J. Lopez

Coral long-term recovery after bleaching: implications for sexual reproduction and physiology.

This study examines long-term effects of coral bleaching on reproduction and physiology of Montipora capitata, finding distinct transcriptomic responses and reproductive impacts between bleached and non-bleached colonies.

Spatial architecture of CD8+ T cells and DC subsets is critical for the response to immune checkpoint inhibitors in melanoma

This study examines the spatial organization of dendritic cell (DC) subsets and their interactions with CD8+ T cells in melanoma patients, finding that proximity between cDC1 and CD8+ T cells correlates with response to immune checkpoint inhibitors.

High Sensitivity Top-down Proteomics Captures Single Muscle Cell Heterogeneity in Large Proteoforms

This study develops a sensitive top-down proteomics method to analyze large proteoforms in single muscle cells, revealing heterogeneity and linking it to muscle fiber types.

Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps

The paper develops a computational pipeline combining Rosetta and cryo-EM to analyze ACE2 receptor traps' binding to SARS-CoV-2 variants, showing high affinity and neutralization capabilities against Omicron and Delta.

An intranasal lentiviral booster broadens immune recognition of SARS-CoV-2 variants and reinforces the waning mRNA vaccine-induced immunity that it targets to lung mucosa

This study shows an intranasal lentiviral booster enhances and broadens immune response to SARS-CoV-2 variants and improves waning mRNA vaccine immunity in the lungs.

Formylglycine-generating enzyme-like proteins constitute a novel family of widespread type VI secretion system immunity proteins

This study identifies Tsi3 as a T6SS immunity protein with an FGE domain, showing it prevents self-intoxication by interacting with Tse3 but is not a functional enzyme.

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

The paper uses cryo-EM and AlphaFold2 to determine the structure of SARS-CoV-2 Nsp2, revealing its zinc-binding site and potential interactions with host proteins.

Beyond single discrete responses: An integrative and multidimensional analysis of behavioral dynamics assisted by Machine Learning

This paper introduces a multidimensional analysis of behavioral dynamics using machine learning to integrate continuous spatial behavior with discrete responses, revealing previously overlooked aspects of behavior.

Killing of Gram-negative and Gram-positive bacteria by a bifunctional cell wall-targeting T6SS effector

Acinetobacter baumannii enhances T6SS effector activity by secreting D-Lys, increasing extracellular pH and killing Gram-negative and Gram-positive bacteria.

Full Brain and Lung Prophylaxis against SARS-CoV-2 by Intranasal Lentiviral Vaccination in a New hACE2 Transgenic Mouse Model or Golden Hamsters

This study shows that an intranasal lentiviral vaccine protects both the respiratory and central nervous systems against SARS-CoV-2 in a new hACE2 transgenic mouse model.

The glycoprotease CpaA secreted by medically relevant Acinetobacter species targets multiple O-linked host glycoproteins

This paper identifies CpaA, a glycoprotease from Acinetobacter species, as a broad-spectrum enzyme that cleaves multiple O-linked human glycoproteins, including those involved in complement activation, and proposes its use in glycoproteomics.

Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes

The paper develops a CoA-based chemoproteomic strategy to optimize probe selectivity and evaluates its application in assessing small molecule acetyltransferase inhibitors.

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.

Intranasal Vaccination with a Lentiviral Vector Strongly Protects against SARS-CoV-2 in Mouse and Golden Hamster Preclinical Models

This study shows that intranasal vaccination with a lentiviral vector encoding the SARS-CoV-2 Spike protein provides strong protection against SARS-CoV-2 in mice and golden hamsters by reducing viral load and inflammation.

Multi-modal single cell analysis reveals brain immune landscape plasticity during aging and gut microbiota dysbiosis

This study uses CITE-seq to analyze brain immune cell plasticity in aged mice with and without gut dysbiosis, revealing transcriptional shifts in monocytes and ILCs linked to neuroinflammation.

UHRF1 upregulation mediates exosome release and tumor progression in osteosarcoma

This study shows that UHRF1 upregulation drives exosome release and tumor progression in osteosarcoma by promoting metastasis and cell mobility.

Peptidoglycan editing provides immunity to Acinetobacter baumannii during bacterial warfare

Acinetobacter baumannii incorporates D-Lysine into its peptidoglycan to gain immunity against T6SS attacks from competitors, though this trait is lost in pathogenic strains due to host enzyme activity.

The tip of the VgrG spike is essential to functional type VI secretion assembly in Acinetobacter baumannii

This study identifies a single amino acid mutation in VgrG that inhibits T6SS function in A. baumannii, suggesting the T6SS is not essential for virulence.

Towards standardization of immune functional assays

The paper validates a standardized immune functional assay method using a healthy volunteer cohort, showing strong host-response correlation and highlighting its potential for clinical use.

Parallel high-performance computing algorithm to generate FEM-compliant volumetric mesh representations of biomolecules at atomic scale

The paper develops a parallel algorithm to generate volumetric meshes of biomolecules for Finite Element Analysis, showing improved speed and accuracy compared to previous methods.

Systematic mapping of drug metabolism by the human gut microbiome

The paper systematically maps drug metabolism by the human gut microbiome, showing 13% of 575 drugs are metabolized by a single microbiome sample.

The diversity, evolution and ecology of Salmonella in venomous snakes

This study investigates Salmonella diversity in venomous snakes, finding 91% prevalence and identifying metabolic differences between subspecies, suggesting a potential role in human Salmonellosis in Africa.

FUN-LOV: Fungal LOV domains for optogenetic control of gene expression and flocculation in yeast

This paper introduces FUN-LOV, an optogenetic switch based on fungal LOV domains, enabling light-controlled gene expression and flocculation in yeast with high temporal resolution and dynamic range.

Activated BAX/BAK enable mitochondrial inner membrane permeabilisation and mtDNA release during cell death

This study shows that BAX/BAK-mediated mitochondrial outer membrane pores widen after MOMP, leading to inner membrane permeabilisation and mtDNA release, which triggers inflammation via cGAS-STING.

Leaf rolling in maize crops: from leaf scoring to canopy level measurements for phenotyping

This study links leaf rolling in maize under water stress to canopy structure changes, enabling high-throughput remote sensing phenotyping.