Biology subjects

Jacobs, S.

Publications and source records attributed to Jacobs, S..

18 recordsLinked to original sources

bioRxiv2026

Residual cohesin function and PARP1 levels determine PARP inhibitor sensitivity in STAG2-deficient cancers

The STAG1 and STAG2 paralogs are mutually exclusive subunits of cohesin, a large protein complex that controls different aspects of genome organization. Loss-of-function mutations in STAG2 are common in a variety of cancers, and have been associated with increased sensitivity to poly(ADP-ribose) polymerase inhibitors (PARPi). This provides a possible entry point for therapeutic exploitation. However, insights in the underlying mechanism and additional determinants of this sensitivity are currently lacking. Here we show that STAG2-deficient cell lines exhibit variable PARPi sensitivity. While wildtype TP53 enhances PARPi sensitivity in RPE1 cells, STAG2 depletion does not trigger p53 or affect PARPi sensitivity in RPE1-TP53wt cells. PARPi sensitivity is determined by the capacity of STAG1 to compensate for the lack of STAG2. It appears that STAG2 is not uniquely required for the PARPi response, and its loss predominantly sensitizes cells through a general defect in cohesin function. PARP trapping underlies this sensitivity and is strongly influenced by basal PARP1 expression levels and further enhanced by oncogenic signaling. Perturbations in sister chromatid cohesion also enhances PARPi sensitivity, correlating with aggravated cohesion defects and increased chromosome breakage. Mechanistically, cohesin impairment does not appear to compromise repair of nickase-induced DNA lesions, suggesting that cohesin-defective cells are particularly vulnerable to a distinct class of lesions associated with trapped PARP. Together, our findings identify residual cohesin function and PARP1 expression as key determinants of PARPi response and suggest that successful clinical application of PARP inhibitors in STAG2-mutant cancers will require biomarker-guided patient stratification rather than STAG2 mutation status alone.

molecular biology↗

bioRxiv2026

Patterns of species richness and endemism in bee and plant communities in California

Understanding the spatial distribution of species and their patterns of endemism is necessary for establishing effective conservation priorities. Despite the vital pollination services bees provide, Californias native bee distribution patterns remain largely unexplored relative to plants and butterflies. We analyzed bee species richness and endemism across California and their concordance with plant distributions. Richness was high across areas of the California Floristic Province, including the Sierra Nevada, San Francisco Bay Area and Central Coast, South Coast Ranges, and the Transverse and Peninsular ranges. Bee endemism was more localized, concentrated in the San Joaquin Valley, eastern Sierra Nevada and adjacent Great Basin, Sierra Nevada foothills, and California deserts. Because richness and endemism appear to operate at different spatial scales and likely respond to different environmental drivers, effective conservation strategies must address both. Additionally, conservation plans that incorporate both plant and bee diversity are needed to achieve more comprehensive biodiversity protection.

ecology↗

bioRxiv2026

Assessment of Leaf-Litter Invertebrate Biodiversity Using High Throughput Sequencing

Leaf litter ecosystems and their fauna are largely understudied, despite their critical ecological roles. Here, we investigate challenges associated with estimating biodiversity in terrestrial leaf litter. Current methodologies for biodiversity assessment are fraught with limitations, amongst the most significant is a decline in taxonomic expertise, complicating the process of species identification and the significant costs associated with species-level morphological identifications. DNA barcoding employs the mitochondrial gene cytochrome c oxidase I (COI) to identify animal species, and DNA metabarcoding facilitates the identification of multiple species without necessitating taxonomic expertise. Recent studies indicate that environmental DNA (eDNA) may exhibit greater sensitivity compared to traditional methods. To test whether these methods work in a real-world application, we sampled leaf litter across a temperate forest/field ecotone. Leaf litter was dried, ground and processed to extract environmental DNA. We evaluated the DNA extraction protocols to test their relative efficacy. We found that the Qiagen Blood and Tissue Kit was the most effective at recovering invertebrate diversity and that there were notable differences in biodiversity between forest and field habitats. Temperature emerged as a significant factor influencing the composition of the communities observed. Our methodology is applicable across various environments for efficient biodiversity assessment and might be particularly beneficial for monitoring pests and invasive species. Our approach offers a cost-effective and timely alternative to conventional biodiversity assessment methods and underscores the significance of accurate assessment methodologies for leaf litter communities.

ecology↗

bioRxiv2026

Prolonged impact of fire on peatland fungi despite rapid recovery of vegetation, prokaryotes, and soil physicochemistry

Climate change is increasing the frequency of wildfires in ecosystems that historically rarely burn, such as wet heaths and peatlands, thereby threatening carbon storage, biodiversity, and ecosystem functioning. We conducted a three-year, multi-level study to assess early post-fire recovery trajectories of soil physicochemical properties, vegetation, and soil microbial communities in a wet peatland-heathland mosaic affected by a flaming wildfire. Using a paired-plot design of burned and adjacent intact plots, we observed immediate spikes in bioavailable nitrogen (NH, NO-) and phosphorus (POlsen) and a reduction in soil moisture in burned plots, yet two years later these parameters had normalized, indicating rapid abiotic recovery. Vegetation was also strongly altered in the year of the fire, quantifiable by a distinct destruction of herb, moss, tree and litter cover. Although initial regrowth was dominated by a relatively fast resprouting of the graminoid Molinia caerulea, its absolute cover in burned plots never exceeded its cover in intact plots, suggesting this species did not expand post-fire. More typical peatland and wet heath species, including ericoid shrubs and Sphagnum mosses, recovered more gradually but largely returned to pre-fire levels within the timespan of our study, highlighting high vegetation resilience. Soil microbial communities showed contrasting responses. Prokaryotic communities shifted immediately after burning but largely recovered within one year. Fungal communities, however, exhibited stronger and more persistent changes and followed a distinct recovery trajectory shaped by succession of immediate and delayed fungal responders. Overall, pyrophilous and fire-tolerant fungi, such as Coniochaeta spp., increased, as did many presumably generalist or opportunistic saprotrophs. Litter and wood-associated saprotrophs as well as many mycorrhizal taxa, however, declined. Ongoing fungal shifts occurred even after soil chemistry and vegetation had largely returned to baseline, reflecting a temporary decoupling between above- and belowground communities that may have cascading effects on ecosystem functioning. In conclusion, our results reveal differential recovery trajectories across the soil-microbiome-vegetation interface and highlight that seemingly rapid abiotic and aboveground biotic recovery can mask prolonged microbial disruptions. We emphasize the importance of multi-level assessments for understanding ecosystem resilience. HighlightsO_LISoil physicochemistry, vegetation and prokaryotes recovered rapidly after a peatland wildfire C_LIO_LIFungal communities lagged behind and followed a slower recovery trajectory C_LIO_LIThe timing and duration of fungal responses to fire varied across taxa and included immediate or delayed as well as short-lived or persistent responders C_LIO_LIThere was a mismatch between vegetation and fungal recovery trajectories, evidenced by a transient post-disturbance decoupling between above- and belowground biotic communities C_LIO_LIPresumed aboveground recovery can mask prolonged belowground disruptions, with potential implications for decomposition, nutrient cycling, and plant-microbe interactions C_LI

ecology↗

bioRxiv2025

Beyond Arrhenius: Nonlinear and negative temperature scaling of biological rates from multi-step mechanisms

Temperature shapes all biological processes, particularly during the early development of ectothermic organisms. A widely used framework for describing temperature dependence is the Arrhenius equation, which predicts an exponential increase in rates with temperature. However, biological rates often deviate from this prediction when measured across broader temperature ranges. While negative apparent activation energies are often attributed to protein denaturation, this cannot explain similar behavior observed at temperatures where enzymes remain stable. These broader scaling patterns remain mechanistically unexplained. Here we present a general Markov chain framework for modeling biological timing as cascades of reversible, temperature-dependent steps. Applying this model to 121 published datasets spanning diverse species, biological timescales, and temperature ranges, we find that a consistent three-zone scaling pattern emerges: Arrhenius-like behavior at low and high temperatures, and a quadratic exponential regime at intermediate temperatures. We show that this pattern arises naturally from differences in activation energies across steps in the network. The quadratic exponential regime is an emergent feature of averaging across many steps and is robust to variation across network realizations. In contrast, Arrhenius-like scaling at the extremes tends to be more variable and originates from smaller sub-networks. Apparent negative activation energies can emerge naturally from the dynamics of multi-step networks, even in the absence of protein denaturation. Our framework provides a unified mechanistic explanation for diverse temperature-scaling behaviors in biology and may help predict how developmental and physiological processes respond to environmental change. Although we focus on development, the model is broadly applicable to biological systems governed by multi-step reaction networks.

systems biology↗

bioRxiv2025

Epistasis at the cell surface: what is the role of Erg3 loss-of-function in acquired echinocandin resistance?

Echinocandins, which target the fungal {beta}-1,3-glucan synthase (Fks), are essential for treating invasive fungal infections, yet resistance is increasingly reported. While resistance typically arises through mutations in Fks hotspots, emerging evidence suggests a contributing role of changes in membrane sterol composition due to ERG3 mutations. Here, we present a clinical case of Nakaseomyces glabratus (Candida glabrata) in which combined mutations in ERG3 and FKS2, but not FKS2 alone, appear to confer echinocandin resistance. Integrated analyses reveal a recurrent association between Erg3 loss-of-function and echinocandin resistance mediated by Fks variation across Candida species, but exclude ERG3 loss-of-function as an independent resistance mechanism. Advances in Fks structural biology and insights into echinocandin-Fks interactions support a model of epistatic crosstalk between membrane sterols and Fks function. Understanding this interaction is crucial, as it may underlie not only acquired echinocandin resistance but also the broader development of multidrug resistance across major antifungal drug classes.

molecular biology↗

bioRxiv2025

Cryopreservation of Human Cortical Organoids Using Vitrification.

Cryopreservation at ultra-low temperatures is a valuable tool for preserving cells and tissues used in research. However, few protocols exist for the preservation of brain organoid models. Current methods for preserving human cortical organoids (hCOs) rely on conventional slow cooling approaches with organoids suspended in a medium containing a cocktail of cryoprotectants. In contrast, we have optimized a vitrification technique previously used to cryopreserve human embryos and oocytes for application to hCOs. We have successfully cryopreserved hCOs that were generated by two different protocols. The vitrified organoids demonstrate a growth rate, cytoarchitecture, cell type composition and electrical activity comparable to non-vitrified controls. Our hCO cryopreservation method provides a useful alternative approach for bio-banking and cross-institutional collaboration using cortical organoids as their model system. Highlights- Human pluripotent stem cell (hPSC) derived hCOs can be cryopreserved using vitrification. - Vitrified hCOs develop similarly to non-vitrified controls. - Vitrified hCOs can be stored long-term and shipped to other institutions. MotivationMany methods of cryopreservation have been developed for the maintenance of cell lines, organoid models and tissues. Most organoid models have been successfully preserved using conventional slow-cooling methods; however, human cortical organoids have been difficult to preserve. Our findings demonstrate that the vitrification of cortical organoids preserves their structure, cell type diversity and function upon rewarming and continued culture.

neuroscience↗

bioRxiv2024

Exploring the use of environment-agent-based models for risk assessment of Great Lakes piping plovers

The Piping Plover Charadrius melodus is an endangered species of shorebird endemic to North America. This species has been the centre of many modelling studies in the last decade. One model type that has been underused in Piping Plover studies is agent-based modelling, which can be used as an accurate risk assessment tool in simulating effects of anthropogenic activities on a given animal species. Recent innovations in ecological modelling have given rise to the environmental agent-based model (enviro-ABM), which efficiently stores information about spatially indexed environmental cells and treat those as agents. This restricts computation to only focus on environmental cells containing the species we are studying, allowing for a more efficient simulation. Using Python, a high-level programming language popular in scientific computing, we develop an enviro-ABM to provide simulations of Piping Plover hatchling growth during a given breeding season. We experiment with increasing levels of human presence and human exclosure size and observe their effects on the growth rate of the simulated Piping Plover hatchlings. Our simulations showed a clear decrease in Piping Plover growth rate as anthropogenic presence increased in the simulated environment. However, when we added a 100 m human exclosure around the nest, the effects of the anthropogenic presence were mitigated at each level. We conclude that an enviro-ABM can be used to assist with conservation and management decisions, with the caveat that the model be constantly updated and informed with results of field studies, especially those pertaining to foraging and energetics of Piping Plovers.

ecology↗

bioRxiv2024

Depletion of skin bacteria by topical antibiotic treatment accelerates onset of Zika virus disease in mice.

Mosquito-borne flaviviruses have emerged as global health threats due to their rapid spread and high disease burden. The initial site of virus replication is the mosquito biting site in the host skin, yet the role of host skin bacteria remains unclear. Here, we observed accelerated progression of Zika virus (ZIKV)-induced disease in mice with depleted skin bacteria by topical antibiotic treatment prior to ZIKV infection. Increased viral loads in the blood, draining lymph node, spleen and brain of antibiotic-treated mice suggested faster ZIKV dissemination. Flow cytometry revealed increased frequencies of T cells in the lymph nodes, along with enhanced activation of T cells in the brain upon antibiotic treatment. The antibiotic-induced phenotype was rescued by restoring the skin bacteria prior to infection. Our findings demonstrate an increased susceptibility to ZIKV infection in mice with depleted skin microbiomes, suggesting a potential role of skin bacteria in modulating the infection outcome.

microbiology↗

bioRxiv2021

Alphavirus and flavivirus infectivity is disrupted by components of the bacterial cell wall

The impact of the host microbiota on arbovirus infections is currently not well understood. Arboviruses are viruses transmitted through the bites of infected arthropods, predominantly mosquitoes or ticks. The first site of arbovirus inoculation is the biting site in the host skin, which is colonized by a complex microbial community that could possibly influence arbovirus infection. We demonstrated that pre-incubation of arboviruses with certain components of the bacterial cell wall, including lipopolysaccharides (LPS) of some Gram-negative bacteria and lipoteichoic acids or peptidoglycan of certain Gram-positive bacteria, significantly reduced arbovirus infectivity in vitro. This inhibitory effect was observed for arboviruses of different virus families, including chikungunya virus of the Alphavirus genus and Zika virus of the Flavivirus genus, showing that this is a broad phenomenon. A modest inhibitory effect was observed following incubation with a panel of heat-inactivated bacteria, including bacteria residing on the skin. No viral inhibition was observed after pre-incubation of cells with LPS. Furthermore, a virucidal effect of LPS on viral particles was noticed by electron microscopy. Therefore, the main inhibitory mechanism seems to be due to a direct effect on the virus particles. Together, these results suggest that bacteria are able to decrease the infectivity of alphaviruses and flaviviruses. ImportanceDuring the past decades the world has experienced a vast increase in epidemics of alphavirus and flavivirus infections. These viruses can cause severe diseases such as hemorrhagic fever, encephalitis and arthritis. Several alpha- and flaviviruses, such as chikungunya virus, Zika virus and dengue virus, are significant global health threats because of their high disease burden, their widespread (re-)emergence and the lack of (good) anti-arboviral strategies. Despite the clear health burden, alphavirus and flavivirus infection and disease are not fully understood. A knowledge gap in the interplay between the host and the arbovirus is the potential interaction with host skin bacteria. Therefore, we studied the effect of (skin) bacteria and bacterial cell wall components on alphavirus and flavivirus infectivity in cell culture. Our results show that certain bacterial cell wall components markedly reduced viral infectivity by directly interacting with the virus particle.

microbiology↗

bioRxiv2021

Drug development of an affinity enhanced, broadly neutralizing heavy chain only antibody that restricts SARS-CoV-2 in hamsters

We have identified camelid single-domain antibodies (VHHs) that cross-neutralize SARS-CoV-1 and -2, such as VHH72, which binds to a unique highly conserved epitope in the viral receptor-binding domain (RBD) that is difficult to access for human antibodies. Here, we establish a protein engineering path for how a stable, long-acting drug candidate can be generated out of such a VHH building block. When fused to human IgG1-Fc, the prototype VHH72 molecule prophylactically protects hamsters from SARS-CoV-2. In addition, we demonstrate that both systemic and intranasal application protects hACE-2-transgenic mice from SARS-CoV-2 induced lethal disease progression. To boost potency of the lead, we used structure-guided molecular modeling combined with rapid yeast-based Fc-fusion prototyping, resulting in the affinity-matured VHH72_S56A-Fc, with subnanomolar SARS-CoV-1 and -2 neutralizing potency. Upon humanization, VHH72_S56A was fused to a human IgG1 Fc with optimized manufacturing homogeneity and silenced effector functions for enhanced safety, and its stability as well as lack of off-target binding was extensively characterized. Therapeutic systemic administration of a low dose of VHH72_S56A-Fc antibodies strongly restricted replication of both original and D614G mutant variants of SARS-CoV-2 virus in hamsters, and minimized the development of lung damage. This work led to the selection of XVR011 for clinical development, a highly stable anti-COVID-19 biologic with excellent manufacturability. Additionally, we show that XVR011 is unaffected in its neutralizing capacity of currently rapidly spreading SARS-CoV-2 variants, and demonstrate its unique, wide scope of binding across the Sarbecovirus clades.

molecular biology↗

bioRxiv2020

High transmissibility and fetal pathogenicity of recent Zika virus strains from the African lineage

The global emergence of Zika virus (ZIKV) in the last decade revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects such as microcephaly. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compared the transmissibility and pathogenicity of seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We found that recent African ZIKV strains largely outperformed their Asian counterparts in mosquito transmission kinetics experiments, which translated into a markedly higher epidemic potential in outbreak computer simulations. In addition, African ZIKV strains were significantly more lethal than Asian ZIKV strains in immunocompromised adult mice. Finally, prenatal infection of immunocompetent mouse embryos with an African ZIKV strain resulted in embryonic death whereas it caused microcephaly with Asian ZIKV strains. Together, our results demonstrate the high epidemic potential and pathogenicity of recent ZIKV strains from Africa. Importantly, they also imply that the African ZIKV lineage could more easily go unnoticed by public health surveillance systems than the Asian ZIKV lineage due to its propensity to cause fetal loss rather than birth defects.

microbiology↗

bioRxiv2020

Antiviral treatment of SARS-CoV-2-infected hamsters reveals a weak effect of favipiravir and a complete lack of effect for hydroxychloroquine

SARS-CoV-2 rapidly spread around the globe after its emergence in Wuhan in December 2019. With no specific therapeutic and prophylactic options available, the virus was able to infect millions of people. To date, close to half a million patients succumbed to the viral disease, COVID-19. The high need for treatment options, together with the lack of small animal models of infection has led to clinical trials with repurposed drugs before any preclinical in vivo evidence attesting their efficacy was available. We used Syrian hamsters to establish a model to evaluate antiviral activity of small molecules in both an infection and a transmission setting. Upon intranasal infection, the animals developed high titers of SARS-CoV-2 in the lungs and pathology similar to that observed in mild COVID-19 patients. Treatment of SARS-CoV-2-infected hamsters with favipiravir or hydroxychloroquine (with and without azithromycin) resulted in respectively a mild or no reduction in viral RNA and infectious virus. Micro-CT scan analysis of the lungs showed no improvement compared to non-treated animals, which was confirmed by histopathology. In addition, both compounds did not prevent virus transmission through direct contact and thus failed as prophylactic treatments. By modelling the PK profile of hydroxychloroquine based on the trough plasma concentrations, we show that the total lung exposure to the drug was not the limiting factor. In conclusion, we here characterized a hamster infection and transmission model to be a robust model for studying in vivo efficacy of antiviral compounds. The information acquired using hydroxychloroquine and favipiravir in this model is of critical value to those designing (current and) future clinical trials. At this point, the data here presented on hydroxychloroquine either alone or combined with azithromycin (together with previously reported in vivo data in macaques and ferrets) provide no scientific basis for further use of the drug in humans.

microbiology↗

bioRxiv2020

STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters

Introductory paragraphSince the emergence of SARS-CoV-2 causing COVID-19, the world is being shaken to its core with numerous hospitalizations and hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that productive SARS-CoV-2 infection in the lungs of mice is limited and restricted by early type I interferon responses. In contrast, we show that Syrian hamsters are highly permissive to SARS- CoV-2 and develop bronchopneumonia and a strong inflammatory response in the lungs with neutrophil infiltration and edema. Moreover, we identify an exuberant innate immune response as a key player in pathogenesis, in which STAT2 signaling plays a dual role, driving severe lung injury on the one hand, yet restricting systemic virus dissemination on the other. Finally, we assess SARS-CoV- 2-induced lung pathology in hamsters by micro-CT alike used in clinical practice. Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients.

microbiology↗

bioRxiv2019

Microscaled Proteogenomic Methods for Precision Oncology

Cancer proteogenomics integrates genomics, transcriptomics and mass spectrometry (MS)-based proteomics to gain insights into cancer biology and treatment efficacy. A proteogenomics approach was therefore developed for frozen core biopsies using tissue-sparing specimen processing with a \"microscaled\" proteomics workflow. For technical proof-of-principle, biopsies from ERBB2 positive breast cancers before and 48-72 hours after the first dose of neoadjuvant trastuzumab-based chemotherapy were analyzed. ERBB2 protein and phosphosite levels, as well as mTOR target phosphosites, were significantly more suppressed upon treatment in cases associated with pathological complete response, suggesting MS-based pharmacodynamics is achievable. Furthermore, integrated analyses indicated potential causes of treatment resistance including the absence of ERBB2 amplification (false-ERBB2 positive) and insufficient ERBB2 activity for therapeutic sensitivity despite ERBB2 amplification (pseudo-ERBB2 positive). Candidate resistance features in true-ERBB2+ cases, including androgen receptor signaling, mucin expression and an inactive immune microenvironment were observed. Thus, proteogenomic analysis of needle core biopsies is feasible and clinical utility should be investigated.

cancer biology↗

bioRxiv2019

Pan-viral protection against arboviruses by targeting inoculation site-based skin macrophages

Arthropod-borne viruses (arboviruses) are important human pathogens for which there are no specific antiviral medicines. The large number of genetically-distinct arbovirus species, coupled with the unpredictable nature of their outbreaks, has made developing virus-specific anti-viral medicines challenging. Instead, we have defined and targeted a key aspect of the host innate immune response to virus at the arthropod bite that is common to all arbovirus infections, potentially circumventing the need for virus-specific therapies at this site. Using mouse models and human skin explants, we identify innate immune responses by dermal macrophages in the skin as a key determinant of disease severity. Post-exposure treatment of the inoculation site by a topical innate immune agonist significantly suppressed both the local and subsequent systemic course of infection and improved clinical outcome in mice to infection with a variety of arboviruses from the Alphavirus, Flavivirus and Orthobunyavirus genuses. In the absence of treatment, anti-viral interferon expression to virus in the skin was restricted to dermal dendritic cells. In contrast, targeting the more populous skin-resident macrophages with an immune agonist elicited protective responses in key cellular targets of virus that otherwise replicated virus to high levels. By defining and targeting a key aspect of the innate immune response to virus at the mosquito bite site, we have shown that it is possible to improve outcome to infection by targeting pathways activated at the site of inoculation, and thereby identified a putative new strategy for limiting disease following infection with a variety of genetically-distinct arboviruses.\n\nOne-sentence summaryWe demonstrate that activation of innate immune responses to arbovirus at the mosquito bite is a limiting factor for preventing efficient systemic dissemination of virus and that therapeutic targeting of skin-resident macrophages can have defining inhibitory effects on the later systemic course.

immunology↗

bioRxiv2018

Analysis of the role of Nidogen/entactin in basement membrane assembly and morphogenesis in Drosophila

Basement membranes (BMs) are thin sheet-like specialized extracellular matrices found at the basal surface of epithelia and endothelial tissues. They have been conserved across evolution and are required for proper tissue growth, organization, differentiation and maintenance. The major constituents of BMs are two independent networks of Laminin and Type IV Collagen interlinked by the proteoglycan Perlecan and the glycoprotein Nidogen/entactin (Ndg). The ability of Ndg to bind in vitro Collagen IV and Laminin, both with key functions during embryogenesis, anticipated an essential role for Ndg on morphogenesis linking the Laminin and Collagen IV networks. This was supported by results from in vitro and cultured embryonic tissues experiments. However, the fact that elimination of Ndg in C. elegans and mice did not affect survival, strongly questioned this proposed linking role. Here, we have isolated mutations in the only Ndg gene present in Drosophila. We find that while, similar to C.elegans and mice, Ndg is not essential for overall organogenesis or viability, it is required for appropriate fertility. We also find, alike in mice, tissue-specific requirements of Ndg for proper assembly and maintenance of certain BMs, namely those of the adipose tissue and flight muscles. In addition, we have performed a thorough functional analysis of the different Ndg domains in vivo. Our results support an essential requirement of the G3 domain for Ndg function and unravel a new key role for the Rod domain in regulating Ndg incorporation into BMs. Furthermore, uncoupling of the Laminin and Collagen IV networks is clearly observed in the larval adipose tissue in the absence of Ndg, indeed supporting a linking role. In light of our findings, we propose that BM assembly and/or maintenance is tissue-specific, which could explain the diverse requirements of a ubiquitous conserved BM component like Nidogen.\n\nAuthor SummaryBasement membranes (BMs) are thin layers of specialized extracellular matrices present in every tissue of the human body. Its main constituents are two networks of Laminin and Type IV Collagen linked by Nidogen (Ndg) and proteoglycans. They form an organized scaffold that regulates organ morphogenesis and function. Mutations affecting BM components are associated with organ dysfunction and several congenital diseases. Thus, a better comprehension of BM assembly and maintenance will not only help to learn more about organogenesis but also to a better understanding and, hopefully, treatment of these diseases. Here, we have used Drosophila to analyse the role of Ndg in BM formation in vivo. Elimination of Ndg in worms and mice does not affect survival, strongly questioning its proposed linking role, derived from in vitro experiments. Here, we show that in the fly Ndg is dispensable for BM assembly and preservation in many tissues, but absolutely required in others. Furthermore, our functional study of the different Ndg domains challenges the significance of some interactions between BM components derived from in vitro experiments, while confirming others, and reveals a new key requirement for the Rod domain in Ndg function and incorporation into BMs.

developmental biology↗

bioRxiv2018

Cell type identity determines transcriptomic immune responses in Arabidopsis thaliana roots.

Root pathogens are a major threat in global crop production and protection strategies are required to sustainably enhance the efficiency of root immunity. Our understanding of root immunity is still limited relative to our knowledge of immune responses in leaves. In an effort to reveal the organisation of immunity in roots, we undertook a cell type-specific transcriptome analysis to identify gene networks activated in epidermis, cortex and pericycle cells of Arabidopsis roots upon treatment with two immunity elicitors, the bacterial microbe-associated molecular pattern flagellin, and the endogenous damage-associated molecular pattern Pep1. Our analyses revealed that both elicitors induced immunity gene networks in a cell type-specific manner. Interestingly, both elicitors did not alter cell identity-determining gene networks. Using sophisticated paired motif promoter analyses, we identified key transcription factor pairs involved in the regulation of cell type-specific immunity networks. In addition, our data show that cell identity networks integrate with cell immunity networks to activate cell type-specific immune response according to the functional capabilities of each cell type.\n\nMaterial Distribution FootnoteThe author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Patrick Schafer (p.schafer@warwick.ac.uk).

plant biology↗