Biology subjects

Cheng, W.

Publications and source records attributed to Cheng, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Specific Pathogen Free Ten Gene-Edited Pig Donor for Xenotransplantation

Xenotransplantation has entered the clinical phase to fulfill the global organ shortage. However, recent clinical studies revealed that the xenograft from current gene-edited (GE) pigs still poses the risk of immune rejection, and biosafety concerns. In this study, we successfully constructed a large batch of 10- (GTKO/CMAHKO/ {beta}4GalNT2KO/hCD46/hCD55/hCD59/hTBM/hEPCR/hCD39/hCD47) GE cloned (GEC) donor pigs by utilizing gene editing and somatic cell cloning technology, and successfully obtained F1 generation. Phenotypic characterization of 10-GEC pigs showed the deletion of three xenoantigens along with expression of seven human transgenes in various tissues. Digital droplet polymerase chain reaction, and whole genome sequencing indicated 2 copies of hCD46/hCD55/hCD59/hTBM/hCD39 and 1 copy of hEPCR/hCD47 in pig genome without significant off-target and damage to the porcine own functional genes. The validation results showed that 10-GEC pigs effectively inhibited the attacks of human antibodies, complement, and macrophages on porcine endothelial cells and alleviated the coagulation abnormalities between pigs and humans. 10-GEC pigs were negative for all zoonotic pathogens (48) including cytomegalovirus, except streptococcal infections. Kidney, heart, and liver xenografts from these 10-GE pigs were transplanted to non-human primates (NHP), which started working normally without hyperacute rejection. Among them, the heart and liver transplant recipient died without resuscitation due to unexpected interruption of oxygen supply, while the 2 kidney transplant recipients survived for 23 and 16 days, respectively. Pathological analysis showed that 10-GE pig kidney xenografts showed mesenchymal congestion, and fibrosis, cellular hyperplasia, with minor antibody and complement deposition, and significantly reduced the infiltration of CD68+ macrophage. In summary, we successfully produced a group of specific pathogen free GEC donor pigs that effectively mitigated immune rejection upon multi-organ transplantation to NHP.

immunology↗

bioRxiv2025

Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution

Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200-300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to surpass this limitation. By physically enlarging tissues, Seq-Scope-X minimizes transcript diffusion effects and increases spatial feature density by an additional order of magnitude. In liver tissue, this approach resolves nuclear and cytoplasmic compartments in nearly every single cell, uncovering widespread differences between nuclear and cytoplasmic transcriptome patterns. Independently confirmed by imaging-based methods, these results suggest that individual hepatocytes can dynamically switch their metabolic roles. Seq-Scope-X is also applicable to non-hepatic tissues such as brain and colon, and can be modified to perform spatial proteomic analysis, simultaneously profiling hundreds of barcode-tagged antibody stains at microscopic resolutions in mouse spleens and human tonsils. These findings establish Seq-Scope-X as a transformative tool for ultra-high-resolution whole-transcriptome and proteome profiling, offering unparalleled spatial precision and advancing our understanding of cellular architecture, function, and disease mechanisms.

genomics↗

bioRxiv2025

DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks

Modeling long-range DNA dependencies is crucial for understanding genome structure and function across a wide range of biological contexts. However, effectively capturing these extensive dependencies, which may span millions of base pairs in tasks such as three-dimensional (3D) chromatin folding prediction, remains a significant challenge. Furthermore, a comprehensive benchmark suite for evaluating tasks that rely on long-range dependencies is notably absent. To address this gap, we introduce DNALO_SCPLOWONGC_SCPLOWBO_SCPLOWENCHC_SCPLOW, a benchmark dataset encompassing five important genomics tasks that consider long-range dependencies up to 1 million base pairs: enhancer-target gene interaction, expression quantitative trait loci, 3D genome organization, regulatory sequence activity, and transcription initiation signals. To comprehensively assess DNALO_SCPLOWONGC_SCPLOWBO_SCPLOWENCHC_SCPLOW, we evaluate the performance of five methods: a task-specific expert model, a convolutional neural network (CNN)-based model, and three fine-tuned DNA foundation models - HyenaDNA, Caduceus-Ph, and Caduceus-PS. We envision DNALO_SCPLOWONGC_SCPLOWBO_SCPLOWENCHC_SCPLOW as a standardized resource with the potential to facilitate comprehensive comparisons and rigorous evaluations of emerging DNA sequence-based deep learning models that account for long-range dependencies.

bioinformatics↗

bioRxiv2024

L2G: Repurposing Language Models for Genomics Tasks

Pre-trained language models have transformed the field of natural language processing (NLP), and their success has inspired efforts in genomics to develop domain-specific foundation models (FMs). However, creating high-quality genomic FMs from scratch is resource-intensive, requiring significant computational power and high-quality pre-training data. The success of large language models (LLMs) in NLP has largely been driven by industrial-scale efforts leveraging vast, diverse corpora and massive computing infrastructure. In this work, we aim to bypass the data and computational bottlenecks of creating genomic FMs from scratch and instead propose repurposing existing LLMs for genomics tasks. Inspired by the recently observed cross-modal transfer phenomenon - where transformers pre-trained on natural language can generalize to other modalities - we introduce L2G, which adapts a pre-trained LLM architecture for genomics using neural architecture search (NAS) and a novel three-stage training procedure. Remarkably, without requiring extensive pre-training on DNA sequence data, L2G achieves superior performance to fine-tuned genomic FMs and task-specific models on more than half of tasks across multiple genomics benchmarks. In an enhancer activity prediction task, L2G further demonstrates its capacity to identify significant transcription factor motifs. Our work not only highlights the generalizability and efficacy of language models in out-of-domain tasks such as genomics, but also opens new avenues for more efficient and less resource-intensive methodologies in genomic research.

bioinformatics↗

bioRxiv2024

SOX2-induced IL-1alpha-mediated immune suppression drives epithelial dysplasia malignant transformation

Squamous cell carcinomas (SCC) are often preceded by potentially malignant precursor lesions, most of which remain benign. The terminal exhaustion phenotypes of effector T-cells and the accumulation of myeloid-derived suppressor cells (MDSC) have been thoroughly characterized in established SCC. However, it is unclear what precancerous lesions harbor a bona fide high risk for malignant transformation and how precancerous epithelial dysplasia drives the immune system to the point of no return. Here we show that expression of SRY-box transcription factor 2 (SOX2) in precancerous lesions imparts an irreversible risk that recruits suppressive myeloid cells by promoting the release of CCL2. We developed a unique genetically engineered mouse model (GEMM) to recapitulate the malignant transformation of epithelial dysplasia to SCC in the oral mucosa with high histologic and phenotypic fidelity. Using a combination of longitudinal human specimens and the Sox2-GEMM, we found that the myeloid cells in precancerous epithelial dysplasia exhibit a distinctive dichotomous profile featuring high levels of IL-1-SLC2A1 and low levels of type-I interferon (IFN-I) signatures, which occurs before SCC emerges histologically. Brief priming of myeloid cells with IL-1 desensitizes them to IFN-I agonists and makes myeloid-derived suppressor cells (MDSC) even more suppressive of T-cell activation. Mechanistically, IL-1 activation represses the expression of DHHC3/7 enzymes, which are responsible for the palmitoylation of stimulator of interferon genes (STING). Early blockade of IL1 signaling using pharmacologic and genetic approaches similarly reduces MDSC and SLC2A1high myeloid cells, suppresses epithelial dysplasia transformation, and extends survival. This work establishes a previously unrecognized SOX2-CCL2-IL1 pathway that leads to irreversible immune escape when precancerous epithelial lesions transform.

cancer biology↗

bioRxiv2024

Neural correlates of device-based sleep characteristics in adolescents

Understanding the brain mechanisms underlying objective sleep patterns in adolescents and their implications for psychophysiological development is a complex challenge. Here, we applied sparse canonical correlation (sCCA) analysis on 3300 adolescents from Adolescent Brain Cognitive Development (ABCD) study, integrating extensive device-based sleep characteristics and multimodal imaging data. We revealed two sleep-brain dimensions: one characterized by later being asleep and shorter duration, linked to decreased subcortical-cortical network functional connectivities; the other showed higher heart rate and shorter light sleep duration, associated with lower brain volumes and decreased functional connectivities. Hierarchical clustering based on brain dimension associated with sleep characteristics revealed three biotypes of adolescents, marked by unique sleep profiles: biotype 1 exhibited delayed and shorter sleep, coupled with higher heart rate during sleep; biotype 3 with earlier and longer sleep, accompanied by lower heart rate; and biotype 2 with intermediate pattern. This biotypic differences also extended to cognition, academic attainment, brain structure and function in a gradient order. Longitudinal analysis demonstrated consistent biotypic differences from ages 9 to14, highlighting enduring cognitive and academic advantages in biotype3. The linked sleep-brain dimensions and the associated biotypes were well replicated in a longitudinal sample of 1271 individuals. Collectively, our novel findings delineate a linkage between objective sleep characteristics and developing brain in adolescents, underscoring their significance in cognitive development and academic attainment, which could serve as references for individuals with sleep difficulties and offer insights for optimizing sleep routines to enhance better cognitive development and school achievement.

neuroscience↗

bioRxiv2024

Unraveling the impact of hyperleptinemia on female reproduction: Insights from transgenic pig model

BackgroundInfertility is a growing global health concern affecting millions of couples worldwide. Among several factors, an extreme body weight adversely affects reproductive functions. Leptin is a well-known adipokine that serves as an endocrine signal between adiposity and fertility. However, the exact mechanisms underlying the effects of high leptin on female reproduction remain unclear. MethodsTransgenic pig overexpressing leptin (11) were produced by back cross and screened for leptin overexpression, and the growth curve, fat deposition, reproductive performance, apoptosis, serum hormones and cholesterol production, RNA sequencing, and single nucleus RNA sequencing of the leptin-overexpressed pigs and control group were evaluated. ResultsTransgenic pig overexpressing leptin (11) were obtained, which exhibited significantly reduced body weight, body size, and back fat thickness. These pigs manifested late onset of puberty (327{+/-}48.5 vs 150{+/-}6.5 days), irregular estrous behavior characterized by increased inter-estrous interval (28.1{+/-}4.2 vs 21.3 {+/-} 0.9 days), and more numbers of mating until pregnancy (at least 3 times). This reproductive impairment in leptin pigs was related to hormonal imbalances characterized by increased levels of FSH, LH, prolactin, E2, P4, and TSH, altered steroidogenesis such as increased levels of serum CE along with steroidogenic markers (STAR, CYP19A), and ovarian dysfunctions manifested by neutrophilic infiltration and low expression of caspase-3 positive cells on leptin pigs ovary. Meanwhile, bulk RNA sequencing of the ovaries also revealed neutrophilic infiltration followed by upregulation of inflammation-related genes. Further, leptin overexpression triggered immune response, suppressed follicle development and luteinization, imposing metabolism dysfunction and hormone imbalance in the ovary by single-nucleus RNA sequencing (snRNA-seq). ConclusionLow body weight in leptin overexpression pigs adversely affects reproductive performance, causing delayed puberty, irregular estrous cycles, and reduced breeding efficiency. This is linked to metabolic imbalances, increased immune response, and altered ovarian functions. This study provided a theoretical basis for the complex mechanisms underlying leptin, and infertility by employing leptin-overexpressed female pigs.

genetics↗

bioRxiv2024

Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics

Spatial transcriptomics (ST) technologies represent a significant advance in gene expression studies, aiming to profile the entire transcriptome from a single histological slide. These techniques are designed to overcome the constraints faced by traditional methods such as immunostaining and RNA in situ hybridization, which are capable of analyzing only a few target genes simultaneously. However, the application of ST in histopathological analysis is also limited by several factors, including low resolution, a limited range of genes, scalability issues, high cost, and the need for sophisticated equipment and complex methodologies. Seq-Scope--a recently developed novel technology--repurposes the Illumina sequencing platform for high-resolution, high-content spatial transcriptome analysis, thereby overcoming these limitations. Here we provide a detailed step-by-step protocol to implement Seq-Scope with an Illumina NovaSeq 6000 sequencing flow cell that allows for the profiling of multiple tissue sections in an area of 7 mm x 7 mm or larger. In addition to detailing how to prepare a frozen tissue section for both histological imaging and sequencing library preparation, we provide comprehensive instructions and a streamlined computational pipeline to integrate histological and transcriptomic data for high-resolution spatial analysis. This includes the use of conventional software tools for single cell and spatial analysis, as well as our recently developed segmentation-free method for analyzing spatial data at submicrometer resolution. Given its adaptability across various biological tissues, Seq-Scope establishes itself as an invaluable tool for researchers in molecular biology and histology. KEY POINTSO_LIThe protocol outlines a method for repurposing an Illumina NovaSeq 6000 flow cell as a spatial transcriptomics array, enabling the generation of high-resolution spatial datasets. C_LIO_LIThe protocol introduces a streamlined data analysis pipeline that produces a spatial digital gene expression matrix suitable for various single-cell and spatial transcriptome analysis methods. C_LIO_LIThe protocol allows for the capture of histology images from the same tissue section subjected to spatial transcriptomics analysis and allows users to precisely align the transcriptome dataset with the histological image using fiducial marks engraved on the flow cell surface. C_LIO_LILeveraging commonly available Illumina equipment, the protocol offers researchers ultra-high submicrometer resolution in spatial transcriptomics analysis with a comprehensive pipeline, rapid turnaround, cost efficiency, and versatility. C_LI

genomics↗

bioRxiv2024

High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation

Skeletal muscle exhibits pronounced cellular and subcellular heterogeneity, but comprehensive spatial mapping has been constrained by cell/nuclei dissociation-based methods that lose tissue architecture and by spatial platforms with insufficient resolution or limited transcriptome coverage. Here we present a high-resolution spatial transcriptomic atlas of mouse soleus muscle in longitudinal sections with unbiased whole-transcriptome coverage, enabling myofiber-resolved transcriptomes while preserving subcellular expression domains across the length of fibers. Combining histology-guided myofiber segmentation with unbiased grid-based mapping, we recover canonical fiber types and reveal widespread hybrid myofiber states in situ, including type IIb-associated signatures that are rare in soleus muscle and evident only when intramyofiber heterogeneity is assessed. At subcellular scale, we delineate the neuromuscular junction (NMJ) as a multi-compartment niche comprising postsynaptic myonuclei and spatially distinct peri-synaptic and myelinating Schwann cell-associated regions, each with characteristic gene programs. Applying this framework to denervation (3 and 7 days) identifies robust fiber-type-specific stress responses, coordinated remodeling of macrophage and fibroblast transcriptomes, and marked intramyofiber heterogeneity, including spatially nonuniform activation of damage-response genes along individual myofibers, with distinct transcriptional domains proximal and distal to the NMJ and associated degenerative histological features. Together, this atlas provides a high-resolution reference for muscle biology and clarifies how denervation reshapes myofiber, synaptic, and stromal-immune programs across cells and within cells in intact tissue.

physiology↗

bioRxiv2024

Enhancing Plant Photosynthesis using Carbon Dots as Light Converter and Photosensitizer

Improving photosynthetic efficiency is pivotal for CO2-based biomanufacturing and agriculture purposes. Despite the progress on photosynthetic biohybrids integrating biocatalysts with synthetic materials, nanomaterials with improved optical and photoelectrochemical properties are still needed to increase the energy-conversion efficiency. Here, we present a novel approach using carbon dots (CDs) as both intracellular photosensitizers and light converters for enhancing solar energy utilization in photosynthetic organisms. The CDs were produced from cyanobacterial biomass and used to convert a broad spectrum of solar irradiation to red light. We demonstrated that the nanosized CDs were incorporated into cyanobacterial cells and transferred light-excited electrons into the photosynthetic electron transfer chain. The biohybrids consisting of the CDs and Synechococcus elongatus exhibited increased growth rates, enhanced activities of both photosystems, and accelerated linear electron transport, compared with the cyanobacterial cells only. The supplementation of the CDs increased CO2-fixation rate and CO2-to-glycerol production by 2.4-fold and 2.2-fold, respectively. Furthermore, the CDs were shown to enhance photosynthesis and promote growth of Arabidopsis thaliana. The fresh weight of plant was increased 1.8-fold by CDs addition. These results reveal that simultaneous photosensitization and spectral modification could substantially improve the efficiency of natural photosynthesis. This study presents CDs as an attractive nanomaterial with great application potential in agriculture and solar-powered biomanufacturing.

synthetic biology↗

bioRxiv2024

Identification of differentially methylated single-nucleotide m6A sites by incorporating site-specific antibody specificity

Various genome-wide and transcriptome-wide technologies are based on antibodies, however, the specificity of antibodies on different targets has not been characterized or considered in the analyses. The antibody-based MeRIP-seq is the most widely used method to determine the locations of N6-methyladenosine (m6A) on RNAs, especially for differential m6A analyses. However, the antibody specificities in different RNA regions and their resulting technical biases in differential m6A analyses have not been evaluated. Here, we evaluated the m6A antibody specificities using 100 pairs of spike-in RNAs with known m6A levels at single sites. Based on two replicates with different m6A levels on spike-in RNAs, we realized the m6A antibody specificities of the m6A sites on spike-in RNAs were greatly varied and mainly determined by the surrounding sequences of the m6A sites. Moreover, the MeRIP-seq signal fold change is the function of the real difference in m6A levels as well as the m6A antibody specificity. We then trained a machine learning model to predict the m6A antibody specificities of given sequences and predicted the m6A specificities of all RNA sequences surrounding the known m6A motif DRACH throughout the human transcriptome. Finally, we developed a Hierarchical statistic model for Differential Analysis of m6A Sites (HDAMS) by taking advantage of the predicted m6A specificities. We found that HDAMS can accurately determine the differentially methylated single-nucleotide m6A sites and the output more functionally relevant results. Our study not only provides a powerful tool for differential m6A analyses but also provides a methodological framework for other antibody-based studies to incorporate antibody specificities.

bioinformatics↗

bioRxiv2024

An integrated signaling threshold initiates IgG response towards virus-like immunogens

Class-switched neutralizing antibody (nAb) production is rapidly induced upon many viral infections. However, due to the presence of multiple components in typical virions, the precise biochemical and biophysical signals from viral infections that initiate nAb responses remain inadequately defined. Using a reductionist system of synthetic virus-like structures (SVLS) containing minimal, highly purified biochemical components commonly found in enveloped viruses, here we show that a foreign protein on a virion-sized liposome can serve as a stand-alone danger signal to initiate class-switched nAb responses in the absence of cognate T cell help or Toll-like receptor signaling but requires CD19, the antigen (Ag) coreceptor on B cells. Introduction of internal nucleic acids (iNAs) obviates the need for CD19, lowers the epitope density (ED) required to elicit the Ab response and transforms these structures into highly potent immunogens that rival conventional virus-like particles in their ability to elicit strong Ag-specific IgG. As early as day 5 after immunization, structures harbouring iNAs and decorated with just a few molecules of surface Ag at doses as low as 100 ng induced all IgG subclasses of Ab known in mice and reproduced the IgG2a/2c restriction that has been long observed in live viral infections. These findings reveal a shared mechanism for nAb response upon viral infection. High ED is capable but not necessary for driving Ab secretion in vivo. Instead, even a few molecules of surface Ag, when combined with nucleic acids within these structures, can trigger strong antiviral IgG production. As a result, the signaling threshold for the induction of neutralizing IgG is set by dual signals originating from both ED on the surface and the presence of iNAs within viral particulate immunogens. One-sentence summaryReconstitution of minimal viral signals necessary to initiate antiviral IgG

immunology↗

bioRxiv2023

FICTURE: Scalable segmentation-free analysis of sub-micron resolution spatial transcriptomics

Spatial transcriptomics (ST) technologies have advanced to enable transcriptome-wide gene expression analysis at submicron resolution over large areas. Analysis of high-resolution ST data relies heavily on image-based cell segmentation or gridding, which often fails in complex tissues due to diversity and irregularity of cell size and shape. Existing segmentation-free analysis methods scale only to small regions and a small number of genes, limiting their utility in high-throughput studies. Here we present FICTURE, a segmentation-free spatial factorization method that can handle transcriptome-wide data labeled with billions of submicron resolution spatial coordinates. FICTURE is orders of magnitude more efficient than existing methods and it is compatible with both sequencing- and imaging-based ST data. FICTURE reveals the microscopic ST architecture for challenging tissues, such as vascular, fibrotic, muscular, and lipid-laden areas in real data where previous methods failed. FICTUREs cross-platform generality, scalability, and precision make it a powerful tool for exploring high-resolution ST.

bioinformatics↗

bioRxiv2023

Quantitative dynamics of intracellular NMN by genetically encoded biosensor

Nicotinamide mononucleotide (NMN) is a major precursor for NAD+ metabolism with promising effects in treating NAD+- and aging-related pathologies. However, measuring live cell NMN dynamics was not possible, leaving key questions in intracellular NMN uptake and regulation unanswered. Here we developed a genetically encoded bioluminescent sensor to quantify subcellular NMN in live cells by fusing engineered NMN-responsive binding domain to bioluminescent and fluorescent proteins from BRET pairs. The sensor dissected the multimechanistic uptake of extracellular NMN and precursors in live cells. We then captured the notably low mitochondrial NMN content and the thereafter vulnerable NMN/NAD+ ratio and SARM1 activation in mitochondria, establishing NMN/NAD+ ratio as an important parameter in evaluating NAD+ boosting strategies. Moreover, we characterized the signature of major NAD+ regulating enzymes on NMN and NMN/NAD+ ratios, in which Slc25a45 was identified to be a potential mitochondrial NMN transporter for its unique fingerprint on mitochondrial NMN/NAD+ ratio.

cell biology↗

bioRxiv2023

In situ cryoET reveals inhibitor-induced perturbations in Pf80S GTPase interactions

Malaria parasites rely heavily on rapid, high fidelity protein synthesis to infect and replicate in human erythrocytes, making translation an attractive target for new antimalarials. Here, we have determined in situ structures of Pf80S ribosomes in thirteen conformational and compositional states from cryoFIB-milled Plasmodium falciparum-infected human erythrocytes across the stages of asexual intraerythrocytic parasite replication. We observe eight active translation intermediates, enabling us to define the native malarial translation elongation cycle, which surprisingly features a bifurcation at the decoding stage of the cycle that has not previously been described. Examination of perturbations in the distribution of ribosomes among these states in the presence of a malaria-specific translation inhibitor suggests that the inhibitor impedes PfeEF2 and PfeEF1 interactions with the ribosome. We integrated our in situ cryoET data with proteomic and ultrastructural data to arrive at a deeper understanding of malarial translation, which will inform development of new therapies.

biophysics↗

bioRxiv2023

Rapid and visual detection of Schistosoma japonicum circulating nucleic acids by CRISPR-Cas12a

BackgroundSchistosomiasis is the second most destructive parasitic disease globally. It poses a serious threat to human health if not diagnosed and treated promptly. However, the current detection methods have limitations due to their dependence on specialized equipments and personnel, and the long detection time, resulting in less-than-ideal detection outcomes. Therefore, more accurate and sensitive assays are required to aid in the control of schistosomiasis. This study aims to develop a rapid and practical method for detecting Schistosoma japonicum circulating nucleic acid by combining the Cas12a protein in the CRISPR (Clustered regularly interspaced short palindromic repeats) system with recombinase-mediated isothermal nucleic acid amplification technology. Methodology/Principal FindingsWe created a CRISPR-Cas12a detection method for Schistosomiasis. SjR2 and SjCHGCS19 genes with repetitive copies in the Schistosoma japonicum genome were targeted for detection. The CRISPR-Cas12a detection method can achieve a detection sensitivity of 1 cp/{micro}L, with no cross-reaction with the other three human-infecting trematode parasites. To vividly simulate clinical patients at different infection stages, we collected rabbits serums at 1 d, 3 d, 1 w, 3 w, 5 w, and 7 w post-infection. Circulating Schistosoma japonicum DNA in the serum can be detected as early as 3 days post-infection. The sample and positive rates of each stage were analyzed and the CRISPR-Cas12a detection method prevailed to Nested-PCR. Additionally, our assay offers flexible results readout options, including lateral test strips. Conclusions/SignificanceThis CRISPR-Cas12a detection method enables sensitive and specific detection of Schistosomiasis by detecting highly repetitive SjR2 and SjCHGCS19 genes. The method was fully validated with rabbits serums collected at different infection stages, which can be applied to monitoring the early infection of schistosomiasis in resource-limited regions. Author SummaryWith the development of schistosomiasis prevention and control efforts in recent years, the prevalence rate and infection intensity of schistosomiasis have decreased, making early and accurate diagnoses more challenging. Combining CRISPR-Cas12a protein with isothermal amplification technology, a detection method for the multi-copy sequences SjR2 and SjCHGCS19 in the genome of Schistosoma japonicum was developed in this study. The results demonstrated that the detection sensitivity of this method could reach 1 cp/{micro}L, with no cross reactivity with three other fluke-like human parasites. In this study, serum samples from 15 rabbits infected with Schistosoma japonicum were used to validate the method. The results demonstrated that rabbits could be identified as early as the third day after infection. CRISPR-Cas12a detection method has a higher positive rate than traditional Nested-PCR. In addition, lateral test strips enable direct observation of our assay results. The aforementioned research findings indicate that the CRISPR-Cas12a-based detection method can be utilized for the early diagnosis of schistosomiasis. In conjunction with the result reading method of the lateral test strips, it also provides a new method for the on-site diagnosis of schistosomiasis in environments with limited access to resources.

bioengineering↗

bioRxiv2023

Scalable Solar-Driven Chemical Production by Semiconductor Biohybrids Synthesized from Wastewater Pollutants

Semiconductors biohybrids integrate the best of biological catalysts and semiconductor nanomaterials for solar-to-chemical conversion. To realize the potential of hybrid systems at the commercial level, it remains an urgent need for cost-competitive and environmentally friendly approaches to scaling up. Here, we successfully tackle this challenge through developing biohybrid route that co-utilize multi-pollutants in wastewater to produce semiconductor biohybrids in-situ for solar-to-chemical production. To achieve cost-effective biohybrid production, we introduced an aerobic sulfate reduction pathway into Vibrio natriegens to enable the direct utilization of the heavy metal ions (i.e., Cd2+), sulfate, and organics in the wastewater to biosynthesize functional semiconductor nanoparticles in living V. natriegens. Furthermore, 2,3-butanediol biosynthetic pathway was introduced into the V. natriegens hybrid to couple the solar energy for enhanced bioproduction. We demonstrated the scalability of this system in a 5-L illuminated fermenter using wastewater as the feedstock, which resulted in production of 13 g/L of 2,3-butanediol. Life cycle analysis showed this specific biohybrid route had a significantly lower cost and reduced CO2 emission compared to both pure sugars fermentation and fossil-based routes. In addition to providing a promising step toward sustainable commercializing semiconductor biohybrids for biomanufacturing, our work may lead to hybrid living matter toward future waste to wealth conversion.

synthetic biology↗

bioRxiv2023

Mechanisms of neutralizing antibody response probed using synthetic virus-like structures

The durability of an antibody (Ab) response is highly important for antiviral vaccines. However, due to the complex compositions of natural virions, the molecular determinants of Ab durability from viral infection or inactivated viral vaccines have been incompletely understood. Here we used a reductionist system of liposome-based virus-like structures to examine the durability of Abs in primary immune responses in mice. This system allowed us to independently vary fundamental viral attributes and to do so without additional adjuvants to model natural viruses. We show that a single injection of antigens (Ags) orderly displayed on a virion-sized liposome is sufficient to induce a long-lived neutralizing Ab (nAb) response. Introduction of internal nucleic acids dramatically modulates the magnitude of long-term Ab responses without alteration of the long-term kinetic trends. These Abs are characterized by exceptionally slow off-rates of [~]0.0005 s-1, which emerged as early as day 5 after injection and these off-rates are comparable to that of affinity-matured monoclonal Abs. A single injection of these structures at doses as low as 100 ng led to lifelong nAb production in BALB/c mice. Thus, a minimal virus-like immunogen can give rise to potent and long-lasting antiviral Abs in a primary response in mice without live infection. This has important implications for understanding both live viral infection and for optimized vaccine design.

immunology↗