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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 ↗223 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
Genome report: sequencing of Helicoverpa- infecting Ophryocystis sp. confirms cryptic diversity and changes in gene content of Lepidoptera-infecting apicomplexan parasites ↗
Abstract Apicomplexan parasites of insects represent a largely unexplored branch of the tree of life. Their small size and lack of informative phenotypic traits can obscure their diversity and many lineage-specific adaptations to different host species. To better understand how these parasites have evolved, we have sequenced and annotated the genome of a neogregarine parasite of moths in the family Noctuidae, including Helicoverpa armigera. This parasite, which we term Helicoverpa-infecting Ophryocystis, has a tiny 8 Megabase genome with only 2,500 predicted protein-coding genes. Using phyloge…
- OpenAlex · Published · First archived
Sampling Weights at Intermediate Temperatures is Optimal for Training Large Language Protein Models ↗
Using a statistical mechanics framework, we investigate the parameter space of transformer models trained on protein sequence data. We sample the loss landscape at varying temperatures using Langevin dynamics to characterize the low-loss manifold and to understand the mechanisms underlying transformers’ superior performance in protein structure prediction. We find that, at variance with networks not based on the attention mechanism, the lack of a first-order-like transition in the loss of the transformer produces a range of intermediate temperatures with good learning properties; this is true…
- Europe PMC · Published · First archived
Towards standards for analysing structural variants from short-read whole genome sequencing data ↗
No widely accepted standard exists for analysing structural variants from short-read whole genome sequencing (WGS) data. We use comprehensive SV truth sets (HG002 T2T-Q100, Platinum Pedigree) and long-read sequencing databases (1KGP-ONT, CoLoRS) to benchmark SV breakpoints and sizes at base pair resolution. Using 30X Illumina WGS data, only five of sixteen individual tools tested reliably output deletions, insertions and duplications that perfectly match the truth sets. Ensemble pipelines (e.g. GATK-SV, MOPline, Parliament2), frequently used in population-scale datasets, reduced perfect matchi
- OpenAlex · Published · First archived
Protein distribution, quantity and quality is optimized by protein intervention in frail community-dwelling older adults during resistance training: a randomized controlled trial ↗
Protein interventions are widely implemented alongside resistance training in older adults. However, research has mainly focused on increasing protein intake, while changes in protein distribution and protein quality remain insufficiently explored. Therefore, this randomized controlled trial investigated the effect of a protein intervention consisting of dietary counselling and protein supplementation during resistance training on protein distribution, quantity and quality in frail community-dwelling older adults. This secondary analysis included 295 frail community-dwelling older adults (mean…
- OpenAlex · Published · First archived
Design of ancestral protein-glutaminase with improved thermal stability ↗
ABSTRACT Protein-glutaminase (PG) from Chryseobacterium proteolyticum is an industrially valuable enzyme for protein deamidation; however, its application is limited because of insufficient thermal stability. Previous rational design studies have enhanced the thermostability of PG but often required labor-intensive, stepwise optimization. In this study, ancestral sequence reconstruction (ASR) was used to engineer thermostable PG variants in a single design step. Eight ancestral PGs were constructed, all of which exhibited enhanced thermal stability compared with that of the wild type. The most…
- OpenAlex · Published · First archived
Hantavirus species detection from viral genome sequences using explainable artificial intelligence techniques ↗
Hantaviruses are important zoonotic pathogens associated with severe human diseases, including hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome. The World Health Organization (WHO) has recognized the importance of strengthening hantavirus surveillance and early detection because of their public health impact. Nevertheless, Artificial Intelligence (AI)-based approaches for hantavirus species identification from viral genome sequences remain largely unexplored. This study developed and evaluated an explainable AI-based approach for hantavirus species identification u…
- OpenAlex · Published · First archived
DipSkmer: Reference-free population genomics with diploid genome skims ↗
Ecologists and conservation biologists rely on genetic diversity as a key essential biodiversity variable (EBV) used to track population health and dynamics, and utilize the population-scaled mutation parameter θ as a key metric of diversity. While whole-genome-sequencing (wgs) is increasingly affordable, it will be considerable time before the full diversity of life is represented by high-quality assembled genomes; even then, constant monitoring will still require repeated sampling across time and space. In contrast, genome skimming (low-coverage, short-read wgs) is highly cost-effective but…
- OpenAlex · Published · First archived
In Vitro Reconstitution of Vertebrate Sonic Hedgehog Protein Cholesterolysis; Native and Engineered Sterol Specificity ↗
Abstract Extracellular secretion of the oncogenic sonic hedgehog signaling ligand is contingent on release from a precursor protein through peptide-bond cholesterolysis, mediated by the hedgehog C-terminal domain, SHhC. In this work, we first describe the in vitro reconstitution of SHhC domains from vertebrate model organisms, Xenopus laevis (Xla) and Danio rerio (Dre). Cholesterolysis is assayed continuously in multiwell plates by monitoring changes in fluorescence resonance energy transfer (FRET) from a bacterially expressed, engineered precursor construct. Using this FRET assay, we found th…
- OpenAlex · Published · First archived
Dietary Fibre in Pea Cotyledon Used as a Protein Source Provides Multidimensional Protection Against Colonic Protein Putrefaction ↗
Background/Objectives: Substitution of plant-based for animal-based protein sources has been recommended to reduce global non-communicable disease burdens, including colorectal cancer. Objective: The goal of this study was to determine possible ways that pea cotyledon may modulate hindgut concentrations of protein putrefaction products implicated in colorectal cancer by comparing diets based on casein, meat or pea cotyledon in a rat model. Method: Rats (n = 8 per treatment) were fed for 9 days on 18.6% protein diets containing casein, meat, or yellow split peas as sole protein sources. Faecal…
- OpenAlex · Published · First archived
Structure- and Exonuclease-Guided Engineering of Cas12o1 Enhances Genome Editing Efficiency and Deletion Outcomes ↗
Abstract Small and efficient CRISPR nucleases hold great promise for genome engineering but often exhibit suboptimal activity and limited control over DNA repair outcomes. Here, we engineer Cas12o1 using a structure- and exonuclease-guided strategy to enhance both editing efficiency and deletion profiles in mammalian cells. Structure-guided arginine-scanning mutagenesis of 42 residues identifies a single substitution, D534R, that markedly improves editing efficiency across multiple genomic loci, outperforming combinatorial variants. In parallel, fusion of T5 exonuclease (T5 exo) profoundly rem…
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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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