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Earlier sources: Biotechnology
This science thread follows biotechnology through original research, public projects, and source reports. Read the evidence below to see which developments are represented in SYMTRI’s archive.
SYMTRI organizes observations from public sources into a living map. Connections reflect shared subject matter; they do not establish causation or endorse a source.
Open in the map ↗238 classified signals in the fourteen-day window. These counts include signals awaiting readable evidence.
Earlier sources
Up to ten sources with readable evidence, ordered by their feed timestamp. These archive sources can be older than the live fourteen-day window. This list is a sample, not a measure of total activity. Dates distinguish paper publication, repository creation, model/dataset activity, Hacker News posts, and KEV catalog additions. “First archived” records when SYMTRI first stored the signal.
- OpenAlex · Published · First archived
Spontaneous mutation rate estimation in the large-genome unicellular eukaryote Euglena gracilis ↗
Abstract The spontaneous mutation rate per nucleotide (µ) is a fundamental parameter shaping genome evolution, yet it remains unknown for many eukaryotic groups. Here, we estimated µ in the freshwater unicellular eukaryote Euglena gracilis, which possesses a 2.4 Gb genome, among the largest reported for unicellular species. We conducted a mutation accumulation experiment using 10 independent MA lines propagated through repeated single-cell bottlenecks and then identified 153 de novo nucleotide mutations. After correction for false negatives, the spontaneous mutation rate was estimated at µ=6.6…
- OpenAlex · Published · First archived
Structure and Function of Archaeal SRP54 Protein Mutants Associated with Human Severe Congenital Neutropenia ↗
Abstract SRP54, a key component of the signal recognition particle, is a highly conserved enzyme both structurally and functionally. The protein plays a vital role in cellular protein translocation by interacting with the translating ribosome and a membrane receptor, thereby aiding protein folding and trafficking. Recent studies have shown that mutations in the SRP54 gene cause severe neutropenia and are associated with an increased risk of pediatric leukemias. Here, we present high-resolution structures of clinically relevant SRP54 mutant proteins from the archaea Pyrococcus furiosus. This wo…
- OpenAlex · Published · First archived
Proteomic identification of secreted protein candidates mediating anti-colorectal cancer activity in a human-derived non-enterotoxigenic Bacteroides fragilis ↗
The contribution of gut microbiota-derived factors to colorectal cancer (CRC) progression has attracted increasing attention; however, the specific bioactive components and their underlying mechanisms remain poorly defined. In this study, an activity-guided fractionation approach combined with proteomic analysis was employed to identify NTBF-derived components associated with anti-proliferative activity in colorectal cancer cells. Bacterial conditioned supernatant was sequentially fractionated by ultrafiltration, solvent extraction, and chromatography, and the antiproliferative activity of eac…
- OpenAlex · Published · First archived
Leviathan: fast, memory-efficient, and scalable taxonomic and pathway profiling for (pan)genome-resolved metagenomics and metatranscriptomics ↗
Functional profiling of meta-omics is essential for understanding microbial communities, yet support for custom genome-resolved reference databases is limited. We introduce Leviathan for integrated taxonomic and functional profiling at both genome and pangenome resolution. Leviathan combines Sylph for ultrafast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA space against (pan)genome-resolved gene catalogs, producing dual metrics per (pan)genome: pathway abundance and graph-based pathway coverage. Benchmarking alignment backends on synthetic…
- OpenAlex · Published · First archived
Design of a novel chimeric multi-epitope vaccine construct against Staphylococcus lugdunensis using pan-genome analysis and immunoinformatics approaches ↗
Abstract Staphylococcus lugdunensis has emerged as an increasingly important opportunistic pathogen associated with invasive infections and rising antimicrobial resistance, creating a need for new preventive approaches. In this study, a reverse-vaccinology strategy integrated with immunoinformatics analyses was applied to genomic datasets derived from 29 complete genomes. Pan-genome evaluation identified 1689 conserved core proteins, from which four surface-associated proteins were prioritized as potential vaccine targets based on their predicted antigenic properties and favorable safety profi…
- OpenAlex · Published · First archived
Whole-genome 5-hydroxymethylation profiling of human neurons for regulatory and biological insight ↗
Abstract While 5-methylcytosine (5mC) DNA methylation is a well-known player in genome stability and transcriptional regulation, the role of 5-hydroxymethylcytosine (5hmC), particularly prevalent in neurons, remains largely unknown. Here, we used long-read Oxford Nanopore Technology (ONT) to profile whole-genome, native 5mC and 5hmC levels in sorted neuronal nuclei samples from human post-mortem brain tissue. Genomic annotation revealed high 5hmC levels in actively transcribed genes and enhancers, which were enriched in neuron-related pathways, with functional variety when stratifying across c…
- OpenAlex · Published · First archived
Polydeoxyribonucleotide attenuates dexamethasone-induced skeletal muscle atrophy by suppressing oxidative stress and regulating muscle protein turnover ↗
Glucocorticoid-induced muscle atrophy is characterized by excessive oxidative stress and disrupted muscle protein homeostasis. Polydeoxyribonucleotide (PDRN) exerts tissue-protective and regenerative effects; however, its therapeutic potential in muscle atrophy remains unclear. This study investigated the protective effects of PDRN against dexamethasone (DEX)-induced muscle atrophy in vitro and in vivo. Differentiated C2C12 myotubes were treated with PDRN in the presence or absence of DEX (100 µM). PDRN showed no cytotoxicity, and concentrations of 10, 25, and 50 µg/mL were selected for subseq…
- OpenAlex · Published · First archived
GRETA: a results database for whole-genome sequencing studies ↗
Whole-genome sequencing in large cohorts generates vast numbers of genetic association results, but integrating and querying them alongside public reference data remains a challenge for the diverse stakeholders involved. To address this challenge, we developed the Genetic REsults daTAbase (GRETA), a relational database that stores in-house association results alongside public reference data and functional annotation resources, facilitating their integration, querying and analysis. Following a requirements-engineering process grounded in user-centred design, we defined product specifications sp…
- OpenAlex · Published · First archived
Mapping Functional Transitions across Protein Homologues from a Single Simulation: Application of gEDES-HM to Adenylate Kinases ↗
Abstract Proteins fluctuate across different conformational states, which constitute a dynamic ensemble that regulates their interaction networks and functions. Predicting the conformational landscape remains a computational challenge, and even more difficult is capturing the link between state distributions and specific functions within protein homologues. Here, we present gEDES-HM (generalized Ensemble Docking with Enhanced sampling of pocket Shape-Homology Modeling), a scalable computational protocol enabling us to remap conformational ensembles obtained from enhanced sampling simulations o…
- Europe PMC · Published · First archived
CropStabDB: a protein stability resource and Engineering Atlas of orthologue-supported substitutions for 30 plant proteomes ↗
Protein stability, the capacity to maintain a folded structure and function, matters as much for transporters and regulators as for enzymes, and heat erodes it. Wheat, rice, maize and soybean supply two-thirds of human caloric intake, and warming reduces yields. Rubisco activase variants selected for thermostability increased photosynthesis, biomass and yield under heat. They came from gene shuffling; no method proposes residues at proteome scale. Genome editing has made such changes routine, yet predictors estimate melting temperature, name no residue, and have not been reported for a plant p
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How to assess evidence about Biotechnology
Check each original source for its methods, release status, limitations, and supporting data. A repository announcement, a preprint, and a published study provide different kinds of evidence. SYMTRI’s subject classification helps discovery; it does not independently validate the source’s claims.
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