bioRxiv : the preprint server for biology最新文献

Rab-dependent membrane trafficking is critical for changing the structure and function of dendritic spines during synaptic plasticity. Here, we developed highly sensitive sensors to monitor Rab protein activity in single dendritic spines undergoing structural long-term potentiation (sLTP) in rodent organotypic hippocampal slices. During sLTP, Rab10 was persistently inactivated (>30 min) in the stimulated spines, whereas Rab4 was transiently activated over ~5 min. Inhibiting or deleting Rab10 enhanced sLTP, electrophysiological LTP and AMPA receptor (AMPAR) trafficking during sLTP. In contrast, disrupting Rab4 impaired sLTP only in the first few minutes, and decreased AMPAR trafficking during sLTP. Thus, our results suggest that Rab10 and Rab4 oppositely regulate AMPAR trafficking during sLTP, and inactivation of Rab10 signaling facilitates the induction of LTP and associated spine structural plasticity.

We report a population of multipotent cells isolated from term human placentas that exhibit clonal expansion and migratory capacity, along with a gene expression profile that indicates immune privilege. Previously known largely for its role in early placentation, the developmental regulator CDX2 marks cells capable of differentiating into cardiomyocytes and vascular lineages. Building on our prior findings that murine Cdx2 cells improved cardiac function in mice after myocardial infarction (MI), we isolated CDX2⁺ cells from placentas of 180 healthy pregnancies. These human CDX2 cells spontaneously generate cardiac and vascular lineages in vitro, in vivo, and express transcriptomic signatures associated with cardiogenesis, vasculogenesis, immune modulation, and chemotaxis. When administered to NOD/SCID mice after MI, the cells restore cardiac function. Additionally, CDX2 cells can be clonally propagated while retaining cardiovascular differentiation potential. Our findings support the therapeutic potential of placental CDX2 cells as an ethically accessible and regenerative strategy for cardiovascular disease.

Characterization of the structural integrity of cortex in adults who have undergone resection for epilepsy treatment has, in some cases, revealed persistent or even accelerated cortical atrophy but, in others, the converse is evident, and atrophy decelerates or even reverses. Whether this variability applies to a pediatric population, for whom postoperative plasticity may be greater than in adulthood, remains to be determined. Furthermore, understanding the morphometrics of this patient population is important, as cognitive gains have been associated with the anatomical status of preserved cortex post-resection. Here, we used high-resolution structural T1 magnetic resonance imaging data to compare the (1) gross anatomy, (2) cortical thickness, volume, and surface area for 34 cortical regions, and (3) volume for nine subcortical regions of 32 pediatric post-surgical cases and 51 healthy controls. Patients with either a preserved right hemisphere (RH) or left hemisphere (LH) had lower total white matter volume and select subcortical structures' volumes, relative to controls; lateral ventricle size of both preserved RH and LH patients was also significantly larger than that of controls. However, relative to controls, only patients with a preserved RH had significantly lower total gray matter volume and lower thickness, volume, and surface area in multiple cortical regions, primarily in frontal and temporal cortex. The differences in preserved RH cortex of LH resection patients may relate to transfer of language function from the resected LH. Our findings lay the foundation for future studies probing associations of the morphometric differences in pediatric epilepsy surgery patients with neuropsychological outcomes.

Understanding how populations evolve requires accounting for both intrinsic fitness, defined by genotype and environment, and ecological interactions that emerge in mixed communities. While evolutionary experiments typically assess fitness in isolation, such monoculture measures may misrepresent dynamics in realistic, interacting populations. Here, we present a game-theoretic framework that explicitly separates intrinsic and ecological contributions to fitness, allowing us to map how ecological interactions can mask, mirror, maintain, or mimic selection driven by genetic differences. We derive analytical conditions for these regimes using deterministic replicator dynamics and validate them in stochastic Wright-Fisher models with mutation and drift. Applying our model to published microbial and cancer co-culture data, we show that real systems span both intrinsic-dominant and ecology-dominant regimes, with ecological effects sometimes reversing or neutralizing intrinsic fitness advantages. These results expose a critical blind spot in experimental design and interpretation, emphasizing the need to account for ecological interactions when inferring evolutionary dynamics and designing therapeutic strategies.

The main olfactory epithelium initiates the process of odor encoding. Recent studies have demonstrated intergenerationally inherited changes in the olfactory system in response to fear conditioning, resulting in increases in olfactory sensory neuron frequencies and altered responses to odors. We investigated changes in the cellular composition of the olfactory epithelium in response to an aversive stimulus. Here, we achieve volumetric cellular resolution to demonstrate that olfactory fear conditioning increases the number of odor-encoding neurons in mice that experience odor-shock conditioning (F0), as well as their unconditioned offspring (F1). We demonstrate that the increase in F0 is due, in part, to the biasing of the stem cell layer of the main olfactory epithelium. Detailed analysis of F1 behavior revealed subtle odor-specific differences between the offspring of unconditioned and conditioned parents, despite the absence of an active aversion to the conditioned odor. Thus, we reveal intergenerational regulation of olfactory epithelium composition in response to olfactory fear conditioning, providing insight into the heritability of acquired phenotypes.

One-sentence summary: Olfactory fear conditioning induces heritable changes to the mouse olfactory system and biases neurogenesis and behavior in both parent and offspring.

DNA origami information storage is a promising alternative to silicon-based data storage, offering a secure molecular cryptography technique that conceals information within arbitrarily folded DNA origami nanostructures. Routing, sliding, and interlacing staple strands lead to the creation of a large 700-bit key size. The realization of practical DNA data storage requires high information density, robust security, and accurate and rapid information retrieval. To meet these requirements, advanced readout techniques and large encryption key sizes are essential. In this study, we report an enhanced DNA origami cryptography protocol to encrypt information in 2D and 3D DNA origami structures, increasing the number of possible scaffold routings and increasing the encryption key size. We employed all-DNA-based steganography with fast readout through high-speed 2D and 3D DNA-PAINT super-resolution imaging, which enables higher information density. By combining 2D and 3D DNA-PAINT data with unsupervised clustering, we achieved an accuracy of up to 89% and high ratios of correct-to-wrong readout, despite the significant flexibility in the 3D DNA origami structure shown by oxDNA simulation. Furthermore, we propose design criteria that ensure complete information retrieval for the DNA origami cryptography protocol. Our findings demonstrate that DNA-based cryptography is a highly secure and versatile solution for transmitting and storing information, making it an attractive choice for the post-silicon era.

Given that age is a significant risk factor for multiple neurodegenerative diseases, investigating normal brain aging may help identify molecular events that may contribute to increased disease risk over time. Single-nucleus RNA sequencing (snRNA-seq) enables analysis of gene expression changes within specific cell-types, potentially offering insights into the molecular mechanisms underlying aging. However, most brain snRNA-Seq datasets used age-matched controls from studies focused on pathological processes and have largely been limited to cortical regions. Therefore, there is a need to investigate the non-pathological aging process in brain regions that are vulnerable to age-related diseases. Here, we report a snRNA-seq study of 6 young (20-30 years) and 7 aged (60-85 years) encompassing four different brain regions: the entorhinal cortex, middle temporal gyrus, subventricular zone, and putamen. We captured over 150,000 nuclei that represented 10 broad cell-types. While we did not find statistically significant differences in cell-type proportions with age, region- and cell-type-specific differential expression analyses identified over 8,000 age-associated genes. Notably, within a given cell-type, most of these associations were region-specific. Functional enrichment analyses of the gene sets for each cell-type-region combination revealed diverse biological processes, including multiple hallmarks of aging, such as proteostasis, interactions with cytokines, vesicular trafficking, metabolism, inflammation, and metal ion homeostasis. Overall, our findings suggest that unique cell-types exhibit distinct transcriptional aging profiles both at the cell-type level and across different brain regions.

Cryptosporidium spp. are parasites that cause severe illness in vulnerable human populations. Obtaining pure and sufficient Cryptosporidium DNA from clinical and environmental samples is a challenging task. Oocysts shed in available fecal samples can be limited in quantity, require purification (biased towards dominant strains), and yield limited DNA (<40 fg/oocyst). Here, we use updated genomic sequences from a broad diversity of human-infecting Cryptosporidium species ( C. cuniculus , C. hominis , C. meleagridis , C. parvum , C. tyzzeri , and C. viatorum ) to develop and validate a set of 100,000 RNA baits (CryptoCap_100k) with the aim of enriching Cryptosporidium spp. DNA from varied samples. Compared to unenriched libraries, CryptoCap_100k increases the percentage of reads mapping to target genome sequences, increases the depth and breadth of genome coverage and the reliability of detecting species and mixed infections within a sample, and allows assessment of genetic variation via SNP calling, while decreasing costs.

Segmenting individual instances of mitochondria from imaging datasets can provide rich quantitative information, but is prohibitively time-consuming when done manually, prompting interest in the development of automated algorithms using deep neural networks. Existing solutions for various segmentation tasks are optimized for either: high-resolution three-dimensional imaging, relying on well-defined object boundaries (e.g., whole neuron segmentation in volumetric electron microscopy datasets); or low-resolution two-dimensional imaging, boundary-invariant but poorly suited to large 3D objects (e.g., whole-cell segmentation of light microscopy images). Mitochondria in whole-cell 3D electron microscopy datasets often lie in the middle ground-large, yet with ambiguous borders, challenging current segmentation tools. To address this, we developed skeleton-oriented object segmentation (SKOOTS)-a novel approach that efficiently segments large, densely packed mitochondria. SKOOTS accurately and efficiently segments mitochondria in previously difficult contexts and can also be applied to segment other objects in 3D light microscopy datasets. This approach bridges a critical gap between existing segmentation approaches, improving the utility of automated analysis of three-dimensional biomedical imaging data. We demonstrate the utility of SKOOTS by applying it to segment over 15,000 cochlear hair cell mitochondria across experimental conditions in under 2 hours on a consumer-grade PC, enabling downstream morphological analysis that revealed subtle structural changes following aminoglycoside exposure-differences not detectable using analysis approaches currently used in the field.

Smith-Lemli-Opitz syndrome (SLOS) is a cholesterol biosynthesis disorder that arises from mutations in the gene DHCR7, leading to decreased production of cholesterol and accumulation of its precursor, 7-dehydrocholesterol. SLOS displays a wide range of neurodevelopmental defects, intellectual disability, and behavioral problems. However, an in-depth study on the temporal changes of gene expression in the developing brains has not been done before. In this work, we carried out the transcriptomic analysis of whole brains from WT and Dhcr7-KO mice at embryonic day 12.5 (E12.5), E14.5, E16.5, and postnatal day 0 (PND0). First, we observed the expected downregulation of the Dhcr7 gene in the Dhcr7-KO brains, as well as changes of other genes involved in cholesterol biosynthesis at all time points. Pathway and GO term enrichment analyses revealed affected signaling pathways and biological processes that were shared amongst time points and unique to individual time points. Specifically, the pathways important for embryonic and neural development, including Hippo, Wnt, and TGF-β signaling pathways, are the most significantly affected at the earliest time point, E12.5. Additionally, neurogenesis-related GO terms were enriched in earlier time points, consistent with the timing of development. Conversely, pathways related to synaptogenesis, which occurs later in development compared to neurogenesis, are significantly affected at the later time points, E16.5 and PND0, including the cholinergic, glutamatergic, and GABAergic synapses. In vitro neurogenesis experiments using GABAergic neuronal precursors isolated from embryonic mouse brain confirmed that loss of Dhcr7 led to decreased proliferation and premature neurogenesis, consistent with the transcriptomic changes.