Bogdan Budnik

Firewalled synthetic commensal blocks horizontal gene transfer in the gut

This paper develops a genetically firewalled Escherichia coli commensal that blocks horizontal gene transfer and viral infections while maintaining high fitness in the gut.

Viscoelastic Niches Shape γδ T-Cell Phenotype and Effector Function

This study shows that matrix viscoelasticity influences γδ T-cell phenotype and function, with slow-relaxing matrices enhancing cytotoxic programs and tumor control.

Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking

This study establishes quality control standards for single-cell proteomics through inter-laboratory benchmarking, identifying software and technical factors affecting data reliability.

Sequestration of growth cone surface proteins by cytoplasmic Lrrtm2 induces de novo amygdala innervation by cerebral cortex associative neurons

The paper identifies how Lrrtm2 sequestration in growth cones disrupts axon guidance, leading to abnormal amygdala innervation in callosal projection neurons, linking Bcl11a deletion to ASD/ID mechanisms.

Human fallopian tube-on-a-chip for preclinical testing of non-hormonal contraceptives with living human sperm

The paper develops a human fallopian tube-on-a-chip model to test non-hormonal contraceptives, showing dose-dependent sperm motility inhibition by TDI-11861.

Endothelial CLK2 as a therapeutic target for acute radiation syndrome

This study identifies CLK2 as a therapeutic target for acute radiation syndrome by showing CLK2 inhibitors protect endothelial cells and reverse radiation injury in human organ models.

Control of Molecular Biochemistry and Cell Injury Responses through Highly Ordered Supramolecular Assembly of Flavonoids

Molecular dynamic simulations reveal flavonoids self-assemble into ordered structures that interact with proteins, modulate enzyme activity, and protect cells from UV-induced injury.

Induction of cervical dysfunction associated with preterm birth by IL-1 and dysbiotic microbiome revealed in human endocervix chips

The paper uses human endocervix chips to show that IL-1 receptor antagonists may prevent preterm labor by reducing cervical dysfunction.

Altered Protein Phosphorylation in a Novel Midbrain Organoid Model for Bipolar Disorder

This study develops a midbrain organoid model for bipolar disorder using patient-derived hiPSCs, identifies dysregulated signaling pathways, and shows lithium reverses some abnormalities.

Cortical projection neurons with distinct axonal connectivity employ ribosomal complexes with distinct protein compositions

The paper identifies subtype-specific ribosomal complex protein compositions in cortical projection neurons during axonal connectivity formation.

Preventing escape and malfunction of recoded cells due to tRNA base changes

The paper shows recoded E. coli can escape faster due to tRNA base changes and introduces kill switches to prevent this.

Synthetic genomes unveil the effects of synonymous recoding

This study uses synthetic genomes to investigate how synonymous codon recoding affects organismal fitness and develops a workflow to overcome lethal effects of codon swaps.

Identification of markers for the isolation of neuron-specific extracellular vesicles

The paper identifies NRXN3 as a neuron-specific marker for isolating extracellular vesicles from biofluids and develops methods to isolate these vesicles for neurological disease research.

Symmetry in levels of axon-axon homophilic adhesion establishes topography in the corpus callosum and development of connectivity between brain hemispheres

The paper identifies topographic principles in the corpus callosum that guide axon connectivity between brain hemispheres through symmetric adhesion molecule levels and co-fasciculation.

Modulation of dysbiotic vaginal complications by cervical mucus revealed in linked human vagina and cervix chips

The paper shows that cervical mucus from Organ Chips protects vaginal chips from inflammation and injury caused by bacterial vaginosis microbiomes, suggesting potential biomarkers and therapeutic targets.

A blood-brain-barrier penetrant AAV gene therapy rescues neurological deficits in mucolipidosis IV mice.

Brain cell type specific proteomics approach to discover pathological mechanisms in the childhood CNS disorder mucolipidosis type IV

The paper uses cell type-specific proteomics in a MLIV mouse model to identify molecular mechanisms and dysregulated pathways in different brain cell types.

Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality

The paper shows that macrophages interact with nascent blood stem cells in zebrafish embryos, influencing their survival and clonality through mechanisms involving calreticulin.

Swapped genetic code blocks viral infections and gene transfer

The paper demonstrates a genetic code reassignment strategy that makes cells resistant to viral infections and prevents horizontal gene transfer by mistranslating viral proteins and relying on synthetic codons.

Formation and recycling of an active epigenetic mark mediated by cell cycle-specific RNAs

The paper shows that cell cycle-specific long noncoding RNAs regulate the establishment and recycling of the acetylated histone H2A.Z epigenetic mark.

Loss of TBK1 activity leads to TDP-43 proteinopathy through lysosomal dysfunction in human motor neurons

This study shows that TBK1 deficiency in human motor neurons causes TDP-43 proteinopathy through lysosomal dysfunction, and restoring TBK1 rescues the pathology.

Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation

SCoPE-MS combines acoustic cell lysis with isobaric tandem-mass-tag carrier channels to quantify over a thousand proteins in single mammalian cells, resolving cancer cell types and stem cell differentiation.

Quantifying homologous proteins and proteoforms

The paper develops a model to accurately quantify proteoform stoichiometries using mass-spectrometry data without external standards.

Automated sample preparation for high-throughput single-cell proteomics

Minimal ProteOmic sample Preparation (mPOP) eliminates cleanup losses in single-cell mass spectrometry proteomics, enabling automated SCoPE-MS profiling that separates mammalian cells by cell type and cell-division-cycle phase.

Dynamic post-transcriptional regulation during embryonic stem cell differentiation

The paper measures mRNA and protein levels during ESC differentiation, revealing widespread discordance and using a kinetic model to identify post-transcriptional regulation.

Differential stoichiometry among core ribosomal proteins

This study quantifies core ribosomal protein stoichiometry in mouse embryonic stem cells and yeast, showing variability influenced by growth conditions and ribosome-mRNA binding.