bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revealing Gene Expression Heterogeneity in a Clonal Population ofTetrahymena thermophilathrough Single-Cell RNA Sequencing
Authors: Kojima Hiroki , Kashiwagi Akiko , Ikegami Takashi 
Published: August 2023

AbstractWe performed single-cell RNA sequencing (scRNA-seq) on a population of 5,000Tetrahymena thermophila, using the 10x Genomics 3’ gene expression analysis, to investigate gene expression variability within this clonal population. Initially, we estimated the 3’-untranslated regions (3’ UTRs), which were absent in existing annotation files but are crucial for the 10x Genomics 3’ gene expression analysis, using the peaks2utr method. This allowed us to create a modified annotation file, which was then utilized in our scRNA-seq analysis. Our analysis revealed significant gene expression variability within the population, even after removing the effect of cell phase-related features. This variability predominantly appeared in six distinct clusters. Through gene ontology and KEGG pathway enrichment analyses, we identified that these were primarily associated with ribosomal proteins, proteins specific to mitochondria, proteins involved in peroxisome-specific carbon metabolism, cytoskeletal proteins, motor proteins, and immobilized antigens.
Phonic Tics in a Rat Model of Tourette Syndrome Enable Research on Symptom-Based DBS
Authors: Sagalajev Boriss , Lennartz Lina , Mokhtari Niloofar , Szpak Mikolaj , Schüller Thomas , Baldermann Juan Carlos , Andrade Pablo , Visser-Vandewalle Veerle , Sesia Thibaut 
Published: August 2023

AbstractThe lack of a rodent model for both motor and phonic tics hinders research on deep brain stimulation (DBS) for refractory Tourette syndrome (TS). Striatal disinhibition with a GABA-A antagonist (bicuculline) was previously shown to induce tic-like hyperkinesia in rats and monkeys, while tic-like vocalizations were studied and confirmed only in the latter. We, therefore, assessed whether vocalizations accompany hyperkinesia also in rats and whether they respond to thalamic DBS. Rats underwent surgical implantation of a unilateral guide cannula targeting the caudate putamen (CPu) or nucleus accumbens (NAc). Additionally, they were implanted with an ipsilateral stimulation electrode targeting the border between the central medial (CM) and ventrolateral (VL) thalamic nuclei. Motor changes and ultrasound vocalizations were recorded and characterized offline. Bicuculline in CPu led to the development of hyperkinesia in the form of arrhythmic, myocloniform shoulder jerks sporadically alternating with episodes of dystonic lordosis. Likewise, bicuculline in NAc resulted in hyperkinesia, but at a much smaller dose and in conjunction with nonsensical vocalizations. DBS of CM/VL, but not adjacent regions, attenuated hyperkinesia. Also, early results indicate that thalamic DBS attenuates vocalizations, yet the hotspot for stimulation remains to be determined. In conclusion, striatal disinhibition leads not only to the development of hyperkinesia but also vocalizations in rats. The resemblance of hyperkinesia to motor tics and vocalizations to phonic tics is evident in their appearance and susceptibility to DBS. Rats can, therefore, be used to study DBS for symptom-based TS therapy.
Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation
Authors: Alston Jhullian J. , Soranno Andrea , Holehouse Alex S. 
Published: August 2023

ABSTRACTIntrinsically disordered regions (IDRs) are critical for cellular function, yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. We focussed here on the first two domains of coronavirus nucleocapsid proteins, the disordered N-terminal domain (NTD) followed by the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system to explore the interplay between an IDR adjacent to a folded domain, and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can – depending on the sequence – either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved fuzzy RNA:protein complex is found across nucleocapsid protein orthologs, despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.
Individual-specific memory reinstatement patterns within human face-selective cortex
Authors: Chen Yvonne Y. , Areti Aruni , Yoshor Daniel , Foster Brett L. 
Published: August 2023

AbstractHumans have the remarkable ability to vividly retrieve sensory details of past events. According to the theory of sensory reinstatement, during remembering, brain regions involved in the sensory processing of prior events are reactivated to support this perception of the past. Recently, several studies have emphasized potential transformations in the spatial organization of reinstated activity patterns. In particular, studies of scene stimuli suggest a clear anterior shift in the location of retrieval activations compared with those during perception. However, it is not clear that such transformations occur universally, with evidence lacking for other important stimulus categories, particularly faces. Critical to addressing these questions, and to studies of reinstatement more broadly, is the growing importance of considering meaningful variations in the organization of sensory systems across individuals. Therefore, we conducted a multi-session neuroimaging study to first carefully map individual participants face-selective regions within ventral temporal cortex (VTC), followed by a second session to examine the correspondence of activity patterns during face memory encoding and retrieval. Our results showed distinct configurations of face-selective regions within the VTC across individuals. While a significant degree of overlap was observed between face perception and memory encoding, memory retrieval engagement exhibited a more selective and constricted reinstatement pattern within these regions. Importantly, these activity patterns were consistently tied to individual-specific neural substrates, but did not show any consistent direction of spatial transformation (e.g., anteriorization). To provide further insight to these findings, we also report on unique human intracranial recordings from VTC under the same experimental conditions. Our findings highlight the importance of considering individual variations in functional neuroanatomy in the context of assessing the nature of cortical reinstatement. Consideration of such factors will be important for establishing general principles shaping the neural transformations that occur from perception to memory.
Development of Cell-Derived Plasma Membrane Vesicles as a Nanoparticle Encapsulation and Delivery System
Authors: Kheradmandi Mahsa , Farnoud Amir M. , Burdick Monica M. 
Published: August 2023

AbstractBackgroundDeveloping non-invasive delivery platforms with a high level of structural and/or functional similarity to biological membranes is highly desirable to reduce toxicity and improve targeting capacity of nanoparticles. Numerous studies have investigated the impacts of physicochemical properties of engineered biomimetic nanoparticles on their interaction with cells, yet technical difficulties have led to the search for better biomimetics, including vesicles isolated directly from live cells. Cell-derived giant plasma membrane vesicles (GPMVs), in particular, offer a close approximation of the intact cell plasma membrane by maintaining the latter’s compositional complexity, protein positioning in a fluid-mosaic pattern, and physical and mechanical properties. Thus, to overcome technical barriers of prior nanoparticle delivery approaches, we aimed to develop a novel method using GPMVs to encapsulate a variety of engineered nanoparticles, then use these core-shell, nanoparticle-GPMV vesicle structures to deliver cargo to other cells.ResultsThe GPMV system in this study was generated by chemically inducing vesiculation in A549 cells, a model human alveolar epithelial line. These cell-derived GPMVs retained encapsulated silica nanoparticles (50 nm diameter) for at least 48 hours at 37 °C. GPMVs showed nearly identical lipid and protein membrane profiles as the parental cell plasma membrane, with or without encapsulation of nanoparticles. Notably, GPMVs were readily endocytosed in the parental A549 cell line as well as the human monocytic THP-1 cell line. Higher cellular uptake levels were observed for GPMV-encapsulated nanoparticles compared to control groups, including free nanoparticles. Further, GPMVs delivered a variety of nanoparticles to parental cells with reduced cytotoxicity compared to free nanoparticles at concentrations that were otherwise significantly toxic.ConclusionsWe have introduced a novel technique to load nanoparticles within the cell plasma membrane during the GPMV vesiculation process. These GPMVs are capable of (a) encapsulating different types of nanoparticles (including larger and not highly-positively charged bodies that have been technically challenging cargoes) using a parental cell uptake technique, and (b) improving delivery of nanoparticles to cells without significant cytotoxicity. Ultimately, endogenous surface membrane proteins and lipids can optimize the physicochemical properties of cell membrane-derived vesicles, which could lead to highly effective cell membrane-based nanoparticle/drug delivery systems.
The roles of RNA editing in cancer immunity through interacting with interferon
Authors: Wu Sijia , Qin Xinyu , Lu Zhennan , Wen Jianguo , Yang Mengyuan , Kim Pora , Zhou Xiaobo , Huang Liyu 
Published: August 2023

AbstractThe interferon-activated tumor innate immunity can be primed by specific double-stranded RNA (dsRNA) sensors upon stimulation. A-to-I RNA editing in the dsRNA regions can have a potential function to regulate interferon-related cancer immunity. A systematical analysis of both the editing enzyme and specific enriched editing region in patients, tissues, and cell lines is performed to reveal the underlying mechanisms. We then validate the preferred editing of dsRNA regions, identify the hyper-editing in severe tumors, and discover the negative effect of editing on cancer immunity. Specifically, RNA editing acts as an inhibitor ofPKR- andMDA5-related interferon pathways through the regulations of miRNAs and RNA-binding proteins and the deactivation of dsRNA sensors. With the alteration of interferons, subsequently, RNA editing represses the infiltration of CD8 and CD4 T cells and reduces the sensitivities of cancer drugs, such as cisplatin. These analyses on A-to-I RNA editing can improve the knowledge of tumorigenesis, immunology, and cancer-targeted immunotherapy.HighlightsThe preferred dsRNA region for RNA editing is validated.Upregulation of RNA editing in severe tumors is discovered.RNA editing inhibits PKR- and MDA5-related cancer immunity.RNA editing represses the infiltration of CD8 and CD4 T cells.RNA editing reduces the sensitivities of cancer drugs.
RFC1AAGGG pentanucleotide repeats form parallel G-quadruplex: structural implications for aberrant molecular cascades in CANVAS
Authors: Wang Yang , Wang Junyan , Yan Zhenzhen , Hou Jianing , Wan Liqi , Yi Jie , Guo Pei , Han Da 
Published: August 2023

AbstractA pentanucleotide repeat expansion (PRE) of (AAGGG)nin the replication factor C subunit 1 (RFC1) gene is recently identified as the genetic cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), and also linked to several other neurodegenerative disorders including the Parkinson’s disease. However, the molecular mechanism by whichRFC1PRE drives pathology remains poorly understood. Here, for the first time we discovered and determined the high-resolution structures of parallel G-quadruplex formed by AAGGG repeats within the pathogenicRFC1PRE, revealing an intriguing conformational plasticity at the 3’-termi that allows stacking of multiple G4s. We further identify a molecular mechanism by which the DNA G4 inRFC1PRE impedes polymerase processivity leading to replication stalling and transcription inhibitionin vitroin a repeat-length-dependent manner, and the transcription inhibition could partially contribute to a reduced gene expression in cells. Our results demonstrate that the DNA G-quadruplex ofRFC1PRE participate in aberrant molecular cascades, and provide an unprecedented high-resolution structural target to discover helicases and ligands that resolve the pathogenic G4 for therapeutic intervention.
A competitive disinhibitory network for robust optic flow processing inDrosophila
Authors: Erginkaya Mert , Cruz Tomás , Brotas Margarida , Steck Kathrin , Nern Aljoscha , Torrão Filipa , Varela Nélia , Bock Davi , Reiser Michael , Chiappe M Eugenia 
Published: August 2023

SummaryMany animals rely on optic flow for navigation, using differences in eye image velocity to detect deviations from their intended direction of travel. However, asymmetries in image velocity between the eyes are often overshadowed by strong, symmetric translational optic flow during navigation. Yet, the brain efficiently extracts these asymmetries for course control. While optic flow sensitive-neurons have been found in many animal species, far less is known about the postsynaptic circuits that support such robust optic flow processing. In the flyDrosophila melanogaster, a group of neurons called the horizontal system (HS) are involved in course control during high-speed translation. To understand how HS cells facilitate robust optic flow processing, we identified central networks that connect to HS cells using full brain electron microscopy datasets. These networks comprise three layers: convergent inputs from different, optic flow-sensitive cells, a middle layer with reciprocal, and lateral inhibitory interactions among different interneuron classes, and divergent output projecting to both the ventral nerve cord (equivalent to the vertebrate spinal cord), and to deeper regions of the fly brain. By combining two-photon optical imaging to monitor free calcium dynamics, manipulating GABA receptors and modeling, we found that lateral disinhibition between brain hemispheres enhance the selectivity to rotational visual flow at the output layer of the network. Moreover, asymmetric manipulations of interneurons and their descending outputs induce drifts during high-speed walking, confirming their contribution to steering control. Together, these findings highlight the importance of competitive disinhibition as a critical circuit mechanism for robust processing of optic flow, which likely influences course control and heading perception, both critical functions supporting navigation.
OSGN-1 is a conserved flavin-containing monooxygenase required to stabilize the intercellular bridge in late cytokinesis
Authors: Goupil Eugénie , Lacroix Léa , Brière Jonathan , Guga Sandra , Saba-El-Leil Marc K. , Meloche Sylvain , Labbé Jean-Claude 
Published: August 2023

AbstractCytokinesis is the last step of cell division and is regulated by the small GTPase RhoA. RhoA activity is required for all steps of cytokinesis, including prior to abscission when daughter cells are ultimately physically separated. Like germ cells in all animals, theC. elegansembryonic germline founder cell initiates cytokinesis but does not complete abscission, leaving a stable intercellular bridge between the two daughter cells. Here we identify and characterizeC. elegansOSGN-1 as a novel cytokinetic regulator that promotes RhoA activity during late cytokinesis. Sequence analyses and biochemical reconstitutions reveal that OSGN-1 is a flavin-containing monooxygenase. Genetic analyses indicate that the monooxygenase activity of OSGN-1 is required to maintain active RhoA at the end of cytokinesis in the germline founder cell and to stabilize the intercellular bridge. Deletion ofOSGIN1in human cells results in an increase in binucleation as a result of cytokinetic furrow regression, and this phenotype can be rescued by expressing a catalytically-active form ofC. elegansOSGN-1, indicating that OSGN-1 and OSGIN1 are functional orthologs. We propose that OSGN-1 and OSGIN1 are novel, conserved monooxygenase enzymes required to maintain RhoA activity at the intercellular bridge during late cytokinesis and thus promote its stability, enabling proper abscission in human cells and bridge stabilization inC. elegansgerm cells.
Using deep long-read RNAseq in Alzheimer’s disease brain to assess medical relevance of RNA isoform diversity
Authors: Heberle Bernardo Aguzzoli , Brandon J. Anthony , Page Madeline L. , Nations Kayla A. , Dikobe Ketsile I. , White Brendan J. , Gordon Lacey A. , Fox Grant A. , Wadsworth Mark E. , Doyle Patricia H. , Williams Brittney A. , Fox Edward J. , Shantaraman Anantharaman , Ryten Mina , Goodwin Sara , Ghiban Elena , Wappel Robert , Mavruk-Eskipehlivan Senem , Miller Justin B. , Seyfried Nicholas T. , Nelson Peter T. , Fryer John D. , Ebbert Mark T. W. 
Published: August 2023

AbstractDue to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical relevance of measuring RNA isoform expression, we sequenced 12 aged human frontal cortices (6 Alzheimer’s disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. Our study uncovered 53 new high-confidence RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. Specific examples includeWDR4(61%; microcephaly),MYL3(44%; hypertrophic cardiomyopathy), andMTHFS(25%; major depression, schizophrenia, bipolar disorder). Other notable genes with new high-confidence isoforms includeCPLX2(10%; schizophrenia, epilepsy) andMAOB(9%; targeted for Parkinson’s disease treatment). We identified 1,917 medically relevant genes expressing multiple isoforms in human frontal cortex, where 1,018 had multiple isoforms with different protein coding sequences, demonstrating the need to better understand how individual isoforms from a single gene body are involved in human health and disease, if at all. Exactly 98 of the 1,917 genes are implicated in brain-related diseases, including Alzheimer’s disease genes such asAPP(Aβ precursor protein; five),MAPT(tau protein; four), andBIN1(eight). As proof of concept, we also found 99 differentially expressed RNA isoforms between Alzheimer’s cases and controls, despite the genes themselves not exhibiting differential expression. Our findings highlight the significant knowledge gaps in RNA isoform diversity and their medical relevance. Deep long-read RNA sequencing will be necessary going forward to fully comprehend the medical relevance of individual isoforms for a “single” gene.
Differential conformational dynamics in two type-A RNA-binding domains drive the double-stranded RNA recognition and binding
Authors: Parvez Firdousi , Sangpal Devika , Paithankar Harshad , Amin Zainab , Chugh Jeetender 
Published: August 2023

AbstractTAR RNA binding protein (TRBP) has emerged as a key player in the RNA interference (RNAi) pathway, wherein it binds to different pre-miRNAs and siRNAs, each varying in sequence and/or structure. We hypothesize that TRBP displays dynamic adaptability to accommodate heterogeneity in target RNA structures. Thus, it is crucial to ascertain the role of intrinsic and RNA-induced protein dynamics in RNA recognition and binding. We have previously elucidated the role of intrinsic and RNA-induced conformational exchange in the double-stranded RNA-binding domain 1 (dsRBD1) of TRBP in shape-dependent RNA recognition. The current study delves into the intrinsic and RNA-induced conformational dynamics of the TRBP-dsRBD2 and then compares it with the dsRBD1 study carried out previously. Remarkably, the two domains exhibit differential binding affinity to a 12 bp dsRNA owing to the presence of critical residues and structural plasticity. Further, we report that dsRBD2 depicts constrained conformational plasticity when compared to dsRBD1. Although, in the presence of RNA, dsRBD2 undergoes induced conformational exchange within the designated RNA-binding regions and other residues, the amplitude of the motions remains modest when compared to those observed in dsRBD1. We propose a dynamics-driven model of the two tandem domains of TRBP, substantiating their contributions to the versatility of dsRNA recognition and binding.Significance StatementExploring the intricacies of RNA-protein interactions by delving into dynamics-based measurements not only adds valuable insights into the mechanics of RNA-protein interactions but also underscores the significance of conformational dynamics in dictating the functional outcome in such tightly regulated biological processes. In this study, we measure intrinsic and RNA-induced conformational dynamics in the second dsRBD, i.e., TRBP-dsRBD2, and compare the same with that carried out in the first dsRBD (TRBP-dsRBD1) of TRBP protein, a key player of the RNAi pathway. The study unveils the differential conformational space accessible to the two domains of TRBP, even though they both adopt a canonical dsRBD fold, thereby affecting how they interact with target RNAs.