Biology subjects

Cortes, D.

Publications and source records attributed to Cortes, D..

5 recordsLinked to original sources

bioRxiv2026

Co-limitation by stable, dynamic and directional habitat features shapes climate vulnerability in an alpine specialist

Alpine ecosystems are among the most climate sensitive on Earth, yet logistical challenges and detection biases often impede robust assessment of alpine dependent species. We investigated habitat associations and density patterns of the Sierra Nevada subspecies of the Gray-crowned Rosy-Finch (Leucosticte tephrocotis dawsoni), an alpine obligate and regional endemic, over five breeding seasons from 2018 to 2022 using hierarchical distance sampling and mark-recapture distance sampling to explicitly account for imperfect detection and spatial heterogeneity. Density estimates tracked annual snowpack variation, ranging from 4.77 individuals/km{superscript 2} in a low snow year to 12.08 individuals/km{superscript 2} in a high snow year. Abundance was highest near persistent snow patches that provide foraging habitat and near cliffs that provide nesting substrate, and declined sharply above approximately 10% woody cover, with densities approaching zero beyond approximately 25%, indicating a steep ecological threshold. In contrast, the proportion of surveyed blocks with detections remained relatively stable across years. Together, these patterns indicate a three timescale co-limitation framework in which breeding habitat is shaped by static features (cliffs), dynamic annual drivers (snowpack), and longer-term directional change (woody encroachment). By linking population density to climate sensitive habitat features, this study provides a high-resolution abundance-based baseline for long term monitoring and offers a framework for evaluating climate vulnerability in alpine and other resource-limited systems. Open Research StatementData necessary to replicate the analyses and results presented in this manuscript will be archived in the Dryad Digital Repository upon acceptance, with no embargo on the material. The R code associated with this manuscript is not novel. All analyses use publicly available packages and functions without modification, including mrds (v2.3.0), unmarked (v1.2.5), tidyverse (v2.0.0), MuMIn (v1.47.5), and standard ggplot2 visualization tools. All code is properly cited within the manuscript and publicly available through CRAN. Complete analysis scripts will be archived in Dryad alongside the data upon acceptance to facilitate full reproducibility of results.

ecology↗

bioRxiv2026

mRNAbow: A versatile gene expression system for multiplexed fluorescent imaging using optimized in vitro transcribed mRNA

Messenger RNA (mRNA) transfection enables rapid, transient protein expression without nuclear entry, providing a powerful alternative to DNA or viral delivery in post-mitotic and otherwise difficult-to-transfect cells. Although in vitro transcribed (IVT) mRNAs have revolutionized therapeutic applications, their adoption in experimental biology remains limited by challenges in synthesis, variability across cell types, and concerns about cytotoxicity. Here, we define design principles that maximize IVT mRNA performance across diverse cellular and organismal systems. Through systematic comparison of capping strategies and base modifications, including N1-methyl-pseudouridine, 5-methylcytidine, and 5-methoxyuridine, we identify modifications that enhance translation while minimizing activation of cellular stress responses. Optimized transcripts drive robust protein expression within four hours, persist for up to one week, and support multiplexed expression of structurally and functionally distinct proteins in mammalian cells, including cancer cell lines, iPSC-derived systems, primary cells, and organoids, as well as in vivo in zebrafish embryos and in less genetically tractable models such as Danionella cerebrum and sea urchin embryos. To further expand accessibility for community use, we developed mRNAbow, a platform for generating low-toxicity mRNAs encoding organelle-targeted fluorescent proteins and biosensors for multiplex imaging, with corresponding plasmids made publicly available. Together, these advances establish a generalizable framework for IVT mRNA design and expand experimental access to synthetic mRNA technologies for dissecting cellular architecture and dynamics.

cell biology↗

bioRxiv2024

Phylogeny, morphology, and behavior of the new ciliate species Stentor stipatus

BackgroundStentor, the genus of large trumpet-shaped ciliates, is well-known for its complex morphology and striking behaviors. Members of this genus are distributed throughout the world in a wide and diverse pool of freshwater ecosystems. Recently, the molecular phylogeny of Stentor has been explored through comparison of 18S small subunit (SSU) ribosomal DNA (rDNA) sequences, clarifying several previously mischaracterized species and species complexes. However, despite their wide distribution, to-date, only about a dozen species of Stentor have been described and verified by phylogenetic means. ResultsHere, we introduce the discovery of a new species within genus Stentor: Stentor stipatus spec. nov., so named for their distinctive cytosolic dark pigmented granules which surround the macronucleus and are also present cortically alongside cortically-distributed green microalgae. We present morphological, phylogenetic, ecological, and behavioral characterizations of these cells. Phylogenetic analysis of S. stipatus spec. nov. by comparison of SSU rDNA sequence suggests it is a distinct species from its closest relative, S. amethystinus. We demonstrate that S. stipatus spec. nov. is capable of habituation in response to repeated mechanical stimulation. Further, S. stipatus spec. nov. exhibits strongly directed positive phototaxis, like its relative S. pyriformis, but with a distinct action spectrum from both S. coeruleus and S. pyriformis. Finally, S. stipatus phototaxis response strength varies in a consistent pattern throughout the day, providing evidence of potential circadian regulation. ConclusionsThis work expands the current understanding of the ecological distribution of and behavioral features present within genus Stentor.

cell biology↗

bioRxiv2019

Bond type and discretization of non-muscle myosin II are critical for simulated contractile dynamics

Molecular motors drive cytoskeletal rearrangements to change cell shape. Myosins are the motors that move, crosslink, and modify the actin cytoskeleton. The primary force generator in contractile actomyosin networks is non-muscle myosin II (NMMII), a molecular motor that assembles into ensembles that bind, slide, and crosslink actin filaments (F-actin). The multivalence of NMMII ensembles and their multiple roles have confounded the resolution of crucial questions including how the number of NMMII subunits affects dynamics, and what affects the relative contribution of ensembles crosslinking versus motoring activities. Since biophysical measurements of ensembles are sparse, modeling of actomyosin networks has aided in discovering the complex behaviors of NMMII ensembles. Myosin ensembles have been modeled via several strategies with variable discretization/coarse-graining and unbinding dynamics, and while general assumptions that simplify motor ensembles result in global contractile behaviors, it remains unclear which strategies most accurately depict cellular activity. Here, we used an agent-based platform, Cytosim, to implement several models of NMMII ensembles. Comparing the effects of bond type, we found that ensembles of catch-slip and catch motors were the best force generators and binders of filaments. Slip motor ensembles were capable of generating force but unbound frequently, resulting in slower contractile rates of contractile networks. Coarse-graining of these ensemble types from two sets of 16 motors on opposite ends of a stiff rod to two binders, each representing 16 motors, reduced force generation, contractility, and the total connectivity of filament networks for all ensemble types. A parallel cluster model (PCM) previously used to describe ensemble dynamics via statistical mechanics, allowed better contractility with coarse-graining, though connectivity was still markedly reduced for this ensemble type with coarse-graining. Together our results reveal substantial trade-offs associated with the process of coarse-graining NMMII ensembles and highlight the robustness of discretized catch-slip ensembles in modeling actomyosin networks. STATEMENT OF SIGNIFICANCEAgent-based simulations of contractile networks allow us to explore the mechanics of actomyosin contractility, which drives many cell shape changes including cytokinesis, the final step of cell division. Such simulations should be able to predict the mechanics and dynamics of non-muscle contractility, however recent work has highlighted a lack of consensus on how to best model the non-muscle myosin II. These ensembles of approximately 32 motors are the key components responsible for driving contractility. Here, we explored different methods for modeling non-muscle myosin II ensembles within the context of contractile actomyosin networks. We show that the level of coarse-graining and the choice of unbinding model used to model motor unbinding under load indeed has profound effects on contractile network dynamics.

cell biology↗

bioRxiv2019

Spherical Spindle Shape Promotes Perpendicular Cortical Orientation by Preventing Isometric Cortical Pulling on both Spindle Poles during C. elegans Female Meiosis

Meiotic spindles are positioned perpendicular to the oocyte cortex to facilitate segregation of chromosomes into a large egg and a tiny polar body. In C. elegans, spindles are initially ellipsoid and parallel to the cortex before shortening to a spherical shape and rotating to the perpendicular orientation by dynein-driven cortical pulling. The mechanistic connection between spindle shape and rotation has remained elusive. Here we used mutants of the microtubule-severing protein katanin to manipulate spindle shape without eliminating cortical pulling. In a katanin mutant, spindles remained ellipsoid, had pointed poles and became trapped in either a diagonal or a parallel orientation. Results indicated that astral microtubules emanating from both spindle poles initially engage in cortical pulling until microtubules emanating from one pole detach from the cortex allowing pivoting of the spindle. The lower viscous drag experienced by spherical spindles prevented recapture of the cortex by astral microtubules emanating from the detached pole. In addition, maximizing contact between pole dynein and cortical dynein stabilizes round poles in a perpendicular orientation. Spherical spindle shape can thus promote perpendicular orientation by two distinct mechanisms.

cell biology↗