Integrating evolution into ecological modelling: accommodating phenotypic changes in agent based models.

PMCID: PMC3733718This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Evolutionary change is a characteristic of living organisms and forms one of the ways in which species adapt to changed conditions. However, most ecological models do not incorporate this ubiquitous phenomenon. We have developed a model that takes a 'phenotypic gambit' approach and focuses on changes in the frequency of phenotypes (which differ in timing of breeding and fecundity) within a population, using, as an example, seasonal breeding. Fitness per phenotype calculated as the individual's contribution to population growth on an annual basis coincide with the population dynamics per phenotype. Simplified model variants were explored to examine whether the complexity included in the model is justified. Outputs from the spatially implicit model underestimated the number of individuals across all phenotypes. When no phenotype transitions are included (i.e. offspring always inherit their parent's phenotype) numbers of all individuals are always underestimated. We conclude that by using a phenotypic gambit approach evolutionary dynamics can be incorporated into individual based models, and that all that is required is an understanding of the probability of offspring inheriting the parental phenotype

Analysis of the impact of broad absorption lines on quasar redshift measurements with synthetic observations

Accurate quasar classifications and redshift measurements are increasingly important to precision cosmology experiments. Broad absorption line (BAL) features are present in 15-20 per cent of all quasars, and these features can introduce systematic redshift errors, and in extreme cases produce misclassifications. We quantitatively investigate the impact of BAL features on quasar classifications and redshift measurements with synthetic spectra that were designed to match observations by the Dark Energy Spectroscopic Instrument (DESI) survey. Over the course of 5 yr, DESI aims to measure spectra for 40 million galaxies and quasars, including nearly three million quasars. Our synthetic quasar spectra match the signal-to-noise ratio and redshift distributions of the first year of DESI observations, and include the same synthetic quasar spectra both with and without BAL features. We demonstrate that masking the locations of the BAL features decreases the redshift errors by about 1 per cent and reduces the number of catastrophic redshift errors by about 80 per cent. We conclude that identifying and masking BAL troughs should be a standard part of the redshift determination step for DESI and other large-scale spectroscopic surveys of quasars

The DESI One-Percent Survey: Constructing Galaxy-Halo Connections for ELGs and LRGs Using Auto and Cross Correlations

In the current Dark Energy Spectroscopic Instrument (DESI) survey, emission line galaxies (ELGs) and luminous red galaxies (LRGs) are essential for mapping the dark matter distribution at N M . We measure the auto and cross correlation functions of ELGs and LRGs at 108.0 M ⊙ from the DESI One-Percent survey. Following Gao et al., we construct the galaxy-halo connections for ELGs and LRGs simultaneously. With the stellar-halo mass relation for the whole galaxy population (i.e., normal galaxies), LRGs can be selected directly by stellar mass, while ELGs can also be selected randomly based on the observed number density of each stellar mass, once the probability z ∼ 0.2 of a satellite galaxy becoming an ELG is determined. We demonstrate that the observed small scale clustering prefers a halo mass-dependent z ∼ 0.2 model rather than a constant. With this model, we can well reproduce the auto correlations of LRGs and the cross correlations between LRGs and ELGs at z ∼ 0.7 z ∼ 1. We can also reproduce the auto correlations of ELGs at deg2 z ∼ 1 (0.6 < z < 1.6 z ∼ 1) in real (redshift) space. Although our model has only seven parameters, we show that it can be extended to higher redshifts and reproduces the observed auto correlations of ELGs in the whole range of ∼1012 M ⊙, which enables us to generate a lightcone ELG mock for DESI. With the above model, we further derive halo occupation distributions for ELGs, which can be used to produce ELG mocks in coarse simulations without resolving subhalos

Changing-look Active Galactic Nuclei from the Dark Energy Spectroscopic Instrument. I. Sample from the Early Data

\ua9 2024. The Author(s). Published by the American Astronomical Society.Changing-look active galactic nuclei (CL AGNs) can be generally confirmed by the emergence (turn-on) or disappearance (turn-off) of broad emission lines (BELs), associated with a transient timescale (about 100 ∼ 5000 days) that is much shorter than predicted by traditional accretion disk models. We carry out a systematic CL AGN search by crossmatching the spectra coming from the Dark Energy Spectroscopic Instrument and the Sloan Digital Sky Survey. Following previous studies, we identify CL AGNs based on Hα, Hβ, and Mg ii at z ≤ 0.75 and Mg ii, C iii], and C iv at z &gt; 0.75. We present 56 CL AGNs based on visual inspection and three selection criteria, including 2 Hα, 34 Hβ, 9 Mg ii, 18 C iii], and 1 C iv CL AGN. Eight cases show simultaneous appearances/disappearances of two BELs. We also present 44 CL AGN candidates with significant flux variation of BELs, but remaining strong broad components. In the confirmed CL AGNs, 10 cases show additional CL candidate features for different lines. In this paper, we find: (1) a 24:32 ratio of turn-on to turn-off CL AGNs; (2) an upper-limit transition timescale ranging from 330 to 5762 days in the rest frame; and (3) the majority of CL AGNs follow the bluer-when-brighter trend. Our results greatly increase the current CL census (∼30%) and would be conducive to exploring the underlying physical mechanism

A striking relationship between dust extinction and radio detection in DESI QSOs: evidence for a dusty blow-out phase in red QSOs

We present the first eight months of data from our secondary target programme within the ongoing Dark Energy Spectroscopic Instrument (DESI) survey. Our programme uses a mid-infrared and optical colour selection to preferentially target dust-reddened quasi-stellar objects (QSOs) that would have otherwise been missed by the nominal DESI QSO selection. So far, we have obtained optical spectra for 3038 candidates, of which ∼70 per cent of the high-quality objects (those with robust redshifts) are visually confirmed to be Type 1 QSOs, consistent with the expected fraction from the main DESI QSO survey. By fitting a dust-reddened blue QSO composite to the QSO spectra, we find they are well-fitted by a normal QSO with up to AV ∼4 mag of line-of-sight dust extinction. Utilizing radio data from the LOFAR Two-metre Sky Survey (LoTSS) DR2, we identify a striking positive relationship between the amount of line-of-sight dust extinction towards a QSO and the radio detection fraction, that is not driven by radio-loud systems, redshift and/or luminosity effects. This demonstrates an intrinsic connection between dust reddening and the production of radio emission in QSOs, whereby the radio emission is most likely due to low-powered jets or winds/outflows causing shocks in a dusty environment. On the basis of this evidence, we suggest that red QSOs may represent a transitional 'blow-out' phase in the evolution of QSOs, where winds and outflows evacuate the dust and gas to reveal an unobscured blue QSO

Regulation of endothelial cell plasticity by TGF-β

Recent evidence has demonstrated that endothelial cells can have a remarkable plasticity. By a process called Endothelial-to-Mesenchymal Transition (EndMT) endothelial cells convert to a more mesenchymal cell type that can give rise to cells such as fibroblasts, but also bone cells. EndMT is essential during embryonic development and tissue regeneration. Interestingly, it also plays a role in pathological conditions like fibrosis of organs such as the heart and kidney. In addition, EndMT contributes to the generation of cancer associated fibroblasts that are known to influence the tumor-microenvironment favorable for the tumor cells. EndMT is a form of the more widely known and studied Epithelial-to-Mesenchymal Transition (EMT). Like EMT, EndMT can be induced by transforming growth factor (TGF)-β. Indeed many studies have pointed to the important role of TGF-β receptor/Smad signaling and downstream targets, such as Snail transcriptional repressor in EndMT. By selective targeting of TGF-β receptor signaling pathological EndMT may be inhibited for the therapeutic benefit of patients with cancer and fibrosis

Mutations in Protein-Binding Hot-Spots on the Hub Protein Smad3 Differentially Affect Its Protein Interactions and Smad3-Regulated Gene Expression

Hub proteins are connected through binding interactions to many other proteins. Smad3, a mediator of signal transduction induced by transforming growth factor beta (TGF-β), serves as a hub protein for over 50 protein-protein interactions. Different cellular responses mediated by Smad3 are the product of cell-type and context dependent Smad3-nucleated protein complexes acting in concert. Our hypothesis is that perturbation of this spectrum of protein complexes by mutation of single protein-binding hot-spots on Smad3 will have distinct consequences on Smad3-mediated responses.We mutated 28 amino acids on the surface of the Smad3 MH2 domain and identified 22 Smad3 variants with reduced binding to subsets of 17 Smad3-binding proteins including Smad4, SARA, Ski, Smurf2 and SIP1. Mutations defective in binding to Smad4, e.g., D408H, or defective in nucleocytoplasmic shuttling, e.g., W406A, were compromised in modulating the expression levels of a Smad3-dependent reporter gene or six endogenous Smad3-responsive genes: Mmp9, IL11, Tnfaip6, Fermt1, Olfm2 and Wnt11. However, the Smad3 mutants Y226A, Y297A, W326A, K341A, and E267A had distinct differences on TGF-β signaling. For example, K341A and Y226A both reduced the Smad3-mediated activation of the reporter gene by ∼50% but K341A only reduced the TGF-β inducibilty of Olfm2 in contrast to Y226A which reduced the TGF-β inducibility of all six endogenous genes as severely as the W406A mutation. E267A had increased protein binding but reduced TGF-β inducibility because it caused higher basal levels of expression. Y297A had increased TGF-β inducibility because it caused lower Smad3-induced basal levels of gene expression.Mutations in protein binding hot-spots on Smad3 reduced the binding to different subsets of interacting proteins and caused a range of quantitative changes in the expression of genes induced by Smad3. This approach should be useful for unraveling which Smad3 protein complexes are critical for specific biological responses

Astrometric Calibration and Performance of the Dark Energy Spectroscopic Instrument Focal Plane

The Dark Energy Spectroscopic Instrument, consisting of 5020 robotic fiber positioners and associated systems on the Mayall telescope at Kitt Peak, Arizona, is carrying out a survey to measure the spectra of 40 million galaxies and quasars and produce the largest 3D map of the universe to date. The primary science goal is to use baryon acoustic oscillations to measure the expansion history of the universe and the time evolution of dark energy. A key function of the online control system is to position each fiber on a particular target in the focal plane with an accuracy of 11 μm rms 2D. This paper describes the set of software programs used to perform this function along with the methods used to validate their performance

Dynamic, Large-Scale Profiling of Transcription Factor Activity from Live Cells in 3D Culture

phenotypes. Taken together, our objective was to develop cellular arrays for dynamic, large-scale quantification of TF activity as cells organized into spherical structures within 3D culture.TF-specific and normalization reporter constructs were delivered in parallel to a cellular array containing a well-established breast cancer cell line cultured in Matrigel. Bioluminescence imaging provided a rapid, non-invasive, and sensitive method to quantify luciferase levels, and was applied repeatedly on each sample to monitor dynamic activity. Arrays measuring 28 TFs identified up to 19 active, with 13 factors changing significantly over time. Stimulation of cells with β-estradiol or activin A resulted in differential TF activity profiles evolving from initial stimulation of the ligand. Many TFs changed as expected based on previous reports, yet arrays were able to replicate these results in a single experiment. Additionally, arrays identified TFs that had not previously been linked with activin A.This system provides a method for large-scale, non-invasive, and dynamic quantification of signaling pathway activity as cells organize into structures. The arrays may find utility for investigating mechanisms regulating normal and abnormal tissue growth, biomaterial design, or as a platform for screening therapeutics