bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic empirical evaluation of individual base editing targets: validating therapeutic targets inUSH2Aand comparison of methods
Authors: Tachida Yuki , Manian Kannan V. , Butcher Rossano , Levy Jonathan M. , Pendse Nachiket , Hennessey Erin , Liu David R. , Pierce Eric A. , Liu Qin , Comander Jason 
Published: October 2024

AbstractBase editing shows promise for the correction of human mutations at a higher efficiency than other repair methods and is especially attractive for mutations in large genes that are not amenable to gene augmentation therapy. Here, we demonstrate a comprehensive workflow for in vitro screening of potential therapeutic base editing targets for theUSH2Agene and empirically validate the efficiency of adenine and cytosine base editor/guide combinations for correcting 35USH2Amutations. Editing efficiency and bystander edits are compared between different target templates (plasmids versus transgenes) and assays (Next generation sequencing versus Sanger), as well as comparisons between unbiased empirical results and computational predictions. Based on these observations, practical assay recommendations are discussed. Finally, a humanized knock-in mouse model was created with the best-performing target, the nonsense mutation c.11864G>A p.(Trp3955*). Split-intein AAV9 delivery of editing reagents resulted in the restoration of USH2A protein and a correction rate of 65 ± 3% at the mutant base pair and of 52 ± 3% excluding bystander amino acid changes. This efficiency compares favorably to a prior genome editing strategy tested in the retina that completed a clinical trial and demonstrates the effectiveness of this overall strategy to identify and test base editing reagents with the potential for human therapeutic applications.
Illuminating root-soil mechanics
Authors: Le Houx James , Fletcher Daniel McKay , Leonardi Alberto , Williams Katherine A. , Walker Nancy , Alvarez-Borges Fernando , Afsar Dizaj Ebrahim , Murthy Madhu , Smith Ronan , Perera Liam , Aslani Navid , James Andrew , Ahmed Sharif , Roose Tiina , Ruiz Siul 
Published: October 2024

ABSTRACTSoil compaction and escalating global drought increase soil strength and stiffness. It remains unclear which plant root biomechanical mechanisms/traits enable growth in these harsh conditions. Here, we combine synchrotron X-ray computed tomography with spatially resolved X-ray diffraction to characterize the biomechanics of a replica root-soil system. We map the strain field around the root tip, finding strong agreement with finite element simulations, thereby demonstrating a promising new in-vivo measurement protocol.
A novel behavioral apparatus for spontaneous exploration and operant conditioning of social information under spatial conditions in rats
Authors: Wise Taylor B. , Templer Victoria L. , Burwell Rebecca D. 
Published: October 2024

ABSTRACTBackgroundEvidence from the fields of evolutionary biology and neuroscience supports the theory that spatial cognition and social cognition share neural mechanisms. Rodent models are widely used to study either spatial or social cognition, but few studies have explored the interactions between the spatial and social cognitive domains due to the lack of appropriate paradigms.New methodOur study introduces the Vertical Maze (VM), a novel behavioral apparatus designed to measure multiple aspects of spatial and social cognition. The VM features a standard 3-chamber maze positioned above multilevel columns allowing for the presentation of conspecifics at varying spatial distances and familiarity levels. This arrangement enables conspecifics to serve as discriminative stimuli for both social and spatial spontaneous and goal-oriented assessments. The three-dimensional design of the VM allows rats to use multisensory cues to judge distance, direction, and social identity of conspecifics.ResultsIn the present study, we found that rats can 1) discriminate the spatial distance of conspecifics located below them in an operant conditioning task, and 2) discriminate social novelty when conspecifics are presented below at the near, middle, and far distances in a spontaneous exploration task. Critically, it was necessary for rats to explore all levels of the maze to perform these discriminations.Comparison with existing methodsThis new method advances the field by permitting the presentation of social information (conspecifics) at different spatial distances. The use of conspecifics to serve as stimuli for both social and spatial discriminations allows more direct comparison of behavioral measures across these information domains. Importantly, the presentation of conspecifics as stimuli below the 3-chamber level of the maze engages auditory, visual, and olfactory systems, encouraging a robust multisensory representation of conspecifics presented at a distance.ConclusionsOur results confirm that the VM is an effective tool for studying both spatial and social cognition, facilitating the development of novel automated tasks in these areas. This new method opens new avenues for investigating the neural and cognitive foundations of spatial and social behavior, as well as for exploring the possibility of shared mechanisms across these cognitive domains.
Glycerol improves the viability of a cryopreserved choanoflagellate
Authors: Chandra Sheel , Rutaganira Florentine U. 
Published: October 2024

AbstractThe colonial choanoflagellateSalpingoeca rosettais a tractable model system for studying the origins of multicellularity, but long-term storage strategies for this species have not been tested. In this study, we probed each stage of cryopreservation (freeze-down, long-term storage, recovery) to identify the optimal protocol for recovery ofS. rosettaand co-cultured bacterial cells. Dimethyl sulfoxide (Me2SO; commonly referred to as DMSO), the current cryoprotective agent (CPA) standard, proved to be worse than glycerol at comparable concentrations. Samples treated with either CPA at 5% showed the poorest recovery. Our results identified 15% glycerol as the most effective CPA for bothS. rosettaandEchinicola pacifica. We also determined that ultra-low temperature freezers can be sufficient for short-term storage. We propose 15% glycerol and liquid phase nitrogen as the standard cryopreservation protocol forS. rosettacultures and as a starting point for testing long-term storage strategies for other choanoflagellates and heterotrophic protists.
Cross-task implications: How hippocampal event boundary responses predict unrelated memory performance
Authors: van Dijk Daphne , Collin Silvy H.P. 
Published: October 2024

AbstractHippocampal responses at event boundaries have been shown to predict memory performance for these events. However, are these hippocampal event boundary responses specific to memory for those particular events, or can they also have predictive power across various memory tasks? We used data from the Cam-CAN project (fMRI data from continuous movie viewing and memory results from an unrelated Famous Faces Task, N = 630) to determine whether hippocampal responses at event boundaries during the continuous movie viewing were indicative of memory performance in the unrelated Famous Faces task using various machine learning algorithms. The results showed that memory performance in the Famous Faces Task could be predicted based on participants’ hippocampal event boundary responses in another task, which suggests that the hippocampal event boundary responses are indicative for general memory performance. This might indicate importance of these hippocampal event boundary responses in terms of general information processing of the human brain.
The challenge of chromatin model comparison and validation - a project from the first international 4D Nucleome Hackathon
Authors: Kubica Jędrzej , Korsak Sevastianos , Clerkin Ariana Brenner , Kouřil David , Schirman Dvir , Yadavalli Anurupa Devi , Banecki Krzysztof , Kadlof Michał , Busby Ben , Plewczynski Dariusz 
Published: October 2024

AbstractThe computational modeling of chromatin structure is highly complex and challenging due to the hierarchical organization of chromatin, which reflects its diverse biophysical principles, as well as inherent dynamism, which underlies its complexity. The variety of methods for chromatin structure modeling, which are based on different approaches, assumptions and scales of modeling, suggests that there is a necessity for a comprehensive benchmark. This inspired us to conduct a project at the NIH-funded 4D Nucleome Hackathon on March 18-21, 2024 at The University of Washington in Seattle, USA. The hackathon provided an amazing opportunity to gather an international, multi-institutional and unbiased group of experts to discuss, understand and undertake the challenges of chromatin model comparison and validation. These challenges seem straightforward in theory, however in practice, they are challenging and ambiguous. To address them, we developed a bioinformatics workflow for chromatin model comparison and validation, in which we use distance matrices to represent chromatin models, and we calculate Spearman correlation coefficients between pairs of matrices to estimate correlations between models, as well as between models and experimental data. During the 4-day hackathon, we tested our workflow on several distinct software packages for chromatin structure modeling and we discovered several challenges that include: 1) different aspects of chromatin biophysics and scales complicate model comparisons, 2) expertise in biology, bioinformatics, and physics is necessary to conduct a comprehensive research on chromatin structure, 3) bioinformatic software, which is often developed in academic settings, is characterized by insufficient support and documentation. Therefore, our work constitutes a way to advance the modeling of the 3D organization of the human genome, while emphasizing the importance of establishing guidelines for software development and standardization.
A genetic framework for RNAi inheritance inCaenorhabditis elegans
Authors: Schreier Jan , Kielisch Fridolin , Ketting René F. 
Published: October 2024

ABSTRACTGene regulation by RNA interference (RNAi) is a conserved process driven by double-stranded RNA (dsRNA). It responds to exogenous cues and drives endogenous gene regulation. InCaenorhabditis elegans, RNAi can be inherited from parents to offspring. While a number of factors have been implicated in this inheritance process, we do not understand how and when they function. Using a new inheritance assay, we establish a hierarchy amongst previously identified inheritance factors. The nuclear argonaute protein HRDE-1 was required for RNAi establishment in parents and offspring, but not for the inheritance process. In contrast, the cytoplasmic argonaute protein WAGO-3 was the only factor essential for inheritance, via sperm and oocyte, while not affecting establishment in either parent or offspring. We propose a cycle between nuclear and cytoplasmic argonaute proteins, where nuclear activity drives most of the silencing and cytoplasmic activity ensures inheritance. Finally, we implicate the RNA helicase ZNFX-1 as a factor that controls the entry of exogenous versus endogenous small RNAs into this cycle, ensuring a proper balance between gene silencing and activity.
The Unique Role of Intracellular Perinuclear β-Adrenergic Receptors in defining Signaling Compartmentation and Pathological Cardiac Remodeling
Authors: Turcotte Moriah Gildart , Samuelsson Anne-Maj , Possidento Sofia M. , Li Jinliang , Qin Zhuyun , Kapiloff Michael S. , Dodge-Kafka Kimberly L. 
Published: October 2024

SummaryThe β-adrenergic receptor is a prototypical G-protein coupled receptor that initiates signaling from the plasma membrane. However, active receptors have been detected within intracellular compartments. The functional significance of these intracellular receptors remains unclear, including whether they regulate distinct cellular processes or function independently of plasma membrane receptors. We show using live cell imaging of primary cardiomyocytes that β-adrenergic receptors localized to Golgi apparatus opposing the outer nuclear membrane are sufficient and necessary for the stimulation of cAMP and calcium signaling within a nanometer scale compartment independent of receptors at other sites. Using compartment-specific activators and inhibitors, we show Golgi β-adrenergic receptors associated with the scaffold protein AKAP6β and the outer nuclear membrane protein nesprin-1α are responsible for pathological gene transcription and the induction of cardiomyocyte hypertrophy. The functional significance of Golgi-localized receptors is demonstrated in mice models of cardiomyopathy, providing proof-of-concept for a compartment-specific therapeutic intervention in Dilated Cardiomyopathy.
A Predictive Model for Compound-Protein Interactions Based on Concatenated Vectorization
Authors: Williams Gareth , Azim Kaz 
Published: October 2024

AbstractBackgroundLarge data sets of compound activity lend themselves to building predictive models based on compound and target structure. The simplest representation of structure is via vectorisation. Compound fingerprint vectorisation has been successfully employed in predicting compound activity classes.ResultsA vector representation of a protein-compound pair based on a concatenation of the compound fingerprint and the protein triplet vector has been used to train random forest and neural network models on multiple datasets of protein-compound interaction together with compound associated transcription and activity profiles. Results for compound-target predictability are comparable with more complex published methodologies.ConclusionA simple intuitive representation of a protein-compound pair can be employed in a variety of machine learning models to gain a predictive handle on the activity of compounds for which there is no activity data. It is hoped that this transparent approach will prove sufficiently portable and simple to implement that drug discovery will be opened up to the wider research community.
Pituitary adenylate cyclase-activating polypeptide (PACAP) overexpression in the paraventricular nucleus of the thalamus alters motivated and affective behavior in female rats
Authors: Carpenter Brody A. , Pirino Breanne E. , Jennings Malcolm C. , Samels Shanna B. , Shah Krisha S. , Maser Joya , Gupta Medha , Barson Jessica R. 
Published: October 2024

ABSTRACTBackgroundPituitary adenylate cyclase-activating polypeptide (PACAP) has been found to be involved in a wide range of motivated and affective behaviors. While the PACAP-38 isoform is more densely expressed than PACAP-27 in most of the brain, PACAP-27 is more highly expressed in the rodent paraventricular nucleus of the thalamus (PVT), where females also have greater expression than males. Notably, the role of PACAP-27 expression in cells of the PVT has not been explored.MethodsAdult, female Long-Evans rats were injected in the PVT with an AAV to increase expression of PACAP or a control AAV. They were then investigated for subsequent gene and peptide levels of PACAP in the PVT; ethanol drinking and preference; sucrose drinking and preference; or locomotor activity in a novel chamber, behavior in a light-dark box, behavior in a novelty suppression of feeding test, locomotor activity in a familiar activity chamber, and behavior in a forced swim test.ResultsGene expression of PACAP was significantly increased in the PVT by four weeks after injection with the PACAP AAV, and this resulted in a specific increase in levels of PACAP-27. Rats injected with the PACAP AAV demonstrated reduced drinking and preference for ethanol under the intermittent-access procedure compared to those injected with the control AAV. In contrast, rats injected with the PACAP AAV showed no significant difference in drinking or preference for sucrose, or in any affective behavior tested, except that they spent less time swimming in the forced swim test.ConclusionsIn light of the low overall level of expression of PACAP-27 in the brain, the ability of PACAP-27 in the PVT to control ethanol drinking, with minimal effects on other motivated or affective behaviors, supports the idea that compounds related to PACAP-27 should be investigated as potential therapeutics for the treatment of alcohol use disorder.
WITHDRAWN: Influence of Shading on the Behavioral Ecology of a Caribbean Alcyonacean Octocoral,Briareum asbestinum, in the Florida Keys, United States
Authors: Draud Savannah , Hoeksema Jason D. , Draud Matthew 
Published: October 2024

Withdrawal StatementThe authors have withdrawn this manuscript because they are in the process of making revisions to the study/manuscript, and do not wish this paper to be considered as finalized at this point. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Enhanced Structural Brain Connectivity Analyses Using High Diffusion-weighting Strengths
Authors: Yu Leyao , Flinker Adeen , Veraart Jelle 
Published: October 2024

AbstractTractography is a unique modality for the in vivo measurement of structural connectivity, crucial for understanding brain networks and neurological conditions. With increasingb-value, the diffusion-weighting signal becomes primarily sensitive to the intra-axonal signal. However, it remains unclear how tractography is affected by this observation. Here, using open-source datasets, we showed that at highb-values, DWI reduces the uncertainty in estimating fiber orientations. Specifically, we found the ratio of biologically-meaningful longer-range connections increases, accompanied with downstream impact of redistribution of connectome and network metrics. However, when going beyondb=6000 s/mm2, the loss of SNR imposed a penalty. Lastly, we showed that the data reaches satisfactory reproducibility withb-value above 1200 s/mm2. Overall, the results suggest that usingb-values above 2500 s/mm2is essential for more accurate connectome reconstruction by reducing uncertainty in fiber orientation estimation, supporting the use of higherb-value protocols in standard diffusion MRI scans and pipelines.
Divergent changes in social stress-induced motivation in male and female mice
Authors: McGraw Megan , Christensen Cooper , Nelson Hailey , Li Ai-Jun , Qualls-Creekmore Emily 
Published: October 2024

AbstractExposure to stressors has been shown to dysregulate motivated behaviors in a bidirectional manner over time. The relationship between stress and motivation is relevant to psychological disorders, including depression, binge eating, and substance abuse; however, this relationship is not well characterized, especially in females, despite their increased risk of these disorders. Social defeat stress is a common model to study stress-induced motivation changes, however, historically this model excluded females due to lack of female-to-female aggression and unreliable male-to-female aggression. Additionally, changes in motivation are often assessed well after stress exposure ends, potentially missing or occluding changes to motivation during stress. Recently, the chronic non-discriminatory social defeat stress (CNSDS) model has demonstrated social defeat of male and female C57BL/6J mice by exposing both mice to an aggressive male CD-1 mouse simultaneously. Here we use this model to directly compare changes in the motivated behavior of male and female mice during and following chronic stress. We hypothesized that motivated behavioral responses would be dysregulated during stress and that the effects would worsen as the stress exposure continued. To monitor motivated behavior, mice had access to a Feeding Experimental Device.3 (FED3), a home cage device for operant responding. Operant responding was monitored prior to, during, and after stress by measuring nose pokes for sucrose pellets on a modified progressive ratio schedule of reinforcement. Our results demonstrated divergent behavioral outcomes between males and female mice in response to stress; where male mice increased motivated behavior during stress only, whereas female mice exhibited a decrease in motivation during and after stress. This study highlights the need to investigate the effects of stress-induced motivation over time, as well as the increased need to understand differences in the stress response in females.HighlightsOperant behaviors were monitored continuously during and after stress exposure.Chronic social stress produced opposite effects on motivation in males and females.Susceptibility to stress only influenced outcomes on female motivated behaviors.
Susceptibility to auditory feedback manipulations and individual variability
Authors: Ozker Muge , Hagoort Peter 
Published: October 2024

AbstractMonitoring auditory feedback from hearing one’s own voice is important for fluent speech production as it enables detection and correction of speech errors. The influence of auditory feedback is best illustrated by manipulating it during speech production. A common temporal manipulation technique, delaying auditory feedback (DAF), leads to disruptions in speech fluency, while a common spectral manipulation technique, perturbing the pitch of auditory feedback (PAF), results in vocal alterations.Previous research involving clinical populations has revealed diverse susceptibility profiles to auditory feedback manipulations, yet the extent of such diversity within the neurotypical population remains unclear. Furthermore, different types of manipulations elicit distinct speech errors (i.e. fluency/coordination versus acoustic errors), which may be processed by distinct error correction mechanisms. It is yet to be understood whether individuals affected by one manipulation are similarly impacted by the other. Lastly, based on evidence from clinical studies, which demonstrated that visual feedback can improve impaired speech production, it is an open question whether visual feedback can alleviate the disruptive effects of altered auditory feedback.We recorded voice samples from 40 neurotypical participants during both a DAF and a PAF task. DAF significantly prolonged articulation duration and increased voice pitch and intensity. In some trials, participants received immediate visual feedback, however visual feedback did not alleviate but rather strengthened the disruptive effects of DAF. During the PAF task, participants adjusted their voice pitch in the opposite direction of the perturbation in majority of the trials to compensate for the perturbation. We assessed susceptibility of the participants to the effects of DAF and PAF by examining articulation duration and compensatory vocal response magnitude, respectively. Susceptibility varied widely among participants for both manipulations, but individuals susceptible to one manipulation did not consistently exhibit susceptibility to the other, indicating distinct processing mechanisms for these different types of auditory feedback manipulations.