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Related Articles from SNS
A digital droplet microarray for measuring tolerance to antibiotics
Antibiotic tolerance enables populations of microbes to survive normally lethal antibiotic concentrations, increasing the likelihood of reinfection and facilitating the evolution of resistance. Tolerance measurements typically involve quantifying viable cells after antibiotic exposure. Existing methods range from accessible but low-throughput approaches, such as plate counting, to higher-throughput but semi-quantitative techniques, such as the TDtest.
DropSynth-Gold: Golden Gate Assembly in Emulsions Extends Multiplexed Gene Libraries to Greater Lengths
The ability to synthesize longer genes at scale remains a central challenge in multiplexed gene synthesis. DropSynth is a pooled gene synthesis platform that enables highly multiplexed, compartmentalized assembly from microarray-derived oligonucleotides, but current implementations rely on polymerase cycling assembly (PCA), which constrains fragment number, construct length, and assembly fidelity. Here we present DropSynth-Gold, an evolution of the DropSynth platform that replaces PCA with...
Optical genome mapping identifies source-associated structural variant differences across early-passage human iPSCs
Background: Induced pluripotent stem cells (iPSCs) are an important model for studying human diseases in vitro. However, previous studies have shown that iPSC reprogramming and extended cell culture can introduce genomic structural variants (SVs). Technologies like karyotyping, CNV microarrays, and whole-genome sequencing have limitations in resolution, sensitivity, or the ability to detect large and complex structural variants compared to optical genome mapping (OGM).
EndoTwin-W: glycodelin-A and CA-125 as non-invasive biomarkers of endometrial receptivity derived from a multiscale computational digital twin
Endometrial receptivity assessment currently requires invasive tissue biopsy, yet recent randomized trials have questioned the clinical utility of biopsy-based approaches. Here we present EndoTwin-W, a four-layer mechanistic computational model that simulates human endometrial remodeling from hormone inputs through receptor binding, pathway scoring, and continuous-time Markov chain cell-state transitions across 17 cell states. Transition rates were optimized against scRNA-seq and microarray...
Genomic-Adjusted Radiation Dose from Bulk RNA Sequencing for Personalized Radiotherapy
Radiotherapy is delivered to more than half of all patients with cancer yet is prescribed using uniform physical doses despite well-established interpatient variability in biological response. The genomic-adjusted radiation dose (GARD), derived from the radiosensitivity index (RSI), integrates tumor transcriptomics with radiation dose to estimate patient-specific treatment effect, and has been clinically validated as a predictor of radiotherapy benefit across diverse disease sites, including...
A prognostic human brain network for diffuse midline glioma
Abstract Diffuse midline gliomas (DMGs) are near-universally lethal tumours of the childhood central nervous system1,2. In animal models, DMGs form brain-wide integrated networks through neuron-to-glioma synapses3,4,5,6 and glioma-to-glioma gap junctional coupling3. This extensive connectivity robustly promotes the growth and invasion of DMG3,4,5,6,7,8,9 and other glial malignancies10,11,12 through paracrine mechanisms and direct neuron-to-glioma synapses.
Interpretable Graph Kolmogorov-Arnold Networks for Multi-Cancer Classification and Biomarker Identification using Multi-Omics Data
arXiv:2503.22939v4 Announce Type: replace Abstract: The integration of heterogeneous multi-omics datasets at a systems level remains a central challenge for developing analytical and computational models in precision cancer diagnostics. This paper introduces Multi-Omics Graph Kolmogorov-Arnold Network (MOGKAN), a deep learning framework that utilizes messenger-RNA, micro-RNA sequences, and DNA methylation samples together with Protein-Protein Interaction (PPI) networks for cancer...
Mitochondria directly interact with the nuclear pore complex
Abstract Mitochondria regulate cellular processes through direct and indirect interactions with other organelles. A well-studied example has been contact with the endoplasmic reticulum at mitochondrial-associated endoplasmic reticulum membranes1, which control pathways including redox and calcium homeostasis2,3. Recent studies have also reported direct mitochondria–nuclear membrane contacts in cancer cells and yeast that promote pro-survival signalling4,5.