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Fang, Y.

Publications and source records attributed to Fang, Y..

At least 91 records · Page 5Linked to original sources

Efficient Coding in Motor Planning

The nervous system utilizes prior information to enhance the accuracy of perception and action. Prevailing models of motor control emphasize Bayesian models, which suggest that the system adjusts the current motor plan by integrating information from previous observations. While Bayesian integration has been extensively examined, those studies usually applied a highly stable and predictable environment. In contrast, in many real-life situations, motor goals change rapidly over time in a relatively unpredictable way, leaving it unclear whether Bayesian integration is useful in those natural environments. An alternative model that leverages prior information to improve performance is efficient coding, which suggests that the motor system maximizes the accuracy by dynamically tuning the allocation of the encoding resources based on environmental statistics. To investigate whether this adaptive mechanism operates in motor planning, we employed center-out reaching tasks with motor goals changing in a relatively unpredictable way, where Bayesian and efficient coding models predict opposite sequential effects. Consistent with the efficient coding model, we found that current movements were biased in the opposite direction of previous movements. These repulsive biases were amplified by intrinsic motor variability. Moreover, movement variability decreased when successive reaches were similar to each other. Together, these effects support the presence of efficient coding in motor planning, a novel mechanism with which the motor system maintains flexibility and high accuracy in dynamic environments.

neuroscience↗

An Iterative Approach to Polish the Nanopore Sequencing Basecalling for Therapeutic RNA Quality Control

Nucleotide modifications deviate nanopore sequencing readouts, therefore generating artifacts during the basecalling of sequence backbones. Here, we present an iterative approach to polish modification-disturbed basecalling results. We show such an approach is able to promote the basecalling accuracy of both artificially-synthesized and real-world molecules. With demonstrated efficacy and reliability, we exploit the approach to precisely basecall therapeutic RNAs consisting of artificial or natural modifications, as the basis for quantifying the purity and integrity of vaccine mRNAs which are transcribed in vitro, and for determining modification hotspots of novel therapeutic RNA interference (RNAi) molecules which are bioengineered (BioRNA) in vivo.

bioinformatics↗

Training Data Diversity Enhances the Basecalling of Novel RNA Modification-Induced Nanopore Sequencing Readouts

Accurately basecalling sequence backbones in the presence of nucleotide modifications remains a substantial challenge in nanopore sequencing bioinformatics. It has been extensively demonstrated that state-of-the-art basecallers are less compatible with modification-induced sequencing signals. A precise basecalling, on the other hand, serves as the prerequisite for virtually all the downstream analyses. Here, we report that basecallers exposed to diverse training modifications gain the generalizability to analyze novel modifications. With synthesized oligos as the model system, we precisely basecall various out-of-sample RNA modifications. From the representation learning perspective, we attribute this generalizability to basecaller representation space expanded by diverse training modifications. Taken together, we conclude increasing the training data diversity as a novel paradigm for building modification-tolerant nanopore sequencing basecallers.

bioinformatics↗

Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating

Cytometry is an advanced technique for simultaneously identifying and quantifying many cell surface and intracellular proteins at a single-cell resolution. Analyzing high-dimensional cytometry data involves identifying and quantifying cell populations based on their marker expressions. This study provided a quantitative review and comparison of various ways to phenotype cellular populations within the cytometry data, including manual gating, unsupervised clustering, and supervised auto-gating. Six datasets from diverse species and sample types were included in the study, and manual gating with two hierarchical layers was used as the truth for evaluation. For manual gating, results from five researchers were compared to illustrate the gating consistency among different raters. For unsupervised clustering, 22 tools were quantitatively compared in terms of accuracy with the truth and computing cost. While no method outperformed all others, several tools, including PAC-MAN, CCAST, FlowSOM, flowClust, and DEPECHE, generally demonstrated strong performance. For supervised auto-gating methods, four algorithms were evaluated, where DeepCyTOF and CyTOF Linear Classifier performed the best. We further provided practical recommendations on prioritizing gating methods based on different application scenarios. This study offers comprehensive insights for biologists to understand diverse gating methods and choose the best-suited ones for their applications.

bioinformatics↗

G-quadruplexes are a source of vulnerability in BRCA2 deficient granule cell progenitors and medulloblastoma

Biallelic pathogenic variants in the essential DNA repair gene BRCA2 causes Fanconi anemia, complementation group FA-D1. Patients in this group are highly prone to develop embryonal tumors, most commonly medulloblastoma arising from the cerebellar granule cell progenitors (GCPs). GCPs undergo high proliferation in the postnatal cerebellum under SHH activation, but the type of DNA lesions that require the function of the BRCA2 to prevent tumorigenesis remains unknown. To identify such lesions, we assessed both GCP neurodevelopment and tumor formation using a mouse model with deletion of exons three and four of Brca2 in the central nervous system, coupled with global Trp53 loss. Brca2{Delta}ex3-4;Trp53-/- animals developed SHH subgroup medulloblastomas with complete penetrance. Whole-genome sequencing of the tumors identified structural variants with breakpoints enriched in areas overlapping G-quadruplexes (G4s). Brca2-deficient GCPs exhibited decreased replication speed in the presence of the G4-stabilizer pyridostatin. Pif1 helicase, which resolves G4s during replication, was highly upregulated in tumors, and Pif1 knockout in primary MB tumor cells resulted in increased genome instability upon pyridostatin treatment. These data suggest that G4s may represent sites prone to replication stalling in highly proliferative GCPs and without BRCA2, G4s become a source of genome instability. Tumor cells upregulate G4-resolving helicases to facilitate rapid proliferation through G4s highlighting PIF1 helicase as a potential therapeutic target for treatment of BRCA2-deficient medulloblastomas.

cancer biology↗

Apoptotic caspases cleave DRP1 to promote mitochondrial fusion and anti-viral immune responses

Apoptosis has been recognized as a suicidal host-defense programmed cell death pathway against invading pathogens. However, recent evidences showed that viruses can employ caspases to cleave and inactivate immune signaling molecules to facilitate infection. Whether caspases can instead promote anti-viral immune responses is currently unknown. Here, we demonstrated that the NSs protein of RVFV triggers activation of apoptotic caspases, which cleave the mitochondrial fission factor DRP1 resulting in mitochondrial elongation. Elongated mitochondria promote MAVS aggregation leading to enhanced anti-viral immunity. Apoptotic caspases, including caspase-3, -6, -7 and -8, cleave DRP1 at the motifs of D500FAD503 and/or AEAD556, suggesting that this cleavage event may occur during infection of different viruses. Indeed, infection of H1N1, SeV and HSV-1 all triggered apoptotic caspases activation to cleave DRP1 promoting anti-viral immune responses. Compared with wild-type DRP1, introduction of caspase-resistant DRP1 strongly attenuated immune responses triggered by virus infection. These results revealed a mechanism through which apoptotic caspases promote anti-viral immunity by regulating mitochondrial morphodynamics.

microbiology↗

Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity

Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics in these viruses remain largely unknown. In this study, we investigated population and intra-population dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed near-automatic computational pipeline generated 1,065 high-quality metagenome-assembled genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community at the study site and distinct dynamics of different viral populations classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. Notably, year-round recovery patterns were observed at the intra-population genetic diversity level for viruses classified as persistent or seasonal. Our results further indicated that the viral genome dynamics were associated with intra-population diversity; specifically, giant viruses with broader niche breadth tended to exhibit greater levels of microdiversity. We argue that greater microdiversity in viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.

microbiology↗

High efficient chromatin conformation capture without pre-enrichment (HiChew) in single cells

This study presents HiChew, a cutting-edge technique for high-efficiency chromatin conformation capture in single cells, without the need for pre-enrichment. This unique approach minimizes the risk of cell or DNA loss. When compared to Dip-C, HiChew captures valid pairs with 4-8 times more efficiency, reducing wastage and saving significant sequencing budget. Furthermore, HiChew delivers a lower false positive ratio, ensuring data accuracy. It also achieves more contacts per cell, enhancing resolution in single cell. HiChews superior performance not only enhances single-cell Hi-C but also streamlines conventional Hi-C, making it more robust than conventional HiC methods. This study also unveils a fascinating mechanism of gene activation in the B compartment of chromatin, providing insight into the elusive aspect of gene expression within this region.

genomics↗

Digital Immunoassay for Rapid Detection of SARS-CoV-2 Infection in a Broad Spectrum of Animals

The ability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to infect a wide-range of species raises significant concerns regarding both human-to-animal and animal-to-human transmission. There is an increasing demand for highly sensitive, rapid, and simple diagnostic assays that can detect viral infection across various species. In this study, we developed a biosensor assay that adapted a monoclonal-antibody (mAb)-based blocking ELISA format into an Activate Capture + Digital Counting (AC + DC)-based immunoassay. The assay employs a photonic crystal (PC) biosensor, gold-nanoparticle (AuNP) tags, SARS-CoV-2 nucleocapsid (N) protein, and specific anti-N mAb to detect antibody responses in animals exposed with SARS-CoV-2. We demonstrated a simple 2-step 15-min test that was capable of detecting as low as 12.5 ng of antibody in controlled standard serum samples. Based on an evaluation of 176 cat serum samples with known antibody status, an optimal percentage of inhibition (PI) cut-off value of 0.588 resulted in a diagnostic sensitivity of 98.3% and a diagnostic specificity of 96.5%. The test is highly repeatable with low variation coefficients of 2.04%, 2.73%, and 4.87% across different runs, within a single run, and on a single chip, respectively. The test was further employed to detect antibody responses in multiple animal species as well as investigate dynamics of antibody response in experimentally infected cats. This test platform provides an important tool for rapid field surveillance of SARS-CoV-2 infection across multiple species.

microbiology↗

Mechanosensitive FHL2 tunes endothelial function

Endothelial tissues are essential mechanosensors in the vasculature and facilitate adaptation to various blood flow-induced mechanical cues. Defects in endothelial mechanoresponses can perturb tissue remodelling and functions leading to cardiovascular disease progression. In this context, the precise mechanisms of endothelial mechanoresponses contributing to normal and diseased tissue functioning remain elusive. Here, we sought to uncover how flow-mediated transcriptional regulation drives endothelial mechanoresponses in healthy and atherosclerotic-prone tissues. Using bulk RNA sequencing, we identify novel mechanosensitive genes in response to healthy unidirectional flow (UF) and athero-prone disturbed flow (DF). We find that the transcription as well as protein expression of Four-and-a-half LIM protein 2 (FHL2) are enriched in athero-prone DF both in vitro and in vivo. We then demonstrate that the exogenous expression of FHL2 is necessary and sufficient to drive discontinuous adherens junction morphology and increased tissue permeability. This athero-prone phenotype requires the force-sensitive binding of FHL2 to actin. In turn, the force-dependent localisation of FHL2 to stress fibres promotes microtubule dynamics to release the RhoGEF, GEF-H1, and activate the Rho-ROCK pathway. Thus, we unravelled a novel mechanochemical feedback wherein force-dependent FHL2 localisation promotes hypercontractility. This misregulated mechanoresponse creates highly permeable tissues, depicting classic hallmarks of atherosclerosis progression. Overall, we highlight crucial functions for the FHL2 force-sensitivity in tuning multi-scale endothelial mechanoresponses.

cell biology↗

Poxvirus A52 is a host range factor for modified vaccinia virus Ankara (MVA) and promotes viral replication by disturbing the formation of autolysosomes

Many members of the poxvirus family are important zoonotic pathogens that pose a significant threat to human and animal health worldwide. Autophagy is a multi-step degradation pathway within cells, and one of its primary biological functions includes the clearance of invading viruses. Nevertheless, the interplay between poxviruses and host cell autophagy has not been fully elucidated. Here, we demonstrate that vaccinia virus (VACV) and lumpy skin disease virus (LSDV) induce incomplete autophagy and inhibit the fusion of autophagosomes and lysosomes, while modified vaccinia virus Ankara (MVA), an attenuated strain of VACV unable to replicate in almost all human cells, does not. Additionally, we screened and identified the VACV protein A52 as a key factor that obstruct the formation of autolysosomes. Mechanistically, A52 interacts with SNAP29 and inhibits its interaction with STX17 and VAMP8, both of which are binding partners of SNAP29 and are essential for complete autophagy. Moreover, A52 promotes the proteasomal degradation of SNAP29, which facilitates viral replication. We further revealed that SNAP29 functions as a restriction factor for MVA, as the suppression of SNAP29 allowed the replication of MVA in human cells. In summary, our data present a molecular mechanism by which poxviruses manipulate the cellular autophagic machinery and provide additional explanation for the restriction of MVA in human cells.

microbiology↗

Pencil Beam Based X-ray Luminescence Computed Tomography Imaging of Deep TargetsThree-dimensionally and Quantitatively

X-ray luminescence computed tomography (XLCT), especially pencil beam based XLCT, has been emerged for more than 15 years because it can image deep targets in tissue with high spatial resolution and high measurement sensitivity. However, its application is limited by long scanning time and the tedious efforts of finite element mesh generation for model based reconstruction. Our previous study has addressed the imaging speed issue. In this study, we propose to reconstruct XLCT with weighted filtered back projection (wFBP) which makes it possible to perform XLCT imaging three dimensionally for complex objects at a high spatial resolution. We have also proposed measurements with multiple detectors to obtain quantitative XLCT images. To evaluate the proposed methods, we have performed numerical simulations and different sets of phantom experiments including phantom experiments with a control contrast target, different concentrations, and different target sizes. We have also successfully reconstructed deep targets with a diameter of approximately 0.15 mm. For the phantom experiments with targets of different concentrations, using a 4-channel XLCT system and the wFBP, we achieved the ratio of 3.8:1.79:1, closely resembling the ground truth ratio of 4:2:1. Lastly, we have, for the first time, reconstructed different 3D targets at high spatial resolution, successfully, including a printed M target, a triangular hollow bar, and a hot background cuboid with "UCM Li Lab" slots. Our results indicate that the proposed wFBP advances the promising XLCT technology and makes it ready for in vivo studies in the future.

bioengineering↗

An intra-family conserved high-order RNA structure within the M ORF is important for arterivirus subgenomic RNA accumulation and infectious virus production

Synthesis of subgenomic RNAs is a strategy commonly used by polycistronic positive sense single-stranded RNA viruses to express 3'-proximal genes. Members of the order of Nidovirales, including coronaviruses and arteriviruses, use a unique discontinuous transcription strategy to synthesize subgenomic RNAs. In this study, in silico synonymous site conservation analysis and RNA structure folding predicted the existence of intra-family conserved high-order RNA structure within the M ORF of arteriviral genomes, which was further determined to be important for the transcription/accumulation of subgenomic RNAs and production of infectious viral particles. Mutations disrupting the stability of the RNA structures significantly decreased the accumulation of multiple subgenomic RNAs. In contrast, the impact of mutagenesis on full-length genomic RNA accumulation was limited. The degree to which wild-type levels of subgenomic RNA accumulation were maintained was found to correlate with the efficiency of infectious virus production. Moreover, the thermo-stability of stems within the high-order RNA structure is also well correlated with viral replication capacity and the maintenance of subgenomic RNA accumulation. This study is the first to report an intra-Arteriviridae conserved high-order RNA structure that is located in a protein-coding region and functions as an important cis-acting element to control the accumulation/transcription of arteriviral subgenomic RNAs. This work suggests a complex regulation mechanism between genome replication and discontinuous transcription in nidoviruses. IMPORTANCEArteriviruses are a group of RNA viruses that infect different animal species. They can cause diseases associated with respiratory/reproductive syndromes, abortion, or haemorrhagic fever. Among arteriviruses, porcine reproductive and respiratory syndrome virus (PRRSV) and equine arteritis virus (EAV) are economically important veterinary pathogens. The challenge in control of arterivirus infection reflects our limited knowledge of viral biology. In this study, we conducted a comprehensive bioinformatical analysis of arteriviral genomes and discovered intra-family conserved regions in the M ORF with a high-order RNA structure. The thermo-stability of the RNA structure influences sgRNA transcription/accumulation and correlates with the level of infectious virus production. Our studies provide a new insight on arterivirus replication mechanism, which may have implications in developing disease control and prevention strategies.

molecular biology↗

Heat stress and recovery induce transcriptomic changes in lactogenic bovine mammary epithelial (MAC-T) cells

Heat stress (HS) in cattle significantly challenges the dairy industry by reducing milk production. However, the molecular mechanism behind mammary gland responses to HS and recovery remains poorly understood. This study aimed to determine the transcriptomic changes in lactogenic bovine mammary epithelial (MAC-T) cells after HS and post-HS recovery. Six culture conditions were analyzed: MAC-T cells cultured in basal medium, cells in lactogenic medium to induce differentiation, differentiated cells at standard temperature (37) or HS (42) for 1 hour. HS cells were collected after incubation at 37 for either 2 or 6 hours to examine the extent of recovery. A total of 1,668 differentially expressed genes (DEGs) were identified. Differentiated cells expressed genes associated with milk lipid synthesis, indicating lactogenic potential. HS suppressed genes involved in cellular differentiation and activated heat shock protein genes. Several transcription factors were identified as potential regulators of HS response. During recovery, chaperon-mediated protein folding genes remained elevated. Apoptosis regulation genes were induced at 2 hours, and cellular homeostasis regulation genes were enriched at 6 hours. Overall, these findings provide a foundation for the molecular mechanisms involved in HS and recovery in cattle.

genomics↗

Spatiotemporal dynamics revealed the dark water community of giant virus from a deep freshwater lake

Giant viruses significantly regulate the ecological dynamics of diverse ecosystems. Although metagenomics has expanded our understanding of their diversity and ecological roles played in marine environments, little is known about giant viruses of freshwater ecosystems. Most previous studies have employed short-read sequencing and therefore resulted in fragmented genomes, hampering accurate assessment of genetic diversity. We sought to bridge this knowledge gap and overcome previous technical limitations. We subjected spatiotemporal (2 depths x 12 months) samples from Lake Biwa to metagenome-assembled genome reconstruction enhanced by long-read metagenomics. This yielded 294 giant virus metagenome-assembled genomes. Of these, 285 included previously unknown species in five orders of nucleocytoviruses and the first representatives of freshwater mirusviruses, which exhibited marked divergence between freshwater- and marine-derived lineages. Notably, 42 (14.3%) genomes were composed of single contigs with completeness values >90%, demonstrating the good performance of our long-read metagenomic assembly. Giant viruses were partitioned across water depths, with most species specific to either the sunlit epilimnion or the dark hypolimnion. Epilimnion-specific members tended to be opportunistic and to exhibit short and intense abundance peaks, in line with the fact that they regulate the surface algal blooms. During the spring bloom, mirusviruses and members of three nucleocytovirus families were among the most abundant giant viruses. In contrast, hypolimnion-specific ones including algaviruses and mirusviruses were typically more persistent in the hypolimnion throughout the water-stratified period, suggesting that they infect hosts specific to the hypolimnion and play previously unexplored ecological roles in dark water-specific microbial ecosystems.

ecology↗

FLASH Irradiation Regulates IFN-β induction by mtDNA via Cytochrome c Leakage

Ultrahigh dose rate radiotherapy (FLASH-RT) is under intensive investigation for its biological benefits. The mechanisms underlying its ability to spare normal tissues while suppress tumor growth still remain controversial. Here we reveal that compared to the low dose rate electron irradiation (0.36 Gy/s), FLASH electron irradiation at 61 or 610 Gy/s enhances the cytochrome c leakage from mitochondria in human breast cells MCF-10A, which elicits substantial caspase activation, suppresses both the cytosolic mitochondrial DNA (mtDNA) accumulation and IFN-{beta} secretion. Besides, the deletion of mtDNA severely decreases the radiation-induced cGAS-STING activation. Conversely, the cytochrome c leakage in carcinoma cells MDA-MB-231 post electron irradiation is limited, especially for the case of FLASH irradiation, resulting in less cytosolic cytochrome c but stronger cGAS-STING activation than those in MCF-10A cells. The enhanced difference of cytochrome c leakage between cancer cells and normal cells post FLASH irradiation indicates a potential mechanism of FLASH effect by regulating the apoptotic and inflammatory pathway.

biophysics↗

Thermotherapy has Sexually Dimorphic Responses in APP/PS1 Mice

A thermoregulatory decline occurs with age due to changes in muscle mass, vasoconstriction, and metabolism that lowers core body temperature (Tc). Although lower Tc is a biomarker of successful aging, we have previously shown this worsens cognitive performance in the APP/PS1 mouse model of Alzheimers disease (AD) [1]. We hypothesized that elevating Tc with thermotherapy would improve metabolism and cognition in APP/PS1 mice. From 6-12 months of age, male and female APP/PS1 and C57BL/6 mice were chronically housed at 23 or 30{degrees}C. At 12 months of age, mice were assayed for insulin sensitivity, glucose tolerance, and spatial cognition. Plasma, hippocampal, and peripheral (adipose, hepatic, and skeletal muscle) samples were procured postmortem and tissue-specific markers of amyloid accumulation, metabolism, and inflammation were assayed. Chronic 30{degrees}C exposure increased Tc in all groups except female APP/PS1 mice. All mice receiving thermotherapy had either improved glucose tolerance or insulin sensitivity, but the underlying processes responsible for these effects varied across sexes. In males, glucose regulation was influenced predominantly by hormonal signaling in plasma and skeletal muscle glucose transporter 4 expression, whereas in females, this was modulated at the tissue level. Thermotherapy improved spatial navigation in male C57BL/6 and APP/PS1 mice, with the later attributed to reduced hippocampal soluble amyloid-{beta} (A{beta})42. Female APP/PS1 mice exhibited worse spatial memory recall after chronic thermotherapy. Together, the data highlights the metabolic benefits of passive thermotherapy, but future studies are needed to determine therapeutic benefits for those with AD.

neuroscience↗

Sediment-associated processes drive spatial variation in ecosystem respiration in the Yakima River basin

Hyporheic zones (HZ) can contribute substantially to total stream ecosystem respiration (ERtot). HZ-focused process-based models may, therefore, effectively predict ERtot across sites, yet this remains untested under variable environmental conditions. Here we evaluate whether spatial variation in HZ respiration predicted via a process-based model explains spatial variation in field-estimates of ERtot across 33 sites in the Yakima River basin in Washington State, USA. We found that HZ respiration predictions did not explain spatial variation in field estimates of ERtot. To investigate further, we partitioned ERtot contributions into water column respiration (ERwc) and sediment-associated respiration (ERsed). ERsed contributed >50% of ERtot at 88% of sites, though relative contributions varied substantially. Despite this dominance, modeled HZ respiration explained neither spatial variation in ERtot nor in ERsed, suggesting that the HZ model alone does not capture the drivers of sediment-associated respiration across these sites. Instead, ERsed spatial variation was primarily explained by gross primary production, stream slope, velocity, and total dissolved nitrogen rather than median grain size, a primary control of HZ respiration predicted by the process-based model. Consistent with recent studies, our results indicate that improving basin-scale ERtot predictions requires integrating hydrologic and biogeochemical processes across hyporheic, benthic, and water column zones.

ecology↗