BackgroundXenomonitoring is an approach of epidemiological infection risk assessment addressing vector-transmitted infections like malaria in hematophagous arthropods. Standardization and automation can facilitate its use even in remote areas. In this study, the suitability of an automated commercial loop-mediated isothermal amplification (LAMP) assay, originally designed for the detection of malaria parasite DNA in human blood, was assessed for its applicability for xenomonitoring purposes.MethodsAn automated generic LAMP assay for malaria detection in human blood was applied with Anopheles spp. samples. The results were compared with commercial generic as well as species-specific real-time PCR.ResultsLAMP identified 15/43 (34.9%, 95% CI (20.1%; 50.9%)) mosquitoes artificially exposed to Plasmodium berghei, while this was the case for 22/43 (51.2%, 95% CI (35.5%; 66.7%)) samples applying real-time PCR. Considerably less discrepancy was observed with Anopheles spp. imported to Germany from field studies with 12/172 pools (7.0%, 95% CI (3.7%; 11.9%)) for LAMP and 13/172 pools (7.6%, 95% CI (4.1%; 12.6%)) for real-time PCR. Single testing and typing of DNA isolates indicated an overall infection rate of 1.2% (20/1711) with Plasmodium falciparum, P. malariae and P. ovale. Low rates of invalid results during a field exercise proved the general suitability of the LAMP approach for use at tropical settings.ConclusionsImperfect sensitivity in case of artificial exposure of mosquitoes to non-human plasmodial species was detected for both compared molecular approaches with slightly lower sensitivity of the LAMP approach. For Anopheles spp. infected with Plasmodium spp. causing human malaria, comparable diagnostic reliability could be shown for both approaches and the LAMP assay was shown to be suitable for application under tropical field conditions.

Recent studies have focused on the role of dying cells in modulating immune function and shaping the local microenvironment. Apoptotic cells release various extracellular vesicles (EVs), such as exosomes and microvesicles, and form apoptotic bodies through membrane blebbing. Despite growing interest in EVs, the effects of EVs derived from apoptotic cells versus those from live cell remain poorly understood.Here, via transmission electron microscopy, nanoparticle tracking analysis, proteomics, and flow cytometry, we characterise the distinct features of EVs from live versus apoptotic cells. Using a model of Schistosoma mansoni infection, characterised by the presence of dying cells due to parasite egg accumulation, we demonstrate that the injection of apoptotic T cell-derived EVs attenuates hepatocyte damage, in contrast to EVs from live T cells.Analysis of the transcriptomic profile of target macrophages and functional assays revealed that apoptotic cell-derived EVs activate nitric oxide-related pathways, which modulate macrophage function. Furthermore, these EVs specifically promoted fibroblast-mediated wound healing in vitro.Collectively, our findings highlight that cell fitness influences EV properties and their immune regulatory function. Investigating the differences between EVs from living and apoptotic cells is essential for advancing our understanding of immune regulation and optimising the development of EV-based therapeutic strategies.

1.6 billion people are currently infected with parasitic worms. Group 2 innate lymphoid cells (ILC2) play a central role in promoting the protective type 2 immunity against these parasites. Here we show that a subpopulation of intestinal ILC2 express the immune checkpoint molecule CD160 in mice infected with the parasitic nematode Strongyloides ratti. CD160+ ILC2 represented a distinct ST2-IL-17RB+Ki-67+ subset that expanded in vivo during S. ratti infection. By contrast, CD160- ILC2 were ST2+IL-17RB-Ki-67- and represented the dominant producers of type 2 cytokines. Upon in vitro stimulation, sorted CD160+ ILC2 progressively lost CD160 expression and acquired cytokine-producing capacity. While CD160-competent RAG KO mice efficiently controlled S. ratti infection with less than 1% of the infective dose remaining by day 10 post-infection, CD160-deficient RAG KO mice failed to expand intestinal ILC2, failed to activate mucosal mast cells and retained high intestinal worm burden for nearly 100 days. Adoptive transfer of CD160-competent ILC2 into S. ratti-infected CD160-deficient RAG KO mice partially restored mast cell activation and reduced intestinal worm burden by 50%. Collectively, these findings identify CD160 expression as a critical checkpoint in the development and expansion of fully functional ILC2 required for effective immunity against intestinal helminth infection.

Background and aims The liver is an immune privileged organ, yet it needs to overcome infections. We aimed to explore the role of the liver-specific microRNA miR-122 in liver immune tolerance. Methods We developed a miR-122 knockout (KO) mouse model and assessed immune, inflammatory, and fibrogenic responses from early postnatal stages. Innate and adaptive immune alterations were studied in miR-122 KO mice. Transcriptomic profiles from autoimmune hepatitis (AIH) patients were compared to these KO mice. Results MiR-122 KO mice developed liver inflammation and fibrosis as early as two weeks of age. An inverse correlation between miR-122 expression and inflammation/fibrosis was observed in both KO mice (p<0.01in both at weeks two (n=6) and three (n=6) of KO mice age) and human AIH samples (p<0.01, n=9). KO mice shared transcriptomic and phenotypic features with human AIH. RNA sequencing identified over 5,000 differentially expressed genes between wt and KO mice, including upregulated chemokines, immune checkpoints, and pro-fibrotic markers. IRF2, a TLR3 transcription factor, was identified as a novel direct target of miR-122. Conclusions MiR-122 is a key regulator of liver immune tolerance, modulating inflammation and fibrosis via distinct pathways. Its absence enhances immune activation and accelerates fibrosis. These findings identify miR-122 as a promising therapeutic target for autoimmune liver diseases. Impact and implication The liver is an immune-privileged organ, an adaptation likely evolved to prevent robust immune responses against material absorbed from the gastrointestinal tract. This tolerance creates a sanctuary for pathogens—including bacteria, hepatitis viruses, and parasites such as Plasmodium—within the liver parenchyma, and similarly permits the development of primary liver malignancy and metastatic seeding. We found that miR-122 regulates hepatic immune tolerance, positioning miR-122 modulation as a potential therapeutic strategy for infectious, autoimmune, malignant, and metastatic liver diseases.

Sequestration of Plasmodium falciparum -infected erythrocytes in the microvasculature is a defining feature of severe malaria and has been closely associated with endothelial activation and vascular dysfunction. However, inflammatory mediators such as tumour necrosis factor alpha (TNF-α) are also abundant during infection and strongly influence endothelial signalling pathways. Here, we investigated the relative contribution of cytoadhesion and inflammatory signalling to endothelial activation using primary human brain endothelial cells. Transcriptomic and microRNA profiling revealed that cytoadhesion alone induces minimal transcriptional changes. In contrast, TNF-α stimulation drives extensive reprogramming of mRNAs and microRNAs associated with endothelial activation and barrier dysfunction. These findings provide a mechanistic framework integrating host inflammatory signalling with parasite cytoadhesion in malaria pathogenesis.

The green seaweed Ulva compressa is a promising model for functional biology. In addition to historical research on growth and development, -omics data and molecular tools for stable transformation are available. However, more efficient tools are needed to study gene function. Here, we expand the molecular toolkit for Ulva. We screened the survival of Ulva and its mutualistic bacteria on 14 selective agents and established that Blasticidin deaminases (BSD or bsr) can be used as selectable markers to generate stable transgenic lines. We show that Cas9 and Cas12a RNPs are suitable for targeted mutagenesis and can generate genomic deletions of up to 20 kb using the marker gene ADENINE PHOSPHORIBOSYLTRANSFERASE (APT). We demonstrate that the targeted insertion of a selectable marker via homology-directed repair or co-editing with APT is possible for nonmarker genes. We evaluated 31 vector configurations and found that the bicistronic fusion of Cas9 to a resistance marker or the incorporation of introns in Cas9 led to the most mutants. We used this to generate mutants in three nonmarker genes using a co-editing strategy. This expanded molecular toolkit now enables us to reliably make gain- and loss-of-function mutants; additional optimizations will be necessary to allow for vector-based multiplex genome editing in Ulva.

Abstract MicroRNAs (miRNAs) control 60% of genes expressed in the human body, but their role in malaria pathogenesis is incompletely understood. For the first time, we demonstrate cell type-specific alterations to the miRNA profiles during the early response to malaria infection in brain and lung endothelial cells (ECs). In brain ECs, incubation with Plasmodium falciparum-infected red blood cells in the ring stage (iRBCs) most significantly affected endocytosis-related miRNAs and mRNAs. Contrastingly, in lung ECs, iRBCs altered electron transport chain-related miRNAs and mRNAs. We also present a novel dataset of inherent differences between microRNA profiles in brain and lung ECs and their secreted extracellular vesicles (EVs). We demonstrated that shear stress affected multiple pathways in brain ECs, which were controlled by numerous human miRNAs. Together, these findings demonstrate that host miRNAs respond to parasite exposure; this is accompanied by stimulation of downstream signaling pathways within the ECs. Therefore, we consider miRNAs to be the initial spark (Code of duty) for the early host-parasite interaction events.

Drought is one of the most devastating causes of yield losses in crops like maize, and the anticipated increases in severity and duration of drought spells due to climate change pose an imminent threat to agricultural productivity. To understand the drought response, phenotypic and molecular studies are typically performed at a given time point after drought onset, representing a steady-state adaptation response. Because growth is a dynamic process, we monitored the drought response with high temporal resolution and examined cellular and transcriptomic changes after rehydration at 4 and 6 days after leaf four appearance. These data showed that division zone activity is a determinant for full organ growth recovery upon rehydration. Moreover, a prolonged maintenance of cell division by the ectopic expression of PLASTOCHRON1 extends the ability to resume growth after rehydration. The transcriptome analysis indicated that GROWTH-REGULATING FACTORS (GRFs) affect leaf growth by impacting cell division duration, which was confirmed by a prolonged recovery potential of the GRF1-overexpression line after rehydration. Finally, we used a multiplex genome editing approach to evaluate the most promising differentially expressed genes from the transcriptome study and as such narrowed down the gene space from 40 to seven genes for future functional characterization.

Protein-protein interactions play an important biological role in every aspect of cellular homeostasis and functioning. Proximity labeling mass spectrometry-based proteomics overcomes challenges typically associated with other methods and has quickly become the current state of the art in the field. Nevertheless, tight control of proximity-labeling enzymatic activity and expression levels is crucial to accurately identify protein interactors. Here, we leverage a T2A self-cleaving peptide and a non-cleaving mutant to accommodate the protein of interest in the experimental and control TurboID setup. To allow easy and streamlined plasmid assembly, we built a Golden Gate modular cloning system to generate plasmids for transient expression and stable integration. To highlight our T2A Split/link design, we applied it to identify protein interactions of the glucocorticoid receptor and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid and non-structural protein 7 (NSP7) proteins by TurboID proximity labeling. Our results demonstrate that our T2A split/link provides an opportune control that builds upon previously established control requirements in the field.

Aging is a multifactorial and complex physiological process, affecting every organ with characteristic manifestations. Understanding the molecular mechanisms that drive aging processes is crucial to targeting age-related disorders. Recent reports suggest that severe post-infection syndromes can partially accelerate aging. However, the underlying gene-encoded regulatory interplay, whether being shared or distinct between aging and infection biology are poorly understood. Here, we employed spatial transcriptomics to establish a multi-organ atlas (brain, heart, kidney, liver, lung, and spleen) across the mouse lifespan (4, 17, and 26 months). Dissecting high-quality fresh-frozen tissue samples at unbiased molecular resolution, we found both organ-specific and cross-organ gene dysregulation upon aging. We identified age-related trajectories in gene expression and cell state, some only detectable within their spatial context, and provide validation at subcellular resolution. The most prominent effect was organ-wide immune system activation with spatially variable severity. We therefore evaluated how aging mimics the expression signatures observed in systemic infection, using spatial transcriptomics slices from young mice infected with Plasmodium berghei ANKA. While on the gene level the effect sizes caused by the infection outweighed those of aging, we reveal a shared activation of the early complement pathway (C4b) and serine protease inhibitors (Serpin gene family) within by phenotype distinct spatial niches. We show that this common RNA signature is driven by tissue-specific cell types and eventually affects protein levels in the aged brain, rendering them a target for future mechanistic and drug discovery studies. Taken together, our study provides a coherent in-depth and cross-organ transcriptomics atlas to systematically study aging and infection in the mouse at spatiotemporal resolution. ### Competing Interest Statement The authors have declared no competing interest.

MicroRNAs (miRNAs) control 60% of genes expressed in the human body, but their role in malaria pathogenesis is incompletely understood. Here, we demonstrate cell type-specific alterations to the miRNA profiles during the early response to malaria infection in brain and lung endothelial cells (ECs). In brain ECs, incubation with Plasmodium falciparum-infected red blood cells in the ring stage (iRBCs) most significantly affected endocytosis-related miRNAs and mRNAs. Contrastingly, in lung ECs, iRBCs altered electron transport chain-related miRNAs and mRNAs. We present a dataset of inherent differences between microRNA profiles in brain and lung ECs and their extracellular vesicles (EVs). We demonstrated that shear stress affected multiple pathways in brain ECs, which were controlled by numerous human miRNAs. Together, these findings indicate that host miRNAs respond to parasite exposure, accompanied by stimulation of downstream signaling pathways within the ECs. Therefore, we consider miRNAs the initial spark for early host-parasite interaction events.

Macrophages are functionally heterogeneous cells essential for apoptotic cell clearance. Apoptotic cells are defined by homogeneous characteristics, ignoring their original cell lineage identity. We found that in an interleukin-4 (IL-4)–enriched environment, the sensing of apoptotic neutrophils by macrophages triggered their tissue remodeling signature. Engulfment of apoptotic hepatocytes promoted a tolerogenic phenotype, whereas phagocytosis of T cells had little effect on IL-4–induced gene expression. In a mouse model of parasite-induced pathology, the transfer of macrophages conditioned with IL-4 and apoptotic neutrophils promoted parasitic egg clearance. Knockout of phagocytic receptors required for the uptake of apoptotic neutrophils and partially T cells, but not hepatocytes, exacerbated helminth infection. These findings suggest that the identity of apoptotic cells may contribute to the development of distinct IL-4–driven immune programs in macrophages.

Infection with the protozoan parasite Trypanosoma cruzi is causative for Chagas disease, which is a highly neglected tropical disease prevalent in Latin America. Humans are primary infected through vectorial transmission by blood-sucking triatomine bugs. The parasite enters the human host through mucous membranes or small skin lesions. Since keratinocytes are the predominant cell type in the epidermis, they play a critical role in detecting disruptions in homeostasis and aiding in pathogen elimination by the immune system in the human skin as alternative antigen-presenting cells. Interestingly, keratinocytes also act as a reservoir for T. cruzi, as the skin has been identified as a major site of persistent infection in mice with chronic Chagas disease. Moreover, there are reports of the emergence of T. cruzi amastigote nests in the skin of immunocompromised individuals who are experiencing reactivation of Chagas disease. This observation implies that the skin may serve as a site for persistent parasite presence during chronic human infection too and underscores the significance of investigating the interactions between T. cruzi and skin cells. Consequently, the primary objective of this study was to establish and characterize the infection kinetics in human primary epidermal keratinocytes (hPEK). Our investigation focused on surface molecules that either facilitated or hindered the activation of natural killer (NK) cells, which play a crucial role in controlling the infection. To simulate the in vivo situation in humans, an autologous co-culture model was developed to examine the interactions between T. cruzi infected keratinocytes and NK cells. We evaluated the degranulation, cytokine production, and cytotoxicity of NK cells in response to the infected keratinocytes. We observed a strong activation of NK cells by infected keratinocytes, despite minimal alterations in the expression of activating or inhibitory ligands on NK cell receptors. However, stimulation with recombinant interferon-gamma (IFN-γ), a cytokine known to be present in significant quantities during chronic T. cruzi infections in the host, resulted in a substantial upregulation of these ligands on primary keratinocytes. Overall, our findings suggest the crucial role of NK cells in controlling acute T. cruzi infection in the upper layer of the skin and shed light on keratinocytes as potential initial targets of infection.

CRISPR/Cas9 is currently the most powerful tool to generate mutations in plant genomes and more efficient tools are needed as the scale of experiments increases. In the model plant Arabidopsis, the choice of the promoter driving Cas9 expression is critical to generate germline mutations. Several optimal promoters have been reported. However, it is unclear which promoter is ideal as they have not been thoroughly tested side by side. Furthermore, most plant vectors still use one of the two Cas9 nuclear localization sequence (NLS) configurations initially reported. We genotyped more than 6000 Arabidopsis T2 plants to test seven promoters and six types of NLSs across 14 targets to systematically improve the generation of single and multiplex inheritable mutations. We found that the RPS5A promoter and bipartite NLS were individually the most efficient components. When combined, 99% of T2 plants contained at least one knockout (KO) mutation and 84% contained 4- to 7-plex KOs, the highest multiplexing KO rate in Arabidopsis to date. These optimizations will be useful to generate higher-order KOs in the germline of Arabidopsis and will likely be applicable to other CRISPR systems as well.

A major advantage of using CRISPR/Cas9 for gene editing is multiplexing, that is, the simultaneous targeting of many genes. However, primary transformants typically contain hetero-allelic mutations or are genetic mosaic, while genetically stable lines that are homozygous are desired for functional analysis. Currently, a dedicated and labor-intensive effort is required to obtain such higher-order mutants through several generations of genetic crosses and genotyping. We describe the design and validation of a rapid and efficient strategy to produce lines of genetically identical plants carrying various combinations of homozygous edits, suitable for replicated analysis of phenotypical differences. This approach was achieved by combining highly multiplex gene editing in Zea mays (maize) with in vivo haploid induction and efficient in vitro generation of doubled haploid plants using embryo rescue doubling. By combining three CRISPR/Cas9 constructs that target in total 36 genes potentially involved in leaf growth, we generated an array of homozygous lines with various combinations of edits within three generations. Several genotypes show a reproducible 10% increase in leaf size, including a septuple mutant combination. We anticipate that our strategy will facilitate the study of gene families via multiplex CRISPR mutagenesis and the identification of allele combinations to improve quantitative crop traits.

Site-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Importantly, recombinases complement the CRISPR-Cas toolbox and provide the additional benefit of high-efficiency DNA editing without generating toxic DNA double-strand breaks, allowing multiple recombination events at the same time. However, only a handful of independent, orthogonal recombination systems are available, limiting their use in more complex applications that require multiple specific recombination events, such as metabolic engineering and genetic circuits. To address this shortcoming, we develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation. Ultimately, we establish a set of 16 orthogonal LoxPsym variants and demonstrate their use for multiplexed genome engineering in both prokaryotes ( E. coli ) and eukaryotes ( S. cerevisiae and Z. mays ). Together, this work yields a significant expansion of the Cre-LoxP toolbox for genome editing, metabolic engineering and other controlled recombination events, and provides insights into the Cre-LoxP recombination process.