An official website of the United States government
Abstract Hosts and their associated microbes can enter into different relationships, which can range from mutualism, where both partners benefit, to exploitation, where one partner benefits at the expense of the other. Many host–microbe relationships have been presumed to be mutualistic, but frequently only benefits to the host, and not the microbial symbiont, have been considered. Here, we address this issue by looking at the effect of host association on the fitness of two facultative members of theDictyostelium discoideummicrobiome (Burkholderia agricolarisandBurkholderia hayleyella). Using two indicators of bacterial fitness, growth rate and abundance, we determined the effect ofD. discoideumonBurkholderiafitness. In liquid culture, we found thatD. discoideumamoebas lowered the growth rate of bothBurkholderiaspecies. In soil microcosms, we tracked the abundance ofBurkholderiagrown with and withoutD. discoideumover a month and found thatB. hayleyellahad larger populations when associating withD. discoideumwhileB. agricolariswas not significantly affected. Overall, we find that bothB. agricolarisandB. hayleyellapay a cost to associate withD. discoideum, butB. hayleyellacan also benefit under some conditions. Understanding how fitness varies in facultative symbionts will help us understand the persistence of host–symbiont relationships. OPEN RESEARCH BADGESThis article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available athttps://openscholarship.wustl.edu/data/15/
more »
« less
Suicidal selection: Programmed cell death can evolve in unicellular organisms due solely to kin selection
AbstractUnicellular organisms can engage in a process by which a cell purposefully destroys itself, termed programmed cell death (PCD). While it is clear that the death of specific cells within amulticellularorganism could increase inclusive fitness (e.g., during development), the origin of PCD inunicellularorganisms is less obvious. Kin selection has been shown to help maintain instances of PCD in existing populations of unicellular organisms; however, competing hypotheses exist about whether additional factors are necessary to explain its origin. Those factors could include an environmental shift that causes latent PCD to be expressed, PCD hitchhiking on a large beneficial mutation, and PCD being simply a common pathology. Here, we present results using an artificial life model to demonstrate that kin selection can, in fact, be sufficient to give rise to PCD in unicellular organisms. Furthermore, when benefits to kin are direct—that is, resources provided to nearby kin—PCD is more beneficial than when benefits are indirect—that is, nonkin are injured, thus increasing the relative amount of resources for kin. Finally, when considering how strict organisms are in determining kin or nonkin (in terms of mutations), direct benefits are viable in a narrower range than indirect benefits. Open Research BadgesThis article has been awarded Open Data and Open Materials Badges. All materials and data are publicly accessible via the Open Science Framework athttps://github.com/anyaevostinar/SuicidalAltruismDissertation/tree/master/LongTerm.
more »
« less
- Award ID(s):
- 1655715
- PAR ID:
- 10460088
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Ecology and Evolution
- Volume:
- 9
- Issue:
- 16
- ISSN:
- 2045-7758
- Format(s):
- Medium: X Size: p. 9129-9136
- Size(s):
- p. 9129-9136
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Nicotinic acetylcholine receptors (nAChRs) are known to play a role in cognitive functions of the hippocampus, such as memory consolidation. Given that they conduct Ca2+and are capable of regulating the release of glutamate and γ‐aminobutyric acid (GABA) within the hippocampus, thereby shifting the excitatory‐inhibitory ratio, we hypothesized that the activation of nAChRs will result in the potentiation of hippocampal networks and alter synchronization. We used nicotine as a tool to investigate the impact of activation of nAChRs on neuronal network dynamics in primary embryonic rat hippocampal cultures prepared from timed‐pregnant Sprague‐Dawley rats. We perturbed cultured hippocampal networks with increasing concentrations of bath‐applied nicotine and performed network extracellular recordings of action potentials using a microelectrode array. We found that nicotine modulated network dynamics in a concentration‐dependent manner; it enhanced firing of action potentials as well as facilitated bursting activity. In addition, we used pharmacological agents to determine the contributions of discrete nAChR subtypes to the observed network dynamics. We found that β4‐containing nAChRs are necessary for the observed increases in spiking, bursting, and synchrony, while the activation of α7 nAChRs augments nicotine‐mediated network potentiation but is not necessary for its manifestation. We also observed that antagonists of N‐methyl‐D‐aspartate receptors (NMDARs) and group I metabotropic glutamate receptors (mGluRs) partially blocked the effects of nicotine. Furthermore, nicotine exposure promoted autophosphorylation of Ca2+/calmodulin‐dependent kinase II (CaMKII) and serine 831 phosphorylation of the α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid receptor (AMPAR) subunit GluA1. These results suggest that nicotinic receptors induce potentiation and synchronization of hippocampal networks and glutamatergic synaptic transmission. Findings from this work highlight the impact of cholinergic signaling in generating network‐wide potentiation in the form of enhanced spiking and bursting dynamics that coincide with molecular correlates of memory such as increased phosphorylation of CaMKII and GluA1. Open science badgesThis article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. More information about the Open Practices badges can be found athttps://cos.io/our-services/open-science-badges/ imagemore » « less
-
dadi-cli: Automated and distributed population genetic model inference from allele frequency spectraAbstract Summarydadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing. Availability and Implementationdadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available athttps://github.com/xin-huang/dadi-cli. dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2https://cacao.jetstream-cloud.org/.more » « less
-
Abstract BackgroundThe pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species. ResultsHere we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations. ConclusionsThe PGV software can be installed via conda or downloaded fromhttps://github.com/ucrbioinfo/PGV. The companion PGV browser athttp://pgv.cs.ucr.educan be tested using example bed tracks available from the GitHub page.more » « less
-
Abstract BackgroundComputational cell type deconvolution enables the estimation of cell type abundance from bulk tissues and is important for understanding tissue microenviroment, especially in tumor tissues. With rapid development of deconvolution methods, many benchmarking studies have been published aiming for a comprehensive evaluation for these methods. Benchmarking studies rely on cell-type resolved single-cell RNA-seq data to create simulated pseudobulk datasets by adding individual cells-types in controlled proportions. ResultsIn our work, we show that the standard application of this approach, which uses randomly selected single cells, regardless of the intrinsic difference between them, generates synthetic bulk expression values that lack appropriate biological variance. We demonstrate why and how the current bulk simulation pipeline with random cells is unrealistic and propose a heterogeneous simulation strategy as a solution. The heterogeneously simulated bulk samples match up with the variance observed in real bulk datasets and therefore provide concrete benefits for benchmarking in several ways. We demonstrate that conceptual classes of deconvolution methods differ dramatically in their robustness to heterogeneity with reference-free methods performing particularly poorly. For regression-based methods, the heterogeneous simulation provides an explicit framework to disentangle the contributions of reference construction and regression methods to performance. Finally, we perform an extensive benchmark of diverse methods across eight different datasets and find BayesPrism and a hybrid MuSiC/CIBERSORTx approach to be the top performers. ConclusionsOur heterogeneous bulk simulation method and the entire benchmarking framework is implemented in a user friendly packagehttps://github.com/humengying0907/deconvBenchmarkingandhttps://doi.org/10.5281/zenodo.8206516, enabling further developments in deconvolution methods.more » « less
