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Candida albicans is a normal resident of the human gut and mucosal microbiomes and also an opportunistic fungal pathogen. It undergoes several morphological transitions, one of which is white-opaque switching, where C. albicans reversibly alternates between two distinct cell types, namely, "white" and "opaque." Each state, which is maintained by a complex transcriptional feedback loop, is heritable through many cell divisions. To date, most research works on interactions between C. albicans and the innate immune system have utilized white cells. In this paper, we examine the response of opaque cells following phagocytosis by murine macrophage cell lines and compare it to the response of white cells. White cells are known to rapidly form hyphae that can rupture macrophages, but we show here that opaque cells continue to proliferate as yeast-form opaque cells within the macrophage. Before phagocytosis, white and opaque cells differ markedly in the mRNAs they express and therefore enter macrophages as two distinct types of cells. We were surprised to observe that, within macrophages, the transcriptional profiles of white and opaque cells became much more similar to each other. This convergence was driven, in part, by the upregulation, in white cells, of a set of genes that were already expressed in opaque cells prior to macrophage exposure. These observations indicate that opaque cells, compared to white cells, are "pre-adapted" for life within host macrophages.IMPORTANCEThe human fungal pathogen Candida albicans undergoes several morphological transitions, one of which is white-opaque switching. Although most research works on interactions between C. albicans and the innate immune system have focused on white cells, opaque cells have been shown to interact with macrophages differently compared to white cells. In this study, we examine the transcriptional response of opaque cells to phagocytosis and compare it to that of white cells. Despite differences in how the two cell types proliferate following phagocytosis, their transcriptional responses strongly overlap, and fewer genes are differentially expressed between white and opaque cells following phagocytosis than observed in media lacking macrophages. Unexpectedly, the responses of both white and opaque cells favor genes that were already upregulated in opaque cells (relative to white cells) before exposure to macrophages; these observations suggest that opaque cells are "pre-adapted" for life within macrophages.

One exciting class of future genetic devices could be those deployed in microbes that join complex microbial environments in the wild. We sought to determine whether genetic parts designed for monoculture are predictable when used in co-culture by testing constitutive Anderson promoters driving the expression of chromoproteins from a plasmid. In Escherichia coli monoculture, a high copy number origin of replication causes stochastic expression regardless of promoter strength, and high constitutive Anderson promoter strength leads to selection for inactivating mutations, resulting in inconsistent chromoprotein expression. Medium- and low-strength constitutive Anderson promoters function more predictably in E. coli monoculture but experience an increase in inactivating mutations when grown in co-culture over many generations with Pseudomonas aeruginosa. Expression from regulated promoters instead of constitutive Anderson promoters can lead to stable expression in a complex wastewater culture. Overall, we show intraspecies selection for inactivating mutations due to a competitive growth advantage for E. coli that do not express the genetic device compared to their peers that retain the functional device. We show additional interspecies selection against the functional device when E. coli is co-cultured with another organism. Together, these two selection pressures create a significant barrier to genetic device function in microbial communities that we overcome by utilizing a regulated E. coli promoter. Future strategies for genetic device design in microorganisms that need to function in a complex microbial environment should focus on regulated promoters and/or strategies that give the microorganism carrying the device a selective or growth advantage.

Importance: First-generation biotechnology focused on genetic devices designed for use in monoculture conditions. One class of next-generation biotechnology devices could be designed to function in complex ecosystems with other organisms, so we sought to create conditions where the genetic device retained function when the organism carrying it is in co-culture with other organisms. We discovered that when the genetic device is a significant resource burden on the organism carrying the device, mutations will be selected for due to intraspecies and interspecies selection pressures, and the device will be rendered non-functional. Therefore, genetic device design for complex ecosystems in next-generation biotechnology needs to balance functionality of the genetic device with the need to reduce resource burden on the organism carrying it.

Intrastrain genetic and phenotypic heterogeneity of Pseudomonas aeruginosa is a hallmark of chronic lung infections in individuals with cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD). Although the coexistence of multiple P. aeruginosa lineages within a single host is well documented, the impact of this heterogeneity on infection microbiogeography remains poorly understood. We previously showed that loss of the lipopolysaccharide (LPS) O-specific antigen (OSA) alters P. aeruginosa aggregate assembly. Since OSA-deficient variants are common in chronic pulmonary infections and associated with increased pathogenesis and immune evasion, we investigated whether intrastrain OSA diversity shapes infection microbiogeography. We constructed mixed populations containing equal ratios of OSA-deficient variants and wild-type (WT) cells and examined aggregate assembly and population structures in a synthetic CF sputum model (SCFM2). To assess OSA heterogeneity in vivo, we used a murine pneumonia model combined with hybridization chain reaction (HCR) RNA-FISH and whole-tissue clearing to visualize spatial organization in the airways. In SCFM2, OSA-deficient variants increased total population size, reduced WT aggregate size, and altered spatial organization. We employed 2-plex HCR RNA-FISH to distinguish WT and OSA-deficient variants in murine lungs. Interestingly, in contrast to in vitro conditions, OSA-deficient cells led to significantly larger WT aggregates in the airways. These findings highlight the role of intrastrain genetic heterogeneity in shaping infection microbiogeography and provide a framework for understanding how population dynamics influence microbial physiology and host-pathogen interactions at the micron scale.IMPORTANCEIntrastrain genetic and phenotypic diversity within Pseudomonas aeruginosa populations is common in chronic pulmonary infections. While this intrastrain heterogeneity is a hallmark of chronic infection, its consequences for the spatial organization of P. aeruginosa within the airways remain unclear. Here, we demonstrate that the loss of O-specific antigen in a subpopulation of P. aeruginosa significantly alters the spatial architecture of P. aeruginosa, without changing the total population size or composition. Using a combination of tissue clearing and hybridization chain reaction RNA-FISH in a murine lung infection model, we mapped the localization of genetically distinct P. aeruginosa variants in mixed populations in vivo. These findings reveal that genetic diversification within a strain can reshape the infection landscape at the micron scale, highlighting the overlooked role of intrastrain dynamics in shaping the microbiogeography of infections and influencing host-pathogen interactions.

When susceptible bacterial cultures are treated with antibiotics, some cells can survive treatment without heritable resistance, giving rise to susceptible daughter cells in a phenomenon termed antibiotic persistence. Current models of fluoroquinolone (FQ) persistence in stationary-phase cultures posit that post-treatment resuscitation is dependent on double-stranded break (DSB) repair through RecA-mediated homology-directed repair. Previously, we reported that stationary-phase P. aeruginosa does not depend on RecA to persist. In this work, we ask whether P. aeruginosa FQ persisters from stationary-phase cultures suffer DSBs at all. We measured DSB formation in Levofloxacin (LVX)-treated cells recovering from treatment using strains expressing fluorescently labeled DSB-binding protein, Gam. We find that, surprisingly, the majority of P. aeruginosa LVX persisters survive treatment without apparent DSBs. Persisters that have evidence of DSBs take longer until their first division compared to persisters without DSBs. Additionally, the fates of their progenies suggest that persisters may cope with DSBs by repair or damage sequestration. These observations pave the way for mechanistic studies into P. aeruginosa FQ persistence and highlight the need for single-cell tools to track FQ-induced damage.

Importance: Pseudomonas aeruginosa is an opportunistic pathogen of significant clinical interest. When susceptible cultures of P. aeruginosa are treated with fluoroquinolone (FQ) antibiotics, some cells survive treatment and regrow in a phenomenon termed antibiotic persistence. Studies in Escherichia coli and other bacterial species suggest that FQ persisters survive by repairing DNA double-stranded breaks (DSBs) after antibiotic removal. In this study, we show that most stationary-phase P. aeruginosa survive by avoiding DSBs rather than repairing them.

DNA ligases are a fundamental class of enzymes required for DNA replication and repair. They catalyze the formation of phosphodiester bonds, specifically at single-strand breaks in double-stranded DNA. The nuclear genome of malaria parasites encodes a single DNA ligase that is likely involved in nuclear and organellar DNA replication and repair. DNA ligase I from Plasmodium falciparum (PfLig1) has been biochemically characterized and shown to possess nick-sealing activity. However, its localization and function in the three genome-containing compartments-the nucleus, apicoplast, and mitochondrion-of the malaria parasites remain unknown. Here, we found that Lig1 is located primarily in the nucleus in both human and rodent malaria parasites throughout the parasite life cycle. Furthermore, we detected its presence in organelles via a chromatin immunoprecipitation-PCR assay. Our attempts to disrupt Plasmodium berghei Lig1 (PbLig1) in the blood stages have failed, indicating that the gene is likely essential. Next, we used an Flp/FRT-based conditional mutagenesis system that silences gene function in sporozoites. We demonstrated that PbLig1 is essential for parasite liver-stage development. Sporozoites lacking PbLig1 invade hepatocytes but arrest growth during mid-liver-stage development. PbLig1 cKO parasites undergo limited nuclear division and present a reduced DNA content that fails to increase beyond mid-liver stage of development. These data suggest that Lig1 is an essential enzyme for parasite blood- and liver-stage development.IMPORTANCEUnlike mammalian cells that possess multiple DNA ligases, the malaria parasite's nuclear genome encodes a single DNA ligase. This single DNA ligase is likely involved in both DNA replication and DNA repair. However, the importance of parasite DNA ligase remains largely unknown. Here, we show that Plasmodium Lig1 is primarily found within the nucleus, but it also exhibits a distribution across parasite organelles. Knockout of PbLig1 in sporozoites abolishes parasite liver-stage development, preventing the formation of hepatic merozoites and ultimately blocking the transition from the liver to the blood stage of infection. More specifically, PbLig1 is essential for nuclear division during hepatic schizogony. These findings enhance our understanding of the role of DNA ligase I in malaria parasite liver-stage development.

Methicillin-resistant Staphylococcus aureus (MRSA) is a high-priority microorganism that necessitates the development of new treatments, as it causes a substantial disease burden and economic impact globally. MRSA colonizes the skin and anterior nares and can potentially become invasive, leading to pneumonia and soft tissue infection. Additionally, MRSA can establish chronic infections in wounds and medical implants, partly due to its ability to form biofilms. Likewise, the skin commensal Staphylococcus epidermidis also causes similar infections, particularly through its ability to form a plastic-binding biofilm. In this study, we used N-benzyl-N-methyldithiocarbamate (BMDC) in combination with copper or zinc to decrease the viability of MRSA in both planktonic and biofilm settings in vitro, as well as to inhibit biofilm formation by S. epidermidis. We used Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES), biomass assessment, colony counts, and metabolism assays to interrogate the state of the bacterium after exposure to metal-BMDC. Furthermore, we compared these metal complexes to the antibiotic vancomycin, one of the current therapeutics used to treat MRSA infections. BMDC enhances copper uptake in bacteria, increasing intracellular copper levels by 70-fold compared to copper alone. Copper intoxication leads to a decrease in metabolic activity that ultimately results in bacterial death. Zinc also combines with BMDC, though likely through a different mechanism, and similarly exerts bactericidal effects. Significantly, both metal-BMDC combinations effectively reduce biofilm formation and eradicate bacteria within established biofilms in vitro, highlighting their potential as promising antimicrobial strategies against MRSA and S. epidermidis biofilms.IMPORTANCEAntimicrobial-resistant bacteria, such as Staphylococcus aureus (MRSA) and Staphylococcus epidermidis, are a significant cause of morbidity and mortality in vulnerable populations, contributing to an escalating health and economic burden. Biofilms are an important reservoir that protects bacteria from immune clearance and antimicrobial agents. However, current strategies to effectively target MRSA biofilms are limited. This research describes a therapeutic approach that can disrupt biofilms in both MRSA and S. epidermidis, thereby enhancing bacterial clearance.

The 5 May 2025 executive order (EO) "Improving the safety and security of biological research" established a federal funding pause for dangerous gain-of-function (DGoF) research, defined as seeking certain experimental outcomes and deemed capable of resulting in significant societal consequences. These moves place institutional biosafety committees central in the identification and self-reporting of DGoF. The previous federal review for research anticipated to result in enhanced potential pandemic pathogens involved a multidisciplinary board, including a bioethicist. From our experience on those boards and based on the EO's mandate to assess the significance of the societal consequences that might result from proposed DGoF research, we suggest a layered review process for the assessment of societal consequences to inform implementation of the EO. In the layered review, proposed research, initially identified based on anticipated experimental outcomes, is confirmed as DGoF through an assessment that is informed by ethical frameworks.

The apicoplast is an essential organelle found in Apicomplexa, a large phylum of intracellular eukaryotic pathogens. The apicoplast produces metabolites that are utilized for membrane biogenesis and energy production. A majority of apicoplast-resident proteins are encoded by the nuclear genome and are trafficked to the apicoplast and are referred to as nuclear-encoded and apicoplast-trafficked (NEAT) proteins. In this study, we characterized a NEAT protein named TgBipA, which is a homolog of the highly conserved prokaryotic translational GTPase BipA. BipA is essential for bacterial survival in stress conditions and functions through interactions with the prokaryotic ribosome, although its role is not fully understood. Through genetic knockouts of TgBipA and immunofluorescence imaging, we show that the loss of TgBipA results in apicoplast genome replication defects, disruption of NEAT trafficking, loss of the apicoplast, and ultimately parasite death. Furthermore, we show through comparative studies that this phenotype closely resembles the delayed death phenomenon observed when inhibiting apicoplast translation. Finally, we show that TgBipA is an active GTPase in vitro, and its GTP hydrolysis activity is critical for its cellular function. Our findings demonstrate that TgBipA is a GTPase that has an essential role in apicoplast maintenance, providing new insights into the cellular processes of the organelle.IMPORTANCEToxoplasma gondii, and many other parasites in the phylum Apicomplexa, are pathogens with significant medical and veterinary importance. Most Apicomplexa contain a non-photosynthetic plastid organelle named the apicoplast. This organelle produces essential metabolites, and perturbation of apicoplast function results in parasite death. The apicoplast contains bacterial-like pathways for apicoplast genome replication and expression. Thus, the discovery of the apicoplast leads to optimism that this organelle would provide a wealth of anti-parasitic drug targets. Therefore, the identification and characterization of new apicoplast proteins could provide new opportunities for therapeutic development. In this study, we characterized the function of a protein called TgBipA, a homolog of a highly conserved bacterial GTPase BipA, which has been implicated in the maturation of the 50S ribosomal subunit and adaptation to cellular stress. We show that TgBipA is essential for apicoplast maintenance and parasite survival.

Mosquito-borne viruses represent a major global public health threat, with transmission dynamics governed by climatic, ecological, and anthropogenic factors. Yantai City, Shandong Province, situated in a warm-temperate monsoon climate zone, shares geographical and ecological characteristics with regions where mosquito-borne viruses are endemic, creating potential for virus introduction. We used metagenomics to systematically analyze viral communities in mosquitoes from the Yantai region. We collected 8,111 mosquitoes representing four genera and six species, with Culex being predominant (89.8%). High-throughput sequencing revealed 11 viral species spanning 9 families, including Peribunyaviridae and Picornaviridae. Notably, Serbia mononega-like virus 1 and Biggievirus Mos11 represent the first reports from China, with quantitative reverse transcription PCR revealing minimum infection rates of 0.34% and 0.68%, respectively. Phylogenetic analysis revealed close relationships to known viral strains, with several isolates potentially representing novel genera or species. Analysis revealed that Culex quinquefasciatus harbored the greatest viral diversity (five species), with significantly higher viral diversity in agricultural versus urban areas (P < 0.001). Several viruses demonstrated cross-species transmission potential, including Zhee mosquito virus, Zhejiang mosquito virus 3, and Culex tritaeniorhynchus rhabdovirus, all detected across multiple mosquito species. While most viruses appear mosquito-specific, several show close phylogenetic relationships to known pathogens, potentially posing public health risks warranting surveillance. This study addresses knowledge gaps regarding mosquito-borne viruses in the Bohai Rim region and provides a scientific foundation for regional viral surveillance and early warning systems.IMPORTANCEMosquito-borne viruses are a significant global health threat, with the potential to cause widespread disease outbreaks. This study investigated the viral diversity within mosquito populations in Yantai, China, and characterized the molecular features of two emerging RNA viruses. These findings highlight the remarkable viral diversity harbored by Culex mosquitoes and reveal higher viral diversity in agricultural areas compared to urban settings. Several identified viruses exhibit cross-species transmission potential and close phylogenetic relationships to known pathogens, suggesting that they may pose public health risks. Understanding these interactions is essential for predicting how environmental changes may affect virus transmission and the resilience of surveillance and control strategies.