Biology subjects

Bahr, A.

Publications and source records attributed to Bahr, A..

6 recordsLinked to original sources

bioRxiv2025

Lipid lowering alone fails to limit atherosclerosis progression and neutrophilic inflammation in middle-aged mice

While cholesterol lowering remains the cornerstone therapy for atherosclerosis and prevention of major adverse cardiovascular events, 33-50% of individuals on lipid-lowering therapy continue to exhibit elevated inflammation. Middle age (MA) represents a critical window for disease acceleration, underscoring a need to better understand non-resolving inflammation in this time frame. We rendered young (2 months) and MA mice (10 months) hypercholesterolemic with an AAV8-PCSK9 virus and fed a western diet (WD). Following 20 weeks on a WD, mice were switched to chow for 6 weeks to mimic lipid-lowering therapy. We found that MA atherosclerotic mice had increased plaque necrosis with increased circulating and bone marrow PMN compared to young mice. Upon lipid lowering, unlike in young mice, MA mice had increased necrosis, and reduced remodeling as well as increased circulating white blood cells and bone marrow hematopoietic stem cell progenitors (HSPCs). Circulating neutrophils correlated with necrosis in MA mice whereas young mice exhibited no correlation. Lipid lowered MA atherosclerotic mice had bone marrow HSPCs and neutrophils that exhibited a more activated phenotype relative to young. Elevated neutrophil-endothelial contacts were observed in the hippocampal vasculature of MA lipid lowered mice. While lipid lowering restrains atheroprogression in young, it is inadequate in MA, failing to reduce systemic inflammation and indicating the need for complementary therapies during this time frame.

immunology↗

bioRxiv2025

Tracking blaKPC Plasmid Dissemination within and between Enterobacterales across Michigan Over a Decade

AbstractblaKPC is endemic among Enterobacterales in the USA. While present on diverse plasmids, blaKPC burden is often associated with the clonal spread of multi-drug resistant (MDR) epidemic lineages. In this study we sought to determine the relative contributions of clonal spread and plasmid transfer to blaKPC burden across Michigan healthcare facilities over a decade. To this end we performed whole-genome sequencing of 1,058 KPC-producing isolates collected from 47 Michigan healthcare facilities between 2013 and 2022, including long-read sequencing for 527 isolates to enable precise plasmid tracking. Analysis with MOB-suite identified 64 distinct KPC plasmid types ("secondary clusters"), with the AK975 broad-host range plasmid being the most prevalent, found in 27% of isolates, spanning 20 species and 92 sequence types. Among genomes with AK975, 30% were from epidemic and 70% non-epidemic lineages, highlighting its broad role in regional blaKPC spread. Epidemic lineages of various species constituted 46% of the study population. Epidemic lineages differed in their primary plasmids, and even within epidemic lineages there were clonal expansions with distinct blaKPC plasmids, including in some cases AK975. These findings highlight two patterns of KPC spread: transmission of epidemic lineages harboring broad-range and lineage-specific KPC plasmids; and broader spread of AK975 among diverse species. Traditional surveillance studies often focus on common MDR lineages, potentially overlooking rare species and lineages that mediate the spread of plasmid-borne antimicrobial resistance (AMR) genes. Here we show how longitudinal studies tracking plasmids across species are essential to understand the pathways leading to AMR infections in hospitals. ImportanceThis decade-long longitudinal study highlights the persistence and spread of key KPC- carrying plasmid across multiple bacterial species in the region, including some uncommon ones. It also emphasizes the differences in KPC plasmids across lineages within the same species. While some lineages acquire multiple plasmids with resistance, they are unable to successfully maintain the plasmids. In contrast, clonal sub-populations of KPC-producing bacteria disseminate selected plasmids, establishing a stable host-plasmid combination. Comprehensive genomic surveillance that includes all pathogenic species and plasmids is crucial to understanding the regional transmission dynamics of plasmid-borne antimicrobial resistance (AMR). While outbreak studies define the blowup of a successful lineage and associated plasmids, longitudinal studies identify the reservoir-species and circulating plasmids in the context of plasmid- borne AMR.

genomics↗

bioRxiv2025

Endothelial Cells retain inflammatory memory through chromatin remodeling

Sepsis survivors face a heightened risk of secondary infections and chronic vascular dysfunction despite clinical recovery, yet the underlying mechanisms remain poorly defined. Our study identifies a novel mechanism of endothelial inflammatory memory, wherein transient inflammatory exposure induces durable chromatin remodeling, priming endothelial cells for exaggerated responses to subsequent inflammatory insults. Utilizing a clinically relevant two-hit mouse model, cecal ligation and puncture (CLP) followed by secondary Streptococcus pneumoniae (SP) infection, we reveal persistent transcriptional activation in endothelial cells (ECs), characterized by amplified expression of inflammatory cytokines, adhesion molecules (e.g., ICAM-1), complement factors, and interferon-stimulated genes. Genome-wide ATAC-seq analyses demonstrated stable chromatin accessibility at key inflammatory loci, indicative of epigenetic priming. Mechanistically, we uncovered a critical role for the AP-1 transcription factor JunB in mediating this epigenetic remodeling. JunB knockdown attenuated chromatin accessibility and subsequent transcriptional amplification upon secondary challenge, pinpointing JunB-driven chromatin modifications as central to endothelial reprogramming. Our findings offer mechanistic insights into how transient inflammation creates lasting epigenetic states within the endothelium, highlighting JunB as a potential therapeutic target to mitigate chronic endothelial dysfunction and increased susceptibility to secondary infections post-sepsis.

cell biology↗

bioRxiv2025

Massively parallel metabarcoding of droplet co-cultures

A systems approach to microbial community ecology requires high-throughput tools for identifying key microbial interactions. While microfluidic droplets enable the high throughput generation, co-cultivation, and sorting of miniaturized co-cultures in sub-nanoliter, uniform water-in-oil emulsions, analyzing composition of individual droplet co-cultures at comparable throughputs has been challenging, particularly with environmentally isolated or less genetically tractable strains. To address this bottleneck, we present Cocoa-seq (combinatorial co-cultivation and amplicon sequencing), a droplet-based microfluidic workflow that enables 16S rRNA gene amplicon sequencing for thousands of droplet co-cultures in parallel. In summary, after co-cultivation of microbial co-cultures in agarose droplets, which are then set and recovered as discrete gel beads, Cocoa-seq pairs individual gel beads with barcoded primer beads in new droplets to produce multiplexed amplicon libraries via droplet PCR for sequencing. To benchmark Cocoa-seq, we used a model two-species co-culture and four-member mock communities with three different compositions. The community profiles derived from Cocoa-seq were qualitatively consistent with fluorescence microscopy-based estimates for the two-species co-culture and correlated well with mock community expectations, even for low-abundance representatives. Attempts to incorporate spike-in 16S standards for quantification of absolute abundance were hindered by PCR stochasticity at the single-molecule level, and we provide a simulation-based explanation of this bias and recommend against relying on spike-ins for quantitative inference. ImportanceResearchers in microbial ecology are increasingly utilizing sub-nanoliter microfluidic droplets to construct, grow, sort, and analyze miniaturized microbial co-cultures to identify and characterize critical microbial interactions. However, while the generation, incubation, and sorting of droplet co-cultures is scalable, analyzing the composition of these droplet co-cultures in large number is much more difficult. We demonstrate and benchmark a workflow for multiplexing 16S rRNA amplicon libraries derived from thousands of individual droplet co-cultures in a single sequencing run. This addition in the arsenal of growing microfluidic capabilities will support future study of critical interactions within complex microbial systems. Study fundingNational Science Foundation (Awards 2120909, 2426415) (awarded to XNL)

microbiology↗

bioRxiv2024

SusC/D-like proteins in Gammaproteobacteria that utilize fructans

Fructans are ubiquitous in terrestrial ecosystems, however, these glycans are unexplored in the marine environment. We have discovered that the Antarctic gammaproteobacterium Pseudoalteromonas distincta is highly adapted to the degradation of fructose-containing substrates. This is enabled by proteins encoded in several genomic regions, including a fructan polysaccharide utilization locus (PUL). In addition to a glycoside hydrolase from family 32 (GH32), the fructan PUL encodes two proteins that have been described as specific for Bacteroidota and were previously unknown for Gammaproteobacteria: a glycan-binding SusD-like protein and a SusC-like TonB-dependent transporter (TBDT), which work as a complex in glycan import. Proteome analyses and biochemistry results suggest that the SusC/D-like proteins of P. distincta shuttle small-sized inulin-type fructans directly into the cell, where they are degraded by a periplasmic exo-active GH32. A SusD-like protein could provide a competitive adavantage in the absence of extracelluar endo-active inulinases. Comparative genomics identified further SusC/D-like proteins in Gammaproteobacteria, most of which are co-encoded with GH32s, indicative of fructan PULs, and are frequently associated with the marine habitat. Our study thus shows the first known exception to the paradigm that only Bacteroidota use SusC/D-like proteins. It further suggests that fructans contribute to the marine glycan pool.

molecular biology↗

bioRxiv2019

Characterization of SETD1A haploinsufficiency in humans and Drosophila defines a novel neurodevelopmental syndrome.

Defects in histone methyltransferases (HMTs) are major contributing factors in neurodevelopmental disorders (NDDs). Heterozygous variants of SETD1A involved in histone H3 lysine 4 (H3K4) methylation were previously identified in individuals with schizophrenia. Here, we define the clinical features of the Mendelian syndrome associated with haploinsufficiency of SETD1A by investigating 15 predominantly pediatric individuals who all have de novo SETD1A variants. These individuals present with a core set of symptoms comprising global developmental delay and/or intellectual disability, subtle facial dysmorphisms, behavioral and psychiatric problems. We examined cellular phenotypes in three patient derived lymphoblastoid cell lines with three variants: p.Gly535Alafs*12, c.4582-2_4582delAG, and p.Tyr1499Asp. These patient cell lines displayed DNA damage repair defects that were comparable to previously observed RNAi-mediated depletion of SETD1A. This suggested that these variants, including the p.Tyr1499Asp in the catalytic SET domain, behave as Loss-of-Function (LoF) alleles. Previous studies demonstrated a role for SETD1A in cell cycle control and differentiation. However, individuals with SETD1A variants do not show major structural brain defects or severe microcephaly, suggesting that defective proliferation and differentiation of neural progenitors is unlikely the single underlying cause of the disorder. We show here that the Drosophila Melanogaster SETD1A orthologue is required in postmitotic neurons of the fly brain for normal memory, suggesting a role in post development neuronal function. Together, this study defines a neurodevelopmental disorder caused by dominant de novo LoF variants in SETD1A and further supports a role for H3K4 methyltransferases in the regulation of neuronal processes underlying normal cognitive functioning.

genetics↗