Biology subjects

Dong, Y.

Publications and source records attributed to Dong, Y..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Comparative population genomics of relictual Caribbean island Gossypium hirsutum

Gossypium hirsutum is the worlds most important source of cotton fiber, yet the diversity and population structure of its wild forms remain largely unexplored. The complex domestication history of G. hirsutum combined with reciprocal introgression with a second domesticated species, G. barbadense, has generated a wealth of morphological forms and feral derivatives of both species and their interspecies recombinants, which collectively are scattered across a large geographic range in arid regions of the Caribbean basin. Here we assessed genetic diversity within and among populations from two Caribbean islands, Puerto Rico (n = 43, five sites) and Guadeloupe (n = 25, one site), which contain putative wild and/or introgressed forms. Using whole-genome resequencing data and a phylogenomic framework derived from a broader genomic survey, we parsed individuals into feral derivatives and truly wild forms. Feral cottons display uneven levels of genetic and morphological resemblance to domesticated cottons, with diverse patterns of genetic variation and heterozygosity. These patterns are inferred to reflect a complex history of interspecific and intraspecific gene flow that is spatially highly variable in its effects. Wild cottons in both Caribbean islands appear to be relatively inbred, especially the Guadeloupe samples. Our results highlight the dynamics of population demographics in relictual wild cottons that experienced profound genetic bottlenecks associated with repeated habitat destruction superimposed on a natural ecogeographical distribution comprising widely scattered populations. These results have implications for conservation and utilization of wild diversity in G. hirsutum.

evolutionary biology↗

bioRxiv2025

FEDRANN: effective overlap graph construction based on dimensionality reduction and approximate nearest neighbors

Overlap detection is a key step in de novo genome assembly pipelines based on the Overlap-Layout-Consensus (OLC) paradigm. However, existing methods for overlap detection either rely on heuristic seed-and-extension strategies or locality-sensitive hashing (LSH), both of which struggle to handle repetitive genomic regions and the computational burden of large-scale datasets. Here, we present FEDRANN, a novel strategy for overlap graph construction that integrates feature extraction, dimensionality reduction (DR), and approximate nearest neighbor (ANN) search. We find the pipeline combining inverse document frequency (IDF) transformation, sparse random projection (SRP), and NNDescent enables accurate detection of overlaps across diverse datasets. We developed an efficient open-source implementation of this pipeline named Fedrann (https://github.com/jzhang-dev/fedrann). Through systematic benchmarking on real long-read sequencing data, we demonstrate that Fedrann produces overlap graphs comparable to or better than those generated by existing state-of-the-art tools, including MECAT2, minimap2, and wtdbg2, while maintaining competitive runtime. Despite being implemented primarily in Python, Fedrann achieves performance on par with tools written in compiled languages, owing to matrix-based representations and C-accelerated numerical libraries. Our results suggest that DR and ANN techniques offer a promising new direction for scalable and accurate overlap detection in long-read assembly and broader sequence similarity search tasks.

bioinformatics↗

bioRxiv2025

Lipidomic signatures in microglial extracellular vesicles during acute inflammation: a gateway to neurological biomarkers

Extracellular vesicles (EVs) are membrane bound vesicles released from all cells throughout the body, including the central nervous system, and are known to carry both membrane-bound proteins and cargo reflective of their cell of origin. EVs show promise as neurological disease biomarkers due to their molecular makeup reflecting their parent-cell composition signature and due to their ability to cross the blood-brain barrier. To-date, the vast majority of research in this field has explored the protein profiles of EVs; however, lipids play an important role not only in the formation of EVs, but also in mediating cellular function and the pathological progression of many neurodegenerative conditions. Herein, we take a critical first step in determining the potential utility of EV lipids as biomarkers in neurological disease. In vitro we exposed BV-2 microglia to either control media or media containing lipopolysaccharides (LPS), a known pro-inflammatory stimulus, for 24 hours then isolated both the cells and their EVs and performed LC-MS/MS. For the first time, we reveal distinct lipidomic changes can differentiate resting vs. pro-inflammatory microglia and their EVs, while distinct lipids are preserved between EVs and their parent cell. Moreover, we add to current literature by demonstrating acute pro-inflammatory activation of microglia results in the activation and suppression of distinct lipidomic pathways. Finally, we demonstrate that analysis of lipid-based relationships between parent cells and their EVs may be a useful tool to infer cellular function. This study is the first of its kind to demonstrate that lipidomic analysis can not only differentiate the functional state of cells in vitro but can also differentiate their EVs. We lay the first brick in a foundation to support future research into EV lipids as novel and exciting biomarker candidates in neurological disease.

neuroscience↗

bioRxiv2025

Decoupling bile acid 7α-dehydroxylation from colonization resistance to Clostridioides difficile

Secondary bile acids, generated through microbial transformation of primary bile acids secreted in bile, play a role in shaping intestinal microbial communities, modulating host immunity, and regulating energy metabolism. In vitro studies have shown that the balance between primary and secondary bile acids strongly affects spore germination, growth, and cellular physiology of Clostridioides difficile, a major nosocomial gut pathogen. In vivo correlations between microbiome composition, bile acid metabolome, and colonization resistance have led to the hypothesis that 7-dehydroxylating bacteria such as Clostridium scindens protect against C. difficile infection by producing secondary bile acids like deoxycholic acid. However, due to the genetic intractability of known 7-dehydroxylating species, direct experimental validation of this causal relationship has been challenging. In this study, we leveraged the first available 7-dehydroxylation-deficient baiH mutant to test the direct role of 7-dehydroxylated bile acid production in C. difficile colonization resistance in vivo. We colonized gnotobiotic mice with isogenic wild-type or baiH strains of the recently described 7-dehydroxylating species Faecalicatena contorta, including wild-type C. scindens-colonized mice as a positive control. Wild-type F. contorta accumulated 7-dehydroxylated bile acids at levels equivalent to C. scindens, in a strictly baiH-dependent manner. However, despite equivalent bile acid profiles, wild-type F. contorta failed to replicate the C. difficile-restrictive phenotype observed with C. scindens. These findings demonstrate that commensal clostridial 7-dehydroxylation alone is not sufficient for enhancing colonization resistance to C. difficile. Our results highlight the existence of additional, potentially bile acid-independent mechanisms by which certain commensals mediate protection, with important implications for microbiota-based therapies. Importance7-dehydroxylated secondary bile acids, including deoxycholic acid and lithocholic acid, produced by commensal clostridia are widely assumed to inhibit the important nosocomial pathogen Clostridioides difficile, yet their precise role in colonization resistance remains unresolved. Using a defined mouse microbiota and an isogenic Faecalicatena contorta strain pair differing in a single 7-dehydroxylation gene (baiH), we show that restoration of secondary bile acid production is not sufficient to delay C. difficile colonization in vivo. This contrasts with the protective effect of Clostridium scindens, which generates a similar bile acid profile. Our findings uncouple bile acid metabolism from protection and suggest that additional, strain-specific functions - such as nutrient competition or antimicrobial production - play a critical role. Understanding these mechanisms is essential for the rational design of next-generation microbiota-based therapies to prevent or treat recurrent C. difficile infection.

microbiology↗

bioRxiv2025

Transcriptome and metabolome analyses reveal novel genetic targets for L-tryptophan overproduction in Corynebacterium glutamicum

Corynebacterium glutamicum is a promising microbial chassis for the industrial production of L-tryptophan, which has exhibited increasing demand due to its diverse applications and high market value. In previous work, we developed an L-tryptophan-overproducing C. glutamicum strain TR26 through multiple rounds of rational metabolic engineering. Here, comparative transcriptome and metabolome analyses were conducted between TR26 and its progenitor strain MB001 to reveal the underlying mechanisms and potential bottlenecks for L-tryptophan production in TR26. Furthermore, by systematically down- and up-regulating differentially expressed genes of interest, two novel genetic targets, glnK and sugR, were identified as being associated with L-tryptophan synthesis. Specifically, the repression of glnK and overexpression of sugR in strain TR26 increased the titer of L-tryptophan by 6.7% and 20.9%, respectively. Gene transcription profiling and intracellular metabolite analysis further suggested that the observed improvements in L-tryptophan synthesis could be attributed to optimized nitrogen transport and metabolism, efficient reallocation of cellular resources and enhanced supply of phosphoenolpyruvate (PEP). This study advances our understanding of the regulation mechanisms governing L-tryptophan synthesis in C. glutamicum and provides valuable insights for further optimization of industrial cell factories.

synthetic biology↗

bioRxiv2025

Two telomere-to-telomere, gap-free genome assemblies and comparisons revealed the conserved key genes associated with sugar accumulation in Rubus genus

For the first time, we assembled two highly continuous, completely gap-free reference genomes of the Rubus subgenus: Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP), which are widely distributed in southern China with similar phenotypic traits (Figures 1A, 1B, and Figure S1), yet ripe fruits display distinct sugar accumulation levels (Table S1), making them ideal candidates for investigating the mechanisms underlying sugar accumulation in the Rubus genus. The XMM (213.53 Mb, 28,204 genes) and DHP (218.26 Mb, 28,569 genes) genomes exhibit close evolutionary relationships, diverging approximately 3.21 Mya. Comparative genomics identified extensive synteny, interspecific structural variations (translocations, inversions, segmental duplications), and presence/absence variation (PAV). Using Hi-C interaction heatmaps and Sanger sequencing, we validated interspecific structural inversions. Additionally, we identified a sugar transporter gene (MFS1), which is present in XMM but absent in DHP. Combined analysis of the gene family expansion/contraction and transcriptome identified two conserved key genes (RhSTP13 and RhSTP7) associated with sugar accumulation in Rubus genus and displayed distinct roles through transient expression assay. To facilitate functional genomics study, we also established a comprehensive Rubus database, RubusDB, a freely accessible repository consolidating all genomic, transcriptomic and phenotypic data of Rubus genus. These findings provide a foundational framework for elucidating the genetic basis of sugar accumulation, genome diversification, and trait improvement in Rubus species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/646780v2_fig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@1baca20org.highwire.dtl.DTLVardef@2c01eaorg.highwire.dtl.DTLVardef@131dc00org.highwire.dtl.DTLVardef@62a04f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFIGURE 1.C_FLOATNO Phenotypic characterization, de novo genome assemblies, variation, and evolution of Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP). (A) Illustration of XMM whole plants, stem, flower bud and flower, respectively. (B) Illustration of DHP whole plants, stem, flower bud and flower, respectively. (C) The chromosome karyotype analysis of XMM. Bar = 10 {micro}m. (D) Circular diagram of XMM and DHP reference genomes. (a) Chromosomes are represented by centromeres (dark red) and telomeres (blue); (b) CEN18 density; (c) CEN17 density; (d) Gene density; (e) TE density; (f) PAV density; (g) SNP density; (h) Collinear lines at the center of diagram highlight homoeologous chromosomes relationships and non-homoeologous regions. (E) Genomic alignments between XMM and DHP. Inversions, duplications and translocations are marked with orange, blue and green ribbons, respectively. (F) Identification of large inversions in chromosome 7 between XMM and DHP. The three heatmaps show the chromatin interaction matrix, including mapping Hi-C data of DHP against DHP genome (left), mapping Hi-C data of DHP against XMM genome (middle) and mapping Hi-C data of XMM against XMM genome (right). The lower panel illustrates gene alignments between XMM and DHP. (G) Synteny, structural rearrangements, monomer, and identity distribution in the 16-20 Mbp region of chromosome 6 between XMM and DHP. (H) Local genome synteny of chromosome 5, with a structural variation that is present only in XMM. The PAV region includes a gene related to sugar transporter (MFS1, XMM05G025540). (I) Gene-level matchings of MFS genes in the PAVs region between XMM and DHP. (J) Phylogenetic relationships and divergence times between raspberries and other Rosaceae species. The black numbers close to the divergence nodes indicate the divergence times and the red bars represent the 95% confidence intervals. The red and black numbers indicate expanded and contracted ortholog groups at the corresponding node. Scale bar corresponds to 10 Mya. C_FIG

genomics↗

bioRxiv2025

Enhancing Tissue-Specific Antiviral Immunity to Disrupt Arbovirus Transmission by Mosquitoes

Arboviruses, including dengue virus (DENV), Zika virus (ZIKV), and chikungunya virus (CHIKV), pose a significant global health and economic burden, with Aedes aegypti serving as their primary vector. Arbovirus infection in Ae. aegypti progresses sequentially through the midgut (MG), carcass (CA), and salivary glands (SG), with each tissue exhibiting distinct antiviral responses. Here, we investigate tissue-specific antiviral mechanisms, focusing on the small interfering RNA (siRNA) pathway in SGs. Our results reveal that SGs possess weaker antiviral defense and are more susceptible to arboviral infection compared to MGs and CAs. Notably, overexpression of Dicer2 (Dcr2), a key component of the siRNA pathway, in SGs leads to a significant decrease in arboviral replication. Conversely, Dcr2 overexpression in fat bodies, the primary tissue in CAs, only moderately suppresses DENV2 infection and has no notable effect on Mayaro virus (MAYV) infection. Remarkably, the simultaneous overexpression of Dcr2 in both MGs and SGs enhances antiviral activity, effectively blocking the transmission of multiple arboviruses. These findings reveal the tissue-specific dynamics of mosquito antiviral immunity and underscore the potential for targeting SG-specific immunity to disrupt arbovirus transmission, providing a promising approach for controlling mosquito-borne diseases.

microbiology↗

bioRxiv2025

Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis

The tight coordination of sulfur metabolism and growth regulation is predicated upon nutrient availability. Central to this balancing act is the utilization of cysteine (Cys) for the formation of methionine (Met) and S-adenosylmethionine (SAM). Plants that are severely deficient in regenerating Met due to reduced methylthioadenosine (MTA) nucleosidase activity experience numerous developmental abnormalities. Here, we assess the developmental, metabolic, and regulatory effects associated with decreased MTA recycling. We show that MTA over-accumulation predominantly occurs in reproductive tissues and leads to reduced levels of Cys, Met, and SAM, as well as elevated S-adenosylhomocysteine. These disruptions of primary sulfur utilization also lead to the misregulation of energy metabolism and altered cell cycle progression. RNA-seq experiments show a general down-regulation of many developmental and reproductive genes. Targeted metabolite analyses demonstrate clear impacts on the methyl index which are reflected in the results of bisulfite-sequencing experiments including global alterations in CG gene-body methylation levels and decreases of CHG and CHH methylation in transposable elements. Our findings demonstrate the broad impacts of MTA metabolism on plant development, sulfur utilization and the maintenance of the methyl index.

plant biology↗

bioRxiv2025

Charting Postnatal Heart Development Using In Vivo Single-Cell Functional Genomics

The transition at birth, marked by increased circulatory demands and rapid growth, necessitates extensive remodeling of the hearts structure, function, and metabolism. This transformation requires precise spatial and temporal coordination among diverse cardiac cell types; central to this process is cardiomyocyte maturation, yet the regulatory mechanisms driving these changes remain poorly understood. Here, we present a temporal and spatial atlas of postnatal hearts by integrating single-nucleus transcriptomics with image-based spatial transcriptomics, which uncovers the dynamic regulatory networks of cardiomyocyte maturation. To functionally interrogate candidate regulators in vivo, we developed Probe-based Indel-detectable Perturb-seq (PIP-seq), a high-throughput platform that uses probe-based chemistry to directly capture sgRNA expression, perturbation status, and transcriptomic profiles at single-nucleus resolution. Applying PIP-seq to postnatal cardiac development identified 21 novel regulators of cardiomyocyte maturation, highlighting critical nodal points in this process. Our study establishes a high-resolution framework for dissecting postnatal heart development, underscoring the integrative and highly ordered roles of microenvironment and intercellular communication in cardiomyocyte maturation. Importantly, PIP-seq enables systematic, high-throughput exploration of gene function and networks underlying complex biological processes in their native in vivo context.

developmental biology↗

bioRxiv2025

Enzyme Co-Scientist: Harnessing Large Language Models for Enzyme Kinetic Data Extraction from Literature

The extraction of molecular annotations from scientific literature is critical for advancing data-driven research. However, traditional methods, which primarily rely on human curation, are labor-intensive and error-prone. Here, we present an LLM-based agentic workflow that enables automatic and efficient data extraction from literature with high accuracy. As a demonstration, our workflow successfully delivers a dataset containing over 91,000 enzyme kinetics entries from around 3,500 papers. It achieves an average F1 score above 0.9 on expert-annotated subsets of protein enzymes and can be extended to the ribozyme domain in fewer than 3 days at less than $90. This method opens up new avenues for accelerating the pace of scientific research.

biochemistry↗

bioRxiv2025

Targeted suppression of type 1 interferon signaling during RNA delivery enhances vaccine-elicited immunity

RNA vaccines have emerged as a breakthrough technology, and one promising modality employs alphavirus-derived self-replicating RNA (repRNA) to express vaccine antigens. However, both the lipid nanoparticles (LNP) commonly used to deliver RNA and virus-like amplification of repRNAs trigger innate immune recognition, especially via type I interferon (IFN) signaling. To modulate IFN responses during vaccination, we formulated LNPs co-delivering antigen-encoding RNA together with siRNA targeting the interferon-/{beta} receptor-1 (IFNAR1). siRNA-mediated repression of IFNAR1 increased antigen expression from repRNAs by >10-fold, increased immune cell infiltration, and increased antigen presenting cell activation in the injection site and draining lymph nodes. Compared to repRNA alone, siRNA/repRNA co-delivery increased serum antibody titers >10-fold, dramatically augmented antigen-specific germinal center (GC) B cell responses, and primed 4.4-fold more antigen-specific T cells. Ifnar1 silencing by siRNA co-delivery similarly enhanced mRNA vaccines. Thus, siRNA co-delivery is a readily translatable approach to substantially enhance the immunogenicity of RNA vaccines.

bioengineering↗

bioRxiv2025

Integrative Analysis of Single-cell and Bulk RNA Sequencing Reveals Macrophage Heterogeneity in Lyme Arthritis

IntroductionLyme arthritis (LA) is a common late-stage manifestation of Lyme disease caused by Borrelia burgdorferi (Bb) infection. Macrophages play a crucial role in LA pathogenesis, yet their heterogeneity and functional states within the arthritic microenvironment remain poorly understood. MethodsWe integrated single-cell RNA sequencing data from ankle joint tissues of Bb-infected C57BL/6 mice with bulk RNA sequencing data from both infected ankle joints and bone marrow-derived macrophages. We developed a LA mouse model and validated key findings through histopathological examination and RT-qPCR analysis. ResultsWe identified nine distinct cell types in the joint microenvironment with significant compositional shifts during disease progression. Analysis of 16,617 Macrophages/Monocytes revealed seven functionally distinct subpopulations with differential responses to infection. Pseudo-time trajectory analysis demonstrated three principal differentiation pathways from monocyte-derived macrophages toward anti-inflammatory, TNF+, and IL1b+ inflammatory phenotypes. Cell-cell communication analysis revealed significantly altered TGF-{beta} signaling networks in LA, with the Tgfb1-(Tglbr1+TgIbr2) axis playing a critical role. GSVA and pathway analyses showed metabolic reprogramming from oxidative phosphorylation toward glycolysis in macrophages during infection. Through integrated analysis and LASSO regression, we identified four characteristic genes (SIRPB1C, FABP5, MMP14, and EGR1) as potential LA biomarkers and developed a diagnostic nomogram with high predictive accuracy. ConclusionOur integrative analysis provides comprehensive insights into macrophage heterogeneity and functional plasticity in LA, identifying characteristic biomarkers and potential therapeutic targets. The metabolic reprogramming and altered TGF-{beta} signaling networks we identified may contribute to disease pathogenesis and offer new avenues for intervention strategies.

genomics↗

bioRxiv2025

IQI: Individualized Quantitative trait loci (QTL) Index

There is currently no standard efficient method to precisely detecting and characterizing the difference of quantitative trait loci (QTL) effect among groups and/or populations at individual level. The main reason is that the traditional global regression based QTL analyses can only derive an overall effect of genetic variants on the quantitative trait in a specific group. It is a big challenge to obtain the individual-level QTL effect, which is necessary for accurate testing and precise characterization. Here, we first proposed an individualized QTL index (IQI) that represents the degree of regulation between genetic variants and the trait for each individual. Based on IQI, Differential QTL (DQ) analysis framework was presented to accurately detect the case-control differences in more detail. In addition, IQI can be a new feature/biomarker applied to various accurate bioinformatics analysis, such as differential analysis, disease prediction, and survival analysis. Overall, IQI affords a new perspective on pathogenic mechanisms and will facilitate the study of genetic regulation more detailedly and precisely.

bioinformatics↗

bioRxiv2025

A Sensitive Soma-localized Red Fluorescent Calcium Indicator for Multi-Modality Imaging of Neuronal Populations In Vivo

Recent advancements in genetically encoded calcium indicators, particularly those based on green fluorescent proteins, have optimized their performance for monitoring neuronal activities in a variety of model organisms. However, progress in developing red-shifted GECIs, despite their advantages over green indicators, has been slower, resulting in fewer options for end-users. In this study, we explored topological inversion and soma-targeting strategies, which are complementary to conventional mutagenesis, to re-engineer a red genetically encoded calcium indicator, FRCaMP, for enhanced in vivo performance. The resulting sensors, FRCaMPi and soma-targeted FRCaMPi (SomaFRCaMPi), exhibit up to 2-fold higher dynamic range and peak {Delta}F/F0 per single AP compared to widely used jRGECO1a in neurons in culture and in vivo. Compared to jRGECO1a and FRCaMPi, SomaFRCaMPi reduces erroneous correlation of neuronal activity in the brains of mice and zebrafish by two- to four-fold due to diminished neuropil contamination without compromising the signal-to-noise ratio. Under wide-field imaging in primary somatosensory and visual cortex in mice with high labeling density (80-90%), SomaFRCaMPi exhibits up to 40% higher SNR and decreased artifactual correlation across neurons. Altogether, SomaFRCaMPi improves the accuracy and scale of neuronal activity imaging at single-neuron resolution in densely labeled brain tissues due to a 2-3-fold enhanced automated neuronal segmentation, 50% higher fraction of responsive cells, up to 2-fold higher SNR compared to jRGECO1a. Our findings highlight the potential of SomaFRCaMPi, comparable to the most sensitive soma-targeted GCaMP, for precise spatial recording of neuronal populations using popular imaging modalities in model organisms such as zebrafish and mice.

neuroscience↗

bioRxiv2025

Wearable Photonic Device for Multiple Biomarker Sampling and Detection Without Blood Draws

Blood draws or phlebotomy using needles have been practiced in clinics for several centuries and it often causes pain, discomfort, and inconvenience. Herein, we create a wearable photonic device by integrating a microlens array (MLA) and an optic microneedle array (OMNA) functionalized with immunobinding capacity for safe and needle-free biomarker sampling and detection. The MLA-integrated OMNA amplified and transmitted LED light at 595 nm into the skin through the OMNA, bypassing the light-absorbing melanin in the epidermal layer, and evenly distributing it in the capillary-enriched dermis. The 595 nm light was preferably absorbed by hemoglobin (Hb) and oxygen-Hb within the capillaries, triggering thermal dilation of capillaries without damaging them or causing petechiae. The light illumination resulted in remarkable increases in the concentrations of various blood biomarkers in the skin owing to capillary dilation and biomarker extravasation. These extravasated biomarkers bound specifically to the OMNA, which was covalently decorated with capture antibodies, each microneedle immobilized with one specific antibody. The multi-functional OMNA was extensively modified to amplify the immunobinding signals and achieve sensitivity superior to that of enzyme-linked immunosorbent assay (ELISA) kits. As a proof of concept, we validated the functionality of the prototype for minimally invasive sampling and precise multiplexed blood biomarker detection in two mouse models to quantify acute inflammation and specific antibody production. This cost-efficient device provides a promising platform for blood-free, multiplexed detection of blood biomarkers.

bioengineering↗

bioRxiv2025

Single cell resolved spatial immune repertoire unveils spatial heterogeneity of lymphoid aggregates in human immune disorders

Adaptive immunity, mediated by T and B cell responses, is essential for defending against infections and cancers while also being implicated in autoimmune diseases. Tracking T and B cell repertoires in situ at single-cell resolution is essential for understanding adaptive immune responses. To address the lack of tools for in situ single-cell T/BCR (XCR) sequencing, we developed Stereo-XCR-seq, an efficient strategy for retrieving and sequencing TCR and BCR from Stereo-seq cDNA libraries at subcellular resolution. Stereo-XCR-seq provides unbiased full-length XCR reads alongside spatial transcriptomics, enabling the identification of heterogeneous lymphoid aggregates with distinct clonal activities in cancers and inflammatory bowel disease (IBD). We identified plasma cell aggregates that differ from tertiary lymphoid structures (TLSs) in both transcriptomic profiles and clonal activities, with spatial positioning potentially mediating unique immune responses. Collectively, Stereo-XCR-seq enables in situ single-cell profiling of T and B cell clonal activities within tissue microenvironments, providing insights into lymphocyte adaption to environmental stimuli. This technology provides potential for advancing our understanding of tissue immunity and the development of therapeutic strategies for immune disorders.

immunology↗

bioRxiv2025

Deciphering Transcription in Cryptosporidium parvum: Polycistronic Gene Expression and Chromatin Accessibility

Once considered rare in eukaryotes, polycistronic mRNA expression has been identified in kinetoplastids and, more recently, green algae, red algae, and certain fungi. This study provides comprehensive evidence supporting the existence of polycistronic mRNA expression in the apicomplexan parasite Cryptosporidium parvum. Leveraging long-read RNA-seq data from different parasite strains and using multiple long-read technologies, we demonstrate the existence of defined polycistronic transcripts containing 2-4 protein encoding genes, several validated with RT-PCR. Some polycistrons exhibit differential expression profiles, usually involving the generation of internal monocistronic transcripts at different times during development. ATAC-seq in sporozoites reveals that polycistronic transcripts usually have a single open chromatin peak at their 5-prime ends, which contains a single E2F binding site motif. Polycistronic genes do not appear enriched for either male or female exclusive genes. This study elucidates a potentially complex layer of gene regulation with distinct chromatin accessibility akin to monocistronic transcripts. This is the first report of polycistronic transcription in an apicomplexan and expands our understanding of gene expression strategies in this medically important organism. SignificanceCryptosporidium parvum is a parasite that causes human gastrointestinal disease, profoundly impacting infants and immunocompromised individuals worldwide. C. parvum isolation, culturing, cloning, and its compact 9.2 Mb genome pose challenges for research. We have discovered that, unlike most eukaryotes, which express one gene per mRNA, C. parvum exhibits widespread polycistronic transcription, whereby 10% of its protein encoding genes are expressed as multiple genes per single mRNA molecule. Mining the published C. parvum single-cell atlas with proxy sequences for polycistronic expression, we observed patterns of polycistron expression that vary with developmental stages, suggesting a role in the parasites lifecycle. By illuminating this unique aspect of C. parvum biology, our findings provide novel insights into Cryptosporidium gene expression.

genetics↗

bioRxiv2025

Adipocyte Aldosterone in Obstructive Sleep Apnea

Aldosterone, a hormone synthesized by the adrenal glands, plays a pivotal role in regulating both blood pressure and electrolyte balance and may contribute to long term cardiovascular risk. Recent findings suggest that adipose tissue might serve as a source for aldosterone production and secretion. Patients suffering from obstructive sleep apnea (OSA) often exhibit elevated blood pressure levels and increased cardiovascular risk. Therefore, we sought to investigate whether increased aldosterone synthesis in fat tissue could contribute to the increase in hypertension and cardiovascular disease in OSA patients. To address this, we conducted a comparative analysis of adipocyte aldosterone level in OSA patients versus Age and BMI matched healthy individuals. Our data revealed no significant differences in aldosterone content between the two groups. Further examination involved measuring the expression of the key enzyme CYP11B2 responsible for aldosterone synthesis. We observed comparable expression levels of CYP11B2 in both the OSA and control groups. To corroborate these findings, we isolated stromal vascular fraction (SVF) from human fat tissues. The SVF cells were cultured in preadipocyte medium and subjected to normoxia and intermittent hypoxia (IH), mimicking OSA conditions as per established protocol. Subsequent analysis of aldosterone levels in cell lysates and conditioned medium revealed no significant differences. Similarly, in vitro examination of CYBP11B2 expression was not different in normoxic versus IH conditions. In conclusion, our study did not discern significant differences in adipocyte aldosterone production and secretion between patients with OSA and matched control subjects, nor in human preadipocytes under normoxic versus IH conditions.

molecular biology↗