Biology subjects

Mueller, B.

Publications and source records attributed to Mueller, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Developing a fluorescent derivative of GagPol as a tool for live-cell imaging of HIV-1 assembly

The HIV-1 assembly process is driven by the structural polyprotein Gag, which forms small cytosolic oligomers that traffic to the plasma membrane. While Gag alone is sufficient to drive particle formation, the incorporation of GagPol, a polyprotein comprising Gag and viral enzymes, is essential for productive infection. Maintenance of the proper Gag:GagPol ratio is crucial for virion infectivity. Yet, the mechanisms regulating their cytosolic interactions remain incompletely understood, in part because most studies rely on ensemble biochemical assays that hide cell-to-cell heterogeneity and lack spatial and temporal resolution. To overcome these limitations and investigate the dynamics of GagPol at the molecule level, we systematically tested different approaches to fluorescently label it. We successfully produced two functional fluorescent GagPol variants: one single-labeled GagPol, and a second double-labeled variant with a fluorescent protein added within Gag, that allows concurrent visualization of Gag and GagPol. These labeled versions, in combination with the use of raster image (cross-) correlation spectroscopy, enabled the quantification of Gag and GagPol relative concentrations and intermolecular interactions at the single-cell level. Overall, these variants set the stage for in-depth investigations of GagPol during HIV assembly providing insights into cytoplasmic trafficking, particle assembly, and the kinetics of these processes. ImportanceThe participation of Gag and GagPol in HIV-1 assembly is central to the generation of infectious virions. While the structural role of Gag and the enzymatic functions of GagPol are well described, little is known regarding the mechanisms underlying their cytosolic interactions, spatial organization, and relative incorporation into assembling particles. Here, we successfully developed two stable fluorescently labeled variants of GagPol; a single labeled variant with a label in the Pol domain and double-labeled construct in which the Gag domain is also tagged. Using these constructs, we can quantitatively investigate Gag and GagPol interactions on the single-cell level. Hence, they provide a framework for a comprehensive study of the oligomerization properties and trafficking of these polyproteins at different stages of HIV-1 assembly, including membrane recruitment and incorporation into nascent virions.

biophysics↗

bioRxiv2026

Mitochondrial COX4I2 drives pericyte-dependent inflammation and emphysema

Chronic obstructive pulmonary disease (COPD) is characterized by neutrophilic inflammation, emphysema, and mild pulmonary hypertension (PH). Oxidative/nitrosative stress are key drivers, but specific mitochondrial mechanisms remain unclear. We show increased expression of the regulatory mitochondrial cytochrome c oxidase subunit 4 isoform 2 (COX4I2) in an early murine model and human COPD. After 8 months of cigarette smoke exposure, Cox4i2-/- mice were completely protected from emphysema but not from PH, associated with reduced nitrosative stress, inflammation, and apoptosis. Using a novel Cox4i2 reporter mouse and in situ hybridization of human lungs, COX4I2 was detected in precapillary ACTA2+ cells and capillary pericytes. COX4I2 promotes mitochondrial reactive oxygen species (mtROS) production in these cells, thereby enhancing neutrophil migration and alveolar type II cell apoptosis, and modulates angiogenesis. In contrast to Cox4i2-/-, mitochondria-targeted antioxidant MitoQ reversed emphysema and PH, suggesting pericyte-specific regulation of COPD pathologies and mtROS inhibition as a therapeutic approach in COPD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/703513v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@83bca4org.highwire.dtl.DTLVardef@d5ebaborg.highwire.dtl.DTLVardef@632d1borg.highwire.dtl.DTLVardef@1267a13_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Phylum-wide propionate degradation and its potential connection to poly- γ-glutamate biosynthesis in Candidatus Cloacimonadota

The candidate phylum Cloacimonadota is frequently detected in anaerobic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood due to the lack of cultured representatives. Metagenomic evidence suggests capacities for amino acid fermentation, cellulose degradation, and production of carbohydrate-active enzymes, with particular interest in their presumed role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from a lab-scale anaerobic baffled reactor fed with sugar beet pulp, where a sharp increase in an uncultured Cloacimonadota OTU coincided with recovery of methanogenesis and enhanced methane production. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of this OTU, complemented by a curated database of 47 genome-resolved Cloacimonadota species. Comparative genomics revealed conserved protein clusters indicative of an alternative mmc pathway, suggesting that this variant of the SPO pathway is a widespread, phylum-specific trait potentially linked to protein degradation and poly-{gamma}-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a primary syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.

microbiology↗

bioRxiv2025

Neuroanatomical Correlates of Negative Symptoms in Schizophrenia

BackgroundSchizophrenia is characterized by widespread structural brain abnormalities, but associations between structural abnormalities and negative symptom severity are not well understood. Negative symptoms have been conceptualized in a hierarchical structure of two second-order dimensions--motivation and pleasure (MAP) and expression (EXP)--and five first-order domains: anhedonia, avolition, and asociality (MAP), and blunted affect and alogia (EXP). A better understanding of the neural circuitry underlying negative symptom dimensions and domains is important given their reported association with poor functional outcome and lack of available treatments. Study DesignThe meta-analysis included 1,591 individuals with schizophrenia across 16 samples with structural imaging and Scale for Assessment of Negative Symptoms data. The study generated correlations of cortical thickness and subcortical volumes with the negative symptom dimensions and domains. Study resultsNegative symptoms showed mainly negative associations with cortical thickness and subcortical volumes. The effect sizes were small but there was a pattern of associations in predominantly frontal lobe cortical thickness and limbic subcortical volumes. The regional correlation patterns of cortical thickness and subcortical volumes with symptom domains support the conceptualized hierarchical structure of negative symptoms: correlations of MAP domains were stronger with the MAP than EXP dimension, and vice versa. Exploratory analyses with receptor densities further supported the hierarchy. ConclusionOur findings reveal small but consistent associations between negative symptom dimensions and predominantly prefrontal region cortical thickness, and limbic region volumes. These findings advance our understanding of the network of anatomical regions that may contribute to the severity of negative symptoms in schizophrenia.

neuroscience↗

bioRxiv2025

Skeletal muscle mitochondrial responses to a single bout and six weeks of high load versus high volume resistance training in previously trained men

The effects of higher-load (HL) versus higher-volume (HV) resistance training (RT) on various molecular outcomes are similar. However, mitochondrial responses remain understudied. Therefore, the purpose of this study was to interrogate mitochondrial mRNA and protein responses to acute and chronic HL versus HV RT. Vastus lateralis biopsies from resistance trained males in two prior studies were assessed. In STUDY 1, 11 college-aged men completed an acute bout of either HL or HV RT exercises to failure. Biopsies were collected at PRE, 3 hours post-, and 6 hours post-exercise. In STUDY 2, 15 college-aged men participated in six weeks of supervised unilateral RT where each leg was assigned to either HL or HV RT. Biopsies were collected from both legs prior to and 72 hours following last training bout of the intervention. Biopsies from both studies were used to assess mitochondrial mRNAs, and STUDY 2 biopsies were assayed for mitochondrial proteins and CS activity. Results from both studies revealed several significant main effects of time but no significant interactions. Additionally, CS activity, a surrogate of mitochondrial content, decreased following chronic RT (p=0.016) but no interaction was observed between the HV and HL leg over time (p=0.882). In conclusion, while RT resulted in both acute mitochondrial mRNA as well as chronic CS activity and mitochondrial protein responses, there were no differences in the HL versus HV paradigms on these outcomes.

physiology↗

bioRxiv2025

Lenacapavir-induced capsid damage exposes HIV-1 genomes from nuclear speckles.

Following cell entry, HIV-1 capsids enter the nucleus by passage through nuclear pores and reach nuclear speckles, where uncoating of the reverse-transcribed genome and integration occur. Here, we characterized the ultrastructure of HIV-1 subviral complexes in nuclei of primary monocyte-derived macrophages and cell lines using live-cell imaging, super-resolution microscopy and correlative light and electron tomography in the absence and presence of capsid-targeting inhibitors Lenacapavir and PF74. Capsid-like structures containing viral DNA as well as broken capsids clustered in nuclear speckles and were displaced from speckles by drug treatment. This was accompanied by alteration of the nuclear capsid structure, with electron-dense protrusions emanating from the narrow end of capsid cones and exposure of complete, or almost complete, genomic HIV-1 DNA. Our data indicate that synthesis of genomic dsDNA can be completed inside the closed HIV-1 capsid, and speckle-associated factors appear to be required to promote genome uncoating. This may ensure that genome uncoating occurs at optimal sites for integration into transcriptionally active chromatin. The results also shed further light on the mechanism of action of Lenacapavir.

microbiology↗

bioRxiv2025

Cap-adjacent 2'-O-ribose methylation of RNA in C. elegans is required for postembryonic growth and germline development in the presence of the decapping exonuclease EOL-1

Cap-adjacent 2-O-ribose methylation (cOMe) of the first two transcribed nucleotides of RNA polymerase II transcripts is a conserved feature in many eukaryotes. In mammals, these modifications are key to a transcript surveillance system that regulates the interferon response, but the broader functions of cOMe remain poorly understood. To understand the role of cOMe in C. elegans, we functionally characterised the methyltransferases (CMTR-1 and CMTR-2) responsible for installing these modifications. These enzymes have distinct expression patterns, protein interaction partners, and loss of function phenotypes. Loss of CMTR-1 causes dramatic reductions in cOMe, impaired growth and sterility. In contrast, animals lacking CMTR-2 are superficially wild-type, though CMTR-2 loss enhances the severity of the cmtr-1 mutant phenotype. Depletion of CMTR-1 causes downregulation of transcripts associated with germline sex determination and upregulation of those involved in the intracellular pathogen response (IPR). We show that absence of the decapping exonuclease, EOL-1, an IPR component, completely suppresses the sterility and growth defects caused of loss of CMTR-1, suggesting that EOL-1 degrades cellular transcripts lacking cOMe. Our work shows the physiological relevance of cOMe in protecting transcripts from decapping exonucleases, raising the possibility that cOMe plays a role in RNA-mediated immune surveillance beyond the vertebrates. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/638824v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1cd906dorg.highwire.dtl.DTLVardef@c4e922org.highwire.dtl.DTLVardef@1a5c2dborg.highwire.dtl.DTLVardef@19be5d8_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Combined cellular and proteomics approach suggest differential processing of native and foreign vibrios in the sponge Halichondria panicea

Phagocytosis is a conserved cellular mechanism for food uptake, defense and general animal-microbe interactions in metazoans. How the discrimination and subsequent processing of different microbes in marine invertebrates is facilitated remains largely unknown. Thereto, we combined a recently developed phagocytic assay with proteomics analysis to compare the phagocytic activity of the sponge Halichondria panicea upon encounter with a native (i.e., H. panicea isolate; Hal 281) and a foreign (i.e., Nematostella vectensis isolate; NJ 1) Vibrio. The sponge cell fraction was recovered after Vibrio exposure of 30 and 60 min and used for cellular (fluorescence-activated cell sorting and microscopy) and proteomics analyses. While the number of phagocytic active cells was similar between the isolates (p = 0.19), the distribution of vibrios over cell types differed (p = 0.02) with the tendency for a higher accumulation of foreign vibrios in small phagocytic cells than the native vibrios. Initially, both vibrios elicited a mitochondrial proteomic response (e.g., TBXASI, CASP7), whereas after 60 min differentially abundant proteins were dominated by lysosomal proteins (e.g., AGA, FUCA, SCARB2) in response to the native compared to immune-related proteins (e.g., AQP9, H2A, SAMHDI) in response to the foreign vibrio. H. panicea may discriminate native and foreign vibrios post-cellular internalization into choanocytes, followed by differential cellular and molecular processing: Native vibrios are readily transferred to archeocytes and elicit a digestive response, whereas foreign vibrios further accumulate before being transferred and provoke an immune response. These findings provide a mechanism for immune specificity in sponges. ImportanceMetazoans recognize and discriminate between native (i.e., associated and/or commonly encountered) and foreign microbes. In marine invertebrates, the mechanisms of microbial discrimination and immune specificity are not well understood. Phagocytosis is a conserved cellular process from amoeba to humans that facilitates the ingestion and digestion of microbial cells and likely plays a role in this discrimination. To elucidate the molecular and cellular basis of immune specificity in marine invertebrates, we examined the differential phagocytic processing of native and foreign Vibrio isolates in a marine sponge. Our findings revealed that both vibrios provoke a generalist mitochondrial protein-mediated response, while native vibrios trigger a digestive response, and foreign vibrios elicit an immune response after being internalized into sponge cells. This study uncovers a mechanism for immune specificity in an early-divergent metazoan and provides a valuable model for studying the evolution of immunity and its role in animal-microbe interactions.

cell biology↗

bioRxiv2024

The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation

HIV-1 particles are released in an immature, non-infectious form. Proteolytic cleavage of the main structural polyprotein Gag into functional domains induces rearrangement into mature, infectious virions. In immature virus particles, the Gag membrane binding domain, MA, forms a hexameric protein lattice that undergoes structural transition upon cleavage into a distinct, mature MA lattice. The mechanism of MA lattice maturation is unknown. Here we show that released spacer peptide 2 (SP2), a conserved peptide of unknown function situated [~]300 residues downstream of MA, binds MA to induce structural maturation. By high-resolution in-virus structure determination of MA, we show that MA does not bind lipid into a side pocket as previously thought, but instead binds SP2 as an integral part of the protein-protein interfaces that stabilise the mature lattice. Analysis of Gag cleavage site mutants showed that SP2 release is required for MA maturation, and we demonstrate that SP2 is sufficient to induce maturation of purified MA on lipid layers in vitro. SP2-triggered MA maturation correlated with faster fusion of virus with target cells. Our results reveal a new, unexpected interaction between two HIV-1 components, provide a high-resolution structure of mature MA, establish the trigger of MA structural maturation, and assign function to the SP2 peptide.

microbiology↗

bioRxiv2022

Natural rubber reduces herbivory and alters the microbiome below ground

O_LILaticifers are hypothesized to mediate both plant-herbivore and plant-microbe interactions. However, there is little evidence for the dual function of these secretory structures. C_LIO_LIWe investigated whether the major constituent of natural rubber, cis-1,4-polyisoprene, a phylogenetically widespread and economically important latex polymer, alters plant resistance and the root microbiome of the Russian dandelion (Taraxacum koksaghyz) under attack of a root herbivore, the larva of the May cockchafer (Melolontha melolontha). C_LIO_LIRubber-depleted transgenic plants lost more shoot and root biomass upon herbivory than normal rubber content near-isogenic lines. M. melolontha preferred to feed on artificial diet supplemented with rubber-depleted rather than normal rubber content latex. Likewise, adding purified cis-1,4-polyisoprene in ecologically relevant concentrations to diet deterred larval feeding and reduced larval weight gain. Metagenomics and metabarcoding revealed that abolishing biosynthesis of natural rubber alters the structure but not the diversity of the rhizosphere and root microbiota in a herbivore-dependent manner. Roots from rubber-depleted plants, however, did not exhibit a higher pathogen load compared to normal rubber content roots. C_LIO_LITaken together, our data demonstrate that natural rubber biosynthesis reduces herbivory and alters the plant microbiota in a herbivore-dependent manner, which highlights the role of plant specialized metabolites and secretory structures in shaping multitrophic interactions. C_LI

plant biology↗

bioRxiv2022

A Glass Phase Plate for Wavelength SensitiveSuperresolution Microscopy

Multicolor localization microscopy typically relies on sequential imaging and bandpass filters to distinguish fluorescent tags, which introduces temporal delays during live imaging, and decreases photon yield. By engineering the point-spread function (PSF), different fluors can be imaged simultaneously and distinguished by their unique patterns, without discarding photons. Here, we insert a silicon-dioxide phase plate at the Fourier plane of the detection path of a wide-field fluorescence microscope to produce distinguishable PSFs (X-PSFs) at different wavelengths. We demonstrate that the resulting PSFs can be localized spatially and spectrally using a statistics-based computational algorithm and can be utilized for hyper-spectral super-resolution microscopy of biological samples. Single PSFs in fixed U2OS cells were acquired using dSTORM with simultaneous illumination of fluors without emission filters. The modified PSF achieves [~]21 nm lateral localization precision (FWHM), [~]17 nm axial precision (FWHM) with an average of 1,800 - 3,500 photons per PSF and a background as high as 130 - 400 photons per pixel. The modified PSF can distinguish up to three fluorescent probes with [~]80 nm peak-to-peak separation between consecutive spectra.

biophysics↗

bioRxiv2022

Explicitly Nonlinear Dynamic Functional Network Connectivity In Resting-State fMRI Data

Most dynamic functional connectivity in fMRI data is focused on linear correlations, and to our knowledge, no study has studied whole brain explicitly nonlinear dynamic relationships within the data. While some approaches have attempted to study overall connectivity more generally using flexible models, we are particularly interested in whether the non-linear relationships, above and beyond linear, are capturing unique information. This study thus proposes an approach to assess the explicitly nonlinear dynamic functional network connectivity derived from the relationship among independent component analysis time courses. Linear relationships were removed at each time point to evaluate, typically ignored, explicitly nonlinear dFNC using normalized mutual information. Simulations showed the proposed method accurately estimated NMI over time, even within relatively short windows of data. Results on fMRI data included 151 schizophrenia patients, and 163 healthy controls showed three unique, highly structured, mostly long-range, functional states that also showed significant group differences. This analysis identifies a higher level of explicitly nonlinear dependencies in transient connectivity within the visual network in healthy controls compared to schizophrenia patients. In particular, nonlinear relationships tend to be more widespread than linear ones. We also find highly significant differences in the relative co-occurrence of linear and explicitly nonlinear states in HC and SZ, suggesting these may be an important aspect of the disorder. Overall, this work suggests that quantifying nonlinear dependencies of dynamic functional connectivity may provide a complementary and potentially valuable tool for studying brain function by exposing relevant variation that is typically ignored.

neuroscience↗

bioRxiv2021

Direct capsid labeling of infectious HIV-1 by genetic code expansion allows detection of largely complete nuclear capsids and suggests nuclear entry of HIV-1 complexes via common routes

The cone-shaped mature HIV-1 capsid is the main orchestrator of early viral replication. After cytosolic entry, it transports the viral replication complex along microtubules towards the nucleus. While it was initially believed that the reverse transcribed genome is released from the capsid in the cytosol, recent observations indicate that a high amount of capsid protein (CA) remains associated with subviral complexes during import through the nuclear pore complex (NPC). Observation of post-entry events via microscopic detection of HIV-1 CA is challenging, since epitope shielding limits immunodetection and the genetic fragility of CA hampers direct labeling approaches. Here, we present a minimally invasive strategy based on genetic code expansion and click chemistry that allows for site-directed fluorescent labeling of HIV-1 CA, while retaining virus morphology and infectivity. Thereby, we could directly visualize virions and subviral complexes using advanced microscopy, including nanoscopy and correlative imaging. Quantification of signal intensities of subviral complexes revealed an amount of CA associated with nuclear complexes in HeLa-derived cells and primary T cells consistent with a complete capsid and showed that treatment with the small molecule inhibitor PF74 did not result in capsid dissociation from nuclear complexes. Cone-shaped objects detected in the nucleus by electron tomography were clearly identified as capsid-derived structures by correlative microscopy. High-resolution imaging revealed dose-dependent clustering of nuclear capsids, suggesting that incoming particles may follow common entry routes.

microbiology↗

bioRxiv2021

Nonlinear Functional Network Connectivity In Resting fMRI Data

In this work, we focus on explicitly nonlinear relationships in functional networks. We introduce a technique using normalized mutual information (MI), that calculates the nonlinear correlation between different brain regions. We demonstrate our proposed approach using simulated data, then apply it to a dataset previously studied in (Damaraju et al., 2014). This resting-state fMRI data included 151 schizophrenia patients and 163 age- and gender-matched healthy controls. We first decomposed these data using group independent component analysis (ICA) and yielded 47 functionally relevant intrinsic connectivity networks. Our analysis showed a modularized nonlinear relationship among brain functional networks that was particularly noticeable in the sensory and visual cortex. Interestingly, the modularity appears both meaningful and distinct from that revealed by the linear approach. Group analysis identified significant differences in nonlinear dependencies between schizophrenia patients and healthy controls particularly in visual cortex, with controls showing more nonlinearity in most cases. Certain domains, including cognitive control, and default mode, appeared much less nonlinear, whereas links between the visual and other domains showed evidence of substantial nonlinear and modular properties. Overall, these results suggest that quantifying nonlinear dependencies of functional connectivity may provide a complementary and potentially important tool for studying brain function by exposing relevant variation that is typically ignored. Further, we propose a method that captures both linear and nonlinear effects in a boosted approach. This method increases the sensitivity to group differences in comparison to the standard linear approach, at the cost of being unable to separate linear and nonlinear effects.

neuroscience↗

bioRxiv2021

Multi-Spatial Scale Dynamic Interactions between Functional Sources Reveal Sex-Specific Changes in Schizophrenia

We introduce an extension of independent component analysis (ICA), called multiscale ICA (msICA), and design an approach to capture dynamic functional source interactions within and between multiple spatial scales. msICA estimates functional sources at multiple spatial scales without imposing direct constraints on the size of functional sources, overcomes the limitation of using fixed anatomical locations, and eliminates the need for model-order selection in ICA analysis. We leveraged this approach to study sex-specific and -common connectivity patterns in schizophrenia. Results show dynamic reconfiguration and interaction within and between multi-spatial scales. Sex-specific differences occur (1) within the subcortical domain, (2) between the somatomotor and cerebellum domains, and (3) between the temporal domain and several others, including the subcortical, visual, and default mode domains. Most of the sex-specific differences belong to between-spatial scale functional interactions and are associated with a dynamic state with strong functional interactions between the visual, somatomotor, and temporal domains and their anticorrelation patterns with the rest of the brain. We observed significant correlations between multi-spatial scale functional interactions and symptom scores, highlighting the importance of multiscale analyses to identify potential biomarkers for schizophrenia. As such, we recommend such analyses as an important option for future functional connectivity studies.

neuroscience↗

bioRxiv2020

SLIDR and SLOPPR: Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data

BackgroundSpliced leader (SL) trans-splicing replaces the 5 end of pre-mRNAs with the spliced leader, an exon derived from a specialised non-coding RNA originating from elsewhere in the genome. This process is essential for resolving polycistronic pre-mRNAs produced by eukaryotic operons into monocistronic transcripts. SL trans-splicing and operons may have independently evolved multiple times throughout Eukarya, yet our understanding of these phenomena is limited to only a few well-characterised organisms, most notably C. elegans and trypanosomes. The primary barrier to systematic discovery and characterisation of SL trans-splicing and operons is the lack of computational tools for exploiting the surge of transcriptomic and genomic resources for a wide range of eukaryotes. ResultsHere we present two novel pipelines that automate the discovery of SLs and the prediction of operons in eukaryotic genomes from RNA-Seq data. SLIDR assembles putative SLs from 5 read tails present after read alignment to a reference genome or transcriptome, which are then verified by interrogating corresponding SL RNA genes for sequence motifs expected in bona fide SL RNA molecules. SLOPPR identifies RNA-Seq reads that contain a given 5 SL sequence, quantifies genomewide SL trans-splicing events and predicts operons via distinct patterns of SL trans-splicing events across adjacent genes. We tested both pipelines with organisms known to carry out SL trans-splicing and organise their genes into operons, and demonstrate that 1) SLIDR correctly detects expected SLs and often discovers novel SL variants; 2) SLOPPR correctly identifies functionally specialised SLs, correctly predicts known operons and detects plausible novel operons. ConclusionsSLIDR and SLOPPR are flexible tools that will accelerate research into the evolutionary dynamics of SL trans-splicing and operons throughout Eukarya and improve gene discovery and annotation for a wide-range of eukaryotic genomes. Both pipelines are implemented in Bash and R and are built upon readily available software commonly installed on most bioinformatics servers. Biological insight can be gleaned even from sparse, low-coverage datasets, implying that an untapped wealth of information can be derived from existing RNA-Seq datasets as well as from novel full-isoform sequencing protocols as they become more widely available.

bioinformatics↗

bioRxiv2020

Maturation of the matrix and viral membrane of HIV-1

Gag - the main structural protein of HIV-1 - is recruited to the plasma membrane for virus assembly by its matrix (MA) domain. Gag is subsequently cleaved into its component domains, causing structural maturation to repurpose the virion for cell entry. We determined the structure and arrangement of MA within immature and mature HIV-1, providing a basis to understand MAs role in virus assembly. Unexpectedly, we found that MA rearranges during maturation, to form a new, hexameric lattice in which the acyl chain of a phospholipid extends out of the membrane to bind a pocket in MA. Our data suggest that proteolytic maturation of HIV-1 not only achieves assembly of the viral capsid surrounding the genome, but extends to repurpose the membrane-bound MA lattice for an entry or post-entry function, and causes partial removal of 2,500 acyl chains from the viral membrane.

microbiology↗

bioRxiv2020

Dissolved organic carbon (DOC) is essential to balance the metabolic demands of four dominant North-Atlantic deepsea sponges

Sponges are ubiquitous components of various deep-sea habitats, including cold water coral reefs and deep-sea sponge grounds. Despite being surrounded by oligotrophic waters, these ecosystems are known to be hotspots of biodiversity and carbon cycling. To assess the role of sponges in the carbon cycling of deep-sea ecosystems, we studied the energy budgets of six dominant deep-sea sponges (the hexactinellid species Vazella pourtalesi, and demosponge species Geodia barretti, Geodia atlantica, Craniella zetlandica, Hymedesmia paupertas and Acantheurypon spinispinosum) in an ex situ aquarium setup. Additionally, we determined morphological metrics for all species (volume, dry weight (DW), wet weight (WW), carbon (C) content, and ash-free dry weight (AFDW)) and provide species-specific conversion factors. Oxygen (O2) removal rates averaged 3.3 {+/-} 2.8 {micro}mol O2 DWsponge h-1 (all values mean {+/-} SD), live particulate (bacterial and phytoplankton) organic carbon (LPOC) removal rates averaged 0.30 {+/-} 0.39 {micro}mol C DWsponge h-1 and dissolved organic carbon (DOC) removal rates averaged 18.70 {+/-} 25.02 {micro}mol C DWsponge h-1. Carbon mass balances were calculated for four species (V. pourtalesi, G. barretti, G. atlantica and H. paupertas) and revealed that the sponges acquired 1.3-6.6 times the amount of carbon needed to sustain their minimal respiratory demands. These results indicate that irrespective of taxonomic class, growth form, and abundance of microbial symbionts, DOC is responsible for over 90 % of the total net organic carbon removal of deep-sea sponges and allows them to sustain in otherwise food-limited environments on the ocean floor.

ecology↗