bluuebunny/crossref_metadata_2025_split huggingface dataset:
GluK2 is a target for gene therapy in drug-resistant Temporal Lobe Epilepsy
Authors: Boileau Céline , Deforges Severine , Peret Angélique , Scavarda Didier , Bartolomei Fabrice , Giles April , Partouche Nicolas , Gautron Justine , Viotti Julio , Janowitz Haley , Penchet Guillaume , Marchal Cécile , Lagarde Stanislas , Trebuchon Agnès , Villeneuve Nathalie , Rumi Julie , Marissal Thomas , Khazipov Roustem , Khalilov Ilgam , Martineau Fanny , Maréchal Marine , Lepine Anne , Milh Mathieu , Figarella-Branger Dominique , Dougy Etienne , Tong Soutsakhone , Appay Romain , Baudouin Stéphane , Mercer Andrew , Smith Jared B. , Danos Olivier , Porter Richard , Mulle Christophe , Crépel Valérie 
Published: April 2023

AbstractObjectiveTemporal lobe epilepsy (TLE) is characterized by recurrent seizures generated in the limbic system, particularly in the hippocampus. In TLE, recurrent mossy fiber sprouting from dentate gyrus granule cells (DGCs) creates an aberrant epileptogenic network between DGCs which operates via ectopically expressed GluK2/GluK5-containing kainate receptors (KARs). TLE patients are often resistant to anti-seizure medications and suffer significant comorbidities; hence there is an urgent need for novel therapies. Previously we have shown that GluK2 knockout mice are protected from seizures. This study aims at providing evidence that downregulating KARs in the hippocampus using gene therapy reduces chronic epileptic discharges in TLE.MethodsWe combined molecular biology and electrophysiology in rodent models of TLE and in hippocampal slices surgically resected from patients with drug-resistant TLE.ResultsHere we confirmed the translational potential of KAR suppression using a non-selective KAR antagonist that markedly attenuated Interictal-like Epileptiform Discharges (IEDs) in TLE patient-derived hippocampal slices. An adeno-associated virus (AAV) serotype-9 vector expressing anti-grik2miRNA was designed to specifically downregulate GluK2 expression. Direct delivery of AAV9-antigrik2miRNA into the hippocampus of TLE mice led to a marked reduction in seizure activity. Transduction of TLE patient hippocampal slices reduced levels of GluK2 protein and, most importantly, significantly reduced IEDs.InterpretationOur gene silencing strategy to knock down aberrant GluK2 expression demonstrates inhibition of chronic seizure in a mouse TLE model and IEDs in cultured slices derived from TLE patients. These results provide proof-of-concept for a gene therapy approach targeting GluK2 KARs for drug-resistant TLE patients.
Design of a stem cell-based therapy for ependymal repair in hydrocephalus associated with germinal matrix hemorrhages
Authors: Rodríguez-Pérez Luis M. , Ojeda-Pérez Betsaida , García-Bonilla María , López-de San Sebastián Javier , González-García Marcos , Fernández-Muñoz Beatriz , Sánchez-Pernaute Rosario , García-Martín María L. , Domínguez-Pinos Dolores , Cárdenas-García Casimiro , Jiménez Antonio J. , Páez-González Patricia 
Published: April 2023

AbstractGerminal matrix hemorrhages (GMH) and the consequent posthemorrhagic hydrocephalus (PHH) are among the most common and severe neurological complications of preterm birth that require lifelong complex neurosurgical care. GMH and PHH provoke disruption of neuroepithelium/ependyma development, a key structure implicated in brain development and homeostasis. Neuroepithelial/ependymal damage causes lifelong cognitive and motor deficits; however, no therapy is directed to recover the damaged ependyma. This study is aimed to test the possibilities of ependymal repair in GMH/PHH using neural stem cells (NSCs) or ependymal progenitors (EpPs). Thus, it sets the basis for a therapeutic approach to treating ependymal damage and preventing brain developmental deficits. GMH/PHH was induced in 4-day-old mice using different experimental procedures involving collagenase, blood, or blood serum injections. PHH severity was characterized using magnetic resonance, immunofluorescence, and protein expression quantification with mass spectrometry. Additionally, a newexvivoapproach using ventricular walls from mice developing moderate and severe GMH/PHH was generated to study ependymal restoration and wall regeneration after stem cell treatments. NSCs or EpPs obtained from newborn mice were transplanted in the explants, and pretreatment with mesenchymal stem cells (MSCs) was tested. Ependymal differentiation and the effect of MSC-conditioned microenvironment were investigated in both explants and primary cultures. In the animals, PHH severity was correlated with the extension of GMH, ependymal disruption, astroglial/microglial reactions, and ventriculomegaly. In the explants, the severity and extension of GMH hindered the survival rates of the transplanted NSCs/EpPs. In the explants affected with GMH, new multiciliated ependymal cells could be generated from transplanted NSCs and, more efficiently, from EpPs. Blood and TNFα negatively affected ciliogenesis in cells expressing Foxj1. Pretreatment with mesenchymal stem cells (MSC) improved the survival rates of EpPs and ependymal differentiation while reducing the edematous and inflammatory conditions in the explants. In conclusion, in GMH/PHH, the ependyma can be restored from either NSC or EpP transplantation, being EpPs in an MSC-conditioned microenvironment more efficient for this purpose. Modifying the neuroinflammatory microenvironment by MSC pretreatment positively influenced the success of the ependymal restoration.
Mouse gingival single-cell transcriptomic atlas: An activated fibroblast subpopulation guides oral barrier immunity in periodontitis
Authors: Kondo Takeru , Gleason Annie , Okawa Hiroko , Hokugo Akishige , Nishimura Ichiro 
Published: April 2023

AbstractPeriodontitis, one of the most common non-communicable diseases, is characterized by chronic oral inflammation and uncontrolled tooth supporting alveolar bone resorption. Its underlying mechanism to initiate aberrant oral barrier immunity has yet to be delineated. Here, we report a unique fibroblast subpopulationactivated toguide oral inflammation (AG fibroblasts) identified in a single-cell RNA sequencing gingival cell atlas constructed from the mouse periodontitis models. AG fibroblasts localized beneath the gingival epithelium and in the cervical periodontal ligament responded to the ligature placement and to the discrete application of Toll-like receptor stimulants to mouse maxillary tissue. The upregulated chemokines and ligands of AG fibroblasts linked to the putative receptors of neutrophils in the early stages of periodontitis. In the established chronic inflammation, neutrophils together with AG fibroblasts appeared to induce type 3 innate lymphoid cells (ILC3s) that were the primary source of interleukin-17 cytokines. The comparative analysis ofRag2-/- andRag2γc-/-mice suggested that ILC3 contributed to the cervical alveolar bone resorption interfacing the gingival inflammation. We propose that AG fibroblasts function as a previously unrecognized surveillant to initiate gingival inflammation leading to periodontitis through the AG fibroblast-neutrophil-ILC3 axis.
MdMYB44-like positively regulates salt and drought tolerance via the MdPYL8-MdPP2CA module in apple
Authors: Chen Cui , Zhang Zhen , Lei Ying-Ying , Chen Wen-Jun , Zhang Zhi-Hong , Li Xiao-Ming , Dai Hong-Yan 
Published: April 2023

AbstractAbscisic acid (ABA) is involved in salt and drought stress responses, but the underlying molecular mechanism remains unclear. Here, we demonstrated that the overexpression ofMdMYB44-like, an R2R3-MYB transcription factor (TF), significantly increases the salt and drought tolerance of transgenic apple and Arabidopsis. MdMYB44-like inhibits the transcription ofMdPP2CA, which encodes a type 2C protein phosphatase that acts as a negative regulator in ABA response, thereby enhancing ABA signaling-mediated salt and drought tolerance. Furthermore, we found that MdMYB44-like and MdPYL8, an ABA receptor, form a protein complex that further enhances the transcriptional inhibition of theMdPP2CApromoter by MdMYB44-like. Significantly, we discovered that MdPP2CA can interfere with the physical association between MdMYB44-like and MdPYL8 in the presence of ABA, partially blocking the inhibitory effect of the MdMYB44-like-MdPYL8 complex on theMdPP2CApromoter. Thus, MdMYB44-like, MdPYL8, and MdPP2CA form a regulatory loop that tightly controls ABA signaling homeostasis under salt and drought stress. Our data revealed a previously unidentified mechanism by which MdMYB44-like precisely modulates ABA-mediated salt and drought tolerance in apple through the MdPYL8-MdPP2CA module.
Optogenetic ion pumps differ with respect to the secondary pattern of K+redistribution
Authors: Parrish R. Ryley , Jackson-Taylor Tom , Voipio Juha , Trevelyan Andrew J. 
Published: April 2023

AbstractWe recently reported that strong activation of the optogenetic chloride pump, Halorhodopsin leads to a secondary redistribution of K+ions into the cell, through tonically open, “leak” K+channels. Here we show that this effect is not unique to halorhodopsin, but is also seen with activation of another electrogenic ion pump, archaerhodopsin. The two opsins differ however in the size of the rebound rise in extracellular potassium, [K+]o, after the end of activation, which is far larger with halorhodopsin than for archaerhodopsin activation. Multiple linear regression modelling indicates that most of the variance in the post-illumination surge in [K+]o was explained by the type of opsin, and almost nothing by the size of the preceding, illumination-induced drop in [K+]o. These data provide additional support for the hypothesis that intense chloride-loading of cells, as occurs naturally following intense bursts of GABAergic synaptic bombardment, or artificially following halorhodopsin activation, is followed by extrusion of both Cl and K+coupled together. We discuss this with respect to the pattern of [K+]o rise that occurs at the onset of seizure-like events.
Transgenerational Epigenetic Inheritance of MHC Class I Gene Expression is Regulated by the CCAAT Promoter Element
Authors: Weissman Jocelyn D. , Kotekar Aparna , Barbash Zohar , Mu Jie , Singer Dinah S. 
Published: April 2023

ABSTRACTTransgenerational epigenetic inheritance is defined as the transmission of traits or gene expression patterns across multiple generations that do not derive from DNA alterations. The effect of multiple stress factors or metabolic changes resulting in such inheritance have been documented in plants, worms and flies and mammals. The molecular basis for epigenetic inheritance has been linked to histone and DNA modifications and non-coding RNA. In this study, we show that mutation of a promoter element, the CCAAT box, disrupts stable expression of an MHC Class I transgene, resulting in variegated expression among progeny for at least 4 generations in multiple independently derived transgenic lines. Histone modifications and RNA polII binding correlate with expression, whereas DNA methylation and nucleosome occupancy do not. Mutation of the CCAAT box abrogates NF-Y binding and results in changes to CTCF binding and DNA looping patterns across the gene that correlate with expression status from one generation to the next. These studies identify the CCAAT promoter element as a regulator of stable transgenerational epigenetic inheritance. Considering that the CCAAT box is present in 30% of eukaryotic promoters, this study could provide important insights into how fidelity of gene expression patterns is maintained through multiple generations.
Pararectus versus ilioinguinal approach for the management of acetabular fractures: A Protocol for Systemic Review and Meta-analysis
Authors: Rajnish Rajesh Kumar , Srivastava Amit , Yadav Sandeep Kumar , Elhence Abhay , Rathor Kuldeep , Gupta Saurabh 
Published: April 2023

AbstractBackgroundAcetabular fractures result from high-energy trauma, and their complex anatomy poses a challenge to surgeons for open reduction and internal fixation of these fractures. The goal of fixation is an anatomical reduction of articular surfaces and stable fixation with minimal damage to vital structures around. The long-term clinical outcomes of these fractures are significantly impacted by selecting an appropriate surgical approach with minimal complications to achieve an anatomical reduction with congruent articular surfaces. The purpose of this review is to compare the outcomes of the pararectus (PR) versus the ilioinguinal (IL) approach for the open reduction and internal fixation (ORIF) of displaced acetabular fractures by looking at the evidence in the existing literature.MethodsA systematic review and meta-analysis will be performed in accordance with the PRISMA guidelines. A primary search will be done through the electronic databases of PubMed/Medline, Embase, Scopus, and the Cochrane Library using a pre-defined search strategy. A comparative study, either randomized control trials (RCTs) or non-randomized trials, which have compared at least one outcome of the internal fixation of acetabular fractures using the PR versus IL approach will be included in the current review.Single-armed non-comparative studies, conference posters, abstracts, case reports, review articles, cadaveric studies, book chapters, technical tips, and biomechanical studies will be excluded. Both qualitative and quantitative data analysis will be performed. Appropriate tables and diagrams will be used to demonstrate the qualitative data presentation, and wherever feasible, a quantitative analysis will be done with the appropriate software. The risk-of-bias assessment for non-randomized comparative studies will be done using the MINORS tool, and the Cochrane Collaborations risk-of-bias tool will be used for RCTs.
Mechanisms of regulation of cryptic prophage-encoded gene products inEscherichia coli
Authors: Ragunathan Preethi T. , Lim Evelyne Ng Kwan , Ma Xiangqian , Massé Eric , Vanderpool Carin K. 
Published: April 2023

AbstractThedicBFoperon of Qin cryptic prophage inEscherichia coliK12 encodes the small RNA (sRNA) DicF and small protein DicB, which regulate host cell division and are toxic when overexpressed. While new functions of DicB and DicF have been identified in recent years, the mechanisms controlling the expression of thedicBFoperon have remained unclear. Under standard laboratory growth conditions, transcription fromdicBp,the major promoter of thedicBFoperon, is repressed by DicA. Here, we discovered that transcription of thedicBFoperon and processing of the polycistronic mRNA is regulated by multiple mechanisms. DicF sRNA accumulates during stationary phase and is processed from the polycistronicdicBFmRNA by the action of both RNase III and RNase E. DicA-mediated transcriptional repression ofdicBpcan be relieved by an antirepressor protein, Rem, encoded on the Qin prophage. Ectopic production of Rem results in cell filamentation due to strong induction of thedicBFoperon and filamentation is mediated by DicF and DicB. Spontaneous derepression ofdicBpoccurs in a subpopulation of cells independent of the antirepressor. This phenomenon is reminiscent of the bistable switch of λ phage with DicA and DicC performing functions similar to CI and Cro, respectively. Additional experiments demonstrate stress-dependent induction of thedicBFoperon. Collectively, our results illustrate that toxic genes encoded on cryptic prophages are subject to layered mechanisms of control, some that are derived from the ancestral phage and some that are likely later adaptations.ImportanceCryptic or defective prophages have lost genes necessary to excise from the bacterial chromosome and produce phage progeny. In recent years, studies have found that cryptic prophage gene products influence diverse aspects of bacterial host cell physiology. However, to obtain a complete understanding of the relationship between cryptic prophages and the host bacterium, identification of the environmental, host or prophage-encoded factors that induce the expression of cryptic prophage genes is crucial. In this study, we examine the regulation of a cryptic prophage operon inEscherichia coliencoding a small RNA and a small protein that are involved in inhibiting bacterial cell division, altering host metabolism, and protecting the host bacterium from phage infections.
FOXL2 interaction with different binding partners regulates the dynamics of ovarian development
Authors: Migale Roberta , Neumann Michelle , Mitter Richard , Rafiee Mahmoud-Reza , Wood Sophie , Olsen Jessica , Lovell-Badge Robin 
Published: April 2023

AbstractThe transcription factor FOXL2 is required in ovarian somatic cells for female fertility. Differential timing ofFoxl2deletion, in embryonic versus adult mouse ovary, leads to distinctive outcomes suggesting different roles across development. Here, we comprehensively investigated FOXL2’s role through a multi-omics approach to characterise gene expression dynamics and chromatin accessibility changes, coupled with genome-wide identification of FOXL2 targets and on-chromatin interacting partners in granulosa cells across ovarian development. We found that FOXL2 regulates more targets postnatally, through interaction with factors regulating primordial follicle activation (PFA) and steroidogenesis. Deletion of one interactor, Ubiquitin specific protease 7 (USP7), induces PFA blockage, impaired ovary development and sterility. Our datasets constitute a comprehensive resource for exploration of the molecular mechanisms of ovarian development and causes of female infertility.
Event-Induced Modulation of Aperiodic Background EEG: Attention-Dependent and Age-Related Shifts in E:I balance, and Their Consequences for Behavior
Authors: Kałamała Patrycja , Gyurkovics Máté , Bowie Daniel C. , Clements Grace M. , Low Kathy A. , Dolcos Florin , Fabiani Monica , Gratton Gabriele 
Published: April 2023

AbstractThe broadband shape of the EEG spectrum, summarized using a 1/fxfunction, is thought to reflect the balance between excitation and inhibition in cortical regions (E:I balance). This balance is an important characteristic of neural circuits and could inform studies of aging, as older adults show a relative inhibitory activity deficit. Thus far, no studies have leveraged the event-related temporal dynamics of 1/fxactivity to better understand the phases of information processing, especially in the context of aging. Here, for the first time, we examined variations of this activity during the foreperiod of a cued flanker task in younger (YA) and older adults (OA), with picture cues varying in task relevance, relative novelty, and valence. We report a biphasic change in the spectral exponent (corresponding to negative slopes in log-log space) after cue presentation, independent of cue-elicited ERPs, with an initial period of increased negativity (indicating cortical inhibition, similar in YA and OA) followed by decreased negativity (indicating cortical excitation, especially in OA). The decrease in the exponent negativity was associated with lower performance and greater congruency costs in the flanker task. Finally, more novel cues reduced the shift towards excitation in OA, partly restoring their E:I balance, and diminishing congruency costs. These findings demonstrate that the broadband shape of the EEG spectrum varies dynamically in a manner that is predictive of subsequent behavior. They also expand our understanding of how neural communication shapes cognition in YA and OA and have implications for neuroscientific models of cognitive processing and age-related cognitive decline.
Acid enhances salt taste by activating the epithelial sodium channel
Authors: Collier Daniel M. , Peterson Zerubbabel J. , Ryan Alan J. , Williford Noah N. , Benson Christopher J. , Snyder Peter M. 
Published: April 2023

AbstractSalt is often used to enhance the flavor of foods and drinks, and in turn, some foods and drinks may intensify the taste of salt. For example, highly acidic carbonated beverages sometimes accompany salty snacks, and margaritas made with acidic citrus are served in salt-rimmed glasses. However, whether and how acid might enhance salt taste remain unknown. Epithelial sodium channels (ENaC) in tongue taste cells detect dietary sodium. We found that acid irreversibly increased ENaC channel activity, with half-maximal activation occurring at pH 2.6. Acid altered ENaC gating by increasing the rate of channel opening and reducing the rate of channel closing. Acidic beverages Coca-Cola® and Pepsi® (pH 2.2-2.4) also stimulated ENaC current but Diet Coke® (pH 3.2) did not. In humans, we found that acid reduced the sodium taste detection threshold. These findings identify a functional interplay between dietary sodium and acid--by modulating ENaC gating, acid enhances salt taste.
Charting spatial ligand-target activity using Renoir
Authors: Rao Narein , Kumar Tanush , Pai Rhea , Mishra Archita , Ginhoux Florent , Chan Jerry , Sharma Ankur , Zafar Hamim 
Published: April 2023

AbstractThe advancement of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics has enabled the inference of cellular interactions in a tissue microenvironment. Despite the development of cell-cell interaction inference methods, there is a lack of methods capable of mapping the influence of ligands on downstream target genes across a spatial topology with specific cell type composition, with the potential to shed light on niche-specific relationship between ligands and their downstream targets. Here we present Renoir for charting the ligand-target activities across a spatial topology and delineating spatial communication niches harboring specific ligand-target activities. Renoir also spatially maps pathway-level activity of ligand-target genesets and identifies domain-specific ligand-target activities. Across spatial datasets with varying resolution (spot to single-cell) ranging from development to disease, Renoir inferred cellular niches with distinct ligand-target interactions, spatially mapped pathway activities, and identified context-specific novel cell-cell interactions. Renoir uncovers biological insights and therapeutically-relevant cellular crosstalk from spatial transcriptomics data.
Label-free Quantification of Host-Cell Protein Impurity in a Recombinant Hemoglobin Reference Material
Authors: Henrion André , Arsene Cristian , Liebl Maik , O’Connor Gavin 
Published: April 2023

AbstractQuantitative analysis depends on pure-substance primary calibrators with known mass fractions of impurity. Here, label-free quantification (LFQ) is being evaluated as a readily available, reliable method for determining the mass fraction of host-cell proteins (HCPs) in bioengineered proteins. For example, hemoglobin-A2 (HbA2) is being used as obtained through overexpression inE.coli.Two different materials had been produced: natural, and U-15N-labeled HbA2. For quantification of impurity, precursorion (MSl-) intensities were integrated over allE.coli-proteins identified, and divided by the intensities obtained for HbA2. This ratio was calibrated against the corresponding results forE.coli-cell lysate, which had been spiked at known mass-ratios to pure HbA2. To demonstrate the universal applicability of LFQ, further proteomes (yeast and human K562) were then alternatively used for calibration and found to produce comparable results. Valid results could also be obtained when the complexity of the calibrator is reduced to a mix of nine proteins, and a minimum of five proteins is estimated to be sufficient to keep the sampling error below l5%. For the studied materials, HbA2-mass fractions of 916±15 mg/g and 922±11 mg/g were found. Value assignment by LFQ thus contributes 1-2% to the overall uncertainty of HbA2-quantification when these materials are used as calibrators. Further purification of the natural HbA2yielded 999.1± 0.15 mg/g, corresponding to ≈ 0.2% of uncertainty contribution, though at a significant loss of material. If an overall-uncertainty of 5% is acceptable for protein-quantification, working with the original materials would definitely be viable, therefore.