Biology subjects

Qi, Y.

Publications and source records attributed to Qi, Y..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Voltage dynamics of dendritic integration and back-propagation in vivo

Neurons integrate synaptic inputs within their dendrites and produce spiking outputs, which then propagate down the axon and back into the dendrites where they contribute to plasticity. Mapping the voltage dynamics in dendritic arbors of live animals is crucial for understanding neuronal computation and plasticity rules. Here we combine patterned channelrhodopsin activation with dual-plane structured illumination voltage imaging, for simultaneous perturbation and monitoring of dendritic and somatic voltage in Layer 2/3 pyramidal neurons in anesthetized and awake mice. We examined the integration of synaptic inputs and compared the dynamics of optogenetically evoked, spontaneous, and sensory-evoked back-propagating action potentials (bAPs). Our measurements revealed a broadly shared membrane voltage throughout the dendritic arbor, and few signatures of electrical compartmentalization among synaptic inputs. However, we observed spike rate acceleration-dependent propagation of bAPs into distal dendrites. We propose that this dendritic filtering of bAPs may play a critical role in activity-dependent plasticity.

neuroscience↗

bioRxiv2023

Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells

CRISPR-Cas9 genome editing has enabled advanced T cell therapies, but occasional loss of the targeted chromosome remains a safety concern. To investigate whether Cas9-induced chromosome loss is a universal phenomenon and evaluate its clinical significance, we conducted a systematic analysis in primary human T cells. Arrayed and pooled CRISPR screens revealed that chromosome loss was generalizable across the genome and resulted in partial and entire loss of the chromosome, including in pre-clinical chimeric antigen receptor T cells. T cells with chromosome loss persisted for weeks in culture, implying the potential to interfere with clinical use. A modified cell manufacturing process, employed in our first-in-human clinical trial of Cas9-engineered T cells,1 dramatically reduced chromosome loss while largely preserving genome editing efficacy. Expression of p53 correlated with protection from chromosome loss observed in this protocol, suggesting both a mechanism and strategy for T cell engineering that mitigates this genotoxicity in the clinic.

cell biology↗

bioRxiv2023

EGGNet, a generalizable geometric deep learning framework for protein complex pose scoring

Computational prediction of molecule-protein interactions has been key for developing new molecules to interact with a target protein for therapeutics development. Past work includes two independent streams of approaches: (1) predicting protein-protein interactions (PPI) between naturally occurring proteins and (2) predicting the binding affinities between proteins and small molecule ligands (aka drug target interaction, or DTI). Studying the two problems in isolation has limited the ability of these computational models to generalize across the PPI and DTI tasks, both of which ultimately involve non-covalent interactions with a protein target. In this work, we developed an Equivariant Graph of Graphs neural Network (EGGNet), a geometric deep learning framework for molecule-protein binding predictions that can handle three types of molecules for interacting with a target protein: (1) small molecules, (2) synthetic peptides and (3) natural proteins. EGGNet leverages a graph of graphs (GoGs) representation constructed from the molecule structures at atomic-resolution and utilizes a multi-resolution equivariant graph neural network (GNN) to learn from such representations. In addition, EGGNet leverages the underlying biophysics and makes use of both atom- and residue-level interactions, which improve EGGNets ability to rank candidate poses from blind docking. EGGNet achieves competitive performance on both a public proteinsmall molecule binding affinity prediction task (80.2% top-1 success rate on CASF-2016) and an synthetic protein interface prediction task (88.4% AUPR). We envision that the proposed geometric deep learning framework can generalize to many other protein interaction prediction problems, such as binding site prediction and molecular docking, helping accelerate protein engineering and structure-based drug development.

synthetic biology↗

bioRxiv2023

Aging Atlas Reveals Cell-Type-Specific Regulation of Pro-longevity Strategies

Organism aging occurs at the multicellular level; however, how pro-longevity mechanisms slow down aging in different cell types remains unclear. We generated single-cell transcriptomic atlases across the lifespan of Caenorhabditis elegans under different pro-longevity conditions (http://mengwanglab.org/atlas). We found cell-specific, age-related changes across somatic and germ cell types and developed transcriptomic aging clocks for different tissues. These clocks enabled us to determine tissue-specific aging-slowing effects of different pro-longevity mechanisms, and identify major cell types sensitive to these regulations. Additionally, we provided a systemic view of alternative polyadenylation events in different cell types, as well as their cell-type-specific changes during aging and under different pro-longevity conditions. Together, this study provides molecular insights into how aging occurs in different cell types and how they respond to pro-longevity strategies.

developmental biology↗

bioRxiv2023

Root associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly influenced the root-associated bacterial communities and root metabolite composition of sorghum. Sorghum NUE was positively correlated with the bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to N stress and indicate that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our study provides new insight into the links between host genetic regulation of root metabolites and root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.

microbiology↗

bioRxiv2023

An Unexpected Role of Neutrophils in Clearing Apoptotic Hepatocytes In Vivo

Billions of apoptotic cells are removed daily in a human adult by professional phagocytes (e.g. macrophages) and neighboring nonprofessional phagocytes (e.g. stromal cells). Despite being a type of professional phagocyte, neutrophils are thought to be excluded from apoptotic sites to avoid tissue inflammation. Here we report a fundamental and unexpected role of neutrophils as the predominant phagocyte responsible for the clearance of apoptotic hepatic cells in the steady state. In contrast to the engulfment of dead cells by macrophages, neutrophils burrowed directly into apoptotic hepatocytes, a process we term perforocytosis, and ingested the effete cells from the inside. The depletion of neutrophils caused defective removal of apoptotic bodies, induced tissue injury in the mouse liver and led to the generation of autoantibodies. Human autoimmune liver disease showed similar defects in the neutrophil-mediated clearance of apoptotic hepatic cells. Hence, neutrophils possess a specialized immunologically silent mechanism for the clearance of apoptotic hepatocytes through perforocytosis, and defects in this key housekeeping function of neutrophils contribute to the genesis of autoimmune liver disease.

physiology↗

bioRxiv2023

TFEB-vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy

Transcription factor EB (TFEB) mediates gene expression through binding to the Coordinated Lysosome Expression And Regulation (CLEAR) sequence. TFEB targets include subunits of the vacuolar ATPase (v-ATPase) essential for lysosome acidification. Single nucleus RNA-sequencing (snRNA-seq) of wild-type and PS19 (Tau) transgenic mice identified three unique microglia subclusters in Tau mice that were associated with heightened lysosome and immune pathway genes. To explore the lysosome-immune relationship, we specifically disrupted the TFEB-v-ATPase signaling by creating a knock-in mouse line in which the CLEAR sequence of one of the v-ATPase subunits, Atp6v1h, was mutated. We show that the CLEAR mutant exhibited a muted response to TFEB, resulting in impaired lysosomal acidification and activity. Crossing the CLEAR mutant with Tau mice led to higher tau pathology but diminished microglia response. These microglia were enriched in a subcluster low in mTOR and HIF-1 pathways and was locked in a homeostatic state. Our studies demonstrate a physiological function of TFEB-v-ATPase signaling in maintaining lysosomal homoeostasis and a critical role of the lysosome in mounting a microglia and immune response in tauopathy and Alzheimers disease.

neuroscience↗

bioRxiv2023

Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA polyubiquitination

The unique arginine dependencies of cancer cell proliferation and survival creates metabolic vulnerability. Here, we investigate the impact of extracellular arginine availability on DNA replication and genotoxic resistance. Using DNA combing assays, we find that when extracellular arginine is limited, cancer cells are arrested at S-phase and DNA replication forks slow or stall instantly until arginine is re-supplied. The translation of new histone H4 is arginine-dependent and impacts DNA replication and the expression of newly synthesized histone H4 is reduced in the avascular nutrient-poor breast cancer xenograft tumor cores. Furthermore, we demonstrate that increased PCNA occupancy and HLTF-catalyzed PCNA K63-linked polyubiquitination protects arginine-starved cells from hydroxyurea-induced, DNA2-catalyzed nascent strand degradation. Finally, arginine-deprived cancer cells are tolerant to genotoxic insults in a PCNA K63-linked polyubiquitination-dependent manner. Together, these findings reveal that extracellular arginine is the "linchpin" for nutrient-regulated DNA replication. Such information could be leveraged to expand current modalities or design new drug targets against cancer.

cancer biology↗

bioRxiv2023

PLANET: A Multi-Objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction

Predicting protein-ligand binding affinity is a central issue in drug design. Various deep learning models have been developed in recent years to tackle this issue, but many of them merely focus on reproducing the binding affinity of known binders. In this study, we have developed a graph neural network model called PLANET (Protein-Ligand Affinity prediction NETwork). This model takes the graph-represented 3D structure of the binding pocket on the target protein and the 2D chemical structure of the ligand molecule as input, and it was trained through a multi-objective process with three related tasks, including deriving the protein-ligand binding affinity, protein-ligand contact map, and intra-ligand distance matrix. To serve those tasks, a large number of decoy non-binders were selected and added to the standard PDBbind data set. When tested on the CASF-2016 benchmark, PLANET exhibited a scoring power comparable to other deep learning models that rely on 3D protein-ligand complex structures as input. It also showed notably better performance in virtual screening trials on the DUD-E and LIT-PCBA benchmark. In particular, PLANET achieved comparable accuracy on LIT-PCBA as the conventional docking program Glide. However, it only took less than 1% of the computation time required by Glide to finish the same job because it did not perform exhaustive conformational sampling. In summary, PLANET exhibited a decent performance in binding affinity prediction as well as virtual screening, which makes it potentially useful for drug discovery in practice.

bioinformatics↗

bioRxiv2022

Abrupt shifts in the plant species richness and community composition along an aridity gradient in the Mongolian grasslands

Aridity, edaphic variables related to aridity, and livestock grazing are major drivers of plant community composition across dryland grasslands. With accounting these factors, little is known about differences in determinants and changing patterns along aridity gradients with different average of aridity. Thus, the comparative investigations of communities without and with grazing in semi-arid and arid regions are suitable to clarify the difference in compositional responses along aridity gradients between potential vegetations and degraded ones with grazing. We investigated compositional changes of communities without/with grazing in semi-arid (north) /arid (south) regions across Mongolia. The compositional changes based on Bray-Curtis dissimilarity were investigated by generalized dissimilarity modeling, including geographic distance, aridity, soil pH, and sand and clay contents as independent variables. The determinants and changing patterns of community composition were compared among the four groups. Aridity had significant impacts on community composition regardless of the regions and the absence/presence of grazing. However, without the dependency on grazing, the difference in response patterns was observed between the regions. The compositional change was steeper especially at the upper edge of aridity rather than the lower edge in the arid region. This indicates the vulnerability of plant communities to aridity shifts due to future climate change in desert steppe of Mongolia. In addition, regardless of the regions, the effects of soil pH on community composition were eliminated by grazing. Because soil pH indirectly affected by aridity shifts can have impacts on community composition of potential vegetations without grazing, the long-term monitoring of vegetation dynamics needs observations of both of communities without and with grazing.

ecology↗

bioRxiv2022

On the origin and evolution of the mosquito male-determining factor Nix

The mosquito family Culicidae is divided into two subfamilies named the Culicinae and Anophelinae. Nix, the dominant male-determining factor, has only been found in the culicines Aedes aegypti and Ae. albopictus, two important arboviral vectors that belong to the subgenus Stegomyia. Here we performed sex-specific whole-genome sequencing and RNAseq of divergent mosquito species and explored additional male-inclusive datasets to investigate the distribution of Nix. Except for the Culex genus, Nix homologs were found in all species surveyed from the Culicinae subfamily, including 12 additional species from three highly divergent tribes comprising 4 genera, suggesting Nix originated at least 133-165 MYA. Heterologous expression of one of three divergent Nix ORFs in Ae. aegypti resulted in partial masculinization of genetic females as evidenced by morphology and doublesex splicing. It is not clear whether insufficient transgene expression or sequence divergence or both are responsible for the lack of phenotype for the other two. Phylogenetic analysis suggests Nix is related to femaleless (fle), a recently described intermediate sex-determining factor found exclusively in anopheline mosquitoes. Nix from all species has a conserved structure, including three RNA-recognition motifs (RRMs), as does fle. However, Nix has evolved at a much faster rate than fle. The RRM3 of both Nix and fle are related to the single RRM of a widely distributed and conserved splicing factor transformer-2 (tra2). RRM3-based phylogenetic analysis suggests this domain in Nix and fle may have evolved from tra2 in a common ancestor of mosquitoes. Our results provide insights into the evolution of sex-determination and homomorphic sex chromosomes in mosquitoes, and will inform broad applications of mosquito-control strategies based on manipulating sex ratios towards the non-biting males.

evolutionary biology↗

bioRxiv2022

A bioelectrical phase transition patterns the first beats of a vertebrate heart

The heart is among the first organs to function in vertebrate development, but its transition from silent to beating has not been directly characterized. Using all-optical electrophysiology, we captured the very first zebrafish heartbeat and analyzed the development of cardiac excitability around this singular event. The first beats appeared suddenly and propagated coherently across the primordial heart. Targeted optogenetic perturbations mapped the development of excitability and conduction before and after the first heartbeats. Measured bioelectrical dynamics support a noisy saddle-node on invariant circle (SNIC) bifurcation as the critical phase transition that starts the heart. Simple models of this bifurcation quantitatively capture cardiac dynamics in space and time through early development, including coherent beating before transcriptional specification of pacemakers. Our work shows how gradual and largely asynchronous development of single-cell bioelectrical properties produces a stereotyped and robust tissue-scale transition from quiescence to coordinated beating.

developmental biology↗

bioRxiv2022

Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution

Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole aging Drosophila. We characterize 163 distinct cell types and perform an in-depth analysis of changes in tissue cell composition, gene expression, and cell identities. We further develop aging clock models to predict the fly age and show that ribosomal gene expression is a conserved predictive factor for age. Combining all aging features, we find unique cell type-specific aging patterns. This atlas provides a valuable resource for studying fundamental principles of aging in complex organisms.

developmental biology↗

bioRxiv2022

cpSRP54 and FtsH cooperate thylakoid membrane associated proteostasis during de-etiolation in Arabidopsis thaliana

The thylakoid membrane protein quality control, which requires the coordination of membrane protein translocation and degradation of unassembled proteins, determines the chloroplast development during de-etiolation. Despite numerous efforts, the regulation of this progress in land plants is largely unknown. Here, we reported the isolation and characterization of pga4 mutants with defects in chloroplast development during de-etiolation. Map-based cloning and complementation assay confirmed that PGA4 encodes the chloroplast signal recognition particle 54 kDa protein (cpSRP54). A heterogeneous LhcB2-GFP was generated as an indicative substrate for cpSRP54-mediated thylakoid translocation. LhcB2-GFP were not assembled into functional complexes, and degraded to a short form dLhcB2-GFP during de-etiolation, through an N-terminal degradation initiated on thylakoid membranes. Further biochemical and genetic evidences demonstrated that the degradation of LhcB2-GFP to dLhcB2-GFP was disrupted in pga4, and var2 mutants caused by mutations in the VAR2/AtFtsH2 subunit of thylakoid FtsH. The yeast two-hybrid assay showed that the N-terminus of LhcB2-GFP which was degraded consequently, interacts with the protease domain of VAR2/AtFtsH2 in yeasts. Moreover, the over-accumulated LhcB2-GFP in pga4 and var2, formed protein aggregates, which were insoluble in mild nonionic detergents. Genetically, cpSRP54 is a new suppressor locus for the leaf variegation phenotype of var2. Those together demonstrated the coordination of cpSRP54 and thylakoid FtsH in maintenance of thylakoid membrane protein quality control during the assembly of photosynthetic complexes, and provided a trackable substrate and product for monitoring the cpSRP54-dependent protein translocation and the FtsH-dependent protein degradation. One Sentence SummaryWe revealed the coordination of cpSRP54 and FtsH in thylakoid membrane protein quality control, and provided a trackable marker for monitoring the activity of cpSRP54 and thylakoid FtsH protease.

plant biology↗

bioRxiv2022

Revealing unexpected mechanisms of complex encoding but simple decoding in motor cortex via task-relevant neural signal distillation

In motor cortex, behaviorally-relevant neural responses are entangled with irrelevant signals, which complicates the study of encoding and decoding mechanisms. It remains unclear whether behaviorally-irrelevant signals could conceal some critical truth. One solution is to accurately separate behaviorally-relevant and irrelevant signals at both single-neuron and single-trial levels, but this approach remains elusive due to the unknown ground truth of behaviorally-relevant signals. Therefore, we propose a framework to define, extract, and validate behaviorally-relevant signals. Analyzing separated signals in three monkeys performing different reaching tasks, we found neural responses previously considered to contain little information actually encode rich behavioral information in complex nonlinear ways. These responses are critical for neuronal redundancy and reveal movement behaviors occupy a higher-dimensional neural space than previously expected. Surprisingly, when incorporating often-ignored neural dimensions, behaviorally-relevant signals can be decoded linearly with comparable performance to nonlinear decoding, suggesting linear readout may be performed in motor cortex. Our findings prompt that separating behaviorally-relevant signals may help uncover more hidden cortical mechanisms.

neuroscience↗

bioRxiv2022

Born with intronless ERF transcriptional factors: C4 photosynthesis inherits a legacy dating back 450 million years

The genus Flaveria, containing species at different evolutionary stages of the progression from C3 to C4 photosynthesis, is used as a model system to study the evolution of C4 photosynthesis. Here, we report chromosome-scale genome sequences for five Flaveria species, including C3, C4, and intermediate species. Our analyses revealed that both acquiring additional gene copies and recruiting ethylene responsive factor (ERF) cis-regulatory elements (CREs) contributed to the emergence of C4 photosynthesis. ERF transcriptional factors (TFs), especially intronless ERF TFs, were co-opted in dicotyledonous C4 species and monocotyledonous C4 species in parallel. These C4 species co-opted intronless ERF TFs originated from the Late Ordovician mass extinction that occurred [~]450 million years ago in coping with environmental stress. Therefore, this study demonstrated that intronless ERF TFs were acquired during the early evolution of plants and provided the molecular toolbox facilitating multiple subsequent independent evolutions of C4 photosynthesis.

evolutionary biology↗

bioRxiv2022

Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs

Blood vasculature represents a complex network of vessels with varying lengths and diameters that are precisely organized in space to allow proper tissue function. Light-sheet fluorescence microscopy (LSFM) is very useful to generate tomograms of tissue vasculature with high spatial accuracy. Yet, quantitative LSFM analysis is still cumbersome and available methods are restricted to single organs and advanced computing hardware. Here, we introduce VesselExpress, an automated software that reliably analyzes six characteristic vascular network parameters including vessel diameter in LSFM data on average computing hardware. VesselExpress is ~100 times faster than other existing vessel analysis tools, requires no user interaction, integrates batch processing, and parallelization. Employing an innovative dual Frangi filter approach we show that obesity induces a large-scale modulation of brain vasculature in mice and that seven other major organs differ strongly in their 3D vascular makeup. Hence, VesselExpress transforms LSFM from an observational to an analytical working tool.

bioinformatics↗

bioRxiv2022

Analysis and Exploration of the Implementation System of Mixed Ownership of Scientific and Technological Achievements in Colleges and Universities

Due to the backwardness of the management model and the rigidity of the system, the current service invention system restricts the transformation of scientific and technological achievements of colleges and universities to a certain extent. The mixed ownership system of university post achievements, which gives universities and inventors the freedom to dispose of the rights of scientific and technological achievements, and fundamentally stimulates the enthusiasm of all the achievement owners to transform their achievements, is an important exploration to promote the transformation of scientific and technological achievements. However, there are still many problems in the implementation of the mixed ownership of scientific and technological achievements in colleges and universities. Through the questionnaire survey and analysis, it is found that the four problems such as defects in the management system for the distribution of rights and interests of scientific and technological achievements, imperfect evaluation indicators of scientific and technological achievements, imbalance in the service system for the transformation of scientific and technological achievements, and lack of authoritative standards for the evaluation of the value of the transformation of scientific and technological achievements are the main problems hindering the development of mixed ownership of the current college post achievements. Based on the existing problems, it is proposed to continue to improve the management system, assessment system and service system of mixed ownership of scientific and technological achievements in colleges and universities. The research results can provide new evidence and policy enlightenment for the development of mixed ownership of scientific and technological achievements in colleges and universities in China.

scientific communication and education↗