bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting bat environmental DNA from water-filled road-ruts in upland forest
Authors: Marshall Nathaniel T. , Symonds Daniel E. , Walker Faith M , Sanchez Daniel E , Couch Zachary L. , Kiser James D. 
Published: June 2022

ABSTRACTDeclines in population and diversity of North American bats are rapidly occurring due to habitat loss, incidental take from various industry projects, and lethal White-nose Syndrome disease. It is critical to accurately census habitat for appropriate conservation measures, yet traditional sampling methodology, such as mist netting and acoustic recordings, can be time-intensive and biased. Instead, a passive sampling tool that does not rely on the a priori knowledge of bat roosts may provide crucial information on bat communities. In the water-limited habitats of forested uplands of the Appalachian Plateau, water-filled road-ruts are important resources for bats. Therefore, we developed an environmental DNA (eDNA) protocol to sample isolated road-ruts that may have the presence of sloughed cellular material from actively drinking bats. The detection of bat eDNA was investigated from a positive control experiment, and across 47 water samples collected in Kentucky and Ohio. Water samples were analyzed using both species-specific quantitative polymerase chain reaction (qPCR) and community metabarcoding methodologies. Using qPCR analysis, we detected eDNA from big brown bat (Eptesicus fuscus) and eastern red bat (Lasiurus borealis) from water-filled road-ruts. While the community metabarcoding approach failed to detect any bat eDNA, many non-target amphibians, birds, and mammals were identified. These results suggest eDNA found within road-ruts provides an additional detection tool for surveying biodiversity across upland forests. Additionally, the use of qPCR increased the detection of rare eDNA targets, which will be crucial for properly implementing future eDNA applications for improving bat conservation efforts across the landscape.Article impact statementEnvironmental DNA provides detection of bats from drinking sources offering a novel survey method for management and conservation efforts
Spatio-temporal dynamics of nuclear CREB1: what does it mean?
Authors: Farias Altamirano Luz E. , Vásquez Elena , Freites Carlos L. , Ibañez Jorge E. , Guido Mario E. , Muñoz Estela M. 
Published: June 2022

AbstractIn the mammalian pineal gland (PG), cyclic AMP responsive element-binding protein 1 (CREB1) participates in the nocturnal melatonin synthesis that rhythmically modulates physiology and behavior. Phosphorylation of CREB1 present in pinealocyte nuclei is one of the key regulatory steps that drives pineal transcription. The spatio-temporal dynamics of CREB1 itself within PG cell types have not yet been documented. In this study we analyzed total CREB1 via Western blot, and the dynamism of CREB1 nuclear distribution in individual rat pinealocytes using fluorescence immunohistochemistry followed by confocal laser-scanning microscopy and quantitative analysis. Total CREB1 levels remained constant in the PG throughout the light:dark cycle. The distribution pattern of nuclear CREB1 did vary, however, among different PG cells. Pinealocytes emerged as having discrete CREB1 domains within their nucleoplasm that were especially distinct. The number, size, and location of CREB1 foci fluctuated among pinealocytes, within the same PG and amongZeitgebertimes. A significantly larger dispersion of CREB1-immunoreactive nuclear sites was found at night. This was not accompanied by changes in the overall transcription activity, which was mostly conserved between the light and dark phases, as shown by the expression of a particular phosphorylated form of the RNA polymerase II (RNAPII-pSer5CTD). Suppression of the nocturnal norepinephrine pulse by chronic bilateral superior cervical ganglionectomy increased CREB1 dispersion in pinealocyte nuclei, as compared to sham-derived cells. In addition, differences in CREB1 distribution were found between sham-operated and non-operated rats at early night. Together, these data suggest that in mature pinealocytes nuclear CREB1 is subjected to a dynamic spatio-temporal distribution. Further studies are necessary to elucidate the underlying mechanisms, including the role of chromatin and interchromatin elements, and to understand the impact of CREB1 reorganization in the pineal transcriptome.
Genotype-environment interactions determine microbiota plasticity inNematostella vectensis
Authors: Baldassarre Laura , Reitzel Adam M. , Fraune Sebastian 
Published: June 2022

AbstractMost multicellular organisms harbor microbial colonizers that provide various benefits to their hosts. Although these microbial communities may be host species- or even genotype-specific, the associated bacterial communities can respond plastically to environmental changes. In this study, we estimated the relative contribution of environment and host genotype to bacterial community composition inNematostella vectensis, an estuarine cnidarian. We isolatedN. vectensispolyps from five different populations along a north-south gradient on the Atlantic coast of the United States and Canada at three different times of the year. While half of the polyps were immediately analyzed for their bacterial composition by 16S rRNA gene sequencing, the remaining polyps were cultured under laboratory conditions for one month. Bacterial community comparison analyses revealed that laboratory maintenance reduced bacterial diversity by fourfold, but maintained a population-specific bacterial colonization. Interestingly, the differences between bacterial communities correlated strongly with seasonal variations, especially with ambient water temperature. To decipher the contribution of both ambient temperature and host genotype to bacterial colonization, we generated 12 clonal lines from six different populations in order to maintain each genotype at three different temperatures for three months. The bacterial community composition of the sameN. vectensisclone differed greatly between the three different temperatures, highlighting the contribution of ambient temperature to bacterial community composition. To a lesser extent, bacterial community composition varied between different genotypes under identical conditions, indicating the influence of host genotype. In addition, we identified a significant genotype x environment interaction determining microbiota plasticity inN. vectensis. From our results we can conclude thatN. vectensis-associated bacterial communities respond plastically to changes in ambient temperature, with the association of different bacterial taxa depending in part on the host genotype. Future research will reveal how this genotype-specific microbiota plasticity affects the ability to cope with changing environmental conditions.
Improving the workflow to crack Small, Unbalanced, Noisy, but Genuine (SUNG) datasets in bioacoustics: the case of bonobo calls
Authors: Arnaud Vincent , Pellegrino François , Keenan Sumir , St-Gelais Xavier , Mathevon Nicolas , Levréro Florence , Coupé Christophe 
Published: June 2022

AbstractDespite the accumulation of data and studies, deciphering animal vocal communication remains highly challenging. While progress has been made with some species for which we now understand the information exchanged through vocal signals, researchers are still left struggling with sparse recordings composing Small, Unbalanced, Noisy, but Genuine (SUNG) datasets. SUNG datasets offer a valuable but distorted vision of communication systems. Adopting the best practices in their analysis is therefore essential to effectively extract the available information and draw reliable conclusions. Here we show that the most recent advances in machine learning applied to a SUNG dataset succeed in unraveling the complex vocal repertoire of the bonobo, and we propose a workflow that can be effective with other animal species. We implement acoustic parameterization in three feature spaces along with three classification algorithms (Support Vector Machine, xgboost, neural networks) and their combination to explore the structure and variability of bonobo calls, as well as the robustness of the individual signature they encode. We underscore how classification performance is affected by the feature set and identify the most informative features. We highlight the need to address data leakage in the evaluation of classification performance to avoid misleading interpretations. Finally, using a Uniform Manifold Approximation and Projection (UMAP), we show that classifiers generate parsimonious data descriptions which help to understand the clustering of the bonobo acoustic space. Our results lead to identifying several practical approaches that are generalizable to any other animal communication system. To improve the reliability and replicability of vocal communication studies with SUNG datasets, we thus recommend: i) comparing several acoustic parameterizations; ii) adopting Support Vector Machines as the baseline classification approach; iii) explicitly evaluating data leakage and possibly implementing a mitigation strategy; iv) visualizing the dataset with UMAPs applied to classifier predictions rather than to raw acoustic features.
Comparative analysis of piRNA sequences, targets and functions in nematodes
Authors: Hertz Hannah L. , Pastore Benjamin , Tang Wen 
Published: June 2022

ABSTRACTPiwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in C. briggsae, a sibling species of the model organism C. elegans. Our analyses define 25,883 piRNA producing-loci in C. briggsae. piRNA sequences in C. briggsae are extremely divergent from their counterparts in C. elegans, yet both species adopt similar genomic organization that drive piRNA expression. By examining production of Piwi-mediated secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to C. elegans, small RNAs targeting ribosomal RNAs or histone transcripts are not hyper-accumulated in C. briggsae Piwi mutants. Instead, we found that transcripts with few introns are prone to small RNA overamplification. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.
Binding Free Energies of Piezo1 Channel Agonists at Protein-Membrane Interface
Authors: Jiang Wenjuan , Zhang Han , Yichun-Lin  , Im Wonpil , Lacroix Jerome J. , Luo Yun Lyna 
Published: June 2022

AbstractMechanosensitive Piezo channels convert mechanical stimuli into biological signals in vertebrates. Piezo1 chemical modulators are anticipated to yield many clinical benefits. To date, Yoda1 is the most potent and widely used Piezo1-selective agonist, yet how Yoda1 interacts with Piezo1 at the protein-membrane interface and stabilizes Piezo1’s open state remains elusive. Here, using a previously identified putative Yoda1 binding site and three molecular dynamics (MD)-based methods, we computed the binding free energies of Yoda1 and its analogs in a Piezo1 cryo-EM closed state and anin silicoopen state. Our computed absolute binding free energy of Yoda1 in the closed state agrees well with the experimentalKdin which Piezo1 is expected to be in a closed state. More importantly, Yoda1 binds the open state better than the closed state, in agreement with its agonist effects. All three methods predicted that Dooku1, a Yoda1 analog, binds the closed state stronger than Yoda1, but binds the open state weaker than Yoda1. These results are consistent with the fact that Dooku1 antagonizes the effects of Yoda1 but lacks the ability to activate Piezo1. The relative binding free energies of seven Yoda1 analogs recapitulate key experimental structure-activity-relationships (SAR). Based on the state-dependent binding free energies, we were able to predict whether a molecule is an agonist or inhibitor and whether a chemical modification will lead to a change in affinity or efficacy. These mechanistic insights and computational workflow designed for transmembrane binders open an avenue to structural-based screening and design of novel Piezo1 agonists and inhibitors.
Geometric effects in gas vesicle buckling under ultrasound
Authors: Salahshoor Hossein , Yao Yuxing , Dutka Przemysław , Nyström Nivin N. , Jin Zhiyang , Min Ellen , Malounda Dina , Jensen Grant J. , Ortiz Michael , Shapiro Mikhail G. 
Published: June 2022

SUMMARYAcoustic reporter genes based on gas vesicles (GVs) have enabled the use of ultrasound to noninvasively visualize cellular function in vivo. The specific detection of GV signals relative to background acoustic scattering in tissues is facilitated by nonlinear ultrasound imaging techniques taking advantage of the sonomechanical buckling of GVs. However, the effect of geometry on the buckling behavior of GVs under exposure to ultrasound has not been studied. To understand such geometric effects, we developed computational models of GVs of various lengths and diameters and used finite element simulations to predict their threshold buckling pressures and post-buckling deformations. We demonstrated that the GV diameter has an inverse cubic relation to the threshold buckling pressure, whereas length has no substantial effect. To complement these simulations, we experimentally probed the effect of geometry on the mechanical properties of GVs and the corresponding nonlinear ultrasound signals. The results of these experiments corroborate our computational predictions. This study provides fundamental insights into how geometry affects the sonomechanical properties of GVs, which, in turn, can inform further engineering of these nanostructures for high-contrast, nonlinear ultrasound imaging.STATEMENT OF SIGNIFICANCEGas vesicles (GVs) are an emerging class of genetically encodable and engineerable imaging agents for ultrasound whose sonomechanical buckling generates nonlinear contrast to enable sensitive and specific imaging in highly scattering biological systems. Though the effect of protein composition on GV buckling has been studied, the effect of geometry has not previously been addressed. This study reveals that geometry, especially GV diameter, significantly alters the threshold acoustic pressures required to induce GV buckling. Our computational predictions and experimental results provide fundamental understanding of the relationship between GV geometry and buckling properties and underscore the utility of GVs for nonlinear ultrasound imaging. Additionally, our results provide suggestions to further engineer GVs to enable in vivo ultrasound imaging with greater sensitivity and higher contrast.
Turicibacterstrains differentially modify bile acids and host lipids
Authors: Lynch Jonathan B. , Gonzalez Erika L. , Choy Kayli , Faull Kym F. , Jewell Talia , Arellano Abelardo , Liang Jennifer , Yu Kristie B. , Paramo Jorge , Hsiao Elaine Y. 
Published: June 2022

ABSTRACTBacteria from theTuricibactergenus are prominent members of the mammalian gut microbiota and are associated with alterations in dietary fat and body weight, but the specific connections between these symbionts and host physiology are poorly understood. We genomically and phenotypically characterized a diverse set of mouse-and human-derivedTuricibacterstrains, and found they group into three clades that differ in their transformations of bile acids. We identifiedTuricibacterbile salt hydrolases that confer strain-specific differences in bile deconjugation. Colonization with individualTuricibacterstrains led to changes in host bile acid profiles, generally aligning with those producedin vitro. Further, colonizing mice with another bacterium expressing bile-modifying genes from these strains decreased serum cholesterol and triglycerides, as well as adipose tissue mass. This work identifies genes that enable diverseTuricibacterstrains to differentially modify host bile acids and lipid metabolism, and positions multipleTuricibacterstrains as candidates for altering host fat biology.MAIN TEXT
Angular speed should be avoided when estimating the speed-curvature power law in movement
Authors: Matić Adam 
Published: June 2022

AbstractThe speed-curvature power law is one of the most studied constraints in biological movement. In many types of movements, there is a strong relationship between instantaneous speed and local curvature. For example, in elliptical trajectories, tangential speed is proportional to curvature raised to the power -1/3, (V∼C-1/3). This phenomenon is known as the “one-thirds power law” and is generally considered to be mathematically equivalent to the “two-thirds power law” that describes the relationship between angular speed and curvature (A∼C2/3); the two formulations are used interchangeably. However, in this paper, analysis of empirical and synthetic data demonstrates that using angular speed instead of tangential speed to estimate the power law tends to result in much stronger correlations, impacting the interpretation of the strength of the relationship, and therefore the existence of the law. Further analysis shows that angular speed and curvature are often trivially correlated, since angular speed is not a purely kinematic variable and depends on curvature. In conclusion, two forms of the law are not equivalent, angular speed should be avoided when expressing the speed-curvature power law.
Ideal free distribution of unequal competitors: spatial assortment and evolutionary diversification of competitive ability
Authors: Netz Christoph , Ramesh Aparajitha , Weissing Franz J. 
Published: June 2022

AbstractIdeal free distribution theory attempts to predict the distribution of well-informed (‘ideal’) and unconstrained (‘free’) foragers in space based on adaptive individual decisions. When individuals differ in competitive ability, a whole array of equilibrium distributions is possible, and it is unclear which of these distributions are most likely. In the first part of our study, we show that strong competitors have an intrinsically stronger preference for highly productive habitat patches than poor competitors. This leads to an equilibrium distribution where the average competitive ability on a patch is strongly correlated with the productivity of the patch. In the second part of our study, we consider what happens if differences in competitive ability are heritable and, hence, subject to natural selection. Under constant environmental conditions, selection eliminates such differences: a single strategy prevails that optimally balances the costs and benefits associated with competitive ability. If the productivity of patches changes during the lifetime of individuals, the spatial assortment of competitors of equal competitive ability gives poor competitors a systematic advantage in times of environmental change, while good competitors benefit from equilibrium conditions. Using evolutionary individual-based simulations, we demonstrate that environmental change may then lead to the diversification of competitive ability.
Following cell type transitions in space and time by combining live-cell tracking and endpoint cell identity in intestinal organoids
Authors: Zheng Xuan , Betjes Max A. , Goos Yvonne J. , Huelsz-Prince Guizela , Clevers Hans , van Zon Jeroen S. , Tans Sander J. 
Published: June 2022

AbstractElucidating the dynamics of cellular differentiation in space and time is key to advancing organoid biology and technology. Direct visualization of differentiation patterns is challenging, however, in part because of the difficulty of simultaneously detecting all relevant cell types by fluorescence imaging. Here we present TypeTracker, which determines the differentiation trajectories of all cells within a region of interest, including their type transitions, growth, divisions, and changes in spatial organization. We show how the lineage tree topology, as determined by automated cell tracking, allows for the retrospective identification of cell types across multiple generations. The data revealed various surprising aspects of intestinal organoid differentiation, including symmetric fate adoption by sister cells, cell type abundance regulated by division, and type commitment of cells occurring prior to their spatial reorganization. Our method can be applied broadly to study other organoid systems and to screen for compounds that affect differentiation programs.
Mapping nanoscale forces and potentials in live cells with microsecond 3D single-particle tracking
Authors: Hou Shangguo , Zhang Chen , Niver Anastasia , Welsher Kevin 
Published: June 2022

Abstract3D single-particle tracking has the potential to resolve the molecular level forces which dictate particle motion in biological systems. However, the information gleaned from 3D single-particle tracking often cannot resolve underlying nanoscale potentials due to limited spatiotemporal resolution. To this end, we introduce an active-feedback 3D tracking microscope that utilizes silver nanoparticles (AgNPs) as probes to study intricate biophysical events in live cells at the nanometer and microsecond scales. Due to this extremely high and durable scattering photon flux of the plasmonic particles, 1 MHz sampling frequency at nanometer precision in all three dimensions can be achieved over an unlimited observation times. In this work, we applied microsecond-sampling, active-feedback 3D single-particle tracking to investigate the interaction between AgNPs and nanoscale filopodium on the live-cell surface. The nanometer precision and microsecond sampling revealed that TAT peptide modified particles visit and dwell at local “hot spots” on the filopodium surface. The high sampling rate further enabled the calculation of the local forces and potentials within these nanoscale hotspots on the cylindrical surface of live cell filopodia. This study presents a promising tool to investigate intracellular biophysical events with unprecedented spatiotemporal resolution and a pipeline to study nanoscale potentials on three-dimensional cellular structures.