Biology subjects

Zhao, J.

Publications and source records attributed to Zhao, J..

At least 271 records · Page 15Linked to original sources

bioRxiv2024

BinDash 2.0: New MinHash Scheme Allows Ultra-fast and Accurate Genome Search and Comparisons

MotivationComparing large number of genomes in term of their genomic distance is becoming more and more challenging because there is an increasing number of microbial genomes deposited in public databases. Nowadays, we may need to estimate pairwise distances between millions or even billions of genomes. Few softwares can perform such comparisons efficiently. ResultsHere we update the multi-threaded software BinDash by implementing several new MinHash algorithms and computational optimization (e.g. Simple Instruction Multiple Data, SIMD) for ultra-fast and accurate genome search and comparisons at trillion scale. That is, we implemented b-bit one-permutation rolling MinHash with optimal/faster densification with SIMD. Now with BinDash 2, we can perform 0.1 trillion (or [~]10^11) pairs of genome comparisons in about 1.8 hours on a descent computer cluster or several hours on personal laptops, a [~]50% or more improvement over original version. The ANI (average nucleotide identity) estimated by BinDash is well correlated with other accurate but much slower ANI estimators such as FastANI or alignment-based ANI. In line with the findings from comparing 90K genomes ([~]10^9 comparisons) via FastANI, the 85% [~] 95% ANI gap is consistent in our study of [~]10^11 prokaryotic genome comparisons via BinDash2, which indicates fundamental ecological and evolutionary forces keeping species-like unit (e.g., > 95% ANI) together. Availability and implementationBinDash is released under the Apache 2.0 license at: https://github.com/zhaoxiaofei/bindash Contactkostas.konstantinidis@gatech.edu Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2024

Microbial Response to Natural Disturbances: Rare Biosphere often plays a role

Understanding how microbial populations respond to disturbances represents a major goal for microbial ecology. While several theories have been advanced to explain microbial community compositional changes in response to disturbances, appropriate data to test these theories is scarce, especially when considering the challenges to define rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to define rare populations, and by borrowing concepts from macroecology, the proportional similarity index (PS index), to define generalists. Using these concepts, we found that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm weather events snaps-in part-due to the response of rare populations, providing support for the insurance hypothesis (i.e., the rare biosphere has the buffering capacity to mitigate the effects of disturbances). Generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis, i.e., disturbance favors generalists. Taken together, our results advance understanding of the mechanisms governing microbial populations dynamics under changing environmental conditions and have potential applications for ecosystem management.

ecology↗

bioRxiv2024

The segmented flavivirus Alongshan virus reduces mitochondrial mass via degrading STAT2 to suppress innate immune response

Alongshan virus (ALSV) is a newly discovered pathogen of the Flaviviridae family, characterized by a multi-segmented genome distantly related to the canonical flaviviruses. Understanding the pathogenic mechanism of the emerging segmented flavivirus is crucial for the development of intervention strategies. Here we show that ALSV can infect multiple mammalian cells and induces the expression of antiviral genes. Moreover, ALSV is sensitive to IFN-{beta} and possesses the ability to counteract type I IFN response. Mechanistically, ALSVs nonstructural protein NSP1 binds to and degrades human STAT2 through an autophagy pathway in a species-dependent manner, resulting in direct inhibition of the expression of interferon-stimulated genes (ISGs). Specifically, NSP1 methyltransferase domain binds to the key sites of F175/R176 located in coiled-coil domain of STAT2. Moreover, NSP1-mediated degradation of STAT2 results in a reduction in mitochondrial mass by disrupting mitochondrial dynamics to induce mitophagy and inhibiting mitochondrial biogenesis, thereby suppressing the innate immune response. Interestingly, inhibiting mitophagy using 3-Methyladenine and enhancing mitochondrial biogenesis using the PPAR{gamma} agonist pioglitazone can reverse NSP1-mediated inhibition of ISGs, suggesting that promoting mitochondrial mass presents an effective antiviral strategy. Our findings elucidate the intricate regulatory crosstalk between ALSV and the hosts innate immune response, providing valuable insights into the pathogenesis and intervention strategy of emerging segmented flavivirus.

microbiology↗

bioRxiv2024

Deep5hmC: Predicting genome-wide 5-Hydroxymethylcytosine landscape via a multimodal deep learning model

5-hydroxymethylcytosine (5hmC), a critical epigenetic mark with a significant role in regulating tissue-specific gene expression, is essential for understanding the dynamic functions of the human genome. Using tissue-specific 5hmC sequencing data, we introduce Deep5hmC, a multimodal deep learning framework that integrates both the DNA sequence and the histone modification information to predict genome-wide 5hmC modification. The multimodal design of Deep5hmC demonstrates remarkable improvement in predicting both qualitative and quantitative 5hmC modification compared to unimodal versions of Deep5hmC and state-of-the-art machine learning methods. This improvement is demonstrated through benchmarking on a comprehensive set of 5hmC sequencing data collected at four time points during forebrain organoid development and across 17 human tissues. Notably, Deep5hmC showcases its practical utility by accurately predicting gene expression and identifying differentially hydroxymethylated regions in a case-control study of Alzheimers disease.

bioinformatics↗

bioRxiv2024

Arginine Di-methylation of RIPK3 Safeguards Necroptosis for Intestinal Homeostasis

The necroptosis mediated by RIPK3 is stringently regulated for intestinal homeostasis. Here we found that mice lacking Prmt5 (Protein arginase methyltransferase 5) in intestinal epithelial cells (IECs) caused premature death with IECs necroptosis, villus atrophy and loss of Paneth cells. This pathology can be partially rescued by antibiotic treatment, germ-free breeding condition and pharmaceutical inhibition of RIPK1 and RIPK3, but aggravated for embryonic lethality by Caspase-8 deficiency, which demonstrating the importance of commensal bacteria and necroptosis for the Prmt5-IEC deficiency. Intriguingly, tumor-necrosis factor (TNF) receptor 1(Tnfr1) deficiency could not completely rescue the pathology, and mice deficit in Z- DNA binding protein 1(ZBP1) exhibited shorter lifespan compared with Prmt5 null mice, suggesting Prmt5 loss might trigger TNFR-RIPK1-depenfent and ZBP1- dependent necroptosis. Mechanically, we identified the 479-arginine residue of RIPK3 di-methylated by PRMT5 was an endogenous checkpoint for necroptosis. Furthermore, RIPK3-R479K mutation had higher affinity with both RIPK1 and ZBP1 by immunoprecipitation and STORM (Stochastic Optical Reconstruction Microscopy) analysis, which might explain the endogenous necroptosis triggered by mutated RIPK3 even without upstream stimuli. Moreover, the peptide of RIPK3-SDMA (Symmetric dimethylarginine of 479) could rescue lethality of Prmt5 lacking mice through necrosome formation inhibition, which demonstrating the great potential for necroptosis-related disease treatment through RIPK3 dimethylation targeting.

cell biology↗

bioRxiv2024

Mice lacking Astn2 have ASD-like behaviors and altered cerebellar circuit properties

Astrotactin 2 (ASTN2) is a transmembrane neuronal protein highly expressed in the cerebellum that functions in receptor trafficking and modulates cerebellar Purkinje cell (PC) synaptic activity. We recently reported a family with a paternally inherited intragenic ASTN2 duplication with a range of neurodevelopmental disorders, including autism spectrum disorder (ASD), learning difficulties, and speech and language delay. To provide a genetic model for the role of the cerebellum in ASD-related behaviors and study the role of ASTN2 in cerebellar circuit function, we generated global and PC-specific conditional Astn2 knockout (KO and cKO, respectively) mouse lines. Astn2 KO mice exhibit strong ASD-related behavioral phenotypes, including a marked decrease in separation-induced pup ultrasonic vocalization calls, hyperactivity and repetitive behaviors, altered social behaviors, and impaired cerebellar-dependent eyeblink conditioning. Hyperactivity and repetitive behaviors were also prominent in Astn2 cKO animals. By Golgi staining, Astn2 KO PCs have region-specific changes in dendritic spine density and filopodia numbers. Proteomic analysis of Astn2 KO cerebellum reveals a marked upregulation of ASTN2 family member, ASTN1, a neuron-glial adhesion protein. Immunohistochemistry and electron microscopy demonstrates a significant increase in Bergmann glia volume in the molecular layer of Astn2 KO animals. Electrophysiological experiments indicate a reduced frequency of spontaneous excitatory postsynaptic currents (EPSCs), as well as increased amplitudes of both spontaneous EPSCs and inhibitory postsynaptic currents (IPSCs) in the Astn2 KO animals, suggesting that pre- and postsynaptic components of synaptic transmission are altered. Thus, ASTN2 regulates ASD-like behaviors and cerebellar circuit properties.

neuroscience↗

bioRxiv2024

Ultraviolet attenuates centromere-mediated meiotic genome stability and alters gametophytic ploidy consistency in flowering plants

Ultraviolet (UV) radiation influences development and genome stability in organisms; however, its impacts on meiosis, a special cell division essential for the delivery of genetic information over generations in eukaryotes, remain not yet elucidated. In this study, we demonstrate that UV attenuates the centromere-mediated meiotic chromosome stability and induces unreduced gametes in Arabidopsis thaliana. We show that UV reduces crossover (CO) rate but does not interfere with meiotic chromosome integrity. Functional centromere-specific histone 3 (CENH3) is required for the obligate CO formation, and plays a role in protection of homolog synapsis and sister-chromatid cohesion under UV stress. Moreover, UV specifically alters the orientation and organization of spindles and phragmoplasts at meiosis II, resulting in meiotic restitution and unreduced gametes. Further, we determine that UV-induced meiotic restitution does not rely on the UV Resistance Locus8-mediated UV perception and the Tapetal Development and Function1- and Aborted Microspores-dependent tapetum development, but occurs possibly via impacted JASON function and downregulated Parallel Spindle1. This study sheds light on the impacts of UV on meiotic genome stability and gametophytic ploidy consistency, which thus may influence genome evolution in flowering plants.

plant biology↗

bioRxiv2024

Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape

Machine learning (ML) is revolutionizing our ability to model the fitness landscape of protein sequences, which is critical to answering fundamental life science questions and addressing important protein engineering applications, such as quantifying the pathogenicity of disease variants, forecasting viral evolution in a pandemic, and engineering new antibodies. Recently, the protein language model (pLM) has emerged as an effective ML tool in deciphering the intrinsic semantics of protein sequences and become the foundation of state-of-the-art ML solutions for many problems in protein biology. However, significant challenges remain in leveraging pLMs for protein fitness prediction, in part due to the disparity between the scarce number of sequences functionally characterized by high-throughput assays and the massive data samples required for training large pLMs. To bridge this gap, we introduce Contrastive Fitness Learning (ConFit), a pLM-based ML method for learning the protein fitness landscape with limited experimental fitness measurements as training data. We propose a novel contrastive learning strategy to fine-tune the pre-trained pLM, tailoring it to achieve protein-specific fitness prediction while avoiding overfitting, even when using a small number (low-N) of functionally assayed mutant sequences for supervised fine-tuning. Evaluated across over 30 benchmark datasets of protein fitness, ConFit consistently provided accurate fitness predictions and outperformed several competitive baseline methods. Further analysis revealed that ConFits capability of low-N learning enabled sample-efficient active learning for identifying high-fitness protein variants. Collectively, our work represents a novel strategy to harness the potential of pLMs to elucidate the protein sequence-function relationship. The source code of ConFit is available at https://github.com/luo-group/ConFit.

bioinformatics↗

bioRxiv2024

Two distinct mechanisms for Nav1.7 null analgesia

Genetic deletion and pharmacological inhibition are distinct approaches to unravelling pain mechanisms, identifying targets and developing new analgesics. Both approaches have been applied to the voltage-gated sodium channels Nav1.7 and Nav1.8. Genetic deletion of Nav1.8 in mice leads to a loss of pain, and antagonists are effective analgesics. Complete embryonic loss of Nav1.7 in humans or in mouse sensory neurons leads to profound analgesia substantially mediated by endogenous opioid signaling, and anosmia that is opioid independent. Autonomic function appears to be normal. Adult deletion of Nav1.7 in sensory neurons also leads to analgesia with diminished sensory neuron excitability but there is no opioid component of analgesia. Pharmacological inhibition of Nav1.7 leads to dramatic side-effects on the autonomic nervous system. Here we compare and contrast the distinct embryonic and adult null mechanisms of Nav1.7 loss-of-function analgesia. We describe an endogenous opioid mechanism of analgesia that provides new opportunities for therapeutic intervention and pain relief. SummaryIn contrast to Nav1.8, Nav1.7, a genetically validated human pain target is unsuitable for small molecule drug development because of its wide spread expression both centrally and peripherally.

neuroscience↗

bioRxiv2024

RNA Splicing Junction Landscape Reveals Abundant Tumor-Specific Transcripts in Human Cancer

RNA splicing is a critical process governing gene expression and transcriptomic diversity. Despite its importance, a detailed examination of transcript variation at the splicing junction level remains scarce. Here, we perform a thorough analysis of RNA splicing junctions in 34,775 samples across multiple sample types. We identified 29,051 tumor-specific transcripts (TSTs) in pan-cancer, with a majority of these TSTs being unannotated. Our findings show that TSTs are positively correlated with tumor stemness and linked to unfavorable outcomes in cancer patients. Additionally, TSTs display mutual exclusivity with somatic mutations and are overrepresented in transposable element-derived transcripts possessing oncogenic functions. Importantly, TSTs can generate neoepitopes that bind to MHC class I molecules for immunotherapy. Moreover, TSTs can be detected in blood extracellular vesicles from cancer patients. Our results shed light on the intricacies of RNA splicing and offer promising avenues for cancer diagnosis and therapy. In briefThis study thoroughly analyzed RNA splicing junctions in 34,775 samples and identified 29,051 tumor-specific transcripts (TSTs), which may serve as novel cancer driver genes, neoantigens, and circulating biomarkers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/579246v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@7e1db2org.highwire.dtl.DTLVardef@1cfbe81org.highwire.dtl.DTLVardef@1e427e1org.highwire.dtl.DTLVardef@1f655f5_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Stimulated Prorocentrum donghaiense cell growth by in-situ mariculture dissolved organic matter

Mixotrophic dinoflagellates frequently cause harmful algal blooms (HAB) in eutrophic mariculture waters that contain diverse excreted dissolved organic matter (DOM). The phagotrophy and the utilization of single organic small molecules have been extensively investigated in the bloom-forming mixotrophic dinoflagellates. However, their ability to utilize the in-situ DOM via absorbtrophy still remains unexplored. Here we examined the growth promotion effect of the in-situ mariculture DOM on Prorocentrum donghaiense, a representative HAB-forming species in coastal waters. Our results showed that the cell growth and photosynthesis of P. donghaiense were significantly promoted under in-situ DOM culture conditions. Additionally, parallel cultures were set up to disclose the potential role of the bacterioplankton in the free-living community (helper), where they aid in the remineralization of the in-situ DOM, and the phycosphere community (competitor), where they compete against the algal host to acquire nutrients from the in-situ DOM. Meanwhile, we determined the cellular stoichiometry under different culture conditions, showing that mariculture DOM can shape cellular stoichiometry significantly. Elevated cellular N (84.96%) and P (48.3%) were observed in spring DOM groups compared with the control groups. For the first time, this study quantifies the efficient utilization of the in-situ DOM via absorbtrophy, indicating the vital role in the outbreak and maintenance of HAB events.

ecology↗

bioRxiv2024

Large-scale multi-omics analyses identified root-microbiome associations underlying plant nitrogen nutrition

The microbiome determines the performance and fitness of the host plant. Nevertheless, the causal interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here we generated 1,341 paired root transcriptome, rhizosphere microbiome and root ionome samples and performed a multi-omics analyses of the host-microbe association at the root-soil interface using 175 rapeseeds (Brassica napus L.) resequenced ecotypes at two field environments. We observed the highest statistically explained variance for root nitrogen uptake among natural ionomic variation by overall transcriptome-wide gene expression and microbial abundance variation. Moreover, we identified significant genome-wide associations for 203 highly heritable amplicon sequence variants (ASVs) at multiple genetic loci regulated by eQTL hotspots associated with nitrogen metabolism components. These associations involved a central bacterial genus (Sphingopyxis), which plays a dominant role on gene regulatory effect on its variation regulated by eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjected Sphingopyxis to whole genome sequencing. Finally, targeted metabolite profiling and confocal imaging assays demonstrated a host-microbiome regulatory effect on Sphingopyxis established by lateral root development and plant nitrogen nutrition. In summary, our integrative approach reveals the genetic basis of host-microbiome trait associations in the transcriptional, nutritional and environmental domains and suggests that the microbiome might have causal effects on root development with implications towards the breeding of nutrient-efficient crops.

plant biology↗

bioRxiv2024

Approximate Nearest Neighbor Graph Provides Fast and Efficient Embedding with Applications in Large-scale Biological Data

Dimension reduction (or embedding), as a popular way to visualize data, has been a fundamental technique in many applications. Non-linear dimension reduction such as t-SNE and UMAP has been widely used in visualizing single cell RNA sequencing data and metagenomic binning and thus receive many attentions in bioinformatics and computational biology. Here in this paper, we further improve UMAP-like non-linear dimension reduction algorithms by updating the graph- based nearest neighbor search algorithm (e.g. we use Hierarchical Navigable Small World Graph, or HNSW instead of K-graph) and combine several aspects of t-SNE and UMAP to create a new non-linear dimension reduction algorithm. We also provide several additional features including computation of LID (Local Intrinsic Dimension) and hubness, which can reflect structures and properties of the underlying data that strongly affect nearest neighbor search algorithm in traditional UMAP-like algorithms and thus the quality of embeddings. We also combined the improved non-linear dimension reduction algorithm with probabilistic data structures such as MinHash-likes ones (e.g., ProbMinHash et.al.) for large-scale biological sequence data visualization. Our library is called annembed and it was implemented and fully parallelized in Rust. We benchmark it against popular tools mentioned above using standard testing datasets and it showed competitive accuracy. Additionally, we apply our library in three real-world problems: visualizing large-scale microbial genomic database, visualizing single cell RNA sequencing data and metagenomic binning, to showcase the performance, scalability and efficiency of the library when distance computation is expensive or when the number of data points is large (e.g. millions or billions). Annembed can be found here: https://github.com/jean-pierreBoth/annembed

bioinformatics↗

bioRxiv2024

A systematic evaluation of computation methods for cell segmentation

Cell segmentation is a fundamental task in analyzing biomedical images. Many computational methods have been developed for cell segmentation and instance segmentation, but their performances are not well understood in various scenarios. We systematically evaluated the performance of 18 segmentation methods to perform cell nuclei and whole cell segmentation using light microscopy and fluorescence staining images. We found that general-purpose methods incorporating the attention mechanism exhibit the best overall performance. We identified various factors influencing segmentation performances, including image channels, choice of training data, and cell morphology, and evaluated the generalizability of methods across image modalities. We also provide guidelines for choosing the optimal segmentation methods in various real application scenarios. We developed Seggal, an online resource for downloading segmentation models already pre-trained with various tissue and cell types, substantially reducing the time and effort for training cell segmentation models.

bioinformatics↗

bioRxiv2024

PI3Kγ promotes neutrophil extracellular trap formation by noncanonical pyroptosis in abdominal aortic aneurysm

BackgroundAbdominal aortic aneurysm (AAA) is one of the most life-threatening cardiovascular diseases while currently lacks effective drug treatment. NETs formation has been proved to be crucial trigger of AAA, so finding its upstream regulatory targets is the key to discovering therapeutic agents for AAA. Methods and Resultswe reveal that PI3Kgmma (PI3K{gamma}) is an upstream signal that regulates NETs formation. Inhibition of PI3K{gamma} reduces the expression of NETs and reduces inflammation in the aortic wall, thereby significantly ameliorating AAA. However, the mechanism of NETs formation regulated by PI3K{gamma} has not been fully elucidated. Using isolated bone marrow neutrophils, we show that PI3K{gamma} deficiency inactivates the noncanonical pyroptosis pathway (Capase11/GSDMD) to inhibit NETs expression, and subsequently found that PI3K{gamma} regulation of noncanonical pyroptosis via anchoring PKA is dependent on cAMP/PKA signaling, but not on classical PI3K/AKT signaling. ConclusionsOur research uncovers the role and mechanism of PI3K{gamma} in AAA development and provides insights into AAA therapy from the perspective of NETs formation.

cell biology↗

bioRxiv2024

Targeting resident astrocytes attenuates neuropathic pain after spinal cord injury

Astrocytes derive from different lineages and play a critical role in neuropathic pain after spinal cord injury (SCI). Whether selective eliminating these main origins of astrocytes in lumbar enlargement could attenuate SCI-induced neuropathic pain remains unclear. Through transgenic mice injected with an adeno-associated virus vector and diphtheria toxin, astrocytes in lumbar enlargement were lineage traced, targeted and selectively eliminated. Pain-related behaviors were measured with an electronic von Frey apparatus and a cold/hot plate after SCI. RNA sequencing, bioinformatics analysis, molecular experiment and immunohistochemistry were used to explore the potential mechanisms after astrocyte elimination. Lineage tracing revealed that the resident astrocytes but not ependymal cells were the main origins of astrocytes-induced neuropathic pain. SCI induced mice to obtain significant pain symptoms and astrocyte activation in lumbar enlargement. Selective resident astrocytes elimination in lumbar enlargement could attenuate neuropathic pain and activate microglia. Interestingly, the type I interferons (IFNs) signal was significantly activated after astrocytes elimination, and the most activated Gene Ontology terms and pathways were associated with the type I IFNs signal which was mainly activated in microglia and further verified in vitro and in vivo. Furthermore, different concentrations of interferon and Stimulator of interferon genes (STING) agonist could activate the type I IFNs signal in microglia. These results elucidate that selectively eliminating resident astrocytes attenuated neuropathic pain associated with type I IFNs signal activation in microglia. Targeting type I IFNs signal is proven to be an effective strategy for neuropathic pain treatment after SCI.

neuroscience↗

bioRxiv2024

Noncaloric monosaccharides induce excessive sprouting angiogenesis in zebrafish via foxo1a-marcksl1a signal

Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar-sweetened beverages. Nevertheless, the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. We have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose, resembling the hyperangiogenic characteristics observed in proliferative diabetic retinopathy (PDR). Utilizing this model, we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels, especially intersegmental vessels (ISVs). The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells (ECs) into tip cells. Single-cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs, proliferating ECs, and a series of upregulated proangiogenic genes. Further analysis and experiments validated that reduced foxo1a mediated the excessive angiogenesis induced by monosaccharides via up-regulating the expression of marcksl1a. This study has provided new evidence showing the negative effects of noncaloric monosaccharides on the vascular system and the underlying mechanisms.

pharmacology and toxicology↗

bioRxiv2024

The N-terminus of Plasmodium falciparum Circumsporozoite Protein Contains Three Non-Overlapping Murine B-cell Epitope Regions

The generation of an anti-malarial vaccine that produces broad, potent, and durable responses is highly desirable to control the burden of Plasmodium falciparum disease. Current vaccines have offered modest efficacy ranging from 50%-70%, likely associated with antibody responses that are relatively short lived and strain specific. Currently approved malaria vaccines, RTS,S and R21, target the repeat region and C-terminal region of Plasmodium falciparum CSP, leaving the N-terminal region of CSP neglected as a target for protective immunogen design. Here, we isolate and express a panel of memory B-cell derived N-terminal CSP-specific monoclonal antibodies (mAbs) from mice immunized with an N-terminal CSP specific immunogen. The characterization of N-terminal specific mAbs including peptide walking and affinity experiments indicate that these antibodies target three distinct sites within the N-terminus of CSP. Site ntCSP-A contains the Region I (RI) cleavage site, which has been previously defined, whereas the remaining two sites are in previously undescribed locations upstream of RI, termed ntCSP-B and ntCSP-C.

immunology↗