P. D. Adams

This study identifies a mitochondria-regulated p53 circuit that links genomic instability and inflammation in senescent cells, showing p53 suppresses inflammation without affecting cell cycle arrest.

The paper identifies a putative rhamnogalacturonan-II CMP-β-Kdo transferase by using CRISPR/Cas9 to generate a callus mutant lacking Kdo, which disrupts RG-II crosslinking and growth.

This study shows HIRA and PML regulate SASP through interactions with p62/SQSTM1 and the cGAS-STING pathway in senescent cells.

This study investigates carbon catabolite repression in Pseudomonas putida M2 during simultaneous sugar and aromatic co-utilization, revealing simultaneous repression by sugars and aromatics and the role of crc and small RNAs.

The paper identifies SGF29 as a novel chromatin regulator of MEIS1 and AML oncogenes, showing its role in leukemogenesis and potential as a drug target.

The paper identifies a Burkholderia polyketoacyl-CoA thiolase with significantly higher TAL production activity than 2-PS, achieving 2.8 g/L in E. coli fermentations.

The paper evaluates high-confidence AlphaFold predictions against experimental crystal structures, showing they are accurate but require experimental validation for detailed structural features.

This paper introduces an iterative AlphaFold method to accelerate crystal structure determination using sequence and crystallographic data, achieving higher accuracy than non-iterative approaches.

The paper identifies WSTF as a nuclear inhibitor of inflammation degraded by autophagy, showing its role in inflammation, cancer, and immune surveillance.

This paper develops a synthetic light harvesting model using modified TMV proteins attached to lipid bilayers, enabling dynamic energy transfer studies.

This study shows PSGL-1 modulates TCF-1/TOX axis to repress metabolism and promote T cell exhaustion in CD8+ T cells, making it a therapeutic target for PD-1/PD-L1 resistant tumors.

The paper assesses microbiome performance in plant cell wall deconstruction using network analysis and identifies key microbial populations and enzymes involved.

The paper improves AlphaFold modeling by incorporating experimental density maps iteratively, resulting in more accurate protein structure predictions.

This study identifies four conserved transcription factors that oppose cell fate reprogramming by controlling chromatin accessibility and gene expression, and shows their potential as therapeutic targets for regenerative medicine.

This study shows that combining MDM2 inhibitors and BET inhibitors synergistically kills AML cells by enhancing p53 activation through BRD4's repressive function.

The paper evaluates cryo-EM model quality using benchmark maps, showing high accuracy and reproducibility across 13 teams and recommending multiple metrics for model assessment.

The paper introduces a re-implemented Ramachandran Z-score and its uncertainty estimation for protein structure validation, advocating its inclusion in structural publications and validation reports.

This paper introduces a density modification method for improving cryo-EM maps by combining half-map information and a model, enhancing map quality and detail visibility.

This study translates dog-to-human aging by identifying conserved epigenetic changes, showing methylation patterns align physiological milestones across species.

This paper investigates the structural mechanism of regioselectivity in a bacterial acyl-CoA dehydrogenase, identifying key residues and structural features responsible for its unique substrate specificity.

This paper shows that Pseudomonas putida can grow on lignolysate from sorghum, using aromatic monomers and other unknown factors like amino acids and ionic liquid.

This paper uses RB-TnSeq to identify novel enzymes in Pseudomonas putida lysine metabolism, revealing new biochemical pathways and functions for DUF1338 proteins.

This study shows that telomere damage independent of length causes cardiomyocyte senescence, leading to cardiac dysfunction, and that clearing senescent cells improves cardiac health.

The paper applies a segmentation method to cryo-EM maps to generate automated models for the 2016 cryo-EM model challenge, achieving varying completeness and RMS distances.

The paper develops a fully automatic method for optimizing and interpreting cryo-EM maps, achieving 71% residue reproduction for high-resolution reconstructions.

The paper develops an algorithm to automatically sharpen cryo-EM maps by optimizing detail and connectivity, showing it improves map quality compared to model-based methods.