Biology subjects

Holdener, C.

Publications and source records attributed to Holdener, C..

4 recordsLinked to original sources

bioRxiv2025

Smoothie: Efficient Inference of Spatial Co-expression Networks from Denoised Spatial Transcriptomics Data

Finding correlations in spatial gene expression is fundamental in spatial transcriptomics, as co-expressed genes within a tissue are linked by regulation, function, pathway, or cell type. Yet, sparsity and noise in spatial transcriptomics data pose significant analytical challenges. Here, we introduce Smoothie, a method that denoises spatial transcriptomics data with Gaussian smoothing and constructs and integrates genome-wide co-expression networks. Utilizing implicit and explicit parallelization, Smoothie scales to datasets exceeding 100 million spatially resolved spots with fast run times and low memory usage. We demonstrate how co-expression networks measured by Smoothie enable precise gene module detection, functional annotation of uncharacterized genes, linkage of gene expression to genome architecture, and multi-sample comparisons to assess stable or dynamic gene expression patterns across tissues, conditions, and time points. Overall, Smoothie provides a scalable and versatile framework for extracting deep biological insights from high-resolution spatial transcriptomics data.

genomics↗

bioRxiv2025

A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection

The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial transcriptomics with paired, high-fidelity long-read sequencing of T and B cell receptors. This method enables the simultaneous analysis of cellular transcriptomes and adaptive immune receptor (AIR) repertoires within their native spatial context. We applied AIR-SPACE to mouse popliteal lymph nodes at five distinct time points after Vaccinia virus footpad infection and constructed a comprehensive map of the developing adaptive immune response. Our analysis revealed heterogeneous activation niches, characterized by Interferon-gamma (IFN-{gamma}) production, during the early stages of infection. At later stages, we delineated sub-anatomical structures within the germinal center (GC) and observed evidence that antibody-producing plasma cells differentiate and exit the GC through the dark zone. Furthermore, by combining clonotype data with spatial lineage tracing, we demonstrate that B cell clones are shared among multiple GCs within the same lymph node, reinforcing the concept of a dynamic, interconnected network of GCs. Overall, our study demonstrates how AIR-SPACE can be used to gain insight into the spatial dynamics of infection responses within lymphoid organs.

immunology↗

bioRxiv2024

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing

Inter-microbial and host-microbial interactions are thought to be critical for the functioning of the gut microbiome, but few tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at one micron resolution. This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA-sequencing. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong inter-microbial interactions at short length scales, shaping of local microbiome niches by the host, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with broadly available commercial platforms for spatial RNA-sequencing, and can therefore be readily adopted to broadly study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.

genomics↗

bioRxiv2019

Acid and Iron Experimental Evolution of Halobacterium sp. NRC-1

BackgroundHalobacterium sp. NRC-1 (NRC-1) is an extremely halophilic archaeon that is adapted to multiple stressors such as UV, ionizing radiation and arsenic exposure. We conducted experimental evolution of NRC-1 under acid stress. NRC-1 was serially cultured in CM+ medium modified by four conditions: optimal pH (pH 7.5), acid stress (pH 6.3), iron amendment (600 M ferrous sulfate, pH 7.5), and acid plus iron (pH 6.3, with 600 M ferrous sulfate). For each condition, four independent lineages of evolving populations were propagated. After 500 generations, 16 clones were isolated for phenotypic characterization and genomic sequencing. ResultsGenome sequences of all 16 clones revealed 378 mutations, of which 90% were haloarchaeal insertion sequences (ISH) and ISH-mediated large deletions. This proportion of ISH events in NRC-1 was five-fold greater than that reported for comparable evolution of E. coli. One acid-evolved clone had increased fitness compared to the ancestral strain when cultured at low pH. Seven of eight acid-evolved clones had a mutation within or upstream of arcD, which encodes an arginine-ornithine antiporter; no non-acid adapted strains had arcD mutations. Mutations also affected the arcR regulator of arginine catabolism, which protects bacteria from acid stress by release of ammonia. Two acid-adapted strains shared a common mutation in bop, which encodes the bacteriorhodopsin light-driven proton pump. Unrelated to pH, one NRC-1 minichromosome (megaplasmid) pNRC100 had increased copy number, and we observed several mutations that eliminate gas vesicles and arsenic resistance. Thus, in the haloarchaeon NRC-1, as in bacteria, pH adaptation was associated with genes involved in arginine catabolism and proton transport. ConclusionsOur study is among the first to report experimental evolution with multiple resequenced genomes of an archaeon. Haloarchaea are polyextremophiles capable of growth under environmental conditions such as concentrated NaCl and desiccation, but little is known about pH stress. Halobacterium sp. NRC-1 (NRC-1) is considered a model organism for the feasibility of microbial life in iron-rich brine on Mars. Interesting parallels appear between the molecular basis of pH adaptation in NRC-1 and in bacteria, particularly the acid-responsive arginine-ornithine system found in oral streptococci.

genetics↗