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Garcia, S.

Publications and source records attributed to Garcia, S..

At least 19 recordsLinked to original sources

No Evidence for a Wakeful Rest Benefit on Associative Memory: A Within-Participant EEG Study

Wakeful rest after learning has been proposed to facilitate memory consolidation compared to engaging in a distraction task, with prior EEG studies linking slow oscillation power during rest to better memory performance. However, replication attempts have yielded mixed results. We investigated whether 10 minutes of wakeful rest would enhance associative memory performance relative to 10 minutes of a hippocampus-dependent auditory short-term memory distraction task, using a within-participant design with continuous EEG recording. We employed both a replication-inspired analytical approach, closely modeled on prior work, and a data-specific approach adapted to our dataset. Contrary to our hypotheses, we found no advantage of rest over distraction on associative memory performance. We did, however, observe an order effect: performance was better for the second learning than the first, and this improvement was more pronounced when rest was performed second compared to first. At the neurophysiological level, neither slow oscillation nor alpha power during the post-learning period correlated with memory performance, regardless of analytical pipeline, although cross-over analyses revealed that the choice of EEG reference influenced the direction of some correlations. At the phenomenological level, self-reported mental activity during rest and distraction, as well as trait daydreaming frequency, were not related to memory outcomes, despite the two conditions inducing distinct subjective cognitive states. Together, these findings do not support a robust benefit of post-learning wakeful rest over a hippocampus-dependent distraction task for associative memory, nor do they replicate prior EEG correlates of consolidation. We discuss methodological factors, including task-learning effects in within-participant designs, the coarseness of averaged spectral power measures, and variability in EEG preprocessing pipelines, that may contribute to inconsistencies across the literature, and we call for greater standardization and transparency in future studies.

neuroscience↗

Cytogenomic signatures of hybridisation in the genus Carpobrotus reveal biased parental dominance

O_LIHybridisation is frequently associated with plant invasions; however, its consequences for genome organisation and chromosome evolution remain poorly understood in invasive species. We investigated the extent of hybridisation in the invasive Carpobrotus edulis--acinaciformis hybrid complex and determined the cytogenomic contribution of parental species in hybrid accessions. C_LIO_LIWe combined whole-genome sequencing, population genomic analyses, genome size estimation, repeatome characterisation, chromosome counting and fluorescence in situ hybridisation to compare parental species and hybrid accessions from South Africa and the Mediterranean Basin. C_LIO_LIPopulation genomic analyses revealed widespread hybridisation and introgression, with most invasive accessions showing admixed ancestries. Pattersons D-statistic supported asymmetric allele sharing towards C. edulis. Hybrid accessions displayed genome sizes indistinguishable from C. edulis, whereas C. acinaciformis possessed significantly larger genomes. Repeatome analyses identified marked differences in repetitive DNA composition, particularly in satellite DNA abundance and chromosomal distribution. A newly identified satellite repeat (CarpoSat) showed contrasting chromosomal patterns between parental species, whereas hybrids resembled C. edulis satellite pattern. C_LIO_LIOur results demonstrate that Carpobrotus hybrid accessions are a swarm of later-generation hybrids and backcrosses showing a strong bias towards C. edulis, indicating asymmetric introgression. These findings highlight the value of integrating cytogenetic and genomic approaches to understand genome evolution in invasive hybrid complexes. C_LI

plant biology↗

AEGIS reveals epitope- and clone-resolved convergence of CNS B and T cell autoreactivity in ROHHAD

Autoimmune diseases arise when B and T lymphocytes lose tolerance to self. Yet in most disorders, the underlying molecular determinants, including autoantibodies, epitopes and lymphocyte clones that drive tissue injury remain undefined. Rapid-onset obesity with hypothalamic dysfunction, hypoventilation and autonomic dysregulation (ROHHAD) is a rare and often fatal pediatric neuroendocrine syndrome with strong evidence of antigen-driven paraneoplastic autoimmunity, including association with the intracellular autoantigen ZSCAN1. However, the effector immune circuit and the epitope-level determinants operating within the hypothalamus and brainstem have remained unknown. To address this challenge in ROHHAD and more broadly in autoimmune disease, we developed the Autoimmune Epitope and immunoGlobulin/Immune-receptor identification System (AEGIS), an integrated framework that links immune repertoires to their cognate self-epitopes. AEGIS combines B cell and T cell receptor profiling from sites of tissue injury with high-resolution epitope mapping, direct sequencing of antigen-specific autoantibodies, in silico antibody-antigen folding, selection, and T cell antigen discovery. Applied to a deeply phenotyped child with ROHHAD, AEGIS revealed a compartmentalized, clonally restricted immune response in which brain-deposited IgG and expanded cerebrospinal fluid B cell and CD4 T cell clonotypes converged on shared ZSCAN1 epitopes, resolved to minimal determinants and peptide-MHC ligands. These findings provide a clone- and epitope-linked mechanistic map of ROHHAD autoimmunity and establish a generalizable framework for identifying candidate pathogenic clones and antigens across diverse autoimmune diseases.

immunology↗

Protein-guided RNA barcoding links transcriptomes to synaptic architecture

Mammalian brain function relies on the precise synaptic architecture of diverse cell types, yet scalable methods for linking a neurons transcriptomic profile to its neuroanatomy remain limited. We present Synapse-seq, an in vivo strategy in which cell-identifying barcoded mRNAs are routed to subcellular compartments via targeting proteins and detected by single-cell and spatial genomics. Using AAV delivery for minimal perturbation of gene expression, we directed barcodes to presynaptic terminals (via synaptophysin) in four distinct circuits, or to postsynaptic sites (via nanobodies to endogenous PSD95) of hippocampal excitatory neurons. In the mouse primary visual cortex, presynaptic Synapse-seq recovered known long-range projections and discovered cortical layer subtypes with distinct thalamic innervation. In the anterior cortex, we elucidated simple topographic rules of corticostriatal innervation: intratelencephalic neurons followed a continuous depth-to-target gradient, while extratelencephalic neurons exhibited striatal collaterals that spatially correlated with medullary innervation. Finally, postsynaptic barcoding of excitatory neurons revealed cell type-specific variation in dendritic architectures across and within hippocampal subfields. These data establish Synapse-seq as a versatile, genomics-based approach for the integrated definition of molecular identity and synaptic organization across mammalian brains.

neuroscience↗

Opening the black box: a modular approach to spike sorting

Spike sorting is an algorithmic process that extracts the activity of individual neurons from extracellular electrophysiology recordings. With the ballooning use of high density probes, such as Neuropixels, this essential processing step is increasingly becoming time consuming and computationally expensive. Although many software tools have been proposed to address spike sorting, they are usually constructed and benchmarked as monolithic "black boxes", making it difficult to factor out the effects of individual algorithmic steps on the final outcome, especially when varying datasets and parameters. To address this issue, we developed a modular and common framework to develop, benchmark and assemble the key computational steps that are used in state-of-the-art spike sorting algorithms. Relying on fast and efficient ground truth generation of biophysically plausible recordings, we show that we are able to individually benchmark and precisely quantify the performance of different steps in a spike sorting pipeline (i.e. peak detection, feature extraction and clustering, and template matching). We then leverage these results to create a modular, component-based spike sorter that can outperform Kilosort 4 on dense and large simulated recordings and produce similar quantitative results on real data. In addition, we find that the major bottleneck of all modern spike sorting pipelines is in the physical motion of probes, regardless of the drift-correction strategy. The component-based spike sorting framework presented here has the potential to foster community engagement in the field by lowering the barrier to contributions and providing a flexible yet powerful framework to construct end-to-end spike sorting solutions.

neuroscience↗

The impact of the invasive Kalanchoe xhoughtonii on vegetated sea cliffs of the Mediterranean coasts with endemic Limonium species

Invasive alien plant species pose a serious threat to biodiversity, especially in ecologically rich regions such as the Mediterranean Basin. Among the most affected habitats are coastal communities, which host many endemic taxa and provide valuable ecosystem services. One such invasive taxa is Kalanchoe xhoughtonii, an allegedly artificial hybrid. This plant, although having demonstrated strong invasive potential, still largely remains unrecognised as a taxon of concern in Mediterranean countries, at least in national official catalogues. In this study, we assess the impact of this hybrid on coastal communities, focusing on the European Union Habitat of Community Interest (HCI) 1240--"vegetated cliffs with endemic statices (Limonium spp.)"--at two sites along the southern coast of Catalonia (NE Iberian Peninsula). Between 2022 and 2025, we conducted field surveys to document the population size, growth stages, and spatial competition with native species. Additionally, we gathered 1,422 iNaturalist occurrences of K. xhoughtonii to map its distribution across the Mediterranean Basin, assess its presence within Natura 2000 protected sites and within protected areas, including the HCI 1240, and determine its potential spread using ensemble ecological niche modelling with bioclimatic variables. Our results show that K. xhoughtonii forms dense monospecific patches in the surveyed areas that compete for space with two native Limonium species in southern Catalonia. Moreover, we confirmed 713 naturalised occurrences in the Mediterranean area, 107 were located within Natura 2000 protected sites and 58 within the HCI 1240 included in protected sites. Ecological niche modelling indicates high climatic suitability across 93% of western and 59% of eastern Mediterranean Natura 2000 sites containing the HCI 1240. The findings of this study highlight the invasive potential of K. xhoughtonii and support its inclusion in national catalogues of invasive species across Mediterranean basin countries. The study calls for systematic monitoring of the spread and ecological impact of this hybrid species in coastal community habitats.

ecology↗

Dedifferentiation-Driven Oncogenic Stemness Promotes Tumor-Sustaining Adaptability in the Intestinal Epithelium

Intestinal tumorigenesis can occur via two distinct routes: bottom-up tumorigenesis occurs from mutations sustained in the Lgr5 stem cells, whereas top-down tumorigenesis is driven by dedifferentiation of epithelial cells near the intestinal lumen. While sporadic human colon adenomas exhibit features of top-down tumorigenesis, their biological determinants remain elusive. Here, using a Smad4 loss-of-function and {beta}-catenin gain-of-function (Smad4LOF:{beta}-cateninGOF) mouse model, we demonstrate that dedifferentiation-derived oncogenic stem cells sustain tumorigenesis more effectively than endogenous mutant stem cells harboring the mutation. The dedifferentiating villi epithelial cells showed early expression of CD44 and Lgr5, supporting oncogenic stemness. Aberrant Notch signaling in the villi epithelium was also detected at the onset of dedifferentiation, suggesting its contribution to dedifferentiation. Single-cell RNA sequencing revealed a distinct population of dedifferentiation-derived stem cells enriched for proliferative, metabolic, and mouse embryonic stem cell-like gene signatures, consistent with enhanced plasticity and tumorigenic potential. These mutant cells exhibited growth factor independence, indicating a capacity for niche-independent proliferation and metabolic adaptation to sustain tumor growth. These findings identify dedifferentiation-driven stemness, aberrant Notch activation, and metabolic plasticity as cooperative mechanisms that promote top-down intestinal tumorigenesis. This study provides insight into how oncogenic dedifferentiation contributes to tumor heterogeneity and persistence and has implications for therapeutic resistance in colorectal cancer.

cancer biology↗

Biocontrol of Calonectria causing root rot in Eucalyptus

Calonectria spp. are among the most important pathogens affecting Eucalyptus production, causing severe root rot and significant losses in nurseries. In this study, we established a collection of locally isolated strains of Trichoderma spp. and Bacillus spp., complemented with commercial formulations, to evaluate their potential as biocontrol agents (BCAs) against Calonectria. Leaf bating in vitro assays were conducted using naturally colonized, non-sterilized substrates to closely simulate nursery conditions. Several locally isolated Trichoderma strains (T3, T5, T6, and T7), as well as two commercial products (PC1 and PC2), consistently reduced the incidence of Calonectria infection, indicating their capacity to decrease pathogen inoculum levels in the substrate. The reproducibility of these effects across independent trials underscores the robustness of Trichoderma as reliable BCAs. Altogether, these findings highlight the potential of locally isolated Trichoderma strains as promising alternatives for managing Calonectria root rot in Eucalyptus nurseries, while reinforcing the need for further trials under commercial greenhouse conditions to confirm their efficacy in real production systems.

microbiology↗

Molecular response to the non-lytic peptide bac7 (1-35) triggers disruption of Klebsiella pneumoniae biofilm

Klebsiella pneumoniae is becoming increasingly difficult to treat as multidrug-resistant (MDR) strains become more prevalent. The formation of biofilm heightens this threat by embedding bacterial cells in a polysaccharide-rich matrix that limits antibiotic penetration. Here we dissect the anti-biofilm bovine host-defense cathelicidin peptide fragment bac7 (1-35), exploring its anti-biofilm mechanism, evaluating its ability to curb dissemination of hypervirulent K. pneumoniae, and testing its breadth of activity against diverse clinical isolates. Transcriptomic profiling revealed that bac7(1-35) simultaneously compromises the bacterial membrane and inhibits ribosomal function, a dual assault that precipitates rapid biofilm collapse and blocks bacterial spread. Further, the peptide eradicated biofilms produced by the strongest MDR clinical isolates in the Multidrug-Resistant Organism Repository and Surveillance Network (MRSN) diversity panel. Although bac7 (1-35) kills bacterial cells via a cytosolic mechanism, membrane interaction profiles varied among MRSN isolates, correlating with differential peptide translocation. In a delayed-treatment murine skin-abscess model, bac7 (1-35) halted in vivo dissemination of the hypervirulent strain NTUH-K2044. Collectively, these results delineate a multifaceted mode of action for bac7 (1-35) and underscore its therapeutic promise against biofilm-associated MDR K. pneumoniae infections. Author SummaryKlebsiella pneumoniae is a top-priority pathogen for new therapies, with many strains already approaching pan-drug resistant status. Biofilm formation further complicates treatment, yet biofilm-active therapeutics have not reached the clinic, in part because we still lack a detailed understanding of how to disrupt these impenetrable structures. Antimicrobial peptides are promising candidates and have shown biofilm-disruption potential. Here we provide mechanistic insight into how a host defense peptide dismantles pre-formed K. pneumoniae biofilms. We find that the peptides dual targeting of bacterial membranes and ribosomes triggers dispersal from the biofilm state and concomitantly downregulates factors required for surface attachment and extracellular matrix production. This mechanism involves a protein that, to our knowledge, has not been characterized in K. pneumoniae. Our findings reveal a switch that can be leveraged to reprogram biofilm maintenance toward dispersal in K. pneumoniae, advancing the path to peptide-based antibiofilm therapeutics.

microbiology↗

Precision Neuromodulation with Real-Time Brain Decoding for Working Memory Enhancement

Transcranial magnetic stimulation (TMS) has transformed non-invasive brain therapies but faces challenges due to variability in outcomes, likely stemming from inter-individual differences in brain function. This study aimed to address this challenge by integrating personalized functional networks (PFNs) derived from functional magnetic resonance imaging (fMRI) with a neural network-based decoder to optimize stimulation in real time during a working memory (WM) task. After identification of individualized stimulation targets, participants completed a TMS/fMRI session, performing a WM task while receiving rTMS at randomized frequencies. Decoder outputs and behavioral data during this session guided selection of optimal and suboptimal stimulation frequencies. Participants then underwent six stimulation sessions (three optimal, three suboptimal) in a randomized crossover design, performing WM and control tasks. The optimal stimulation improved WM performance by the final session, with no improvement observed in the control task. Additionally, the decoder output predicted behavioral performance on the WM task, both during the TMS/fMRI and neuromodulation sessions. These findings show that neural network-guided closed-loop neuromodulation can improve TMS effectiveness, marking a step forward in personalized brain stimulation. HIGHLIGHTSO_LIClosed-loop TMS guided by real-time brain decoding enhances post-stimulation behavioral effects. C_LIO_LIIndividualized functional connectivity networks enable targeted neuromodulation C_LIO_LIOptimal stimulation boosted working memory performance over sub-optimal C_LIO_LIBrain decoder readouts predicted behavioral performance C_LI

neuroscience↗

Extracellular superoxide production is a widespread photoacclimation strategy in phytoplankton

Phytoplankton control the habitability of Earth. These photosynthetic microorganisms serve as the base of marine food webs, produce approximately half of the planets oxygen, and regulate climate by sequestering carbon dioxide from the atmosphere. As global changes accelerate through the Anthropocene, phytoplankton communities face multiple stressors, including warming, shifting patterns in ocean circulation and structure, and associated perturbations in levels of light exposure. The health and functioning of the oceans depends on phytoplankton community responses to these stressors; however, the physiological processes involved in light stress are not fully understood. Here, we surveyed sixteen representative phytoplankton and show that most produce extracellular superoxide, an otherwise damaging reactive oxygen species, as a widespread strategy to acclimate to light stress. Indeed, all species regulated extracellular superoxide production as a function of light exposure, which was modeled with a modified photosynthesis-irradiance (PE) curve. Furthermore, the flavoenzyme inhibitor DPI quenched extracellular superoxide production and lead to declines in viability and photosynthetic health in thirteen out of sixteen species. The negative effect of DPI on photosynthetic health was stronger with increasing light, consistent with inhibition of a photoprotective process. Taken together, these results support the hypothesis that phytoplankton mitigate light stress through enzyme-mediated production of extracellular superoxide. These results imply that daytime rates of biological superoxide production in the marine environment are substantially underestimated by dark measurements. Furthermore, phytoplankton photoacclimation may alter superoxide production rates in future oceans impacted by changes in water column structure and light exposure.

microbiology↗

Detection of Infectious Murine Norovirus on Fresh Produce through a Novel CRISPR/Cas13-based Sensitive Assay

Current standard food detection methods do not distinguish between infectious and non-infectious norovirus leading to uncertainty in the interpretation and management of a norovirus positive food sample. These methods also require expensive RT-qPCR based equipment. In contrast, CRISPR-based, compared to RT-qPCR based, detection methods yield similar sensitivity and specificity and are generally less expensive. The aim of this study was to detect norovirus with an intact capsid, a proxy for infectivity, through a CRISPR-Cas13a based detection method in conjunction with acapsid integrity assay. Our CRISPR method detected murine norovirus (MNV-1), with an intact capsid, at a limit of detection of 2.59 log10 gc/ 25 g (5 gc/ rx). This method did not cross-react with other targets (synthetic hepatitis A virus; human norovirus GI, GII; rotavirus). Compared with RT-qPCR, this CRISPR based method showed an increased sensitivity when detecting low copy numbers of RNase-pretreated MNV-1 in lettuce and blueberries samples. This is the first report describing a CRISPR-based detection of potentially infectious viruses in food samples.

microbiology↗

Odor-evoked respiratory responses throughout development in sighted and blind mice

Congenital blindness affects olfactory function depending on developmental stage. However, when studying the ontogeny of olfactory abilities, not all behaviors are expressed at every age making the longitudinal comparisons difficult. Odor-evoked respiratory responses, which are unlearned and do not require complex motor coordination, may serve as sensitive measures of olfactory abilities throughout ontogeny. Using a non-invasive measure of respiration in an olfactory perceptual paradigm, we assessed odor-evoked respiratory responses in a model of congenital blindness at 3 ages, infant, juvenile and adult, in the same mice and in both males and females. We demonstrated the differential outcome of two respiratory parameters (i.e. frequency and amplitude) in a mouse model of congenital blindness. We showed that blind mice have similar olfactory abilities than sighted mice throughout ontogeny but display enhanced sniffing frequency and amplitude, starting at the juvenile age for the latter one, that may help them better explore their environment. We also demonstrated that respiratory frequency is a robust index of age and of olfactory detection, habituation and discrimination at all ages. On the other side, respiratory amplitude does not provide a proxy of olfactory performance at all ages, however, it does highlight differences between sexes and phenotypes associated with visual deprivation. To conclude, our data highlight that respiratory parameters can be used as a complementary approach to assess olfactory performance throughout development and provide an index of olfactory plasticity.

neuroscience↗

The Winner Takes It All: a single genotype of Kalanchoe xhoughtonii is a global invader

Background and AimsInvasive alien plant species pose a global challenge, and their impact is amplified by globalisation and the accelerating pace of climate change. In mild-climate regions, drought-tolerant invasive plants showing broad environmental tolerance have a competitive advantage. One example is Kalanchoe xhoughtonii (Crassulaceae), popularly known as "mother of millions". It is a hybrid resulting from the interploid cross between K. daigremontiana and K. delagoensis, both native to Madagascar. Kalanchoe xhoughtonii, propagated as an ornamental plant, has emerged as a global invader in less than a century. Four morphotypes of this hybrid have been identified, with different ploidy levels and varying invasive capacities. Here we aim to investigate the genomic variability behind the invasion success of Kalanchoe xhoughtonii. MethodsWe sampled 57 accessions of Kalanchoe xhoughtonii, K. daigremontiana, K. delagoensis and closely related taxa, including old herbarium materials, from all over the world. We analysed genome size, chromosome numbers, sequenced the whole genome, analysed the complete plastome sequence of each accession, and studied the diversity of the ribosomal RNA genes. We also performed a detailed phylogenomic study using nuclear BUSCO genes. Key ResultsOur study reveals the genetic and cytogenetic variability between morphotypes, and shows that a single tetraploid genotype (morphotype A) dominates all populations, emerging as the first reported clonal hybrid capable of worldwide colonisation. Morphotype A shows a striking genetic uniformity, high phenotypic plasticity, and extremely high rates of vegetative reproduction, representing an example of a "general-purpose genotype". ConclusionsThe astonishing reproductive capacity, broad adaptability and the speed at which K. xhoughtonii is colonising new regions by clonal spread highlight the importance of understanding hybridisation and polyploidy in the invasion of ecosystems. Our findings call for the need for risk assessments before developing new hybrids for ornamental plant breeding that may exhibit invasive characteristics.

plant biology↗

Viscoelastic HyA Hydrogel Promotes Recovery of Muscle Quality and Vascularization in a Murine Model of Delayed Rotator Cuff Repair

Rotator cuff tears are among the most common musculotendinous injuries with high risk of permanent functional disability. Following surgical repair, sub-optimal patient outcomes are directly correlated with poor muscle quality; namely, injury site fatty infiltration (FI), fibrosis, and muscle atrophy. Muscle resident fibro-adipogenic progenitor cells (FAPs) have been identified as key regulators of post-injury skeletal muscle regeneration and repair by maintaining a promyogenic environment. In this work, human-derived FAPs (hFAPs) were encapsulated into hyaluronic acid (HyA)-based hydrogels functionalized with bsp-RGD(15) cell adhesion peptide, heparin, and a matrix metalloproteinase (MMP)-cleavable crosslinker. Hydrogel-encapsulated hFAPs increased expression of the promyogenic marker UCP1 and production of the anti-inflammatory cytokine IL-10, while downregulating the expression of the fibrotic marker SMA over time. A murine model of unilateral rotator cuff transection, denervation, and delayed repair was treated with the HyA hydrogel or PBS and compared to a contralateral, non-injured control limb. Muscle histology 6 weeks post-repair revealed that the hydrogel reduced fibrosis, FI, and muscle atrophy while supporting vascularization of the injured tissue region. Collectively, these results suggest that the hydrogel alone can promote muscle regeneration in a clinically relevant delayed repair model of rotator cuff tear, which we hypothesize is due to controlled FAP differentiation into promyogenic lineages.

bioengineering↗

Pleasant smells: a privileged gateway to soothing autonomic responses and improving brain-body rhythm coupling

Aromatherapy commonly uses odors to improve well-being through their evocation of positive emotions. Although knowledge in this area is often very empirical, the olfactory stimulus has different properties which, taken together, could explain why it can relax. First, olfactory sense have a direct access to the limbic system, without thalamic relay processing, which confers it a strong emotional valence. Second, when appreciated, odors can slow down breathing and cardiac rates. Third, when slow and deep, breathing can entrain brain activity, due to the mechano-sensitivity of olfactory receptors to airflows. We hypothesized that, thanks to these properties, pleasant odors could enhance the subjective feeling of relaxation, slow down body rhythms, and facilitate entrainment of brain activity by respiration. Comparing the effects of a personally pleasant odor to a personally pleasant music on psychological, physiological and neuronal responses, we showed a tendency for both odors and music to enhance subjective relaxation. However, only pleasant odors were able to 1) decrease heart rate while increasing its variability, and 2) decrease respiratory rate while enhancing the respiratory drive of brain activities, regardless of the music tempo. Overall, we demonstrated that the positive emotion evoked by a personally pleasant smell is sufficient to evoke an olfactomotor response, which, by slowing breathing, synchronizes respiration, fluctuations of heart rate and brain activity.

neuroscience↗

De novo RNA base editing in plant organelles with engineered synthetic P-type PPR editing factors

In plant mitochondria and chloroplasts, cytidine-to-uridine RNA editing plays a crucial role in regulating gene expression. While natural PLS-type PPR proteins are specialized in this process, synthetic PPR proteins offer significant potential for targeted RNA editing. In this study, we engineered chimeric editing factors by fusing synthetic P-type PPR guides with the DYW cytidine deaminase domain of a moss mitochondrial editing factor, PPR56. These designer PPR editors (dPPRe) elicited efficient and precise de novo RNA editing in Escherichia coli, and in Nicotiana benthamiana chloroplasts and mitochondria. Chloroplast transcriptome-wide analysis of the most efficient dPPRe revealed minimal off-target effects, with only three non-target C sites edited due to sequence similarity with the intended target. This study introduces a novel and precise method for RNA base editing in plant organelles, paving the way for new approaches in gene regulation applicable to plants and potentially other organisms.

synthetic biology↗

Enhancing Statistical Power While Maintaining Small Sample Sizes in Behavioral Neuroscience Experiments Evaluating Success Rates

Studies with low statistical power reduce the probability of detecting true effects and often lead to overestimated effect sizes, undermining the reproducibility of scientific results. While several free statistical software tools are available for calculating statistical power, they often do not account for the specialized aspects of experimental designs in behavioral studies that evaluate success rates. To address this gap, we developed "SuccessRatePower" a free and user-friendly power calculator based on Monte Carlo simulations that takes into account the particular parameters of these experimental designs. Using "SuccessRatePower", we demonstrated that statistical power can be increased by modifying the experimental protocol in three ways: 1) reducing the probability of succeeding by chance (chance level), 2) increasing the number of trials used to calculate subject success rates, and, in some circumstance, 3) employing statistical analyses suited for discrete values. These adjustments enable even studies with small sample sizes to achieve high statistical power. Finally, we performed an associative behavioral task in mice, confirming the simulated statistical advantages of reducing chance levels and increasing the number of trials in such studies

neuroscience↗