Biology subjects

Qiu, Z.

Publications and source records attributed to Qiu, Z..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

RTM-align: an improved RNA alignment tool with enhanced short sequence performance via post-standardization and fragment alignment

Understanding the three-dimensional structure of RNA is crucial for studying various biological processes. Accurate alignment and comparison of RNA structures are essential for illustrating RNA functionality and evolution. The existing RNA alignment tools suffer from limitations such as size-dependency of scoring functions and inadequate handling of short RNA fragments, leading to the conflicting interpretation of structural and functional relationships among RNA molecules. Hence, we introduce RTM-align, a novel RNA structural alignment tool enhanced for short RNAs. RTM-align employs the RTM-score, which integrates post-standardization to ensure size-independence and utilizes a fragment alignment strategy that improves alignment accuracy by concentrating on structural motifs and local structural elements. Benchmarking results demonstrate that RTM-align outperforms existing tools in RNA structure comparison, offering a universal scoring scale regardless of RNA length. The improvement is particularly evident in evaluating predicted structures for CASP15 RNA targets, with significant enhancements observed for the short RNA target R1117. RTM-align is expected to significantly improve the accuracy and reliability of RNA structure alignment and comparison, thereby aiding in the deeper understanding and discovery of novel RNA functions and their interactions in biological systems. RTM-align is now available at https://github.com/BEAM-Labs/RTM-align.

bioinformatics↗

bioRxiv2024

Pi-PrimeNovo: An Accurate and Efficient Non-Autoregressive Deep Learning Model for De Novo Peptide Sequencing

Peptide sequencing via tandem mass spectrometry (MS/MS) is fundamental in proteomics data analysis, playing a pivotal role in unraveling the complex world of proteins within biological systems. In contrast to conventional database searching methods, deep learning models excel in de novo sequencing peptides absent from existing databases, thereby facilitating the identification and analysis of novel peptide sequences. Current deep learning models for peptide sequencing predominantly use an autoregressive generation approach, where early errors can cascade, largely affecting overall sequence accuracy. And the usage of sequential decoding algorithms such as beam search suffers from the low inference speed. To address this, we introduce{pi} -PrimeNovo, a non-autoregressive Transformer-based deep learning model designed to perform accurate and efficient de novo peptide sequencing. With the proposed novel architecture,{pi} -PrimeNovo achieves significantly higher accuracy and up to 69x faster sequencing compared to the state-of-the-art methods. This remarkable speed makes it highly suitable for computation-extensive peptide sequencing tasks such as metaproteomic research, where{pi} -PrimeNovo efficiently identifies the microbial species-specific peptides. Moreover,{pi} -PrimeNovo has been demonstrated to have a powerful capability in accurately mining phosphopeptides in a non-enriched phosphoproteomic dataset, showing an alternative solution to detect low-abundance post-translational modifications (PTMs). We suggest that this work not only advances the development of peptide sequencing techniques but also introduces a transformative computational model with wide-range implications for biological research.

bioinformatics↗

bioRxiv2024

KAT6A deficiency impairs cognitive functions through suppressing RSPO2/Wnt signaling in hippocampal CA3

Intellectual disability (ID) affects [~]2% of the general population and is often genetic in origin. ID-associated genes are enriched for epigenetic factors, including those encoding the largest family of histone lysine acetyltransferases (KAT5-KAT8). Among them is KAT6A, whose de novo heterozygous mutations cause KAT6A Syndrome (or Arboleda-Tham Syndrome), with ID as a common clinical feature. However, the underlying molecular mechanisms remain elusive. Here, we show that haploinsufficiency of Kat6a impairs learning and memory in mice, and specific deletion of Kat6a in excitatory neurons recapitulates the hippocampus-dependent memory deficits. Unexpectedly, KAT6A deficiency results in impaired synaptic structure and plasticity in hippocampal CA3, but not in CA1 region. Combining single-nucleus RNA-sequencing and chromatin analysis, we identify a CA3-enriched gene Rspo2, encoding a Wnt activator R-spondin 2, as a key transcriptional target of KAT6A. Moreover, deletion of Rspo2 in excitatory neurons phenocopies the loss of Kat6a, resulting in defective Wnt/{beta}-catenin signaling and synaptic plasticity in CA3, and abnormal cognitive behaviors in mice. Importantly, restoring RSPO2 expression in CA3 pyramidal neurons rescues the deficits in Wnt signaling and learning-associated behaviors in Kat6a mutant mice. Collectively, our results demonstrate that KAT6A plays a critical role in regulating synaptic plasticity and memory formation through RSPO2-mediated Wnt signaling in hippocampal CA3, shedding new light on the fundamental mechanisms of ID and providing potential therapeutic targets for the treatment of KAT6A Syndrome and related neurodevelopmental diseases.

neuroscience↗

bioRxiv2023

Mechanical Netrin-1-DCC Coupling Mediates Netrin-1-induced Axonal Haptotaxis

The growth cone, a motile structure located at the tip of growing axon, senses extracellular guidance cues and translates them into directional forces that drive axon outgrowth and guidance. Axon guidance directed by chemical cues on the extracellular adhesive substrate is termed haptotaxis. Recent studies reported that netrin-1 on the substrate functions as a haptotactic axon guidance cue. However, the mechanism mediating netrin-1-induced axonal haptotaxis remains unclear. Here, we demonstrate that substrate-bound netrin-1 induces axonal haptotaxis by facilitating physical interactions between the netrin-1 receptor, DCC, and the adhesive substrates. DCC serves as an adhesion receptor for netrin-1. The clutch molecule shootin1a interacted with DCC, linking it to actin filament retrograde flow at the growth cone. Speckle imaging analyses showed that DCC underwent either grip (stop) and retrograde slip on the adhesive substrate. The grip state was more prevalent on netrin-1-coated substrate compared to the control substrate polylysine, thereby transmitting larger traction force on the netrin-1-coated substrate. Furthermore, disruption of the linkage between actin flow and DCC by shootin1 knockout impaired netrin-1-induced axonal haptotaxis. These findings indicate that the directional force for netrin-1-induced haptotaxis is exerted on the substrates through the mechanical coupling between netrin-1 and DCC which occurs asymmetrically under the growth cone.

cell biology↗

bioRxiv2023

IRF8-mutant B cell lymphoma evades immunity through a CD74-dependent deregulation of antigen processing and presentation in MHC CII complexes

In diffuse large B-cell lymphoma (DLBCL), the transcription factor IRF8 is the target of a series of potentially oncogenic events, including, chromosomal translocation, focal amplification, and super-enhancer perturbations. IRF8 is also frequently mutant in DLBCL, but how these variants contribute to lymphomagenesis is unknown. We modeled IRF8 mutations in DLBCL and found that they did not meaningfully impact cell fitness. Instead, IRF8 mutants, mapping either to the DNA-binding domain (DBD) or c-terminal tail, displayed diminished transcription activity towards CIITA, a direct IRF8 target. In primary DLBCL, IRF8 mutations were mutually exclusive with mutations in genes involved in antigen presentation. Concordantly, expression of IRF8 mutants in murine B cell lymphomas uniformly suppressed CD4, but not CD8, activation elicited by antigen presentation. Unexpectedly, IRF8 mutation did not modify MHC CII expression on the cell surface, rather it downmodulated CD74 and HLA- DM, intracellular regulators of antigen peptide processing/loading in the MHC CII complex. These changes were functionally relevant as, in comparison to IRF8 WT, mice harboring IRF8 mutant lymphomas displayed a significantly higher tumor burden, in association with a substantial remodeling of the tumor microenvironment (TME), typified by depletion of CD4, CD8, Th1 and NK cells, and increase in T-regs and Tfh cells. Importantly, the clinical and immune phenotypes of IRF8-mutant lymphomas were rescued in vivo by ectopic expression of CD74. Deconvolution of bulk RNAseq data from primary human DLBCL recapitulated part of the immune remodeling detected in mice and pointed to depletion of dendritic cells as another feature of IRF8 mutant TME. We concluded that IRF8 mutations contribute to DLBCL biology by facilitating immune escape.

cancer biology↗

bioRxiv2023

Large-scale population genomics of Malayan pangolins reveals deep diversification and a new species

BackgroundArchipelagos and oceanic islands often present high percentage of endemism due to rapid speciation. The Malayan pangolin is a species distributing at both mainland (southern Yunnan, China) and oceanic islands via Malayan peninsula, which may result in deep differentiation among populations. In-depth investigation of population structure and genetic consequences for such species is of vital importance for their protection and conservation, practically for the critically endangered Malayan pangolin that is suffering from poaching, illegal trade, and habitat loss. ResultsHere we carried out a large-scale population genomic analysis for Malayan pangolins, and revealed three highly distinct genetic populations in this species, two of which are now being reported for the first time. Based on multiple lines of genomic and morphological evidence, we postulate the existence of a new pangolin species (Manis_1). Genetic diversity and recent inbreeding were both at a moderate level for both Malayan pangolins and Manis_1, but mainland Malayan pangolins presented relatively lower genetic diversity, higher inbreeding and fitness cost than island populations. ConclusionsWe found extremely deep and graded differentiation in Malayan pangolins, with two newly discovered genetic populations and a new pangolin species that is closely related to the Philippine pangolin than the typical Malayan pangolin, but a distant relative of the Indian pangolin. Anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins, but mainland Malayan pangolins should be paid more attention for conservation due to higher genetic risks than island populations.

genomics↗

bioRxiv2023

Mecp2 Fine-tunes Quiescence Exit by Targeting Nuclear Receptors

Quiescence (G0) maintenance and exit are crucial for tissue homeostasis and regeneration in mammals. Here, we show that methyl-CpG binding protein 2 (Mecp2) expression is cell cycle-dependent and negatively regulates quiescence exit in cultured cells and in an injury-induced liver regeneration mouse model. Specifically, acute reduction of Mecp2 is required for efficient quiescence exit, as deletion of Mecp2 accelerates, while overexpression of Mecp2 delays quiescence exit, and forced expression of Mecp2 after Mecp2 conditional knockout rescues cell cycle reentry. The E3 ligase Nedd4 mediates the ubiquitination and degradation of Mecp2, and thus facilitates quiescence exit. Genome-wide study uncovered the dual role of Mecp2 in preventing quiescence exit by transcriptionally activating metabolic genes while repressing proliferation-associated genes. Particularly, disruption of two nuclear receptors (NRs), Rara or Nr1h3, accelerates quiescence exit, mimicking the Mecp2 depletion phenotype. Our studies unravel a previously unrecognized role for Mecp2 as an essential regulator of quiescence exit and tissue regeneration.

cell biology↗

bioRxiv2023

Sleep maintains excitatory synapse diversity in the cortex and hippocampus

How sleep deprivation affects cognition remains elusive. Synaptome mapping of excitatory synapses in 125 regions of the mouse brain revealed that sleep deprivation selectively reduces synapse diversity in the cortex and hippocampus. Sleep deprivation targeted specific types and subtypes of excitatory synapses while maintaining total synapse density. Altered synaptic responses to neural oscillations in a computational model suggest that sleep prevents cognitive impairments by maintaining normal brain synaptome architecture.

neuroscience↗

bioRxiv2023

Srcap Haploinsufficiency Induced Autistic-Like Behaviors in Mice through Disruption of Satb2 Expression

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with significant genetic predispositions. Among these, loss-of-function mutations of the chromatin remodeling gene SRCAP have been identified in individuals with ASD, but their pathogenic mechanisms have yet to be fully elucidated. In this study, we established a germline mutant mouse model harboring a heterozygous frameshift mutation in the Srcap gene (Srcap+/-). The Srcap+/- mice exhibited notable impairments in social novelty, repetitive and stereotyped behaviors, anxiety, and learning and memory deficits. We observed a decreased number of parvalbumin (PV)-expressing neurons in their retrosplenial cortex (RSC) and dentate gyrus (DG). Furthermore, abnormalities in dendritic structure, synaptic density, and synaptic transmission were noted in the DG of Srcap+/- mice. RNA sequencing revealed that the expression of 27 genes, implicated in ASD, was dysregulated in the Srcap haploinsufficiency mice. Among these genes, we found that Srcap haploinsufficiency resulted in decreased Satb2 expression due to diminished H2A.z-binding within the promoter region of Satb2. Remarkably, intervention through retro-orbital injection of AAV vectors expressing Satb2 in newborn Srcap+/- mice reversed autistic-like behaviors and developmental defects in the RSC and DG regions. Similarly, in adolescent Srcap+/- mice, stereotactic injection of AAV expressing Satb2 into the RSC ameliorated deficits in social novelty. Collectively, these findings highlight the crucial role of the Srcap in neurodevelopment by regulating Satb2 expression, particularly impacting the development of RSC and DG regions.

neuroscience↗

bioRxiv2023

Unravelling Biosynthesis and Biodegradation Potentials of Microbial Dark Matters in Hypersaline Lakes

Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology, new drugs and therapies, and environmental remediation. However, the vast majority of uncultured microbial species along with their metabolic capacities in extreme environments remain obscured. To unravel the metabolic potentials of these microbial dark matters (MDMs), we investigated four deep-inland hypersaline lakes with largely diversified environmental parameters in Xinjiang Uygur Zizhiqu, China. Metagenomic binning obtained 3,030 metagenome-assembled genomes (MAGs) spanning 82 phyla, of which 2,363 MAGs could not be assigned to a known genus. These unknown MAGs were abundantly observed with distinct taxa among lakes, possibly linked to the diversification of physiochemical conditions. Analysis of biosynthetic potentials identified 9,635 biosynthesis gene clusters (BGCs), of which 9,403 BGCs were considered novel. We found that some MAGs from putatively novel phyla consistently comprised enriched BGCs, which may have substantial potentials in biotechnological applications. In addition, biodegradation potentials such as dehalogenation, anaerobic ammonium oxidation (Anammox), polycyclic aromatic hydrocarbon (PAH), and plastic degradation were found in new microbial clades from hypersaline lakes. These findings substantially expanded the genetic repository of biosynthesis and biodegradation potentials, which can further assist the development of new and innovative applications in biotechnology.

microbiology↗

bioRxiv2023

Differential modulation on neural activity related to flankers during face processing: a visual crowding study

The modulations of visual awareness on the processing of emotional faces have been mainly investigated in masking experiments where stimuli were presented for different durations as an integral process to the masking technique. In this visual crowding study, we manipulated the perceivability of a central crowded face (either a fearful or a neutral face) by varying the similarity between the central face and the surrounding flanker stimuli. We presented participants with pairs of visual clutters and recorded their electroencephalography during an emotion judgement task. In an upright flanker condition where both the target face and flanker faces were upright faces (high similarity), participants were less likely to report seeing the central target face, and their P300 was weakened, compared to a scrambled flanker condition where scrambled face images were used as flankers (low similarity). Additionally, at around 120ms post-stimulus, a posterior negativity was found for the upright flanker condition, compared to the scrambled flanker condition, however only for fearful face targets. We concluded that early neural responses seem to be affected by the perceptual characteristics of both target and flanker stimuli whereas neural activity at a later stage is associated with post-perceptual evaluation of the stimuli in this visual crowding paradigm.

neuroscience↗

bioRxiv2023

Faces capture spatial attention only when we want them to: an inattentional blindness EEG study

Previous research on emotional face processing has shown that emotional faces such as fearful faces may be processed without visual awareness. However, evidence for nonconscious attention capture by fearful faces is limited. In fact, studies using sensory manipulation of awareness (e.g., backward masking paradigms) have shown that fearful faces do not attract attention during subliminal viewings nor when they were task-irrelevant. Here, we used a three-phase inattentional blindness paradigm and electroencephalography to examine whether faces (fearful and neutral) capture attention under different conditions of awareness and task-relevancy. We found that the electrophysiological marker for attention capture, the N2-posterior-contralateral (N2pc), was elicited by face stimuli only when participants were aware of the faces and when they were task-relevant (phase 3). When participants were unaware of the presence of faces (phase 1) or when the faces were irrelevant to the task (phase 2), no N2pc was observed. Together with our previous work, we concluded that fearful faces, or faces in general, do not attract attention unless we want them to.

neuroscience↗

bioRxiv2023

Attentional capture by fearful faces requires consciousness and is modulated by task-relevancy: a dot-probe EEG study

In the current EEG study, we used a dot-probe task in conjunction with backward masking to examine the neural activity underlying awareness and spatial processing of fearful faces and the neural processes for subsequent cued spatial targets. We presented face images under different viewing conditions (subliminal and supraliminal) and manipulated the relation between a fearful face in the pair and a subsequent target. Through both mass univariate analysis and multivariate pattern analysis, we found that fearful faces can be processed to an extent where they attract spatial attention only when they are presented supraliminally and when they are task-relevant. The spatial attention capture by fearful faces also modulated the processing of subsequent lateralised targets that were spatially congruent with the fearful face, in both behavioural and neural data. There was no evidence for nonconscious processing of the fearful faces in the current paradigm. We conclude that spatial attentional capture by fearful faces requires visual awareness and it is modulated by top-down task demands.

neuroscience↗

bioRxiv2023

The mechanosensitive ion channel Piezo1 contributes to ultrasound neuromodulation

Transcranial low-intensity ultrasound is a promising neuromodulation modality, with the advantages of non-invasiveness, deep penetration, and high spatiotemporal accuracy. However, the underlying biological mechanism of ultrasonic neuromodulation remains unclear, hindering the development of efficacious treatments. Here, the well-known Piezo1, was studied through a conditional knockout mouse model as a major molecule for ultrasound neuromodulation ex vivo and in vivo. We showed that Piezo1 knockout in the right motor cortex of mice significantly reduced ultrasound-induced neuronal calcium responses, limb movement and muscle EMG responses. We also detected higher Piezo1 in the central amygdala (CEA) which were found more sensitive to ultrasound stimulation than that of cortex. Knocking out the Piezo1 in CEA neurons showed a significant reduction of response under ultrasound stimulation while knocking out astrocytic Piezo1 showed no obvious changes in neuronal responses. Additionally, we excluded an auditory confound by monitoring auditory cortical activation and using smooth waveform ultrasound with randomized parameters to stimulate P1KO ipsilateral and contralateral regions of the same brain and recording evoked movement in the corresponding limb. Thus, we demonstrate that Piezo1 is functionally expressed in different brain regions, and that it is an important mediator of ultrasound neuromodulation in the brain, laying the ground for further mechanistic studies of ultrasound.

neuroscience↗

bioRxiv2023

ATP-releasing SWELL1 channel in spinal microglia contributes to neuropathic pain

Following peripheral nerve injury, extracellular ATP-mediated purinergic signaling is crucial for spinal cord microglia activation and neuropathic pain. However, the mechanisms of ATP release remain poorly understood. Here, we show that volume-regulated anion channel (VRAC) is an ATP-releasing channel and is activated by inflammatory mediator sphingosine-1-phosphate (S1P) in microglia. Mice with microglia-specific deletion of Swell1 (also known as Lrrc8a), a VRAC essential subunit, had reduced peripheral nerve injury-induced increase in extracellular ATP in spinal cord. The mutant mice also exhibited decreased spinal microgliosis, dorsal horn neuronal hyperactivity, and both evoked and spontaneous neuropathic pain-like behaviors. We further performed high-throughput screens and identified an FDA-approved drug dicumarol as a novel and potent VRAC inhibitor. Intrathecal administration of dicumarol alleviated nerve injury-induced mechanical allodynia in mice. Our findings suggest that ATP-releasing VRAC in microglia is a key spinal cord determinant of neuropathic pain and a potential therapeutic target for this debilitating disease.

physiology↗

bioRxiv2022

A patterned human heart tube organoid model generated by pluripotent stem cell self-assembly

Human pluripotent stem cells can recapitulate significant features of mammalian organ development in vitro, including key aspects of heart development. We hypothesized that the organoids thus created can be made substantially more relevant by mimicking aspects of in utero gestation, leading to higher physiological and anatomical resemblance to their in vivo counterparts. Here, we report steps towards generating developmentally inspired maturation methodologies to differentiate early human heart organoids into patterned heart-tube-like structures in a reproducible and high-throughput fashion by complete self-organization. The maturation strategy consists of the controlled and stepwise exposure to metabolic (glucose, fatty acids) and hormonal signals (T3, IGF-1) as present during early heart development. These conditions elicit important transcriptomic, cellular, morphological, metabolomic, and functional changes over a 10-day period consistent with continuously increasing heart complexity, maturation, and patterning. Our data reveals the emergence of atrial and ventricular cardiomyocyte populations, valvular cells, epicardial cells, proepicardial-derived cells, endothelial cells, stromal cells, conductance cells, and cardiac progenitors, all of them cell types present in the primitive heart tube. Anatomically, the organoids elongate and develop well-differentiated atrial and ventricular chambers with compacted myocardial muscle walls and a proepicardial organ. For the first time in a completely self-organizing heart organoid, we show anterior-posterior patterning due to an endogenous retinoic acid gradient originating at the atrial pole, where proepicardial and atrial populations reside, mimicking the developmental process present within the primitive heart tube. Collectively, these findings highlight the ability of self-organization and developmental maturation strategies to recapitulate human heart development. Our patterned human heart tube model constitutes a powerful in vitro tool for dissecting the role of different cell types and genes in human heart development, as well as disease modeling congenital heart defects, and represents a step forward in creating fully synthetic human hearts.

bioengineering↗

bioRxiv2022

Decoding Neural Patterns for the Processing of Fearful Faces under Different Visual Awareness Conditions: A Multivariate Pattern Analysis

Mixed findings have been reported for the nonconscious processing of fearful faces. Here, we used multivariate pattern analysis on electroencephalography data from three backward masking experiments to decode the conscious and nonconscious processing of fearful faces. Three groups of participants were shown pairs of faces that were presented either subliminally (16 ms) or supraliminally (266 ms) and were required to complete tasks where the face stimuli were either task-relevant (Experiment 1) or task-irrelevant (Experiments 2 and 3). We decoded the neural activity to examine the temporal dynamics of visual awareness, and to investigate whether the presence and location of a fearful face were processed when levels of awareness varied. The results reveal that the spatial location of fearful faces can be decoded from neural patterns only when they are consciously seen and relevant to participants task. Nevertheless, the processing of the mere presence of fearful faces can occur in the absence of visual awareness, and the related neural patterns can be generalised to the conscious, non-spatial processing of fearful faces. Additionally, the flexibility of spatial attention seems to modulate the processing of fearful faces.

neuroscience↗

bioRxiv2022

Now you see it: fixation-related electrical potentials during a free visual search task reveal the timing of visual awareness

It has been repeatedly claimed that emotional faces capture attention readily, and that they are processed without awareness. Yet some observations cast doubt on these assertions. Part of the problem may lie in the experimental paradigms employed. Here, we used a free viewing visual search task and simultaneously recorded electroencephalography and eye-movements. Fixation-related potentials were computed for fearful and neutral facial expressions, and the electrical response compared when participants were aware or unaware of the fixated stimulus. We showed that the P300 increased across repeated fixations on the unseen targets, culminating in a conscious report, likely reflecting evidence accumulation. Awareness of the stimulus was associated with electrical changes emerging at around 130 ms, with emotions of the stimulus being dissociated only after awareness had arisen. These results suggest that the earliest electrical correlate of awareness emerges at around 130 ms in visual search and that emotion processing requires visual awareness.

neuroscience↗