bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial transcriptome of developmental mouse brain reveals temporal dynamics of gene expressions and heterogeneity of the claustrum
Authors: Hara Yuichiro , Kumamoto Takuma , Yoshizawa-Sugata Naoko , Hirai Kumiko , Xianghe Song , Kawaji Hideya , Ohtaka-Maruyama Chiaki 
Published: April 2023

ABSTRACTDuring the development of the mammalian cerebral cortex, numerous neurons are arranged in a six-layer structure with an inside-out fashion to form the neocortex and wire neural circuits. This process includes cell proliferation, differentiation, migration, and maturation, supported by precise genetic regulation. To understand this sequence of processes at the cellular and molecular levels, it is necessary to characterize the fundamental anatomical structures by gene expression. However, markers established in the adult brain sometimes behave differently in the fetal brain, actively changing during development. Spatial transcriptomes yield genome-wide gene expression profiles from each spot patterned on tissue sections, capturing RNA molecules from fresh-frozen sections and enabling sequencing analysis while preserving spatial information. However, a deeper understanding of this data requires computational estimation, including integration with single-cell transcriptome data and aggregation of spots on the single-cell cluster level. The application of such analysis to biomarker discovery has only begun recently, and its application to the developing fetal brain is largely unexplored. In this study, we performed a spatial transcriptome analysis of the developing mouse brain to investigate the spatiotemporal regulation of gene expression during development. Using these data, we conducted an integrated study with publicly available mouse data sets, the adult brain’s spatial transcriptome, and the fetal brain’s single-cell transcriptome. Our data-driven analysis identified novel molecular markers of the choroid plexus, piriform cortex, thalamus, and claustrum. In addition, we revealed that the internal structure of the embryonic claustrum is composed of heterogeneous cell populations.
SorLA restricts TNFα release from microglia to shape glioma-supportive brain microenvironment
Authors: Kaminska Paulina , Ovesen Peter L. , Jakiel Mateusz , Obrebski Tomasz , Schmidt Vanessa , Bieniek Magdalena , Anink Jasper , Paterczyk Bohdan , Draminski Michal , Jensen Anne Mette Gissel , Piatek Sylwia , Andersen Olav M. , Aronica Eleonora , Willnow Thomas E. , Kaminska Bozena , Dabrowski Michal J. , Malik Anna R. 
Published: April 2023

AbstractSorLA, encoded by the geneSORL1, is an intracellular sorting receptor of the VPS10P domain receptor gene family. Although SorLA is best recognized for its ability to shuttle target proteins between intracellular compartments in neurons, recent data suggest that also its microglial expression can be of high relevance for the pathogenesis of brain diseases, including glioblastoma (GBM). Here we interrogated the impact of SorLA on the functional properties of glioma-associated microglia and macrophages (GAMs). In the GBM microenvironment, GAMs are re-programmed and in turn lose the ability to elicit anti-tumor responses. Instead, they acquire glioma-supporting phenotype, which is a key mechanism promoting glioma progression. Our analysis of scRNA-seq data from GBM patients revealed that the pro-tumorigenic and pro-inflammatory properties of GAMs are linked to high and lowSORL1expression, respectively. Using cell models, we confirm that SorLA levels are differentially regulated by the presence of glioma cells and by inflammatory cues. We further show that SorLA acts as a sorting receptor for the pro-inflammatory cytokine TNFα to restrain its secretion from microglia. As a consequence, loss of SorLA enhanced the pro-inflammatory potential of microglia, having a remarkable impact on glioma progression. In a murine model of glioma, SorLA-deficient mice develop smaller tumors and show hallmarks of anti-tumor response including altered microglia morphology, enhanced necroptosis, and massive neutrophil influx into the tumor parenchyma. Our findings indicate that SorLA is a key player in shaping the phenotype of GAMs, and its depletion can unlock an anti-tumor response.Significance statementOur study provides insight into the mechanisms shaping the tumor microenvironment in glioblastoma (GBM), the most prevalent and aggressive brain malignancy in adults. Poor prognosis in GBM largely results from the properties of the glioma milieu that blocks the anti-tumor response. We show that SorLA restricts release of the pro-inflammatory cytokine TNFα from microglia, thereby hampering their anti-glioma response. SorLA depletion reinforces the pro-inflammatory properties of tumor microenvironment and inhibits glioma growth. These findings have significant implications for our understanding of glioma biology, indicating SorLA-TNFα interaction as a potential target in GBM therapies. They also offer a new perspective on SorLA activities in microglia which emerge as highly relevant not only for the pathogenesis GBM, but also of other brain diseases such as Alzheimer’s disease.
Structural bases for the Charcot–Marie–Tooth disease induced by single amino acid substitutions of myelin protein zero
Authors: Sakakura Masayoshi , Tanabe Mikio , Mori Masaki , Takahashi Hideo , Mio Kazuhiro 
Published: April 2023

AbstractMyelin protein zero (MPZ or P0) is a major transmembrane protein expressed in peripheral compact myelin and functions to glue membranes to form multiple layered membranes characteristic of myelin. Intermembrane adhesion is mediated by homophilic interactions between the extracellular domains (ECDs) of MPZ molecules. Single amino acid substitutions in an ECD cause demyelinating neuropathy, known as Charcot–Marie–Tooth disease (CMT); however, the mechanisms by which such substitutions induce the disease are not well understood. To address this issue, we constructed a novel assay to evaluate the membrane-stacking activity of ECD using ECD-immobilized nanodiscs. Using this novel “nanomyelin” system, we found that octameric (8-meric) ECDs with a stacked-rings-like configuration are responsible for membrane adhesion. Two inter-ECD interactions,cisand head-to-head, are essential to constituting the 8-mer and, consequently, to gluing the membranes. This result was further reinforced by the observation that the CMT-related N87H substitution at thecisinterface abolished membrane-adhesion activity. In contrast, the CMT-related D32G and E68V variants of ECD retained membrane-stacking activity, whereas their thermal stability was reduced compared to that of the WT. Reduced thermal stability may lead to impairment of the long-term stability of ECD and the layered membranes of myelin.
SUBTLE: An unsupervised platform with temporal link embedding that maps animal behavior
Authors: Kwon Jea , Kim Sunpil , Kim Dong-Kyum , Joo Jinhyeong , Kim SoHyung , Cha Meeyoung , Lee C. Justin 
Published: April 2023

AbstractWhile huge strides have recently been made in language-based machine learning, the ability of artificial systems to comprehend the sequences that comprise animal behavior has been lagging behind. In contrast, humans instinctively recognize behaviors by finding similarities in behavioral sequences. Here, we develop an unsupervised behavior-mapping framework, SUBTLE (spectrogram-UMAP-based temporal-link embedding), to capture comparable behavioral repertoires from 3D action skeletons. To find the best embedding method, we devise a temporal proximity index as a metric to gauge temporal representation in the behavioral embedding space. The method achieves the best performance compared to current embedding strategies. Its spectrogram-based UMAP clustering not only identifies subtle inter-group differences but also matches human-annotated labels. SUBTLE framework automates the tasks of both identifying behavioral repertoires like walking, grooming, standing, and rearing, and profiling individual behavior signatures like subtle inter-group differences by age. SUBTLE highlights the importance of temporal representation in the behavioral embedding space for human-like behavioral categorization.One Sentence SummaryUnsupervised behavior-mapping from 3D action skeletons achieves superior performance, captures behavioral repertoires, and identifies inter-group differences, emphasizing how temporal representation is critical in the behavioral embedding space.
Identification of differentially recognized T cell epitopes in the spectrum ofMtbinfection
Authors: Panda Sudhasini , Morgan Jeffrey , Cheng Catherine , Saito Mayuko , Gilman Robert H. , Ciobanu Nelly , Crudu Valeriu , Catanzaro Donald G , Catanzaro Antonino , Rodwell Timothy , Perera Judy S.B. , Chathuranga Teshan , Gunasena Bandu , DeSilva Aruna D. , Peters Bjoern , Sette Alessandro , Lindestam Arlehamn Cecilia S. 
Published: April 2023

AbstractTuberculosis caused byMycobacterium tuberculosisis one of the leading causes of death from a single infectious agent. Identifying dominant epitopes and comparing their reactivity in different tuberculosis (TB) infection states can help design diagnostics and vaccines. We performed a proteome-wide screen of 20,610Mtbderived peptides in 21 Active TB (ATB) patients 3-4 months post-diagnosis of pulmonary TB (mid-treatment) using an IFNγ and IL-17 Fluorospot assay. Responses were mediated exclusively by IFNγ and identified a total of 137 unique epitopes, with each patient recognizing, on average, 8 individual epitopes and 22 epitopes (16%) recognized by 2 or more participants. Responses were predominantly directed against antigens part of the cell wall and cell processes category. Testing 517 peptides spanning TB vaccine candidates and ESAT- 6 and CFP10 antigens also revealed differential recognition between ATB participants mid-treatment and healthy IGRA+ participants of several vaccine antigens. An ATB-specific peptide pool consisting of epitopes exclusively recognized by participants mid-treatment, allowed distinguishing participants with active pulmonary TB from healthy interferon-gamma release assay (IGRA)+/- participants from diverse geographical locations. Analysis of longitudinal samples indicated decreased reactivity during treatment for pulmonary TB. Together, these results show that a proteome-wide screen of T cell reactivity identifies epitopes and antigens that are differentially recognized depending on theMtbinfection stage. These have potential use in developing diagnostics and vaccine candidates and measuring correlates of protection.
Comparative gene expression analysis of differentiated terminal and lateral haustoria of the obligate root parasitic plantPhelipanche ramosa(Orobanchaceae)
Authors: Brun Guillaume , Leman Julia K. H. , Wicke Susann 
Published: April 2023

AbstractBranched broomrape (Phelipanche ramosa, Orobanchaceae) is the most important parasitic weed of oilseed and vegetable crops in Europe. Deciphering the parasite’s basic biology and genetics underpinning adaptations to parasitism are essential for effective weed management. Here, we compared the gene expression profiles of differentiated terminal haustoria, formed immediately after the germination ofP. ramosawith those of the parasite’s adventitious roots and lateral haustoria, which develop on the latter as it grows. Principal component analysis and functional annotation of differentially expressed genes indicate a greater transcriptional similarity between adventitious roots and lateral haustoria compared to terminal haustoria. Genes involved in hydrogen peroxide catabolic processes and mucilage metabolic processes were more abundant in lateral haustoria compared to adventitious roots, indicating that secondary host attachment involves secretion of adhesive compounds, cell wall modification, and a termination of the developmental program associated with root growth. In terminal haustoria, phytohormonal signaling pathways for post-germination growth and meristem development were the most prominent expression profile difference to lateral haustoria. Besides this, wide similarity of expressed genes between lateral and terminal haustoria suggest overlapping pathways underlying haustorium differentiation and a conserved functional relevance of both haustoria types at maturity. Together, our study provides first insights into the transcriptional landscapes of the primary organs securingP.ramosa’s nutritional success. However, more research is needed to investigate whether the parasite’s various haustorium types differ in their sensitivities to environmental stimuli and whether transcriptional divergence in terminal and lateral haustoria ofP. ramosareflect differences regarding their developmental origin.
Impact of light on task-evoked pupil responses during cognitive tasks
Authors: Campbell Islay , Beckers Elise , Sharifpour Roya , Berger Alexandre , Paparella Ilenia , Balda Aizpurua Jose Fermin , Koshmanova Ekaterina , Mortazavi Nasrin , Sherif Siya , Vandewalle Gilles 
Published: April 2023

AbstractLight has many non-image-forming functions including modulation of pupil size and stimulation of alertness and cognition. Part of these non-image-forming effects may be mediated by the brainstem locus coeruleus. The processing of sensory inputs can be associated with a transient pupil dilation that is likely driven in part by the phasic activity of the locus coeruleus. Here, we aimed to characterise the task-evoked pupil response associated with auditory inputs under different light levels and across two cognitive tasks. We continuously monitored the pupil of 20 young healthy participants (24.05y ±4.0; 14 women) while they completed an attentional and an emotional auditory task whilst exposed to repeated 30-to-40s-blocks of light interleaved with darkness periods. Blocks could either consist of monochromatic orange light [0.16 melanopic Equivalent Daylight Illuminance (EDI) lux] or blue-enriched white light of three different levels [37, 92, 190 melanopic EDI lux; 6500K]. For the analysis 15 and then 14 participants were included in the attentional and emotional tasks respectively. Generalized Linear Mixed Models showed a significant main effect of light level on the task-evoked pupil responses triggered by the attentional and emotional tasks (p≤.0001). The impact of light was different for the target vs. non-target stimulus of the attentional task but was not different for the emotional and neutral stimulus of the emotional task. Despite a smaller sustained pupil size during brighter light blocks, a higher light level triggers a stronger task-evoked pupil response to auditory stimulation, presumably through the recruitment of the locus coeruleus.
Multimodal mismatch responses in associative but not primary visual cortex support hierarchical predictive coding in cortical networks
Authors: Van Derveer Alice B , Ross Jordan M. , Hamm Jordan P. 
Published: April 2023

AbstractA key function of the mammalian neocortex is to process sensory data in the context of current and past stimuli. Primary sensory cortices, such as V1, respond weakly to stimuli that typical in their context but strongly to novel stimuli, an effect known as “deviance detection”. How deviance detection occurs in associative cortical regions that are downstream of V1 is not well-understood. Here we investigated parietal associative area (PTLp) responses to auditory, visual, and audio-visual mismatches with two-photon calcium imaging and local field potential recordings. We employed basic unisensory auditory and visual oddball paradigms as well as a novel multisensory oddball paradigm, involving typical parings (VaAc or VbAd) presented at p=.88 with rare “deviant” pairings (e.g. VaAd or VbAc) presented at p=.12. We found that PTLp displayed robust deviance detection responses to auditory-visual mismatches, both in individual neurons and in population theta and gamma-band oscillations. In contrast, V1 neurons displayed deviance detection only to visual deviants in a unisensory context, but not to auditory or auditory-visual mismatches. Taken together, these results accord with a predictive processing framework for cortical responses, wherein modality specific prediction errors (i.e. deviance detection responses) are computed in functionally specified cortical areas and feed-forward to update higher brain regions.
Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency
Authors: Haudiquet Matthieu , Nucci Amandine , Bris Julie Le , Bonnin Rémy A. , Domingo-Calap Pilar , Rendueles Olaya , Rocha Eduardo P.C. 
Published: April 2023

SummaryBacterial evolution is affected by mobile genetic elements such as phages and conjugative plasmids, which may provide novel adaptive traits but also incur in fitness costs. Infection by these elements is affected by the bacterial capsule. Yet, its importance has been difficult to quantify and characterise because of the high diversity of bacterial genomes regarding confounding mechanisms such as anti-viral systems. We swapped capsule loci betweenKlebsiella pneumoniaestrains to quantify their effect on transfer of conjugative plasmids and phages independently of the genetic background. Capsule swaps systematically invert phage susceptibility, demonstrating that serotypes are key determinants of phage infection. Capsule types also affect conjugation efficiency in both donor and recipient cells depending on the serotype, a mechanism shaped by the capsule volume and depending on the structure of the conjugative pilus. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The pili least sensitive to capsules (F-like) are also the most frequent in the species’ plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how the traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.Graphical abstract
Chromatin context-dependent regulation and epigenetic manipulation of prime editing
Authors: Li Xiaoyi , Chen Wei , Martin Beth K. , Calderon Diego , Lee Choli , Choi Junhong , Chardon Florence M. , McDiarmid Troy , Kim Haedong , Lalanne Jean-Benoît , Nathans Jenny F. , Shendure Jay 
Published: April 2023

ABSTRACTPrime editing is a powerful means of introducing precise changes to specific locations in mammalian genomes. However, the widely varying efficiency of prime editing across target sites of interest has limited its adoption in the context of both basic research and clinical settings. Here, we set out to exhaustively characterize the impact of thecis-chromatin environment on prime editing efficiency. Using a newly developed and highly sensitive method for mapping the genomic locations of a randomly integrated “sensor”, we identify specific epigenetic features that strongly correlate with the highly variable efficiency of prime editing across different genomic locations. Next, to assess the interaction oftrans-acting factors with thecis-chromatin environment, we develop and apply a pooled genetic screening approach with which the impact of knocking down various DNA repair factors on prime editing efficiency can be stratified bycis-chromatin context. Finally, we demonstrate that we can dramatically modulate the efficiency of prime editing through epigenome editing,i.e.altering chromatin state in a locus-specific manner in order to increase or decrease the efficiency of prime editing at a target site. Looking forward, we envision that the insights and tools described here will broaden the range of both basic research and therapeutic contexts in which prime editing is useful.
Functional whole genome screen of nutrient-starvedMycobacterium tuberculosisidentifies genes involved in antibiotic tolerance
Authors: Matern William M. , Harris Harley T. , Danchik Carina , McDonald Marissa , Patel Gopi , Srivastava Aashish , Ioerger Thomas R. , Bader Joel S. , Karakousis Petros C. 
Published: April 2023

AbstractMycobacterium tuberculosis(Mtb), the causative agent of tuberculosis (TB), poses a global health challenge and is responsible for over a million deaths each year. Current treatment is lengthy and complex, and new, abbreviated regimens are urgently needed.Mtbadapts to nutrient starvation, a condition experienced during host infection, by shifting its metabolism and becoming tolerant to the killing activity of bactericidal antibiotics. An improved understanding of the mechanisms mediating antibiotic tolerance inMtbcan serve as the basis for developing more effective therapies. We performed a forward genetic screen to identify candidateMtbgenes involved in tolerance to the two key first-line antibiotics, rifampin and isoniazid, under nutrient-rich and nutrient-starved conditions. In nutrient-rich conditions, we found 220 mutants with differential antibiotic susceptibility (218 in the rifampin screen and 2 in the isoniazid screen). FollowingMtbadaptation to nutrient starvation, 82 mutants showed differential antibiotic susceptibility (80 in the rifampin screen and 2 in the isoniazid screen). Using targeted mutagenesis, we validated the rifampin-hypersusceptible phenotype under nutrient starvation inMtbmutants lacking the following genes:ercc3,moeA1,rv0049, andrv2179c. These findings shed light on potential therapeutic targets, which could help shorten the duration and complexity of antitubercular regimens.ImportanceTreatment ofMtbinfection requires a long course of combination antibiotics, likely due to subpopulations of tolerant bacteria exhibiting decreased susceptibility to antibiotics. Identifying and characterizing the genetic pathways involved in antibiotic tolerance is expected to yield therapeutic targets for the development of novel TB treatment-shortening regimens.