The 18S rRNA gene has emerged as the primary molecular marker for amplicon-based characterization of microalgal communities, including in wastewater treatment systems, yet trade-offs between short- and long-read approaches remain poorly defined. We systematically compared V8V9 short-read sequencing (Illumina MiSeq), full-length long-read sequencing with ss5ss3 primers (PacBio Sequel II), and computationally extracted V8V9 regions from […]
The vacuolar tauopathy-associated mutation D395G confers redox sensitivity to p97/VCP
The multifunctional AAA+ ATPase p97/VCP is a pivotal regulator of cellular proteostasis, extracting polyubiquitinated substrates from protein complexes or organelle membranes for proteasomal degradation. Mutations in p97 are linked to a broad spectrum of neurodegenerative disorders, including multisystem proteinopathy and amyotrophic lateral sclerosis. Here, we provide insights into the basis of dysfunction in p97D395G, implicated […]
EasyCAPS: A web tool for restriction-based genotyping and rational CRISPR-Cas9 donor design
Tracking Single Nucleotide Polymorphisms (SNPs) following CRISPR-Cas9 genome editing is a critical yet often labor-intensive step in modern genetic research. Although Sanger sequencing is the conventional method for definitive confirmation, it typically requires substantial time to generate results. In contrast, PCR-based restriction methods like CAPS (Cleaved Amplified Polymorphic Sequence) and dCAPS (derived CAPS) offer rapid […]
The Synthetic Epitope Atlas: High-Throughput Design and Validation of De Novo Antibody-Antigen Complexes
De novo antibody design models lack sufficient training data to reliably generalize. We demonstrate scalable generation of structural training data for machine learning-driven antibody design by linking in silico designs of antibody-antigen complexes to high-throughput experimental binding validation. Using AlphaSeq, a yeast-based platform for measuring protein binding affinities, we measure the affinity and specificity of […]
ASO-mediated mRNA silencing enables functional analysis and selective depletion of the human microbiota Prevotellaceae
The Prevotellaceae family comprises abundant, taxonomically diverse bacteria of the human microbiota that exhibit remarkable intraspecies variability and distinct phenotypes during host-microbe interactions. Yet functional investigations are hampered by the limited genetic tractability of this medically important bacterial family, rendering it understudied. Here, we apply antisense oligomer (ASO) technology to selectively inhibit translation of single […]
Divergent effects of target protein stabilisation versus overproduction on PROTAC activity
Protein degrader drugs such as PROTACs are being advanced as therapeutics targeted against oncogenic proteins. During tumorigenesis, oncogenic proteins can become constitutively activated via mechanisms including gene amplification, which increases protein production, and point mutations, which can extend protein half-life. Few experimental studies have addressed how disease-associated changes in target protein homeostasis influence PROTAC activity. […]
Methods for evaluating bacterial dispersal on hyphal networks
In heterogeneous environments, the hyphae of filamentous fungi and oomycetes can facilitate the dispersal of other microorganisms. The use of these fungal highways (FH) is regulated by both physical and biological factors with their interplay resulting in variable capabilities of different microbes to establish FH. Several devices have been developed to test the movement of […]
Pauses in a fast-paced life: Intermittent hovering in hummingbirds
Hummingbirds are known for sustained hovering powered by rapid and continuous wingbeats. Here, we describe and quantify a novel flight behavior, intermittent hovering, in which hovering hummingbirds momentarily pause their wing motion mid-air but maintain their vertical position in space, keeping their wings fully extended at the end of the upstroke. We present the first […]
Suitable seasons: Global monthly habitat suitability for the arbovirus vectors Aedes aegypti and Aedes albopictus in 1975-2024
The mosquito species Aedes aegypti and Aedes albopictus are the primary vectors of the arboviruses dengue, Zika, and chikungunya. Expansion of these vectors into previously non-endemic regions due to climate and environmental changes has accelerated global burden from arboviral diseases. To combat this, predictive models accurately mapping Aedes habitats are essential for epidemiological modelling, effective […]
Modular Deep Learning for Direct RNA Sequence Design via Self-Contained RNA Units
RNA sequence design is a pivotal challenge in synthetic biology, yet state-of-the-art deep learning methods face a fundamental bottleneck: the scarcity of high-resolution 3D structures. To compensate for limited training data, existing approaches like NA-MPNN and RiboDiffusion employ computationally expensive autoregressive or iterative diffusion sampling, substantially limiting their throughput and scalability. In this work, we […]
Molecular Dynamic simulations of Aβ42 dimers with solid-state NMR restraints capture the key structural motifs in Aβ42 fibrillation pathways
Formation of the beta-amyloid (Abeta) plaques is a pathological hallmark of Alzheimer’ s disease (AD), and is believed to be a primary cause of dementia in elderly individuals. In the present work, we simulated the conformational evolution of Abeta42 dimers in solution and in membrane-like environment to explore the folding of Abeta42 along fibrillation. The […]
Relative Index of Chimeric Expression (RICE) Analysis: A Quantitative Approach for Chimeric RNAs Using FusionBlaster
Chimeric RNA molecules, which contain nucleotide sequences originating from multiple genes, are generated by chromosomal rearrangements, transcriptional read-throughs, or trans-splicing between separate parental transcripts. Chimeric RNAs have been functionally validated in both pathological and normal healthy physiological contexts indicating the biological significance of chimeric RNA expression. There is, however, currently no standard for computationally quantifying […]