bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artoo-Detoo: What imitating a Star Wars droid reveals on allospecific vocal imitation in parrots and starlings
Authors: Dam Nick C.P. , Honing Henkjan , Spierings Michelle J. 
Published: October 2024

AbstractVocal production learning is a widespread and remarkable phenomenon. However, the underlying mechanisms of allospecific vocal imitation are poorly understood. Parrots and corvids are well known for their imitation abilities, but imitation accuracy has not yet been studied across species in a comparative context. We compared imitation accuracy between nine parrot species and European starlings based on imitation of monophonic and multiphonic sounds, produced by the Star Wars droid R2-D2. Our results show that starlings were better at imitating multiphonic sounds than parrots. However, no difference in imitation accuracy was found between parrots and starlings when imitating monophonic sounds. The differences in imitating accuracy are likely based on a physiological difference in syrinx anatomy, rather than on perceptual or cognitive differences between starlings and parrots. Between our nine tested parrot species, we found that parrots with larger brains (e.g., African greys and amazon parrots) were less accurate at imitating monophonic sounds than smaller brained budgerigars and cockatiels. The use of citizen science in our study shows the great potential this has to expand data collection beyond traditional studies. These findings contribute to a deeper understanding of the evolution of communication complexity in vocal learners.Significance StatementVocal imitation is a hallmark of complex communication in animals, yet the mechanisms driving species differences remain poorly understood. By comparing vocal imitation across nine parrot species and European starlings, we demonstrate, for the first time, that differences in syrinx anatomy, rather than cognitive or perceptual capacities, underlie species-specific variation in imitation accuracy. Contrary to traditional expectations, smaller-brained parrots outperformed larger-brained species in monophonic sound imitation. These findings challenge assumptions that brain size is directly linked to imitation accuracy and offer insights into the evolution of complex communication. We used citizen science to create a uniquely large dataset of species imitating the same source, demonstrating the powerful potential of this approach to broaden research in comparative cognition and vocal learning.
The ratio between experimental and theoretical localization precision of single molecules is sensor-dependent and typically larger than one
Authors: Brenlla-Lopez Alfonso , Deen Laila , Annibale Paolo 
Published: October 2024

AbstractSince the advent of stochastic localization microscopy approaches in 2006, the number of studies employing this strategy to investigate the sub-diffraction limit features of fluorescently labeled structures in biology, biophysics and solid state samples has increased exponentially. Underpinning all these approaches is the notion that the position of single molecules can be determined to high precision, provided enough photons are collected. The determination of exactly how precisely, has been demanded to formulas that try to approximate the so-called Cramer Rao Lower Bound based on input parameters such as the number of photons collected from the molecules, or the size of the camera pixel. These estimates should however be matched to the experimental localization precision, which can be easily determined if instead of looking at single beads, we study the distance between a pair. We revisit here a few key works, observing how these theoretical determinations tend to routinely underestimate the experimental localization precision, of the order of a factor two. A software-independent metric to determine, based on each individual setup, the appropriate value to set on the localization error of individual emitters is provided.
Context-dependent Rhythmicity in Chimpanzee Displays
Authors: van der Vleuten Bas , Hovenkamp Veerle , Varkevisser Judith , Spierings Michelle 
Published: October 2024

AbstractRhythm is an important component of human language and music production. Rhythms like isochrony (intervals spaced equally in time), are also present in vocalisations of certain non-human species, including several birds and mammals. This study aimed to identify rhythmic patterns with music-based methods within display behaviour of chimpanzees (Pan troglodytes), humans’ closest living relatives. Behavioural observations were conducted on individuals from two zoo-housed colonies. We found isochronous rhythms in vocal (e.g. pants, grunts and hoots), as well as in motoric (e.g. swaying and stomping) behavioural sequences. Among individuals, variation was found in the duration between onsets of behavioural elements, resulting in individual-specific tempi. Despite this variation in individual tempi, display sequences were consistently structured with stable, isochronous rhythms. Overall, directed displays, targeted at specific individuals, were less isochronous than undirected displays. The presence of rhythmic patterns across two independent colonies of chimpanzees, suggests that underlying mechanisms for rhythm production may be shared between humans and non-human primates. This shared mechanism indicates that the cognitive requirements for rhythm production potentially preceded human music and language evolution.
Recovery from Spreading Depolarization is slowed by aging and accelerated by antioxidant treatment in locusts
Authors: Robertson R. Meldrum , Wang Yuyang 
Published: October 2024

AbstractSpreading depolarization (SD) temporarily shuts down neural processing in nervous systems with effective blood brain barriers. In mammals this is usually pathological in response to energetic stress. In insects a very similar process is induced by abiotic environmental stressors and can be beneficial by conserving energy. Age is a critical factor for predicting the consequences of SD in humans. We investigated the effect of aging on SD in an insect model of SD and explored the contribution of oxidative stress. Aging slowed the recovery of intact locusts from asphyxia by water submersion. In semi-intact preparations we monitored SD by recording the DC potential across the blood brain barrier in response to bath application of the Na+/K+-ATPase inhibitor, ouabain. Treatment with ouabain induced changes to the DC potential that could be separated into two distinct components: a slow, permanent negative shift, similar to the negative ultraslow potential recorded in mammals and human patients, as well as rapid, reversible negative DC shifts (SD events). Aging had no effect on the slow shift but increased the duration of SD events from ∼0.6 minutes in young locusts to ∼0.9 minutes in old ones. This was accompanied by a decrease in the rate of recovery of DC potential at the end of the SD event, from ∼1.5 mV/s (young) to ∼0.6 mV/s (old). An attempt to generate oxidative stress using rotenone was unsuccessful, but pretreatment with the antioxidant, N-acetylcysteine amide, had opposite effects to those of aging, reducing duration (control ∼1.1 minutes, NACA ∼0.7 minutes) and increasing rate of recovery (control ∼0.5 mV/s, NACA ∼1.0 mV/s) suggesting that it prevented oxidative damage occurring during the ouabain treatment. The antioxidant also reduced the rate of the slow negative shift. We propose that the aging locust nervous system is more vulnerable to stress due to a prior accumulation of oxidative damage. Our findings also strengthen the notion that insects provide useful models for the investigation of cellular and molecular mechanisms underlying SD in mammals.Significance StatementAnoxia and similar energetic crises trigger a shutdown of central neural processing in a process of spreading depolarization (SD) which is generally pathological in mammals and protective in insects. We show that some variability in the consequences of SD in an insect model can be attributed to age, such that older animals are slower to recover. Moreover, preventing oxidative stress with an antioxidant speeds recovery. These findings demonstrate a role for oxidative stress in contributing to the vulnerability of the aging insect CNS in energetic emergencies.Abstract FigureGraphical Abstract of Robertson and Wang - Locust Spreading Depolarization
Astrocytic HIV-1 Nef expression decreases glutamate transporter expression in the nucleus accumbens and increases cocaine-seeking behavior in rats
Authors: Pla-Tenorio Jessalyn , Velazquez-Perez Bethzaly , Mendez-Borrero Yainira , Cruz-Rentas Myrella , Sepulveda-Orengo Marian , Noel Richard J. 
Published: October 2024

AbstractCocaine use disorder is an intersecting issue in populations with HIV-1, further exacerbating the clinical course of the disease, contributing to neurotoxicity and neuroinflammation. Cocaine and HIV neurotoxins play roles in neuronal damage during neuroHIV progression by disrupting glutamate homeostasis in the brain. Even with cART, HIV-1 Nef, an early viral protein expressed in approximately 1% of infected astrocytes, remains a key neurotoxin. This study investigates the relationship that exists between Nef, glutamate homeostasis, and cocaine in the NAc, a critical brain region associated with drug motivation and reward. Using a rat model, we compared the effects of astrocytic Nef and cocaine by molecular analysis of glutamate transporters in the NAc. We further conducted behavioral assessments for cocaine self-administration to evaluate cocaine-seeking behavior. Our findings indicate that both cocaine and Nef independently decrease the expression of the glutamate transporter GLT-1 in the NAc. Additionally, rats with astrocytic Nef expression exhibited increased cocaine-seeking behavior but demonstrated sex dependent molecular differences after behavioral paradigm. In conclusion, our results suggest the expression of Nef intensifies cocaine-induced alterations in glutamate homeostasis in the NAc, potentially underlying increased cocaine-seeking. Understanding these interactions better may inform therapeutic strategies for managing cocaine use disorder in HIV-infected individuals.
Balance performance in aged mice is dependent on unipolar brush cells
Authors: Kizeev Gabrielle , Witteveen Isabelle , Balmer Timothy 
Published: October 2024

AbstractThe vestibular processing regions of the cerebellum integrate vestibular information with other sensory modalities and motor signals to regulate balance, gaze stability, and spatial orientation. A class of excitatory glutamatergic interneurons known as unipolar brush cells (UBCs) are highly concentrated within the granule cell layer of these regions. UBCs receive vestibular signals directly from primary vestibular afferents and indirectly from mossy fibers. Each UBC excites numerous granule cells and could contribute to computations necessary for balance-related motor function. Prior research has implicated UBCs in motor function, but their influence on balance performance remains unclear, especially in aged mice that have age-related impairment. Here we tested whether UBCs contribute to motor coordination and balance by disrupting their activity with chemogenetics in aged and young mice. Age-related balance deficits were apparent in mice > 6 months old. Disrupting the activity of a subpopulation of UBCs caused aged mice to fall off a balance beam more frequently and altered swimming behaviors that are sensitive to vestibular dysfunction. These effects were not seen in young (7-week-old) mice. Thus, disrupting the activity of UBCs impairs mice with age-related balance issues and suggest that UBCs are essential for balance and vestibular function in aged mice.
A piRNA regulating oogenesis and embryo development in cockroaches
Authors: Gonzalvo Judit , Farrus Nuria , Escudero Jorge , Pujal David , Bau Josep , Piulachs Maria-Dolors 
Published: October 2024

AbstractThe PIWI-interacting RNAs (piRNAs) are small non-coding RNAs ranging from 26 to 31 nucleotides. Initially, piRNA functions were associated with repressing transposable elements as part of a mechanism that maintains genomic stability across evolution. However, in the last years, new regulatory functions for piRNAs have been identified. Now, we investigated the regulatory role of piRNAs in insect oogenesis and embryo development. We studied the expression and function of piRNA-83679, one the most abundantly expressed piRNA inBlattella germanicaadult ovaries. piRNA-83679 is expressed in germinal and somatic cells in adult ovaries during the gonadotropic cycle, and is maternally provided to the egg. Using an antisense oligonucleotide (ASO), we reduced piRNA-83679 levels inB. germanicaadult females, enabling the study of its functions. piRNA-83679 depletion affected the expression of different ecdysone and chorion genes in the ovary, and the organization of the F-actin fibers in the basal pole of the follicle cells of the basal ovarian follicle. As a result, the eggs were not correctly encapsulated in the ootheca. Moreover, piRNA-83679 depletion delayed oviposition and affected embryo development, especially in the early stages.
Early experience affects foraging behavior of wild fruit-bats more than their original behavioral predispositions
Authors: Rachum Adi , Harten Lee , Assa Reut , Goldshtein Aya , Chen Xing , Gonceer Nesim , Yovel Yossi 
Published: October 2024

AbstractThere are immense consistent inter-individual differences in animal behavior. While many studies have documented such behavioral differences, often referred to as individual personalities, little research has focused on the underlying causes and on determining whether they are innate or based on individual experience. Moreover, most studies on animal personalities have described consistent differences in behavior under laboratory conditions. We aimed to examine the impact of the early experienced environment on individual animal behavior, and to compare it to that of the individual’s original genetic predisposition. Additionally, we explored the correlation between personality traits measured indoors and the animal’s outdoor behavior. We studied Egyptian fruit bats, in which vast behavioral variability and plasticity have already been demonstrated. We raised bats in a captive colony under either enriched or impoverished environments and assessed their personality under controlled laboratory conditions. We then released the bats into the wild and tracked their foraging using GPS. Bats that had experienced an enriched environment during early life displayed increasing boldness and exploratory behavior when foraging outdoors, demonstrating how early-life experience can affect adult behavior. The individuals’ original predispositions did not predict their later foraging behavior. Our findings shed new light on the interplay between innate and experienced-based effects on individual behavior.
HEXIM1 homodimer binds two sites on 7SK RNA to release autoinhibition for P-TEFb inactivation
Authors: Yang Yuan , Murrali Maria Grazia , Wang Yaqiang , Galvan Sabrina , Ajjampore Neha , Feigon Juli 
Published: October 2024

AbstractHexim proteins are RNA-dependent regulators whose main target is 7SK long non-coding RNA, a major regulator of eukaryotic mRNA transcription. 7SK RNPs control available intracellular concentrations of the kinase P-TEFb (Cdk9–CyclinT1/2) by sequestering it in an inactive form. Active P-TEFb phosphorylates NELF, DSIF, and the RNA polymerase II CTD to transition it from promoter-proximal pausing to productive elongation. P-TEFb associates with 7SK RNP via Hexim, which directly binds 7SK RNA. However, free Hexim is in an autoinhibited state that cannot inactivate P-TEFb, and how Hexim autoinhibition is released by 7SK remains unknown. Here, we show that one Hexim1 homodimer binds two sites on linear 7SK RNA in a manner that exposes the Cdk9 binding sites, which are otherwise masked within the autoinhibited dimer. These results provide mechanistic insights into Hexim–RNA specificity and explain how P-TEFb can be effectively regulated to respond to changing levels of transcriptional signaling.
Spinal cerebrospinal fluid contacting neurons are a conserved sensory neuronal population along the mouse spinal cord
Authors: Elysa Crozat , Edith Blasco , Jorge Ramirez-Franco , Priscille Riondel , Nina Jurčić , Riad Seddik , Caroline Michelle , Jérôme Trouslard , Nicolas Wanaverbecq 
Published: October 2024

Cerebrospinal Fluid contacting neurons (CSF-cNs) are present in all vertebrates around the medullo-spinal central canal. They are GABAergic, selectively express PKD2L1, a member of the TRP channel superfamily, and are thought to represent a novel sensory system intrinsic to the central nervous system. Using histology, we found that CSF-cNs form a homogeneous population, distributed along the whole spinal cord and mainly located in the ventral region of the central canal. Patch-clamp recordings reveal conserved intrinsic properties and voltage-dependent conductance expression. Spinal CSF-cNs express PKD2L1 channels and ASICs, acting as sensory receptors for extracellular pH changes. They express both inhibitory (GABAA, glycine) and excitatory (glutamate, cholinergic) synaptic receptors as well as functional GABABand muscarinic receptors, but not glutamatergic metabotropic ones, to modulate Ca2+channels.CSF-cNs represent a functionally homogeneous population that might integrates sensory signals along the central canal to modulate body functions by regulating local spinal networks. Demonstrating such a function represents the future challenge in the field.
Time-Space Resolved Fluorescence Spectroscopy in LiveChlamydomonasCells under Light-Harvesting Regulation
Authors: Fujita Yuki , Zhang Xianjun , Ye Shen , Shibata Yutaka 
Published: October 2024

ABSTRACTWe report here a technical advancement that enables time-resolved fluorescence spectroscopy in spatially resolved domains of a living cell at low temperatures. The technique is based on a combination of the self-developed cryo-confocal microscope system and the streak-camera technology. An instrumental response time of ca. 24 ps was achieved. This technique was applied to reveal the light-harvesting dynamics in local domains within singleChlamydomonas reinhardtiicells. Organisms performing oxygenic photosynthesis, likeChlamydomonas, have evolved a regulation mechanism called state transitions (ST), which maintains the excitation balance between PSI and PSII. ST relies on the shuttling of light-harvesting chlorophyll protein complex II (LHCII) between the two PSs. In the present experiment, cells were induced either to state1, where LHCII is bound to PSII, or state2, where LHCII moved and is bound to PSI. After the induction of ST, cells were immediately cooled to ca. 80 K, where PSI and PSII show clearly separated fluorescence emission bands, enabling the visualization of these components separately. Based on kinetic analyses of the time-resolved fluorescence spectra in both PSI-rich and PSII-rich local domains, we concluded that (1) the intracellular inhomogeneity in the PSII/PSI fluorescence ratio comes from that in the PSII/PSI stoichiometry, not from that in the antenna sizes of the PSs, and (2) the antenna size of PSI in state2 cells may larger in intact cells than that of the isolated PSI-LHCI-LHCII super-complex reported so far.
Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation
Authors: Wu Jiangbo , Dasetty Siva , Beckett Daniel , Wang Yihang , Xue Weizhi , Skóra Tomasz , Bidone Tamara C. , Ferguson Andrew L. , Voth Gregory A. 
Published: October 2024

ABSTRACTMicrotubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5’-triphosphate) to GDP (guanosine-5’-diphosphate) within theβ-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the “equation-free” multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments × 8 heterodimers) comprising ∼21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 μs unbiased all-atom simulation, we interleave coarse projective “equation-free” jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 μs. Our 5.875 μs of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whetherβ-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. The approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution.SIGNIFICANCEThe dynamic instability of microtubules (MTs) is essential for a plethora of biological functions, from cell division to intracellular transport. Despite their importance, current computational models often struggle to handle the large-scale, long-term dynamics of all-atom simulations. This computational study employs the “equation-free” method to accelerate relaxation of the all-atom structures of MT tips in both GDP and GTP states which nearly halves the computational demands of simulating very large biomolecular systems. Our findings expose subtle but crucial structural differences between GDP-bound and GTP-bound MTs, particularly in the number of protofilament clusters, and is consistent with a relatively stronger lateral interactions in GTP-bound MT tips.
Distinct cortical spatial representations learned along disparate visual pathways
Authors: Lian Yanbo , LaChance Patrick A. , Malmberg Samantha , Hasselmo Michael E. , Burkitt Anthony N. 
Published: October 2024

AbstractRecent experimental studies have discovered diverse spatial properties, such as head direction tuning and egocentric tuning, of neurons in the postrhinal cortex (POR) and revealed how the POR spatial representation is distinct from the retrosplenial cortex (RSC). However, how these spatial properties of POR neurons emerge is unknown, and the cause of distinct cortical spatial representations is also unclear. Here, we build a learning model of POR based on the pathway from the superior colliculus (SC) that has been shown to have motion processing within the visual input. Our designed SC-POR model demonstrates that diverse spatial properties of POR neurons can emerge from a learning process based on visual input that incorporates motion processing. Moreover, combining SC-POR model with our previously proposed V1-RSC model, we show that distinct cortical spatial representations in POR and RSC can be learnt along disparate visual pathways (originating in SC and V1), suggesting that the varying features encoded in different visual pathways contribute to the distinct spatial properties in downstream cortical areas.Conflict of interest statementThe authors declare no competing financial interests.