Biology subjects

Han, J.

Publications and source records attributed to Han, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Absolute Quantification of Aging-Associated Glycans in IgG for Biological Age Prediction: Insights from Glycomics and Transcriptomics

Immunoglobulin G (IgG) N-glycans have been identified as associated with aging; however, previous studies predominantly quantified changes based on the relative percentages of each glycan within the total glycan pool, neglecting the absolute concentration changes of individual glycans. Additionally, relative quantification can limit practical applications, as these often require absolute concentration measurements for consistent and interpretable biomarker values. In this study, we introduce a novel strategy for discovering aging-associated IgG glycans and establishing a prediction model based on their absolute concentration alteration. We employed a glycome quantification technology to identify the alteration in IgG glycan amount in natural aging and anti-aging (caloric restriction) models, discovering aging-related glycans. The glycomics analysis revealed key features: downregulation of bisected glycan GP3 (F(6)A2B) and upregulation of digalactosylated glycan GP8 (F(6)A2G2). These glycan changes showed significant fold changes from an early stage. Using external standards of these two glycans, we subsequently measured the absolute concentrations of them, allowing us to establish a predictive model, abGlycoAge, for biological aging. The abGlycoAge index suggested a younger state under caloric restriction, with an average age reduction of 3.9-14 weeks. Additionally, we performed RNA sequencing on splenic B cells of mice, suggesting Derl3, Smarcb1, Ankrd55, Tbkbp1 and Slc38a10 could contribute to the alteration of GP3 and GP8 in aging. This analysis enhances our understanding of glycan alterations, accounts for individual variability, and aids in designing effective anti-aging strategies. These findings highlight the crucial roles of the GP3 and GP8 as potential biomarkers for aging and health.

biochemistry↗

bioRxiv2024

Oral delivery of semaglutide and tirzepatide using milk-derived small extracellular vesicles

Therapeutic proteins and peptides have revolutionized modern biomedicine. However, the large size and complex structure of these macromolecules preclude their oral administration, greatly limiting their applications in patient care. Biochemical degradation in the gastrointestinal tract, mucus, and cellular barrier are the major obstacles to oral development. Small extracellular vesicles (sEVs) are natural nano lipid vesicles serving as essential vehicles for intercellular communication. sEVs are resistant to biochemical degradation, permeable to mucus barriers, and can penetrate cellular barriers. sEVs are thus considered the next-generation vehicles with the potential for oral peptide/protein drug delivery. Herein, we report the use of milk-derived sEVs as delivery vehicles to achieve successful and highly efficient oral delivery of two therapeutic GLP-1 receptor agonists, semaglutide and tirzepatide. We showed that semaglutide and tirzepatide can be efficiently loaded onto sEVs in vitro, and oral gavage of semaglutide-loaded sEVs or tirzepatide-loaded sEVs can effectively lower blood glucose levels in db/db mouse models. This study demonstrates that sEVs is a platform technology for oral peptide drug delivery and opens a new avenue for oral peptide/protein therapeutics delivery.

pharmacology and toxicology↗

bioRxiv2024

Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation

All great apes differ karyotypically from humans due to the fusion of chromosomes 2a and 2b, resulting in human chromosome 2. Yet, the structure, function, and evolutionary history of the genomic regions associated with this fusion remain poorly understood. Here, we analyze finished telomere-to-telomere chromosomes in great apes and macaques to show that the fusion was associated with multiple pericentric inversions, segmental duplications (SDs), and the rapid turnover of subterminal repetitive DNA. We characterized the fusion site at single-base-pair resolution and identified three distinct SDs that originated more than 5 million years ago. These three distinct SDs were differentially distributed among African great apes as a result of incomplete lineage sorting (ILS) and lineage-specific duplication. Most conspicuously, one of these SDs shares homology to a hypomethylated SD spacer sequence present in hundreds of copies in the subterminal heterochromatin of chimpanzees and bonobos. The fusion in human was accompanied by a systematic degradation of the three divergent -satellite arrays representing the ancestral centromere creating five distinct structural haplotypes in humans. CRISPR/Cas9-mediated depletion of the fusion site in human cell lines significantly alters the expression of 108 genes, indicating a potential regulatory consequence to this human-specific karyotypic change.

evolutionary biology↗

bioRxiv2024

FaDAM3 and FaDAM4 are candidate genes for the regulation of seasonal dimorphism in cultivated strawberry

Cultivated strawberry (Fragaria ananassa) exhibits seasonal dimorphism between the summer and winter seasons. Under the influence of short day conditions, the winter morphology is induced, which includes shorter petioles, smaller and thicker leaves with higher concentrations of chlorophyll and higher density of trichomes. In peach (Prunus persica) the Dormancy-Associated MADS-box (DAM) gene family is involved in the regulation of winter dormancy, which closely resembles strawberry seasonal dimorphism in terms of timing and environmental regulation. In strawberry, six genes exist with close homology to the peach DAM genes. We analyzed the amino acid and coding sequences of these genes, and designated them FaDAM1-4 and FaSVP1-2. We found that there are three pairs of highly similar paralogs within the strawberry genome that exhibit similar expression patterns, although expression levels vary. FaDAM3 and FaDAM4 exhibit expression patterns that are consistent with seasonal dimorphism. We conclude that FaDAM3 and FaDAM4 are candidate genes for the regulation of seasonal dimorphism in strawberry.

plant biology↗

bioRxiv2024

Functional and epitope specific monoclonal antibody discovery directly from immune sera using cryoEM

Antibodies are crucial therapeutics, comprising a significant portion of approved drugs due to their safety and clinical efficacy. Traditional antibody discovery methods are labor-intensive, limiting scalability and high-throughput analysis. Here, we improved upon our streamlined approach combining structural analysis and bioinformatics to infer heavy and light chain sequences from electron potential maps of serum-derived polyclonal antibodies (pAbs) bound to antigens. Using ModelAngelo, an automated structure-building tool, we accelerated pAb sequence determination and identified sequence matches in B cell repertoires via ModelAngelo derived Hidden Markov Models (HMMs) associated with pAb structures. Benchmarking against results from a non-human primate HIV vaccine trial, our pipeline reduced analysis time from weeks to under a day with higher precision. Validation with murine immune sera from influenza vaccination revealed multiple protective antibodies. This workflow enhances antibody discovery, enabling faster, more accurate mapping of polyclonal responses with broad applications in vaccine development and therapeutic antibody discovery.

immunology↗

bioRxiv2024

A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell populations, we developed a benchmark containing mosaic variants in the Genome in a Bottle Consortium (GIAB) HG002 reference material DNA from a large batch of a normal lymphoblastoid cell line. First, we used a somatic variant caller with high coverage (300x) Illumina whole genome sequencing data from the Ashkenazi Jewish trio to detect variants in HG002 not detected in at least 5% of cells from the combined parental data. These candidate mosaic variants were subsequently evaluated using >100x BGI, Element, and PacBio HiFi data. High confidence candidate SNVs with variant allele fractions above 5% were included in the HG002 draft mosaic variant benchmark, with 13/85 occurring in medically relevant gene regions. We also delineated a 2.45 Gbp subset of the previously defined germline autosomal benchmark regions for HG002 in which no additional mosaic variants >2% exist, enabling robust assessment of false positives. The variant allele fraction of some mosaic variants is different between batches of cells, so using data from the homogeneous batch of reference material DNA is critical for benchmarking these variants. External validation of this mosaic benchmark showed it can be used to reliably identify both false negatives and false positives for a variety of technologies and detection algorithms, demonstrating its utility for optimization and validation. By adding our characterization of mosaic variants in this widely-used cell line, we support extensive benchmarking efforts using it in simulation, spike-in, and mixture studies.

bioinformatics↗

bioRxiv2024

Structural basis of broad protection against influenza virus by a human antibody targeting the neuraminidase active site via a recurring motif in CDR H3

Influenza viruses evolve rapidly, driving seasonal epidemics and posing global pandemic threats. While neuraminidase (NA) has emerged as a vaccine target, shared molecular features of NA antibody responses are still not well understood. Here, we describe cryo-electron microscopy structures of the broadly protective human antibody DA03E17, which was previously identified from an H1N1-infected donor, in complex with NA from A/H1N1, A/H3N2, and B/Victoria-lineage viruses. DA03E17 targets the highly conserved NA active site using its long CDR H3, which features a DR (Asp-Arg) motif that engages catalytic residues and mimics sialic acid interactions. We further demonstrate that this motif is conserved among several NA active site-targeting antibodies, indicating a common receptor mimicry strategy. We also identified potential antibody precursors containing this DR motif in all donors of a healthy human donor BCR database, highlighting the prevalence of this motif and its potential as vaccine targeting. Our findings reveal shared molecular features in NA active site-targeting antibodies, offering insights for NA-based universal influenza vaccine design.

immunology↗

bioRxiv2024

Behaviorally-relevant features of observed actions dominate cortical representational geometry in natural vision

We effortlessly extract behaviorally relevant information from dynamic visual input in order to understand the actions of others. In the current study, we develop and test different classes of models to better understand the neural representational geometries supporting action understanding. Using fMRI, we measured brain activity as participants viewed a diverse set of 90 different video clips depicting social and nonsocial actions in real-world contexts. We developed five behavioral models using arrangement tasks: two models reflecting behavioral judgments of the purpose (transitivity) and the social content (sociality) of the actions depicted in the video stimuli; and three models reflecting behavioral judgments of the visual content (people, objects, and scene) depicted in still frames of the stimuli. We evaluated how well these models predict neural representational geometry and tested them against semantic models based on verb and nonverb embeddings and visual models based on gaze and motion energy. Our results revealed that behavioral models of action meaning/purpose (transitivity, sociality) better reflect neural representational geometry than behavioral models of object, person, and scene features, as well as semantic and visual models throughout much of cortex. The sociality and transitivity models captured a large portion of unique variance throughout the action observation network, extending into regions not typically associated with action perception, like ventral temporal cortex. Overall, these findings expand our understanding of the action observation network and indicate that the social content and purpose of observed actions are predominant in cortical representation.

neuroscience↗

bioRxiv2024

Task-induced internal bodily rather than brain states regulate human self-perception

A fundamental ability for us is to identify and distinguish with others, known as the self, whose neural substrate is hard to identify by external self-related stimuli because of possible interference from internal self-related states of both body and brain. Using the same stimuli, we ruled out this dilemma by manipulating human subjects performing own- and celebrity-face discrimination tasks to induce self-related and non-self-related states, respectively. Results showed that stimulus-driven sensory sensory differences among own-, celebrity-, and stranger-faces were independent of task-induced internal states, whereas their perceptual differences were strongly modulated by these states. Intriguingly, we further found that subjects bodily (indexed by heartbeat-evoked potentials) rather than brain (indexed by pre-stimulus -powers) states not only predicated their self-perception but also moderated the relationship between external stimuli and self-perception. Our results reveal for the first time an adaptive self-perception, shaped by not only external stimuli but also internal states, especially the interoception.

neuroscience↗

bioRxiv2024

Distribution-preserved compression of single-cell atlases for privacy-protected data dissemination and novel cell type discovery

We introduce SUREv2, a tool for constructing lightweight, transmittable, and privacy-preserving references from single cell atlases. SUREv2 introduces a compressed data structure that maintain the distribution of cells within these atlases and develops an out-of-reference scoring method for identifying novel cell populations. This user-friendly tool shall enhance the analysis of single cell datasets by providing a consistent, privacy-focused reference framework.

bioinformatics↗

bioRxiv2024

Building a single cell transcriptome-based coordinate system for cell ID with SURE

The growing scale of single cell data demands standardized cell identification. We develop SURE, a data-driven method that establishes a cell coordinate system through optimally-sized metacells exhibiting enhanced transcriptional homogeneity. This approach enables precise cellular state characterization while providing three key atlas functionalities: zero-shot query-to-reference mapping, out-of-atlas detection, and cell type annotation. SUREs hierarchical assembly pipeline successfully integrates large-scale atlas datasets, as demonstrated by constructing the Human Blood Metacell Atlas (HBMCA) from 5 million cells. Our method addresses the fundamental challenge of consistent cell positioning across diverse experimental contexts, facilitating robust comparative analyses between healthy and disease states.

bioinformatics↗

bioRxiv2024

Characteristic of KPC-14, a KPC Variant Conferring Resistance to Ceftazidime-Avibactam in the Extensively Drug-resistant ST463 Pseudomonas aeruginosa Clinical Isolate

We studied two KPC-14 variants from clinical Pseudomonas aeruginosa isolates, C137 and C159, to better understand genomic diversity, mechanisms, and genes that confer antibiotic resistance and pathogenicity. C137 and C159, a sequence type 463 ExoU-positive multidrug-resistant strain, were concurrently resistant to carbapenems and ceftazidime-avibactam (CZA). Both strains possessed five intrinsic antimicrobial resistance genes (fosA, catB7, crpP, blaPAO, and a blaOXA-486 variant), as well as the blaKPC-14 gene in the chromosome. In strain C137, blaKPC-14 gene was situated on the plasmid pC137. KPC-14-harbouring transformants of pC137 exhibited resistance to CZA and restored sensitivity to carbapenems, signifying a "see-saw" effect. Both strains demonstrated the expression of the blaKPC-14 gene, concurrent inactivation of the outer membrane protein OprD, overexpression of the efflux pump MexX, and a pronounced capacity for biofilm formation. The genomic environment of KPC-14 consisted of IS26/IS26/TnpR_Tn3/ISKpn27/ISKpn6/IS26, which was classified as pseudo-compound transposons (PCTs). Plasmid pC137 closely resembled the previously described plasmid p94, which possesses the same genomic architecture, implying that IS26-mediated PCTs may store a variety of resistance genes, including blaKPC-2 and KPC variants, and were currently disseminating in the region. The KPC-14 variant presents significant challenges for clinical treatment. The blaKPC-14 gene, carried by the PCTs, was integrated into the chromosome, exhibiting stability throughout bacterial inheritance. Our research highlights the necessity for improved clinical surveillance of Klebsiella pneumoniae carbapenemase-producing P. aeruginosa.

molecular biology↗

bioRxiv2024

Acetic acid induces osmotic imbalances in drug-resistant bacteria synergistically enhancing cobalt-doped carbon quantum dots bactericidal efficiency

When pathogenic bacteria colonise a wound, they can create an alkaline ecological niche which selects for their survival by creating an inflammatory environment which restricts healthy wound healing to proceed. To aid healing, wound acidification has been exploited to disrupt this process and stimulate fibroblast growth, increase wound oxygen concentrations, minimise proteolytic activity and re-stimulate the host immune system. Within this study, we have developed unique cobalt doped carbon quantum dot nanoparticles which work together with mild acetic acid creating a potent synergistic antimicrobial therapy. The acidic environment alters the osmotic balance of microorganisms forcing them to swell and speed up the internalisation of the ultra-small particles. The particles hyperpolarise the bacterial membranes and generate damaging peroxidase species resulting in cellular lysis. In mice, cobalt doped carbon quantum dots remove MRSA infection while allowing wounds to heal at equivalent rates to uninfected wounds. This work demonstrates how synergistic antimicrobial treatment strategies can be successfully used to combat antimicrobial resistant infections.

microbiology↗

bioRxiv2024

Estimating and correcting index hopping misassignments in single-cell RNA-seq data

BackgroundIndex hopping causes read assignment errors in data from multiplexed sequencing libraries. This issue has become more prevalent with the widespread use of high-capacity sequencers and highly multiplexed single-cell RNA sequencing (scRNA- seq). ResultsWe conducted deep, plate-based scRNA-seq on a mixed population of mouse skin cells. Analysis of transcriptomes from 1152 cells identified four distinct cell types. To estimate the error rate in sample assignment due to index hopping, we employed differential expression analysis to identify signature genes that were highly and specifically expressed in each cell type. We quantified the proportion of misassigned reads by examining the detection rates of signature genes in other cell types. Remarkably, regardless of gene expression levels, we estimated that 0.65% of reads per gene were assigned to incorrect cell across our data. To computationally compensate for index hopping, we developed a simple correction method wherein, for each gene, 0.65% of the librarys average expression level was subtracted from the expression in each cell. This correction had notable effects on transcriptome analyses, including increased cell-cell clustering distance and alterations in intermediate state assignments of cell differentiation. ConclusionsIndex hopping misassignments are measurable and can impact the experimental interpretation of sequencing results. We devised a straightforward method to estimate and correct for the index hopping rate by quantifying misassigned genes in distinct cell types within an scRNA-seq library. This approach can be applied to any barcoded, multiplexed scRNA-seq library containing cells with distinct expression profiles, allowing for correction of the expression matrix before conducting biological analysis.

genomics↗

bioRxiv2024

Elucidating the metabolic roles of isoflavone synthase-mediated protein-protein interactions in yeast

Transient plant enzyme complexes formed via protein-protein interactions (PPIs) play crucial regulatory roles in secondary metabolism. Complexes assembled on cytochrome P450s (CYPs) are challenging to characterize metabolically due to difficulties in decoupling the PPIs metabolic impacts from the CYPs catalytic activities. Here, we developed a yeast-based synthetic biology approach to elucidate the metabolic roles of PPIs between a soybean-derived CYP, isoflavone synthase (GmIFS2), and other enzymes in isoflavonoid metabolism. By reconstructing multiple complex variants with an inactive GmIFS2 in yeast, we found that GmIFS2-mediated PPIs can regulate metabolic flux between two competing pathways producing deoxyisoflavonoids and isoflavonoids. Specifically, GmIFS2 can recruit chalcone synthase (GmCHS7) and chalcone reductase (GmCHR5) to enhance deoxyisoflavonoid production or GmCHS7 and chalcone isomerase (GmCHI1B1) to enhance isoflavonoid production. Additionally, we identified and characterized two novel isoflavone O-methyltransferases interacting with GmIFS2. This study highlights the potential of yeast synthetic biology for characterizing CYP-mediated complexes.

synthetic biology↗

bioRxiv2024

A top-down insular cortex circuit crucial for non-nociceptive fear learning

Understanding how threats drive fear memory formation is crucial to understanding how organisms adapt to environments and treat threat-related disorders like PTSD. While traditional Pavlovian conditioning studies have provided valuable insights, the exclusive reliance on electric shock as a threat stimulus has limited our understanding of diverse threats. To address this, we developed a conditioning paradigm using a looming visual stimulus as an unconditioned stimulus (US) in mice and identified a distinct neural circuit for visual threat conditioning. Parabrachial CGRP neurons were necessary for both conditioning and memory retrieval. Upstream neurons in the posterior insular cortex (pIC) responded to looming stimuli, and their projections to the parabrachial nucleus (PBN) induced aversive states and drove conditioning. However, this pIC-to-PBN pathway was not required for foot-shock conditioning. These findings reveal how non-nociceptive visual stimuli can drive aversive states and fear memory formation, expanding our understanding of aversive US processing beyond traditional models.

neuroscience↗

bioRxiv2024

Accurate Cell Abundance Quantification using Multi-positive and Unlabeled Self-learning

Quantifying the abundance of different cell types in pathological samples can help to uncover the correlations between cell composition and pathological conditions, offering deeper insights into the roles of different cell types in complex diseases. Conventional methods for cell abundance estimation often employ unsupervised clustering or supervised learning to identify cell types and estimate their proportions. However, these methods face challenges in accurately quantifying cell abundances, as clustering results could be unreliable and supervised methods may misclassify cell types not presented in the training data. We introduce CleverXMBD1 (denoted as Clever) for quantifying cell abundance from complex samples using a multi-class classifier trained with a confidence-based multi-positive and unlabeled loss function. Our evaluations show that Clever consistently and substantially outperforms existing methods in quantifying cell type abundance across multiple single cell datasets derived from different modalities, including CyTOF and image mass cytometry.

bioinformatics↗

bioRxiv2024

Maximum vertical height during wing flapping of laying hens captured with a depth camera

Cage-free housing systems for laying hens, and their accompanying guidelines, legislation, and audits, are becoming more common around the world. Cage-free regulations often specify requirements for floor space and cage height, but the availability of three-dimensional space can vary depending on system configurations. Little research has looked at how much vertical space a hen occupies while flapping her wings, which is arguably her most space-intensive behavior. Therefore, the objective of this study was to use a depth sensing camera to measure the maximum vertical height hens reach when wing flapping without physical obstructions. Twenty-eight individually caged Hy-line W36 hens at 45 weeks of age were evaluated. A ceiling-mounted depth camera was centered above a test pen and calibrated prior to collecting data. During testing, one hen at a time was placed in the test pen and recorded flapping her wings. From depth footage, the minimum distance between pixels was obtained for each frame, and we computed the maximum vertical height reached by each hen. Results for vertical space used during a wing flapping event showed that hens reached a maximum height of 51.0 {+/-} 4.7 cm. No physical measures correlated with maximum height obtained from the depth camera (P>0.05). Hens in this study were from a single strain, were old enough to have keel damage, and were cage-reared and housed, preventing us from generalizing the results too far. However, depth cameras provide a useful approach to measure how much space laying hens of varying strains, ages, and rearing/housing methods need to perform dynamic behaviors.

animal behavior and cognition↗