Miracle-dz/UniFAR-FTUs huggingface dataset:
The plant immune receptors NRG1.1 and ADR1 are calcium influx channels

Plant nucleotide-binding leucine-rich repeat receptors (NLRs) regulate immunity and cell death. RPW8 domain-containing “helper” NLRs (RNLs) are required by many “sensor” NLRs. Our crystal structure of the RNL N REQUIREMENT GENE 1.1 (NRG1.1) N-terminal signaling domain resembled that of the resting state plant resistosome-forming HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) and the animal MIXED-LINEAGE KINASE-LIKE (MLKL) cation channel. Active NRG1.1 oligomerized, was enriched in plasma membrane puncta and conferred cytoplasmic Ca2+ influx in plant and human HeLa cells. NRG1.1-dependent Ca2+ influx and cell death were sensitive to Ca2+ channel blockers. Ca2+ influx and cell death mediated by NRG1.1 and ACTIVATED DISEASE RESISTANCE 1 (ADR1), another RNL, required conserved negatively charged N-terminal residues. Thus, RNLs apparently form influx channels to directly regulate cytoplasmic [Ca2+] and consequent cell death. One Sentence Summary A specific class of plant immune receptors function as calcium-permeable channels upon activation to induce cell death.
Regulation of plasmodesmata at specific cell-cell interfaces

Precise exchange of information and resources among cells is essential for multicellular organisms. Intercellular communication among diverse cell types requires differential mechanisms to achieve the specific regulation. Despite the significance of intercellular communication, it is largely unknown how the communication between different cells is regulated. Here, we report that two members of plasmodesmata-located proteins modulate plasmodesmata at two distinct cell-cell interfaces.
Nothing in evolution makes sense except in the light of parasites

The emergence of parasites in evolving replicating systems appears to be inevitable. Parasites emerge readily in models and laboratory experiments of the hypothesised earliest replicating systems: the RNA world. Phylogenetic reconstructions also suggest very early evolution of viruses and other parasitic mobile genetic elements in our biosphere. The evolution of such parasites would lead to extinction unless prevented by compartmentalisation or spatial pattern formation, and the emergence of multilevel selection. Today and apparently since the earliest times, many intricate defence and counter-defence strategies have evolved. Here we bring together for the first time automata chemistry models and spatial RNA world models, to study the emergence of parasites and the evolving complexity to cope with the parasites. Our system is initialised with a hand-designed program string that copies other program strings one character at a time, with a small chance of point mutation. Almost immediately, short parasites arise; these are copied more quickly, and so have an evolutionary advantage. Spatial pattern formation, in the form of chaotic waves of replicators followed by parasites, can prevent extinction. The replicators also become shorter, and so are replicated faster. They evolve a mechanism to slow down replication, which reduces the difference of replication rate of replicators and parasites. They also evolve explicit mechanisms to discriminate copies of self from parasites; these mechanisms become increasingly complex. Replicators speciate into lineages and can become longer, despite the fitness cost that entails. We do not see a classical co-evolutionary arms-race of a replicator and a parasite lineage: instead new parasite species continually arise from mutated replicators, rather than from evolving parasite lineages. Finally we note that evolution itself evolves, for example by effectively increasing point mutation rates, and by generating novel emergent mutational operators. The inevitable emergence of parasites in replicator systems drives the evolution of complex replicators and complex ecosystems with high population density. Even in the absence of parasites, the evolved replicators outperform the initial replicator and the early short replicators. Modelling replication as an active computational process opens up many degrees of freedom that are exploited not only to meet environmental challenges, but also to modify the evolutionary process itself.
Efficient Agony Based Transfer Learning Algorithms for Survival Forecasting

Progression modeling is a mature subfield of cancer bioinformatics, but it has yet to make a proportional clinical impact. The majority of the research in this area has focused on the development of efficient algorithms for accurately reconstructing sequences of (epi)genomic events from noisy data. We see this as the first step in a broad pipeline that will translate progression modeling to clinical utility, with the subsequent steps involving inferring prognoses and optimal therapy programs for different cancers and using similarity in progression to enhance decision making. In this paper we take some initial steps in completing this pipeline. As a theoretical contribution, we introduce a polytime-computable pairwise distance between progression models based on the graph-theoretic notion of “agony”. Focusing on a particular progression model we can then use this agony distance to cluster (dis)similarities via multi-dimensional scaling. We recover known biological similarities and dissimilarities. Finally, we use the agony distance to automate transfer learning experiments and show a large improvement in the ability to forecast time to death.
The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis

The microbiomes of tropical corals are actively studied using 16S rRNA gene amplicons to understand microbial roles in coral health, metabolism, and disease resistance. However, primers targeting bacterial and archaeal 16S rRNA genes may also amplify organelle rRNA genes from the coral, associated microbial eukaryotes, and encrusting organisms. In this manuscript, we demonstrate that standard workflows for annotating microbial taxonomy severely under-annotate mitochondrial sequences in 1272 coral microbiomes from the Earth Microbiome Project. This issue prevents annotation of >95% of reads in some samples and persists when using either Greengenes or SILVA taxonomies. Worse, mitochondrial under-annotation varies between species and across anatomy, biasing comparisons of α- and β-diversity. By supplementing existing taxonomies with diverse mitochondrial rRNA sequences, we resolve ~97% of unique unclassified sequences as mitochondrial, without increasing misannotation in mock communities. We recommend using these extended taxonomies for coral microbiome analysis and encourage vigilance regarding similar issues in other hosts.
On bridging paired-end RNA-seq data

Motivation The widely-used high-throughput RNA-sequencing technologies (RNA-seq) usually produce paired-end reads. We explore if full fragments can be computationally reconstructed from the sequenced two ends—a problem here we refer to as bridging. Solving this problem provides longer, more informative RNA-seq reads, and hence benefits downstream RNA-seq analysis such as transcriptome assembly and expression quantification. However, bridging is a challenging and complicated task owing to alternative splicing, transcript noises, and sequencing errors. It remains unclear if the data itself provides sufficient information for accurate bridging, let alone proper models and efficient algorithms that characterize and determine the true bridges. Algorithmic Results We studied this problem in two settings: reference-based bridging, which assumes reads alignments are available and reconstructs the alignments of full fragments, and de novo bridging, which reconstructs sequences of entire fragments from sequences of the two ends. We proposed a novel mathematical formulation that works for both settings—to seek a path in an underlying graph data structure (i.e., splice graph for reference-based bridging, and compacted de Bruijn graph for de novo bridging) such that its bottleneck weight is maximized. This formulation characterizes true bridges and is efficient in filtering out false bridges. This formulation admits optimal substructure property, and hence efficient dynamic programming algorithms can be designed. For reference-based bridging, we designed such an algorithm to calculate the top N bridging paths, followed by a voting approach to select one using the distribution of fragment length. For de novo bridging, we designed a new truncated Dijkstra’s algorithm. To further speed up, we proposed a novel algorithm that reuses the shortest path tree to avoid running the truncated Dijkstra’s algorithm from scratch for all vertices. These innovations result in scalable algorithms that can bridge all paired-end reads in a compacted de Bruijn graph with millions of vertices. Experimental Results We showed that paired-end RNA-seq reads can be accurately bridged to a large extend. Our reference-based bridging tool could correctly bridge more than 79.6% of reads. For de novo bridging, high precision was observed with varied sensitivity. We also showed that bridging can improve reference-based transcript assembly: the improvement was significant (up to 14.4% measured with adjusted precision), and universal in all combinations with different aligners and assemblers. Availability Implementations of the algorithms for reference-based and de novo bridging are available at https://github.com/Shao-Group/rnabridge-align and https://github.com/Shao-Group/rnabridge-denovo, respectively. Scripts, datasets, and documentations that can reproduce the experimental results in this manuscript are available at https://github.com/Shao-Group/rnabridge-test.
An integrated multi-wavelength SCATTIRSTORM microscope combining TIRFM and IRM modalities for imaging cellulases and other processive enzymes

We describe a multimodal SCATTIRSTORM microscope for visualizing processive enzymes moving on immobilized substrates. The instrument combines Interference Reflection Microscopy (IRM) with multi-wavelength Total Internal Reflectance Fluorescence Microscopy (TIRFM). The microscope can localize quantum dots with a precision of 2.8 nm at 100 frames/s, and was used to image the dynamics of the cellulase, Cel7a interacting surface-immobilized cellulose. The instrument, which was built with off-the-shelf components and controlled by custom software, is suitable for tracking other degradative enzymes such as collagenases, as well as motor proteins moving along immobilized tracks.
An Adeno-Associated Viral vector encoding Neurotrophin 3 injected into affected forelimb muscles modestly improves sensorimotor function after contusive mid-cervical spinal cord injury

Traumatic spinal cord injury (SCI) in humans occurs most frequently in the cervical spine where it can cause substantial sensorimotor impairments to upper limb function. The altered input to spinal circuits below the lesion leads to maladaptive reorganisation which often leads to hyperreflexia in proprioceptive circuits. Neurotrophin 3 (NT3) is growth factor essential for the development of proprioceptive neurons. We have previously shown that following bilateral corticospinal tract axotomy, intramuscular delivery of an Adeno-Associated Viral vector encoding NT3 (AAV-NT3) induces proprioceptive circuit reorganisation linked to functional recovery. To assess its therapeutic effects following a clinically relevant bilateral C5-C6 contusion in rats, AAV-NT3 was injected intramuscularly into the dominant limb 24 hours after injury and forelimb function was assessed over 13 weeks. The injury generated hyperreflexia of a distal forelimb proprioceptive circuit. There was also loss of fine motor skills during reach-and-grasp and walking on a horizontal ladder. Ex vivo magnetic resonance imaging (MRI) revealed atrophy of the spinal cord and white matter disruption throughout the lesion site together with extensive loss of grey matter. Unexpectedly, animals treated with AAV-NT3 had a slightly smaller lesion in the regions close to the epicentre compared to PBS treated animals. Rats treated with AAV-NT3 showed subtly better performance on the horizontal ladder and transient benefits on reach-and-grasp. AAV-NT3 did not normalise hyperreflexia in a treated muscle. The treatment increased the amount of NT3 in treated muscles but, unexpectedly, serum levels were only elevated in a small subset of animals. These results show that this dose and delivery of AAV-NT3 may generate subtle improvements in locomotion but additional treatments will be required to overcome the widespread sensorimotor deficits caused by contusion injury.
cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae

The cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of “universal” PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus and the 23 newer genera showed that cpn60-based sequence relationships were consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, “universal” barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework. Significance and Impact of the Study The genus Lactobacillus recently underwent a major reorganization resulting in the definition of 23 new genera. Lactobacilli are widespread in environmental and host-associated microbiomes and are exploited in food and biotechnology applications, making methods for their accurate identification desirable. Here we show that the combination of a reference sequence database, “universal” barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.
MYC promotes immune-suppression in TNBC via inhibition of IFN signaling

Immune checkpoint inhibitor (ICI) treatment has thus far shown limited efficacy in triple-negative breast cancer (TNBC) patients, presumably due to sparse or unresponsive tumor-infiltrating lymphocytes. We reveal a strong correlation between MYC expression and loss of immune signatures in human TNBC. In mouse models of BRCA1-proficient and -deficient TNBC, MYC overexpression dramatically decreased lymphocyte infiltration in tumors, along with immune signature loss. Likewise, MYC overexpression suppressed inflammatory signaling induced by BRCA1/2 inactivation in human TNBC cell lines. Moreover, MYC overexpression prevented the recruitment and activation of lymphocytes in co-cultures with human and mouse TNBC models. Chromatin immunoprecipitation (ChIP)-sequencing revealed that MYC directly binds promoters of multiple interferon-signaling genes, which were downregulated upon MYC expression. Finally, MYC overexpression suppressed induction of interferon signaling and tumor growth inhibition by a Stimulator of Interferon Genes (STING) agonist. Together, our data reveal that MYC suppresses innate immunity and facilitates immune escape, explaining the poor immunogenicity of MYC-overexpressing TNBCs. Statement of Significance MYC suppresses recruitment and activation of immune cells in TNBC by repressing the transcription of interferon genes. These findings provide a mechanistic rationale for the association of high MYC expression levels with immune exclusion in human TNBCs, which might underlie the relatively poor response of many TNBCs to ICI.
Intrinsic Gating Behavior of Voltage-Gated Sodium Channels Predetermines Regulation by Auxiliary β-subunits

Voltage-gated sodium (Nav) channels mediate rapid millisecond electrical signaling in excitable cells. Auxiliary subunits, β1-β4, are thought to regulate Nav channel function through covalent and/or polar interactions with the channel’ s voltage-sensing domains. How these interactions translate into the diverse and variable regulatory effects of β-subunits remains unclear. Here, we find that the intrinsic movement order of the voltage-sensing domains during channel gating is unexpectedly variable across Nav channel isoforms. This movement order dictates the channel’ s propensity for closed-state inactivation, which in turn modulates the actions of β1 and β3. We show that the differential regulation of skeletal muscle, cardiac, and neuronal Nav channels is explained by their variable levels of closed-state inactivation. Together, this study provides a unified mechanism for the regulation of all Nav channel isoforms by β1 and β3, which explains how the fixed structural interactions of auxiliary subunits can paradoxically exert variable effects on channel function.
Towards a systematic characterization of protein complex function: a natural language processing and machine-learning framework

It is a general assumption of molecular biology that the ensemble of expressed molecules, their activities and interactions determine biological processes, cellular states and phenotypes. Quantitative abundance of transcripts, proteins and metabolites are now routinely measured with considerable depth via an array of “OMICS” technologies, and recently a number of methods have also been introduced for the parallel analysis of the abundance, subunit composition and cell state specific changes of protein complexes. In comparison to the measurement of the molecular entities in a cell, the determination of their function remains experimentally challenging and labor-intensive. This holds particularly true for determining the function of protein complexes, which constitute the core functional assemblies of the cell. Therefore, the tremendous progress in multi-layer molecular profiling has been slow to translate into increased functional understanding of biological processes, cellular states and phenotypes. In this study we describe PCfun, a computational framework for the systematic annotation of protein complex function using Gene Ontology (GO) terms. This work is built upon the use of word embedding— natural language text embedded into continuous vector space that preserves semantic relationships— generated from the machine reading of 1 million open access PubMed Central articles. PCfun leverages the embedding for rapid annotation of protein complex function by integrating two approaches: (1) an unsupervised approach that obtains the nearest neighbor (NN) GO term word vectors for a protein complex query vector, and (2) a supervised approach using Random Forest (RF) models trained specifically for recovering the GO terms of protein complex queries described in the CORUM protein complex database. PCfun consolidates both approaches by performing the statistical test for the enrichment of the top NN GO terms within the child terms of the predicted GO terms by RF models. Thus, PCfun amalgamates information learned from the gold-standard protein-complex database, CORUM, with the unbiased predictions obtained directly from the word embedding, thereby enabling PCfun to identify the potential functions of putative protein complexes. The documentation and examples of the PCfun package are available at https://github.com/sharmavaruns/PCfun. We anticipate that PCfun will serve as a useful tool and novel paradigm for the large-scale characterization of protein complex function.
MIA 3 / TANGO 1 enables efficient secretion by constraining COPII vesicle budding

20 Complex machinery is required to drive secretory cargo export from the endoplasmic reticulum. In vertebrates, this includes transport and Golgi organization protein 1 (TANGO1), encoded by the Mia3 gene. Here, using genome engineering of human cells light microscopy, secretion assays, and proteomics, we show loss of Mia3/TANGO1 results in formation of numerous vesicles and a loss of early secretory pathway integrity. This restricts secretion not only of large proteins like procollagens but of all 25 types of secretory cargo. Our data shows that Mia3/TANGO1 constrains the propensity of COPII to form vesicles promoting instead the formation of the ER-Golgi intermediate compartment. Thus, Mia3/TANGO1 facilities the secretion of complex and high volume cargoes from vertebrate cells.
Bacteriophage self-counting in the presence of viral replication

Significance Viral dormancy, in which the infected cell is not killed but rather becomes the long-term residence of the parasite, is a hallmark of viruses across kingdoms from bacteriophages to HIV. When and how viruses decide to opt for this lifestyle remains mysterious. Phage lambda, which serves as a paradigm for viral dormancy, is reported to count the number of coinfecting viruses and then uses this value to assess the abundance of potential hosts and decide whether to become dormant. Here, we use a single-cell measurement of viruses and messenger RNA together with mathematical modeling to illuminate how lambda performs this task. When host cells are in low abundance, temperate bacteriophages opt for dormant (lysogenic) infection. Phage lambda implements this strategy by increasing the frequency of lysogeny at higher multiplicity of infection (MOI). However, it remains unclear how the phage reliably counts infecting viral genomes even as their intracellular number increases because of replication. By combining theoretical modeling with single-cell measurements of viral copy number and gene expression, we find that instead of hindering lambda’s decision, replication facilitates it. In a nonreplicating mutant, viral gene expression simply scales with MOI rather than diverging into lytic (virulent) and lysogenic trajectories. A similar pattern is followed during early infection by wild-type phage. However, later in the infection, the modulation of viral replication by the decision genes amplifies the initially modest gene expression differences into divergent trajectories. Replication thus ensures the optimal decision—lysis upon single-phage infection and lysogeny at higher MOI.
Longitudinal high-resolution imaging through a flexible intravital imaging window

A fully flexible imaging window acting as an implantable transparent “second skin” upgrades in vivo imaging. Intravital microscopy (IVM) is a powerful technique that enables imaging of internal tissues at (sub)cellular resolutions in living animals. Here, we present a silicone-based imaging window consisting of a fully flexible, sutureless design that is ideally suited for long-term, longitudinal IVM of growing tissues and tumors. Crucially, we show that this window, without any customization, is suitable for numerous anatomical locations in mice using a rapid and standardized implantation procedure. This low-cost device represents a substantial technological and performance advance that facilitates intravital imaging in diverse contexts in higher organisms, opening previously unattainable avenues for in vivo imaging of soft and fragile tissues.