bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of odorants on perception of sweetness by honey bees
Authors: Pel Allyson V. , Van Nest Byron N. , Hathaway Stephanie R. , Fahrbach Susan E. 
Published: August 2023

AbstractOrganic volatiles produced by fruits can result in overestimation of sweetness by humans, but it is unknown if a comparable phenomenon occurs in other species. Honey bees collect nectar of varying sweetness at different flowering plants. Bees discriminate sugar concentration and generally prefer higher concentrations; they encounter floral volatiles as they collect nectar, suggesting that they, like humans, could be susceptible to sweetness enhancement by odorant. In this study, limonene, linalool, geraniol, and 6-methyl-5-hepten-2-ol were tested for their ability to alter behaviors related to perception of sweetness by honey bees. Honey bees were tested in the laboratory using proboscis extension response-based assays and in the field using feeder-based assays. In the laboratory assays, 6-methyl-5-hepten-2-ol and geraniol, but neither linalool nor limonene, significantly increased responses to low concentrations of sucrose compared with no odorant conditions in 15-day and 25-day-old adult worker honey bees, but not in 35-day-old bees. Limonene reduced responding in 15-day-old bees, but not in the older bees. There was no odorant- based difference in performance in field assays comparing geraniol and limonene with a no odorant control. The interaction of the tested plant volatiles with sucrose concentration revealed in laboratory testing is therefore unlikely to be a major determinant of nectar choice by honey bees foraging under natural conditions. Because geraniol is a component of honey bee Nasonov gland pheromone as well as a floral volatile, its impact on responses in the laboratory may reflect conveyance of different information than the other odorants tested.
Decrease in reaction time for volleyball athletes during saccadic eye movement task: An associative analysis with evoked potentials
Authors: Costa Élida , Gongora Mariana , Bittencourt Juliana , Marinho Victor , Cagy Mauricio , Teixeira Silmar , Nicoliche Eduardo , Fernandes Isabelle , Wienecke Jacob , Ribeiro Pedro , Gupta Daya S. , Velasques Bruna , Budde Henning 
Published: August 2023

AbstractAimThe current study investigated the differences to event-related potential and reaction time under two groups (athletesvs. non-athletes).Material and MethodsThe P300 was analyzed for Fz, Cz and Pz electrodes in thirty-one healthy volunteers divided into two groups (volleyball athletes and non-athletes). In addition, the participants performed a saccadic eye movement task to measure reaction time.ResultsThe EEG analysis showed that the athletes in comparison to the no-athletes has differences of the P300 in the frontal area (p=0.021). In relation to reaction time, the results show lower reaction time for athletes (p=0.001).ConclusionsThe volleyball athletes may present a greater allocation of attention during the execution of the inhibition task, since they have a lower reaction time for responses when compared to non-athletes.
Embryonic life histories in annual killifish: adapted to what?
Authors: Van Dooren Tom JM 
Published: August 2023

AbstractAdaptation requires an evolving strategy and an environment. Given an environment, we predict or estimate which strategies are adapted. Given a strategy, we want to know in which environments it might be adapted. Example calculations aiming to determine such environments, named evolutionarily singular environments ESE, are presented using lab data on embryonic life histories ofAustrolebiasannual killifish. Annual killifish embryos can arrest development and survive desiccation of temporary ponds in the soil. They might implement diversified bet-hedging, generally seen as an adaptation to uncertain environments. Using parameter estimates and parsimonious assumptions, a population dynamical model is constructed with explicit developmental stages. Using invasion fitness gradients of rates of development and hatching probabilities, it is investigated whether these could be adapted to pond filling regimes with gradual filling and drying and deterministic within-year variation only. The life history as a whole is not adapted to the regular within-year annual cycles investigated, with one or two periods where reproduction can occur. Faster development rates were always favoured, just as in constant environments. Only for hatching probabilities, pond filling regimes were found which made their invasion fitness sensitivities zero. However, the observed trait values did not have long-term evolutionary stability in these ESE. Therefore, neither the developmental rates nor the hatching strategy seem adapted to within-year patterns of environmental change.
Quantifying the Influence of the Actin Cytoskeleton on Ion Transport in Dendritic Spines by Homogenization of the Poisson-Nernst-Planck Equations
Authors: Eberhardt Florian 
Published: August 2023

AbstractDendritic spines are filled with a very dense actin cytoskeleton. However, due to their small size, the impact of this mesh on biophysical parameters has not been studied so far, and it remains unclear to what extent it might affect ion flow in dendritic spines. Only recently has the three-dimensional internal structure of dendritic spines been quantified in great detail in electron microscopic tomography data. Based on these results, we estimate the effect of the spine actin cytoskeleton on diffusion and permittivity. We apply a method called homogenization to estimate effective diffusion tensors and permittivity tensors in Poisson-Nernst-Planck (PNP) equations. We find that the volume taken up by the intracellular structure alone cannot explain the changes in these biophysical parameters. The characteristic architecture of the intracellular space in dendritic spines will reduce the diffusion of ions by 33% to 46% and the permittivity by 30% to 42%, compared to values found for the cytosol free of intracellular structures.These results can be used to improve computational studies using PNP equations and help to better interpret experimental results of electrical and chemical compartmentalization.
In-depth immunometabolic profiling by measuring cellular protein translation inhibition via bioorthogonal noncanonical amino acid tagging (CENCAT)
Authors: Vrieling Frank , van der Zande Hendrik J.P. , Naus Britta , Smeehuijzen Lisa , Ignacio Bob J. , Bonger Kimberly M. , Van den Bossche Jan , Kersten Sander , Stienstra Rinke 
Published: August 2023

AbstractMotivationExtracellular Flux (XF) analysis has been a key technique in immunometabolism research, measuring cellular oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) to determine immune cell metabolic profiles. However, XF analysis has several limitations, including the need for purified adherent cells, relatively high cell numbers, and specialized equipment. Recently, a novel flow cytometry-based technique called SCENITH (Single Cell Energetic metabolism by profiling Translation inhibition) was introduced, which measures the inhibition of cellular protein synthesis as a proxy for metabolic activity in single cells. A limitation of this technique is its reliance on fluorescent staining of intracellular puromycin, a toxic antibiotic. To address this, we propose an alternative approach using biorthogonal noncanonical amino acid tagging (BONCAT) to measure protein synthesis.SummaryThe field of immunometabolism has revealed that cellular energy metabolism significantly contributes to immune cell function. Disturbances in immune cell metabolism have been associated with various diseases, including obesity, atherosclerosis, and cancer. To further advance immunometabolic research, developing novel methods to study the metabolism of immune cells in complex samples is essential. Here, we introduce CENCAT (Cellular Energetics through Non-Canonical Amino acid Tagging). This technique utilizes click-labeling of alkyne-bearing non-canonical amino acids (ncAAs) to measure protein synthesis inhibition as a proxy of metabolic activity. CENCAT successfully reproduced known metabolic signatures of immune cell activation. Specifically, LPS/IFNγ-induced classical activation increased glycolytic capacity, and IL-4-induced alternative activation enhanced mitochondrial dependence in human primary macrophages. The assay’s applicability was further explored in more complex samples, including peripheral blood mononuclear cells (PBMCs) from healthy volunteers, which revealed diverse metabolic rewiring in immune cell subsets upon stimulation with different activators. Finally, CENCAT was used to analyze the cellular metabolism of murine tissue-resident immune cells from various organs. Principal component analysis (PCA) revealed tissue-specific clustering based on metabolic profiles, likely driven by microenvironmental priming of tissue-resident immune cells. In conclusion, CENCAT offers valuable insights into immune cell metabolic responses and presents a powerful platform for studying immune cell metabolism in complex samples and tissue-resident immune populations in both human and murine studies.
Social attention across development in common ravens and carrion crows
Authors: Miller Rachael , Boeckle Markus , Ridgway Sophie , Richardson James , Uhl Florian , Bugnyar Thomas , Schwab Christine 
Published: August 2023

ABSTRACTUnderlying social learning and other important aspects of successful adaptation to social life is social awareness, where individuals are required to pay attention and respond flexibly to others in their environment. We tested the influence of social context (alone, affiliate, non-affiliate, heterospecific) on behavioural interactions (manipulation, caching, head & body out of sight i.e. barrier use) with food and objects during development at fledging (1-2 months), juvenile (3-8 months) and sub-adult (14-18 months old) in 10 carrion crows (Corvus corone; C. cornix) and nine common ravens (C. corax). These species are closely related, generalist corvids and subjects were all hand-reared and housed in highly comparable conditions. Both species will routinely cache, i.e. hide food and other items for later recovery, and engage in cache-pilfering (stealing) strategies. They will interact and ‘play’ with objects, potentially as part of developing social bonding and/or physical skills. We found that corvid behaviour was influenced by social context, with birds showing higher frequency of ‘head & body out of sight’ behaviour while others were observing than when alone, suggesting they have an awareness of other’s presence and respond by using barriers when interacting with items. There were no differences based on observer identity, supporting an interpretation of item interaction and play potentially driving development of physical skills in this setting. There were developmental effects, including increased manipulation and use of barriers as juveniles as well as increased caching with age. Ravens generally cached more than crows. Objects were manipulated more frequently than food, while barriers were used more with food, indicating that food was more likely to be actively hidden while objects may promote open play. We discuss our findings in relation to other social and developmental influences on behaviour and the wider ramifications for identifying the drivers of play in animals.
Constitutive activity of ionotropic glutamate receptors via hydrophobic substitutions in the ligand-binding domain
Authors: Seljeset Sandra , Sintsova Oksana , Wang Yuhong , Harb Hassan Y. , Lynagh Timothy 
Published: August 2023

SUMMARYNeurotransmitter ligands electrically excite neurons by activating ionotropic glutamate receptor (iGluR) ion channels. Knowledge of the iGluR amino acid residues that dominate ligand-induced activation would enable the prediction of function from sequence. We therefore explored the molecular determinants of activity in rat NMDA-type iGluRs (NMDA receptors), complex heteromeric iGluRs comprising two glycine-binding GluN1 and two glutamate-binding GluN2 subunits, using amino acid sequence analysis, mutagenesis, and electrophysiology. We find that a broadly conserved aspartate residue controls both ligand potency and channel activity, to the extent that certain substitutions at this position bypass the need for ligand-binding in GluN1 subunits, generating NMDA receptors activated solely by glutamate. Furthermore, we identify a homomeric iGluR from the placozoanTrichoplax adhaerensthat has utilized native mutations of this crucial residue to evolve into a leak channel that is inhibited by neurotransmitter binding, pointing to a dominant role of this residue throughout the iGluR superfamily.
NaV1.6 inhibition drives the efficacy of voltage-gated sodium channel inhibitors to prevent electrically induced seizures in both wild type andScn8aN1768D/+gain-of-function mice
Authors: Johnson JP , Focken Thilo , Tari Parisa Karimi , Dube Celine , Goodchild Samuel J , Andrez Jean-Christophe , Bankar Girish , Burford Kristen , Chang Elaine , Chowdhury Sultan , Christabel Jessica , Dean Richard , de Boer Gina , Dehnhardt Christoph , Gong Wei , Grimwood Michael , Hussainkhel Angela , Jia Qi , Khakh Kuldip , Lee Stephanie , Li Jenny , Lin Sophia , Lindgren Andrea , Lofstrand Verner , Mezeyova Janette , Nelkenbrecher Karen , Shuart Noah Gregory , Sojo Luis , Sun Shaoyi , Waldbrook Matthew , Wesolowski Steven , Wilson Michael , Xie Zhiwei , Zenova Alla , Zhang Wei , Scott Fiona , Cutts Alison J , Sherrington Robin P , Winquist Raymond , Cohen Charles J , Empfield James R 
Published: August 2023

AbstractInhibitors of voltage-gated sodium channels (NaVs) are important anti-epileptic drugs, but the contribution of specific channel isoforms is unknown since available inhibitors are nonselective. We created a series of compounds with diverse selectivity profiles enabling block of NaV1.6 alone or together with NaV1.2. Mice with a heterozygous gain-of-function mutation (N1768D/+) in Scn8a (encoding NaV1.6) responded with a tonic-clonic seizure to a mild 6 Hz stimulus that was innocuous to wild-type mice. Pharmacologic inhibition of NaV1.6 inScn8aN1768D/+mice prevented seizures. Inhibitors were also effective in a direct current maximal electroshock seizure assay in wild-type mice. NaV1.6 inhibition correlated with efficacy in both models, even without inhibition of other CNS NaVisoforms. Our data suggest NaV1.6 inhibition is a driver of efficacy for NaVinhibitor anti-seizure medicines. Selective NaV1.6 inhibitors may provide targeted therapies for human Scn8a developmental and epileptic encephalopathies and better tolerated treatments for idiopathic epilepsies.Graphical Abstract
Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third generation sequencing
Authors: Gajski Domagoj , Wolff Jonas O. , Melcher Anja , Weber Sven , Prost Stefan , Krehenwinkel Henrik , Kennedy Susan R. 
Published: August 2023

AbstractPhylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.HighlightsDNA barcoding is an invaluable tool for fast and accurate taxonomic classificationExisting DNA barcodes are still insufficient for obtaining well-supported phylogeniesWe present a protocol that produces long amplicons of unlinked loci for spidersAmplicons are sequenced at very low cost per specimen with ONT MinIONOur recovered phylogeny is largely consistent with that of high-cost approaches.
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions
Authors: Sun Heqi , Wang Jianmin , Wu Hongyan , Lin Shenggeng , Chen Junwei , Wei Jinghua , Lv Shuai , Xiong Yi , Wei Dong-Qing 
Published: August 2023

ABSTRACTProtein-protein interactions (PPIs) are essential for various biological processes and diseases. However, most existing computational methods for identifying PPI modulators require either target structure or reference modulators, which restricts their applicability to novel PPI targets. To address this challenge, we propose MultiPPIMI, a sequence-based deep learning framework that predicts the interaction between any given PPI target and modulator. MultiPPIMI integrates multimodal representations of PPI targets and modulators, and uses a bilinear attention network to capture inter-molecular interactions. Experimental results on our curated benchmark dataset show that MultiPPIMI achieves an average AUROC of 0.837 in three cold-start scenarios, and an AUROC of 0.994 in the random-split scenario. Furthermore, the case study show that MultiPPIMI can assist molecular simulations in screening inhibitors of Keap1/Nrf2 PPI interactions. We believe that the proposed method provides a promising way to screen PPI-targeted modulators.
KAT8 compound inhibition inhibits the initial steps of PINK1-dependant mitophagy
Authors: de Talhouët Capucine , Esteras Gallego Noemi , Soutar Marc , O’Callaghan Benjamin , Plun-Favreau Helene 
Published: August 2023

AbstractIt has recently been shown thatKAT8, a genome-wide association study (GWAS) candidate risk gene for Parkinson’s Disease, is involved in PINK1/Parkin-dependant mitophagy. TheKAT8gene encodes a lysine acetyltransferase and represents the catalytically active subunit of the non-specific lethal (NSL) epigenetic remodelling complex. In the current study, we show that contrary to KAT5 inhibition, dual inhibition of KAT5 and KAT8 via the MG149 compound inhibits the initial steps of the PINK1-dependant mitophagy process. More specifically, our study shows that following mitochondrial depolarisation induced by mitochondrial toxins, MG149 treatment inhibits PINK1-dependant mitophagy initiation by impairing PINK1 activation, and subsequent phosphorylation of Parkin and ubiquitin. While this inhibitory effect of MG149 on PINK1-activation is potent, MG149 treatment in the absence of mitochondrial toxins is sufficient to depolarise the mitochondrial membrane, recruit PINK1 and promote partial downstream recruitment of the autophagy receptor p62, leading to an increase in mitochondrial delivery to the lysosomes. Altogether, our study provides additional support for KAT8 as a regulator of mitophagy and autophagy processes.
Is your data alignable? Principled and interpretable alignability testing and integration of single-cell data
Authors: Ma Rong , Sun Eric D. , Donoho David , Zou James 
Published: August 2023

AbstractSingle-cell data integration can provide a comprehensive molecular view of cells, and many algorithms have been developed to remove unwanted technical or biological variations and integrate heterogeneous single-cell datasets. Despite their wide usage, existing methods suffer from several fundamental limitations. In particular, we lack a rigorous statistical test for whether two high-dimensional single-cell datasets are alignable (and therefore should even be aligned). Moreover, popular methods can substantially distort the data during alignment, making the aligned data and downstream analysis difficult to interpret. To overcome these limitations, we present a spectral manifold alignment and inference (SMAI) framework, which enables principled and interpretable alignability testing and structure-preserving integration of single-cell data. SMAI provides a statistical test to robustly determine the alignability between datasets to avoid misleading inference, and is justified by high-dimensional statistical theory. On a diverse range of real and simulated benchmark datasets, it outperforms commonly used alignment methods. Moreover, we show that SMAI improves various downstream analyses such as identification of differentially expressed genes and imputation of single-cell spatial transcriptomics, providing further biological insights. SMAI’s interpretability also enables quantification and a deeper understanding of the sources of technical confounders in single-cell data.
Investigating experimental storage methodologies for the understudied intermediate recalcitrant seed of Northern Wild Rice (Zizania palustrisL.)
Authors: Mickelson A. , McGilp L. , Kimball J. 
Published: August 2023

AbstractThe maintenance of plant genetic diversity is an essential target for conservation and breeding efforts. However, the ability to store seed varies between species with those that are more easily stored being overrepresented in seed banks. Northern Wild Rice (NWR;Zizania palustris) has intermediately recalcitrant seed which, along with its dormancy period, makes it more challenging to store long term. This study evaluated alternate storage treatments, including water changes, aeration, and the shift from submerged to moist seed, to extend the longevity of NWR seed in storage compared to current best management practices. Monthly water changes were the most effective storage treatment, maintaining greater than ∼ 50% viability for over 28 months. There was a negative correlation found between aerated treatments with high dissolved oxygen and seed viability. Submerged to moist storage was only effective for ∼16 months. Control treatments maintained relatively high viability (≥ 58%) through 21 months of storage. However, by 28 months, monthly water change seed had significantly higher viability (57.6%) compared to either the standard control (37.2%) or the bucket control (28.9%), suggesting that this treatment is more efficacious than standard storage conditions for maintaining seed viability of NWR.
An end-to-end workflow for non-destructive 3D pathology
Authors: Bishop Kevin W. , Barner Lindsey A. Erion , Han Qinghua , Baraznenok Elena , Lan Lydia , Poudel Chetan , Gao Gan , Serafin Robert B. , Chow Sarah S.L. , Glaser Adam K. , Janowczyk Andrew , Brenes David , Huang Hongyi , Miyasato Dominie , True Lawrence D. , Kang Soyoung , Vaughan Joshua C. , Liu Jonathan T.C. 
Published: August 2023

AbstractRecent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end protocol covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. While 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol will focus on a fluorescent analog of hematoxylin and eosin (H&E), which remains the most common stain for gold-standard diagnostic determinations. We present our guidelines for a broad range of end-users (e.g., biologists, clinical researchers, and engineers) in a simple tutorial format.