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Biology subjects

Zhao, H.

Publications and source records attributed to Zhao, H..

At least 253 records · Page 14Linked to original sources

Brain implantation of tissue-level-soft bioelectronics 1 via embryonic development

The design of bioelectronics capable of stably tracking brain-wide, single-cell, and millisecond-resolved neural activities in the developing brain is critical to the study of neuroscience and neurodevelopmental disorders. During development, the three-dimensional (3D) structure of the vertebrate brain arises from a 2D neural plate1,2. These large morphological changes previously posed a challenge for implantable bioelectronics to track neural activity throughout brain development3-9. Here, we present a tissue-level-soft, sub-micrometer-thick, stretchable mesh microelectrode array capable of integrating into the embryonic neural plate of vertebrates by leveraging the 2D-to-3D reconfiguration process of the tissue itself. Driven by the expansion and folding processes of organogenesis, the stretchable mesh electrode array deforms, stretches, and distributes throughout the entire brain, fully integrating into the 3D tissue structure. Immunostaining, gene expression analysis, and behavioral testing show no discernible impact on brain development or function. The embedded electrode array enables long-term, stable, brain-wide, single-unit-single-spike-resolved electrical mapping throughout brain development, illustrating how neural electrical activities and population dynamics emerge and evolve during brain development.

bioengineering↗

Enhancing lipid production in plant cells through high-throughput genome editing and phenotyping via a scalable automated pipeline

Plant bioengineering is a time-consuming and labor-intensive process, with no guarantee of achieving the desired trait. Here we report a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB). FAST-PB achieves gene cloning, genome editing, and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrate that FAST-PB can streamline the Golden Gate cloning process, with the capacity to construct 96 vectors in parallel. To prove the concept, using FAST-PB, we first found that PEG2050 significantly increases transfection efficiency by over 45%. To validate the pipeline, we established a reporter-gene-free method for CRISPR editing via mutation of HCF136, affecting cellular chlorophyll fluorescence. Next, we applied this pipeline for lipid production and found that diverse lipids were significantly enhanced up to sixfold through introducing multi-gene cassettes via CRISPR activation, and regenerated plant using this platform. Lastly, we harnessed FAST-PB to achieve high-throughput single-cell lipid profiling through the integration of MALDI-MS with the biofoundry, and differentiated engineered and unengineered cells using the single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering, and change what is possibly using single-cell metabolomics in plants.

synthetic biology↗

Skeleton-forming responses of reef-building corals under ocean acidification

Ocean acidification is increasing in frequency and is considered one of the most important causes of severe damage to global coral reefs. Therefore, there is an urgent need to study the impact of acid stress on the growth patterns of major reef-building corals. Here, we studied the skeleton forming strategies of four widely distributed coral species in a simulated acidified habitat with a pH of 7.6-7.8. We reconstructed and visualized the skeleton building process, quantified elemental calcium loss, and determined gene expression changes. The results suggest that different reef-building corals have diverse growing strategies in acidified seawater. A unique cavity-like forming process starts from the inside of the skeletons of Acropora muricata, which sacrifices skeleton density to protect its polyp-canal system. The forming patterns in Pocillopora damicornis, Montipora capricornis, and M. foliosa were characterized by osteoporosis, exhibiting disordered skeletal structures, insufficient synthesis of adhesion proteins, and low bone mass, correspondingly. In addition, we found that skeletal areas near coral polyps suffered less and had later acidified damage than other skeletal areas in the colony. These results help to understand the skeleton-forming strategies of several major coral species under acid stress, thereby laying a foundation for coral reef protection and restoration under increasing ocean acidification.

ecology↗

CosGeneGate Selects Multi-functional and Credible Biomarkers for Single-cell Analysis

Selecting representative genes or marker genes to distinguish cell types is an important task in single-cell sequencing analysis. Although many methods have been proposed to select marker genes, the genes selected may have redundancy and/or do not show cell-type-specific expression patterns to distinguish cell types. Here we present a novel model, named CosGeneGate, to select marker genes for more effective marker selections. CosGeneGate is inspired by combining the advantages of selecting marker genes based on both cell-type classification accuracy and marker gene specific expression patterns. We demonstrate the better performance of the marker genes selected by CosGeneGate for various downstream analyses than the existing methods with both public datasets and newly sequenced datasets. The non-redundant marker genes identified by CosGeneGate for major cell types and tissues in human can be found at the website as follows: https://github.com/VivLon/CosGeneGate/blob/main/marker gene list.xlsx.

bioinformatics↗

Enhanced Thompson Sampling by Roulette Wheel Selection for Screening Ultra-Large Combinatorial Libraries

Chemical space exploration has gained significant interest with the increase in available building blocks, which enables the creation of ultra-large virtual libraries containing billions or even trillions of compounds. However, the challenge of selecting most suitable compounds for synthesis arises, and one such challenge is hit expansion. Recently, Thompson sampling, a probabilistic search approach, has been proposed by Walters et al. to achieve efficiency gains by operating in the reagent space rather than the product space. Here, we aim to address some of its shortcomings and propose optimizations. We introduce a warmup routine to ensure that initial probabilities are set for all reagents with a minimum number of molecules evaluated. Additionally, a roulette wheel selection is proposed with adapted stop criteria to improve sampling efficiency, and belief distributions of reagents are only updated when they appear in new molecules. We demonstrate that a 100% recovery rate can be achieved by sampling 0.1% of the fully enumerated library, showcasing the effectiveness of our proposed optimizations.

bioinformatics↗

Production of four-gene (GTKO/hCD55/hTBM/hCD39)-edited donor pigs and kidney xenotransplantation

BackgroundThe number of multigene-modified donor pigs for xenotransplantation is increasing with the advent of gene editing technologies. However, which gene combination is suitable for which organ transplantation remains unclear. MethodsIn this study, we utilized CRISPR/Cas9 gene editing technology, PiggyBac transposon system and somatic cell cloning to construct GTKO/hCD55/hTBM/hCD39 four-gene-edited cloned (GEC) pigs and performed kidney transplantation from pig to rhesus monkey to evaluate the effectiveness of these GEC pigs. ResultsFirst, 107 cell colonies were obtained through drug selection, of which 7 were 4-GE colonies. Two colonies were selected for somatic cell nuclear transfer, resulting in 7 fetuses, of which 4 were GGTA1 biallelic knockout. Both fetuses had higher expression of hCD55, hTBM and hCD39. Therefore, these two fetuses were selected for two consecutive rounds of cloning, resulting in a total of 97 live piglets. After phenotype identification, the GGTA1 gene of these pigs was inactivated, and hCD55, hTBM and hCD39 were expressed in cells and multiple tissues. Furthermore, the numbers of monkey IgM and IgG binding to the peripheral blood mononuclear cells (PBMCs) of the 4-GEC pigs were markedly reduced. Moreover, 4-GEC porcine PBMCs had greater survival rates than those from wild-type pigs through complement-mediated cytolysis assays. In pig-to-monkey kidney xenotransplantation, the kidney xenograft successfully survived for 11 days. All physiological and biochemical indicators were normal, and no hyperacute rejection or coagulation abnormalities were found after transplantation. ConclusionThese results indicate that the GTKO/hCD55/hTBM/hCD39 four-gene modification effectively alleviates immune rejection, and the pig kidney can functionally support the recipient monkeys life.

genetics↗

Production and functional verification of 8-gene (GGTA1, CMAH, β4GalNT2, hCD46, hCD55, hCD59, hTBM, hCD39)-edited donor pigs for xenotransplantation

Gene-edited pig-to-human xenotransplantation continues to make breakthroughs and is expected to enter clinic to solve the global shortage of donor organs. However, which gene combination is suitable for which organ transplantation remains unclear. In this study, we utilized CRISPR/Cas9 gene editing technology, PiggyBac transposon system and somatic cell cloning to construct GTKO/CMAHKO/{beta}4GalNT2KO/hCD46/hCD55/hCD59/hCD39/hTBM 8 gene-edited cloned (GEC) donor pigs, and performed pig to non-human primate (NHP) transplantation to evaluate the effectiveness of these GEC pigs. The multiple vectors were co-transfected into fetal fibroblasts of Diannan miniature pig with O blood type, and 25 colonies were screened out, and one of them carried GGTA1, CMAH and {beta}4GalNT2 biallelic knockout and integration of hCD46, hCD55, hCD59, hTBM and hCD39 genes, which was used as a donor cell for cloning, and a 33-day-old viable fetus was obtained. The fetus was identified and confirmed for normal karyotype and the absence of three xenogeneic antigens -Gal, Neu5Gc and Sda, and expression of hCD46, hCD55, hCD59, hTBM and hCD39 genes, then the recloning was carried out and 28 cloned piglets were obtained by natural delivery. Molecular identification at DNA, mRNA and protein levels showed that 8 gene editing (GE) was successful in these GEC piglets. Moreover, antigen-antibody binding assay and complement-dependent cytotoxicity assay demonstrated that 8GE effectively reduced the immune incompatibility and kidney xenograft survived up to 15 and 17 days into two NHPs, respectively. During this period, the recipient serum antibodies IgA and IgM, complements C3 and C4, coagulation indicators PT, APTT, TT and FIB, as well as most electrolytes and liver function indicators remained relatively stable. The 24-hour urine output and serum creatinine remained normal at a period of post-transplantation. These results indicated that the 8GEC pigs effectively alleviated immune rejection and exerted life-supporting kidney function in the recipient.

genetics↗

Unraveling the impact of hyperleptinemia on female reproduction: Insights from transgenic pig model

BackgroundInfertility is a growing global health concern affecting millions of couples worldwide. Among several factors, an extreme body weight adversely affects reproductive functions. Leptin is a well-known adipokine that serves as an endocrine signal between adiposity and fertility. However, the exact mechanisms underlying the effects of high leptin on female reproduction remain unclear. MethodsTransgenic pig overexpressing leptin (11) were produced by back cross and screened for leptin overexpression, and the growth curve, fat deposition, reproductive performance, apoptosis, serum hormones and cholesterol production, RNA sequencing, and single nucleus RNA sequencing of the leptin-overexpressed pigs and control group were evaluated. ResultsTransgenic pig overexpressing leptin (11) were obtained, which exhibited significantly reduced body weight, body size, and back fat thickness. These pigs manifested late onset of puberty (327{+/-}48.5 vs 150{+/-}6.5 days), irregular estrous behavior characterized by increased inter-estrous interval (28.1{+/-}4.2 vs 21.3 {+/-} 0.9 days), and more numbers of mating until pregnancy (at least 3 times). This reproductive impairment in leptin pigs was related to hormonal imbalances characterized by increased levels of FSH, LH, prolactin, E2, P4, and TSH, altered steroidogenesis such as increased levels of serum CE along with steroidogenic markers (STAR, CYP19A), and ovarian dysfunctions manifested by neutrophilic infiltration and low expression of caspase-3 positive cells on leptin pigs ovary. Meanwhile, bulk RNA sequencing of the ovaries also revealed neutrophilic infiltration followed by upregulation of inflammation-related genes. Further, leptin overexpression triggered immune response, suppressed follicle development and luteinization, imposing metabolism dysfunction and hormone imbalance in the ovary by single-nucleus RNA sequencing (snRNA-seq). ConclusionLow body weight in leptin overexpression pigs adversely affects reproductive performance, causing delayed puberty, irregular estrous cycles, and reduced breeding efficiency. This is linked to metabolic imbalances, increased immune response, and altered ovarian functions. This study provided a theoretical basis for the complex mechanisms underlying leptin, and infertility by employing leptin-overexpressed female pigs.

genetics↗

Ferroptosis mediates the progression of hyperuricemic nephropathy by activating RAGE signaling

Hyperuricemic nephropathy (HN) represents a prevalent complication arising from hyperuricemia, typified by tubular dysfunction, inflammation, and progressive renal fibrosis, whose pathogenic mechanisms remain enigmatic. Ferroptosis, a newly elucidated iron-dependent form of regulated cell death, plays a role in various disease states. However, its involvement in HN has seldom been explored. In this study, we observed indications of ferroptosis in the renal tissues of urate oxidase knockout (UOX-/-) mice, a model of hyperuricemia, as evidenced by increased iron deposition and reduced expression of glutathione peroxidase 4 (GPX4). These findings suggest a substantial role of ferroptosis in the pathogenesis of HN. To further explore this hypothesis, UOX-/- mice were administered Ferrostatin-1, a known inhibitor ferroptosis. This treatment markedly ameliorated tubular injury, necrosis, and inflammatory cell infiltration, mitigated renal fibrosis, reinstated the expression of proteins associated with ferroptosis in renal tissues, and reduced iron overload, lipid peroxidation, and mitochondrial damage in UOX-/- mice. Additionally, we found that receptor for advanced glycation end products (RAGE) propagates ferroptosis-induced renal injury, inflammation and fibrosis, albeit without directly facilitating ferroptosis. Finally, ferroptosis and RAGE upregulation were validated in renal tissues of patients with hyperuricemia-related kidney disease. Collectively, our research elucidates the critical contribution of ferroptosis to HN pathogenesis, indicating that therapeutic strategies targeting ferroptosis and the related RAGE signaling may offer novel therapeutic approaches for managing this condition.

ecology↗

Intestinal microbiome dysbiosis increases Mycobacteria pulmonary colonization in mice by regulating the Nos2-associated pathways

AbstractIncreasing researches reveal gut microbiota was associated with the development of tuberculosis. How to prevent or reduce Mycobacterium tuberculosis colonization in the lungs is a key measure to prevent tuberculosis. However, the data on gut microbiota preventing Mycobacterium colonization in the lungs were scarce. Here, we established the clindamycin-inducing intestinal microbiome dysbiosis and fecal microbial transplantation models in mice to identify gut microbiotas effect on Mycobacteriums colonization in the mouse lungs and explore its potential mechanisms. The results showed that clindamycin treatment altered the diversity and composition of the intestinal bacterial and fungal microbiome, weakened the trans-kingdom network interactions between bacteria and fungi, and induced gut microbiome dysbiosis in the mice. Gut microbiota dysbiosis increases intestinal permeability and enhances the susceptibility of Mycobacterium colonization in the lungs of mice. The potential mechanisms were gut microbiota dysbiosis altered the lung transcriptome and increased Nos2 expression through the "gut-lung axis". Nos2 high expression disrupts the intracellular antimicrobial and anti-inflammatory environment by increasing the concentration of NO, decreasing the levels of ROS and Defb1 in the cells, and resulting in promoting Mycobacteria colonization in the lungs of mice. The present study raises a potential strategy for reducing the risks of Mycobacteria infections and transmission by regulating the gut microbiome balance.

microbiology↗

Singular Odorant Receptor Expression Orchestrated by Promoter Activation Specificity in Apis Mellifera Olfactory Sensory Neurons

Honeybee, positioned as an outgroup of flies and mosquitos, have exhibited intriguing duplications and expansions of OR genes in genomic studies. However, little is known about how the OR genes are expressed and regulated in honeybee olfactory sensory neurons (OSNs). In this study, we utilized a single-cell multi-omics approach to profile the transcriptome and chromatin accessibility in Apis mellifera antennal nuclei, aiming to elucidate OR gene expression and its underlying regulatory mechanisms. Our systematical analysis unveiled a similar singular expression pattern of ligand-specific receptors in Apis mellifera OSNs, parallel with those observed in Drosophila melanogaster. Mechanistically, we discovered that promoter activation of OR genes orchestrates receptor expression patterns. For instance, although multiple adjacent OR genes are co-expressed with a single active promoter through polycistronic transcription, only the first OR gene could produce functional receptor protein, as supported by transcriptome quantification in OSNs. Additionally, we found that co-expression of receptor proteins might occur only when co-expressed OR genes possess multiple accessible promoters. This scenario is less common than expected, considering the number and evolutionary age of OR genes in Apis mellifera, suggesting a selection favoring the specialization of rapidly expanded OR genes in Apis mellifera. Overall, our study provides significant insights into the insect olfaction system and the regulatory mechanisms of OR genes expression.

neuroscience↗

Generators of the frequency-following response in the subthalamic nucleus: implications for non-invasive deep brain stimulation

While Deep Brain Stimulation (DBS) is effective treatment for several movement disorders, non-invasive stimulation modes have major clinical relevance. We report on a novel method holding potential for non-invasive subthalamic nucleus (STN) stimulation. We used an auditory frequency-following response task (FFR), a popular tool for studying the auditory brainstem as the neural response in the cortical and midbrain generator, as it precisely reflects the ongoing dynamics of a speech or non-speech sound. We recorded EEG and DBS electrodes from 5 patients, in 4 from the STN, and one from the anterior thalamus and a number of cortical and subcortical areas located in the hippocampus and frontal regions, during an FFR at a frequency higher than the upper limit of phase-locking in the cortex (333Hz). Our results revealed a neural response local to the STN, but not other structures. This finding is novel. Auditory perception in the basal ganglia is rather unexplored, and the STN generator of the FFR has likely gone unseen due to the limitations of our tools and research focus. The potential clinical implications are far-reaching. Future research should investigate whether auditory stimuli at common electrical stimulation frequencies and waveforms of electrical DBS stimulation can induce clinical improvement.

neuroscience↗

Curved light sheet microscopy for centimeter-scale cleared tissues imaging

Imaging large cleared tissues requires scaling the throughput of imaging techniques. Here we introduce curved light sheet microscope to perform optical sectioning with curved light sheets. This concept addresses the long-standing field curvature problem and lowers the barriers in designing high-throughput objectives. Leveraging a customized objective, the curved light sheet microscope achieves diffraction-limited resolution (1.0 m laterally and 2.5 m axially) and uniform contrast over a field of view of more than 1 x 1 cm2 and is compatible with various tissue clearing techniques. Imaging an entire intact cleared mouse brain at 0.625 x 0.625 x 1.25 m3 voxel size takes less than 3 hours and image tiling is not required. We share full optics description of the objective and report imaging neuronal and vascular networks and tracing brain-wide long-distance axonal projections in intact mouse brains.

bioengineering↗

The robust, high-throughput, and temporally regulated roxCre and loxCre reporting systems for genetic modifications in vivo

Cre-loxP technology, a cornerstone in fate mapping and in vivo gene function studies, faces challenges in achieving precise and efficient conditional mutagenesis through inducible systems. This study introduces two innovative genetic tools designed to overcome these limitations. The first, roxCre, enables DreER-mediated Cre release, paving the way for intersectional genetic manipulation that permits increased precision and efficiency. The second, loxCre, facilitates conditional gene targeting by allowing CreER lines to induce Cre expression with significantly enhanced efficiency. These tools incorporate a fluorescent reporter for genetic lineage tracing, simultaneously revealing efficient gene knockout in cells marked by the reporter. These strategies hold great potential for precise and efficient exploration of lineage-specific gene functions, marking a significant advancement in genetic research methodologies.

genetics↗

Plant Accessible Tissue Clearing Solvent System (PATCSOS) for 3-D Imaging of Whole Plants

Tissue clearing is a technique to make the inner structure of opaque tissue visible to achieve 3-dimensional (3-D) tissue imaging by unifying the refractive indexes of most of the cell components. Tissue clearing is widely used in animal tissue imaging, where whole body 3-D imaging has been realized. However, it has not been widely used in plant research. Most plant tissue clearing protocols have their disadvantages, including low efficiency, not being fluorescence-friendly and poor transparency on tissues with a high degree of lignification. In this work, we developed a new plant tissue clearing method for whole plant imaging, named Plant Accessible Tissue Clearing Solvent System (PATCSOS), which was based on the Polyethylene Glycol-associated Solvent System (PEGASOS). The PATCSOS method realized extensive transparency of plant tissues, including the flower, leaf, stem, root, and seed of Arabidopsis thaliana, with high efficiency. The PATCSOS method consists of four main steps: fixation, decolorization/delipidation, dehydration, and clearing. Subsequently a rapid and efficient clearing of mature plant tissue can be achieved. With PATCSOS, we can image Arabidopsis seedling in their entirety in 3-D using endogenous cellulose autofluorescence. Whats more, the PATCSOS method is compatible with fluorescence protein imaging and GUS staining, which greatly expands the applicability of this method. We also imaged intact Nicotiana benthamiana leaf and Zea mays embryos. Our results showed that the PATCSOS clearing method is an excellent tool to study plant development and cell biology.

plant biology↗

Gra-CRC-miRTar: The pre-trained nucleotide-to-graph neural networks to identify potential miRNA targets in colorectal cancer

Colorectal cancer (CRC) is the third most diagnosed cancer and the second deadliest cancer worldwide representing a major public health problem. In recent years, increasing evidence has shown that microRNA (miRNA) can control the expression of targeted human messenger RNA (mRNA) by reducing their abundance or translation, acting as oncogenes or tumor suppressors in various cancers, including CRC. Due to the significant up-regulation of oncogenic miRNAs in CRC, elucidating the underlying mechanism and identifying dysregulated miRNA targets may provide a basis for improving current therapeutic interventions. In this paper, we proposed Gra-CRC-miRTar, a pre-trained nucleotide-to-graph neural network framework, for identifying potential miRNA targets in CRC. Different from previous studies, we constructed two pre-trained models to encode RNA sequences and transformed them into de Bruijn graphs. We employed different graph neural networks to learn the latent representations. The embeddings generated from de Bruijn graphs were then fed into a Multilayer Perceptron (MLP) to perform the prediction tasks. Our extensive experiments show that Gra-CRC-miRTar achieves better performance than other deep learning algorithms and existing predictors. In addition, our analyses also successfully revealed 172 out of 201 functional interactions through experimentally validated miRNA-mRNA pairs in CRC. Collectively, our effort provides an accurate and efficient framework to identify potential miRNA targets in CRC, which can also be used to reveal miRNA target interactions in other malignancies, facilitating the development of novel therapeutics.

bioinformatics↗

BAITSAO: Building A Foundation Model for Drug Synergy Analysis Powered by Language Models

Drug synergy prediction is a challenging and important task in the treatment of complex diseases including cancer. In this manuscript, we present a novel unified Model, known as BAITSAO, for tasks related to drug synergy prediction with a unified pipeline to handle different datasets. We construct the training datasets for BAITSAO based on the context-enriched embeddings from Large Language Models for the initial representation of drugs and cell lines. After demonstrating the relevance of these embeddings, we pre-train BAITSAO with a large-scale drug synergy database under a multi-task learning framework with rigorous selections of tasks. We demonstrate the superiority of the model architecture and the pre-trained strategies of BAITSAO over other methods through comprehensive benchmark analysis. Moreover, we investigate the sensitivity of BAITSAO and illustrate its unique functions including new drug discoveries, drug combinations-gene interaction, and multi-drug synergy predictions.

bioinformatics↗

The neuroendocrine transition in prostate cancer is dynamic and dependent on ASCL1

Lineage plasticity is a recognized hallmark of cancer progression that can shape therapy outcomes. The underlying cellular and molecular mechanisms mediating lineage plasticity remain poorly understood. Here, we describe a versatile in vivo platform to identify and interrogate the molecular determinants of neuroendocrine lineage transformation at different stages of prostate cancer progression. Adenocarcinomas reliably develop following orthotopic transplantation of primary mouse prostate organoids acutely engineered with human-relevant driver alterations (e.g., Rb1-/-; Trp53-/-; cMyc+ or Pten-/-; Trp53-/-; cMyc+), but only those with Rb1 deletion progress to ASCL1+ neuroendocrine prostate cancer (NEPC), a highly aggressive, androgen receptor signaling inhibitor (ARSI)-resistant tumor. Importantly, we show this lineage transition requires a native in vivo microenvironment not replicated by conventional organoid culture. By integrating multiplexed immunofluorescence, spatial transcriptomics and PrismSpot to identify cell type-specific spatial gene modules, we reveal that ASCL1+ cells arise from KRT8+ luminal epithelial cells that progressively acquire transcriptional heterogeneity, producing large ASCL1+;KRT8- NEPC clusters. Ascl1 loss in established NEPC results in transient tumor regression followed by recurrence; however, Ascl1 deletion prior to transplantation completely abrogates lineage plasticity, yielding adenocarcinomas with elevated AR expression and marked sensitivity to castration. The dynamic feature of this model reveals the importance of timing of therapies focused on lineage plasticity and offers a platform for identification of additional lineage plasticity drivers.

cell biology↗