Category Citation

We recently reported that the antimicrobial activity of rifabutin against Acinetobacter baumannii is best modeled by the use of RPMI for in vitro susceptibility testing. Here, we define the effects of medium on the susceptibility and frequency of resistance emergence in a panel of A. baumannii, Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa clinical isolates. Only A. baumannii was hypersusceptible to rifabutin in vitro and in vivo using a Galleria mellonella infection model. In vitro, the frequency of resistance emergence was greater when the bacteria were selected on RPMI versus tryptic soy agar (TSA) or Mueller-Hinton II (MHII) agar plates.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/34817233

LKB1 is among the most frequently altered tumor suppressors in lung adenocarcinoma. Inactivation of Lkb1 accelerates the growth and progression of oncogenic KRAS-driven lung tumors in mouse models. However, the molecular mechanisms by which LKB1 constrains lung tumorigenesis and whether the cancer state that stems from Lkb1 deficiency can be reverted remains unknown. To identify the processes governed by LKB1 in vivo, we generated an allele which enables Lkb1 inactivation at tumor initiation and subsequent Lkb1 restoration in established tumors. Restoration of Lkb1 in oncogenic KRAS-driven lung tumors suppressed proliferation and led to tumor stasis.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/37696956/

Nearly all essential nuclear processes act on DNA packaged into arrays of nucleosomes. However, our understanding of how these processes (for example, DNA replication, RNA transcription, chromatin extrusion and nucleosome remodeling) occur on individual chromatin arrays remains unresolved. Here, to address this deficit, we present SAMOSA-ChAAT: a massively multiplex single-molecule footprinting approach to map the primary structure of individual, reconstituted chromatin templates subject to virtually any chromatin-associated reaction. We apply this method to distinguish between competing models for chromatin remodeling by the essential imitation switch (ISWI) ATPase SNF2h: nucleosome-density-dependent spacing versus fixed-linker-length nucleosome clamping.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/37696956

Concurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of California (PacBio) single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90-99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/38724748/

Genome instability is a hallmark of cancer crucial for tumor heterogeneity and is often a result of defects in cell division and DNA damage repair. Tumors tolerate genomic instability, but the accumulation of genetic aberrations is regulated to avoid catastrophic chromosomal alterations and cell death. In ovarian cancer tumors, claudin-4 is frequently upregulated and closely associated with genome instability and worse patient outcomes. However, its biological association with regulating genomic instability is poorly understood. Here, we used CRISPR interference and a claudin mimic peptide to modulate the claudin-4 expression and its function in vitro and in vivo. We found that claudin-4 promotes a tolerance mechanism for genomic instability through micronuclei generation in tumor cells.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/38867360/

Alterations in the interplay between the nucleus and the cell cycle during cancer development lead to a state of genomic instability, often accompanied by observable morphologic aberrations. Tumor cells can regulate these aberrations to evade cell death, either by preventing or eliminating genomic instability. In epithelial ovarian cancer, overexpression of claudin-4 significantly contributes to therapy resistance through mechanisms associated with genomic instability regulation. However, the molecular mechanisms underlying claudin-4 overexpression in epithelial ovarian cancer remain poorly understood. In this study, we modified claudin-4 expression and employed a unique claudin mimic peptide to investigate claudin-4’s function.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/39625235/

The Rab40 subfamily of proteins consists of unique small monomeric GTPases that form CRL5-based ubiquitin E3 ligase complexes and regulate ubiquitylation of specific target proteins. Recent studies have shown that Rab40 proteins play an important role in regulating cell migration, but the underlying mechanisms of how the Rab40-CRL5 complex functions are still not fully understood. In this study, we identified AMBRA1 as a novel binding partner of Rab40 GTPases and show that this interaction mediates a bidirectional crosstalk between the CRL4 and CRL5 E3 ligases.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/40110710/

Stenotrophomonas maltophilia is responsible for a growing number of nosocomial infections and is difficult to treat owing to limited antibiotic susceptibilities. However, there are numerous recently published examples where traditional susceptibility testing methodology fails to accurately predict in vivo efficacy. We sought to determine if there were efficacious antibiotics against S. maltophilia that have been overlooked due to specious in vivo resistance determined by traditional in vitro methods. Antibiotic resistance testing was performed utilizing conventional and nutrient-limited media. Antibiotics with discordant minimum inhibitory concentrations (MICs) between the two media were selected for further experimentation.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/40401937/

Usutu virus (USUV) is an emerging mosquito-borne flavivirus known to induce neuroinvasive disease in birds, mice, and humans in European and African countries. The mechanisms of infection and dissemination remain poorly understood. Thus, elucidating how USUV spreads in a susceptible host is crucial for identifying therapeutic targets. To investigate host defenses against USUV, we generated an infectious clone of the TC508 isolate. After characterizing its replication dynamics in cultured cells from multiple species, we investigated its pathogenesis in an array of mice with genetic perturbations.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/40694555/

Intramuscular fat (IMF) refers to the adipose tissue located between muscle fibers and is a major determinant of meat quality in cattle. The cellular origin of bovine intramuscular adipocytes remains unclear. Therefore, the objective of this study was to investigate this origin. We derived single-preadipocyte clones from IMF and subcutaneous fat (SF) of cattle through single-cell cloning and subsequent validation of their potential to differentiate into adipocytes.

View the full article and citation at: https://pubmed.ncbi.nlm.nih.gov/41294860/