DNA's Role in Bioimaging, Preeclampsia Prediction, Viral Identification, Immunotherapy, Neuron Mapping, Bioremediation, and Gut Health

Recent scientific papers explore diverse applications of DNA research and human genetics. These studies span bioimaging, preeclampsia prediction, viral identification, immunotherapy, neuron mapping, bioremediation, and gut health. **Bioimaging:** A new tool, μSAM [micro-SAM], enhances bioimaging by unifying image analysis solutions. It supports 2D [two-dimensional] and volumetric segmentation, combining interactive and automatic methods. User studies demonstrate competitive performance for cell segmentation and improved results for volumetric segmentation and tracking. The tool is available at https://github.com/computational-cell-analytics/micro-sam/. **Preeclampsia Prediction:** Nucleosome profiling of cell-free DNA (cfDNA) can accurately estimate fetal fraction (FF) and predict preeclampsia risk. The approach, applicable to low-coverage sequencing data, shows potential for scalability and cost-effectiveness. A study using PDNAS [prenatal diagnosis by non-invasive analysis of single chromosomes] sequence data obtained Institutional Review Board approval. Preeclampsia diagnosis followed American College of Obstetricians and Gynecologists criteria, focusing on early-onset (EPE) and late-onset preterm birth (LPE-PB) cases. **Viral Identification:** A study characterized the virome [all the viruses] within rice plants using 17,115 rice transcriptomes [RNA sequences]. Homology-based approaches identified 104,753 putative viral contigs [overlapping DNA segments], with 1525 non-redundant RdRPs [RNA-dependent RNA polymerase] representing RNA viral vOTUs [species-level viral operational taxonomic units]. Phylogenetic analyses classified novel viruses, many associated with fungi and invertebrates, indicating potential origins from rice endophytic fungi and rice-feeding insects. **Immunotherapy:** INO-3107, a DNA immunotherapy, showed promise in treating recurrent respiratory papillomatosis (RRP) [growth of tumors in the respiratory tract] related to HPV-6 and HPV-11. A Phase 1/2 trial demonstrated safety, efficacy, and immune responses. The study enrolled 32 patients, with 81.3% showing a clinical response. T-cell responses were induced, and RNA sequencing of airway tissue samples indicated significant enrichment of interferon responses. **Neuron Mapping:** A study identified and spatially registered an outlying subiculum neuron subtype [part of the hippocampus]. Analysis of single-cell RNA sequencing data revealed a distinct subtype expressing Ly6g6e. These ovoid neurons project to the anteroventral and anteromedial nuclei of the anterior thalamic nuclei (ATN) [areas of the brain], exhibiting specialized dendritic morphology and heightened intrinsic excitability. In vivo calcium imaging showed sustained activity correlating with novel object encounters. **Bioremediation:** Effective transgene biocontainment [preventing the spread of genetically modified organisms] is crucial for bioremediation [using living organisms to clean up pollution]. A study engineered Drosophila melanogaster [fruit flies] and zebrafish to express E. coli merA and merB enzymes for mercury detoxification. The engineered organisms showed enhanced mercury volatilization and reduced toxicity, demonstrating a potential strategy for mercury bioremediation. **Gut Health:** A gut-on-a-chip model was developed to study intestinal epithelial physiology. The model integrates multiple cell types, extracellular matrix, shear forces, and mechanical stretch. Transcriptional profiles of the gut-on-a-chip model exposed to faecal samples from melanoma patients revealed distinct responses based on immunotherapy responsiveness, highlighting the potential for predicting treatment outcomes and dissecting microbiome-host interactions. **Tecovirimat Sensitivity:** A study mapped F13/tecovirimat contacts to estimate tecovirimat sensitivity of clinical isolates. The structural data, molecular dynamics simulations and the battery of assays developed here will pave the way for the development of these novel antivirals active against tecovirimat-resistant strains. **Trace Elements and Cancer:** High whole blood burdens of Pb, Cr and Mn, as well as patients being male or with tumor metastases, had shorter OS (all P < 0.05; Fig. 6A-E). Subsequently, multivariable Cox proportional hazard regression analysis identified blood levels of Mn, Pb and Zn, as well as gender, as independent prognostic factors for OS with hazard ratios (HR) of 2.66 (95% CI 1.28-5.52), 2.13 (95% CI 1.06-4.27), 0.19 (95% CI 0.07-0.51) and 0.37 (95% CI 0.14-0.93), respectively (Fig. 7A). **T-cell Responses:** Aggregate assessment of ELISpot, flow cytometry and significant T-cell clonal expansion data determined that 100% of patients (32/32) exhibited peripheral immune response during the conduct of the study (Fig. 2E). Taken together these results suggest that INO-3107 robustly engaged peripheral T-cells, inclusive of the induction of HPV-6 and HPV-11-specific activity. **Genetic Origin:** Based on autosomal data, although all Fudamen individuals show high levels of middle reaches of Yellow River-related ancestry as previously published historical period Shandong populations, 2 Fudamen individuals require ~5% Western Eurasian/Central Asian-related ancestry to describe their ancestry composition best. To the best of our knowledge, it is the first evidence of such ancestry in Shandong, the eastern part of today's China. Moreover, the admixture pattern is also reflected by the presence of both west and east Eurasian-specific mtDNA and Y chromosomal haplogroups in Fudamen people. The estimated admixture time is also consistent with periods when Sogdians and other non-Han populations were active in ancient China. These genomic findings suggest that intermarriage with Han Chinese involved the Sinicization process of the Hu people. **Self-Organized Resetting:** We illustrate the rich dynamic behavior inherent to self-organized resetting schemes by focusing on the paradigmatic example of cooperative resetting. This example involves a many-particle system driven by two dynamics: the accumulation of noise governed by a stochastic process for each constituent, and random events of pair-wise resetting to their respective average (Fig. 1b). We show that self-organized, cooperative resetting leads to a stationary state with bounded variance if interactions are sufficiently long-ranged.