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Gruber, A.

Publications and source records attributed to Gruber, A..

16 recordsLinked to original sources

First community challenge for automated virus taxonomy

The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all fifteen ranks of the virus taxonomy. We led an open community challenge for the computational taxonomic classification of viruses and assembled a dataset of virus sequences combining expert-curated and metagenomic sequences. Seventeen teams contributed a total of thirty-four automated, fully reproducible classification pipelines. Most tools correctly assigned viruses belonging to established species, genera, or families, but viruses that are unclassified at those lower ranks remain challenging. This study provides datasets, open-source software, novel approaches, and recommendations to benchmark computational taxonomic classification of viruses, and support organizing the many viruses discovered in big omics data.

microbiology↗

Crystalline guanine packed within vacuoles serves as nitrogen store in Chromera velia

Nitrogen is an important element for all living organisms. Photoautotrophic organisms need to assimilate nitrogen from the environment, therefore changes in nitrogen availability have a strong influence on their growth and metabolism. Many microalgae have been known to contain crystalline inclusions, and recently, it has been shown that many of these consist of purines like guanine and thus must be linked to the cellular nitrogen metabolisms. The alveolate alga Chromera velia contains such guanine crystals, and during its lifecycle, the alga is thought to be subjected to strong changes in external nitrogen availability. Here, we investigated the formation or decline of crystalline guanine in dependence of the availability of inorganic nitrogen in the growth medium. Cells were examined using polarised light microscopy, Raman micro-spectroscopy, chromatography (HPLC), transmission and scanning electron microscopy. The cellular guanine crystal content decreased during nitrogen starvation and increased upon transfer of the cells back to standard growth medium containing nitrate. Raman micro-spectroscopy showed that the crystals were composed of anhydrous guanine in beta-polytype. They appear in unspecific positions throughout the cell, and staining with the green dye Lysotracker DND-26 suggests that they are within vacuoles. Stacks of crystals could be observed in cells via freeze fracture and freeze etching electron microscopy, which unambiguously showed a membrane around the crystal aggregates, in a similar arrangement as has been shown for guanine storage vacuoles (GSV) in Chlamydomonas reinhardtii. We developed a method to isolate the guanine crystals from whole cells, and were able to obtain crystals which retained their flat, plate-like structure, matching the electron microscopic observations from whole cells. The isolated crystals were shown to consist of nitrogen rich compounds via energy-dispersive X-ray (EDX) analysis, and Raman micro-spectroscopy confirmed that they consist of guanine.

cell biology↗

Versatile Learning without Synaptic Plasticity in a Spiking Neural Network

Learning in the brains cerebral cortex is widely attributed to synaptic plasticity among cortical neurons. However, a growing body of evidence suggests that alternative processes, such as modulation of intrinsic excitability or gating by subcortical inputs, may also serve as important learning mechanisms. We developed the Bias Adaptive Neural Firing Framework (BANFF) as a simplified model of such phenomena embodied by a learnable bias current for each neuron of a rate-based network. Here, we extend this framework to spiking neural networks. We show that learning such biases enables one recurrent spiking neural network with fixed and random synaptic weights to perform well on nine tasks spanning classification, regression, and closed-loop dynamical systems mimicry. The network learnt a unique bias set for each task, and unlike recurrent synapse-based learning, new learning did not interfere with previous learning. The network was robust to non-stationary F-I curves (spike frequency adaptation), and biases could be learned with a learning algorithm (e-prop) that is more biologically plausible than stock gradient descent. Overall, we show that the BANFF can be extended from rate-based to spiking neural networks, maintaining good multi-task performance with a single network of spiking neurons.

neuroscience↗

Direct Training of Networks of Morris-Lecar Neurons withBackprop

Spiking Neural Networks (SNNs) have the potential to replicate the brains computational efficacy by explicitly incorporating action potentials or "spikes", which is not a feature of most artificial neural networks. However, training SNNs is difficult due to the non-differentiable nature of the most common spiking models: integrate-and-fire neurons. This study investigates if some of the difficulty in training SNNs arises from the use of integrate-and-fire neurons, rather than smoother alternatives, like conductance-based neurons. To that end, we considered networks of Morris-Lecar (ML) neurons, a conductance-based neuron model which is differentiable. Networks were built using kinetic synaptic models that smoothly link presynaptic voltage dynamics directly to postsynaptic conductance changes, ensuring that all components remain fully differentiable. Switching to biophysically detailed models of synapses and neurons enabled direct end-to-end training through Backpropagation Through Time (BPTT). Biophysically detailed networks were successfully trained on image classification, regression, and time series prediction tasks. These results demonstrate the feasibility of employing biophysically detailed differentiable point neuron models to create SNNs that function as more accurate paradigms for the study of neural computations and learning. Further, this work confirms that some aspects of the difficulty in translating gradient-based learning algorithms from machine learning may arise from model choice, rather than SNNs being intrinsically difficult to train. 1. Author summaryThe brains information-processing efficiency arises in part from neurons communicating via discrete spikes. Spiking Neural Networks (SNNs) mimic this process at the neuronal level but have been difficult to train as most machine learning algorithms are not directly applicable. Most SNNs use integrate-and-fire neurons, a modelling framework that simplifies spikes into non-differentiable, abrupt voltage changes, which makes them difficult to train with powerful, standard AI training methods that use derivatives to compute gradients (e.g. Backprop). In our work, we asked if this difficulty could be overcome by considering end-to-end differentiable spiking neural networks. We used completely differentiable SNNs using the Morris-Lecar neuron, a biophysically detailed neuron model that produces smooth spikes, along with differentiable kinetic synapses. With the entire network being mathematically differentiable, we found that we could train it directly using standard backpropagation through time on different tasks (regression, classification, and chaotic time series prediction). This work demonstrates that the use of integrate-and-fire models may be limiting applications of machine learning algorithms towards understanding how learning functions in the brain.

neuroscience↗

HIF1α-dependent induction of the T-Type calcium channel CaV3.2 mediates hypoxia-induced neuronal hyperexcitability

Post-stroke epilepsy (PSE) is a leading cause of acquired epilepsy in adults, yet the molecular mechanisms linking post-ischemic hypoxia to neuronal hyperexcitability remain poorly understood. The transcription factor hypoxia-inducible factor 1 (HIF1) is a central mediator of the cellular response to hypoxia and may contribute to epileptogenesis by regulating ion channel expression. Here, we identify the T-type calcium channel CaV3.2 (encoded by Cacna1h) as a direct transcriptional target of HIF1 and demonstrate its role in hypoxia-induced network hyperexcitability. Oxygen-glucose deprivation followed by reoxygenation (OGD/R) induced a persistent increase in neuronal firing rate. In murine and human organotypic brain slices, hypoxia led to a marked increase in HIF1 and Cacna1h expression at both transcript and protein levels. Using neuronal cell lines and primary cortical neurons we show that HIF1 activation through HIF1 overexpression, consistently increases Cacna1h expression. In NS20Y cells, overexpression of a normoxia-stable HIF1 variant increased Cacna1h promoter activity in both fluorescent and dual-luciferase reporter assays. The same effect was observed in primary cortical neurons, where HIF1 overexpression also elevated network activity measured by multielectrode array recordings, replicating the effect of the OGD/R model. Together, these results establish HIF1 as a key transcriptional regulator of CaV3.2 in neurons and reveal a conserved hypoxia-HIF1-CaV3.2 pathway that enhances neuronal excitability. This mechanism may underlie hypoxia-induced network hyperactivity and contribute to the pathogenesis of post-ischemic epileptogenesis, offering a potential molecular target for intervention.

neuroscience↗

Rapidly Reconfigurable Dynamic Computing in Neural Networks with Fixed Synaptic Connectivity

Learning and memory in the brains neocortex have long been hypothesised to be primarily mediated by synaptic plasticity. Extensive research in artificial neural networks has shown that training networks by adjusting connection weights faces computational challenges, including large parameter spaces and the tendency of new learning to interfere with previous learning (catastrophic forgetting). We propose that the brain, which is resistant to these challenges, can also learn by modulating the excitability of each neuron in a network rather than changing synaptic strengths. We show here that learning a task-specific set of bias currents enables a feedforward or recurrent network with fixed and randomly assigned connections to perform well on and switch between dozens of tasks, including regression, classification, autonomous time series generation, a game and robotic control. Bias-only learning also provides a novel mechanistic explanation for representational drift. It directly links the noise robustness of neuronal representations on short and long time scales to the ability of neural circuits to preserve learned information while remaining adaptable. We postulate that subcortical structures, such as the basal ganglia or cerebellum, may provide similar bias inputs to the neocortex for rapid task learning and robustness against interference.

neuroscience↗

A melancholy machine: simulated synapse loss induces depression-like behaviors in deep reinforcement learning

Deep Reinforcement Learning is a branch of artificial intelligence that uses artificial neural networks to model reward-based learning as it occurs in biological agents. Here we modify a Deep Reinforcement Learning approach by imposing a suppressive effect on the connections between neurons in the artificial network - simulating the effect of dendritic spine loss as observed in major depressive disorder (MDD). Surprisingly, this simulated spine loss is sufficient to induce a variety of MDD-like behaviors in the artificially intelligent agent, including anhedonia, increased temporal discounting, avoidance, and an altered exploration/exploitation balance. Furthermore, simulating alternative and longstanding reward-processing-centric conceptions of MDD (dysfunction of the dopamine system, altered reward discounting, context-dependent learning rates, increased exploration) does not produce the same range of MDD-like behaviors. These results support a conceptual model of MDD as a reduction of brain connectivity (and thus information-processing capacity) rather than an imbalance in monoamines - though the computational model suggests a possible explanation for the dysfunction of dopamine systems in MDD. Reversing the spine-loss effect in our computational MDD model can lead to rescue of rewarding behavior under some conditions. This supports the search for treatments that increase plasticity and synaptogenesis, and the model suggests some implications for their effective administration. Significance statementSimulating dendritic spine loss in a deep reinforcement learning agent causes the agent to exhibit a surprising range of depression-like behaviors. Simulating spine restoration allows rewarding behavior to be re-learned. This computational model sees Major Depressive Disorder as a reversible loss of brain capacity, providing some insights on pathology and treatment.

neuroscience↗

Enabling functionality and translation fidelity characterization of mRNA-based vaccines with a platform-based, antibody-free mass spectrometry detection approach

The success of mRNA-based therapeutics and vaccines can be attributed to their rapid development, adaptability to new disease variants, and scalable production. Modified ribonucleotides are often used in mRNA-based vaccines or therapeutics to enhance stability and reduce immunogenicity. However, substituting uridine with N1-methylpseudouridine has recently been shown to result in +1 ribosomal frameshifting that induces cellular immunity to the translated off-target protein. To accelerate vaccine development, it is critical to have analytical methods that can be rapidly brought online to assess the functionality and translation fidelity of mRNA constructs. Here, a platform-based, antibody-free method was developed using cell-free translation (CFT) and liquid chromatography-tandem mass spectrometry (MS) that can detect, characterize, and provide relative quantification of antigen proteins translated from mRNA vaccine drug substance. This workflow enabled the evaluation of mRNA subjected to thermal stress as well as bivalent (i.e., two mRNA encoding different antigen variants) drug substance. Additionally, the MS detection approach exhibited high sensitivity and specificity by accurately identifying all six translated proteins and their relative abundances in a dose-dependent manner following transfection of human cells with a hexavalent mRNA mixture encapsulated in lipid nanoparticles (LNPs), despite significant protein sequence homology. Expanding on these efforts, we show the utility of the CFT-MS approach in identifying the presence and junction of +1 ribosomal frameshifting resulting from N1-methylpseudouridation. Overall, this CFT-MS methodology offers a valuable analytical tool for the development and production of mRNA-based vaccines by facilitating the evaluation of mRNA quality and functionality while ensuring accurate translation of antigen proteins. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/594137v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@e4c7a7org.highwire.dtl.DTLVardef@1efddd1org.highwire.dtl.DTLVardef@cbfcbaorg.highwire.dtl.DTLVardef@1ae1acc_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Changes in functional connectivity preserve scale-freeneuronal and behavioral dynamics

Does the brain optimize itself for storage and transmission of information and if so, how? The critical brain hypothesis is based in statistical physics and posits that the brain self-tunes its dynamics to a critical point or regime to maximize the repertoire of neuronal responses. Yet, the robustness of this regime, especially with respect to changes in the functional connectivity, remains an unsolved fundamental challenge. Here, we show that both scale-free neuronal dynamics and self-similar features of behavioral dynamics persist following significant changes in functional connectivity. Specifically, we find that the psychedelic compound ibogaine that is associated with an altered state of consciousness fundamentally alters the functional connectivity in the retrosplenial cortex of mice. Yet, the scale-free statistics of movement and of neuronal avalanches among behaviorally-related neurons remain largely unaltered. This indicates that the propagation of information within biological neural networks is robust to changes in functional organization of sub-populations of neurons, opening up a new perspective on how the adaptive nature of functional networks may lead to optimality of information transmission in the brain.

neuroscience↗

Whole genome sequencing of 2,023 colorectal cancers reveals mutational landscapes, new driver genes and immune interactions

To characterise the somatic alterations in colorectal cancer (CRC), we conducted whole-genome sequencing analysis of 2,023 tumours. We provide the most detailed high-resolution map to date of somatic mutations in CRC, and demonstrate associations with clinicopathological features, in particular location in the large bowel. We refined the mutational processes and signatures acting in colorectal tumorigenesis. In analyses across the sample set or restricted to molecular subtypes, we identified 185 CRC driver genes, of which 117 were previously unreported. New drivers acted in various molecular pathways, including Wnt (CTNND1, AXIN1, TCF3), TGF-{beta}/BMP (TGFBR1) and MAP kinase (RASGRF1, RASA1, RAF1, and several MAP2K and MAP3K loci). Non-coding drivers included intronic neo-splice site alterations in APC and SMAD4. Whilst there was evidence of an excess of mutations in functionally active regions of the non-coding genome, no specific drivers were called with high confidence. Novel recurrent copy number changes included deletions of PIK3R1 and PWRN1, as well as amplification of CCND3 and NEDD9. Putative driver structural variants included BRD4 and SOX9 regulatory elements, and ACVR2A and ANKRD11 hotspot deletions. The frequencies of many driver mutations, including somatic Wnt and Ras pathway variants, showed a gradient along the colorectum. The Pks-pathogenic E. coli signature and TP53 mutations were primarily associated with rectal cancer. A set of unreported immune escape driver genes was found, primarily in hypermutated CRCs, most of which showed evidence of genetic evasion of the anti-cancer immune response. About 25% of cancers had a potentially actionable mutation for a known therapy. Thirty-three of the new driver genes were predicted to be essential, 17 possessed a druggable structure, and nine had a bioactive compound available. Our findings provide further insight into the genetics and biology of CRC, especially tumour subtypes defined by genomic instability or clinicopathological features.

genomics↗

Bioluminescent Synthetic Cells Communicate with Natural Cells and Self-Activate Light-Responsive Proteins

Development of regulated cellular processes and signaling methods in synthetic cells is essential for their integration with living materials. Light is an attractive tool to achieve this, but the limited penetration depth into tissue of visible light restricts its usability for in-vivo applications. Here, we describe the synthesis and application of blue-light-generating synthetic cells using bioluminescence, dismissing the need for an external light source. First, the lipid membrane and internal composition of light-producing synthetic cells were optimized to enable high-intensity emission. Next, we show these cells capacity for triggering bioprocesses in natural cells by initiating asexual sporulation of dark-grown mycelial cells of the fungus Trichoderma atroviride in a quorum-sensing like mechanism. Finally, we demonstrate regulated transcription and membrane recruitment in synthetic cells using bioluminescent self-activating fusion proteins. These functionalities pave the way for deploying synthetic cells as embeddable microscale light sources that are capable of activating engineered processes inside tissues.

bioengineering↗

Germline loss-of-function variants in the base-excision repair gene MBD4 cause a Mendelian recessive syndrome of adenomatous colorectal polyposis and acute myeloid leukaemia

Inherited defects in base-excision repair (BER) predispose to adenomatous polyposis and colorectal cancer (CRC), yet our understanding of this important DNA repair pathway remains incomplete. By combining detailed clinical, histological and molecular profiling, we reveal biallelic germline loss-of-function (LOF) variants in the BER gene MBD4 to predispose to adenomatous polyposis and -uniquely amongst CRC predisposition syndromes- to myeloid neoplasms. Neoplasms from MBD4-deficient patients almost exclusively accumulate somatic CpG>TpG mutations, resembling mutational signature SBS1. MBD4-deficient adenomas harbour mutations in known CRC driver genes, although AMER1 mutations were more common and KRAS mutations less frequent. We did not find an increased risk for colorectal tumours in individuals with a monoallelic MBD4 LOF variant. We suggest that this condition should be termed MBD4-associated neoplasia syndrome (MANS) and that MBD4 is included in testing for the genetic diagnosis of polyposis and/or early-onset AML.

genetics↗

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

The novel betacoronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after initially emerging in Wuhan, China. Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. To our knowledge, this is the first meta-analysis to predict host factors that play a specific role in SARS-CoV-2 pathogenesis, distinct from other respiratory viruses. We identified differentially expressed genes, isoforms and transposable element families specifically altered in SARS-CoV-2 infected cells. Well-known immunoregulators including CSF2, IL-32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were overexpressed. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1, PABPC1 and eIF4b, which may play important roles in the viral life cycle. We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19. The host factors we identified likely represent important mechanisms in the disease profile of this pathogen, and could be targeted by prophylactics and/or therapeutics against SARS-CoV-2. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/225581v3_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@15ca5a6org.highwire.dtl.DTLVardef@17f455forg.highwire.dtl.DTLVardef@a39f50org.highwire.dtl.DTLVardef@306ec1_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

Muscle mechanics and energy expenditure of the triceps surae during rearfoot and forefoot running

Forefoot running is advocated to improve running economy because of increased elastic energy storage than rearfoot running. This claim has not been assessed with methods that predict the elastic energy contribution to positive work or estimate muscle metabolic cost. The purpose of this study was to compare the mechanical work and metabolic cost of the gastrocnemius and soleus between rearfoot and forefoot running. Seventeen rearfoot and seventeen forefoot runners ran over-ground with their habitual footfall pattern (3.33-3.68m*s-1) while collecting motion capture and ground reaction force data. Ankle and knee joint angles and ankle joint moments served as inputs into a musculoskeletal model that calculated the mechanical work and metabolic energy expenditure of each muscle using Hill-based muscle models with contractile (CE) and series elastic (SEE) elements. A mixed-factor ANOVA assessed the difference between footfall patterns and groups (=0.05). Forefoot running resulted in greater SEE mechanical work in the gastrocnemius than rearfoot running but no differences were found in CE mechanical work or CE metabolic energy expenditure. Forefoot running resulted in greater soleus SEE and CE mechanical work and CE metabolic energy expenditure than rearfoot running. The metabolic cost associated with greater CE velocity, force production, and activation during forefoot running may outweigh any metabolic energy savings associated with greater SEE mechanical work. Therefore, there was no energetic benefit at the triceps surae for one footfall pattern or the other. The complex CE-SEE interactions must be considered when assessing muscle metabolic cost, not just the amount of SEE strain energy.

bioengineering↗

Description and charactrization of the Amazonian entomopathogenic bacterium Photorhabdus luminescens MN7

Many isolates of the genus Photorhabdus have been reported around the world. Here we describe the first Brazilian Photorhabdus isolate, found in association with the entomopathogenic nematode Heterorhabditis baujardi LPP7, from the Amazonian forest in Monte Negro (RO, Brazil). The new isolate can be grouped with the Hb-Hm clade of P. luminescens subsp. luminescens, close to the new subspecies P. luminescens subsp. sonorensis. P. luminescens MN7 has several characteristics expected of variant form I cells, such as the presence of intracellular crystals, secretion of hydrolytic enzymes (lipases and proteases) and bioluminescence. Although H. baujardi LPP7 is not prolific when compared to H. bacteriophora HP88, P. luminescens MN7 is clearly pathogenic and probably secretes the same toxins as P. luminescens subsp. luminescens W14, when fed to larvae of the greater wax moth Galleria mellonella. This behavior is different from what is found in Photorhabdus luminescens subsp. laumondii HP88, which was used as a control in our experiments, and P. l. subsp. laumondii TT01. Besides the toxin secretion, P. luminescens MN7 secretes proteolytic polypeptides that have molecular masses different from those found in P. l. subsp. laumondii TT01. Finally, the crude extract from spent culture medium was shown to contain 3,5-dihydroxy-4-isopropyl-cis-stilbene and 1,3,8-trihydroxy-9,10-anthraquinone as the major compounds, similarly to other Photorhabdus luminescens strains.

microbiology↗

Mitochondrial targeting of glycolysis in a major lineage of eukaryotes

Glycolysis is a major cytosolic catabolic pathway that provides ATP for many organisms1. Mitochondria play an even more important role in the provision of additional cellular ATP for eukaryotes2. Here, we show that in many stramenopiles, the C3 part of glycolysis is localised in mitochondria. We discovered genuine mitochondrial targeting signals on the six last enzymes of glycolysis. These targeting signals are recognised and sufficient to import GFP into mitochondria of a heterologous host. Analysis of eukaryotic genomes identified these targeting signals on many glycolytic C3 enzymes in a large group of eukaryotes found in the SAR supergroup3, in particular the stramenopiles. Stramenopiles, or heterokonts, are a large group of ecologically important eukaryotes that includes multi- and unicellular algae such as kelp and diatoms, but also economically important oomycete pathogens such as Phytophthora infestans. Confocal immunomicroscopy confirmed the mitochondrial location of glycolytic enzymes for the human parasite Blastocystis. Enzyme assays on cellular fractions confirmed the presence of the C3 part of glycolysis in Blastocystis mitochondria. These activities are sensitive to treatment with proteases and Triton X-100 but not proteases alone. Our work clearly shows that core cellular metabolism is more plastic than previously imagined and suggests new strategies to combat stramenopile pathogens such as the causative agent of late potato blight, P. infestans.

evolutionary biology↗