Biology subjects

Yu, H.

Publications and source records attributed to Yu, H..

At least 235 records · Page 13Linked to original sources

bioRxiv2023

Learning regular cross-trial shifts of the target location in serial search involves awareness: an eye-tracking study

People can learn, and utilize, not only static but also dynamic (cross-trial) regularities in the positioning of target items in parallel, pop-out visual search. However, while static target-location learning also works in serial search, acquiring dynamic regularities seems prevented by the demands imposed by item-by-item scanning. Also, questions have been raised regarding a role of explicit awareness for utilizing (at least) dynamic regularities to optimize performance. The present study re-investigated whether dynamic regularities may be learned in serial search when regular shifts of the target location occur frequently, and whether such learning would correlate with awareness of the dynamic rule. To this end, we adopted the same regularity used by Yu et al. (2023) to demonstrate dynamic learning in parallel search: a cross-trial shift of the target location in, e.g., clockwise direction within a circular array in 80% of the trials, which was compared to irregular shifts in the opposite (e.g., counterclockwise; 10%) or some other, random direction (10%). The results showed that [2/3] of participants learned the dynamic regularity, with their performance gains correlating with awareness: the more accurately they estimated how likely the target shifted in the frequent direction, the greater their gains. Importantly, part of the gains accrued already early during search: a large proportion of the very first and short-latency eye movements was directed to the predicted location, whether or not the target appeared there. We discuss whether this rule-driven behavior is causally mediated by conscious control. (248 words).

neuroscience↗

bioRxiv2023

Prediction of DNA i-Motifs Via Machine Learning

i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and strength of putative iMs vary dramatically. Much previous research on iM has focused on assessing the iM folding properties using biophysical experiments. However, there are no dedicated computational tools for predicting the folding status and strength of iM structures. Here, we introduce a machine learning pipeline, iM-Seeker, to predict both folding status and structural stability of DNA iMs. The programme iM-Seeker incorporates a Balanced Random Forest classifier trained on genome-wide iMab antibody-based CUT&Tag sequencing data to predict the folding status and an Extreme Gradient Boosting regressor to estimate the folding strength according to both literature biophysical data and our in-house biophysical experiments. iM-Seeker predicts DNA iM folding status with a classification accuracy of 81% and estimates the folding strength with coefficient of determination (R2) of 0.642 on the test set. Model interpretation confirms that the nucleotide composition of the C-rich sequence significantly affects iM stability, with a positive correlation with sequences containing cytosine and thymine and a negative correlation with guanine and adenine. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/571121v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@11f4398org.highwire.dtl.DTLVardef@18eb7e9org.highwire.dtl.DTLVardef@cc49c6org.highwire.dtl.DTLVardef@1ff91a8_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Role of Dusp5 KO on Vascular Properties of Middle Cerebral Artery in Rats

Vascular aging influences hemodynamics, elevating risks for vascular diseases and dementia. We recently demonstrated that knockout (KO) of Dusp5 enhances cerebral and renal hemodynamics and cognitive function. This improvement correlates with elevated pPKC and pERK1/2 levels in the brain and kidneys. Additionally, we observed that Dusp5 KO modulates the passive mechanical properties of cerebral and renal arterioles, associated with increased myogenic tone at low pressure, enhanced distensibility, greater compliance, and reduced stiffness. The present study evaluates the structural and mechanical properties of the middle cerebral artery (MCA) in Dusp5 KO rats. We found that vascular smooth muscle cell layers and the collagen content in the MCA wall are comparable between Dusp5 KO and control rats. The internal elastic lamina in the MCA of Dusp5 KO rats exhibits increased thickness, higher autofluorescence intensity, smaller fenestrae areas, and fewer fenestrations. Despite an enhanced myogenic response and tone of the MCA in Dusp5 KO rats, other passive mechanical properties, such as wall thickness, cross-sectional area, wall-to-lumen ratio, distensibility, incremental elasticity, circumferential wall stress, and elastic modulus, do not significantly differ between strains. These findings suggest that while Dusp5 KO has a limited impact on altering the structural and mechanical properties of MCA, its primary role in ameliorating hemodynamics and cognitive functions is likely attributable to its enzymatic activity on cerebral arterioles. Further research is needed to elucidate the specific enzymatic mechanisms and explore potential clinical applications in the context of vascular aging.

physiology↗

bioRxiv2023

PIEZO2-dependent rapid pain system in humans and mice.

The PIEZO2 ion channel is critical for transducing light touch into neural signals but is not considered necessary for transducing acute pain in humans. Here, we discovered an exception - a form of mechanical pain evoked by hair pulling. Based on observations in a rare group of individuals with PIEZO2 deficiency syndrome, we demonstrated that hair-pull pain is dependent on PIEZO2 transduction. Studies in control participants showed that hair-pull pain triggered a distinct nocifensive response, including a nociceptive reflex. Observations in rare A{beta} deafferented individuals and nerve conduction block studies in control participants revealed that hair-pull pain perception is dependent on A{beta} input. Single-unit axonal recordings revealed that a class of cooling-responsive myelinated nociceptors in human skin is selectively tuned to painful hair-pull stimuli. Further, we pharmacologically mapped these nociceptors to a specific transcriptomic class. Finally, using functional imaging in mice, we demonstrated that in a homologous nociceptor, Piezo2 is necessary for high-sensitivity, robust activation by hair-pull stimuli. Together, we have demonstrated that hair-pulling evokes a distinct type of pain with conserved behavioral, neural, and molecular features across humans and mice.

neuroscience↗

bioRxiv2023

Evolution is All You Need in Promoter Design and Optimization

Predicting the strength of promoters and guiding their directed evolution is a crucial task in synthetic biology. This approach significantly reduces the experimental costs in conventional promoter engineering. Previous studies employing machine learning or deep learning methods have shown some success in this task, but their outcomes were not satisfactory enough, primarily due to the neglect of evolutionary information. In this paper, we introduce the Chaos-Attention net for Promoter Evolution (CAPE) to address the limitations of existing methods. We comprehensively extract evolutionary information within promoters using chaos game representation and process the overall information with DenseNet and Transformer. Our model achieves state-of-the-art results on two kinds of distinct tasks. The incorporation of evolutionary information enhances the models accuracy, with transfer learning further extending its adaptability. Furthermore, experimental results confirm CAPEs efficacy in simulating in silico directed evolution of promoters, marking a significant advancement in predictive modeling for prokaryotic promoter strength. Our paper also presents a user-friendly website for the practical implementation of in silico directed evolution on promoters.

synthetic biology↗

bioRxiv2023

Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04

Drug resistance poses a significant challenge in the development of effective therapies against SARS-CoV-2. Here, we identified two double mutations, M49K/M165V and M49K/S301P, in the 3C-like protease (3CLpro) that confer resistance to a novel non-covalent inhibitor, WU-04. Crystallographic analysis indicates that the M49K mutation destabilizes the WU-04 binding pocket, impacting the binding of WU-04 more significantly than the binding of 3CLpro substrates. The M165V mutation directly interferes with WU-04 binding. The S301P mutation, which is far from the WU-04 binding pocket, indirectly affects WU-04 binding by restricting the rotation of 3CLpros C-terminal tail and impeding 3CLpro dimerization. We further explored 3CLpro mutations that confer resistance to two clinically used inhibitors: ensitrelvir and nirmatrelvir, and revealed a trade-off between the catalytic activity, thermostability, and drug resistance of 3CLpro. We found that mutations at the same residue (M49) can have distinct effects on the 3CLpro inhibitors, highlighting the importance of developing multiple antiviral agents with different skeletons for fighting SARS-CoV-2. These findings enhance our understanding of SARS-CoV-2 resistance mechanisms and inform the development of effective therapeutics.

microbiology↗

bioRxiv2023

DREDge: robust motion correction for high-density extracellular recordings across species

High-density microelectrode arrays (MEAs) have opened new possibilities for systems neuroscience in human and non-human animals, but brain tissue motion relative to the array poses a challenge for downstream analyses, particularly in human recordings. We introduce DREDge (Decentralized Registration of Electrophysiology Data), a robust algorithm which is well suited for the registration of noisy, nonstationary extracellular electrophysiology recordings. In addition to estimating motion from spikes in the action potential (AP) frequency band, DREDge enables automated tracking of motion at high temporal resolution in the local field potential (LFP) frequency band. In human intraoperative recordings, which often feature fast (period <1s) motion, DREDge correction in the LFP band enabled reliable recovery of evoked potentials, and significantly reduced single-unit spike shape variability and spike sorting error. Applying DREDge to recordings made during deep probe insertions in nonhuman primates demonstrated the possibility of tracking probe motion of centimeters across several brain regions while simultaneously mapping single unit electrophysiological features. DREDge reliably delivered improved motion correction in acute mouse recordings, especially in those made with an recent ultra-high density probe. We also implemented a procedure for applying DREDge to recordings made across tens of days in chronic implantations in mice, reliably yielding stable motion tracking despite changes in neural activity across experimental sessions. Together, these advances enable automated, scalable registration of electrophysiological data across multiple species, probe types, and drift cases, providing a stable foundation for downstream scientific analyses of these rich datasets.

neuroscience↗

bioRxiv2023

Neurophysiological Features of STN LFP underlying Sleep Fragmentation in Parkinson's Disease

BackgroundSleep fragmentation is a persistent problem throughout the course of Parkinsons disease (PD). However, the related neurophysiological patterns and the underlying mechanisms remained unclear. MethodWe recorded subthalamic nucleus (STN) local field potentials (LFPs) using DBS with real-time wireless recording capacity from thirteen PD patients undergoing a one-night polysomnography recording, one month after DBS surgery before initial programming and when the patients were Off-Medication. The STN LFP features that characterized different sleep stages, correlated with arousal and sleep fragmentation index, and preceded stage transitions during N2 and REM sleep were analyzed. ResultsBoth beta and low gamma oscillations in NREM sleep increased with the severity of sleep disturbance (arousal index (ArI)-betaNREM: r=0.9,p=0.0001) and sleep fragmentation index (SFI)-betaNREM: r=0.6,p=0.0301; SFI-gammaNREM: r=0.6,p=0.0324). We next examined the low-to-high power ratio, which was the power ratio of theta oscillations to beta and low gamma oscillations, and found it to be an indicator of sleep fragmentation (ArI-LHPRNREM: r=-0.8,p=0.0053; ArI-LHPRREM: r=-0.6,p=0.0373; SFI-LHPRNREM: r=-0.7,p=0.0204; SFI-LHPRREM: r=-0.6,p=0.0428). In addition, long beta bursts (>0.25s) during NREM stage 2 were found preceding the completion of transition to stages with more cortical activities (towards Wake/N1/REM compared with towards N3 (p<0.01)) and negatively correlated with STN spindles, which were detected in STN LFPs with peak frequency distinguishable from long beta bursts (STN spindle: 11.5Hz, STN long beta bursts: 23.8Hz), in occupation during NREM sleep ({beta} = -0.24,p<0.001). ConclusionFeatures of STN LFPs help explain neurophysiological mechanisms underlying sleep fragmentations in PD, which can inform new intervention for sleep dysfunction. What is already known on this topicBeta oscillation, which is a biomarker for rigidity and bradykinesia during awake, significantly reduced during NREM sleep compared to REM or awake. Researches from MPTP non-human primate model suggested increased beta oscillation in basal ganglia contributed to insomnia in PD, however evidence in human patients is still lacking. What this study addsBeta and low gamma band activities in STN LFPs during sleep recorded from human PD patients correlated with severity of sleep impairment. The low-high power ratio can serve as a biomarker for sleep fragmentation. Besides, pathological beta bursts and physiological sleep spindles can be detected in STN LFP during NREM sleep and distinguishable from each other. How this study might affect research, practice or policyThese findings enhance our understanding of the electrophysiological mechanisms that underlie sleep fragmentation in Parkinsons disease. The study also has implications on the design of closed-loop DBS: we may need to take multiple frequency band activities into consideration and differentiate pathological beta oscillation from the sleep spindles.

physiology↗

bioRxiv2023

Dual Ethanolamine Head Groups in Ionizable Lipids Facilitate Phospholipid-free Stable Nanoparticle Formulation for Augmented and Safer mRNA Delivery

The accelerated advent of mRNA-based therapeutics and vaccines, highlighted by the battle against SARS-CoV-2, underscores the urgency to refine lipid nanoparticles (LNPs) for efficient mRNA delivery. In this work, we introduce a novel series of ionizable lipids characterized by double ethanolamine head groups, significantly amplifying mRNA binding affinity. A succinct three-component formulation is subsequently delineated, obviating the conventional dependency on phospholipids inherent in traditional four-component LNPs. Intriguingly, this formulation enables particle formation under neutral pH conditions, a notable departure from the acidic milieu traditionally required, attributable to the enhanced nonionic interactions predominating in mRNA encapsulation. The resultant particles exhibit exceptional stability, superior mRNA encapsulation efficiency, and maintain robust delivery efficacy. When deployed as a vaccine platform, the formulation elicited pronounced humoral and T-cell immune responses, concurrently exhibiting a favorable toxicity profile with a reduced induction of pro-inflammatory cytokines such as IL-6. Our exploration suggests that by fine-tuning the non-electrostatic interactions between the ionizable lipid and mRNA, the dynamics of particle formation can be considerably divergent from the prevailing paradigms of mRNA-LNP formation, hinting at a broader horizon for lipid optimization within the realm of mRNA delivery systems.

bioengineering↗

bioRxiv2023

Olfactory learning in Drosophila requires O-GlcNAcylation of mushroom body ribosomal subunits

O-GlcNAcylation is a dynamic post-translational modification that diversifies the proteome. Its dysregulation is associated with neurological disorders that impair cognitive function, and yet identification of phenotype-relevant candidate substrates in a brain-region specific manner remains unfeasible. By combining an O-GlcNAc binding activity derived from Clostridium perfringens OGA (CpOGA) with TurboID proximity labeling in Drosophila, we developed an O-GlcNAcylation profiling tool that translates O-GlcNAc modification into biotin conjugation for tissue-specific candidate substrates enrichment. We mapped the O-GlcNAc interactome in major brain regions of Drosophila and found that components of the translational machinery, including many ribosomal subunits, were abundantly O-GlcNAcylated in the mushroom body, the computational center of the Drosophila brain. Hypo-O-GlcNAcylation induced by ectopic expression of active CpOGA in the mushroom body decreased local ribosomal activity, leading to olfactory learning deficits that could be rescued by increasing ribosome biogenesis. Our study reveals that O-GlcNAcylation contributes to the links between protein synthesis and cognitive function in the brain learning center, and provides a useful tool for future dissection of tissue-specific functions of O-GlcNAcylation in Drosophila.

cell biology↗

bioRxiv2023

Bayesian optimization of separation gradients to maximize the performance of untargeted LC-MS

Liquid chromatography (LC) with gradient elution is a routine practice for separating complex chemical mixtures in mass spectrometry (MS)-based untargeted analysis. Despite its prevalence, systematic optimization of LC gradients has remained challenging. Here we develop a Bayesian optimization method, BAGO, for autonomous and efficient LC gradient optimization. BAGO is an active learning strategy that discovers the optimal gradient using limited experimental data. From over 100,000 plausible gradients, BAGO locates the optimal LC gradient within ten sample analyses. We validated BAGO on six biological studies of different sample matrices and LC columns, showing that BAGO can significantly improve quantitative performance, tandem MS spectral coverage, and spectral purity. For instance, the optimized gradient increases the count of annotated compounds meeting quantification criteria by up to 48.5%. Furthermore, applying BAGO in a Drosophila metabolomics study, an additional 57 metabolites and 126 lipids were annotated. The BAGO algorithms were implemented into user-friendly software for everyday laboratory practice and a Python package for its flexible extension.

bioinformatics↗

bioRxiv2023

Insights into Phakopsora pachyrhizi effector-effector interactions

The multifaceted role of pathogen-encoded effectors in plant-pathogen interactions is complex and not fully understood. Effectors operate within intricate host environments, interacting with host proteins and other effectors to modulate virulence. The complex interplay between effectors raises the concept of metaeffectors, where some effectors regulate the activity of others. While previous research has demonstrated the importance of effector repertoires in pathogen virulence, only a limited number of studies have investigated the interactions between these effectors. This study explores the interactions among Phakopsora pachyrhizi effector candidates (PpECs). P. pachyrhizi haustorial transcriptome analysis identified a collection of predicted PpECs. Among these, PpEC23 was found to interact with PpEC48, prompting further exploration into their potential interaction with other effectors. Here, we utilized a yeast-two-hybrid screen to explore protein-protein interactions between PpECs. A split-luciferase complementation assay also demonstrated that these interactions could occur within soybean cells. Interestingly, PpEC48 displayed the ability to interact with several small cysteine-rich proteins (SCRP), suggesting its affinity for this specific class of effectors. We show that these interactions involve a histidine-rich domain within PpEC48, emphasizing the significance of structural motifs in mediating effector interactions. The unique nature of PpEC48, showing no sequence matches in other organisms, suggests its relatively recent evolution and potential orphan gene status. Our work reveals insights into the intricate network of interactions among P. pachyrhizi effector-effector interactions.

plant biology↗

bioRxiv2023

Cooperative progression of colitis and leukemia modulated by clonal hematopoiesis via PTX3/IL-1β pro-inflammatory signaling

Clonal hematopoiesis (CH) is considered an important risk factor for all-cause mortality and the development of multiple chronic diseases including hematological neoplasms, cardiovascular diseases, and potentially a range of autoimmune or immune-deficiency diseases. Mutations in TET2 are one of the first identified, most important, and prevalent genetic drivers of CH. However, cooperative factors and mechanisms underlying TET2-deficiency related CH (TedCH) remain largely unknown. Recently, it has been suggested that certain diseases occurred before TedCH and promote TedCH trajectory on the contrary, indicating that diseases in non-hematopoietic organs may act as environmental non-genetic drivers of CH. To clarify the relationships between immune-dysfunctional diseases and CH, here we tested the impact of various challenges on TedCH. We found that expedited TedCH depended on establishment of an inflammatory environment. Primary or chimeric Tet2-mutant mice spontaneously developed co-symptoms reminiscent of human chronic colitis and myeloid leukemia, which was exacerbated by feeding with DSS, an experimental inducer of ulcerative colitis. Single cell RNA-seq (scRNA-seq) analysis reveals in depth the damage of colon in the Tet2-mutant mice in physiological conditions or fed with DSS, along with increase of dysbacteriosis indicated by gut microbiome analysis. Results from colon scRNA-seq from both mouse and human highlight the important roles of PTX3/IL-1{beta} pro-inflammatory signaling in promoting colitis or leukemia. Finally, TedCH trajectory and inflammation in colon and bone marrow were ameliorated by treatment of IL-1R1 inhibitor Anakinra. Our study suggests that PTX3/IL-1{beta} signaling and clonal hematopoiesis cooperate and play important roles in gut-bone marrow axis and related diseases including colitis and leukemia. HighlightsO_LICertain environmental factors, such as Dextran Sulfate Sodium (DSS), an experimental inducer of ulcerative colitis, promote TedCH C_LIO_LIColitis and leukemia are spontaneously and simultaneously developed in Tet2-defficient primary or chimeric mice, along with increased pathogenic gut microbiomes, indicating an aberrant gut-bone marrow axis in the mutant mice. C_LIO_LISingle cell RNA-seq analysis reveals enhanced PTX3, a soluble pattern recognition molecule and IL-1{beta} pro-inflammatory signaling in colitis and leukemia. C_LIO_LIThe In vivo function of the PTX3/IL-1{beta} pro-inflammatory signaling in TedCH is indicated in human colitis and validated in experimental settings. C_LI

immunology↗

bioRxiv2023

Multiple cis-regulatory elements control prox1a expression in distinct lymphatic vascular beds

Lymphatic vessels play a role in several physiological and pathological processes including tissue fluid homeostasis, dietary fat absorption, immunosurveillance, and immunomodulation. During embryonic development, lymphatic endothelial cell (LEC) precursors are distinguished from blood endothelial cells by the expression of the transcription factor Prospero-related homeobox 1 (PROX1). PROX1 is essential for lymphatic vascular network formation in mouse and zebrafish. The initiation of PROX1 expression precedes LEC sprouting and migration, serving as the definitive marker of specified LECs. Despite its crucial role in lymphatic development, the upstream regulation of PROX1 in LECs remains to be uncovered. SOX18 and COUP-TFII are thought to regulate Prox1 expression in mice by binding to its promoter region. However, how the specificity of Prox1 expression to LECs is achieved remains to be studied in detail. In this study, we analysed evolutionary conservation and chromatin accessibility to identify enhancer sequences located in the proximity of zebrafish prox1a active in developing LECs. We confirmed the functional role of the identified sequences through CRISPR/Cas9 mutagenesis of a lymphatic valve enhancer. The deletion of this genomic region results in impaired valve morphology and function. Overall, our results reveal the intricate control of prox1a expression through a collection of enhancers. Ray-finned fish-specific distal enhancers drive pan-lymphatic expression, while vertebrate-conserved proximal enhancers refine expression in functionally distinct subsets of lymphatic vessels. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/550483v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@fed780org.highwire.dtl.DTLVardef@f62a8dorg.highwire.dtl.DTLVardef@163b04corg.highwire.dtl.DTLVardef@1cb7f87_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

The role of neutrophil typing in homeostatic resilience protective model of inflammatory preconditioning

Sepsis is a systemic inflammatory response syndrome (SIRS) characterized by a dysregulated host response to infection that results in organ dysfunction. The response of neutrophils to early inflammation is critical, interferon regulatory factors 4 (IRF4) and interferon regulatory factors 5 (IRF5) are expressed in most cell types of the immune system, but the relationship between the role of IRF4 and IRF5 in preconditioning-protected septic peritonitis mouse model and neutrophils response remains unknown. In this study, we used an E.coli-induced septic peritonitis mouse model and zebrafish model to explore the relationship between neutrophil inflammation and IRF subtype changes in the process of septic peritonitis. Mechanistically, we found that the protein complex formed by polymorphonuclear neutrophils (PMN) and IRF5/MyD88 can secrete pro-inflammatory factors and directly kill invading bacteria. Author SummaryNumerous animal and clinical sepsis studies have shown that markedly impaired recruitment of neutrophils to sites of infection and failure to clear bacteria contribute to excessive inflammation and increased mortality in sepsis. In our previous work, we established an Escherichia coli (E.coli) lethal septic peritonitis model and a preconditioning-protected septic peritonitis mouse model. In the early stage of septic peritonitis, a large number of PMN infiltrate the peritoneal cavity, which produces an inflammatory response to invasive bacteria. In this study, the switching process between pro-inflammatory and anti-inflammatory attracted our attention. Our research shows that IRF5-IRF4 regulatory axis leads to a PMN phenotype switch in sepsis and the expression of IRF5 and IRF4 was related to PMN pro-inflammatory (N1 type) and anti-inflammatory (N2 type) phenotypes, respectively.

immunology↗

bioRxiv2023

Local CpG-Stat3 siRNA treatment improves antitumor effects of checkpoint inhibitors

Immune checkpoint blockade (ICB) therapy has significantly benefited patients with several types of solid tumors and some lymphomas. However, many of the treated patients do not have durable clinical response. It has been demonstrated that rescuing exhausted CD8+ T cells is required for ICB-mediated antitumor effects. We recently developed an immunostimulatory strategy based on silencing STAT3 while stimulating immune responses by CpG, ligand for Toll-like receptor 9 (TLR9). The CpG-small interfering RNA (siRNA) conjugates efficiently enter immune cells, silencing STAT3 and activating innate immunity to enhance T-cell mediated antitumor immune responses. In the present study, we demonstrate that blocking STAT3 through locally delivered CpG-Stat3 siRNA enhances the efficacies of the systemic PD-1 and CTLA4 blockade against mouse A20 B cell lymphoma. In addition, locally delivered CpG-Stat3 siRNA combined with systemic administration of PD-1 antibody significantly augmented both local and systemic antitumor effects against mouse B16 melanoma tumors, with enhanced tumor-associated T cell activation. Overall, our studies in both B cell lymphoma and melanoma mouse models demonstrate the potential of combinatory immunotherapy with CpG-Stat3 siRNA and checkpoint inhibitors as a therapeutic strategy for B cell lymphoma and melanoma.

immunology↗

bioRxiv2023

DARTsort: A modular drift tracking spike sorter for high-density multi-electrode probes

With the advent of high-density, multi-electrode probes, there has been a renewed interest in developing robust and scalable algorithms for spike sorting. Current spike sorting approaches, however, struggle to deal with noisy recordings and probe motion (drift). Here we introduce a modular and interpretable spike sorting pipeline, DARTsort (Drift Aware Registration and Tracking), that builds upon recent advances in denoising, spike localization, and drift estimation. DARTsort integrates a precise estimate of probe drift over time into a model of the spiking signal. This allows our method to be robust to drift across a variety of probe geometries. We show that our spike sorting algorithm outperforms a current state-of-the-art spike sorting algorithm, Kilosort 2.5, on simulated datasets with different drift types and noise levels. Open-source code can be found at https://github.com/cwindolf/dartsort.

neuroscience↗

bioRxiv2023

Butyrate Protects against SARS-CoV-2-induced Tissue Damage in Golden Hamsters.

Butyrate, produced by gut microbe during dietary fiber fermentation, plays anti-inflammatory and antioxidant effects in chronic inflammation diseases, yet it remains to be explored whether butyrate has protective effects against viral infections. Here, we demonstrated that butyrate alleviated tissue injury in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected golden hamsters with supplementation of butyrate before and during the infection. Butyrate-treated hamsters showed augmentation of type I interferon (IFN) response and activation of endothelial cells without exaggerated inflammation. In addition, butyrate regulated redox homeostasis by enhancing the activity of superoxide dismutase (SOD) to inhibit excessive apoptotic cell death. Therefore, butyrate exhibited an effective prevention against SARS-CoV-2 by upregulating antiviral immune responses and promoting cell survival. IMPORTANCESince SARS-CoV-2 has caused severe disease characterized by acute respiratory distress syndrome (ARDS) in humans, it is essential to develop therapeutics based on relieving such severe clinical symptoms. Current therapy strategies mainly focus on individuals who have COVID-19, however, there is still a strong need for prevention and treatment of SARS-CoV-2 infection. This study showed that butyrate, a bacterial metabolite, improved the response of SARS-CoV-2-infected hamsters by reducing immunopathology caused by impaired antiviral defenses and inhibiting excessive apoptosis through reduction in oxidative stress.

microbiology↗