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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 ↗233 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
Identifying conserved G protein-coupled receptor protein interactions independent of heterotrimeric G proteins and β-arrestins ↗
Abstract The canonical paradigm of G protein-coupled receptor (GPCR) signaling recognizes G proteins, β-arrestins, and GPCR kinases (GRKs) as the primary transducers that shape GPCR signaling. However, multiple studies have demonstrated that other interacting proteins regulate GPCR function in addition to these pathways, termed GPCR-interacting proteins (GIPs). The atypical chemokine receptor 3 (ACKR3) does not couple to G proteins, and β-arrestins have been shown to be dispensable for many of its functions. Here, we employed proximity labeling to identify proteins that interact with ACKR3 in…
- OpenAlex · Published · First archived
Heat shock protein genes Hsp70 and DnaJA1 are key contributors to thermotolerance and development in predatory ladybeetle Propylaea japonica ↗
Global climate change has increased the frequency of extreme high-temperature events, underscoring the need to elucidate thermotolerance mechanisms in natural enemy insects for effective biological control. The ladybird Propylaea japonica is a predominant predator in South-East Asia and a successful biocontrol agent, yet the molecular basis of its heat resistance remains unknown. Here we cloned full-length cDNAs of three heat shock protein genes (pjhsp70, pjDnaJA1, and pjhsp21) from P. japonica using transcriptomic data. We characterized their sequences, inferred phylogenetic relationships, an…
- OpenAlex · Published · First archived
PrePssmCas: fusing pre-trained features and PSSM features for Cas protein classification ↗
Abstract Background Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins play a vital role in prokaryotic adaptive immune systems, defending against foreign genetic material. However, the classification of CRISPR-Cas systems remains challenging due to limited direct identification techniques. Distinct classes of Cas proteins perform different roles, offering an opportunity for system classification through their identification. The accurate identification of specific Cas proteins is therefore essential for advancing CRISPR-Cas system classifica…
- OpenAlex · Published · First archived
Fermented protein foods as modulators of the gut-muscle axis: mechanisms, evidence, and future directions ↗
Abstract Skeletal muscle has a profound influence on metabolic health, functional capacity and resilience across the lifespan. Beyond dietary protein and physical activity, the gut microbiome may have the capacity to impact skeletal muscle mass and function through the bidirectional network termed the gut-muscle axis (GMA). Fermented protein foods (FPFs) are protein rich matrices transformed by microbial activity that integrate modified protein structures, bioactive peptides, and live microorganisms, or components thereof, which could modulate skeletal muscle physiology. Here, we review mechan…
- OpenAlex · Published · First archived
RCSB PDB AI Help Desk: retrieval-augmented generation for protein structure deposition support ↗
Abstract Motivation Structural biologists have contributed more than 260,000 experimentally determined three-dimensional structures of biological macromolecules to the Protein Data Bank. Incoming depositions are validated and biocurated by approximately 20 expert biocurators at the collaborating data centers worldwide. Biocurators at the Research Collaboratory for Structural Bioinformatics Protein Data Bank, who process more than 40% of global depositions, face growing difficulty sustaining efficient Help Desk operations, having received roughly 19,000 depositor messages across some 8,000 entr…
- arXiv · Published · First archived
ProteoEM: probabilistic protein abundance estimation from iterative affinity traces ↗
Single-molecule affinity mapping enables molecular-level measurement of proteins and proteoforms, but imperfect and nonspecific probe binding makes individual affinity traces compatible with multiple molecular identities. Accurate abundance estimation therefore requires apportionment of ambiguous traces by weight rather than assignment to a single candidate. We developed ProteoEM, an expectation-maximization framework for weighted proteoform quantification, inspired by transcript abundance estimation methods for RNA sequencing and released as an open-source Python package. ProteoEM evaluates e…
- arXiv · Published · First archived
PFArena: Benchmarking Language Models for Protein Modification ↗
Protein modification requires navigating an immense sequence space, yet wet-lab validation remains low-throughput and costly. Although computational paradigms including protein language models (PLMs), large language models (LLMs), and LLM-based agents have shown promise in protein modification, their relative efficacy across realistic experimental decision-making settings remains unclear. To bridge this gap, we introduce PFArena, a benchmark comprising four controlled task interfaces that cover single-mutant generation and multi-mutant ranking. By providing varying levels of mutation fitness d…
- OpenAlex · Published · First archived
Surveillance of antibiotic-resistant bacteria integrating whole genome sequencing and epidemiological information – a global, systematic review, 2012–2023 ↗
Abstract Background Epidemiologic surveillance is one pillar in the global efforts to stop the spread of antibiotic-resistant bacteria (ARB) and increasingly includes whole genome sequencing (WGS). However, no review systematically examined the characteristics of such surveillance systems until February 2025. We conducted a systematic review to identify and describe routine surveillance systems of ARB, that integrate WGS and epidemiological information. Methods A protocol was developed and published on PROSPERO. We searched 8 databases and Google. Included articles needed to report on a nation…
- OpenAlex · Published · First archived
GenPTM: a generalizable framework for protein post-translational modification information extraction from the scientific literature ↗
Abstract Background Protein post-translational modification (PTM) plays a pivotal role in cellular activities and biological processes. Although several databases curate PTM information, most cover only a limited number of PTMs. Although the scientific literature continues to accumulate a vast amount of PTM-related knowledge, these databases are not updated regularly. This growing information gap highlights the need for automated information extraction (IE) systems that can identify modified proteins and their specific amino acid sites directly from the literature. While numerous PTMs have bee…
- OpenAlex · Published · First archived
Uncovering potential autotrophs in coal seams: characterization, enrichment, and genome-resolved metabolisms of a subsurface coal seam microbiome ↗
ABSTRACT Biological transformation of inorganic carbon into organic compounds is an extremely important biosynthetic process, and many organisms catalyze this reaction autotrophically, using CO 2 as the sole carbon source. Natural autotrophic pathways are diverse, as are the organisms that employ them, driven in part by the varied ecological niches they inhabit. One understudied ecological niche, coal seams, contains autotrophic acetogens that catalyze an intermediate step in the conversion of coal to methane. Here, we characterize the geochemistry and microbiology of coal seam produced water…
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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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