Biology subjects

Johnson, J.

Publications and source records attributed to Johnson, J..

At least 19 recordsLinked to original sources

bioRxiv2026

The Salmonella effector SspH2 disrupts F-actin cytoskeletal organization to inhibit macrophage migration

The facultative intracellular pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) causes gastroenteritis in humans and persistent infections in animals, enabling widespread environmental reservoirs. Intracellular survival of S. Typhimurium depends on a suite of type III secretion system effectors encoded within Salmonella Pathogenicity Island 2 (SPI-2), many of which also impair host cell migration. Among these, SspH2 is a novel E3 ubiquitin ligase (NEL) effector, but how it inhibits host cell movement has remained unclear. By using a combination of time-lapse microscopy and wound-healing assays, we show that SspH2 is required for S. Typhimurium to fully suppress migration of macrophage-like RAW264.7 cells and that conditional expression of SspH2 alone is sufficient to restrict their movement. SspH2 expression led to a marked reduction in F-actin and fewer cells containing higher-order F-actin structures, indicating cytoskeletal remodeling. In contrast, the catalytically inactive mutant SspH2C580A had no effect, demonstrating that E3 ligase activity is essential for these phenotypes. Knockdown of the host cytoskeletal factor vinculin, a core component of podosomes and focal adhesions, mimicked SspH2's effect on cell migration. When vinculin expression was reduced, SspH2 did not further inhibit migration, suggesting that SspH2 requires vinculin-associated F-actin-rich structures to block cell migration. These findings reveal a new pathway by which S. Typhimurium limits host cell movement, potentially enhancing immune evasion and fitness within the host.

microbiology↗

bioRxiv2026

Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma

The genomic landscape of osteosarcoma, the most common bone cancer worldwide, is among the most structurally complex of all human malignancies. The identification of recurrent and functionally consequential patterns has thus remained a challenge. Across 236 whole-genome sequencing osteosarcoma samples, we uncovered five genomic hotspots of clustered structural variation collectively altered in 58% of tumors. Four were associated with amplification of oncogenes ( MYC , CCND3 , CCNE1 , CDK4) , while the fifth mapped largely upstream of TP53 . Hotspot events showed coordinated patterns of co-occurrence and mutual exclusivity with each other and with tumor suppressor alterations, suggesting genomic context-specific selection. We found localized transcriptional dysregulation at hotspot event loci, and single cells harboring these events converged on a neural crest-like program, linking these structural alterations to a less differentiated cell state. These events were also detectable non-invasively through liquid biopsies and displayed ongoing structural evolution throughout disease progression, a finding with potential clinical utility. Our results provide novel insight into how complex rearrangements shape oncogenesis in osteosarcoma, with broader relevance to other cancers characterized by complex genomes.

cancer biology↗

bioRxiv2026

Regional cerebral arterial elasticity is associated with cardiovascular health in cognitively healthy older adults

Ageing is often associated with a decline in cardiovascular and cerebrovascular health. This study examines the relationship between cerebral arterial elasticity and measures of cardiovascular health, as well as longitudinal changes in cerebral arterial elasticity over a 1.5 year interval. The pulse relaxation function (PReFx) is a measure of regional cerebral arterial elasticity derived using diffuse optical tomography (pulse-DOT). PReFx was measured over the anterior brain, including the frontal lobes and anterior sections of temporal and parietal regions that are especially vulnerable to vascular and cognitive ageing. We examined relationships between PReFx and measures of four cardiovascular risk factors (CVRF; i.e., hypertension, cholesterol, diabetes, obesity), as well as CVRF burden (i.e., number of CVRFs) in the highly active and cognitively healthy ACTIVate cohort (60-70 years). We replicated the well-established relationship between PReFx and both age and cardiorespiratory fitness, and examined associations between PReFx, measures of cardiovascular health and CVRF burden. Higher CVRF burden was linearly associated with lower cerebral arterial elasticity. The relationship between age and cerebral arterial elasticity was partially mediated by pulse pressure, an index of hypertension. PReFx declined significantly in as little as 1.5 years, and the effect did not vary with baseline level of any of the four CVRFs. We conclude that PReFx shows promise as a putative biomarker for monitoring cerebrovascular ageing in healthy older adults.

neuroscience↗

bioRxiv2026

Efficient colonic colonization by Campylobacter jejuni requires the heme receptor ChuA

Previous research demonstrated that Campylobacter jejuni encodes a heme utilization system that facilitates heme-dependent growth under iron-limiting conditions and that transcription of this system is induced during human infection. Despite these observations, it remained unknown whether the heme transport system is required for colonization and disease in a susceptible host. To address this, we created individual non-polar deletion mutants of each component of the heme transport system and examined their ability to promote heme-dependent growth and iron uptake. From this work, we found that only the heme receptor, ChuA, was required for heme-dependent growth and iron acquisition, which supports the earlier work of another group. Further, we examined whether intestinal colonization, immune activation, and pathology were altered during infection with these mutants. After establishing that elevated heme and chuABCD expression occur during C. jejuni infection of IL-10-/- mice, we found that a mutant of the heme receptor, ChuA, exhibited significantly reduced colonization of the colon. In addition, we found that neutrophil and circulating monocyte recruitment were significantly reduced in the colon during infection with the ChuA mutant, but that populations of self-maintaining tissue macrophages remained high. Loss of ChuA reduced colonic colonization and was accompanied by diminished innate immune cell recruitment and intestinal pathology. Together, these findings identify ChuA-dependent heme acquisition as a key determinant of efficient colonic colonization and the associated inflammatory disease.

microbiology↗

bioRxiv2026

Partial epithelial-to-mesenchymal transition mediates profound gap closure through growth and fluidization

Epithelial gap closure is essential for maintaining tissue integrity during development and wound healing. Previous studies have shown that closure of small gaps is driven by actomyosin purse-string contraction and traction forces generated at the gap edge. Here, we show that millimeter-scale circular gap closure in mouse epicardial (MEC1) monolayers is driven primarily by growth-mediated compressive stresses. Compared with MDCK monolayers, MEC1 cells close gaps more rapidly with reduced undulation near gap edge through coordinated tissue-wide extension-contraction. The collective closing dynamics can be modulated by partial epithelial-mesenchymal transition induction and Rho kinase inhibition. By integrating tissue and cell kinematic analyses, traction-force mapping, and a continuum framework that decomposes tissue strain rates into growth-, elastic-, and fluidity-related contributions, we reveal that growth-generated compression drives inward tissue flow, while elastic cell elongation and fluid-like tissue remodeling through cell-cell intercalation act synergistically to accommodate deformation and promote robust collective gap closure.

biophysics↗

bioRxiv2026

Cohesin residence time gates 3D genome response to histone hyperacetylation

Cohesin-mediated loop extrusion and chromatin state-dependent compartmentalization are major drivers of three-dimensional (3D) genome organization. Although epigenomic perturbations are widely assumed to reshape chromatin architecture, the mechanisms that determine how changes in chromatin state are translated into structural reorganization remain poorly understood. Here, we identify cohesin residence time as a key regulator of the genomes architectural response to histone hyperacetylation induced by histone deacetylase inhibition (HDACi). Acute depletion of RAD21 or CTCF weakens chromatin loops but preserves HDACi-induced changes in compartmentalization, contact-scaling behavior, and loop density. In contrast, perturbation of cohesin loading or release produces opposing effects: NIPBL depletion sensitizes and amplifies architectural responses to HDACi, whereas WAPL loss renders the genome largely refractory to HDACi-induced remodeling, suppressing changes in compartments and loop density while stabilizing CTCF-anchored loops. These distinct architectural outcomes occur despite comparable levels of HDACi-induced histone hyperacetylation across genotypes, indicating that differential epigenomic input is not responsible for the observed effects. Together, our findings demonstrate that dynamic cohesin turnover, rather than cohesin chromatin association alone, governs whether epigenomic perturbations are converted into higher-order genome reorganization. These results establish cohesin residence time as a molecular gate linking chromatin state to 3D genome architecture and reveal a previously unrecognized principle underlying chromatin architecture plasticity.

genomics↗

bioRxiv2026

Internalized Components of Membrane Attack Complexes Disrupt Proteostasis and Acquire Alarmin-Like Properties

Immune effects of membrane attack complexes (MAC) have been widely attributed to their abilities to cause cell death. Here, we show that the MAC component, C9, forms non-cytolytic aggregates with pro-inflammatory effects. Intracellular aggregates of C9 are detected within inflamed tissues of patients in association with endothelial cell (EC) activation but not increased cell death. We identify NUMBL as a Rab35 effector that directly binds surface-bound C9 to promote C9 internalization and entry into the endolysosomal pathway. Within acidified endolysosomes, C9 forms insoluble aggregates that are targeted for degradative aggrephagy in a process that activates NF-{kappa}B. For C9 aggrephagy to occur, ZFYVE21, a Rab5 effector, complexes with RNF34 to bridge C9 aggregates to LC3B+ aggresome membranes. We detect C9 aggregates in vivo, and we show that a ZFYVE21-RNF34 signaling axis is required for C9 aggrephagy and NF-{kappa}B -dependent EC activation in three separate mouse models. Mice with conditional loss of ZFYVE21 in ECs show reduced aggregraphy, resulting in attenuated systemic inflammation and reduced tissue injury following skin transplantation. Our data show that the C9 component of MACs forms intracellular aggregates with alarmin-like properties.

biochemistry↗

bioRxiv2026

Improved model representation of the photosynthetic light reactions reduces estimates of global gross primary productivity

The assimilation of carbon dioxide by plants can be predicted by the Farquhar, von Caemmerer and Berry model of photosynthesis. This largely mechanistic model is central to understanding how plants influence Earths climate. However, it represents the use of light by photosynthesis using an empirical formulation. Johnson and Berry proposed an alternative mechanistic formulation based on the functioning of the cytochrome b6f complex that includes key steps in light harvesting and electron transport. We compared both formulations using photosynthetic light response measurements from 146 C3 species spanning arctic to tropical biomes and implemented them in the terrestrial biosphere model ELM-FATES to simulate global photosynthesis. The Johnson and Berry formulation better fitted the measured response of leaf-level photosynthesis to light, and predicted lower photosynthetic rates at intermediate light levels, which decreased global estimations of terrestrial photosynthesis by 8%. Our findings support adopting the Johnson and Berry formulation to improve model representation of global carbon cycle modeling.

plant biology↗

bioRxiv2026

Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants

Understanding how transcription factor binding site (TFBS) position influences gene regulation remains a fundamental challenge in plants. Here, we integrate conserved multiDAP TFBS maps for 244 transcription factors (TFs) with single-nucleus chromatin accessibility, cell type-resolved gene expression, and hormone-response datasets across Brassicaceae species to determine how TFBS position relates to regulatory function. Although conserved TFBSs are enriched near transcription start sites (TSSs), TSS-proximal accessibility poorly predicts cell type-specific expression. Instead, cell type-specific expression correlates best with conserved TFBSs embedded in cell type-restricted chromatin, with TF family-specific distributions across distal promoters and introns. In contrast, TSS-proximal TFBSs in broadly accessible chromatin are associated with rapid transcriptional responses to abiotic and biotic stress hormones. Coding sequence TFBSs mark a distinct regulatory context in which the same DNA sequence encodes both amino acid sequence and TF motifs, including evidence that CDS-localized ABR1 binding may contribute to repression during hormone response. Finally, distal upstream regions contain conserved multi-family TF clusters with enhancer-like features overlapping rare cell type-specific accessible chromatin and enriched near genes controlling embryonic, meristematic, and hormone-dependent developmental patterning. Together, these results support a positional grammar in which TFBS position and chromatin context jointly partition developmental, stress-responsive, and repressive regulatory output in plants.

genomics↗

bioRxiv2026

Lactate promotes IL-8 secretion in human alveolar macrophages through GPR132 and lipid metabolic reprogramming

Alveolar macrophages are the primary lung immune cell. They play a crucial role in both maintenance of tissue homeostasis and the initiation of inflammation, secreting multiple immune mediators including the chemokine interleukin-8 (IL-8). Inflammatory settings are often characterised by tissue hypoxia, increased glycolytic rates and lactate secretion, yet how lactate influences alveolar macrophage function remains unclear. Here we investigated how lactate, once considered a waste-product, shapes alveolar macrophage function. To do so, primary human alveolar macrophages (hAMs) and a combination of flow cytometry, ELISA/Luminex, western blot, light microscopy, bioluminescence resonance energy transfer (BRET) and analysis of publicly available datasets were used to understand the role of lactate in lung pathological environments. We demonstrate that hAMs sense extracellular lactate via the expression of different lactate transporters (e.g. MCT1, MCT4) and receptors (i.e. GPR132). Lactate treatment of hAMs increased IL-8 secretion in a MCT1-dependent manner. Lipid metabolism and lipid droplet formation, as well as direct lactate-driven GPR132 signalling were required for lactate-dependent IL-8 release. Our findings uncover a previously unrecognised dual mechanism by which lactate orchestrates immune regulation in hAMs. Specifically, lactate-driven IL-8 production requires two distinct lactate-driven processes: uptake via MCT1, which reprograms lipid metabolism, and signaling through the lactate receptor GPR132. This functional integration of lactate transport and receptor-mediated signaling provides new mechanistic insight into lactates role in hAM biology and highlights potential targets for therapeutic intervention.

immunology↗

bioRxiv2025

Cysteine protease cathepsin B promotes high population density-induced mutagenesis, driving genome evolution and competitive growth in response to the crowding stress

In a wide variety of species from invertebrates to mammals, overpopulation has been shown to induce low fertility and high mortality. Although density-dependent population regulation is widespread in the animal kingdom, the underlying molecular mechanisms remain poorly understood. We show here that C. elegans animals respond to the crowding stress by secreting CPR-4, a homologue of human cathepsin B cysteine protease, to promote chromosomal DNA damage in germ cells, leading to high density-induced deficiencies that include increased embryonic lethality and larval arrest and decreased brood size. CPR-4 mediates these crowding responses through the insulin-like growth factor receptor DAF-2, multiple components in the insulin signaling pathway, and the SKN-1/Nrf transcription factor. Whole genome sequencing analyses of animals from 10 generations of continual growth in the crowded condition reveal that CPR-4-induced DNA damage produces an average of 2.9 more de novo genome mutations per animal per generation and a 75% increase in mutation rate compared with animals grown in the uncrowded condition. CPR-4-induced mutagenesis also facilitates evolution of the genomes through multi-generational crowding selection, leading to biased mutation distributions towards the intergenic regions over the gene bodies and crowd-inducible growth advantage. Our findings suggest that CPR-4 acts as a crucial crowd-responding factor to induce chromosomal DNA damage, leading to density-dependent deficiencies, increased genome mutation rates, and genome evolution and competitive growth of animals in response to the crowding stress.

developmental biology↗

bioRxiv2025

Region-specific associations between cerebral arterial elasticity and grey matter volume: Evidence for lateral prefrontal vulnerability

BackgroundAgeing is associated with increased cardiovascular health risks and disproportionate atrophy in frontotemporal brain. Regional cerebral arterial elasticity correlates with regional grey matter volume, with stronger associations frontally and in older adults. Cardiorespiratory fitness (CRF) is linked to preserved brain structure and greater arterial elasticity, while sex differences exist in the timing of vascular versus structural changes. This study examines whether regional cerebral arterial elasticity in frontotemporal cortex mediates the association between age and corresponding grey matter volume decline, and whether sex and/or CRF moderate this relationship. MethodsWe analysed data from 162 healthy adults (60-70 years) with structural MRI and diffuse optical tomography of the cerebral arterial pulse (Pulse-DOT) from the ACTIVate cohort. CRF was estimated from demographic and physiological measures. Pulse Relaxation Function (PReFx), an optical index of regional arterial elasticity, was measured across 28 frontal, temporal, and parietal regions of interest (ROI). Grey matter (GM) volume was quantified for corresponding ROIs. Mediation and moderated mediation models tested whether PReFx mediated the relationship between age and GM volume at bilateral frontal and temporal ROIs, and whether biological sex or CRF moderated this relationship. ResultsRegional bivariate correlations identified associations between age, PReFx and GM volume across multiple ROIs, which PReFx and GM volume being associated primarily in left frontal and temporal areas. PReFx partially mediated the effect of age on GM volume in a left mid-inferior frontal ROI, accounting for approximately 16% of the total age effect and this relationship was only evident in females. Although higher CRF was associated with greater PReFx, it did not moderate the relationship between age, PReFx and GM volume. ConclusionsConsistent with cascade models of neurovascular aging, cerebral arterial stiffening was found to partially explain the effect of increasing age on frontal GM volume, even in this highly age-restricted and high functioning cohort. This effect was only significant over the left prefrontal cortex, consistent with greater vulnerability of frontal brain and associated cognitive functions. It was also exclusively present in females, who had better cardiovascular health, larger grey matter volume and greater arterial elasticity than males. These findings are consistent with pulse-DOT measures of cerebral arterial elasticity being more sensitive to subclinical brain structural variability.

neuroscience↗

bioRxiv2025

Detection and Characterization of West Nile Virus with evidence of Transovarial Transmission in the Coastal region, Kenya

BackgroundWest Nile virus (WNV) is a mosquito-borne flavivirus of global public health significance, maintained in an enzootic cycle between birds and mosquitoes, with humans and other mammals as incidental hosts. Understanding WNV circulation in diverse mosquito populations is critical for predicting and mitigating outbreaks. This study investigated mosquito populations from coastal Kenya, where WNV was detected, genetically characterized, and evidence of transovarial transmission in Aedes aegypti was observed. MethodsMosquitoes were collected from Kwale, Kilifi, Mombasa, and Isiolo counties (n=14,105) and pooled by species and location (1,596 pools). Pools were inoculated on Vero E6 cells, followed by RNA extraction, Illumina MiSeq sequencing, and preliminary analysis on CZ-ID. Reads were quality-controlled (PrinseqLite v0.20.4), assembled de novo (MEGAHIT v1.2.9), and analyzed via BLAST. Phylogenetic reconstruction used Maximum Likelihood, and codon-level selection pressure was evaluated using FEL, MEME, and FUBAR on Datamonkey. ResultsWNV was detected in ten pools: eight Lineage 1a and two Lineage 2. Virus isolates came from Culex pipiens, Culex univittatus, Anopheles funestus, Aedes aegypti, and Eretmapodites chrysogaster. Notably, one Lineage 1a isolate from a male Aedes aegypti confirmed transovarial transmission. Six codons were under diversifying selection, NS2B gene was found to carry the V103A mutation. ConclusionWNV in coastal Kenyan mosquitoes revealed transovarial transmission in Aedes aegypti. Lineage-specific evolution, codons under positive selection, and the NS2B:V103A mutation demonstrate ongoing viral adaptation. These findings highlight the need for continued genomic surveillance and targeted vector studies to guide WNV control strategies in Kenya and the wider region. ImportanceWest Nile virus (WNV) remains a globally important arbovirus, yet genomic and experimental data from under-sampled regions such as coastal East Africa are limited. This study provides the first integrated molecular and genotypic characterization of WNV circulating along the Kenyan coast, revealing the co-detection of Lineage 1a and the first identification of Lineage 2 in this region. By combining field surveillance, whole-genome sequencing, evolutionary analyses, and lineage-specific replication assays across multiple vertebrate and mosquito cell lines, we demonstrate clear genetic and biological differences with implications for transmission and adaptation. Importantly, the detection of WNV in a male Aedes aegypti mosquito and recovery of full genomes offers compelling evidence of transovarial transmission, a mechanism that may support viral maintenance independent of vertebrate hosts. These findings expand current knowledge of WNV ecology in Africa and underscore the need for continued genomic surveillance to detect emerging variants and inform public health strategies.

genomics↗

bioRxiv2025

Life history and infection susceptibility parameters of Drosophila species reared on a common diet

The fruit fly Drosophila is a powerful model organism for many biological questions. While Drosophila melanogaster has been the most widely used species owing to its versatile genetic tools, comparative studies also take advantage of the rich evolutionary, ecological, and behavioural diversity of Drosophilidae. This model system has only benefitted from the sequencing of hundreds of genomes assembled to chromosome level, and rich array of publicly-available datasets. However, labs that typically use just D. melanogaster can have difficulties adopting other species into their experiments due to unique dietary needs and care regimens. While dedicated research groups can rear dozens of fly species, this often requires preparing a variety of food media, which can be logistically taxing. In this study, we report an agar food recipe that we have used to rear >70 species of Drosophilidae (Prop recipe). This list includes ecological specialists such as D. sechellia, major pest species including D. suzukii, cactophiles, slime flux feeders, detritivores, and even mushroom-feeding species of the Quinaria and Testacea groups. This food recipe uses only standard powdered ingredients and molasses, and is already in use by one commercial transgenic injection provider. We provide life history parameters for dozens of species reared on this recipe, including comparisons in a subset of species across a variety of diets, finding fly fitness to be comparable or better on the Prop recipe among tested species. We further provide comparative data for 42 species after systemic infection by Acetobacter bacteria. However, unexpectedly, we found a striking interaction of diet and the microbiota that impacts susceptibility to infection in species-specific fashion. Our results suggest certain experiment types may be impacted by diet due to the microbiome that the diet itself supports. By providing rearing advice, life history parameters, and this infection dataset and experience, we hope to enable researchers to take advantage of the diversity of Drosophila as a model system for evolutionary research.

evolutionary biology↗

bioRxiv2025

Smooth Muscle Cell-Specific TGFβ2 Protects Against Thoracic Aortic Aneurysm and Dissection in Mice

ObjectiveThoracic aortic aneurysm and dissection (TAAD) are major complications of Loeys- Dietz syndrome caused by heterozygous TGFB2 mutations. While Tgfb2 knockout mice die at birth and adult heterozygotes develop late, non-dissecting or non-rupturing aneurysms, the role of vascular smooth muscle cell (SMC)-derived TGF{beta}2 in postnatal aortic homeostasis and disease remains undefined. Approach and ResultsWe generated tamoxifen-inducible, SMC-specific Tgfb2 conditional knockout mice (Tgfb2cKO) by crossing Tgfb2flox alleles with Myh11CreERT2 and ROSAmT/mG lineage reporter mice. Tgfb2 deletion was induced at 4 weeks of age. Tgfb2cKO mice developed rapidly progressive aneurysms involving both ascending and descending aortas, with intramural dissection and/or rupture at the proximal descending aorta. Lineage tracing confirmed loss of Tgfb2-deficient SMCs during disease progression. Histological and morphometric analyses revealed elastic fiber fragmentation, SMC loss and de-differentiation, medial thickening, adventitial fibrosis, and accumulation of collagen and proteoglycans. Molecular profiling demonstrated reduced expression of SMC contractile genes (Acta2, Myh11), increased fibrillar collagen (Col1a1) expression, early suppression of SMAD2/3 phosphorylation and increased non-canonical TGF{beta} signaling via p38 and pERK1/2 MAPK pathways. ConclusionsThese findings demonstrate that TGF{beta}2 derived from vascular SMCs is essential for postnatal aortic wall homeostasis by preserving SMC differentiation, maintaining extracellular matrix integrity, and supporting and preserving a proper balance of both canonical and non-canonical TGF{beta} signaling. Loss of SMC-specific Tgfb2 precipitates medial degeneration, aneurysm formation, dissection, and rupture, providing direct mechanistic insight into TGFB2-associated aortopathy and establishing a robust novel genetic mouse model for evaluating targeted therapies in TAAD. HighlightsO_LIPostnatal, SMC-specific Tgfb2 deletion in mice caused rapidly progressive thoracic aortic aneurysms, dissections, and fatal rupture. C_LIO_LILoss of Tgfb2 disrupts SMC contractile phenotype and ECM homeostasis, leading to medial degeneration, elastin fragmentation, and abnormal collagen/proteoglycan accumulation. C_LIO_LICanonical TGF{beta}-SMAD signaling is suppressed, while MAPK pathways are activated, indicating ligand-specific signaling imbalance. C_LIO_LIFindings highlight TGF{beta}2 as a central regulator of postnatal aortic homeostasis and suggest that targeted ligand-specific therapeutic strategies may better preserve aortic wall stability. C_LI SignificanceThis study identifies smooth muscle cell-derived TGF{beta}2 as a critical, nonredundant regulator of postnatal aortic wall integrity, linking its loss to thoracic aortic aneurysm, dissection, and rupture, and highlighting TGF{beta}2 ligand-specific signaling as a targeted therapeutic target. Graphical AbstractSmooth muscle cell-derived TGF{beta}2 maintains postnatal aortic wall homeostasis by preserving contractile gene expression, elastin architecture, and balanced ECM remodeling. Conditional deletion of Tgfb2 in SMCs shifts signaling from canonical SMAD2/3 to MAPK pathways, leading to medial degeneration, progressive aneurysm, dissection, and rupture--highlighting TGF{beta}2 as a nonredundant, ligand-specific regulator and potential therapeutic target in thoracic aortopathy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/679917v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1ef41d3org.highwire.dtl.DTLVardef@ca8feborg.highwire.dtl.DTLVardef@aebce4org.highwire.dtl.DTLVardef@1f3599b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Cell Line Development for Bispecific Antibodies: Better Predictability Through Transposases

Bispecific antibodies are at the forefront of biopharmaceutical drug development. With over 100 different molecular architectures combined with diverse individual subunit sequences, choosing the most suitable structure and predicting the ideal subunit expression ratios for successful heterodimerization is a significant challenge. In this paper, we demonstrate that the recently described cell line development paradigm shift (Rajendran et al. 2021), enabled by the Leap-In transposon platform, can be extended to the development of bispecific monoclonal antibody-producing cell substrates (stable clones and pools). The key features are 1) Parental pools reliably predict the derivative clonal productivity and clonal heterodimer fractions. 2) Clonal productivity and clonal heterodimer fraction remained stable for at least 60 population doublings. 3) Depending on the products biophysicochemical properties, the stable pools exhibit variable productivity stability. 4) Heterodimer fractions remain stable in the Leap-In mediated stable pools independently of the productivity stability of the pools. 5) Structures and subunit ratios can be triaged at stable pool level, and 6) Due to the homogeneous clonal productivity distribution, only a small number ([~]50) of clones need to be isolated and characterized.

bioengineering↗

bioRxiv2025

Establishing a standardized genetic toolkit for the radiation-resistant extremophile Deinococcus radiodurans

Deinococcus radiodurans is a highly radiation-resistant extremophile with potential for biomanufacturing and bioremediation in harsh environments, including extraterrestrial settings. However, genetic engineering in this organism has been constrained by limited genetic tools. Here, we establish a comprehensive genetic toolkit for D. radiodurans that enables tunable gene regulation with genome-engineering tools. We have standardized a library of 36 constitutive promoter sequences sourced from the native D. radiodurans genome and from synthetic sources, spanning 45-fold range gene expression in the context of plasmids. We have also identified 136 variants of ribosome binding sites (RBS), variants using a high-throughput screen for precise translational control across a 963-fold range of expression when used in our plasmid-based system. Additionally, we have developed a codon-optimizer script that we leverage to improve the function of four fluorescent proteins in D. radiodurans. Next, we characterized 9 small molecule-inducible promoter systems, and identified four key inducible promoter systems that achieve between 3-fold and 12-fold signal amplification, as well as titratability across induction concentrations in D. radiodurans. To engineer the D. radiodurans genome, we present a novel method for gene integrations, compatible with de novo sequences, up to 3kB in length, doing so with 87% efficiency. Lastly, we repurpose the RNA-directed nuclease, TnpB, as a novel post-transcriptional tool for programmable gene repression analogous to CRISPRi-based systems, and this tool can achieve up to 70% repression of its target. Collectively, this toolkit provides modular, standardized components for both plasmid engineering and chromosomal engineering in D. radiodurans to improve its genetic tractability and to facilitate its deployment. TOC Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/658681v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@c961deorg.highwire.dtl.DTLVardef@1386776org.highwire.dtl.DTLVardef@10977aorg.highwire.dtl.DTLVardef@1490931_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Benchmarking Spectral Library and Database Search Approaches for Metaproteomics Using a Ground-Truth Microbiome Dataset

Mass spectrometry-based metaproteomics, the identification and quantification of thousands of proteins expressed by complex microbial communities, has become pivotal for unraveling functional interactions within microbiomes. However, metaproteomics data analysis encounters many challenges, including the search of tandem mass spectra against a protein sequence database using proteomics database search algorithms. We used a ground-truth dataset to assess a spectral library searching method against established database searching approaches. Mass spectrometry data collected by data-dependent acquisition (DDA-MS) was analyzed using database searching approaches (MaxQuant and FragPipe), as well as using Scribe with Prosit predicted spectral libraries. We used FASTA databases that included protein sequences from microbial species present in the ground-truth dataset along with background protein sequences, to estimate error rates and assess the effects on detection, peptide-spectral match quality, and quantification. Using the Scribe search engine resulted in more proteins detected at a 1% false discovery rate (FDR) compared to MaxQuant or FragPipe, while FragPipe detected more peptides verified by PepQuery. Scribe was able to detect more low-abundance proteins in the microbiome dataset and was more accurate in quantifying the microbial community composition. This research provides insights and guidance for metaproteomics researchers aiming to optimize results in their analysis of DDA-MS data.

bioinformatics↗