Miracle-dz/UniFAR-FTUs huggingface dataset:
Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus

First identified in 2002, diphtheritic stomatitis (DS) is a devastating disease affecting yellow-eyed penguins (Megadyptes antipodes, or hoiho in te reo Māori). The disease is associated with oral lesions in chicks and has caused significant morbidity and mortality. DS is widespread among yellow-eyed penguin chicks on mainland New Zealand yet appears to be absent from the subantarctic population. Corynebacterium spp. have previously been suspected as a causative agent yet, due to inconsistent cultures and inconclusive pathogenicity, its role in DS is unclear. Herein, we used a metatranscriptomic approach to identify potential causative agents of DS by revealing the presence and abundance of all viruses, bacteria, fungi and protozoa - together, the infectome. Oral and cloacal swab samples were collected from presymptomatic, symptomatic and recovered chicks along with a control group of healthy adults. Two novel viruses from the Picornaviridae were identified, one of which - yellow-eyed penguin megrivirus - was highly abundant in chicks irrespective of health status but not detected in healthy adults. Tissue from biopsied oral lesions also tested positive for the novel megrivirus upon PCR. We found no overall clustering among bacteria, protozoa and fungi communities at the genus level across samples, although Paraclostridium bifermentans was significantly more abundant in oral microbiota of symptomatic chicks compared to other groups. The detection of a novel and highly abundant megrivirus has sparked a new line of enquiry to investigate its potential association with DS.
Viruses in Laboratory Drosophila and Their Impact on Host Gene Expression

Drosophila melanogaster has one of the best characterized antiviral immune responses among invertebrates. However, relatively few easily-transmitted natural virus isolates are available, and so many Drosophila experiments have been performed using artificial infection routes and artificial host-virus combinations. These may not reflect natural infections, especially for subtle phenotypes such as gene expression. Here, to explore the laboratory virus community and to better understand how natural virus infections induce changes in gene expression, we analyse seven publicly available D. melanogaster transcriptomic sequencing libraries that were originally sequenced for projects unrelated to virus infection. We find ten known viruses—including five that have not been experimentally isolated—but no previously unknown viruses. Our analysis of host gene expression found numerous genes were differentially expressed in flies that were naturally infected with a virus. For example, flies infected with nora virus showed patterns of gene expression consistent with intestinal vacuolization and host attempted repair via the upd3 JAK/STAT pathway. We also found marked sex-differences in virus-induced differential gene expression. Our results show that natural virus infection in laboratory Drosophila does indeed induce detectable changes in gene expression, suggesting that this may form an important background condition for experimental studies in the laboratory.
Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs

We introduce a novel metagenomics assembler for high-accuracy long reads. Our approach, implemented as metaMDBG, combines highly efficient de Bruijn graph assembly in minimizer space, with both a multi-k′ approach for dealing with variations in genome coverage depth and an abundance-based filtering strategy for simplifying strain complexity. The resulting algorithm is more efficient than the state-of-the-art but with better assembly results. metaMDBG was 1.5 to 12 times faster than competing assemblers and requires between one-tenth and one-thirtieth of the memory across a range of data sets. We obtained up to twice as many high-quality circularised prokaryotic metagenome assembled genomes (MAGs) on the most complex communities, and a better recovery of viruses and plasmids. metaMDBG performs particularly well for abundant organisms whilst being robust to the presence of strain diversity. The result is that for the first time it is possible to efficiently reconstruct the majority of complex communities by abundance as nearcomplete MAGs.
The Role of Phylogenetic Structure on Canidae Lineage Distribution and Trait Variation across the Globe

Aim Understanding the spatial structuring of ecological communities requires us to consider the interplay between evolutionary history and environmental factors. In this study, we investigated the influence of Canidae phylogenetic structure on the distribution and trait patterns of lineages across the planet. Location Americas, Africa, Eurasia. Time period 12 million years ago – present. Major taxa studied Canidae. Methods Using distribution data and phylogenetic information for 37 Canidae species, we employed phylogenetic fuzzy-weighting to compare assemblages based on their phylogenetic similarity. Results Our results revealed distinct global patterns of body size, body mass, range size, habitat type, and evolutionary distinctiveness among lineages. We also identified the shared contributions of phylogenetic structure and temperature to trait variation using variance partitioning analysis. The PCPS axes highlighted the influence of phylogenetic relationships on Canidae assemblages, particularly in South America. Main conclusions Notably, the study challenges the applicability of Bergmann’s and Rapoport’s rules in explaining canids’ sizes and range sizes geographic variation across continents, emphasizing the importance of phylogenetic information. The unique diversification history of Canidae in South America and Africa and their diverse environmental conditions likely contribute to the observed trait patterns that make both continents so distinguished when compared to N. America and Eurasia. Our findings underscore the need to incorporate phylogenetic information in models assessing trait variation across geographic scales for unbiased estimations.
Evolution from mixed to fixed handedness in mirror-image flowers: insights from adaptive dynamics

Mirror-image flowers (enantiostyly) involve a form of sexual asymmetry in which a flower’s style is deflected either to the left or right side, with a pollinating anther orientated in the opposite direction. This curious floral polymorphism, which was known but not studied by Charles Darwin, occurs in at least 11 unrelated angiosperm families and represents a striking example of adaptive convergence in form and function associated with cross-pollination by insects. In several lineages, dimorphic enantiostyly (one stylar orientation per plant, both forms occurring within populations) has evolved from monomorphic enantiostyly, in which all plants can produce both style orientations. We use a modelling approach to investigate the emergence of dimorphic enantiostyly from monomorphic enantiostyly under gradual evolution. We show using adaptive dynamics that depending on the balance between inbreeding depression following geitonogamy, pollination efficiency and plant density, dimorphism can evolve from an ancestral monomorphic population. In general, the newly emergent dimorphic population is stable against invasion of a monomorphic mutant. However, our model predicts that under certain ecological conditions, e.g., a decline of pollinators, dimorphic enantiostyly may revert to a monomorphic state. We demonstrate using population genetics simulations that the observed evolutionary transitions are possible assuming a plausible genetic architecture.
Calcium and Integrin-binding protein 2 (CIB2) controls force sensitivity of the mechanotransducer channels in cochlear outer hair cells

Calcium and Integrin-Binding Protein 2 (CIB2) is an essential subunit of the mechano-electrical transduction (MET) complex in mammalian auditory hair cells. CIB2 binds to pore-forming subunits of the MET channel, TMC1/2 and is required for their transport and/or retention at the tips of mechanosensory stereocilia. Since genetic ablation of CIB2 results in complete loss of MET currents, the exact role of CIB2 in the MET complex remains elusive. Here, we generated a new mouse strain with deafness-causing p.R186W mutation in Cib2 and recorded small but still measurable MET currents in the cochlear outer hair cells. We found that R186W variant causes increase of the resting open probability of MET channels, steeper MET current dependence on hair bundle deflection (I-X curve), loss of fast adaptation, and increased leftward shifts of I-X curves upon hair cell depolarization. Combined with AlphaFold2 prediction that R186W disrupts one of the multiple interacting sites between CIB2 and TMC1/2, our data suggest that CIB2 mechanically constraints TMC1/2 conformations to ensure proper force sensitivity and dynamic range of the MET channels. Using a custom piezo-driven stiff probe deflecting the hair bundles in less than 10 µs, we also found that R186W variant slows down the activation of MET channels. This phenomenon, however, is unlikely to be due to direct effect on MET channels, since we also observed R186W-evoked disruption of the electron-dense material at the tips of mechanotransducing stereocilia and the loss of membrane-shaping BAIAP2L2 protein from the same location. We concluded that R186W variant of CIB2 disrupts force sensitivity of the MET channels and force transmission to these channels.
Mitochondrial-Derived Compartments Remove Surplus Proteins from the Outer Mitochondrial Membrane

The outer mitochondrial membrane (OMM) creates a boundary that imports most of the mitochondrial proteome while removing extraneous or damaged proteins. How the OMM senses aberrant proteins and remodels to maintain OMM integrity remains unresolved. Previously, we identified a piecemeal autophagic mechanism called the mitochondrial-derived compartment (MDC) that removes a subset of the mitochondrial proteome. Here we show that MDCs specifically sequester proteins localized only at the OMM, providing an explanation for how select mitochondrial proteins are removed by MDCs. Remarkably, selective sorting into MDCs also occurs within the OMM, as subunits of the translocase of the outer membrane (TOM) complex are excluded from MDCs unless assembly of the TOM complex is impaired. Considering that overloading the OMM with mitochondrial membrane proteins or mistargeted tail-anchored membrane proteins induces MDCs to form and sequester these proteins, we propose that one functional role of MDCs is to create an OMM-enriched trap that segregates and sequesters excess proteins from the mitochondrial surface. SUMMARY Wilson and colleagues observe that mitochondrial-derived compartments (MDCs) selectively incorporate proteins from only the outer mitochondrial membrane (OMM), and robustly sequester both excess and mistargeted proteins into this OMM-enriched domain, suggesting MDCs act to remove surplus hydrophobic cargo from mitochondria.
Multimodal Imaging for Validation and Optimization of Ion Channel-Based Chemogenetics in Nonhuman Primates

Chemogenetic tools provide an opportunity to manipulate neuronal activity and behavior selectively and repeatedly in nonhuman primates (NHPs) with minimal invasiveness. Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) are one example that is based on mutated muscarinic acetylcholine receptors. Another channel-based chemogenetic system available for neuronal modulation in NHPs uses pharmacologically selective actuator modules (PSAMs), which are selectively activated by pharmacologically selective effector molecules (PSEMs). To facilitate the use of the PSAM/PSEM system, the selection and dosage of PSEMs should be validated and optimized for NHPs. To this end, we used a multimodal imaging approach. We virally expressed excitatory PSAM (PSAM4-5HT3) in the striatum and the primary motor cortex (M1) of two male macaque monkeys, and visualized its location through positron emission tomography (PET) with the reporter ligand [18F]ASEM. Chemogenetic excitability of neurons triggered by two PSEMs (uPSEM817 and uPSEM792) was evaluated using [18F]fluorodeoxyglucose-PET imaging, with uPSEM817 being more efficient than uPSEM792. Pharmacological magnetic resonance imaging (phMRI) showed that increased brain activity in the PSAM4-expressing region began ∼13 min after uPSEM817 administration and continued for at least 60 min. Our multimodal imaging data provide valuable information regarding the manipulation of neuronal activity using the PSAM/PSEM system in NHPs, facilitating future applications. SIGNIFICANCE STATEMENT Like other chemogenetic tools, the ion channel-based system called pharmacologically selective actuator module/pharmacologically selective effector molecule (PSAM/PSEM) allows remote manipulation of neuronal activity and behavior in living animals. Nevertheless, its application in nonhuman primates (NHPs) is still limited. Here, we used multitracer positron emission tomography (PET) imaging and pharmacological magnetic resonance imaging (phMRI) to visualize an excitatory chemogenetic ion channel (PSAM4-5HT3) and validate its chemometric function in macaque monkeys. Our results provide the optimal agonist, dose, and timing for chemogenetic neuronal manipulation, facilitating the use of the PSAM/PSEM system and expanding the flexibility and reliability of circuit manipulation in NHPs in a variety of situations.
Prioritized imputed sequence variants from multi-population GWAS improve prediction accuracy for sea lice count in Atlantic salmon (Salmo salar)

Sea lice infestation is one of the major fish health problems during the grow-out phase in Atlantic salmon (Salmo salar) aquaculture. In this study, we integrated different genomic approaches, including whole-genome sequencing (WGS), genotype imputation and meta-analysis of genome-wide association studies (GWAS), to identify single-nucleotide polymorphisms (SNPs) associated with sea lice count in Atlantic salmon. Different sets of trait-associated SNPs were prioritized and compared against randomly chosen markers, based on the accuracy of genomic predictions for the trait. Lice count phenotypes and dense genotypes of five breeding populations challenged against sea lice were used. Genotype imputation was applied to increase SNP density of challenged animals to WGS level. The summary statistics from GWAS of each population were then combined in a meta-analysis to increase the sample size and improve the statistical power of associations. Eight different genotyping scenarios were considered for genomic prediction: 70K_array: 70K standard genotyping panel; 70K_priori: 70K SNPs with the highest p-values identified in the meta-analysis; 30K_priori: 30K SNPs with the highest p-values identified in the meta-analysis; WGS: SNPs imputed to whole-genome sequencing level; and the remaining four scenarios were the same SNP sets with a linkage disequilibrium (LD) pruning filter: 70K_array_LD; 70K_priori_LD; 30K_priori_LD and WGS_LD, respectively. Genomic prediction accuracy was evaluated using a five-fold cross-validation scheme in two different populations excluding them from the meta-analysis to remove possible validation-reference bias. Results showed significant genetic variation for sea lice counting in Atlantic salmon across populations, with heritabilities ranging from 0.06 to 0.24. The meta-analysis identified several SNPs associated with sea lice resistance, mainly in Ssa03 and Ssa09 chromosomes. Genomic prediction using the GWAS-based prioritized SNPs showed higher accuracy compared to using the standard SNP array in most of scenarios, achieving up to 57% increase in accuracy. Accuracy of prioritized scenarios was higher for the 70K_priori in comparison to 30K_priori. The use of WGS data in genomic prediction presented marginal or negative accuracy gain compared to the standard SNP array. The LD-pruning filter presented no benefits, reducing accuracy in most of scenarios. Overall, our study demonstrated the potential of prioritized of imputed sequence variants from multi-population GWAS meta-analysis to improve prediction accuracy for sea lice count in Atlantic salmon. The findings suggest that incorporating WGS data and prioritized SNPs from GWAS meta-analysis can accelerate the genetic progress of selection for polygenic traits in salmon aquaculture.
Gene editing of putative cAMP and Ca2+-regulated proteins using an efficient cloning-free CRISPR/Cas9 system in Trypanosoma cruzi

Trypanosoma cruzi, the agent of Chagas disease, must adapt to a diversity of environmental conditions that it faces during its life cycle. The adaptation to these changes is mediated by signaling pathways that coordinate the cellular responses to the new environmental settings. Cyclic AMP (cAMP) and Calcium (Ca2+) signaling pathways regulate critical cellular processes in this parasite, such as differentiation, osmoregulation, host cell invasion and cell bioenergetics. Although the use of CRISPR/Cas9 technology prompted reverse genetics approaches for functional analysis in T. cruzi, it is still necessary to expand the toolbox for genome editing in this parasite, as for example to perform multigene analysis. Here we used an efficient T7RNAP/Cas9 strategy to tag and delete three genes predicted to be involved in cAMP and Ca2+ signaling pathways: a putative Ca2+/calmodulin-dependent protein kinase (CAMK), Flagellar Member 6 (FLAM6) and Cyclic nucleotide-binding domain/C2 domain-containing protein (CC2CP). We endogenously tagged these three genes and determined the subcellular localization of the tagged proteins. Furthermore, the strategy used to knockout these genes allow us to presume that TcCC2CP is an essential gene in T. cruzi epimastigotes. Our results will open new venues for future research on the role of these proteins in T. cruzi.
DNA recognition and induced genome modification by a hydroxymethyl-γ tail-clamp peptide nucleic acid

Peptide nucleic acids (PNA) can target and stimulate recombination reactions in genomic DNA. We have reported that gamma (γ)-PNA oligomers possessing the diethylene glycol γ-substituent show improved efficacy over unmodified PNAs in stimulating recombination-induced gene modification. However, this structural modification poses a challenge because of the inherent racemization risk in O-alkylation of the precursory serine side chain. To circumvent this risk and improve γPNA accessibility, we explore the utility of γPNA oligomers possessing the hydroxymethyl-γ moiety for gene editing applications. We demonstrate that a γPNA oligomer possessing the hydroxymethyl modification, despite weaker preorganization, retains the ability to form a hybrid with the double-stranded DNA target of comparable stability and with higher affinity to that of the diethylene glycol-γPNA. When formulated into poly(lactic-co-glycolic acid) nanoparticles, the hydroxymethyl-γPNA stimulates higher frequencies (≥ 1.5-fold) of gene modification than the diethylene glycol γPNA in mouse bone marrow cells.
Estimating 4D Data Associations Towards Spatial-Temporal Mapping of Growing Plants for Agricultural Robots

Our world is non-static, and robots should be able to track its changing geometry. For tracking changes, data asso-ciations between 3D points over time are key. In this paper, we investigate the problem of associating 3D points on plant organs from different mapping runs over time while the plants grow. We achieve a high spatial-temporal matching performance by combining 3D RGB-D SLAM, visual place recognition, and 2D/3D matching exploiting background knowledge. We showcase our approach in a real agricultural glasshouse used to grow sweet peppers, using RGB-D observations from a mobile robot traversing the environment. Our experiments suggest that with our approach, we can robustly make data associations in highly repetitive scenes and under changing geometries caused by plant growth. We see our approach as an important step towards spatial-temporal data association for robotic agriculture.
High-resolution volumetric imaging constrains compartmental models to explore synaptic integration and temporal processing by cochlear nucleus globular bushy cells

Globular bushy cells (GBCs) of the cochlear nucleus play central roles in the temporal processing of sound. Despite investigation over many decades, fundamental questions remain about their dendrite structure, afferent innervation, and integration of synaptic inputs. Here, we use volume electron microscopy (EM) to construct synaptic maps that precisely specify convergence ratios and synaptic weights for auditory- nerve innervation and accurate surface areas of all postsynaptic compartments. Detailed biophysically-based compartmental models can help develop hypotheses regarding how GBCs integrate inputs to yield their recorded responses to sound. We established a pipeline to export a precise reconstruction of auditory nerve axons and their endbulb terminals together with high-resolution dendrite, soma, and axon reconstructions into biophysically-detailed compartmental models that could be activated by a standard cochlear transduction model. With these constraints, the models predict auditory nerve input profiles whereby all endbulbs onto a GBC are subthreshold (coincidence detection mode), or one or two inputs are suprathreshold (mixed mode). The models also predict the relative importance of dendrite geometry, soma size, and axon initial segment length in setting action potential threshold and generating heterogeneity in sound-evoked responses, and thereby propose mechanisms by which GBCs may homeostatically adjust their excitability. Volume EM also reveals new dendritic structures and dendrites that lack innervation. This framework defines a pathway from subcellular morphology to synaptic connectivity, and facilitates investigation into the roles of specific cellular features in sound encoding. We also clarify the need for new experimental measurements to provide missing cellular parameters, and predict responses to sound for further in vivo studies, thereby serving as a template for investigation of other neuron classes.
Compact Multiple-Way Power-Dividing Network with Bandpass-Filtering Response Using Spiral Resonators

ABSTRACT A new type of multiple-way out-of-phase power-dividing network with bandpass-filtering response using spiral resonators is proposed. The basic structure unit is a compact two-way out-of-phase power divider with bandpass-filtering response. The introduction of two identical spiral-type resonators can generate transmission zeros in the lower or upper stopband to implement the bandpass-filtering function. Impedance matching and out-of-phase performance are analyzed by using the even- and odd-mode method based on four-port network theory. A four-way out-of-phase power-dividing network with bandpass-filtering response is constructed and designed according to the basic two-way out-of-phase power-dividing structure. The simulated and measured results of the fabricated out-of-phase bandpass-filtering power-dividing network demonstrate the reasonable performance of impedance matching, amplitude balance, and bandpass-filtering function.
Plasmonic circuits for manipulating optical information

Abstract Surface plasmons excited by light in metal structures provide a means for manipulating optical energy at the nanoscale. Plasmons are associated with the collective oscillations of conduction electrons in metals and play a role intermediate between photonics and electronics. As such, plasmonic devices have been created that mimic photonic waveguides as well as electrical circuits operating at optical frequencies. We review the plasmon technologies and circuits proposed, modeled, and demonstrated over the past decade that have potential applications in optical computing and optical information processing.