Biology subjects

Wu, B.

Publications and source records attributed to Wu, B..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

High-resolution diploid 3D genome reconstruction using Pore-C data

In diploid organisms, spatial variations between homologous chromosomes are essential to many biological phenomena. Currently, it is still challenging to efficiently reconstruct a high-quality diploid 3D human genome. Here, we introduce Dip3D, reconstructing the diploid 3D human genome using Pore-C data of one sample. Dip3D has solved multiple problems in genome-wide SNV calling and haplo-tagging caused by the high sequencing error rates in Pore-C type data. Dip3D capitalizes on the high-order chromosomal interaction characteristics, enabling robust haplotype imputation and intricate haplotype-specific 3D structure discovery. Dip3D outperforms previous methods in data utilization rate, contact matrix resolution, and completeness by one order of magnitude. Moreover, Dip3D allows capturing haplotype high-order interactions that are unseen in Hi-C type data. We demonstrated the identified haplotype substructures such as Topologically Associating Domains (TADs) in the constructed 3D human genome, and unraveled connections between genic haplotype-specific high-order interactions and imbalanced allelic expression.

genomics↗

bioRxiv2023

Sex differences in discrimination behavior and orbitofrontal engagement during context-gated reward prediction

Animals, including humans, rely on contextual information to interpret ambiguous stimuli. Impaired context processing is a hallmark of several neuropsychiatric disorders, including schizophrenia, autism spectrum disorders, post-traumatic stress disorder, and addiction. While sex differences in the prevalence and manifestations of these disorders are well established, potential sex differences in context processing remain uncertain. Here we examined sex differences in the contextual control over cue-evoked reward seeking and its neural correlates, in rats. Male and female rats were trained in a bidirectional occasion-setting preparation in which the validity of two auditory reward-predictive cues was informed by the presence, or absence, of a visual contextual feature (LIGHT: X+ / DARK: X- / LIGHT: Y- / DARK: Y+). Females were significantly slower to acquire contextual control over cue-evoked reward seeking. However, once established, the contextual control over behavior was more robust in female rats; it showed less within-session variability (less influence of prior reward) and greater resistance to acute stress. This superior contextual control achieved by females was accompanied by an increased activation of the orbitofrontal cortex compared to males. Critically, these behavioral and neural sex differences were specific to the contextual modulation process and not observed in simple, context-independent, reward prediction tasks. These results indicate a sex-biased trade-off between the speed of acquisition and the robustness of performance in the contextual modulation of cued reward seeking. The different distribution of sexes along the fast learning {leftrightarrow} steady performance continuum might reflect different levels of engagement of the orbitofrontal cortex, and might have implications for our understanding of sex differences in psychiatric disorders.

neuroscience↗

bioRxiv2023

Structure-based self-supervised learning enables ultrafast prediction of stability changes upon mutation at the protein universe scale

Predicting free energy changes ({Delta}{Delta}G) is of paramount significance in advancing our comprehension of protein evolution and holds profound implications for protein engineering and pharmaceutical development. Traditional methods, however, often suffer from limitations such as sluggish computational speed or heavy reliance on biased training datasets. These challenges are magnified when aiming for accurate {Delta}{Delta}G prediction across the vast universe of protein sequences. In this study, we present Pythia, a self-supervised graph neural network tailored for zero-shot {Delta}{Delta}G predictions. In comparative benchmarks with other self-supervised pre-training models and force field-based methods, Pythia outshines its contenders with superior correlations while operating with the fewest parameters, and exhibits a remarkable acceleration in computational speed, up to 105-fold. The efficacy of Pythia is corroborated through its application in predicting thermostable mutations of limonene epoxide hydrolase (LEH) with significant higher experimental success rates. This efficiency propels the exploration of 26 million high-quality protein structures. Such a grand-scale application signifies a leap forward in our capacity to traverse the protein sequence space and potentially enrich our insights into the intricacies of protein genotype-phenotype relationships. We provided a web app at https://pythia.wulab.xyz for users to conveniently execute predictions. Keywords: self-supervised learning, protein mutation prediction, protein thermostability

bioinformatics↗

bioRxiv2023

Conditional Protein Denoising Diffusion Generates Programmable Endonucleases

Deep learning-based methods for generating functional proteins address the growing need for novel biocatalysts, allowing for precise tailoring of functionalities to meet specific requirements. This emergence leads to the creation of highly efficient and specialized proteins with wide-ranging applications in scientific, technological, and biomedical domains. This study establishes a pipeline for protein sequence generation with a conditional protein diffusion model, namely CPDiffusion, to deliver diverse sequences of proteins with enhanced functions. CPDiffusion accommodates protein-specific conditions, such as secondary structure and highly conserved amino acids (AAs). Without relying on extensive training data, CPDiffusion effectively captures highly conserved residues and sequence features for a specific protein family. We applied CPDiffusion to generate artificial sequences of Argonaute (Ago) proteins based on the backbone structures of wild-type (WT) Kurthia massiliensis Ago (KmAgo) and Pyrococcus furiosus Ago (PfAgo), which are complex multi-domain programmable endonucleases. The generated sequences deviate by up to nearly 400 AAs from their WT templates. Experimental tests demonstrated that the majority of generated proteins show unambiguous activity in DNA cleavage for both KmAgo and PfAgo, with many of them exhibiting superior activity as compared to the WT. These findings underscore CPDiffusions remarkable success rate to generate novel sequences for proteins of complex structures and functions in a single step with enhanced activity. This approach facilitates the design of enzymes with multi-domain molecular structures and intricate functions through in silico generation and screening, all accomplished without any supervision from labeled data.

bioengineering↗

bioRxiv2023

Evidence for gene transfer between mycoviruses and their host: Curvulaviridae as a case study

Gene transfer between distinct evolutionary lineages has been recognized as a frequent event occurring between viruses and their hosts. This phenomenon has been studied to some extent in animal and plant viruses, not so much in the case of mycoviruses, for which the evolutionary origins of their proteins remain poorly understood. In this study, we have tested the hypothesis of a mosaic origin for mycoviruses genomes, with the RNA-dependent RNA-polymerase (RdRp) being of viral origin and the coat protein (CP) resulting from one or more transfer events from the host genome. Firstly, phylogenetic trees were constructed for the RdRps and the CPs from a selection of viruses to address for possible incongruent evolutionary histories. Moreover, a PSI-BLAST search using the CP sequences from the different mycovirus groups retrieved hypothetical proteins (HP) with many orthologues in fungal genomes showing significant sequence homology with the CP from the members within the Curvulaviridae family. The structures of these HPs, predicted in silico using AlphaFold, tend to show high similarity with viral CPs suggesting the occurrence of gene transfer between viruses and fungi, although no clear function has been yet attributed to these genes in the host. Phylogenetic analyses suggest that this gene transfer could have occurred in multiple independent events. Additional selection analysis supports the notion that the most parsimonious explanation is the transfer of the HP from the host to an ancestral viral genome followed by fast evolution to accommodate the newly acquired protein to function as a CP.

microbiology↗

bioRxiv2023

Validation of human telomere length trans-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as novel human telomere length regulation genes

Telomere length genome-wide association studies (GWAS) have become well-powered to detect novel genes in telomere length regulation. However, no prior work has validated these putative novel genes to confirm the contribution of GWAS loci to telomere length regulation. We conducted a trans-ancestry meta-analysis of 211,369 individuals. Through enrichment analyses of chromatin state and cell-type heritability we identified blood and immune cells as the most relevant cell type to examine telomere length association signals. We validated specific GWAS associations by overexpressing KBTBD6, a component of an E3 ubiquitin ligase complex, and POP5, a component of the Ribonuclease P/MRP complex, and demonstrating that both lengthened telomeres as predicted by our statistical analyses. CRISPR/Cas9 deletion of the predicted causal regions of these association peaks in K562 immortalized blood cells reduced expression of these genes, demonstrating that these loci are related to transcriptional regulation of KBTBD6 and POP5, respectively. Together our results demonstrate the utility of telomere length GWAS in the identification of novel telomere length regulation mechanisms and highlight the importance of the proteasome-ubiquitin pathway in telomere length regulation.

genetics↗

bioRxiv2023

Mn2+-Induced Structural Flexibility Enhances the Entire Catalytic Cycle and the Cleavage of Mismatches in Prokaryotic Argonaute Proteins

Prokaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+ bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+ in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined. By combining experimental and computational methods, this study reveals that unbound Mn2+ in solution enhances the flexibility of diverse pAgo proteins. This increase in flexibility through decreasing the number of hydrogen bonds, induced by Mn2+, leads to higher affinity for substrates, thus facilitating cleavage. More importantly, Mn2+-induced structural flexibility increases the mismatch tolerance between guide-target pairs by increasing the conformational states, thereby enhancing the cleavage of mismatches. Further simulations indicated that the enhanced flexibility in linkers triggers conformational changes in the PAZ domain for recognizing various lengths of nucleic acids. Additionally, Mn2+-induced dynamic alterations of the protein cause a conformational shift in the N domain and catalytic sites towards their functional form, resulting in a decreased energy penalty for target release and cleavage. These findings demonstrate that the dynamic conformations of pAgo proteins, resulting from the presence of the unbound Mn2+ in solution, significantly promote the catalytic cycle of endonucleases and the tolerance of cleavage to mismatches. This flexibility enhancement mechanism serves as a general strategy employed by Ago proteins from diverse prokaryotes to accomplish their catalytic functions and provide useful information for Ago-based precise molecular diagnostics.

biophysics↗

bioRxiv2023

Whole genome sequencing reveals autooctoploidy in the Chinese sturgeon and its evolutionary trajectories

The Order Acipenseriformes, which include sturgeons and paddlefishes, represent "living fossils" with complex genomes that are good models for understanding whole genome duplication (WGD) and ploidy evolution in fishes. Here we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species that also represents a poorly understood ploidy group in Acipenseriformes. Our results show that A. sinensis is a complex autooctoploid species containing four kinds of octovalents (8 n), a hexavalent (6 n), two tetravalents (4 n), and a divalent (2 n). We propose based on an analysis taking into account delayed rediploidization that its octoploid genome composition results from two rounds of homologous whole genome duplications (WGDs), and further provide insight into the timing of its ploidy evolution. This study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy composition and evolutionary trajectories of polyploidy fishes.

genomics↗

bioRxiv2023

A Rapid Inducible RNA Decay system reveals fast mRNA decay in P-bodies

RNA decay plays a crucial role in regulating mRNA abundance and gene expression. Modulation of RNA degradation is imperative to investigate an RNAs function. However, information regarding where and how RNA decay occurs remains scarce, partially because existing technologies fail to initiate RNA decay with the spatiotemporal precision or transcript specificity required to capture this stochastic and transient process. Here, we devised a general method that employs inducible tethering of regulatory protein factors to target RNAs and modulate their metabolism. Specifically, we established a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNA within minutes. The fast and synchronous induction enabled direct visualization of mRNA decay dynamics in cells with spatiotemporal precision previously unattainable. When applying RIDR to endogenous ACTB mRNA, we observed rapid formation and disappearance of RNA granules, which coincided with pre-existing processing bodies (P-bodies). We measured the time-resolved RNA distribution in P-bodies and cytoplasm after induction, and compared different models of P-body function. We determined that mRNAs rapidly decayed in P-bodies upon induction. Additionally, we validated the functional role of P-bodies by knocking down specific a P-body constituent protein and RNA degradation enzyme. This study determined compartmentalized RNA decay kinetics for the first time. Together, RIDR provides a valuable and generalizable tool to study the spatial and temporal RNA metabolism in cells.

molecular biology↗

bioRxiv2023

Biomaterial based implants caused remote liver fatty deposition through activated blood-derived Kupffer cells

Understanding the foreign-body response (FBR) of biomaterials is a prerequisite for the prediction of its clinical application, and the present assessments mainly rely on in vitro cell culture and in situ histopathology. However, remote organs responses after biomaterials implantation is unclear. Here, by leveraging body-wide-transcriptomics data, we performed in-depth systems analysis of biomaterials - remote organs crosstalk after abdominal implantation of polypropylene and silk fibroin using a rodent model, demonstrating local implantation caused remote organs responses dominated by acute-phase responses, immune system responses and lipid metabolism disorders. Of note, liver function was specially disturbed, defined as hepatic lipid deposition. Combining flow cytometry analyses and liver monocyte recruitment inhibition experiments, we proved that blood derived monocyte-derived Kupffer cells in the liver underlying the mechanism of abnormal lipid deposition induced by local biomaterials implantation. Moreover, from the perspective of temporality, the remote organs responses and liver lipid deposition of silk fibroin group faded away with biomaterial degradation and restored to normal at end, which highlighted its superiority of degradability. These findings were further indirectly evidenced by human blood biochemical examination from 141 clinical cases of hernia repair using silk fibroin mesh and polypropylene mesh. In conclusion, this study provided knowledge of biomaterials-body interactions. It is of great important for future development of biomaterial devices for clinical application. One Sentence SummaryAbdominal local biomaterials implantation induces remote organ fatty deposition through activated blood-derived Kupffer cells.

pharmacology and toxicology↗

bioRxiv2023

Bidirectional transcription at the PPP2R2B gene locus in spinocerebellar ataxia type 12

OBJECTIVESpinocerebellar ataxia type 12 (SCA12) is a neurodegenerative disease caused by expansion of a CAG repeat in the PPP2R2B gene. Here we tested the hypothesis that the PPP2R2B antisense (PPP2R2B-AS1) transcript containing a CUG repeat is expressed and contributes to SCA12 pathogenesis. METHODSExpression of PPP2R2B-AS1 transcript was detected in SCA12 human induced pluripotent stem cells (iPSCs), iPSC-derived NGN2 neurons, and SCA12 knock-in mouse brains using strand-specific RT-PCR (SS-RT-PCR). The tendency of expanded PPP2R2B-AS1 (expPPP2R2B-AS1) RNA to form foci, a marker of toxic processes involving mutant RNAs, was examined in SCA12 cell models by fluorescence in situ hybridization. The toxic effect of expPPP2R2B-AS1 transcripts on SK-N-MC neuroblastoma cells was evaluated by caspase 3/7 activity. Western blot was used to examine the expression of repeat associated non-ATG-initiated (RAN) translation of expPPP2R2B-AS1 transcript in SK-N-MC cells. RESULTSThe repeat region in PPP2R2B gene locus is bidirectionally transcribed in SCA12 iPSCs, iPSC-derived NGN2 neurons, and SCA12 mouse brains. Transfected expPPP2R2B-AS1 transcripts are toxic to SK-N-MC cells, and the toxicity may be mediated, at least in part, by the RNA secondary structure. The expPPP2R2B-AS1 transcripts form CUG RNA foci in SK-N-MC cells. expPPP2R2B-AS1 transcript is translated in the Alanine ORF via repeat-associated non-ATG (RAN) translation, which is diminished by single nucleotide interruptions within the CUG repeat, and MBNL1 overexpression. INTERPRETATIONThese findings suggest that PPP2R2B-AS1 contributes to SCA12 pathogenesis, and may therefore provide a novel therapeutic target for the disease.

neuroscience↗

bioRxiv2023

Few-shot learning: temporal scaling in behavioral and dopaminergic learning

Learning the causes of rewards is necessary for survival. Thus, it is critical to understand the mechanisms of such a vital biological process. Cue-reward learning is controlled by mesolimbic dopamine and improves with spacing of cue-reward pairings. However, whether a mathematical rule governs such improvements in learning rate, and if so, whether a unifying mechanism captures this rule and dopamine dynamics during learning remain unknown. Here, we investigate the behavioral, algorithmic, and dopaminergic mechanisms governing cuereward learning rate. Across a range of conditions in mice, we show a strong, mathematically proportional relationship between both behavioral and dopaminergic learning rates and the duration between rewards. Due to this relationship, removing up to 19 out of 20 cue-reward pairings over a fixed duration has no influence on overall learning. These findings are explained by a dopamine-based model of retrospective learning, thereby providing a unified account of the biological mechanisms of learning.

neuroscience↗

bioRxiv2023

Implantable flexible multielectrode arrays for multi-site sensing of serotonin tonic levels

Real-time multi-channel measurements of tonic serotonin (5-hydroxytryptamine, 5-HT) concentrations across different brain regions are of utmost importance to the understanding of 5-HTs role in anxiety, depression, and impulse control disorders, which will improve the diagnosis and treatment of these neuropsychiatric illnesses. Chronic sampling of 5-HT is critical in tracking disease development as well as the time course of pharmacological treatments. Despite their value, in vivo chronic multi-site measurements of 5-HT have not been reported. To fill this technological gap, we batch fabricated implantable glassy carbon (GC) microelectrode arrays (MEAs) on a flexible SU-8 substrate to provide an electrochemically stable and biocompatible device/tissue interface. Then, to achieve multi-site detection of tonic 5-HT concentrations, we incorporated the poly(3,4-ethylenedioxythiophene)/functionalized carbon nanotube (PEDOT/CNT) coating on the GC microelectrodes in combination with a new square wave voltammetry (SWV) approach, optimized for selective 5-HT measurement. In vitro, the PEDOT/CNT coated GC microelectrodes achieved high sensitivity towards 5-HT, good fouling resistance in the presence of 5-HT, and excellent selectivity towards the most common neurochemical interferents. In vivo, our PEDOT/CNT-coated GC MEAs were able to successfully detect basal 5-HT concentrations at different locations of the CA2 hippocampal region of mice in both anesthetized and awake head-fixed conditions. Furthermore, the implanted PEDOT/CNT-coated MEA achieved stable detection of tonic 5-HT concentrations for one week. Finally, histology data in the hippocampus shows reduced tissue damage and inflammatory responses compared to stiff silicon probes. To the best of our knowledge, this PEDOT/CNT-coated GC MEA is the first implantable flexible multisite sensor capable of chronic in vivo multi-site sensing of tonic 5-HT. This implantable MEA can be custom-designed according to specific brain region of interests and research questions, with the potential to combine electrophysiology recording and multiple analyte sensing to maximize our understanding of neurochemistry. HighlightsO_LIPEDOT/CNT-coated GC microelectrodes enabled sensitive and selective tonic detection of serotonin (5-HT) using a new square wave voltammetry (SWV) approach C_LIO_LIPEDOT/CNT-coated GC MEAs achieved multi-site in vivo 5-HT tonic detection for one week. C_LIO_LIFlexible MEAs lead to reduced tissue damage and inflammation compared to stiff silicon probes. C_LI

bioengineering↗

bioRxiv2022

A Versatile Deep Graph Contrastive Learning Framework for Single-cell Proteomics Embedding

The advance of single-cell proteomics sequencing technology sheds light on the research in revealing the protein-protein interactions, the post-translational modifications, and the proteoform dynamics of proteins in a cell. However, the uncertainty estimation for peptide quantification, data missingness, severe batch effects and high noise hinder the analysis of single-cell proteomic data. It is a significant challenge to solve this set of tangled problems together, where existing methods tailored for single-cell transcriptome do not address. Here, we proposed a novel versatile framework scPROTEIN, composed of peptide uncertainty estimation based on a multi-task heteroscedastic regression model and cell embedding learning based on graph contrastive learning designed for single-cell proteomic data analysis. scPROTEIN estimated the uncertainty of peptide quantification, denoised the protein data, removed batch effects and encoded single-cell proteomic-specific embeddings in a unified framework. We demonstrate that our method is efficient for cell clustering, batch correction, cell-type annotation and clinical analysis. Furthermore, our method can be easily plugged into single-cell resolved spatial proteomic data, laying the foundation for encoding spatial proteomic data for tumor microenvironment analysis.

bioinformatics↗

bioRxiv2022

Bursting Translation on Single mRNAs in Live Cells

Stochasticity has emerged as a mechanism to control gene expression. Much of this so-called "noise" has been attributed to bursting transcription. However, the stochasticity of translation has not similarly been investigated due to a lack of enabling imaging technologies. We developed techniques to track single mRNAs and their translation in live cells for hours, allowing measurement of previously uncharacterized translation dynamics. We applied genetic and pharmacological perturbations to control translation kinetics. Like transcription, translation is not a constitutive process but instead cycles between inactive and active states or "bursts". But unlike transcription, which is largely frequency modulated, complex structure in the 5-untranslated region alters burst amplitude. Bursting frequency can be controlled through cap-proximal sequences and trans-acting factors such as eIF4F. We coupled single molecule imaging with stochastic modeling to deduce the fundamental kinetic parameters of translational bursting, a new dimension of translational control. HighlightsO_LILong-term tracking of single mRNAs reveals multi-state, bursting translation C_LIO_LIStructure in the 5-untranslated region modulates translational burst amplitude C_LIO_LI5-cap proximal sequences modulate translational burst frequency C_LIO_LImTOR signaling adjusts translation bursting to respond to environmental cues C_LI

molecular biology↗

bioRxiv2022

Vascular endothelial growth factor A contributes to the increasing of mammalian respiratory epithelial permeability induced by Pasteurella multocida infection

Infections with Pasteurella multocida can cause significant zoonotic respiratory problems in both humans and animals. In vivo tests in mouse infection models were used to investigate the mechanisms of respiratory epithelial barrier dysfunction during respiratory bacterial infection with these pathogens. Results revealed that P. multocida infection significantly increased epithelial permeability and increased expression of vascular endothelial growth factor A (VEGFA) and endothelial nitric oxide synthase (eNOS) in murine tracheae and lungs. In murine lung epithelial cell (MLE-12) models, P. multocida infection decreased the expression of tight junctions (ZO-1) and adherens junctions ({beta}-catenin, E-cadherin), but induced the activation of the hypoxia-inducible factor-1 (HIF-1) and VEGFA signaling. When expression of HIF-1 is suppressed, the induction of VEGFA and ZO-1expression by P. multocida infection is decreased. We also found that intervention of HIF-1 and VEGFA signaling affected infection outcomes caused by respiratory bacteria in mouse models. Most importantly, we demonstrated that P. multocida infection increased permeability of human respiratory epithelial cells and this process was associated with the activation of the HIF-1 and VEGFA signaling and likely contributes to the pathogenesis of P. multocida in humans. ImportanceMammalian respiratory epithelium forms the first line of defense against infections with Pasteurella multocida, an important zoonotic respiratory pathogen. In this study, we found P. multocida infection increased respiratory epithelial permeability and promoted the induction of the hypoxia-HIF-1-VEGFA axis in both mouse and murine cell models. Similar findings were also demonstrated in human respiratory epithelial cells. The results from this study gain important knowledge about the pathogenesis of P. multocida causing infections in both animals and humans.

microbiology↗

bioRxiv2022

Nanosecond pulsed electric field ablates rabbit VX2 liver tumors in a non-thermal manner versus radiofrequency ablation

BackgroundLiver tumor remains an important cause of cancer-related death. Nanosecond pulsed electric fields (nsPEFs) are advantageous in the treatment of melanoma and pancreatic cancer, but their therapeutic application on liver tumors need to be further studied. MethodsHep3B cells were treated with nsPEFs. The biological behaviors of cells were detected by Cell Counting Kit-8, 5-ethynyl-20-deoxyuridine, and transmission electron microscopy (TEM) assays. In vivo, rabbit VX2 liver tumor models were ablated by ultrasound-guided nsPEFs and radiofrequency ablation (RFA). Contrast-enhanced ultrasound (CEUS) was used to evaluate the ablation effect. HE staining and Masson staining were used to evaluate the tissue morphology after ablation. Immunohistochemistry was performed to determine the expression of Ki67, proliferating cell nuclear antigen, and -smooth muscle actin at different time points after ablation. ResultsThe cell viability of Hep3B cells was continuously lower than that of the control group within 3 days after pulse treatment. The proliferation of Hep3B cells was significantly affected by nsPEFs. TEM showed that Hep3B cells underwent significant morphological changes after pulse treatment. In vivo, CEUS imaging showed that nsPEFs could completely ablate model rabbit VX2 liver tumors. After nsPEFs ablation, the area of tumor fibrosis and the expression of Ki67, proliferating cell nuclear antigen, and -smooth muscle actin were decreased. However, after RFA, rabbit VX2 liver tumor tissue showed complete necrosis, but the expression of PCNA and -smooth muscle actin did not decrease compared to the tumor group. ConclusionsnsPEFs can induce Hep3B cells apoptosis and ablate rabbit VX2 liver tumors in a non-thermal manner versus RFA. The ultrasound contrast agent can monitor immediate effect of nsPEF ablation. This study provides a basis for the clinical study of nsPEFs ablation of liver cancer.

cancer biology↗

bioRxiv2022

Integrated microprism and micro-electrode array for chronic in vivo two-photon imaging and electrophysiology across all cortical layers

Electrophysiology is a vital tool in neuroscience research with increasing translational value. It is used to record or modulate neuronal activity with high temporal but lower spatial resolution. Optical technologies, such as two-photon microscopy (TPM) can complement electrophysiological recordings with large-scale imaging at cellular resolution. Combining these two provides a powerful platform to elucidate and coordinate multimodal functions. Prior attempts have been limited to the superficial brain from a top-down optical view. Here, we describe a novel combination of transparent microelectrode arrays (MEAs) with glass microprisms for simultaneous electrophysiology and optical imaging of all cortical layers in a vertical plane. We tested our device in Thy1-GCaMP6 mice for over 4 months and demonstrated its capability for multisite single-unit recording, microstimulation, and simultaneous TPM calcium imaging. Using this setup, we reveal how amplitude, frequency, and depth of microstimulation impact neural activation patterns across the cortical column. This work presents a multimodal tool that extends integrated electrophysiology and optical imaging from the superficial brain to the whole cortical column, opening new avenues of neuroscience research and neurotechnology development.

bioengineering↗