Biology subjects

Zhang, M.

Publications and source records attributed to Zhang, M..

At least 415 records · Page 23Linked to original sources

bioRxiv2023

Comprehensive catalogs for microbial genes and metagenome-assembled genomes of the swine lower respiratory tract microbiome identify the relationship of microbial species with lung lesions

Understanding the community structure and functional capacity of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about it owing to the difficulty in obtaining microbial samples from the lower respiratory tract. Here we collected 745 microbial samples from the porcine lower respiratory tract by harvesting 675 pigs, and constructed a gene catalog containing 10,337,194 nonredundant genes, of which only 30% could be annotated taxonomically. We obtained 397 metagenome-assembled genomes (MAGs) including 111 MAGs with high-quality. These 397 MAGs were further clustered into 292 species-level genome bins (SGBs), among which 56% SGBs are unknown with current databases. Combining with the lung lesion phenotype, we found that Mycoplasma hyopneumoniae strains and the adhesion-related virulence factors harboring in their genomes were significantly associated with porcine lung lesions, implying the role of adhesion and overgrowth of pathogenic M. hyopneumoniae in host lung diseases. This study provided important resources for the study of porcine lower respiratory tract microbiome and lung health.

microbiology↗

bioRxiv2023

T2T-YAO: a Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese

Since its initial release in 2001, the human reference genome has been continuously improved in both continuity and accuracy, and the recently-released telomere-to-telomere version--T2T-CHM13--reaches its top quality after 20 years of effort. However, T2T-CHM13 does not represent an authentic diploid human genome, but rather one derived from a simplified, nearly homozygous genome of a hydatidiform mole cell line. To address this limitation and provide an alternative pertinent to the Chinese population, the largest ethnic group in the world, we have assembled a complete diploid human genome of a male Han Chinese, T2T-YAO, which includes telomere-to-telomere assemblies for all the 22+X+M and 22+Y chromosomes in his two haploids inherited separately from his parents. Both haplotypes contain no artificial sequences or model nucleotides and possess a high quality comparable to CHM13, with fewer than one error per [~]14 Mb. Derived from the individual who lives in the aboriginal region of Han Chinese, T2T-YAO shows clear ancestry and potential genetic continuity from the ancient ancestors of the Han population. Each haplotype of T2T-YAO possesses [~]340 Mb exclusive sequences and [~]3100 unique genes as compared to CHM13, and their genome sequences show greater genetic distance to CHM13 than to each other in terms of nucleotide polymorphism and structural variations. The construction of T2T-YAO would serve as a high-quality diploid reference that enables precise delineation of genomic variations in a haplotype-sensitive manner, which could advance our understandings in human evolution, hereditability of diseases and phenotypes, especially within the context of the unique variations of the Chinese population.

genetics↗

bioRxiv2023

Single cell RNA analysis uncovers the cell differentiation trajectories and functionalization for air breathing of frog lung

The evolution and development of vertebrate lungs have received extensive concerns for the significance in terrestrial adaptation. Amphibians possess the most primitive lungs among tetrapods, underscoring the evolutionary importance of lungs in bridging the transition from aquatic to terrestrial life. However, the intricate process of cell differentiation during amphibian lung development is still lacking. Using single cell RNA-seq, we identified 21 cell types in the developing lung of a land-dwelling frog (Microhyla fissipes). We elucidated that single type of alveolar epithelial cells (AECs) existed in amphibian and the diversity of AECs may correspond to the capacity for terrestrial adaptation in tetrapods. Based on pseudotime trajectories analysis, we revealed previously unrecognized developmental-specific transition cell states of epithelial and endothelial cells supporting the rapid morphogenesis of lung during metamorphic climax. We illustrated the cellular and molecular processes during lung functionalization. These findings uncover the cell differentiation trajectories and functionalization for air breathing of frog lungs and highlight the evolutionary peculiarity of the primitive lungs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/549571v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@d3188aorg.highwire.dtl.DTLVardef@f049feorg.highwire.dtl.DTLVardef@189f98borg.highwire.dtl.DTLVardef@15e3857_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Experience sampling reveals the role that covert goal states play in task-relevant behavior.

Cognitive neuroscience has gained insight into covert states using experience sampling. Traditionally, this approach has focused on off-task states, however, task-relevant states are also maintained via covert processes. Our study examined whether experience sampling can also provide insights into covert goal-relevant states that support task performance. To address this question, we developed a neural state-space, using dimensions of brain function variation, that allows neural correlates of overt and covert states to be examined in a common analytic space. We use this to describe brain activity during task performance, its relation to covert states identified via experience sampling, and links between individual variation in overt and covert states and task performance. Our study established activity patterns within association cortex emphasizing the fronto-parietal network both during target detection and a covert state of deliberate task focus which was associated with better task performance. In contrast, periods of vigilance and a covert off-task state were both linked to activity patterns emphasizing the default mode network. Our study shows experience sampling can not only describe covert states that are unrelated to the task at hand, but can also be used to highlight the role fronto-parietal regions play in the maintenance of covert task-relevant states.

neuroscience↗

bioRxiv2023

AAV-mediated Delivery of Plakophilin-2a Arrests Progression of Arrhythmogenic Right Ventricular Cardiomyopathy in Murine Hearts: Preclinical Evidence Supporting Gene Therapy in Humans

BackgroundPathogenic variants in plakophilin-2 (PKP2) cause arrhythmogenic right ventricular cardiomyopathy (ARVC), a disease characterized by life-threatening arrhythmias and progressive cardiomyopathy leading to heart failure. No effective medical therapy is available to prevent and/or arrest the disease. We tested the hypothesis that AAV-mediated delivery of the human PKP2 gene to an adult mammalian heart deficient in PKP2 can arrest disease progression and significantly prolong survival. MethodsExperiments were carried out using a cardiac-specific, tamoxifen (TAM)-activated PKP2 knockout murine model (PKP2-cKO). The potential therapeutic, AAVrh.74-PKP2a (RP-A601), is a recombinant AAVrh.74 gene therapy viral vector encoding the human PKP2 variant A (PKP2a). AAVrh.74-PKP2a was delivered to adult mice by a single tail vein injection either before or after TAM-activated PKP2-cKO. PKP2 expression was confirmed by molecular and histopathologic analyses. Cardiac function and disease progression were monitored by survival analyses, echocardiography and electrocardiography. ResultsConsistent with prior findings, loss of PKP2 expression caused 100% mortality within 50 days after TAM injection. In contrast, AAVrh.74-PKP2a-mediated PKP2a expression resulted in 100% survival for more than 5 months (at study termination). Echocardiographic analysis revealed that AAVrh.74-PKP2a prevented right ventricle dilation, arrested left ventricle functional decline, and mitigated arrhythmia burden. Molecular and histological analysis showed AAVrh.74-PKP2a- mediated transgene mRNA and protein expression and appropriate PKP2 localization at the cardiomyocyte intercalated disc. Importantly, therapeutic benefit was shown in mice receiving AAVrh.74-PKP2a after disease onset. ConclusionThese preclinical data demonstrate the potential for AAVrh.74-PKP2a (RP-A601) as a therapeutic for PKP2-related ARVC in both early and more advanced stages of disease.

physiology↗

bioRxiv2023

The canonical single-stranded DNA binding protein SSB is not an essential replication protein but an RNA chaperon in the hyperthermophilic archaeon Saccharolobus islandicus REY15A

Single-stranded DNA binding proteins (SSBs) have been regarded as indispensable factors in all three domains of life since they play vital roles in DNA replication. Herein, we report that genes coding for the canonical SSB (SisSSB) and the non-canonical SSB (SisDBP) in the hyperthermophilic archaeon Saccharolobus islandicus REY15A can both be deleted. The growth is not affected, and the cell cycle progression and genome stability of the deletion strains is not impaired, suggesting that SisSSB and SisDBP are not essential for cell viability. Interestingly, at a lower temperature (55{degrees}C), the protein level of SisSSB increases [~]1.8 fold in the wild type and the growth of {Delta}Sisssb and {Delta}Sisssb{Delta}Sisdbp is retarded. SisSSB exhibits melting activity on dsRNA and DNA/RNA hybrid in vitro and unwinding RNA hairpin in Escherichia coli. Furthermore, the core SisSSB domain is able to complement the absence of the cold shock proteins CspABGE in E. coli, suggesting that SisSSB functions as RNA chaperon. We show that a two-fold overexpression of SisSSB is beneficial to the cell growth at lower temperature, but it has detrimental effect on the cell growth and cell cycle progression at normal growth temperature, which differs from bacterial Csp proteins. Importantly, these in vitro and in vivo activities are conserved in SSB subtype SSB-1 in Crenarchaeota species that lack bacterial Csp homologs. Overall, we have clarified the function of the archaeal canonical SSB which does not function as a DNA processing factor, but plays a role in processes requiring dsRNA or DNA/RNA hybrid unwinding.

microbiology↗

bioRxiv2023

Augmented Super-Resolution Radial Fluctuations (aSRRF) Pushing the Limits of Structured Illumination Microscopy

Structured illumination microscopy (SIM) is a versatile super-resolution technique known for its compatibility with a wide range of probes and fast implementation. While 3D SIM is capable of achieving a spatial resolution of [~]120 nm laterally and [~]300 nm axially, attempting to further enhance the resolution through methods such as nonlinear SIM or 4-beam SIM introduces complexities in optical configurations, increased phototoxicity, and reduced temporal resolution. Here, we have developed a novel method that combines SIM with augmented super-resolution radial fluctuations (aSRRF) utilizing a single image through image augmentation. By applying aSRRF reconstruction to SIM images, we can enhance the SIM resolution to [~]50 nm isotopically, without requiring any modifications to the optical system or sample acquisition process. Additionaly, we have incorporated the aSRRF approach into an ImageJ plugin and demonstrated its versatility across various fluorescence microscopy images, showcasing a remarkable two-fold resolution increase.

cell biology↗

bioRxiv2023

Bestrophin-4 relays Hes4 and interacts with Twist1 to suppress epithelial-to-mesenchymal transition in colorectal cancer cells

AbstractBestrophin isoform 4 (BEST4) is a newly identified subtype of the calcium-activated chloride channel family. Analysis of colonic epithelial cell diversity by single cell RNA-sequencing has revealed the existence of a cluster of BEST4+ mature colonocytes in humans. However, if the role of BEST4 is involved in regulating tumour progression remains largely unknown. In this study, we demonstrate that BEST4 overexpression attenuates cell proliferation, colony formation, and mobility in colorectal cancer (CRC) in vitro, and impedes the tumor growth and the liver metastasis in vivo. BEST4 is coexpressed with hairy/enhancer of split 4 (Hes4) in the nucleus of cells, and Hes4 signals BEST4 by interacting with the upstream region of the BEST4 promoter. BEST4 is epistatic to Hes4 and downregulates Twist1, thereby inhibiting epithelial-to-mesenchymal transition (EMT) in CRC. Conversely, knockout of BEST4 using CRISPR/Cas9 in CRC cells revitalises tumor growth and induces EMT. Furthermore, the low level of the BEST4 mRNA is correlated with advanced and the worse prognosis, suggesting its potential role in regulating CRC progression.

cancer biology↗

bioRxiv2023

Exploiting the therapeutic vulnerability of IDH-mutant gliomas with zotiraciclib

Isocitrate dehydrogenase (IDH)-mutant gliomas have distinctive metabolic and biological traits that may render them susceptible to targeted treatments. Here, by conducting a high-throughput drug screen, we pinpointed a specific susceptibility of IDH-mutant gliomas to zotiraciclib (ZTR). ZTR exhibited selective growth inhibition across multiple IDH-mutant glioma in vitro and in vivo models. Mechanistically, ZTR at low doses suppressed CDK9 and RNA Pol II phosphorylation in IDH-mutant cells, disrupting mitochondrial function and NAD+ production, causing oxidative stress. Integrated biochemical profiling of ZTR kinase targets and transcriptomics unveiled that ZTR-induced bioenergetic failure was linked to the suppression of PIM kinase activity. We posit that the combination of mitochondrial dysfunction and an inability to adapt to oxidative stress resulted in significant cell death upon ZTR treatment, ultimately increasing the therapeutic vulnerability of IDH-mutant gliomas. These findings prompted a clinical trial evaluating ZTR in IDH-mutant gliomas towards precision medicine (NCT05588141). HighlightsO_LIZotiraciclib (ZTR), a CDK9 inhibitor, hinders IDH-mutant glioma growth in vitro and in vivo. C_LIO_LIZTR halts cell cycle, disrupts respiration, and induces oxidative stress in IDH-mutant cells. C_LIO_LIZTR unexpectedly inhibits PIM kinases, impacting mitochondria and causing bioenergetic failure. C_LIO_LIThese findings led to the clinical trial NCT 05588141, evaluating ZTR for IDH-mutant gliomas. C_LI

cancer biology↗

bioRxiv2023

Bipartite left-right sided endocrine system: processing of contralateral effects of brain injury

The crossed descending neural tracts set a basis for contralateral effects of brain injury. In addition, the left-right side-specific effects of the unilateral brain lesions may be mediated by neurohormones through the humoral pathway as discovered in animals with disabled descending motor tracts. We here examined if counterparts of the endocrine system that convey signals from the left and right brain injuries differ in neural and molecular mechanisms. In rats with completely transected cervical spinal cords a unilateral injury of the hindlimb sensorimotor cortex produced hindlimb postural asymmetry with contralateral hindlimb flexion, a proxy for neurological deficit. The effects of the left and right side brain lesions were differently inhibited by antagonists of the {delta}-, {kappa}- and {micro}-opioid receptors suggesting differential neuroendocrine control of the left-right side-specific hormonal signaling. Bilateral deafferentation of the lumbar spinal cord eliminated hormone-mediated effects of the left-side brain injury but not the right-side lesion suggesting their afferent and efferent mechanisms, respectively. Analysis of gene-gene co-expression patterns identified the left and right side-specific gene regulatory networks that were coordinated across the hypothalamus and lumbar spinal cord through the humoral pathway. The coordination was ipsilateral and perturbed by brain injury. These findings suggest that the neuroendocrine system that conveys left-right side-specific hormonal messages from injured brain is bipartite, contributes to contralateral neurological deficits through asymmetric neural mechanisms, and enables ipsilateral coordination of molecular processes across neural areas along the neuraxis. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=173 HEIGHT=200 SRC="FIGDIR/small/546857v2_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1d0ad6org.highwire.dtl.DTLVardef@b273f8org.highwire.dtl.DTLVardef@1dbac79org.highwire.dtl.DTLVardef@118599c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

The Sde phosphoribosyl-linked ubiquitin transferases exploit reticulons to protect the integrity of the Legionella-containing vacuole

Legionella pneumophila grows within host cells by forming a specialized membrane-bound compartment via the Icm/Dot type IV secretion system (T4SS). T4SS translocated Sde proteins promote phosphoribosyl-linked ubiquitination (pR-Ub) of several mammalian cell proteins, including Rtn4. In response to modification, Rtn4 forms tubular ER aggregates around the Legionella-containing vacuole (LCV). The loss of sde together with sdhA results in severe vacuole disruption at early infection timepoints. We tested if Rtn4 modification allowed it to serve as a physical barrier to protect its degradation from host-derived disruptive compartments. The challenge of the rtn4-/- macrophages with {Delta}sdhA partially phenocopied the challenge of rtn4+/+ with {Delta}sde{Delta}sdhA, indicating that Rtn4 plays a role in protecting LCV integrity. Depletion of rtn1 in rtn4-/- macrophages potentiated vacuole permeability when compared to rtn4-/- macrophages, consistent with Sde targeting multiple reticulon family members to support vacuole integrity. These results indicate that L. pneumophila exploits Rtn4 in cooperation with Rtn1 to establish a replication niche by promoting Sde-mediated tubular ER aggregates, arguing that these proteins function as a physical barrier during early steps of LCV biogenesis.

microbiology↗

bioRxiv2023

Immortalization and transformation of primary cells mediated by engineered ecDNAs

Focal gene amplifications are among the most common cancer-associated mutations, but their evolution and contribution to tumorigenesis have proven challenging to recapitulate in primary cells and model organisms. Here we describe a general approach to engineer large (>1 Mbp) focal amplifications mediated by extrachromosomal circular DNAs (ecDNAs, also known as "double minutes") in a spatiotemporally controlled manner in cancer cell lines and in primary cells derived from genetically engineered mice. With this strategy, ecDNA formation can be coupled with expression of fluorescent reporters or other selectable markers to enable the identification and tracking of ecDNA-containing cells. We demonstrate the feasibility of this approach by engineering MDM2-containing ecDNAs in near-diploid human cells, showing that GFP expression can be used to track ecDNA dynamics under physiological conditions or in the presence of specific selective pressures. We also apply this approach to generate mice harboring inducible Myc- and Mdm2-containing ecDNAs analogous to those spontaneously occurring in human cancers. We show that the engineered ecDNAs rapidly accumulate in primary cells derived from these animals, promoting proliferation, immortalization, and transformation.

cancer biology↗

bioRxiv2023

snoRNA-guided tRNA 2'-O-methylation controls codon-biased gene expression and cellular states

snoRNAs are a large family of noncoding (nc)RNAs present across eukaryotes and archaea. While a subset of them guide 2-O- methylation (Nm) and pseudouridylation ({Psi}) of rRNAs and snRNAs, targets of most snoRNAs remain unknown. Here we used PARIS2 to map snoRNA targets, revealing an extensive and conserved snoRNA-tRNA interaction network. Using optimized denatured RiboMeth-seq (dRMS), we discovered snoRNA-guided Nm sites in ncRNAs, including tRNAs. Loss of snoRNAs and their associated 2-O-methyltransferase FBL reduced tRNA modifications and increased fragmentation. CRISPR knockout of the D97/D133 family of snoRNAs reduced the activity and levels of several target tRNAs, including elongator (e)Met-CAU, leading to codon-biased transcriptome and translatome in human cells. The codon-biased gene expression tipped the balance between the dichotomous cellular states of proliferation and differentiation, and skewed germ layer potential of mouse embryonic stem cells. Together, we discovered a snoRNA-guided tRNA modification mechanism controlling codon-biased gene expression and cellular states.

biochemistry↗

bioRxiv2023

In Vitro Culture Alters Cell Lineage Composition and Cellular Metabolism of Bovine Blastocyst

Profiling transcriptome at single cell level of bovine blastocysts derived in vivo (IVV), in vitro from conventional culture medium (IVC), and reduced nutrient culture medium (IVR) has enabled us to reveal cell lineage segregation, during which forming inner cell mass (ICM), trophectoderm (TE), and an undefined population of transitional cells. Only IVV embryos had well-defined ICM, indicating in vitro culture may delay the first cell fate commitment to ICM. Differences between IVV, IVC and IVR embryos were mainly contributed by ICM and transitional cells. Pathway analysis by using the differentially expressed genes of these non-TE cells between groups pointed to highly active metabolic and biosynthetic processes, with reduced cellular signaling and membrane transport in IVC embryos, which may lead to reduced developmental potential. IVR embryos had lower activities in metabolic and biosynthetic processes, but increased cellular signaling and membrane transport, suggesting these cellular mechanisms may contribute to the improved blastocyst development compared to IVC embryos. However, the IVR embryos had compromised development when compared to IVV embryos with notably over-active membrane transport activities that led to impaired ion homeostasis. Summary StatementSingle-cell transcriptomic analysis of bovine blastocysts produced in vivo, and in vitro in conventional and reduced nutrient conditions reveals the effect of culture environments on embryo developmental potential.

developmental biology↗

bioRxiv2023

The involvement of the human prefrontal cortex in the emergence of visual awareness

Exploring the neural mechanisms of awareness is a fundamental task of cognitive neuroscience. There is an ongoing dispute regarding the role of the prefrontal cortex (PFC) in the emergence of awareness, which is partially raised by the confound between report- and awareness-related activity. To address this problem, we designed a visual awareness task that can minimize report-related motor confounding. Our results show that saccadic latency is significantly shorter in the aware trials than in the unaware trials. Local field potential (LFP) data from 6 patients consistently show early (200-300 ms) awareness-related activity in the PFC, including event-related potential and high-gamma activity. Moreover, the awareness state can be reliably decoded by the neural activity in the PFC since the early stage, and the neural pattern is dynamically changed rather than being stable during the representation of awareness. Furthermore, the enhancement of dynamic functional connectivity, through the phase modulation at low frequency, between the PFC and other brain regions in the early stage of the awareness trials may explain the mechanism of conscious access. These results indicate that the PFC is critically involved in the emergence of awareness.

neuroscience↗

bioRxiv2023

Flexible Analysis of Spatial Transcriptomics Data (FAST): A Deconvolution Approach

MotivationSpatial transcriptomics is a state-of-art technique that allows researchers to study gene expression patterns in tissues over the spatial domain. As a result of technical limitations, the majority of spatial transcriptomics techniques provide bulk data for each sequencing spot. Consequently, in order to obtain high-resolution spatial transcriptomics data, performing deconvolution becomes essential. Deconvolution enables the determination of the proportions of different cell types along with the corresponding gene expression levels for each cell type within each spot. Most existing deconvolution methods rely on reference data (e.g., single-cell data), which may not be available in real applications. Current reference-free methods encounter limitations due to their dependence on distribution assumptions, reliance on marker genes, or the absence of leveraging histology and spatial information. Consequently, there is a critical demand for the development of highly adaptable, robust, and user-friendly reference-free deconvolution methods capable of unifying or leveraging case-specific information in the analysis of spatial transcriptomics data. ResultsWe propose a novel reference-free method based on regularized non-negative matrix factorization (NMF), named Flexible Analysis of Spatial Transcriptomics (FAST), that can effectively incorporate gene expression data, spatial coordinates, and histology information into a unified deconvolution framework. Compared to existing methods, FAST imposes fewer distribution assumptions, utilizes the spatial structure information of tissues, and encourages interpretable factorization results. These features enable greater flexibility and accuracy, making FAST an effective tool for deciphering the complex cell-type composition of tissues and advancing our understanding of various biological processes and diseases. Extensive simulation studies have shown that FAST outperforms other existing reference-free methods. In real data applications, FAST is able to uncover the underlying tissue structures and identify the corresponding marker genes.

bioinformatics↗

bioRxiv2023

Deep learning and host variable embedding augment microbiome-based simultaneous detection of multiple diseases

Microbiome has emerged as a promising indicator or predictor of human diseases. However, previous studies typically labeled each specimen as either healthy or with a specific disease, ignoring the prevalence of complications or comorbidities in actual cohorts, which may confound the microbial-disease associations. For instance, a patient may suffer from multiple diseases, making it challenging to detect their health status accurately. Furthermore, host phenotypes such as physiological characteristics and lifestyles can alter the microbiome structure, but this information has not yet been fully utilized in data models. To address these issues, we propose a highly explainable deep learning (DL) method called Meta-Spec. Using a deep neural network (DNN) based approach, it encodes and embeds the refined host variables with microbiome features, enabling the detection of multiple diseases and their correlations simultaneously. Our experiments showed that Meta-Spec outperforms regular machine learning (ML) strategies for multi-label disease screening in several cohorts. More importantly, Meta-Spec can successfully detect comorbidities that are often missed by regular ML approaches. In addition, due to its high interpretability, Meta-Spec captures key factors that shape disease patterns from host variables and microbial members. Hence, these efforts improve the feasibility and sensitivity of microbiome-based disease screening in practical scenarios, representing a significant step towards personalized medicine and better health outcomes.

bioinformatics↗

bioRxiv2023

SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis.

The morphology of protein assemblies impacts their behavior and contributes to beneficial and aberrant cellular responses. While single-molecule localization microscopy provides the required spatial resolution to investigate these assemblies, the lack of universal robust analytical tools to extract and quantify underlying structures limits this powerful technique. Here we present SEMORE, a semi-automatic machine learning framework for universal, system and input-dependent, analysis of super-resolution data. SEMORE implements a multi-layered density-based clustering module to dissect biological assemblies and a morphology fingerprinting module for quantification by multiple geometric and kinetics-based descriptors. We demonstrate SEMORE on simulations and diverse raw super-resolution data; time-resolved insulin aggregates and imaging of nuclear pore complexes. SEMORE extracts and quantifies all protein assemblies enabling classification of heterogeneous insulin aggregation pathways and NPC geometry in minutes. SEMORE is a general analysis platform for super-resolution data, and being the first time-awar e framework can also support the rise of 4D super-resolution data.

biophysics↗