Biology subjects

Smiley, A.

Publications and source records attributed to Smiley, A..

6 recordsLinked to original sources

bioRxiv2026

Pauses in a fast-paced life: Intermittent hovering in hummingbirds

Hummingbirds are known for sustained hovering powered by rapid and continuous wingbeats. Here, we describe and quantify a novel flight behavior, intermittent hovering, in which hovering hummingbirds momentarily pause their wing motion mid-air but maintain their vertical position in space, keeping their wings fully extended at the end of the upstroke. We present the first systematic account of flap-pauses and wing coloration across hummingbirds, and evaluate potential morphological and ecological correlates, as well as evolutionary patterns in the expression of this behavior. Slow-motion footage from 86 species spanning all nine major hummingbird clades shows that at least 45 species exhibited flap-pauses during sustained hovering. Phylogenetic comparative analyses revealed that hovering pauses are evolutionarily conserved and significantly associated with both greater body mass and longer wings. Furthermore, we found that the 16 species in our study with colored underwings also exhibit significantly longer wings. The convergence of intermittent hovering, wing elongation, and chromatic traits leads us to hypothesize that this flight behavior plays a role in visual and/or auditory communication.

evolutionary biology↗

bioRxiv2024

Single-chain nanobody inhibition of Notch and avidity enhancement utilizing the β-pore forming toxin Aerolysin

Notch plays critical roles in developmental processes and disease pathogenesis, which has led to numerous efforts to modulate its function with small molecules and antibodies. Here we present a nanobody inhibitor of Notch signaling, derived from a synthetic phage-display library targeting the notch Negative Regulatory Region (NRR). The nanobody inhibits Notch signaling in a luciferase reporter assay and in Notch-dependent hematopoietic progenitor cell differentiation assay, despite a modest 19uM affinity for Notch. We addressed the low affinity by fusion to a membrane-associating domain derived from the {beta}-Pore forming toxin Aerolysin, resulting in a significantly improved IC50 for Notch inhibition. The nanobody-aerolysin fusion inhibits proliferation of T-ALL cell lines with similar efficacy to other Notch pathway inhibitors. Overall, this study reports the development of a Notch inhibitory antibody, and demonstrates a proof-of-concept for a generalizable strategy to increase the efficacy and potency of low-affinity antibody binders.

biochemistry↗

bioRxiv2024

Estimating wingbeat frequency on hummingbirds by using a no-labeling learning computer vision approach

SynopsisWingbeat frequency estimation is an important aspect for the study of avian flight, energetics, and behavioral patterns, among others. Hummingbirds, in particular, are ideal subjects to test a method for this estimation due to their fast wing motions and unique aerodynamics, which results from their ecological diversification, adaptation to high-altitude environments, and sexually selected displays. Traditionally, wingbeat frequency measurements have been done via "manual" image/sound processing. In this study, we present an automated method to detect, track, classify, and monitor hummingbirds in high-speed video footage, accurately estimating their wingbeat frequency using computer vision techniques and signal analysis. Our approach utilizes a zero-shot learning algorithm that eliminates the need for labeling during training. Results demonstrate that our method can produce automated wingbeat frequency estimations with minimal supervision, closely matching those performed by trained human observers. This comparison indicates that our method can, in some scenarios, achieve low or zero error compared to a human, making it a valuable tool for flight analysis. Automating video analysis can assist wingbeat frequency estimation by reducing processing time and, thus, lowering barriers to analyze biological data on fields such as aerodynamics, foraging behavior, and signaling.

bioinformatics↗

bioRxiv2024

Sequence-directed covalent protein-RNA linkages using engineered HUH-Tags

Replication-initiating HUH-endonucleases (Reps) are enzymes that form covalent bonds with single-stranded DNA (ssDNA) in a sequence specific manner to initiate rolling circle replication. These nucleases have been co-opted for use in biotechnology as sequence specific protein-ssDNA bioconjugation fusion partners dubbed HUH-tags. Here, we describe the engineering and in vitro characterization of a series of laboratory evolved HUH-tags capable of forming robust sequence-directed covalent bonds with unmodified RNA substrates. We show that promiscuous Rep-RNA interaction can be enhanced through directed evolution from nearly undetectable levels in wildtype enzymes to robust reactivity in final engineered iterations. Taken together, these engineered HUH-tags represent a promising platform for enabling site-specific protein-RNA covalent bioconjugation in vitro, potentially mediating a host of new applications and offering a valuable addition to the HUH-tag repertoire.

biochemistry↗

bioRxiv2023

Winging it: Unveiling how hummingbirds alter their flying kinematics during molt.

Hummingbirds are well known for their hovering flight, one of the most energetically expensive modes of locomotion among animals. Molt is a costly event in the annual cycle, in which birds replace their feathers, including all their primary feathers which, in hummingbirds, comprise most of the area of the wing. Despite this, the effects of molt on hovering flight are not well known. Here, we examined high-speed videos (14 individuals of three species from the Colombian Andes recorded at 1200 FPS) comparing molting and non-molting hummingbirds wing kinematics and wingtip trajectories. We found that molting hummingbirds extended their wings in sharper angles during both downstroke and upstroke compared to non-molting individuals (10{degrees} vs 20{degrees}, and 15{degrees} vs 29{degrees}, respectively), while other flight parameters remained unchanged. Our findings show that hummingbirds are capable of sustaining hovering flight kinematics even under impressive wing area reductions by adjusting their wing flapping behavior.

biophysics↗

bioRxiv2022

Oxygen availability drives blood traits and the cell number-size tradeoff across Andean hummingbirds

Predictable trait variation across environmental gradients suggests that adaptive evolution repeatedly finds the same solution to a challenge. Trait-environment associations can reflect long-term, genetic evolution across phylogenies, or short-term, plastic responses of individuals. When phylogenetic and population-level patterns match, it implies consistency between the long timescale of adaptation and the short timescale of acclimatization. Alternatively, genetic adaptation can find solutions that break the rules of trait-environment covariation. For example, blood-hemoglobin concentration ([Hb]) increases at high elevations in animals, but genetic adaptations in some populations have been shown to augment tissue oxygenation while curtailing hemoglobin production, altering this predictable [Hb]-elevation association. Here, we tested whether species adaptation to elevation generally alters trait-environment relationships for blood. To do this, we measured blood traits of 1,217 individuals representing 77 species of Andean hummingbirds, across a 4,600 m elevational gradient. We used hierarchical Bayesian modeling to estimate blood trait responses to elevation, environmental temperature, precipitation, individual and species characteristics, and phylogeny. Strikingly, the effects of elevation on [Hb] and hematocrit (Hct) were nearly identical for individuals and species, implying that rules of elevational blood variation are set by physics of gas exchange in the hummingbird respiratory system and are unchanged by species adaptation. However, when we looked at mechanisms of [Hb] adjustment--by changes in red blood cell size or number--we did find a signal of species adaptation: To adjust [Hb], species at low and high elevations, respectively, tended to adjust cell size, whereas species at mid-elevations tended to adjust cell number. Despite scale-independent elevational variation in [Hb] and Hct, the species-specific balance of red blood cell size versus number appears to have been affected by adaptations that distinguish hummingbird species living at moderate versus high elevations.

evolutionary biology↗