spatial domain detection

Three-dimensional mapping of human lung fibrosis identifies spatial coupling between tissue microarchitecture and maladaptive repair states

This study maps human lung fibrosis in 3D, showing how structural changes in tissue microarchitecture drive maladaptive repair states and disease progression.

A single-cell transcriptomic atlas of paper wasp brains highlights Kenyon cells' role in social behavior

The paper uses single-cell transcriptomics to analyze brain cells in paper wasps, showing that Kenyon cells vary with social roles and respond to social interactions.

Measuring neuronal input-output operations in vivo with random access projection microscopy

This paper introduces SLAP2, a high-speed microscope for measuring submicron synapses and dendritic voltage in behaving mice, revealing nonlinear input-output amplification in neurons.

Quantum Dot-Based Non-invasive Monitoring of Sinusoidal Endothelial Scavenger Function in Steatohepatitis

This study develops a non-invasive method using quantum dots to assess liver sinusoidal endothelial cell scavenger function in MASH, showing reduced retention correlates with disease progression.

Lymphangiogenesis is Critical for Healing and Survival in a Murine Model of Laryngotracheal Injury

This study shows that lymphangiogenesis is essential for healing and survival after laryngotracheal injury in mice, as blocking it leads to worse outcomes.

Mitotic centromeres organize in repeat-subunits with specialized histone landscape and multi-domain architecture as revealed by expansion microscopy

The paper uses expansion microscopy to reveal the repeat-subunit organization and multi-domain architecture of human mitotic centromeres, including specialized histone modifications.

Single-probe, amplification-free multiplex mRNA PNA-FISH maps bacterial gene expression in intact three-dimensional biofilms

This paper develops a single-probe, amplification-free PNA-FISH method to map bacterial gene expression in 3D biofilms, showing it accurately captures transcriptional changes without amplification.

Dissection of the contribution of bushy cell delays to sound localization in juvenile and adult Mongolian gerbils

This study examines how delays in bushy cell axons contribute to sound localization in Mongolian gerbils, finding developmental changes in delay patterns and their impact on interaural time difference processing.

Quantifying subcellular organization from localization to co-occurrence with InSpace

InSpace quantifies subcellular organization by preserving localization and molecular co-occurrence, revealing spatial programs in B and plasma cells across cancers.

Divergent Pontine and Cerebellar Pathology in Preterm Infants With Necrotizing Enterocolitis

This study identifies divergent brain pathology in preterm infants with NEC, showing distinct cellular and molecular changes in the pons and cerebellum.

Recurrent mitotic error and purifying selection shape chromosomal mosaicism across human tissues

This study identifies mosaic chromosomal alterations in healthy human tissues, revealing tissue-specific patterns of mitotic errors and purifying selection across aging.

Individual-specific recovery of the healthy human gut microbiota after antibiotics

The paper shows that the human gut microbiota recovers to an individual-specific state after antibiotics, not to a generic healthy state.

Single-base mapping of m6A in lncRNAs reveals a distinct landscape linked to transposable elements and RNA processing

The paper maps m6A modifications in lncRNAs at single-base resolution, revealing distinct patterns linked to transposable elements, RNA structure, and splicing.

Host specificity, seasonality, and urbanicity shape the gut microbiome of a synanthropic insect

This study examines how host plant, season, and urbanization affect the gut microbiome of soapberry bugs, finding that host plant is the primary driver of microbial community structure.

Molecular control of replication licensing speed by c-MYC

This study identifies c-MYC as a non-canonical origin licensing accelerator, showing it increases licensing speed through TRRAP/GCN5 and histone H1 eviction, particularly in heterochromatin.

Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains

The paper introduces ATLAS, a method to map transcriptional differences across genetic backgrounds in mouse brains, revealing significant cell type distribution changes between sexes and genetic models.

Visualizing the Epigenetic Landscape of Aging and Cellular Reprogramming: Optimized ATAC-see for Cells and Tissues

The paper optimizes ATAC-see for high-throughput chromatin accessibility imaging in aging and reprogramming, revealing age-related chromatin changes and reprogramming-induced remodeling.

Decoder-FFPE-seq enables sensitive, genome-wide spatial transcriptomics of archival tissues at single-cell resolution

Decoder-FFPE-seq improves sensitivity and resolution for spatial transcriptomics in FFPE tissues, enabling analysis of rare genes and tumor microenvironments.

Somatostatin-excitatory coordination emerges with dexterous motor skill learning

The paper shows that SST neurons become selectively coordinated with behaviorally relevant excitatory populations during motor skill learning.

Tissue-specific transcriptomic responses to early Toxoplasma gondii infection in sheep during congenital toxoplasmosis

This study examines early transcriptomic responses to Toxoplasma gondii infection in pregnant sheep, identifying tissue-specific immune and stress pathways linked to fetal loss.

Brain representations of visual short-term memories during healthy human aging: occipital decline and frontoparietal compensation

This study investigates age-related changes in visual short-term memory using fMRI decoding, finding that visual cortex representations weaken with age and load, while frontoparietal regions compensate by strengthening during memory maintenance.

Accumulation of FAM98B and tRNA-Splicing Ligase Complex Proteins in Neuronal Intranuclear Inclusions in Spinocerebellar ataxia type 4.

The paper examines the localization of tRNA-splicing ligase complex proteins in SCA4 pontine neurons, finding their accumulation in neuronal intranuclear inclusions.

A CTCF-LDHB axis converts nuclear lactate availability into an H3K18 acylation switch that directs alternative splicing in hypoxic breast cancer

Development of auxin reporters in oilseed rape (Brassica napus)

This study develops auxin reporters for oilseed rape to visualize and quantify auxin distribution and signaling during development and stress.

Spatial Landscape of Pregnancy-Associated Triple Negative Breast Cancer and Mammary Gland Involution

This study compares transcriptional differences between pre- and post-involution PA-TNBC tissues using spatial transcriptomics, identifying distinct inflammatory and chromatin remodeling patterns in post-involution tumors.

Two closely related RNA helicases, UAP56 and URH49, couple mRNA splicing and export pathways with their distinct complexes

This study identifies three splicing regulation patterns mediated by UAP56 and URH49 and their association with mRNA export pathways.

Metabolic and transcriptional responses reveal co-option of symbiotic processes during early soybean-soybean cyst nematode interaction

This study identifies metabolic and transcriptional changes in soybean during soybean cyst nematode infection, revealing immune system remodeling and co-option of symbiotic processes.

Dose-dependent transcriptional responses of marine prokaryotes to Fe-rich colloids of glacial and non-glacial origin in the Kerguelen region (Southern Ocean)

This study examines how marine prokaryotes respond transcriptionally to Fe-rich colloids from glacial and non-glacial sources, revealing contrasting growth and metabolic responses.

Gene context shapes spatial organization and transcriptional heterogeneity of extrachromosomal DNA in cancer cells

This study investigates how gene context influences the spatial organization and transcriptional behavior of extrachromosomal DNA in cancer cells using a new imaging method called FLAGx.

Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogen Plasmodium falciparum

The paper maps m6A modifications and polyadenylation events in Plasmodium falciparum mRNAs, identifying stage-specific m6A sites and their potential role in 3' end processing.