using-human-differentially-expressed-gene-lists-to-perform-downstream

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

This protocol outlines a multi-step computational pipeline for identifying potential therapeutic targets from RNA-sequencing data, including installation ...

Brigham Young University

Machines powered by artificial intelligence increasingly mediate our social, cultural, economic and political interactions. Understanding the behaviour of artificial intelligence systems is essential to our ability to control their actions, reap their benefits and minimize their harms. Here we argue that this necessitates a broad scientific research agenda to study machine behaviour that incorporates and expands upon the discipline of computer science and includes insights from across the sciences. We first outline a set of questions that are fundamental to this emerging field and then explore the technical, legal and institutional constraints on the study of machine behaviour.

Machine behaviour.

Preeclampsia (PE) is a complex pregnancy-specific disorder characterized by hypertension, proteinuria, and systemic inflammation, posing significant risks to maternal and fetal health. This study investigates the role of growth arrest-specific protein 6 (Gas6) in PE pathogenesis using a rat model. Gas6 administration induces hallmark PE features, including hypertension, proteinuria, and significant alterations in placental gene expression. Transcriptomic analysis revealed changes in pathways related to extracellular matrix remodeling, interleukin signaling, and oxidative stress, highlighting their contribution to PE pathology. Key findings include the upregulation of Fam111a, linked to oxidative stress and DNA replication, and the downregulation of Clca4, associated with ion transport and cellular homeostasis. Protein-level validation through immunofluorescence confirmed these alterations, reinforcing their mechanistic roles in placental dysfunction. Enrichment analysis further identified significant disruptions in extracellular matrix organization and intercellular signaling. These results underscore the pivotal role of Gas6 in exacerbating placental oxidative stress and systemic inflammation. Importantly, therapeutic inhibition of the Gas6/AXL axis using small-molecule inhibitors mitigated PE-like symptoms, highlighting its potential as a therapeutic target. This study provides novel insights into the molecular underpinnings of Gas6-mediated placental dysfunction and supports the development of targeted therapies to improve PE outcomes.

Transcriptomic Insights into Gas6-Induced Placental Dysfunction: Gene Targets for Preeclampsia Therapy.

Bacteriophage Lilbunny is a siphovirus infecting  strain mc155. It was isolated from compost of rabbit fecal matter. The genome of Lilbunny belongs to the A6 subcluster and is 50,789 bp, containing 95 open reading frames, 52.6% of which encode proteins with predicted functions, and three tRNA genes.

Genome sequence of cluster A6 bacteriophage Lilbunny, isolated using  mc155.

Fastidio is an F1 subcluster bacteriophage in the  class, infecting  strain mc²155. The genome is 55,839 base pairs in length and contains several putative novel open reading frames. The isolation, annotation, and analysis of Fastidio, together with other bacteriophages, improve our knowledge of phage diversity.

Genome sequence of cluster F1  phage Fastidio.

Payneful, Marchy, Hami1, and Sorpresa are A1 subcluster tailed bacteriophages belonging to the  class that infect  strain mc155. They are consistent with other A1 subcluster phages based on their genome length and guanine-cytosine content. Their genomes contain six novel open reading frames.

Genome sequences of four A1 subcluster  bacteriophages.

Thunderbird, Gwilliam, and Jiraiya are mycobacteriophages in the B1 subcluster that infect  strain . The genomes of these three phages are ~69 kb in length. Studying these phages will enhance our understanding of subcluster B1 mycobacteriophages, their genes, their putative functions, and potential impact as mycobacterial therapeutic agents.

Genome sequence of cluster B1  phages Thunderbird, Gwilliam, and Jiraiya.

Mycobacteriophages Policronamos and Palpatine are tailed phages infecting the  mc155 strain. The genome for Policronamos is 75,894 bp long with 146 open reading frames (ORFs), while the Palpatine genome is 75,809 bp long with 140 ORFs. The gene synteny of both mycobacteriophages closely matches other phage genomes in subcluster E.

Article	Year
Machine behaviour. Nature\| PubMed ID: 31019318	2019
Transcriptomic Insights into Gas6-Induced Placental Dysfunction: Gene Targets for Preeclampsia Therapy. Cells\| PubMed ID: 39996749	2025
Genome sequence of cluster A6 bacteriophage Lilbunny, isolated using mc155. Microbiology resource announcements\| PubMed ID: 40079615	2025
Genome sequence of cluster F1 phage Fastidio. Microbiology resource announcements\| PubMed ID: 40105350	2025
Genome sequences of four A1 subcluster bacteriophages. Microbiology resource announcements\| PubMed ID: 40130901	2025
Genome sequence of cluster B1 phages Thunderbird, Gwilliam, and Jiraiya. Microbiology resource announcements\| PubMed ID: 40587621	2025
Complete genome sequences of mc155 cluster E bacteriophages Policronamos and Palpatine. Microbiology resource announcements\| PubMed ID: 40698953	2025

Matthew Jackson

Biography

JoVE Journal Publications

Other Publications