Biology subjects

Fei, X.

Publications and source records attributed to Fei, X..

14 recordsLinked to original sources

bioRxiv2026

TiSAM: fusing spatial and histopathology foundation models for whole-slide image segmentation

Semantic segmentation of whole-slide images (WSIs) quantifies tissue composition and architecture, but existing models require extensive annotation and lose accuracy as the number of tissue classes increases or on heterogeneous, cross-scanner datasets. Here, we present the Tissue Segment Anything Model (TiSAM), which fuses SAM3 spatial features with UNI2-h pathology features within a multi-scale decoder. Because public benchmarks contain few tissue classes, we release MegaMouse, comprising 36,833 annotations of 52 tissue classes from 12 mouse organs, and an 11-class human pancreas dataset. TiSAM achieved the highest overall performance across four public datasets compared to existing convolutional neural network and vision transformer models, maintained high accuracy on MegaMouse, and maintained high accuracy in the human pancreas dataset when trained on as few as 5 annotated WSIs where previous integrations of SAM with pathology foundation models did not. TiSAM segmentations were also more consistent across eight slide scanners compared to other models. These results establish TiSAM as a general and highly adaptable framework for tissue segmentation, enabling studies containing many tissue classes, limited annotations, or images from multiple scanners.

bioinformatics↗

bioRxiv2026

Causal event structure shapes convergent reactivation signatures in human cortex and language model

Humans adapt to changing environments by understanding the latent causal structure of events, and modern large language models (LLMs) increasingly exhibit analogous abilities. However, elucidating how causal knowledge is represented and integrated in the human brain and in LLMs poses a substantial challenge for cognitive science. To address this, we combine topological analysis of representational manifolds with neuroscientific analyses of reactivation. We find that event-level causal relations modulate temporally structured neural reactivation in the human brain, particularly in the angular gyrus, precuneus and prefrontal cortex. By contrast, LLMs express these relations through positionally structured representational reactivation. Despite these differences, the resulting reactivation patterns exhibit similar intrinsic manifold structure across the two systems. Together, these findings suggest that the human brain and LLM share a common principle for organizing causal knowledge.

neuroscience↗

bioRxiv2025

The Human Hippocampus Is Involved in Auditory Short-Term Memory Trace Formation

The human hippocampus has been claimed to play an important role in long-term memory, or episodic memory, but its contribution to short-term memory remains debated. Here, we demonstrate human hippocampal involvement in auditory short-term memory (ASTM) trace formation. We used a classic oddball paradigm and intracranial recordings across various human brain areas. High frequency activities evoked by deviant stimuli in subjects indicate the generation of ASTM trace. Analysis of auditory response latencies across the hippocampus, insula, and temporal, parietal, and frontal lobes revealed the early processing of ASTM trace at a pre-attention stage. Granger causality analysis further showed that ASTM trace processing engages hierarchical cortical areas and clarified their interactions. Bottom-up signals flow from the insula and auditory temporal regions to the frontal lobe early on, followed by top-down information from the frontal lobe to the hippocampus, inferior temporal lobe, and insula at a later pre-attentive stage. Critically, Bayesian model selection of dynamic causal modeling revealed that deviant stimuli selectively enhanced the effectiveness of top-down connections to the hippocampus, thereby facilitating ASTM trace formation. These results provide compelling evidence that the human hippocampus contributes to auditory short-term memory at a pre-attention stage and suggests a challenge to entrenched beliefs in the classification of memory systems.

neuroscience↗

bioRxiv2023

The Cognitive Critical Brain: Modulation of Criticality in Task-Engaged Regions

The constantly evolving world necessitates a brain that can adapt and respond to rapid changes. The brain, conceptualized as a system performing cognitive functions through collective neural activity, has been shown to maintain a resting state characterized by near-critical neural activity, poised to respond to external stimuli. The dynamic adaptation of nearcriticality during various tasks, however, remains poorly understood. In this study, we utilized the prototypical Hamiltonian Ising model to investigate the modulation of near-criticality in neural activity at the cortical subsystem level during cognitive tasks. Specifically, we theoretically simulated cortical 2D-Ising models in silico using structural MRI data and empirically estimated the system state in vivo using functional MRI data. First, our findings corroborated previous studies that the resting state is typically near-critical as captured by the Ising model. Notably, we found that cortical subsystems changed their criticality levels heterogeneously during a naturalistic movie-watching task, where visual and auditory cortical regions were fine-tuned closer to criticality. A more fine-grained analysis of the ventral temporal cortex during an object recognition task revealed that only regions selectively responsive to a specific object category were tuned closer to criticality when processing that object category. In conclusion, our study supports the cognitive critical brain hypothesis that modulating the criticality of subsystems within the hierarchical modular brain may be a general mechanism for achieving diverse cognitive functions.

neuroscience↗

bioRxiv2022

The SspB adaptor drives structural changes in the AAA+ ClpXP protease during ssrA-tagged substrate delivery

Energy-dependent protein degradation by the AAA+ ClpXP protease helps maintain protein homeostasis in organisms ranging from simple bacteria to humans. In E. coli and many other proteobacteria, the SspB adaptor assists ClpXP in degrading ssrA-tagged polypeptides produced as a consequence of tmRNA-mediated ribosome rescue. By tethering these incomplete ssrA-tagged proteins to ClpXP, SspB facilitates their efficient degradation at low substrate concentrations. How this process occurs structurally is unknown. Here, we present a cryo-EM structure of the SspB adaptor bound to a GFP-ssrA substrate and to ClpXP. This structure provides evidence for simultaneous contacts of SspB and ClpX with the ssrA tag within the tethering complex, allowing direct substrate handoff concomitant with the initiation of substrate translocation. Furthermore, our structures reveal that binding of the substrate*adaptor complex induces unexpected conformational changes within the spiral structure of the AAA+ ClpX hexamer and its interaction with the ClpP tetradecamer. SIGNIFICANCEIntercellular proteases, including ClpXP, degrade damaged or unneeded proteins. Peptide tags allow specific protein substrates to be recognized by the ClpX unfoldase/translocase component of ClpXP and by an adaptor, SspB, which tethers itself to ClpX and enhances ClpXP degradation of the tagged protein. Our cryo-EM structure of ClpXP bound to SspB and a tagged substrate shows that SspB and ClpX simultaneously contact the degradation tag and reveal changes in the structure of ClpX and its interaction with ClpP. These structural changes appear to be a prelude to an initial ClpX translocation step that pulls the substrate away from SspB and initiates degradation by allowing substrate unfolding and further translocation of the unfolded substrate into the proteolytic chamber of ClpP.

biochemistry↗

bioRxiv2022

A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation

Intracellular proteases must be specific to avoid degrading the wrong proteins. Here, we present cryo-EM structures of E. coli ClpXP, a AAA+ protease, which reveal that the axial channel of ClpX is closed prior to the binding and subsequent translocation of a protein substrate. An open-channel ClpX mutation stimulates degradation of casein, a non-specific substrate, indicating that channel closure contributes to increased degradation specificity. We demonstrate that ClpX activates ClpP cleavage of a degron-free decapeptide by a channel-independent mechanism, in which the peptide substrate appears to pass through a symmetry mismatched gap in the interface between ClpX and ClpP before entering the degradation chamber via the axial portal of ClpP. The peptide products of ClpXP protein degradation are likely to exit the chamber by the reverse route.

biochemistry↗

bioRxiv2022

HSP90.6 is involved in grain filling via carbon and nitrogen metabolism in maize.

Carbon and nitrogen are the two most abundant nutrients in all living things, and their metabolism maintains normal plant growth. However, the molecular mechanism underlying carbon and nitrogen metabolism remains largely unknown. Here, we found that HSP90.6 is involved in the metabolism of carbon and nitrogen. We performed gene cloning and functional characterization of a maize EMS mutant ehsp90.6, whose kernels were small. HSP90.6 encodes heat shock protein 90.6, which has a single-amino acid mutation within its HATPase_c domain. Transcriptome profiling showed that the expression of amino acid biosynthesis- and carbon metabolism-related genes was significantly downregulated in hsp90.6. HSP90.6 is involved in the 26S proteasome degradation pathway, which affects nitrogen recycling to regulate amino acid synthesis; this occurs by interactions between HSP90.6 and the 26S proteasome subunits RPN6 and PBD2 (PRC2). The loss of HSP90.6 significantly reduced the activity of the 26S proteasome, resulting in the accumulation of ubiquitinated proteins and defects in nitrogen recycling. Moreover, HSP90.6 interacted with the 14-3-3 protein GF14-6 to participate in carbon metabolism. Together, these findings revealed that HSP90.6 regulates nutrient metabolism in maize seeds by affecting 26S proteasome-mediated nitrogen recycling and GF14-6-mediated carbon metabolism. One sentence summaryHSP90.6 is involved in nutrient metabolism via 26S proteasome-mediated protein degradation to promote nitrogen recycling and GF14-6 protein-mediated carbon metabolism. The author responsible for the distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (https://academic.oup.com/plcell/pages/General-Instructions) is Weibin Song (songwb@cau.edu.cn). HighlightsO_LIHATPase_c is necessary for HSP90.6 to regulate maize kernel development. C_LIO_LIHSP90.6 is involved in nitrogen recycling via the 26S proteasome degradation pathway. C_LIO_LIHSP90.6 interacts with the 14-3-3 protein GF14-6 to affect carbon metabolism. C_LI IN A NUTSHELLO_ST_ABSBackgroundC_ST_ABSSeeds are the main harvested organs of maize. Understanding the regulatory mechanism of grain filling is helpful to cultivate high-quality and high-yield maize. In the past few years, the regulatory network of grain filling has been explored through multiple means, including transcriptomic, proteomic and functional genomic techniques. Many genes that control grain filling through different mechanisms have been cloned, such as CTLP1 (Choline Transporter-like Protein 1), OS1 (Opaque Endosperm and Small Germ 1), and MN6 (Miniature Seed6). To identify new genes involved in maize grain filling, ethyl methanesulfonate (EMS) was used to induce mutations, and the ehsp90.6 mutant, which exhibited abnormal kernel development, was isolated by bulked segregant analysis RNA sequencing (BSR). QuestionWhy does the single-amino acid mutation of HSP90.6 affect grain size, and how does the loss of HSP90.6 affect grain filling? FindingsA single-amino acid mutant (ehsp90.6) and knockout mutant (hsp90.6) were obtained. We found that HSP90-6 was involved in the regulation of maize grain filling. A single-single amino acid mutation in the HATPase_c domain reduced the ATPase activity of HSP90.6, resulting in smaller grains. The functional loss of HSP90.6 resulted in the expression of amino acid biosynthesis- and carbon metabolism-related genes being significantly downregulated in hsp90.6. We indicated that HSP90.6 is involved in the 26S proteasome degradation pathway, which affects nitrogen recycling to regulate amino acid synthesis by interacting with the 26S proteasome subunits RPN6 and PBD2 (PRC2). Moreover, HSP90.6 was found to interact with the 14-3-3 protein GF14-6 to participate in carbon metabolism. Next stepsTo further verify that the interaction between HSP90.6 and 26S proteasome subunits and GF14-6 affects grain filling, knockout validation of RPN6, PBD2 (PRC2) and GF14-6 will be performed. In addition, since GF14-6 interacts with the phosphorylated proteins, we will determine the phosphorylation site of HSP90.6. Due to the important role of HSP90 family proteins in plant development, there are other regulatory pathways that need to be explored.

plant biology↗

bioRxiv2022

AAA+ protease-adaptor structures reveal altered conformations and ring specialization

ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here, we present high-resolution cryo-EM structures of ClpAPS complexes showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two structural classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated and tucked away from the channel, and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies demonstrate new structures and functions for key AAA+ elements. In addition to ClpAPS delivery, pore-loop tucking may be used broadly by AAA+ unfoldases, for example during enzyme pausing/unloading.

biophysics↗

bioRxiv2020

Structural basis of ClpXP recognition and unfolding of ssrA-tagged C-degron substrates

When ribosomes fail to complete normal translation, all cells have mechanisms to ensure degradation of the resulting partial proteins to safeguard proteome integrity. In E. coli and other eubacteria, the tmRNA system rescues stalled ribosomes and adds an ssrA tag or degron to the C-terminus of the incomplete protein, which directs degradation by the AAA+ ClpXP protease. Here, we present cryo-EM structures of ClpXP bound to the ssrA degron. C-terminal residues of the ssrA degron initially bind in the top of an otherwise closed ClpX axial channel and subsequently move deeper into an open channel. For short-degron protein substrates, we show that unfolding can occur directly from the initial closed-channel complex. For longer-degron substrates, our studies illuminate how ClpXP transitions from specific recognition into a nonspecific unfolding and translocation machine. Many AAA+ proteases and protein-remodeling motors are likely to employ similar multistep recognition and engagement strategies.

biophysics↗

bioRxiv2019

Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate

ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the E. coli enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results.

biophysics↗

bioRxiv2019

Identification of microRNA-target interactions for antioxidant defense response under drought stress by high-throughput sequencing in Zanthoxylum bungeanum Maxim.

When the plant is in an unfavorable environment such as drought or high temperature, it will accumulate a large amount of active oxygen, which will seriously affect the normal growth and development of the plant. The antioxidant system can remove the reactive oxygen species produced under drought conditions and so mitigate oxidative damage. We examined the trends of antioxidant enzymes, miRNAs and their target genes in Zanthoxylum bungeanum under drought stress. According to the changes of antioxidant enzymes, miRNAs and their target genes expression patterns of Zanthoxylum bungeanum under drought stress, an interaction model was constructed to provide a reference for further understanding of plant antioxidant mechanism. The results indicate that under drought stress, POD, CAT, APX, proline, MDA and related genes all show positive responses to drought, while SOD and its genes showed a negative response. It is speculated that in the antioxidant process of Zanthoxylum bungeanum, POD, CAT, and APX play a major role, and SOD plays a supporting role. In addition, the expression levels of miRANs and their target genes were basically negatively correlated, indicating that miRNAs are involved in the regulation of the antioxidant system of Zanthoxylum bungeanum.

cell biology↗

bioRxiv2019

Presynaptic MAST Kinase Controls Bidirectional Post-SynapticResponses to Convey Stimulus Valence in C. elegans

Presynaptic plasticity is known to modulate the strength of synaptic transmission. However, it remains unknown whether regulation in presynaptic neurons alters the directionality -positive or negative-of postsynaptic responses. We report here that the C. elegans homologs of MAST kinase, Stomatin and Diacylglycerol kinase act in a thermosensory neuron to elicit in its postsynaptic neuron an excitatory or inhibitory response that correlates with the valence of thermal stimuli. By monitoring neural activity of the valence-coding interneuron in freely behaving animals, we show that the alteration between excitatory and inhibitory responses of the interneuron is mediated by controlling the balance of two opposing signals released from the presynaptic neuron. These alternative transmissions further generate opposing behavioral outputs necessary for the navigation on thermal gradients. Our findings reveal the previously unrecognized capability of presynaptic regulation to evoke bidirectional postsynaptic responses and suggest a molecular mechanism of determining stimulus valence.

neuroscience↗

bioRxiv2019

Drought Affects the Antioxidant System and Stomatal Aperture in Zanthoxylum bungeanum Maxim.

When under drought, plants activate a range of self-protective responses. Among these are activation of the antioxidant system and changes in stomatal aperture. The antioxidant system can remove the reactive oxygen species produced under drought conditions and so mitigate oxidative damage. Water becomes a severely limiting resource for plants suffering drought stress, so they generally close their stomata to reduce water loss. We examined changes in the activities of the antioxidant enzymes and altered gene expression patterns in Zanthoxylum bungeanum plants exposed to drought by irrigation with 20% PEG6000. We also recorded changes in stomatal aperture as the drought persisted. Relationships between the antioxidant system and stomatal aperture were analyzed in relation to gene expression. The results indicate that under drought stress, POD, CAT, APX, proline, MDA and related genes all show positive responses to drought, while SOD and its genes showed a negative response. The relationship between drought duration and stomatal aperture was considered. Stomatal aperture declines exponentially as drought duration increases.

cell biology↗

bioRxiv2018

Shifted balance of dorsal versus ventral striatal communication with frontal reward and regulatory regions in cannabis dependence

The transition from voluntary to addictive behavior is characterized by a loss of regulatory control in favor of reward driven behavior. Animal models indicate that this process is neurally underpinned by a shift in ventral to dorsal striatal control of behavior, however this shift has not been directly examined in humans. Against this background the present resting state fMRI study employed a two-step approach to (1) precisely map striatal alterations using a novel, data-driven network classification strategy combining Intrinsic Connectivity Contrast (ICC) with Multivoxel Pattern Analysis (MVPA) and, (2) to determine whether a ventral to dorsal striatal shift in connectivity with reward and and regulatory control regions can be observed in abstinent (28 days) male cannabis-dependent individuals (n = 24) relative to matched controls (n = 28). Network classification revealed that the groups can be reliably discriminated by global connectivity profiles of two striatal regions that mapped onto the ventral (nucleus accumbens) and dorsal striatum (caudate). Subsequent functional connectivity analysis demonstrated a relative shift between ventral and dorsal striatal communication with fronto-limbic regions that have been consistently involved in reward processing (rostral ACC) and executive / regulatory functions (dorsomedial PFC). Specifically, in the cannabis dependent subjects connectivity between the ventral striatum with the rostral ACC increased, whereas both striatal regions were uncoupled from the regulatory dorsomedial PFC. Together these findings suggest a shift in the balance between dorsal and ventral striatal control in cannabis dependence. Similar changes have been observed in animal models and may promote the loss of control central to addictive behavior.

neuroscience↗