Biology subjects

Serrano, A.

Publications and source records attributed to Serrano, A..

18 recordsLinked to original sources

bioRxiv2026

Pseudocryptic diversity within the Phakellia robusta species complex: description of Phakellia pallida sp. nov. and Phakellia pusilla sp. nov.

The genus Phakellia comprises predominantly fan-shaped deep-sea sponges, but its species diversity and boundaries remain unresolved. Here, we use an integrative approach combining morphological and molecular data to investigate the Phakellia robusta species complex and describe two new species, Phakellia pallida sp. nov. and Phakellia pusilla sp. nov. Overlap in external and spicular morphology makes these taxa challenging to identify. Molecular analyses based on mitochondrial (cox1) and nuclear (28S) markers support the recognition of the three taxa as distinct species, and reveal their close evolutionary relationship. The two new species co-occur in the NE Atlantic Ocean and the Mediterranean Sea, with overlapping depth ranges, although P. pallida sp. nov. is generally found at greater depths. Our results also suggest that several previous records of P. robusta from the Mediterranean and southern parts of the NE Atlantic may instead correspond to either P. pallida sp. nov. or P. pusilla sp. nov., indicating that its distribution requires reassessment. In addition, a group I intron previously reported in the cox1 gene of P. robusta was polymorphically detected at the same insertion site in some, but not all, individuals of P. pusilla sp. nov., but it was absent from P. pallida sp. nov. individuals. Overall, our results reveal pseudocryptic diversity within Phakellia and highlight the value of integrative approaches for resolving species boundaries and reassessing deep-sea sponge diversity and distributions.

zoology↗

bioRxiv2026

Seven amino acids gate transcriptional activation by a minimal MarA Helix turn-helix DNA-binding domain

Prokaryotic transcription factors (TFs) lie at the core of antimicrobial resistance, controlling genes that let bacteria survive antibiotic exposure. The AraC/XylS family of TFs is defined by a ~99-residue DNA-binding domain composed of two helix-turn-helix (HTH) motifs. While this two-motif architecture is considered the minimal functional unit, the striking sequence and structural similarity between both HTH motifs raises the question of whether it evolved from a single ancestral HTH domain. Here, we designed two C-terminal truncations of MarA, comprising a single HTH motif, differing by seven-residues (IRSRKMT). Electrophoretic-mobility shift assays reveal that both constructs specifically bind the marbox sequence as reconstituted dimers, while size-exclusion chromatography shows they exist in a monomer-dimer equilibrium in solution. Despite retaining DNA-binding capacity, the truncations diverge functionally: while MarA64 (including IRSRKMT) activates transcription and confers regular erythromycin tolerance, MarA57 (lacking IRSRKMT) yields a transcriptionally inactive complex that suppresses reporter expression below baseline, suggesting competitive promoter occupancy. Molecular dynamics simulations and AlphaFold models suggest that the IRSRKMT extension forms an -helical element stabilizing a transcriptionally productive dimer interface. Conversely, its loss disrupts quaternary assembly, alters DNA bending, and misaligns RNA polymerase-contacting residues. Furthermore, free dimers explore non-productive conformations, suggesting that functional dimerization occurs upon DNA engagement. These findings establish that a single, correctly dimerized HTH domain is sufficient for both DNA binding and transcriptional activation, providing a structural rationale for short AraC/XylS-like proteins and offering a tuneable scaffold for synthetic biology and novel anti-virulence strategies.

molecular biology↗

bioRxiv2026

DLL3 expression predicts response and long-term outcome in small cell lung cancer patients treated with tarlatamab

Background: Small cell lung cancer (SCLC) is an aggressive, high-grade neuroendocrine carcinoma (hgNEC) with poor prognosis. Tarlatamab, a DLL3-targeting T cell engager was approved in 2024 for relapsed SCLC, with almost doubled overall survival benefit compared to chemotherapy. However, over half of patients do not respond to tarlatamab and others develop resistance within months. With multiple DLL3-targeting therapies in clinical trials, there are currently no validated predictive biomarkers to identify patients most likely to benefit from tarlatamab. In this study, we evaluate baseline DLL3 IHC level in patients as a predictive biomarker to tarlatamab clinical outcome. Methods: We assembled a cohort of 138 patients within IRB-approved MD Anderson GEMINI database (PA13-0589) with DLL3 expression by CLIA-validated immunohistochemistry (IHC), and those treated with tarlatamab from 7/1/2024 to 3/30/2026. Only those with DLL3 IHC results and treated with tarlatamab were included in this predictive biomarker study. All DLL3 levels were reported as percentage cells with cytoplasmic or surface DLL3 expression, including 24 with additional intensity score and H-score calculation. demographic, clinical, and outcome data were collected. Systemic and intracranial response data were assessed by RECIST and mRANO BM criteria respectively. Longitudinal liquid biopsies were taken from a subset of patients for circulating tumor DNA (ctDNA) and (Cytometry by Time-of-Flight) CyTOF analyses. Results: In the predictive biomarker cohort of 54 patients with SCLC treated with tarlatamab, Median DLL3% level in tarlatamab treated cohort was 75%. Median follow-up time was 9.9 months, median time on tarlatamab treatment (ToT) was 5.8 months. At the data cut-off, 61% (33 out of 54) patients were alive. Kaplan-Meier curve stratified by DLL3 % of <=75% vs. >75 showed significant longer ToT and a trend toward longer median OS (mOS). In DLL3>75% compared to DLL3 <=75%: mToT was 10.1 months vs. 2.9 months (p=0.036), mOS: not reached vs. 9.5 months (p= 0.066). Among 41 patients who completed one cycle of tarlatamab treatment and were eligible for systemic (extra-cranial) response per RECIST criteria; we observed partial response (PR) in 51% (21) patients, stable disease (SD) in 22% (9) patients; and progressive disease (PD) in 27% (11) patients. The median DLL3 % in those with PR vs. PD were 80% vs. 40% (p=0.006); median DLL3% comparing PR and SD were 80% vs. 60% (p=0.051). Among 35 patients evaluable for intracranial response, best objective response prior to any brain radiation were 5 (14%) CR,11(31%) PR, 8 (23%) SD and 11 (31%) PD. 9 received brain radiation (8 SRS, 1 WBRT) during tarlatamab to achieve better intracranial control while systemic control is maintained. DLL3% does not appear to be correlated with intracranial response. Longitudinal ctDNA and CyTOF analyses showed persistent ctDNA positivity, as well as increasing NEUROD1 subtype cells in circulating tumor cells in post-tarlatamab progression samples. We additionally profiled DLL3 expression by IHC in 138 patients with SCLC and found heterogenous DLL3 expression, with Median DLL3% of 70% across different biopsy sites. Conclusions: Our data suggests DLL3 expression in patients with SCLC is heterogeneous and not ubiquitous, with median DLL3 IHC of 70%. DLL3 IHC predicts objective response and long-term outcome with tarlatamab. In addition, dynamic monitoring of ctDNA level and CTCs by CyTOF are suggestive of development of tarlatamab resistance, however further studies with larger cohort of paired longitudinal samples are needed to validate the novel blood-based biomarkers. To our knowledge, this study is the first to validate DLL3 IHC as a predictive biomarker for tarlatamab in SCLC, which leads the way for optimizing treatment selection and combinatorial therapies for the subset of patients less likely to respond to tarlatamab.

cancer biology↗

bioRxiv2026

A modular generalist-specialist AI framework for ROI selection across spatial profiling workflow

Selection of regions of interest (ROIs) is often a crucial step in spatial molecular profiling and many pathology tasks, with substantial implications for research reproducibility and biological interpretability. To provide a reproducible and adaptive framework for AI-guided ROI selection, we developed a modular generalist-specialist solution across spatial profiling platforms. In a cohort comprising 55 tumor types from 160 tissue donors profiled using NanoString Digital Spatial Profiling and multiplex immunofluorescence, we first established a protein-profiling reference atlas capturing compartment-specific immune, checkpoint, stromal, and proliferation patterns. We then developed an AI Specialist Task-Oriented Model for ROI Selection (ASTROS) and tested comprehensive benchmarks considering specialist-only (ASTROS), generalist-only (PLIP/GFM), and hybrid generalist-specialist strategies, showing that the latter provides a balanced tradeoff across slide-level signal preservation, pathologist-reference concordance, within-slide placement consistency, and large-slide computational efficiency. We further demonstrated the feasibility of virtual staining for ROI preview and modular ROI placement for other spatial omics technologies, Visium and Visium HD workflows. Together, these results support our proposed framework to enable ROI selection responding to unmet needs for reducing inter-rater variability, reproducibility, and versatility in spatial profiling experiments.

pathology↗

bioRxiv2026

A new mechanism of regulation of LIM kinases, LIMK1 and LIMK2, modulates their activity on cofilin and actin filament remodelling

LIM kinases, LIMK1 and LIMK2, play a crucial role in cytoskeleton dynamics. They are involved in many physiological processes but also in several pathologies such as cancer, neuronal diseases and neurofibromatosis. Although LIM kinases appear as promising therapeutic targets, they remain undruggable. A better understanding of their activity and regulation is thus required to better design efficient targeted therapies. Here, we have shown the impact of a single amino acid on LIMK activity on cofilin, their main substrate in actin filament remodelling. We demonstrated that Y632 and Y630, for LIMK1 and LIMK2 respectively, mediate LIMK dimerization, resulting in their transphosphorylation. This process seems to be a prerequisite for their canonical phosphorylation on their respective T508 and T505 residues within the activation loop. These Tyrosine are not phosphorylated, their aromatic nature is rather critical to ensure proper LIMK activity on cofilin. These results bring new insights into LIMK molecular features.

Molecular Biology↗

bioRxiv2025

Tolerance to the antifungal drug fluconazole is mediated by tuning cytoplasmic fluidity

Treatment failure rates for fungal infections cannot be explained simply by increased rates of drug resistance. Antifungal drug tolerance, the ability of a susceptible isolate to grow in the presence of inhibitory drug concentrations, relies upon a broad set of stress response pathways and can contribute to antifungal drug treatment failures. As the physical properties of the cytoplasm are critical for diverse cellular processes, we investigated whether cytoplasmic mesoscale fluidity is linked to antifungal tolerance, taking advantage of a fluorescent microrheological probe. Here, we show either using fluconazole, a common drug that inhibits ergosterol biosynthesis, or mutants in the ergosterol biosynthesis pathway, that cytoplasmic fluidity decreased and could be reversed upon drug removal. Reducing ribosome concentration decreased drug tolerance and restored cytoplasmic fluidity, highlighting a link between tolerance and cytoplasmic crowding and/or viscosity. However, growth in fluconazole did not increase ribosome concentrations; rather growth in fluconazole increased the number of dormant, hibernating ribosomes, cytoplasmic protein concentration, viscosity and condensate formation. Specifically, growth in fluconazole resulted in a substantial increase in processing bodies (P-bodies), whose presence correlated with azole tolerance. Furthermore, we found a substantial increase in cell-cell heterogeneity in all biophysical, biochemical and molecular outputs analyzed. Together, our results reveal that changes in the physical properties of the cytoplasm occur in response to antifungal drug and suggest that these changes, as well as increased cell-cell heterogeneity, are crucial for survival in fungistatic drugs.

microbiology↗

bioRxiv2025

Uncoupling of nutrient sensing and cell size control by specific defects in ceramide structure

Ceramides are essential structural lipids whose chemical diversity arises from variations in acyl-chain length and sphingoid base modifications, yet how these structural features couple metabolic state to growth regulation remains unclear. In Saccharomyces cerevisiae, the TORC2-Ypk1/2 signaling axis coordinates plasma membrane homeostasis with cellular growth; however, the precise lipid-derived signals that modulate this pathway remain incompletely characterized. Here, we establish that the structural integrity of very-long-chain fatty acid (VLCFA)-containing ceramides is a critical determinant of nutrient-dependent cell size modulation and TORC2 activity. Disruption of VLCFA elongation elevates Ypk1/2 pT662, consistent with increased TORC2 output, in both nutrient conditions. We further discovered that yeast mutants in VLCFA elongation (elo3{Delta}), fail to modulate their cell size in response to nutrient deprivation. To separate VLCFA elongation from ceramide production, we expressed mammalian ceramide synthases with defined acyl-chain preferences. Ceramides with C24-C26 chains (CerS3) supported near-normal nutrient-dependent size modulation, whereas production of C22-C24 ceramides (CerS2) phenocopied elongation mutants, leading to hyperactive TORC2 signaling and defective size regulation. Remarkably, cells producing C18 ceramides retained size control despite elevated TORC2 activity, revealing that basal signaling and size regulation can be uncoupled. Furthermore, we identify a distinct role for hydroxylation. While sur2{Delta} mutants exhibited size regulation defects resembling elongation mutants, they retained normal nutrient-responsive TORC2 signaling. Conversely, scs7{Delta} mutants maintained normal size regulation but displayed reduced basal TORC2 activity. This striking uncoupling suggests that while the TORC2 pathway senses acyl chain length, sphingoid base hydroxylation is biophysically required downstream for the execution of cell size remodeling. Our findings demonstrate that distinct structural features of ceramides differentially regulate nutrient sensing, signaling intensity, and the mechanical execution of cell size control.

cell biology↗

bioRxiv2025

YAP1 defines an emergent, plastic population of relapsed small cell lung cancer

Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy characterized by rapid onset of chemoresistance and poor clinical outcomes. Transcriptional heterogeneity among treatment-naive SCLC tumors underlies four transcriptional subtypes, each with distinct clinical vulnerabilities. Though previously hypothesized to delineate a distinct subtype, expression of YAP1 is largely absent from treatment-naive, pure SCLC. To characterize relapsed SCLC, circulating tumor DNA, circulating tumor cells, and core needle biopsies from SCLC patients and preclinical models following resistance to standard-of-care therapies were analyzed. In contrast to treatment-naive SCLC, these analyses reveal an emergent YAP1-positive cell population that coincides with treatment resistance. These YAP1-positive cells exhibit characteristics of drug tolerant persister cells, including senescence, stemness, and plasticity, as YAP1 positive cells largely abandon features characteristic of SCLC to adopt those of large-cell neuroendocrine carcinoma (LCNEC). As a result of this SCLC-like to LCNEC-like evolution, YAP1-positive cells lack several clinically relevant SCLC surface targets (i.e., DLL3, SEZ6), but are enriched for others (i.e., B7-H3, TROP2). We propose a model where YAP1 expressing cells emerge with SCLC treatment resistance and characterize a tenacious subpopulation capable of diverging from the treatment naive lineage and adopting features to evade therapeutic response.

cancer biology↗

bioRxiv2025

Genetic barcoding uncovers the clonal makeup of solid and liquid biopsies

Intra-tumoral heterogeneity (ITH) is fueling tumor progression in breast cancer, as specific clones present within a tumor may have a selective advantage to colonize distant organs and escape therapy. Accurate sampling of ITH is therefore a pressing challenge in clinical oncology, to adequately predict recurrence and inform rational and personalized therapies. Here we used cellular barcoding to track the spatio-temporal composition of human breast cancer clones in six preclinical models - across two cell lines and four patient derived xenografts (PDXs). This allowed direct side-by-side quantitative comparison not only of intra-tumor clonal composition, but also of how that composition was reflected in needle biopsies and cell-free DNA (cfDNA). These analyses highlighted several clinically relevant findings. First, the use of orthogonal genetic and optical barcoding revealed that clonal diversity in the center of non-necrotic primary tumors was significantly higher compared to their periphery. Second, cfDNA barcode analysis suggested that DNA shedding in the vasculature varied largely, not only depending on necrosis and tumor burden, but also between models. Third, combining information captured in both solid and liquid biopsies can provide a more robust assessment of tumor clonal composition. Taken together, these results showcases the utility of these barcoded models to optimize the use of solid and liquid biopsies as surrogate markers of ITH.

cancer biology↗

bioRxiv2025

CertPrime: a new oligonucleotide design tool for gene synthesis

The design of oligonucleotides with uniform hybridisation temperatures is essential for successful gene synthesis. However, current computational tools for oligonucleotide design face significant limitations, including difficulties in processing long DNA sequences, poor adaptability to specific experimen- tal conditions, limited control over oligonucleotide length, and challenges in minimising spurious dimer formation. To address these issues, we devel- oped CertPrime, an innovative tool designed for scalable and efficient han- dling of long DNA sequences. CertPrime enables precise customisation of experimental parameters, provides flexibility to limit the maximum oligonu- cleotide length, and generates designs with reduced deviations in melting temperatures across overlapping regions compared to existing tools. We experimentally compared CertPrime designs with benchmark design meth- ods for a complex DNA sequence and found that CertPrime design led to more efficient gene assembly, significantly reducing the occurrence of non- specific bands. These results make CertPrime a powerful and versatile tool for oligonucleotide design in gene synthesis applications. HighlightsO_LICertPrime improves oligonucleotide design by minimising melting-temperature deviations and spurious dimer formation. C_LIO_LIThe new tool enhances gene-synthesis efficiency, allowing a precise con- trol over oligonucleotide lengths and experimental parameters. C_LIO_LICertprime is a scalable tool capable of designing over 99% of the human genome with optimized sequence assembly C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/650686v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@2032aaorg.highwire.dtl.DTLVardef@1de509borg.highwire.dtl.DTLVardef@7e2148org.highwire.dtl.DTLVardef@bb3dd2_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Cullin-RING ligase BioE3 reveals molecular-glue-induced neosubstrates and rewiring of the endogenous Cereblon ubiquitome

BackgroundThe specificity of the ubiquitination process is mediated by the E3 ligases. Discriminating genuine substrates of E3s from mere interacting proteins is one of the major challenges in the field. We previously developed BioE3, a biotin-based approach that uses BirA-E3 fusions together with ubiquitin fused to a low-affinity AviTag to obtain a site-specific and proximity-dependent biotinylation of the substrates. We proved the suitability of BioE3 to identify targets of RING and HECT-type E3 ligases. MethodsBioE3 experiments were performed in HEK293FT and U2OS stable cell lines expressing TRIPZ-bioGEFUb transiently transfected with BirA-cereblon (CRBN). Cells were seeded using biotin-free media, adding a short-biotin pulse. We evaluated the applicability of the BioE3 system to CRBN and molecular glues by western blot and confocal microscopy, blocking the proteasome with bortezomib, inhibiting NEDDylation with MLN4924 and treating the cells with pomalidomide. For the identification of endogenous substrates and neosubstrates we analyzed the eluates of streptavidin pull-downs of BioE3 experiments by LC-MS/MS. Analysis of targets which ubiquitination changes significantly upon treatment was done using two-sided Students t-test. Orthogonal validations were performed by histidine pull-down, GFP-trap and computational modelling. ResultsHere we demonstrate that BioE3 is suitable for the multi-protein complex Cullin-RING E3s ligases (CRLs), the most utilized by targeted protein degradation strategies. Choosing CRBN as proof of concept, one of the substrate receptors of CRL4 E3 ligase, we identified both endogenous substrates and novel neosubstrates upon pomalidomide treatment, including CSDE1 which contains a G-loop motif potentially involved in the binding to CRBN in presence of pomalidomide. Importantly, we observed a major rearrangement of the endogenous ubiquitination landscape upon treatment with this molecular glue. ConclusionsThe ability of BioE3 to detect and compare both substrates and neosubstrates, as well as how substrates change in response to treatments, will facilitate both target and off-target identifications and offer a broader characterization and validation of targeted protein degradation degraders, like molecular glues and PROTACs.

cell biology↗

bioRxiv2024

Comparison of imaging-based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed, paraffin-embedded tumor samples

Imaging-based spatial transcriptomics (ST) is evolving rapidly as a pivotal technology in studying the biology of tumors and their associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. In this study, we used serial 5-m sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma tumor samples in tissue microarrays to compare the performance of the single cell ST platforms CosMx, MERFISH, and Xenium (uni/multi-modal) platforms in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx Digital Spatial Profiler, and hematoxylin and eosin staining data for the same samples. In addition to objective assessment of automatic cell segmentation and phenotyping, we performed pixel-resolution manual evaluation of phenotyping to carry out pathologically meaningful comparison between ST platforms. Our study detailed the intricate differences between the ST platforms, revealed the importance of parameters such as tissue age and probe design in determining the data quality, and suggested reliable workflows for accurate spatial profiling and molecular discovery.

bioinformatics↗

bioRxiv2024

Dynamic cytoplasmic fluidity during morphogenesis in a human fungal pathogen

The molecular crowding of the cytoplasm impacts a range of cellular processes. Using a fluorescent microrheological probe (GEMs), we observed a striking decrease in molecular crowding during the yeast to filamentous growth transition in the human fungal pathogen Candida albicans. This decrease in crowding is due to a decrease in ribosome concentration that results in part from an inhibition of ribosome biogenesis, combined with an increase in cytoplasmic volume; leading to a dilution of the major cytoplasmic crowder. Moreover, our results suggest that inhibition of ribosome biogenesis is a trigger for C. albicans morphogenesis.

cell biology↗

bioRxiv2023

A live-cell ergosterol reporter for visualization of the effects of fluconazole on a human fungal pathogen

Ergosterol, an essential plasma membrane amphipathic lipid, is a major component of the fungal plasma membrane. Most fungal pathogens are sensitive to azole drugs that target ergosterol biosynthesis and resistance/tolerance to azoles is increasingly problematic. Candida albicans is the most prevalent etiology of candidiasis and, in this fungal pathogen, ergosterol rich sub-domains are likely to include sphingolipids, as well as specific membrane proteins, such as multidrug transporters. To investigate the dynamics of ergosterol during the cell cycle and whether drug treatment affects these dynamics in this opportunistic pathogen, we adapted the D4H (domain 4 of the perfringolysin O bacterial toxin) reporter for studying sterol-rich membrane domains. We show that D4H provides a direct readout for the cellular effects of fluconazole and that highly polarized ergosterol is not critical for budding or filamentous growth.

microbiology↗

bioRxiv2022

Cytosolic pH controls fungal MAPK signaling and pathogenicity

In fungi, ambient pH acts as a key regulator of development and virulence. The vascular wilt pathogen Fusarium oxysporum uses host alkalinization to promote infection of plant hosts through activation of the invasive growth mitogen-activated protein kinase (MAPK) Fmk1. The molecular events underlying pH-driven MAPK regulation are unknown. Using the ratiometric GFP-based pH sensor pHluorin, we find that both F. oxysporum and Saccharomyces cerevisiae respond to extracellular alkalinization or acidification with a transitory shift in cytosolic pH (pHc) and rapid changes in phosphorylation levels of the three fungal MAPKs Fmk1, Mpk1/Slt2 (cell wall integrity) and Hog1 (hyperosmotic stress). Pharmacological inhibition of the essential plasma membrane H+-ATPase Pma1, which leads to pHc acidification, is sufficient to trigger reprogramming of MAPK phosphorylation even in the absence of an extracellular pH shift. Screening of a subset of S. cerevisiae mutants identified the sphingolipid-regulated AGC kinase Ypk1/2 as a key upstream component of pHc-modulated MAPK responses. We further show that acidification of pHc in F. oxysporum leads to an increase of the long chain base (LCB) sphingolipid dihydrosphingosine (dhSph) and that exogenous addition of dhSph activates Mpk1 phosphorylation. Our results reveal a pivotal role of pHc in the regulation of MAPK signaling and suggest new ways to control fungal growth and pathogenicity.

microbiology↗

bioRxiv2020

The Cell Wall Integrity MAPK pathway controls actin cytoskeleton assembly during fungal somatic cell fusion.

Somatic cell fusion in Neurospora crassa depends on two MAP kinases, MAK-1 and MAK-2, but their precise contributions to directed growth have remained unclear. Using analog-sensitive alleles and live-cell imaging, we found that MAK-1 activity is required for RAC-1 activation and polarized actin assembly, while MAK-2 controls the positioning of RAC-1 and actin at the fusion tips. Inhibition of MAK-1 disrupted cell communication, prevented actin focus formation, and blocked membrane recruitment of MAK-2 and SO. In contrast, MAK-2 inhibition caused SO and actin to shift to alternative cortical sites, showing that MAK-2 regulates their spatial orientation rather than activation. Actin disruption with latrunculin A eliminated MAK-2 and SO recruitment, confirming its essential role in their localization. Importantly, MAK-1 controlled actin polymerization only during tropic growth, not during general hyphal extension, and acted upstream of RAC-1. These findings establish complementary roles for MAK-1 and MAK-2 in directing RAC-1-dependent actin dynamics during fungal cell fusion. Summary statementMAK-1 activates the Rho GTPase RAC-1 to drive actin polymerization, while MAK-2 orients this RAC-1/actin complex toward the fusion partner, defining complementary MAPK roles in somatic cell fusion.

cell biology↗

bioRxiv2020

Magnetosomes could be protective shields againstmetal stress in magnetotactic bacteria

Magnetotactic bacteria are aquatic microorganisms with the ability to biomineralise membrane-enclosed magnetic nanoparticles, called magnetosomes. These magnetosomes are arranged into a chain that behaves as a magnetic compass, allowing the bacteria to align in and navigate along the Earths magnetic field lines. According to the magneto-aerotactic hypothesis, the purpose of producing magnetosomes is to provide the bacteria with a more efficient movement within the stratified water column, in search of the optimal positions that satisfy their nutritional requirements. However, magnetosomes could have other physiological roles, as proposed in this work. Here we analyse the role of magnetosomes in the tolerance of Magnetospirillum gryphiswaldense MSR-1 to transition metals (Co, Mn, Ni, Zn, Cu). By exposing bacterial populations with and without magnetosomes to increasing concentrations of metals in the growth medium, we observe that the tolerance is significantly higher when bacteria have magnetosomes. The resistance mechanisms triggered in magnetosome-bearing bacteria under metal stress have been investigated by means of x-ray absorption near edge spectroscopy (XANES). XANES experiments were performed both on magnetosomes isolated from the bacteria and on the whole bacteria, aimed to assess whether bacteria use magnetosomes as metal storages, or whether they incorporate the excess metal in other cell compartments. Our findings reveal that the tolerance mechanisms are metal-specific: Mn, Zn and Cu are incorporated in both the magnetosomes and other cell compartments; Co is only incorporated in the magnetosomes, and Ni is incorporated in other cell compartments. In the case of Co, Zn and Mn, the metal is integrated in the magnetosome magnetite mineral core.

microbiology↗

bioRxiv2018

Seidr: A toolkit for calculation of crowd networks

Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and dataset dependent biases of published methods. Furthermore, it has been shown that aggregating networks from multiple methods provides improved results. Despite this, few usable and scalable software tools have been implemented to perform such best-practice analyses. Here, we present Seidr (stylized Seithr), a software toolkit designed to assist scientists in gene regulatory and gene co-expression network inference. Seidr creates community networks to reduce algorithmic bias and utilizes noise corrected network backboning to prune noisy edges in the networks. Using benchmarks in real-world conditions across three eukaryotic model organisms, Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana, we show that individual algorithms are biased toward functional evidence for certain gene-gene interactions. We further demonstrate that the community network is less biased, providing robust performance across different standards and comparisons for the model organisms. Finally, we apply Seidr to a network of drought stress in Norway spruce (Picea abies (L.) H. Krast) as an example application in a non-model species. We demonstrate the use of a network inferred using Seidr for identifying key components, communities and suggesting gene function for non-annotated genes.

bioinformatics↗