bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cochlear transcriptome analysis of an outbred mouse population (CFW)
Authors: Boussaty Ely Cheikh , Tedeschi Neil , Novotny Mark , Ninoyu Yuzuru , Du Eric , Draf Clara , Zhang Yun , Manor Uri , Scheuermann Richard H. , Friedman Rick 
Published: February 2023

AbstractAge-related hearing loss (ARHL) is the most common cause of hearing loss and one of the most prevalent conditions affecting the elderly worldwide. Despite evidence from our lab and others about its polygenic nature, little is known about the specific genes, cell types and pathways involved in ARHL, impeding the development of therapeutic interventions. In this manuscript, we describe, for the first time, the complete cell-type specific transcriptome of the aging mouse cochlea using snRNA-seq in an outbred mouse model in relation to auditory threshold variation. Cochlear cell types were identified using unsupervised clustering and annotated via a three-tiered approach - first by linking to expression of known marker genes, then using the NS-Forest algorithm to select minimum cluster-specific marker genes and reduce dimensional feature space for statistical comparison of our clusters with existing publicly-available data sets on the gEAR website (https://umgear.org/), and finally, by validating and refining the annotations using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types expanding the number of defined cochlear cell types by more than two times. Importantly, we show significant specific cell type increases and decreases associated with loss of hearing acuity implicating specific subsets of hair cell subtypes, ganglion cell subtypes, and cell subtypes withing the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.
Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex
Authors: Deng Chengyu , Whalen Sean , Steyert Marilyn , Ziffra Ryan , Przytycki Pawel F. , Inoue Fumitaka , Pereira Daniela A. , Capauto Davide , Norton Scott , Vaccarino Flora M. , Pollen Alex , Nowakowski Tomasz J. , Ahituv Nadav , Pollard Katherine S. 
Published: February 2023

AbstractNucleotide changes in gene regulatory elements are important determinants of neuronal development and disease. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated thecis-regulatory activity of 102,767 sequences, including differentially accessible cell-type specific regions in the developing cortex and single-nucleotide variants associated with psychiatric disorders. In primary cells, we identified 46,802 active enhancer sequences and 164 disorder-associated variants that significantly alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning, we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.One Sentence SummaryWe identify 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids.
Colour polymorphism and conspicuousness do not increase speciation rates in Lacertids
Authors: de Solan Thomas , Sinervo Barry , Geniez Philippe , David Patrice , Crochet Pierre-André 
Published: February 2023

AbstractConspicuous body colours and colour polymorphism have been hypothesized to increase rates of speciation. Conspicuous colours are evolutionary labile, and often involved in intraspecific sexual signalling and thus may provide a raw material from which reproductive isolation can easily evolve, while polymorphism could favour rapid evolution of new lineages through morphic speciation. Here, we investigated the influence of the presence/absence of conspicuous colourations, and of colour polymorphism on the speciation of Lacertids. We used several state-dependent diversification models, and showed that, regardless of the methods, conspicuous colourations and colour polymorphism were not related to species speciation. While the lack of correlation between conspicuous colourations and speciation rates is in line with most of the literature testing this hypothesis, the results for colour polymorphism contradict previous studies, and question the generality of the morphic speciation hypothesis.
STUN: forward-time Simulation on TUnable fitNess landscapes in recombining populations
Authors: Amado André , Li Juan , Bank Claudia 
Published: February 2023

AbstractUnderstanding the population genetics of complex polygenic traits during adaptation is challenging. Here, we implement a forward-in-time population-genetic simulator (STUN) based on Wright-Fisher dynamics. STUN is a flexible and user-friendly software package for simulating the polygenic adaptation of recombining haploid populations using either new mutations or standing genetic variation. STUN assumes that populations adapt to sudden environmental changes by undergoing selection on a new fitness landscape. With pre-implemented fitness landscape models like Rough Mount Fuji, NK, Block, additive, and House-of-Cards, users can explore the effect of different levels of epistasis (ruggedness of the fitness landscape). Custom fitness landscapes and recombination maps can also be defined. STUN empowers both experimentalists and advanced programmers to study the evolution of complex polygenic traits and to dissect the adaptation process.Availability and implementationSTUN is implemented in Rust. Its source code is available athttps://github.com/banklab/STUN, which also includes a link to the software’s manual and binary files for Linux, macOS and Windows. Upon publication, the code will also be archived on Zenodo and a doi will be provided here.
The Zinc-BED transcription factor Bedwarfed promotes proportional dendritic growth and branching through transcriptional and translational regulation inDrosophila
Authors: Bhattacharjee Shatabdi , Iyer Eswar Prasad R. , Iyer Srividya Chandramouli , Nanda Sumit , Rubaharan Myurajan , Ascoli Giorgio A. , Cox Daniel N. 
Published: February 2023

AbstractDendrites are the primary points of sensory or synaptic inputs to a neuron and play an essential role in synaptic integration and neural function. Despite the functional importance of dendrites, relatively less is known about the underlying mechanisms regulating cell-type specific dendritic patterning. Herein, we have dissected functional roles of a previously uncharacterized gene,CG3995, in cell-type specific dendritic development inDrosophila melanogaster.CG3995, which we have namedbedwarfed(bdwf), encodes a zinc-finger BED-type protein which is required for proportional growth and branching of dendritic arbors, exhibits nucleocytoplasmic expression, and functions in both transcriptional and translational cellular pathways. At the transcriptional level, we demonstrate a reciprocal regulatory relationship between Bdwf and the homeodomain transcription factor (TF) Cut. We show that Cut positively regulates Bdwf expression and that Bdwf acts as a downstream effector of Cut-mediated dendritic development, whereas overexpression of Bdwf negatively regulates Cut expression in multidendritic sensory neurons. Proteomic analyses revealed that Bdwf interacts with ribosomal proteins and disruption of these proteins produced phenotypically similar dendritic hypotrophy defects as observed inbdwfmutant neurons. We further demonstrate that Bdwf and its ribosomal protein interactors are required for normal microtubule and F-actin cytoskeletal architecture. Finally, our findings reveal that Bdwf is required to promote protein translation and ribosome trafficking along the dendritic arbor. Taken together, these results provide new insights into the complex, combinatorial and multi-functional roles of transcription factors (TFs) in directing diversification of cell-type specific dendritic development.
A novel rotavirus reverse genetics platform supports flexible insertion of exogenous genes and enables rapid development of a high-throughput neutralization assay
Authors: Wei Jiajie , Radcliffe Scott , Lu Meiqing , Li Yuan , Cassaday Jason , Newhard William , Heidecker Gwendolyn J , Rose William A , He Xi , Freed Daniel , Citron Michael , Espeseth Amy , Wang Dai 
Published: February 2023

AbstractDespite the success of rotavirus vaccines, rotaviruses are still one of the leading causes of diarrheal diseases, resulting in significant childhood morbidity and mortality especially in low- and middle-income countries. Reverse genetics system enables the manipulation of the rotavirus genome and opens the possibility of using rotavirus as an expression vector for heterologous proteins such as vaccine antigens and therapeutic payloads. Here, we identified three positions in rotavirus genome, the C terminus of NSP1, NSP3 and NSP5, for reporter gene insertion. By using rotavirus expressing GFP, we developed a high-throughput neutralization assay and revealed the pre-existing immunity against rotavirus in human and other animal species. Our work shows the plasticity of rotavirus genome and establishes a high-throughput assay for interrogating humoral immune responses, benefiting the design of next-generation rotavirus vaccines and the development of rotavirus-based expression platforms.
Virotest: a bioinformatics pipeline for virus identification in plants
Authors: Gonzalez-Ibeas Daniel 
Published: February 2023

AbstractHigh-throughput DNA sequencing is being introduced as an emerging technology for viral diagnosis. Despite several tools being available, lack of standardized bioinformatic pipelines and price are major limitations for its implementation. Many extant tools focus on the assembly of virus-derived small RNAs into contigs and their subsequent annotation. Better sensitivity has been reported by several studies when this approach is complemented with read mapping on known viral genome sequences as an ancillary step, requiring less number of reads and allowing price optimization during DNA sequencing. This publication introducesvirotest, a bioinformatics pipeline for the identification of viruses in plants from small RNA data. The tool prioritizes read mapping over sequence assembly for the purpose of obtaining better sensitivities and requiring lower sequencing depths.
Functional significance of PUF partnerships inC. elegansgermline stem cells
Authors: Ferdous Ahlan S. , Costa Dos Santos Stephany J. , Kanzler Charlotte R. , Shin Heaji , Carrick Brian H. , Crittenden Sarah L. , Wickens Marvin , Kimble Judith 
Published: February 2023

AbstractPUF RNA-binding proteins are conserved stem cell regulators. Four PUF proteins govern self-renewal ofC. elegansgermline stem cells together with two intrinsically disordered proteins, LST-1 and SYGL-1. Based on yeast two-hybrid results, we proposed a composite self-renewal hub in the stem cell regulatory network, with eight PUF partnerships and extensive redundancy. Here, we investigate LST-1–PUF and SYGL-1–PUF partnerships and their molecular activities in their natural context – nematode stem cells. We confirm LST-1–PUF partnerships and their specificity to self-renewal PUFs by co-immunoprecipitation and show that an LST-1(AmBm) mutant defective for PUF-interacting motifs does not complex with PUFs in nematodes. LST-1(AmBm) is used to explore the functional significance of the LST-1–PUF partnership. Tethered LST-1 requires the partnership to repress expression of a reporter RNA, and LST-1 requires the partnership to co-immunoprecipitate with NTL-1/Not1 of the CCR4-NOT complex. We suggest that the partnership provides multiple molecular interactions that work together to form an effector complex on PUF target RNAs. Comparison of PUF-LST-1 and Pumilio–Nanos reveals fundamental molecular differences, making PUF–LST-1 a distinct paradigm for PUF partnerships.Summary statementPartnerships between PUF RNA-binding proteins and intrinsically disordered proteins are essential for stem cell maintenance and RNA repression.
Assessing the performance of the Cell Painting assay across different imaging systems
Authors: Tromans-Coia Callum , Jamali Nasim , Abbasi Hamdah Shafqat , Giuliano Kenneth A. , Hagimoto Mai , Jan Kevin , Kaneko Erika , Letzsch Stefan , Schreiner Alexander , Sexton Jonathan Z. , Suzuki Mahomi , Trask O. Joseph , Yamaguchi Mitsunari , Yanagawa Fumiki , Yang Michael , Carpenter Anne E. , Cimini Beth A. 
Published: February 2023

AbstractQuantitative microscopy is a powerful method for performing phenotypic screens from which image-based profiling can extract a wealth of information, termed profiles. These profiles can be used to elucidate the changes in cellular phenotypes across cell populations from different patient samples or following genetic or chemical perturbations. One such image-based profiling method is the Cell Painting assay, which provides morphological insight through the imaging of eight cellular compartments. Here, we examine the performance of the Cell Painting assay across multiple high-throughput microscope systems and find that all are compatible with this assay. Furthermore, we determine independently for each microscope system the best performing settings, providing those who wish to adopt this assay an ideal starting point for their own assays. We also explore the impact of microscopy setting changes in the Cell Painting assay and find that few dramatically reduce the quality of a Cell Painting profile, regardless of the microscope used.
Finite Element Modeling of Residual Hearing after Cochlear Implant Surgery in Chinchillas
Authors: Castle Nicholas , Liang Junfeng , Smith Matthew , Petersen Brett , Matson Cayman , Eldridge Tara , Zhang Ke , Lee Chung-Hao , Liu Yingtao , Dai Chenkai 
Published: February 2023

AbstractCochlear implant (CI) surgery is one of the most utilized treatments for severe hearing loss. However, the effects of a successful scala tympani insertion on the mechanics of hearing are not yet fully understood. This paper presents a finite element (FE) model of the chinchilla inner ear for studying the interrelationship between the mechanical function and the insertion angle of a CI electrode. This FE model includes a three-chambered cochlea and full vestibular system, accomplished using μ-MRI and μ-CT scanning technology. This model’s first application found minimal loss of residual hearing due to insertion angle after CI surgery and indicates that it is a reliable and helpful tool for future application in CI design, surgical planning, and stimuli setup.
Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex
Authors: Huuki-Myers Louise , Spangler Abby , Eagles Nick , Montgomery Kelsey D. , Kwon Sang Ho , Guo Boyi , Grant-Peters Melissa , Divecha Heena R. , Tippani Madhavi , Sriworarat Chaichontat , Nguyen Annie B. , Ravichandran Prashanthi , Tran Matthew N. , Seyedian Arta ,   PsychENCODE consortium, Hyde Thomas M. , Kleinman Joel E. , Battle Alexis , Page Stephanie C. , Ryten Mina , Hicks Stephanie C. , Martinowich Keri , Collado-Torres Leonardo , Maynard Kristen R. 
Published: February 2023

AbstractThe molecular organization of the human neocortex has been historically studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally-defined spatial domains that move beyond classic cytoarchitecture. Here we used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex (DLPFC). Integration with paired single nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we map the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains. Finally, we provide resources for the scientific community to explore these integrated spatial and single cell datasets atresearch.libd.org/spatialDLPFC/.SummaryGeneration of a molecular neuroanatomical map of the human prefrontal cortex reveals novel spatial domains and cell-cell interactions relevant for psychiatric disease.
Mixed IgG Fc immune complexes exhibit blended binding profiles and refine FcR affinity estimates
Authors: Tan Zhixin Cyrillus , Lux Anja , Biburger Markus , Varghese Prabha , Lees Stephen , Nimmerjahn Falk , Meyer Aaron S. 
Published: February 2023

AbstractImmunoglobulin (Ig)G antibodies coordinate immune effector responses by selectively binding to target antigens and then interacting with various effector cells via the Fcγ receptors. The Fc domain of IgG can promote or inhibit distinct effector responses across several different immune cell types through variation based on subclass and Fc domain glycosylation. Extensive characterization of these interactions has revealed how the inclusion of certain Fc subclasses or glycans results in distinct immune responses. During an immune response, however, IgG is produced with mixtures of Fc domain properties, so antigen-IgG immune complexes are likely to almost always be comprised of a combination of Fc forms. Whether and how this mixed composition influences immune effector responses has not been examined. Here, we measured Fcγ receptor binding to immune complexes of mixed Fc domain composition. We found that the binding properties of the mixed-composition immune complexes fell along a continuum between those of the corresponding pure cases. Binding quantitatively matched a mechanistic binding model, except for several low-affinity interactions mostly involving IgG2. We found that the affinities of these interactions are different than previously reported, and that the binding model could be used to provide refined estimates of these affinities. Finally, we demonstrated that the binding model can predict effector-cell elicited platelet depletion in humanized mice, with the model inferring the relevant effector cell populations. Contrary to the previous view in which IgG2 poorly engages with effector populations, we observe appreciable binding through avidity, but insufficient amounts to observe immune effector responses. Overall, this work demonstrates a quantitative framework for reasoning about effector response regulation arising from IgG of mixed Fc composition.Summary pointsThe binding behavior of mixed Fc immune complexes is a blend of the binding properties for each constituent IgG species.An equilibrium, multivalent binding model can be generalized to incorporate immune complexes of mixed Fc composition.Particularly for low-affinity IgG-Fcγ receptor interactions, immune complexes provide better estimates of affinities.The FcγR binding model predicts effector-elicited cell clearance in humanized mice.
Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites
Authors: Dimitriou Nikolaos M. , Flores-Torres Salvador , Kyriakidou Maria , Kinsella Joseph Matthew , Mitsis Georgios D. 
Published: February 2023

AbstractCell sedimentation in 3D hydrogel cultures refers to the vertical migration of cells towards the bottom of the space. To explain this poorly understood phenomenon, we conducted a multiscale experimental and mathematical examination of 3D cancer growth in triple negative breast cancer cells. Migration was examined in the presence and absence of Paclitaxel, in high and low adhesion environments and in the presence of fibroblasts. The observed behaviour was modeled by hypothesizing active migration due to self-generated chemotactic gradients. Our results confirmed this hypothesis, whereby migration was regulated by the MAPK and TGF-β pathways. The mathematical model enabled us to describe the experimental data in absence (normalized error< 40%) and presence of Paclitaxel (normalized error< 10%), suggesting inhibition of random motion and advection in the latter case. Inhibition of sedimentation in low adhesion and co-culture experiments further supported the conclusion that cells actively migrated downwards due to the presence of signals produced by cells already attached to the adhesive glass surface.
Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis
Authors: Rosenberger George , Li Wenxue , Turunen Mikko , He Jing , Subramaniam Prem S , Pampou Sergey , Griffin Aaron T , Karan Charles , Kerwin Patrick , Murray Diana , Honig Barry , Liu Yansheng , Califano Andrea 
Published: February 2023

AbstractAberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. By leveraging progress in proteomic technologies and network-based methodologies, over the past decade, we developed VESPA—an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations—and used it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogation of tumor-specific enzyme/substrate interactions accurately inferred kinase and phosphatase activity, based on their inferred substrate phosphorylation state, effectively accounting for signal cross-talk and sparse phosphoproteome coverage. The analysis elucidated time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring that was experimentally confirmed by CRISPRko assays, suggesting broad applicability to cancer and other diseases.
Highly sensitivein vivodetection of dynamic changes in enkephalins following acute stress
Authors: Mikati Marwa O. , Erdmann-Gilmore Petra , Connors Rose , Conway Sineadh M. , Malone Jim , Woods Justin , Sprung Robert W. , Townsend R. Reid , Al-Hasani Ream 
Published: February 2023

AbstractEnkephalins are opioid peptides that modulate analgesia, reward, and stress.In vivodetection of enkephalins remains difficult due to transient and low endogenous concentrations and inherent sequence similarity. To begin to address this we previously developed a system combining in vivo optogenetics with microdialysis and a highly sensitive mass spectrometry-based assay to measure opioid peptide release in freely moving rodents (Al-Hasani, 2018, eLife). Here we show improved detection resolution and stabilization of enkephalin detection, which allowed us to investigate enkephalin release during acute stress. We present an analytical method for real-time, simultaneous detection of Met- and Leu-Enkephalin (Met-Enk & Leu-Enk) in the mouse Nucleus Accumbens shell (NAcSh) after acute stress. We confirm that acute stress activates enkephalinergic neurons in the NAcSh using fiber photometry and that this leads to the release of Met- and Leu-Enk. We also demonstrate the dynamics of Met- and Leu-Enk release as well as how they correlate to one another in the ventral NAc shell, which was previously difficult due to the use of approaches that relied on mRNA transcript levels rather than post-translational products. This approach increases spatiotemporal resolution, optimizes the detection of Met-Enkephalin through methionine oxidation, and provides novel insight into the relationship between Met- and Leu-Enkephalin following stress.