Biology subjects

Shan, S.

Publications and source records attributed to Shan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

UcTCRp: a TCRβ-based framework for quantitative MAIT- and iNKT-associated repertoire-state profiling

MAIT and iNKT cells are conventionally identified using invariant or semi-invariant TCR chains, antigen-loaded tetramers, or transcriptomic phenotypes. These requirements limit their detection in public and clinical immune-repertoire datasets that contain only TCR{beta} sequences. Here we present UcTCRp, a TCR{beta}-only framework for profiling MAIT- and iNKT-associated repertoire states in bulk immune repertoires. UcTCRp integrates V-gene context and CDR3{beta} sequence features using a transformer-based representation pretrained on more than one million TCR{beta} sequences and supervised with curated cross-species MAIT, iNKT and conventional T cell references. The framework defines conserved model-informative TCR{beta} features, uses V-matched negative sampling to reduce germline-segment shortcuts, and generalizes across independent human and mouse datasets. In paired scRNA-seq/scTCR-seq datasets, UcTCRp recovered transcriptome-defined MAIT and iNKT cells and identified additional MAIT-like candidates supported by receptor evidence but missed by expression-only annotation. Bulk calibration against paired single-cell references and synthetic spike-in experiments established operating characteristics for repertoire-level abundance estimation. These results establish unpaired TCR{beta} repertoires as an actionable substrate for reconstructing unconventional T cell-associated immune states, enabling archived repertoire resources to be repurposed for systems-level studies of tissue immunity, disease and therapeutic response.

bioinformatics↗

bioRxiv2026

An orthogonal near-infrared optical switch for wireless neuromodulation in freely behaving mice

Modulating neuronal activity with light is a powerful tool for neuroscience research. However, currently available technologies often require invasive fibers for delivery of visible light, causing tissue damage and limiting behavioral studies. Although near-infrared (NIR) neuronal modulation improves tissue penetration depth, sustained NIR illumination during neuromodulation raises significant concerns about photothermal effects. Here, we introduce a dual-wavelength near-infrared switch (Dual-NIR Switch) that uses two transcranial NIR inputs to initiate and terminate neuronal activation, enabling tether-free neuromodulation in freely moving mice. Dual-NIR Switch employs orthogonal dichromatic upconversion nanoparticles that emit blue and green light under 980 nm and 808 nm excitation, respectively, to activate and inactivate the step-function opsin SOUL. Therefore, transient 980 nm NIR illumination initiates neuronal excitation, which will remain excited without further stimulation but will be rapidly terminated on demand by a subsequent 808 nm illumination. Upon transcranial 980 nm and 808 nm NIR illuminations in freely moving mice, we achieve on-demand control of behavioral paradigms across tunable timescales, ranging from seconds to minutes and even extending to sub-hour durations. By eliminating the need for sustained NIR irradiation, Dual-NIR Switch offers an on-demand, duration-tunable neuromodulation tool for both basic neuroscience and potential therapeutic applications in treating brain diseases.

neuroscience↗

bioRxiv2025

A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

Carya glabra (2n = 4x = 64), also known as pignut hickory, is a widely distributed species in the walnut family (Juglandaceae). Native to the central and eastern United States and southeastern Canada, C. glabra plays an important ecological role as a common upland forest species; it is closely related to several economically valuable nut trees, including C. illinoinensis (pecan). A deeper understanding of the genetics of C. glabra is essential for studying its evolutionary history and biology, with potential implications for agricultural improvement of pecan. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased, representing the first assembled polyploid genome in the genus Carya. A total of 64 pseudochromosomes were assembled and phased into four haplotypes. The haplotype A assembly spans 600.4 Mb, comprises 55.0% repetitive sequences, and contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Functional annotation assigned 94.3% of haplotype A genes to gene families, and 79.7% and 86.3% of genes were annotated with Gene Ontology terms and protein domains, respectively; 635 putative plant disease resistance genes were found in haplotype A. The other three haplotypes exhibited similarly high-quality annotation metrics. Our genomic analyses also suggest that C. glabra is an autotetraploid. Comparative genomic analyses revealed high collinearity among the four haplotypes of C. glabra and the published genomes of three other Carya species, although structural variation among the genomes of these species was identified. In addition, we provide an improved chloroplast genome assembly and the first mitochondrial genome for C. glabra. Importantly, most members of the research team are undergraduate students; the sequenced individual is located in McCarty Woods, a Conservation Area on the University of Florida campus. This work highlights the value of genome assembly efforts as powerful tools for teaching genomics and supporting conservation initiatives. This first high-quality reference genome for C. glabra provides a valuable resource for studying Carya, a genus of significant ecological and economic importance. Article summaryCarya glabra (pignut hickory) is a common upland forest species in North America. This species is a member of the walnut family (Juglandaceae), which includes many economically important nut trees. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased. The haplotype A assembly contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Our genomic analyses suggest that C. glabra is an autopolyploid. We also provide chloroplast and mitochondrial genome assemblies. This nuclear genome provides a valuable resource for studying Carya, a genus of significant ecological and economic importance.

genomics↗

bioRxiv2025

Keratinocyte VISTA attenuates UV light-induced skin injury by suppressing cutaneous type I interferon (IFN-I) response

Persistent production of type I interferons (IFN-Is) is a hallmark of cutaneous lupus erythematosus (CLE). Ultraviolet (UV) light stimulates IFN-I response in the skin and exacerbates CLE. Here, we identify V-type immunoglobulin domain-containing suppressor of T cell activation (VISTA) as a negative regulator of both basal and UV-induced IFN-I responses in the skin and show that VISTA limits skin photosensitivity in an IFN-I- dependent manner, in part through Stimulator of Interferon Genes (STING). Furthermore, we demonstrate a novel role for VISTA in keratinocytes both at steady state and in response to UV light. Conditional deletion of VISTA in epidermal keratinocytes results in >10-fold increase in the basal skin IFN-I score and a heightened UV-induced skin injury score, which is dependent on IFN-I signaling. VISTA-targeting monoclonal antibodies suppress UV-induced IFN-I response in human keratinocytes and in mice expressing human VISTA in vivo, which also reduces UV-induced skin injury score. Our findings highlight VISTA as a potential therapeutic target for suppressing IFN-I responses in cutaneous lupus patients who suffer from UV-induced skin inflammation.

immunology↗

bioRxiv2025

Leveraging Bayesian Networks for Consensus Network Construction and Multi-Method Feature Selection to Decode Disease Prediction

Constructing reliable microbiome co-occurrence networks and identifying disease-associated taxa remain major challenges in microbiome research due to variability introduced by different inference algorithms. To overcome these limitations, we present CMIMN, a novel R package that uses a Bayesian network framework based on conditional mutual information to infer robust microbial interaction networks. To further enhance reliability, we construct a consensus microbiome network by integrating results from CMIMN and three widely used methods--SPIEC-EASI, SPRING, and SPARCC. This consensus approach, which overlays and weights edges shared across methods, reduces inconsistencies and provides a more biologically meaningful view of microbial relationships. In addition, we introduce a multi-method framework for identifying disease-associated microbial taxa by combining machine learning and network-based feature selection. Our ML pipeline applies distinct algorithms and identifies key taxa based on their consistent importance across models. Complementing this, we employ two network-based strategies that prioritize taxa based on centrality differences between clean tubers and scab-infected tubers networks, as well as a composite scoring system that ranks nodes using integrated network metrics. Our results show that CMIMN achieves high robustness in network inference, and that the consensus network further improves stability and interpretability. The multi-method feature selection framework enhances confidence in identifying biologically relevant taxa linked to potato common scab disease. Notably, we identify Bacteroidota, WPS-2, and Proteobacteria at the Phylum level; Actinobacteria, AD3, Bacilli, Anaerolineae, and Ktedonobacteria at the Class level; and C0119, Defluviicoccales, Bacteroidales, and Ktedonobacterales at the Order level as key taxa associated with disease status.

systems biology↗

bioRxiv2025

Dentification of the Sorghum TMCO Gene Family and Differential Expression Analysis Under Aphid Infestation

The three-domain multicopper oxidase (TMCO) family, the largest subfamily of multicopper oxidases, plays a crucial role in plant growth, development, and responses to biotic stresses. To investigate the expression characteristics of the SbTMCO gene family under aphid infestation, a genome-wide identification and analysis of TMCO family members in sorghum were conducted using bioinformatics methods. Transcriptome data and qRT-PCR were utilized to preliminarily examine sorghums responses to aphid stress. The results revealed 42 TMCO genes in the sorghum genome, distributed across 10 chromosomes and classified into five subgroups. Members within the same subgroup displayed similar physicochemical properties, gene structures, and conserved motifs. Collinearity analysis suggested that tandem duplication and segmental duplication were the primary drivers of TMCO gene expansion in sorghum. Cis-acting element analysis identified multiple jasmonic acid (MeJA) and abscisic acid (ABA) responsive elements among SbTMCO genes. Gene expression analysis, based on RNA-seq and qRT-PCR, confirmed the relative expression levels of TMCO genes under aphid stress. This study establishes a foundation for exploring the anti-aphid functions of SbTMCO genes and provides recommendations and directions for further research on this gene family.

molecular biology↗

bioRxiv2025

Effective in vivo RNA base editing via engineered cytidine deaminase APOBECs fused with PUF proteins

Base editing stands at the forefront of genetic engineering, heralding precise genetic modifications with broad implications. While CRISPR-based DNA and RNA base editing systems capitalize on sgRNA-guided specificity and diverse deaminase functionalities, the pursuit of efficient C-to-U RNA editing has been hampered by the inherent constraints of cytidine deaminases. Here, we report an RNA base editing platform by refining cytidine deaminases, termed professional APOBECs (ProAPOBECs), through systematic enhancements and AI-driven protein engineering. ProAPOBECs demonstrate unprecedented catalytic versatility, particularly fused with RNA-recognizing Pumilio and FBF (PUF) proteins. We present the first effective use of RNA base editing in the brain with ProAPOBECs in Mef2c mutant mice, a model for autism. The AAV-mediated RNA base editing via ProAPOBEC not only corrects genetic mutation in mRNAs but significantly alleviates autistic-like behaviors in the mice. This work introduces a pioneering collection of RNA base editing instruments, emphasizing their therapeutic potential in combatting genetic disorders.

molecular biology↗

bioRxiv2024

Better Prior Distribution for Antibody Complementarity-Determining Regions Design

Designing antibodies with desired binding specificity and affinity is essential for pharmaceutical research. While diffusion-based models have advanced the co-design of the Complementarity-Determining Regions (CDRs) sequences and structures, challenges remain, including non-informative prior distribution, incompatibility with discrete amino acid types, and impractical computational cost in large-scale sampling. To address these, we proposed FlowDesign, a sequence-structure co-design approach based on Flow Matching, offering: (1) Flexible selection of prior distributions; (2) Direct matching of discrete distributions; (3) Enhanced computational efficiency for large-scale sampling. By leveraging various priors, data-driven structural models proved the most informative. FlowDesign outperformed baselines in Amino Acid Recovery (AAR), RMSD, and Rosetta energy. We also applied FlowDesign to design antibodies targeting the HIV-1 receptor CD4. FlowDesign yielded antibodies with improved binding affinity and neutralizing potency compared to the antibody Ibalizumab across multiple HIV mutants, validated by Biolayer Interferometry (BLI) and pseudovirus neutralization. This highlights FlowDesigns potential in antibody and protein design. A record of this papers Transparent Peer Review process is included in the Supplemental Information.

bioinformatics↗

bioRxiv2023

Srcap Haploinsufficiency Induced Autistic-Like Behaviors in Mice through Disruption of Satb2 Expression

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with significant genetic predispositions. Among these, loss-of-function mutations of the chromatin remodeling gene SRCAP have been identified in individuals with ASD, but their pathogenic mechanisms have yet to be fully elucidated. In this study, we established a germline mutant mouse model harboring a heterozygous frameshift mutation in the Srcap gene (Srcap+/-). The Srcap+/- mice exhibited notable impairments in social novelty, repetitive and stereotyped behaviors, anxiety, and learning and memory deficits. We observed a decreased number of parvalbumin (PV)-expressing neurons in their retrosplenial cortex (RSC) and dentate gyrus (DG). Furthermore, abnormalities in dendritic structure, synaptic density, and synaptic transmission were noted in the DG of Srcap+/- mice. RNA sequencing revealed that the expression of 27 genes, implicated in ASD, was dysregulated in the Srcap haploinsufficiency mice. Among these genes, we found that Srcap haploinsufficiency resulted in decreased Satb2 expression due to diminished H2A.z-binding within the promoter region of Satb2. Remarkably, intervention through retro-orbital injection of AAV vectors expressing Satb2 in newborn Srcap+/- mice reversed autistic-like behaviors and developmental defects in the RSC and DG regions. Similarly, in adolescent Srcap+/- mice, stereotactic injection of AAV expressing Satb2 into the RSC ameliorated deficits in social novelty. Collectively, these findings highlight the crucial role of the Srcap in neurodevelopment by regulating Satb2 expression, particularly impacting the development of RSC and DG regions.

neuroscience↗

bioRxiv2023

INKILN is a novel long noncoding RNA promoting vascular smooth muscle inflammation

BackgroundActivation of vascular smooth muscle cells (VSMCs) inflammation is vital to initiate vascular disease. However, the role of human-specific long noncoding RNAs (lncRNAs) in VSMC inflammation is poorly understood. MethodsBulk RNA-seq in differentiated human VSMCs revealed a novel human-specific lncRNA called INflammatory MKL1 Interacting Long Noncoding RNA (INKILN). INKILN expression was assessed in multiple in vitro and ex vivo models of VSMC phenotypic modulation and human atherosclerosis and abdominal aortic aneurysm (AAA) samples. The transcriptional regulation of INKILN was determined through luciferase reporter system and chromatin immunoprecipitation assay. Both loss- and gain-of-function approaches and multiple RNA-protein and protein-protein interaction assays were utilized to uncover the role of INKILN in VSMC proinflammatory gene program and underlying mechanisms. Bacterial Artificial Chromosome (BAC) transgenic (Tg) mice were utilized to study INKLIN expression and function in ligation injury-induced neointimal formation. ResultsINKILN expression is downregulated in contractile VSMCs and induced by human atherosclerosis and abdominal aortic aneurysm. INKILN is transcriptionally activated by the p65 pathway, partially through a predicted NF-{kappa}B site within its proximal promoter. INKILN activates the proinflammatory gene expression in cultured human VSMCs and ex vivo cultured vessels. Mechanistically, INKILN physically interacts with and stabilizes MKL1, a key activator of VSMC inflammation through the p65/NF-{kappa}B pathway. INKILN depletion blocks ILI{beta}-induced nuclear localization of both p65 and MKL1. Knockdown of INKILN abolishes the physical interaction between p65 and MKL1, and the luciferase activity of an NF-{kappa}B reporter. Further, INKILN knockdown enhances MKL1 ubiquitination, likely through the reduced physical interaction with the deubiquitinating enzyme, USP10. INKILN is induced in injured carotid arteries and exacerbates ligation injury-induced neointimal formation in BAC Tg mice. ConclusionsThese findings elucidate an important pathway of VSMC inflammation involving an INKILN/MKL1/USP10 regulatory axis. Human BAC Tg mice offer a novel and physiologically relevant approach for investigating human-specific lncRNAs under vascular disease conditions.

molecular biology↗

bioRxiv2022

Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages

SARS-CoV-2 variants of concern (VOCs), especially the latest Omicron, have exhibited severe antibody evasion. Broadly neutralizing antibodies with high potency against Omicron are urgently needed for understanding working mechanisms and developing therapeutic agents. In this study, we characterized previously reported F61, which was isolated from convalescent patients infected with prototype SARS-CoV-2, as a broadly neutralizing antibody against all VOCs including Omicron BA.1, BA.1.1, BA.2, BA.3 and BA.4 sublineages by utilizing antigen binding and cell infection assays. We also identified and characterized another broadly neutralizing antibody D2 with epitope distinct from that of F61. More importantly, we showed that a combination of F61 with D2 exhibited synergy in neutralization and protecting mice from SARS-CoV-2 Delta and Omicron BA.1 variants. Cryo-EM structures of the spike-F61 and spike-D2 binary complexes revealed the distinct epitopes of F61 and D2 at atomic level and the structural basis for neutralization. Cryo-EM structure of the Omicron-spike-F61-D2 ternary complex provides further structural insights into the synergy between F61 and D2. These results collectively indicated F61 and F61-D2 cocktail as promising therapeutic antibodies for combating SARS-CoV-2 variants including diverse Omicron sublineages.

biochemistry↗

bioRxiv2022

Broadly neutralizing and protective nanobodies against diverse sarbecoviruses

As SARS-CoV-2 Omicron and other variants of concern continue spreading around the world, development of antibodies and vaccines to confer broad and protective activity is a global priority. Here, we report on the identification of a special group of nanobodies from immunized alpaca with exceptional breadth and potency against diverse sarbecoviruses including SARS-CoV-1, Omicron BA.1, and BA.2. Crystal structure analysis of one representative nanobody, 3-2A2-4, revealed a highly conserved epitope between the cryptic and the outer face of the receptor binding domain (RBD). The epitope is readily accessible regardless of RBD in "up" or "down" conformation and distinctive from the receptor ACE2 binding site. Passive delivery of 3-2A2-4 protected K18-hACE2 mice from infection of authentic SARS-CoV-2 Delta and Omicron. This group of nanobodies and the epitope identified should provide invaluable reference for the development of next generation antibody therapies and vaccines against wide varieties of SARS-CoV-2 infection and beyond.

immunology↗

bioRxiv2022

Whole-brain in vivo base editing reverses autistic-like behaviors in mice

Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder associated with deficits in social communication and stereotypical behaviors. Numerous ASD-related genetic mutations have been identified and genome editing methods have been developed but successful genome editing in the whole-brain scale to alleviate autistic-like behaviors in animal models has not been achieved. Here we report the development of a new CRISPR-mediated cytidine base editor (CBE) system, which converts C{middle dot}G base pairs to T{middle dot}A. We demonstrate the effectiveness of this system by targeting an ASD-associated de novo mutation in the MEF2C gene (c.104T>C, p.L35P). We constructed a Mef2c L35P knock-in mouse and observed that Mef2c L35P heterozygous mice displayed autistic-like behaviors, including deficits in social behaviors and repetitive behaviors. We programmed the CBE to edit the C{middle dot}G base pairs of the mutated Mef2c gene (c.104T>C, p.L35P) to T{middle dot}A base pairs and delivered it via a single dose intravenous injection of blood brain barrier (BBB)-crossing AAV-PHP.eB vector into the mouse brain. This treatment restored MEF2C protein levels and reversed impairments in social interactions and repetitive behaviors in Mef2c L35P heterozygous mice. Together, this work presents an in vivo gene editing strategy in which correcting a single nucleotide mutation in the whole-brain scale could be successfully achieved, further providing a new therapeutic framework for neurodevelopmental disorders.

neuroscience↗

bioRxiv2021

SARS-CoV-2 hijacks neutralizing dimeric IgA for enhanced nasal infection and injury

Robust severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in nasal turbinate (NT) accounts for high viral transmissibility, yet whether neutralizing IgA antibodies can control it remains unknown. Here, we evaluated receptor binding domain (RBD)-specific monomeric B8-mIgA1 and B8-mIgA2, and dimeric B8-dIgA1 and B8-dIgA2 against intranasal SARS-CoV-2 challenge in Syrian hamsters. These antibodies exhibited comparably potent neutralization against authentic virus by competing with human angiotensin converting enzyme-2 (ACE2) receptor for RBD binding. While reducing viruses in lungs, pre-exposure intranasal B8-dIgA1 or B8-dIgA2 led to 81-fold more infectious viruses and severer damage in NT than placebo. Virus-bound B8-dIgA1 and B8-dIgA2 could engage CD209 as an alternative receptor for entry into ACE2-negative cells and allowed viral cell-to-cell transmission. Cryo-EM revealed B8 as a class II neutralizing antibody binding trimeric RBDs in 3-up or 2-up/1-down conformation. Therefore, RBD-specific neutralizing dIgA engages an unexpected action for enhanced SARS-CoV-2 nasal infection and injury in Syrian hamsters.

microbiology↗

bioRxiv2021

Single-dose AAV-based vaccine induces a high level of neutralizing antibodies and provides long-term protection against SARS-CoV-2 in rhesus macaques

Coronavirus disease 2019 (COVID-19), which is triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, continues to threaten global public health. Developing a vaccine that only requires single immunization but provides long-term protection for the prevention and control of COVID-19 is important. Here, we developed an adeno-associated virus (AAV)-based vaccine expressing a stable receptor-binding domain (SRBD) protein. The vaccine requires only a single shot but provides effective neutralizing antibodies (NAbs) over 598 days in rhesus macaques (Macaca mulatta). Importantly, our results showed that the NAbs were kept in high level and long lasting against authentic wild-type SARS-CoV-2, Beta, Delta and Omicron variants using plaque reduction neutralization test. Of note, although we detected pre-existing AAV2/9 antibodies before immunization, the vaccine still induced high and effective NAbs against COVID-19 in rhesus macaques. AAV-SRBD immune serum also efficiently inhibited the binding of ACE2 with RBD in the SARS-CoV-2 B.1.1.7 (Alpha), B.1.351 (Beta), P.1/P.2 (Gamma), B.1.617.2 (Delta), B.1.617.1/3(Kappa), and C.37 (Lambda) variants. Thus, these data suggest that the vaccine has great potential to prevent the spread of SARS-CoV-2.

immunology↗

bioRxiv2021

SENP1 in the retrosplenial agranular cortex regulates core autistic-like symptoms in mice

Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder, in which core symptoms are defects of social interaction and evidently repetitive behaviors. Although around 50-70 % of ASD patients have comorbidity of intellectual disabilities (ID) or developmental delay (DD), there are some ASD patients who exhibit only core symptoms but without ID/DD, raising the question whether there are genetic components and neural circuits specific for core symptoms of ASD. Here, by focusing on ASD patients who do not show compound ID or DD, we identified a de novo heterozygous gene-truncating mutation of the Sentrin-specific peptidase1 (SENP1) gene, coding the small ubiquitin-like modifiers (SUMO) deconjugating enzyme, as a potentially new candidate gene for ASD. We found that Senp1 haploinsufficient mice exhibited core symptoms of autism such as deficits in social interaction and repetitive behaviors, but normal learning and memory ability. Moreover, we found that the inhibitory and excitatory synaptic functions were severely affected in the retrosplenial agranular (RSA) cortex of Senp1 haploinsufficient mice. Lack of Senp1 led to over SUMOylation and degradation of fragile X mental retardation protein (FMRP) proteins, which is coded by the FMR1 gene, also implicated in syndromic ASD. Importantly, re-introducing SENP1 or FMRP specifically in RSA fully rescued the defects of synaptic functions and core autistic-like symptoms of Senp1 haploinsufficient mice. Together, these results demonstrated that disruption of the SENP1-FMRP regulatory axis in the RSA may cause core autistic symptoms, which provide a candidate brain region of ASD for potential therapeutic intervene by neural modulation approaches.

neuroscience↗

bioRxiv2020

SlicerMorph: An open and extensible platform to retrieve, visualize and analyze 3D morphology

Large scale digitization projects such as #ScanAllFishes and oVert are generating high-resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. MorphoSource currently hosts tens of thousands of 3D scans of eukaryotes. Along with the data from similarly scoped projects such as 10kPhenomes, DigiMorph and many others, soon hundreds of thousands of specimens that represent biodiversity of extinct and extant organisms will be conveniently available to researchers. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyze them. Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration, and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research. Another relevant concern is that ultimate derivative data from individual research projects (e.g., 3D models of segmentation) are shared in formats that do not preserve the correct spatial scale of the data. In this paper, we present our effort to tackle challenges biologists face when conducting 3D specimen-based research. We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python-scriptable open-source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open-access 3D models or import users own 3D volumes, to annotate 3D curve and patch-based landmarks, generate canonical templates, conduct geometric morphometric analyses of 3D organismal form using both landmark-driven and landmark-free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology, and extensive links to the existing tutorials are provided as supplemental material. Our goal is to establish a community of organismal biologists centered around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort.

evolutionary biology↗

bioRxiv2020

Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution

In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the "down" conformation, indicating they are more prone to adopt this receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. Through structure and sequence comparisons, we identified critical residues in the RBD that underlie the different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes and propose that N-linked glycans serve as conformational control elements of the RBD. These results collectively indicate that strong RBD-ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection.

biophysics↗