Biology subjects

Yamaguchi, H.

Publications and source records attributed to Yamaguchi, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Detection of endogenous MR1B protein in human 293F cells by immunoaffinity enrichment and two-dimensional western blotting

MR1B is a splice variant of the MHC class Ib molecule MR1 that lacks the 3 extracellular domain and has been reported to modulate MR1-mediated antigen presentation to mucosal-associated invariant T (MAIT) cells in transfected cells. Although MR1B transcripts are widely expressed, MR1B protein has been reported only in transfected overexpression systems; whether endogenous MR1B protein is present has remained unknown. Here we report the detection of endogenous MR1B protein. Immunoaffinity enrichment of 293F cell lysate (447 mg total protein) followed by two-dimensional electrophoresis and western blotting gave immunoreactive spots at the MR1A (~40 kDa) and MR1B (~27-30 kDa) reference coordinates established from recombinant cells, whose MR1 identity was confirmed by mass spectrometry. The spots were detected with two antisera raised against regions on opposite sides of the deleted segment and were absent with the corresponding pre-immune sera; detection with the C-terminal antiserum was obtained once. The 27-30 kDa spot lies on the basic side of the MR1A spot, the direction predicted for loss of the 3 domain and opposite to that predicted for a modeled, unmodified N-terminal fragment of similar mass. Mass spectrometry identified MR1 only in the recombinant reference spots, so the endogenous assignment rests on immunoreactivity and two-dimensional position. Endogenous MR1B protein is detected in 293F cells under non-overexpression conditions.

immunology↗

bioRxiv2026

Repeated intermittent clenbuterol administration induces exposure history-dependent proteomic remodeling in mouse skeletal muscle

Clenbuterol (CB), a {beta}2-adrenergic receptor agonist, is known to increase skeletal muscle mass. However, because its effects are influenced by treatment duration, dose, and {beta}-adrenergic receptor responsiveness, it remains unclear how extended intermittent CB exposure alters the skeletal muscle proteome. In this study, we established a repeated intermittent CB administration model in mice and compared the effects of single and repeated CB exposure on plantaris muscle using label-free quantitative proteomics. Repeated CB exposure produced a more evident muscle-weight response than single exposure under the same long-term experimental timeline. Proteomic profiling revealed that repeated CB exposure was not a simple reproduction or amplification of the single CB response, but was associated with distinct changes in sarcomere-associated, tissue-remodeling-related, membrane-trafficking-related, and metabolic proteins. Integrated response-class analysis further identified multiple patterns of protein regulation, including shared CB-responsive proteins and proteins preferentially identified as changed under repeated CB conditions. Immunoblotting validated representative proteins from these response classes: Klhl40 and Napa as shared CB-responsive proteins, Galectin-3 as a strongly CB-responsive remodeling-related protein, and Rab18 as a protein change more clearly detected under repeated CB conditions. Together, these findings indicate that repeated intermittent CB exposure induces exposure history-dependent proteomic remodeling in skeletal muscle. This study provides a resource for understanding the molecular consequences of repeated CB exposure and for future mechanistic studies of {beta}2-adrenergic stimulation-induced skeletal muscle adaptation.

molecular biology↗

bioRxiv2026

Aberrant ciliogenesis induced by enhanced BMP signaling causes heterotopic ossification

Bone morphogenetic protein (BMP) signaling is a principal driver of heterotopic ossification (HO), yet how aberrant BMP activity structurally reprograms cellular signaling machinery to develop HO remains unclear. Here, we identify BMP signaling as a direct upstream regulator of ciliogenesis that coordinates a multi-stage, pro-osteochondrogenic signaling relay during HO. Using a conditional gain-of-function BMP mouse model (Acvr1Q207D/+), we demonstrate that enhanced BMP signaling promotes primary cilium biogenesis and axonemal elongation through canonical Smad1/5/9-dependent transcriptional activation of intraflagellar transport (IFT) Ift20, a core component of the IFT machinery. Rather than operating via a singular downstream cascade, these elongated cilia establish a sensitized signaling hub. Genetic disruption of ciliary Hedgehog (Hh) transduction via Smoothened (Smo) deletion reveals that ciliary Hh signaling is dispensable for initial tissue condemnation but required for the subsequent proliferative expansion and maturation of HO. Conversely, complete genetic ablation of the ciliary structure via Ift20 deletion, or early pharmacological inhibition of ciliogenesis, significantly attenuates HO. Notably, this BMP-IFT20-cilia axis is functionally conserved within injury-responsive, PDGFR-positive fibro-adipogenic progenitor (FAP) populations harboring the clinically authentic Acvr1R206H/+ mutation responsible for fibrodysplasia ossificans progressiva (FOP) in mice. Together, these findings reveal that BMP signaling drives HO by structurally expanding the primary cilium, establishing a novel mechanism for HO development. SignificanceGrowth factor signaling instructs cellular behavior during tissue regeneration, but how they regulate cellular organelles to induce pathological fates remains poorly understood. This study reveals that Bone Morphogenetic Protein (BMP) signaling functions as a direct architectural regulator of the primary cilium, a critical cellular antenna. We show that BMP signaling directly transactivates intraflagellar transport machinery to structurally elongate the cilium, creating a sensitized signaling hub that drives heterotopic ossification. Our findings introduce a novel BMP-driven organelle regulation mechanism and establish a targetable cellular vulnerability to mitigate ectopic bone formation.

developmental biology↗

bioRxiv2026

Efficient generation of hematopoietic progenitor cells from human pluripotent stem cells by robotic automation

Differentiation of human pluripotent stem cells (hPSCs) into therapeutic cell types requires stringent control of developmental signals, but conventional manual operations introduce substantial intra- and inter-operator variability. While automation can reduce such variability, fixed systems often lack compatibility with the dynamic, stage-specific, and format-diverse manipulations required for hPSC culture and differentiation. Here, we establish a flexible robotic platform to standardize a stroma- and xeno-free embryoid body (EB)-based hematopoietic progenitor cell (HPC) differentiation process and integrate machine learning (ML) to optimize key process parameters including the concentrations of multiple signaling molecules. Despite intrinsic biological stochasticity and technical complexity associated with EB formation, the robotic platform substantially reduced experimental variation. ML-guided, unbiased exploration not only identified combinations of signaling inputs that markedly improved the efficiency and reproducibility of HPC differentiation and subsequent natural killer cell generation, but also illuminated key signaling logic underlying early human hematopoietic development. Together, these results demonstrate that data-driven robotic automation can uncover optimal culture conditions that are difficult to identify through conventional human-driven experimentation.

developmental biology↗

bioRxiv2026

Synergistic and Redundant Information Dynamics Exhibit Dissociable Alterations Across Major Psychiatric Disorders

Deficits in neural information integration are hypothesized to underlie diverse psychiatric symptoms, yet the specific patterns of alteration across different disorders remain unclear. In this study, we decomposed information dynamics between brain regions into synergistic and redundant components using a recent information-theoretical approach based on the idea of Partial Information Decomposition applied to resting-state fMRI data from patients with schizophrenia (SZ), autism spectrum disorder (ASD), and attention-deficit/hyperactivity disorder (ADHD). Our analysis revealed distinct disorder-specific profiles: SZ and ASD exhibited a widespread reduction in synergy, whereas ADHD showed a contrasting increase. Furthermore, ASD was uniquely characterized by a significant reduction in redundancy. Meta-analytic functional annotation using NeuroSynth associated synergy with higher-order cognitive functions and redundancy with lower-level sensorimotor processing. To investigate multivariate organization of these patterns that distinguish psychiatric diagnoses, we employed Linear Discriminant Analysis (LDA). This analysis demonstrated that synergy and redundancy partially capture distinct dimensions of network variation, exhibiting substantial complementarity in their multivariate structure. While redundancy overlapped considerably with correlation-based connectivity, synergy reflected additional structure not fully represented by conventional measures. Together, these findings indicate that decomposing information dynamics provides complementary perspectives on large-scale network organization, offering a refined framework for characterizing psychiatric disorders.

neuroscience↗

bioRxiv2025

Loop engineering and activity improvement of TEV protease by a phagemid-based selection system

Loop engineering of enzymes remains challenging due to high flexibility and conformational complexity, posing a bottleneck for deep-learning-based design. Here, we constructed mutant libraries for three loops of TEV protease to assess combining directed evolution with deep learning. Using an M13 phagemid-based selection system, the three libraries were screened, resulting in a Loop 1 variant (HyperTEV60/L1) that significantly enhanced the Michaelis constant (Km) of the HyperTEV60 scaffold, a highly active mutant identified by ProteinMPNN. Structural modeling suggested that a single-residue deletion and substitution in Loop 1 expands the substrate binding pocket, accounting for the improved Km. Although the catalytic efficiency kcat/Km of HyperTEV60/L1 was only marginally higher than HyperTEV60, due to a kcat decrease, our results reveal that the phagemid-based selection system tended to find variants optimizing Km. This study demonstrates that combining deep-learning-based global optimization with localized directed evolution maximizes the probability of discovering distinct, high-performance enzyme variants.

bioengineering↗

bioRxiv2025

Hypoxia-Induced Metabolic Reprogramming and Markings of Cell Fate in Concentric Arterial Hypertrophy

Chronic inhibition of the renin-angiotensin system (RAS), while widely used to treat hypertension, can lead to an underrecognized form of vascular disease marked by concentric arteriolar and arterial hypertrophy (CAAH). Here, using two lineage-traced mouse models of genetic renin deletion and sustained RAS blockade, we uncover a pathogenic cascade initiated by renin-lineage cell fate reprogramming. Loss of endocrine identity and transformation of smooth muscle cells drives a shift toward a fibrotic, inflammatory, and secretory phenotype that remodels the extracellular matrix and promotes vascular thickening and luminal narrowing. Integrated transcriptomic, proteomic, and metabolomic profiling revealed a hypoxia-linked metabolic switch--characterized by succinate accumulation and NAD+ depletion--coupled to Hif activation and disease progression. We identify Cdh13 and collagens (including Col1a1 and Col12a1) as early urinary biomarkers and define a 10-gene molecular signature of CAAH with potential clinical application. These findings establish renin-lineage cell plasticity and metabolic dysfunction as central drivers of CAAH and nominate candidate biomarkers for early detection and therapeutic targeting in RAS-inhibited patients.

physiology↗

bioRxiv2025

Renin Cells Drive Kidney Neurovascular Development and Arterial Remodeling when Renin Activity is Deficient

Renin cells synthesize and release the hormone-enzyme renin to regulate blood pressure and fluid-electrolyte homeostasis. Their function and identity depend on communication with surrounding cells and nerve fibers within complex kidney structure. Because renin cells are rare -0.01 % of kidney cells-conventional histological approaches cannot capture their interaction with nerve fibers and surrounding cells within the nephron and its vasculature. Using a novel ultrabright renin cell-specific tdTomato reporter mouse, high-resolution 3D imaging, and single-cell RNA-Seq, we mapped the interactions of renin cells with growing axons during normal kidney vascular development, in response to threats to homeostasis, and a severe arterial disease caused by a defective renin enzyme. During embryonic kidney development, stromal and renin cell progenitors assemble the arterioles, express axon attractants and neurotrophins that establish the precise innervation of renin cells and arterioles in a centrifugal pattern. Hypotension and sodium depletion led to an increase in the volume and number of renin cells along the arterioles. Renin enzymatic deficiency led to hypertrophy and endocrine transformation of renal arterioles, aberrant axon sprouting and sympathetic hyperinnervation suggesting a feed-forward mechanism whereby renin cells and axons co-induce each other, orchestrate neurovascular development and arteriolar remodeling when renin cells are over stimulated.

developmental biology↗

bioRxiv2025

NT5DC2 downregulation suppresses monoamine oxidase activity and increases catecholamine levels in PC12D cells

Back groundGenome-wide association studies have revealed the involvement of 5-nucleotidase domain-containing protein 2 (NT5DC2) in neuropsychiatric disorders such as schizophrenia and bipolar disorder; however, its function remains unclear. Recently, we found that NT5DC2 downregulation in PC12D cells increases catecholamine synthesis by promoting the activity of tyrosine hydroxylase and that monoamine oxidase A (MAO A) might bind to NT5DC2 using Affinity Purification-Mass Spectroscopy. Methods and ResultsWe investigated the role of NT5DC2 for MAO A activity in PC12D cells. Western blot analysis revealed that NT5DC2 primarily binds to the non-phosphorylated form of MAO A. siRNA-mediated NT5DC2 downregulation reduced MAO A activity, leading to decreased dopamine metabolism and increased noradrenaline synthesis. ConclusionOur findings suggest that NT5DC2 could affect both tyrosine hydroxylase and MAO A activity to control catecholamine synthesis. Therefore, our study provides valuable insights into disorders associated with catecholamine dysregulation, such as Parkinsons disease and neuropsychiatric disorders.

neuroscience↗

bioRxiv2025

Bright Cells, and Inefficient Enzymatic Activity in a Renin Hypomorph Mouse

Juxtaglomerular (JG) cells are crucial regulators of blood pressure and fluid-electrolyte homeostasis. Under normal conditions, renin secretion by JG cells is sufficient to maintain homeostasis. However, under physiological stress such as narrowing of one of the renal arteries, heart failure, dehydration, or chronic administration of renin-angiotensin system (RAS) inhibitors, additional cells along the renal arterioles are transformed to the renin phenotype to meet the demands for renin and regain homeostasis. In cases of prolonged and persistent stimulation of renin cells, concentric arteriolar hypertrophy develops. The study of renin cell identity, plasticity and function often requires the isolation of this rare cell type. Here, we report on the generation of a mouse model to label renin-expressing cells with a bright fluorescent reporter under control of the Ren1c locus for the tracking and isolation of renin cells. Kidneys from adult heterozygous (Het) Ren1ctdTomato/+ mice showed tdTomato signal confined to the JG area under basal conditions, and extending along the afferent arterioles and in the intraglomerular mesangium upon treatment with captopril + low-salt diet to induce the endocrine transformation of renin cells. Unexpectedly, homozygous (Homo) Ren1ctdTomato/tdTomato mice exhibited increased tdTomato signal that extended along the afferent arterioles and into the mesangium even under normal physiological conditions, with progressive thickening of the kidney arterioles with age. Despite reduced renin immunostaining in the renal cortex, Ren1ctdTomato/tdTomato Homo mice exhibited significantly higher kidney Ren1 mRNA and circulating renin levels when compared to Het controls. Moreover, Homo mice showed significantly lower blood pressure measured under anesthesia and angiotensin I (Ang I) plasma levels, indicating compromised renin activity. In addition, Homo mice developed interstitial fibrosis and compromised kidney function. The concentric arteriolar hypertrophy phenotype observed in these mice is identical to that described when RAS is genetically or pharmacologically inhibited, including the presence of mutations in the renin gene. Unlike mice with global deletion of renin, these animals did not require neonatal saline injections to survive and did not develop other kidney abnormalities, indicating that the bicistronic approach rendered a renin hypomorphic mouse. Ren1ctdTomato mice constitute an excellent model for the bright and strong labeling of renin-expressing cells and for the study of the mechanisms involved in the development of concentric vascular hypertrophy under RAS inhibition. In addition, this model may provide a better understanding of factors controlling renin protein folding, stability, packaging, and release.

physiology↗

bioRxiv2025

Harmonizing Inter-Site Differences in T1-Weighted Images Using CycleGAN

IntroductionWhen neuroimaging studies using magnetic resonance imaging (MRI) are conducted across multiple centers, they often encounter inter-site differences in MRI equipment and protocols leading to biases and confounding effects in MRI measurements. There are existing techniques for correcting these site effects, i.e., harmonization, but they have limitations, including the need for preprocessing of MRI data, which involves processes such as spatial normalization. Deep learning-based methods have emerged as potential alternatives that can handle site effects without the need for preprocessing steps. In this study, we propose a novel method based on the generative adversarial network (GAN) framework, CycleGAN, that effectively addresses inter-site differences in T1-weighted images with minimal preprocessing requirements. We compare the harmonization efficacy of CycleGAN with that of the commonly used method ComBat. MethodsWe trained the proposed CycleGAN method and the comparative ComBat method using data from 40 subjects at each of two sites. To evaluate the effectiveness of the two methods, we used data from nine subjects who underwent imaging at both sites. We assessed harmonization performance at the image level using the structural similarity index (SSIM) and peak signal-to-noise ratio (PSNR). Additionally, we evaluated harmonization results at the feature level by analyzing regional cortical thickness and volume data. Cohens d was employed to quantify the differences between feature values. ResultsAt the image level, the ComBat method decreased the median baseline SSIM value from 0.86 (interquartile range [IQR], 0.02) to 0.84 (IQR, 0.02), whereas the proposed CycleGAN method maintained the SSIM value at 0.86 (IQR, 0.02). For PSNR, the baseline value was 18.33 (IQR, 1.78), which decreased to 15.30 (IQR, 2.20) after applying ComBat, but increased to 19.58 (IQR, 3.12) with the proposed CycleGAN method. These findings indicate that CycleGAN preserved the structural and signal similarity of the images. At the feature level, the effect size for cortical thickness decreased from 0.97 (IQR, 1.79) to 0.91 (IQR, 1.54) after applying ComBat, whereas the proposed CycleGAN method yielded an effect size of 1.05 (IQR, 1.14). For cortical volume, the effect size decreased from 0.95 (IQR, 1.78) to 0.69 (IQR, 1.00) after applying ComBat, and decreased to 0.88 (IQR, 0.74) with the CycleGAN method. Compared with baseline, Cohens d was significantly lower with both ComBat (p = 0.000002) and CycleGAN (p = 0.028) with no significant difference between the two methods, indicating similar performance of the two methods under the study conditions. ConclusionThe results underscore the ability of CycleGAN to harmonize data without explicit normalization and emphasize the potential impact of the normalization process on harmonization procedures. Our findings suggest that CycleGAN holds promise as a harmonization technique in multi-site neuroimaging studies.

neuroscience↗

bioRxiv2024

Angiotensin II elicits robust calcium oscillations coordinated within juxtaglomerular cell clusters to suppress renin secretion.

BACKGROUNDJuxtaglomerular (JG) cells are sensors that control blood pressure (BP) and fluid-electrolyte homeostasis. They are arranged as clusters at the tip of each afferent arteriole. In response to a decrease in BP or extracellular fluid volume, JG cells secrete renin, initiating an enzymatic cascade that culminates in the production of angiotensin II (AngII), a potent vasoconstrictor that restores BP and fluid-electrolyte homeostasis. In turn, AngII exerts negative feedback on renin release concomitantly with increased intracellular Ca2+, preventing excessive circulating renin and hypertension. However, within their native structural organization, the intricacies of intracellular Ca2+ signaling dynamics and their sources remain uncharacterized. METHODSWe generated mice expressing the JG cell-specific genetically encoded Ca2+ indicator (GCaMP6f) to investigate Ca2+ dynamics within JG cell clusters ex vivo and in vivo. For ex vivo Ca2+ imaging, acutely prepared kidney slices were perfused continuously with a buffer containing variable Ca2+ and AngII concentrations {+/-} Ca2+ channel inhibitors. For in vivo Ca2+ image capture, native mouse kidneys were imaged in situ using multi-photon microscopy with and without AngII administration. ELISA measurements of renin concentrations determined acute renin secretion ex vivo and in vivo, respectively. RESULTSEx vivo Ca2+ imaging revealed that JG cells exhibit robust and coordinated intracellular oscillatory signals with cell-cell propagation following AngII stimulation. AngII dose-dependently induced stereotypical burst patterns characterized by consecutive Ca2+ spikes, which inversely correlated with renin secretion. Pharmacological channel inhibition identified key sources of these oscillations: endoplasmic reticulum Ca2+ storage and release, extracellular Ca2+ uptake via ORAI channels, and intercellular communication through gap junctions. Blocking ORAI channels and gap junctions reduced AngII inhibitory effect on renin secretion. In vivo Ca2+ imaging demonstrated robust intracellular and intercellular Ca2+ oscillations within JG cell clusters under physiological conditions, exhibiting spike patterns consistent with those measured in ex vivo preparations. Administration of AngII enhanced the Ca2+ oscillatory signals and suppressed acute renin secretion in vivo. CONCLUSIONAngII elicits coordinated intracellular and intercellular Ca2+ oscillations within JG cell clusters, ex vivo and in vivo. The effect is driven by endoplasmic reticulum-derived Ca2+ release, ORAI channels, and gap junctions, leading to suppressed renin secretion.

cell biology↗

bioRxiv2024

Fitness translocation: improving variant effect prediction with biologically-grounded data augmentation

Data scarcity limits the characterization of protein fitness landscapes and the development of accurate variant effect prediction models. To address this challenge, we introduce fitness translocation, a data augmentation strategy that generates synthetic variants for a target protein by leveraging variant fitness data previously measured in homologous proteins. Using embeddings from protein language models, the method computes the difference between each homolog variant and its wild type and applies these offsets to the target wild-type embedding to create synthetic variants in embedding space. We illustrate the utility of fitness translocation in the context of variant effect prediction on three protein families: IGPS, GFP, and SARS-CoV-2 spike proteins, across different models and training data sizes. Fitness translocation consistently improves predictive performance, particularly under limited training data, and is effective even when augmenting with remote homologs sharing as little as 35% sequence identity. These results illustrate how biologically grounded data augmentation can expand and diversify protein fitness landscapes, supporting more data-efficient protein engineering. The code is available at https://github.com/adrienmialland/ProtFitTrans.

bioinformatics↗

bioRxiv2024

Differential clearance rate of proteins encoded on a self-amplifying mRNA vaccine in muscle and lymph nodes

ARCT-154, a recently approved self-amplifying mRNA (saRNA) vaccine, has been shown in clinical trials to induce higher levels of neutralizing antibodies and sustain them for a longer time than the conventional mRNA vaccine BNT162b2. However, the scientific evidence explaining this superiority remain elusive. Hence, we explored the temporal changes in spike protein and replicase components following a single dose of ARCT-154 vaccination in mice. The encoded spike protein reached its highest level approximately 3 days after vaccination and quickly disappeared from the rectus femoris muscle, the injection site. Although the spike protein levels also peaked at an early time point in the lymph nodes, it remained detectable 28 days after the vaccination and then disappeared by 44 days after the vaccination. Expression of nsP1, nsP2 and nsP4 was observed in the injected muscle and/or the lymph nodes for up to 15 days post-vaccination. These data suggest that prolonged expression of spike proteins in lymph nodes may, if not entirely, be responsible for the induction of higher and prolonged levels of neutralizing antibodies by the saRNA vaccine.

molecular biology↗

bioRxiv2024

Intestinal helminth skews DC2 development towards regulatory phenotype to counter the anti-helminth immune response.

The intestinal immune system maintains a balance between active immunity needed for protection and tolerance towards harmless antigens. Dendritic cells (DCs) found in the intestinal mucosa are key to the adaptive arm of these immunoregulatory events. DCs sample antigens in the tissue and then migrate to the draining lymph nodes, where they prime the T cells that then migrate back to the tissue as effector or regulatory cells. Intestinal DC are highly heterogeneous, and it remains unclear exactly which subsets induces the different kinds of immune response, or what signalling molecules and cellular mechanisms are involved. Here, we have studied these issues using Heligmosomoides polygyrus bakeri (Hpb) infection in mice, a model which is uniquely suited to dissecting this regulatory circuit in the gut, where it drives type 2 protective immunity at the same time as inhibiting other aspects of the immune response. Here, we characterise intestinal DC during Hpb infection for the first time. We observed a dynamical change of intestinal DC populations throughout the course of infection that correlated with altered phenotype and function. In particular, Hpb infection saw a rise in a population of CD103+ DC2 that retained a potent ability to drive Tregs during the infection and unlike CD103-DC2, had a reduced ability to induce pro-inflammatory immune response. Furthermore, transcriptional analysis revealed that TGF{beta} signalling may be responsible for some of the changes observed. This was confirmed in vitro, where supplementation TGF{beta} or Hpb-produced TGF{beta} mimic (TGM) replicated the immunomodulatory effects seen in DCs in vivo. Together, these results present a mechanistic explanation of how helminths such as Hpb may modulate host immune responses by altering the differentiation and function of local DCs. Furthermore, our work provides the basis for understanding immune homeostasis in the intestine at the molecular and cellular levels. Thus, this work fills out a crucial gap in our knowledge of basic biology underlining the DC decision between pro- and anti-inflammatory immune response in the central circuit of adaptive immune response.

immunology↗

bioRxiv2024

Heterogeneous local structures of the microtubule lattice revealed by cryo-ET and non-averaging analysis

Microtubule cytoskeletons play pivotal roles in various cellular processes, including cell division and locomotion, by dynamically changing their length and distribution in cells through tubulin polymerization/depolymerization. Recent structural studies have revealed the polymorphic lattice structure of microtubules closely correlate with the microtubule dynamics, but the studies were limited to averaged structures. To reveal the transient and localized structures, such as GTP-cap, we developed several non-averaging methods for cryogenic electron tomography to precisely measure the longitudinal spacing and helical twisting of individual microtubule lattices at the tubulin subunit level. Our analysis revealed that polymerizing and depolymerizing ends share a similar structure with regards to lattice spacing. The most distinctive property specific to the polymerizing plus end was left-handed twisting in the inter-dimer interface, suggesting that the twisting might accelerate fast polymerization at the plus ends. Our analysis uncovered the heterogeneity of native microtubules and will be indispensable for the study of microtubules dynamics under physiological contexts or during specific cellular events.

biophysics↗

bioRxiv2024

An efficient inducible model for the control of gene expression in renin cells

BackgroundFate mapping and genetic manipulation of renin cells have relied on either non-inducible Cre lines that can introduce developmental effects of gene deletion or BAC transgene-based inducible models that may be prone to spurious and/or ectopic gene expression. MethodsWe generated an inducible mouse model in which CreERT2 is under the control of the endogenous Akr1b7 gene, an independent marker of renin cells. ResultsWe evaluated the pattern of Cre expression in Akr1b7CreERT2/+;R26RmTmG/+ mice in which Akr1b7+/renin+ cells become GFP+ upon tamoxifen administration. At E18.5 and P5, GFP was found in Juxtaglomerular cells, along the arterioles, and in the glomerular mesangium. In adult kidneys, GFP was present mainly in Juxtaglomerular cells. In mice treated with captopril and a low sodium diet to induce recruitment of renin cells, GFP extended along the afferent arterioles and in the mesangium. In addition, we deleted renin in adult mice and found a marked reduction in kidney renin expression and mean arterial pressure in mutant animals. When subjected to a homeostatic threat, mutant mice were unable to recruit renin+ cells. Most importantly, mice with renin deletion induced in the adult developed concentric vascular hypertrophy ruling out potential developmental effects on the vasculature due to the lack of renin. ConclusionsRenin can be efficiently and specifically deleted in renin cells in adult life using our conditional model. Akr1b7CreERT2 mice constitute an excellent model for the fate mapping of renin cells and for the spatial and temporal control of gene expression in renin cells.

physiology↗

bioRxiv2024

The Brain Tells a Story: Unveiling Distinct Representations of Semantic Content in Speech, Objects, and Stories in the Human Brain with Large Language Models

In recent studies, researchers have used large language models (LLMs) to explore semantic representations in the brain; however, they have typically assessed different levels of semantic content, such as speech, objects, and stories, separately. In this study, we recorded brain activity using functional magnetic resonance imaging (fMRI) while participants viewed 8.3 hours of dramas and movies. We annotated these stimuli at multiple semantic levels, which enabled us to extract latent representations of LLMs for this content. Our findings demonstrate that LLMs predict human brain activity more accurately than traditional language models, particularly for complex background stories. Furthermore, we identify distinct brain regions associated with different semantic representations, including multi-modal vision-semantic representations, which highlights the importance of modeling multi-level and multi-modal semantic representations simultaneously. We will make our fMRI dataset publicly available to facilitate further research on aligning LLMs with human brain function. Please check out our webpage at https://sites.google.com/view/llm-and-brain/.

neuroscience↗