Biology subjects

Han, Y.

Publications and source records attributed to Han, Y..

At least 217 records · Page 12Linked to original sources

bioRxiv2022

Physiologic and nanoscale distinctions define glutamatergic synapses in tonic vs phasic neurons

Neurons exhibit a striking degree of functional diversity, each one tuned to the needs of the circuitry in which it is embedded. A fundamental functional dichotomy occurs in activity patterns, with some neurons firing at a relatively constant "tonic" rate, while others fire in bursts - a "phasic" pattern. Synapses formed by tonic vs phasic neurons are also functionally differentiated, yet the bases of their distinctive properties remain enigmatic. A major challenge towards illuminating the synaptic differences between tonic and phasic neurons is the difficulty in isolating their physiological properties. At the Drosophila neuromuscular junction (NMJ), most muscle fibers are co-innervated by two motor neurons, the tonic "MN-Ib" and phasic "MN-Is". Here, we employed selective expression of a newly developed botulinum neurotoxin (BoNT-C) transgene to silence tonic or phasic motor neurons. This approach revealed major differences in their neurotransmitter release properties, including probability, short-term plasticity, and vesicle pools. Furthermore, Ca2+ imaging demonstrated ~two-fold greater Ca2+ influx at phasic neuron release sites relative to tonic, along with enhanced synaptic vesicle coupling. Finally, confocal and super resolution imaging revealed that phasic neuron release sites are organized in a more compact arrangement, with enhanced stoichiometry of voltage-gated Ca2+ channels relative to other active zone scaffolds. These data suggest that distinctions in active zone nano-architecture and Ca2+ influx collaborate to differentially tune glutamate release at synapses of tonic vs phasic neuronal subtypes.

neuroscience↗

bioRxiv2022

The pan-genome and local adaptation of Arabidopsis thaliana

Arabidopsis thaliana has been used as a model species for research in a diverse collection of plant species. However, previous studies based on single reference genomes and short-read sequencing data are restricted to detecting variable genes and large structural variation (SV) underlying local adaptation. Here we de novo assemble high-quality chromosomal genomes of 38 A. thaliana ecotypes (with 6 relict ones) using PacBio-HiFi long-read sequencing. From these newly assembled genomes, we annotate several thousand new genes through pan-genomic analysis in comparison to the previous reference genome. The identified variable genes are mainly enriched in and associated with ecological adaptation and this species substantially expands its gene repertoire for local adaptation. We construct a graph-based pan-genome and identify 62,525 SVs which overlap with 14,243 genes. These genes are enriched in multiple ecological adaptation functions, including secondary metabolic processes, enzyme regulation, and biotic/abiotic stimulus. For example, a 566 bp insertion in the promoter of the light-adaptation KNAT3 gene was specific to the high-altitude relict Tibet-0 ecotype. This SV reduces the expression level of KNAT3 and promotes A. thaliana adaptation to habitats high in light radiation. In addition, compared with the SNPs, the SVs identified in this study captured the missing heritability and we detected novel SV associations with environmental variables in their native range, highlighting the value of SVs in environmental adaptation. The genome resources presented here will help pinpoint genetic changes that include both SVs and the ecotype-specific genes for local adaptation of A. thaliana and increase our understanding of the molecular mechanisms in this model species to respond to varied habitats.

genomics↗

bioRxiv2022

Fortuitous Somatic Mutations during Antibody Evolution Endow Broad Neutralization against SARS-CoV-2 Omicron Variants

Striking antibody evasion by emerging circulating SARS-CoV-2 variants drives the identification of broadly neutralizing antibodies (bNAbs). However, how a bNAb acquires increased neutralization breadth during antibody evolution is still elusive. Here, we identified a clonally-related antibody family from a convalescent individual. One of the members, XG005, exhibited potent and broad neutralizing activities against SARS-CoV-2 variants, while the other members showed significant reductions in neutralization breadth and potency, especially against the Omicron sublineages. Structural analysis visualizing the XG005-Omicron spike binding interface revealed how crucial somatic mutations endowed XG005 with greater neutralization potency and breadth. A single administration of XG005 with extended half-life, reduced antibody-dependent enhancement (ADE) effect, and increased antibody product quality, exhibited a high therapeutic efficacy in BA.2- and BA.5-challenged mice. Our results provided a natural example to show the importance of somatic hypermutation during antibody evolution for SARS-CoV-2 neutralization breadth and potency.

immunology↗

bioRxiv2022

Nigral-specific increase in ser31 tyrosine hydroxylase phosphorylation offsets dopamine loss and forestalls hypokinesia onset during progressive nigrostriatal neuron loss

Mechanisms that augment dopamine (DA) signaling to compensate for tyrosine hydroxylase (TH) loss and delay motor impairment in Parkinsons disease remain unidentified. The rat nigrostriatal pathway was unilaterally-lesioned by 6-OHDA to determine whether differences in DA content, TH protein, TH phosphorylation, or D1 receptor expression in striatum or substantia nigra (SN) aligned with onset of hypokinesia at two time points. At 7 days, DA and TH loss in striatum exceeded 95%, whereas DA was unaffected in SN, despite [~]60% TH loss. At 28 days, hypokinesia was established. At both time points, ser31 TH phosphorylation increased only in SN, corresponding to less DA versus TH loss. ser40 TH phosphorylation was unaffected in striatum or SN. By day 28, D1 receptor expression increased only in lesioned SN. These results indicate that increased ser31 TH phosphorylation and D1 receptor in the SN, not striatum, augment DA signaling against TH loss to mitigate hypokinesia. Highlights-Despite >90% TH and DA loss in striatum, open-field locomotor activity did not decrease -Early after lesion, DA and TH loss in striatum exceeded 90%. In contrast, DA loss did not occur despite 60% TH loss in substantia nigra (SN). -TH loss was progressive in the SN, with loss also spreading contralateral to lesion. -Loss of TH protein in SN preceded cell loss ipsilateral and contralateral to lesion, indicating first stages of nigrostriatal neuron loss begin with loss of TH protein loss. -TH phosphorylation at ser31 in SN was associated with less, if any, DA loss compared to TH protein loss. -TH phosphorylation at ser40 did not change in either region and at any time during TH loss, suggesting no contribution to differences in DA loss against TH loss. -Expression of the D1 receptor increased 2.5-fold in the SN late, but not early, after lesion, suggesting a post-synaptic receptor response to offset DA loss in SN. -No increases in TH phosphorylation or D1 receptor expression in striatum at any time after lesion induction, indicating that compensatory mechanisms occur only in substantia nigra, but not in striatum, to delay onset of hypokinesia.

neuroscience↗

bioRxiv2022

Bright and sensitive red voltage indicators for imaging action potentials in brain slices and pancreatic islets

As fast developing tools for observing cellular membrane potential, red-emitting genetically encoded voltage indicators (GEVIs) reduce auto-fluorescence background, allow multiplexed recordings, and enable all-optical electrophysiology, but have been limited by either insensitivity or dimness. Here, we report a pair of red GEVIs, Cepheid1b/s, with improved sensitivity, brightness, and photostability. Cepheid1 indicators faithfully report cellular excitability in pancreatic islets and neural activity in acute brain slices.

neuroscience↗

bioRxiv2022

Functional gradients reveal altered functional segregation in patients with amnestic mild cognitive impairment and Alzheimer' s disease

BackgroundAlzheimers disease (AD) and amnestic mild cognitive impairment (aMCI) are associated with disrupted functional organization in brain networks, yet the finer changes in the topological organization in aMCI and AD remain to be investigated. Connectome gradients are a new tool representing brain functional topological organization in a low-dimensional space to smoothly capture the human macroscale hierarchy. MethodsHere, we examined altered topological organization in aMCI and AD by connectome gradient mapping. We further quantified functional segregation by gradient dispersion. Then, we systematically compared the alterations observed in aMCI and AD patients with those in normal controls (NCs) in a two-dimensional functional gradient space from both the whole-brain level and module level. ResultsCompared with NCs, the first gradient, which described the neocortical hierarchy from unimodal to transmodal regions, showed a distributed and significant suppression in AD patients, while abnormalities were only limited to local regions in aMCI patients. The second gradient showed a decreased pattern in the somatomotor module in both aMCI and AD patients. Furthermore, gradient dispersion showed significant decreases in AD patients at both the global level and module level, whereas this alteration was limited only to limbic areas in aMCI. Notably, we demonstrated that suppressed gradient dispersion in aMCI and AD patients was associated with cognitive scores. ConclusionsChanges in functional gradients could reflect different degrees of altered brain network segregation in aMCI and AD. These findings provide new evidence for altered brain hierarchy in aMCI and AD, which strengthens our understanding of the progressive mechanism of cognitive decline.

neuroscience↗

bioRxiv2022

Single-cell gene expression and chromatin accessibility profiling of human pancreatic islets at basal and stimulatory conditions nominates mechanisms of type 1 diabetes genetic risk

Type 1 diabetes (T1D) is a complex autoimmune disease characterized by the loss of pancreatic islet beta cells. The mechanisms of T1D genetic risk remain poorly understood. Here, we present a multi-omic integrative study of single-cell/nucleus molecular profiles of gene expression and chromatin accessibility in the same biological samples from healthy and beta cell autoantibody+ (AAB+) human pancreatic islets to characterize mechanisms of islet-mediated T1D genetic risk. We additionally performed single-cell/nucleus multi-omic profiling of healthy islets under two stimulatory conditions used as in vitro models of T1D (cytokine cocktail and CVB4 infection) to evaluate how environmental exposures recapitulate multi-omic signatures of T1D. In total, we analyzed 121,272 cells/nuclei across 34 libraries, identifying 10 distinct cell types. We identified cell-type-specific and disease-associated cis-regulatory elements and nominated likely target genes. We provide evidence that T1D genetic risk is mediated through multiple pancreatic cell populations, including islet endocrine cells (beta, alpha, gamma, and delta), exocrine acinar and ductal cells, and immune cells. Finally, we identified three independent T1D risk variants acting through pancreatic islet endocrine cells at the TOX, RASGRP1, and DLK1/MEG3 loci. Together, this work improves our understanding of how non-coding genetic variants encode T1D risk through a complex interplay of different cell types in the pancreas.

genomics↗

bioRxiv2022

Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing

A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host new endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector to transmit RTIV and found RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover.

pathology↗

bioRxiv2022

Baculoviral COVID-19 Delta DNA vaccine cross-protects against SARS-CoV2 variants in K18-ACE2 transgenic mice

After severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) made the world tremble with a global pandemic, SARS-CoV2 vaccines were developed. However, due to the coronaviruss intrinsic nature, new variants emerged, such as Delta and Omicron, refractory to the vaccines derived using the original Wuhan strain. We developed an HERV-enveloped recombinant baculoviral DNA vaccine against SARS-CoV2 (AcHERV-COVID19S). A non-replicating recombinant baculovirus that delivers the SARS-CoV2 spike gene showed a protective effect against the homologous challenge in a K18-hACE2 Tg mice model; however, it offered only a 50% survival rate against the SARS-CoV2 Delta variant. Therefore, we further developed the AcHERV-COVID19 Delta vaccine (AcHERV-COVID19D). Cross-protection experiments revealed that mice vaccinated with the AcHERV-COVID19D showed 100% survival upon challenge with Delta and Omicron variants and 71.4% survival against prototype SARS-CoV2. These results support the potential of the viral vector vaccine, AcHERV-COVID19D, in preventing the spread of coronavirus variants such as Omicron and SARS-CoV2 variants. Author SummaryAfter the SARS-CoV2 pandemic, it is known that the existing vaccine has diminished efficacy against the emerging variants. We developed a baculoviral COVID19 DNA vaccine for the Delta variant (AcHERV-COVIS19D). Compared to AcHERV-COVID19S, designed to protect from the prototype of SARS-CoV2, AcHERV-COVID19D elicited higher humoral and cellular immunity and showed perfect protection against SARS-CoV2 delta strain and Omicron challenge. The broad and robust cellular immunity of the AcHERV-COVID19D vaccine appears to have played a significant role in the cross-protection of the Omicron variant. Our AcHERV-COVID19D can be a potential vaccine against emerging SARS-CoV2 variants.

immunology↗

bioRxiv2022

TRAF6 modulates PD-L1 expression through YAP1-TFCP2 signaling in melanoma

BackgroundImmunotherapy represented by the programmed death-1 (PD-1)/ligand 1 (PD-L1) monoclonal antibodies has led tumor treatment into a new era. However, the low overall response rate and high incidence of drug resistance largely damage the clinical benefits of existing immune checkpoint therapies. Recent studies correlate the response to PD-1/PD-L1 blockade with PD-L1 expression levels in tumor cells. Hence, identifying molecular targets and pathways controlling PD-L1 protein expression and stability in tumor cells is a major priority. MethodsIn this study, we first performed a Stress and Proteostasis CRISPR interference library-based screening to identify PD-L1 positive modulators. We then used in vitro and in vivo assays to investigate the biological function and mechanism of TRAF6 and its downstream YAP1/TFCP2 signaling in malignant melanoma. ResultsHere, we identified TRAF6 as a critical regulator of PD-L1 in melanoma cells. Suppression of TRAF6 expression down-regulates PD-L1 expression on the membrane surface of melanoma cells. We also found that PD-L1 protein abundance is regulated by YAP1/TFCP2 transcriptional complex. TRAF6 stabilizes YAP1 by K63 poly-ubiquitination modification, subsequently promoting the formation of YAP1/TFCP2 and PD-L1 transcription. Furthermore, inhibition of TRAF6 by Bortezomib enhanced cytolytic activity of CD8+ T cells by reduction of endogenous PD-L1. Notably, Bortezomib enhances anti-tumor immunity to an extent that is comparable to anti-PD-1 mAb therapies with no obvious toxicity. ConclusionsThese findings uncover a novel molecular mechanism for regulating PD-L1 protein abundance by a E3 ligase in cancer cells and reveal the potential of using TRAF6 inhibitors to stimulate internal anti-tumor immunological effect for TRAF6-PD-L1 overexpressing cancers.

cancer biology↗

bioRxiv2022

Ancient DNA Reveals China as a Historical Genetic Melting Pot in Tiger Evolution

The contrast between the tigers (Panthera tigris) 2-3 My age and extant tigers coalescence approximately 110,000 years ago suggests an ancient demographic bottleneck. Here we collected over 60 extinct specimens across mainland Asia and generated whole genome sequences from a 10,600-year-old Russian Far East (RFE) specimen (RUSA21, 8{xi} coverage), 14 South China tigers (0.1-12{xi}), three Caspian tigers (4-8{xi}), plus 17 new mitogenomes. RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some 8,000-10,000-year-old RFE mitogenomes are basal to all tigers, one 2,000-year-old specimen resembles present Amur tigers. The Caspian tiger likely dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modeling suggested Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, Eastern China became a genetic melting pot to foster divergent lineages to merge into South China tigers and other subsequent northern subspecies to develop. Genomic information retrieved from ancient tigers hence sheds light on the species full evolutionary history leading to nine modern subspecies and resolves the natural history of surviving tigers.

evolutionary biology↗

bioRxiv2022

High-throughput TCRB enrichment sequencing of human cord blood exhibited a distinct fetal T cell repertoire in the third trimester of pregnancy

Study questionWhat are the molecular characteristics during the maturation process of the human fetal immune system in the third trimester of pregnancy? Summary answerBoth the diversity and length of complementarity determining region 3 (CDR3s) in the fetal TCRB repertoire were less than those of adult CDR3s, and the fetal CDR3 length increased with gestation weeks in late pregnancy. What is known alreadyThe adaptive immune system recognizes various pathogens based on a large repertoire of T-cell receptors (TCR repertoire), but the maturation dynamics of the fetal TCR repertoire in the third trimester are largely unknown. The CDR3is the most diversified segment in the T-cell receptor {beta} chain (TCRB) that binds and recognizes the antigen. Study design, size, and durationThis was a basic research to assess the composing characteristics of TCRBs in core blood and the dynamic pattern with fetal development in the third trimester of pregnancy. Participants/materials, setting methodsHigh-throughput TCRB-enrichment sequencing was utilized to characterize the TCRB repertoire of cord blood at 24~38 weeks of gestational age (WGA) with nonpreterm fetuses and to investigate their difference compared with that of adult peripheral blood. Main results and the role of chanceCompared to the adult control, the fetal TCRB repertoire had a 4.8-fold lower number of unique CDR3s, a comparable Shannon diversity index (p=0.7387), a lower mean top clone rate (p < 0.001) and a constrictive top 1000 unique clone rates. Although all kinds of TCRBV and TCRBJ genes present in adult CDR3s were identified in fetuses, nearly half of these fragments showed a significant difference in usage. Moreover, the fetal TCRB repertoire held a shorter CDR3 length, and the CDR3 length showed a progressive increase with fetal development. Jensen-Shannon (JS) divergences of TCRBV and TCRBJ gene usage in dizygotic twins were much lower than those in unrelated pairs. In the parental-fetal pair, JS divergence of TCRBV gene usage was not obviously different, while that of TCRBJ gene usage was only slightly lower. Limitations, reasons for cautionThe sample size is limited due to the limited accessibility to cord blood in late pregnancy with healthy nonpreterm fetuses. Wider implications of the findingsOur findings reveal the unique properties of fetal TCRB repertoires in the third trimester, fill the gap in our understanding of the maturation process of prenatal fatal immunity, and deepen our understanding of the immunologically relevant problems in neonates. Study funding/competing interest(s)This work was supported by the National Natural Science Foundation of China (82171661) and Tianjin Municipal Science and Technology Special Funds for Enterprise Development (NO. 14ZXLJSY00320). The authors declare that they have no competing interests.

genetics↗

bioRxiv2022

Learning representations for image-based profiling of perturbations

Measuring the phenotypic effect of treatments on cells through imaging assays is an efficient and powerful way of studying cell biology, and requires computational methods for transforming images into quantitative data that highlight phenotypic outcomes. Here, we present an optimized strategy for learning representations of treatment effects from high-throughput imaging data, which follows a causal framework for interpreting results and guiding performance improvements. We use weakly supervised learning (WSL) for modeling associations between images and treatments, and show that it encodes both confounding factors and phenotypic features in the learned representation. To facilitate their separation, we constructed a large training dataset with Cell Painting images from five different studies to maximize experimental diversity, following insights from our causal analysis. Training a WSL model with this dataset successfully improves downstream performance, and produces a reusable convolutional network for image-based profiling, which we call Cell Painting CNN-1. We conducted a comprehensive evaluation of our strategy on three publicly available Cell Painting datasets, discovering that representations obtained by the Cell Painting CNN-1 can improve performance in downstream analysis for biological matching up to 30% with respect to classical features, while also being more computationally efficient.

bioinformatics↗

bioRxiv2022

Structural basis of a high-affinity antibody binding to glycoprotein region with consecutive glycosylation sites

Consecutive glycosylation sites occur in both self and viral proteins. Glycan-shielding of underneath peptide region is a double-edged sword, that avoids immune attack to self-proteins, but helps viruses including HIV-1 and SARS-CoV2 to escape antibody binding. Here we report a high-affinity antibody, 16A, binding to linear peptide containing consecutive glycosylation sites. Co-crystallization of 16A Fab and glycopeptides with GalNAc modifications at different sites showed that STAPPAHG is the sequence recognized by 16A antibody. GalNAc modification at Threonine site on STAPPAHG sequence significantly increased the affinity of Fab binding by 30.6 fold (KD=6.7nM). The increased affinity is conferred by hydrophilic and pi-stacking interactions between the GalNAc residue on Threonine site and a Trp residue from the CDR1 region of the heavy chain. Furthermore, molecular modeling suggested that GalNAc on T site causes more favorable conformation for antibody binding. These results showed that glycan modification most proximal to linear peptide core epitope significantly increases antigenicity of a glycopeptide epitope. The antibody recognition mode by peptide-binding CDR groove with a glycan-binding edge, may shed light on designing of linear glycopeptide-based vaccines for cancer and viral diseases. TeaserA high-affinity antibody was found to bind densely glycosylated glycoprotein region by a peptide binding groove of the antibodys variant region, with a glycan-binding edge specific to glycosylation site most proximal to core peptide epitope.

immunology↗

bioRxiv2022

Targeting c-Jun is a potential therapy of luminal breast cancer bone metastasis

Luminal breast cancer has the highest bone metastasis frequency among all breast cancer subtypes, but its metastatic mechanism has not been elucidated because of the lack of appropriate metastatic cell lines. The study aim was to characterize high-osteolytic bone metastatic MCF7-BM cell lines and extract c-Jun, a novel bone metastasis marker. We found that c-Jun was upregulated in MCF7-BM cells, and its deficiency was associated with suppression of the cell migration, transformation, and stemness of BM cells. In vivo, c-Jun-deficient MCF7-TAM67 cells exhibited weaker bone metastatic ability. Additionally, c-Jun overexpression in MCF7-BM cells led to a tumor-migration promotion cycle in the bone microenvironment possibly by enhancing calcium-induced migration and releasing the osteoclast activator BMP5. Inhibition of c-Jun by JNK-IN-8, a JNK inhibitor, effectively reduced tumorigenesis activities and bone metastatic tumors. Our results indicate the potential benefits of a therapy that targets c-Jun to prevent or minimize luminal breast cancer bone metastasis.

cancer biology↗

bioRxiv2022

TREE-QMC: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees

Summary methods are one of the dominant approaches for estimating species trees from genome-scale data. However, they can fail to produce accurate species trees when the input gene trees are highly discordant due to gene tree estimation error as well as biological processes, like incomplete lineage sorting. Here, we introduce a new summary method TREE-QMC that offers improved accuracy and scalability under these challenging scenarios. TREE-QMC builds upon the algorithmic framework of QMC (Snir and Rao 2010) and its weighted version wQMC (Avni et al. 2014). Their approach takes weighted quartets (four-leaf trees) as input and builds a species tree in a divide-and-conquer fashion, at each step constructing a graph and seeking its max cut. We improve upon this methodology in two ways. First, we address scalability by providing an algorithm to construct the graph directly from the input gene trees. By skipping the quartet weighting step, TREE-QMC has a time complexity of O(n3k) with some assumptions on subproblem sizes, where n is the number of species and k is the number of gene trees. Second, we address accuracy by normalizing the quartet weights to account for "artificial taxa," which are introduced during the divide phase so that solutions on subproblems can be combined during the conquer phase. Together, these contributions enable TREE-QMC to outperform the leading methods (ASTRAL-III, FASTRAL, wQFM) in an extensive simulation study. We also present the application of these methods to an avian phylogenomics data set.

evolutionary biology↗

bioRxiv2022

Accurate background reduction in adaptive optical 3D-STED nanoscopy by dynamic phase switching

Stimulated emission depletion (STED) fluorescence nanoscopy allows the three-dimensional (3D) visualization of nanoscale subcellular structures, providing unique insights into their spatial organization. However, 3D-STED imaging and quantification of dense features are obstructed by the low signal-to-background ratio (SBR), resulting from optical aberrations and out-of-focus background. Here, combining with adaptive optics, we present an easy-to-implement and flexible method to improve SBR by dynamic phase switching. By switching to a counterclockwise vortex phase mask and a top-hat one with an incorrect inner radius, the depletion pattern features a nonzero-intensity center, enabling accurate background recordings. When the recorded background is subtracted from the aberration-corrected 3D-STED image, the SBR in dense sample areas can be improved by a factor of 3-6 times. We demonstrate our method on various dense subcellular structures, showing more advantages than the software-based background subtraction algorithms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/497623v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@7aacd6org.highwire.dtl.DTLVardef@1e91f14org.highwire.dtl.DTLVardef@1f774acorg.highwire.dtl.DTLVardef@10ccf5d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Bento: A toolkit for subcellular analysis of spatial transcriptomics data

The spatial organization of molecules in a cell is essential for performing their functions. Spatial transcriptomics technologies have opened the door to characterization of cellular and subcellular organization. While current computational methods focus on discerning tissue architecture, cell-cell interactions and spatial expression patterns, these approaches are limited to investigating spatial variation at the multicellular scale. We present Bento, a Python toolkit that fully takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three fundamental analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. To demonstrate the toolkit, we apply these methods to a variety of datasets including U2-OS cells (MERFISH), 3T3 cells (seqFISH+), and treated cardiomyocytes (Molecular Cartography). We quantify RNA localization changes in cardiomyocytes identifying mRNA depletion of critical cardiac disease-associated genes RBM20 and CACNB2 from the endoplasmic reticulum upon doxorubicin treatment. The Bento package is a member of the open-source Scverse ecosystem, enabling integration with other single-cell omics analysis tools.

bioinformatics↗