P. D. Adams

Linked regulation of genome integrity and senescence-associated inflammation by p53

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.

A putative rhamnogalacturonan-II CMP-β-Kdo transferase identified using CRISPR/Cas9 gene edited callus to circumvent embryo lethality.

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.

Histone chaperone HIRA, Promyelocytic Leukemia (PML) protein and p62/SQSTM1 coordinate to regulate inflammation during cell senescence.

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

Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2

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.

High Density Domain-Focused CRISPR Screens Reveal Novel Epigenetic Regulators of HOX/MEIS Activation in Acute Myeloid Leukemia

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.

A highly active Burkholderia polyketoacyl-CoA thiolase for production of triacetic acid lactone

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.

AlphaFold predictions are valuable hypotheses, and accelerate but do not replace experimental structure determination

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

Accelerating crystal structure determination with iterative AlphaFold prediction

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

Nuclear autophagy interactome unveils WSTF as a constitutive nuclear inhibitor of inflammation

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

A membrane-associated light harvesting model is enabled by functionalized assemblies of gene-doubled TMV proteins

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

PSGL-1 directs early TCR signaling to repress metabolism and promote T cell exhaustion by modulating the TCF-1/TOX axis in CD8+ T cells.

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.

Assessing Comparative Microbiome Performance in Plant Cell Wall Deconstruction Using Multi-omics-Informed Network Analysis

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

Improved AlphaFold modeling with implicit experimental information

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

Conserved Transcription Factors Control Chromatin Accessibility and Gene Expression to Maintain Cell Fate Stability and Restrict Reprogramming of Differentiated Cells

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.

BRD4-mediated repression of p53 is a target for combination therapy in AML

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

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

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.

A global Ramachandran score identifies protein structures with unlikely stereochemistry

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.

Improvement of cryo-EM maps by density modification

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.

Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks

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

Structural mechanism of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase

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.

The response of Pseudomonas putida to a complex lignolysate

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.

Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

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

Cryo-Electron tomography 3D structure and nanoscale model of Arabidopsis thaliana cell wall

Cryo-electron tomography and mechanical simulations revealed cell wall 3D architecture, optimized for flexibility/ductility.

Length-independent telomere damage drives cardiomyocyte senescence

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

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

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.

A fully automatic method yielding initial models from high-resolution electron cryo-microscopy maps

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

Automated map sharpening by maximization of detail and connectivity

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.