit River selects for evolved CYP1A and p53 responses in wild brown bullhead (Ameiurus nebulosus) populations

<div> <div> In a previous study, adaptive responses to a single polycyclic aromatic hydrocarbon (PAH), benzo[a]pyrene (BaP), were identified in brown bullhead (Ameiurus nebulosus) captured from contaminated sites across the Great Lakes. The tumor suppressor p53 and phase I toxin metabolizing CYP1A genes showed a protective and refractory response, respectively, up to the F1 generation (Williams and Hubberstey, 2014). As an extension to the first study, bullhead were exposed to sediment collected from sites along the Detroit River to see if these adaptive responses are attainable when fish from a contaminated site are exposed to a mixture of contaminants, instead of a single compound. p53 and CYP1A proteins were measured in both studies with the addition of phase II glutathione-s-transferase (GST) activity in the second. Three treatment groups were measured: acute (treated immediately), cleared (depurated for three months and subsequent treatment), and farm raised F1 offspring. All three treatment groups were exposed to clean and contaminated sediment for 24 and 96 hours. Acute fish from contaminated sites exposed to contaminated sediment revealed an initial elevated p53 response that was not reached in cleared fish exposed to contaminated sediment. Instead, cleared and F1 bullhead from clean and contaminated sites had overlapping p53 expression patterns in response to contaminated sediment by 96 hours. Acute fish from contaminated sites exposed to contaminated sediment revealed refractory CYP1A expression, which disappeared in cleared fish and whose F1 refractory response overlapped with clean site F1 offspring. Decreasing GST activity was evident in both clean and contaminated fish over time, with clean site fish responding to contaminated sediment more deliberately. By 96 hours, the response patterns of F1 offspring from clean and contaminated sites to clean and contaminated sediment exposures were similar. </div> <div> Because p53, CYP1A and GST activity responses to contaminated sediment dosing overlapped in clean and contaminated farm-raised F1 offspring, these results suggest that contaminated fish have acclimated to the contaminants present in their environments by reaching a tolerance threshold and no evidence of adaptation was detected in these biomarkers. </div> </div>

High-speed video observations of needles evolving into negative leaders in a positive cloud-to-ground lightning flash

The data supports the manuscript entitled “High-speed video observations of needles evolving into negative leaders in a positive cloud-to-ground lightning flash”. The high-speed video data files of the positive cloud-to-ground lightning (20200603_082539, denoted F20065) of *.cihx and *.avi can be opened by Photron Camera Control software (Photron Fastcam Viewer) that can be download from this link: https://photron.com/photron-support/ In addition, MATLAB can open the *.mat file (electric field change data), and Microsoft Excel can open the *.xlsx file (Guangdong-Hong Kong-Macao Lightning Location data (20200603082523-20200603082556). The data can be used freely for scientific purposes with the appropriate citation.

The evolvement of ULVZ at LLSVP margins--selected models with various buoyancy number and compositional viscosity

This tar.gz file is created and uploaded for the submission of the manuscript titled 'The evolvement of dense ULVZs at LLSVP margins and implications' to the journal Geophysical Research Letters. This tar.gz file is for selected models with various buoyancy number (B) and compositional viscosity (etaC), which are described and compared with the reference model (in doi 10.5281/zenodo.8394637) in the manuscript. The collection includes the raw output data and post-processed data illustrated in Figures 3.  1. the /scratch directory This directory contains the raw output data of three models listed below. All models are calculated by CitcomS (modified from the CitcomS-3.3.1 version) and the data follows the CitcomS output convention. Please read the description of a previous upload (doi 10.5281/zenodo.8394637, titled 'The evolvement of ULVZ at LLSVP margins--reference model with B=3.0 and etaC=1.0') for more information. The ULVZ-v1B6_h10l10/ directory: the model with B=6.0 and etaC=1.0, illustrated in the top panel of Figure 3  The ULVZ-v1B1-5_h10l10/ directory: the model with B=1.5 and etaC=1.0, illustrated in the middle panel of Figure 3  The ULVZ-v01B3_h10l10/ directory: the model with B=3.0 and etaC=0.1, illustrated in the bottom panel of Figure 3  2. the data_plots/ directory: data extracted from the raw outputs and plotted in Figure 3. The time frame of 14800 is for the left column in Figure 3, and the other time frames are for the right column in Figure 3.   temperature: *temp* files composition: *comp* files velocity: *velo_Sv* files density anomaly: *density* files

The evolvement of ULVZ at LLSVP margins--supporting materials

This tar.gz file is created and uploaded for the submission of the manuscript titled 'The evolvement of dense ULVZs at LLSVP margins and implications' to the journal Geophysical Research Letters. This tar.file contains four directories /F1, /F2, /F3, /F4 with data used to plot Figures 1, 2, 3, 4, respectively, in the supporting material. The data follows the same convention as that in doi10.5281/zenodo.8394882 and 10.5281/zenodo.8394637.