J. Spencer

Dynamical Responses Predict a Distal Site that Modulates Activity in an Antibiotic Resistance Enzyme

The paper uses dynamical simulations and experiments to identify a distal site in an antibiotic resistance enzyme that modulates activity when mutated.

Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of oesophageal cancer

The paper investigates how CDKN2A and other 9p21 gene losses influence oesophageal cancer progression, finding context-dependent effects on survival and immune infiltration.

Harvesting and amplifying gene cassettes confers cross-resistance to critically important antibiotics

The paper shows that gene cassettes in an integron, amplified by IS26, confer resistance to amikacin and piperacillin/tazobactam, often leaving meropenem as the last-resort antibiotic.

Electric fields determine carbapenemase activity in class A β-lactamases

The paper investigates how electric fields in class A β-lactamases influence carbapenemase activity using molecular dynamics simulations and identifies key positions that correlate with enzyme efficiency.

Unanticipated interacting features of human gut-associated lymphoid tissues link microbiota, intestinal immunity and autoimmunity

The paper identifies DN2 B cells in human GALT that interact with DC expressing DNASE1L3 and C1Q, linking microbiota, immunity, and autoimmunity.

Inhibition mechanism and antiviral activity of an α-ketoamide based SARS-CoV-2 main protease inhibitor

This study identifies RAY1216, a slow-tight SARS-CoV-2 Mpro inhibitor with improved pharmacokinetics and antiviral activity compared to PF-07321332, currently in phase III clinical trials.

Tautomer-specific deacylation and {Omega}-loop flexibility explain carbapenem-hydrolyzing, broad-spectrum activity of the KPC-2 β-lactamase

This study identifies how tautomer-specific deacylation and {Omega}-loop flexibility enable KPC-2 β-lactamase to efficiently hydrolyze carbapenems, revealing structural and energetic mechanisms for its broad-spectrum activity.

Small Molecule G-quadruplex Ligands are Antibacterial Candidates for Gram-negative Bacteria

The paper identifies a G-quadruplex ligand, L9, as a potential antibacterial agent against multi-drug resistant E. coli, showing superior activity and distinct mechanism compared to existing ligands.

Disrupted Peyer's patch microanatomy in COVID-19 including germinal centre atrophy independent of local virus

This study examines the impact of COVID-19 on ileal Peyer's patches, finding disrupted microanatomy and germinal centre atrophy independent of local viral load.

ChAdOx1 nCoV-19 (AZD1222) vaccine elicits monoclonal antibodies with potent cross-neutralizing activity against SARS-CoV-2 viral variants

This study isolates monoclonal antibodies from a vaccinated individual and shows they neutralize multiple SARS-CoV-2 variants effectively.

Green Fluorescent Carbon Dots as Targeting Probes for LED-Dependent Bacterial Killing

This paper demonstrates that green fluorescent carbon dots can label and kill Gram-positive and Gram-negative bacteria when combined with LED light exposure.

Two subsets of human marginal zone B cells resolved by global analysis of lymphoid tissues and blood

The paper identifies two distinct subsets of human marginal zone B cells through global analysis of lymphoid tissues and blood, revealing differences in their biology and distribution.

Allosteric communication in Class A β-lactamases occurs via Cooperative Coupling of Loop Dynamics

This study identifies allosteric communication pathways in Class A β-lactamases using molecular dynamics simulations, showing how amino acid substitutions affect enzyme activity and antibiotic resistance.

Immunogenomic profile of colorectal cancer response to immune checkpoint blockade

This study identifies immunogenomic features predicting response to immune checkpoint blockade in colorectal cancer, showing that high clonality and immune escape mechanisms are more important than mutational burden.

Human marginal zone B cell development from early T2 progenitors

The paper identifies an IgMhi developmental trajectory in human B cell maturation that connects T2 progenitors to marginal zone B cells and links its disruption to severe SLE.