Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid adaptation to human protein kinase R by a unique genomic rearrangement in rhesus cytomegalovirus

Cytomegaloviruses (CMVs) are generally unable to cross species barriers, in part because prolonged coevolution with one host species limits their ability to evade restriction factors in other species. However, the limitation in host range is incomplete. For example, rhesus CMV (RhCMV) can replicate in human cells, albeit much less efficiently than in rhesus cells. Previously we reported that the protein kinase R (PKR) antagonist encoded by RhCMV, rTRS1, has limited activity against human PKR but is nonetheless necessary and sufficient to enable RhCMV replication in human fibroblasts (HF). We now show that knockout of PKR in human cells or treatment with the eIF2B agonist ISRIB, which overcomes the translational inhibition resulting from PKR activation, augments RhCMV replication in HF, indicating that human PKR contributes to the inefficiency of RhCMV replication in HF. Serial passage of RhCMV in HF reproducibly selected for viruses with improved fitness in human cells. The evolved viruses contain an inverted duplication of the terminal 6.8 kb of the genome, including rTRS1. The duplication replaces ~11.8 kb just downstream of an internal sequence element, pac1-like, which is very similar to the pac1 cleavage and packaging signal found near the terminus of the genome. Plaque-purified evolved viruses produced at least twice as much rTRS1 as the parental RhCMV and blocked the PKR pathway more effectively in HF. Southern blots revealed that unlike the parental RhCMV, viruses with the inverted duplication isomerize in a manner similar to HCMV and other herpesviruses that have internal repeat sequences. The apparent ease with which this duplication event occurs raises the possibility that the pac1-like site, which is conserved in Old World monkey CMV genomes, may serve a function in facilitating rapid adaptation to evolutionary obstacles. AUTHOR SUMMARY Rhesus macaque CMV (RhCMV) is an important model for human CMV (HCMV) pathogenesis and vaccine development. Therefore, it is important to understand the similarities and differences in infectivity and interaction of these viruses with their host species. In contrast to the strict species-specificity of HCMV, RhCMV is able to cross species barriers to replicate in human cells. We know from past work that a component of this broader host range is RhCMV’s ability to counteract both the rhesus and human versions of a key antiviral factor. Here we delve further into the mechanisms by which RhCMV can adapt to counteract human cellular defenses. We find that RhCMV appears to be poised to undergo a specific genomic rearrangement that facilitates increased replication efficiency in human cells. Besides providing insights into CMV species-specificity and host barriers to cross-species transmission, this work also provides more generalized clues about viral adaptative mechanisms.
Cryopreservation of Hydractinia symbiolongicarpus Sperm to Support Community-Based Repository Development for Preservation of Genetic Resources

Hydractinia symbiolongicarpus is an emerging model organism in which cutting-edge genomic tools and resources are being developed for use in a growing number of research fields. However, one limitation of this model system is the lack of long-term storage for genetic resources. Our goal in this study was to establish a generalizable approach to sperm cryopreservation that would support future repository development and could be applied to many species according to available resources. Our approach was to: 1) Assess sperm characteristics and standardize collection and processing; 2) Assess acute toxicity to cryoprotectants, and 3) Evaluate and refine freezing conditions to permit post-thaw fertilization and produce viable offspring. By following this approach, we found that Hydractinia sperm incubated in 5% DMSO, equilibrated at 4°C for 20 min, and cooled at a rate of 20°C/min to - 80°C at a cell concentration of 108-109/mL in 0.25-mL aliquots were able to fertilize 150-300 eggs which yielded offspring that could metamorphose into juvenile polyps. In addition, improvements were made for processing sperm using a customized 3-D printed collection system. Other opportunities for improvement include optimizing the volumetric sperm-to-egg ratio for fertilization. Establishing repository capabilities for the Hydractinia research community will be essential for future development, maintenance, protection, and distribution of genetic resources. More broadly, this application-based approach highlights the long-term value of establishing repository-level resources that can be expanded to fit community needs.
Tonic dopamine, uncertainty and basal ganglia action selection

To make optimal decisions in uncertain circumstances flexible adaption of behaviour is required; exploring alternatives when the best choice is unknown, exploiting what is known when that is best. Using a detailed computational model of the basal ganglia, we propose that switches between exploratory and exploitative decisions can be mediated by the interaction between tonic dopamine and cortical input to the basal ganglia. We show that a biologically detailed action selection circuit model of the basal ganglia, endowed with dopamine dependant striatal plasticity, can optimally solve the explore-exploit problem, estimating the true underlying state of a noisy Gaussian diffusion process. Critical to the model’s performance was a fluctuating level of tonic dopamine which increased under conditions of uncertainty. With an optimal range of tonic dopamine, explore-exploit decision making was mediated by the effects of tonic dopamine on the precision of the model action selection mechanism. Under conditions of uncertain reward pay-out, the model’s reduced selectivity allowed disinhibition of multiple alternative actions to be explored at random. Conversely, when uncertainly about reward pay-out was low, enhanced selectivity of the action selection circuit was enhanced, facilitating exploitation of the high value choice. When integrated with phasic dopamine dependant influences on cortico-striatal plasticity, the model’s performance was at the level of the Kalman filter which provides an optimal solution for the task. Our model provides an integrative account of the relationship between phasic and tonic dopamine and the action selection function of the basal ganglia and supports the idea that this subcortical neural circuit may have evolved to facilitate decision making in non-stationary reward environments, allowing a number of experimental predictions with relevance to abnormal decision making in neuropsychiatric and neurological disease.
Glypicans specifically regulate Hedgehog signaling through their interaction with Ihog in cytonemes

The conserved family of Hedgehog (Hh) signaling proteins plays a key role in cell-cell communication in development, tissue repair and cancer progression. These proteins can act as morphogens, inducing responses dependent on the ligand concentration in target cells located at a distance. Hh proteins are lipid modified and thereby have high affinity for membranes, which hinders the understanding of their spreading across tissues. Direct contact between cell membranes by filopodia-like structures (also known as cytonemes) could be the simplest explanation for Hh dispersal. To better understand this signaling mechanism, we have analyzed in Drosophila the interaction between the glypicans that, besides for other pathways, are necessary for Hh signaling, plus the adhesion molecules and Hh coreceptors Ihog and Boi. We describe that glypicans (Dally and Dally-like protein) are required to maintain Ihog, but not Boi, protein levels. We also show that ectopic Ihog stabilizes cytonemes through its interaction with glypicans, and we determine that two Ihog fibronectin III domains are essential for this interaction. Our data suggest that this interaction with Ihog in cytonemes confers the specificity of glypicans for Hh signaling.
Nsp1 of SARS-CoV-2 Stimulates Host Translation Termination

The Nsp1 protein of SARS-CoV-2 regulates the translation of host and viral mRNAs in cells. Nsp1 inhibits host translation initiation by binding to the entry channel of the 40S ribosome subunit. The structural study of SARS-CoV-2 Nsp1-ribosomal complexes reported post-termination 80S complex containing Nsp1 and the eRF1 and ABCE1 proteins. Considering the presence of Nsp1 in the post-termination 80S ribosomal complex simultaneously with eRF1, we hypothesized that Nsp1 may be involved in translation termination. We show the direct influence of Nsp1 on translation termination. Using a cell-free translation system and reconstituted in vitro translation system, we reveal that Nsp1 stimulates translation termination in the stop codon recognition stage. We identify that activity of Nsp1 in translation termination is localized in its N-terminal domain. The data obtained will enable an investigation of new classes of potential therapeutic agents from coronavirus infection competing with Nsp1 for binding with the termination complex.
Multivariate Genetic Analysis

The goal of multivariate genetic analysis is to estimate the causes of genetic and environmental covariation between phenotypes. As with univariate modeling, when data from genetically informative relatives such as twins are available, the genetic and environmental components of covariation can be separated by a technique which is analogous to factor analysis (Martin & Eaves,). This is achieved by making use of the additional information in the cross-correlations between relatives for different traits (or same traits measured at different times) and can allow researches to estimate the extent to which genetic and environmental influences are shared in common by several traits or are trait specific. The various forms of multivariate analyses covered in this section include the Cholesky decomposition, common and independent genetic pathway models, and genetic simplex modeling. This section will give the reader an appreciation for the flexibility of SEM approaches to address more complicated questions beyond simpler univariate decompositions. Keywords: Cholesky decomposition; common pathway; covariation; factor analysis; independent pathway; multivariate genetic analysis; simplex modelling
Neural network fast-classifies biological images using features selected after their random-forests-importance to power smart microscopy

Artificial intelligence is nowadays used for cell detection and classification in optical microscopy, during post-acquisition analysis. The microscopes are now fully automated and next expected to be smart, to make acquisition decisions based on the images. It calls for analysing them on the fly. Biology further imposes training on a reduced dataset due to cost and time to prepare the samples and have the datasets annotated by experts. We propose here a real-time image processing, compliant with these specifications by balancing accurate detection and execution performance. We characterised the images using a generic, high-dimensional feature extractor. We then classified the images using machine learning for the sake of understanding the contribution of each feature in decision and execution time. We found that the non-linear-classifier random forests outperformed Fisher’s linear discriminant. More importantly, the most discriminant and time-consuming features could be excluded without any significant loss in accuracy, offering a substantial gain in execution time. We offer a method to select fast and discriminant features. In our assay, a 79.6 ± 2.4 % accurate classification of a cell took 68.7 ± 3.5 ms (mean ± SD, 5-fold cross-validation nested in 10 bootstrap repeats), corresponding to 14 cells per second, dispatched into 8 phases of the cell cycle using 12 feature-groups and operating a consumer market ARM-based embedded system. Interestingly, a simple neural network offered similar performances paving the way to faster training and classification, using parallel execution on a general-purpose graphic processing unit.
Dengue virus protease activity modulated by dynamics of protease cofactor

The viral protease domain (NS3pro) of dengue virus is essential for virus replication and its cofactor NS2B is indispensable for the proteolytic function. Although several NS3pro-NS2B complex structures have been obtained, the dynamic property of the complex remains poorly understood. Using NMR relaxation techniques, here we found that NS3pro-NS2B exists in both closed and open conformations which are in dynamic equilibrium on a sub-millisecond timescale in aqueous solution. Our structural information indicates that the C-terminal region of NS2B is disordered in the open conformation but folded in the closed conformation. Using mutagenesis, we showed that the closed-open conformational equilibrium can be shifted by changing NS2B stability. Moreover, we revealed that the proteolytic activity of NS3pro-NS2B correlates well with the population of the closed conformation. Our results suggest that the closed-open conformational equilibrium can be used by both nature and man to control the replication of dengue virus. Statement of Significance The dengue virus protease is an attractive target for drug development against dengue fever as it is essential for virus replication. However, its structure-based drug development has been unsuccessful due to the shallow substrate-binding pocket. The study presented here demonstrates for the first time that the protease activity can be reduced dramatically by shifting the closed-open conformational equilibrium of the protease in complex with its cofactor from the majority of a closed conformation to the majority of an open conformation. Moreover, our work clarifies the structure of the open conformation which has been elusive for a long time. Our results also suggest an alternative method for designing protease inhibitors based on the closed-open conformational equilibrium.
IOCBIO Sparks detection and analysis software

Analysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic calcium sparks detection from line scan confocal images. The developed software is tailored for detecting only calcium sparks, allowing us to design a graphical user interface specifically for this task. The software enables detecting sparks automatically as well as adding, removing, or adjusting regions of interest marking each spark. The results of the analysis are stored in an SQL database, allowing simple integration with statistical tools. We have analyzed the performance of the algorithm using a large set of synthetic images with varying spark sizes and noise levels and also compared the analysis results with results obtained by software established in the field. The use of our software is illustrated by an analysis of the effect of isoprenaline (ISO) on spark frequency, amplitude, and spatial and temporal characteristics. For that, cardiomyocytes from C57BL/6 mice were used. We demonstrated an increase in spark frequency, tendency of having larger spark amplitudes, sparks with a longer duration, and occurrence of multiple sparks from the same site in the presence of ISO. We also show that the duration and the width of sparks with the same amplitude were similar in the absence and presence of ISO. The software was released as an open source repository and is available for free use and collaborative development.
HERC1 Regulates Breast Cancer Cells Migration and Invasion

Tumor cell migration and invasion into adjacent tissues is one of the hallmarks of cancer and the first step towards secondary tumors formation, which represents the leading cause of cancer-related deaths. This process is considered an unmet clinical need in the treatment of this disease, particularly in breast cancers characterized by high aggressiveness and metastatic potential. In order to identify and characterize genes with novel functions as regulators of tumor cell migration and invasion, we performed a genetic loss-of-function screen using a shRNA library directed against the Ubiquitin Proteasome System (UPS) in a highly invasive breast cancer derived cell line. Among the candidates, we validated HERC1 as a gene regulating cell migration and invasion. Furthermore, using animal models, our results indicated that HERC1 silencing affects primary tumor growth and lung colonization. Finally, we conducted an in-silico analysis using publicly available protein expression data and observed an inverse correlation between HERC1 expression levels and breast cancer patients’ overall survival. Altogether, our findings demonstrate that HERC1 might represent a novel therapeutic target for the development or improvement of breast cancer treatment.
Illusory size perception with stimuli from animal experiments of surround modulation

Visual illusions have long been studied because the illusory effect they induce is believed to tell us something important on how the visual system processes visual information. Here, we modified a classic visual illusion, the Delboeuf illusion, so that it resembled a type of stimulus commonly used in experiments investigating surround modulation. We then performed a small set of psychophysical experiments in order to determine if the classical Delboeuf illusion effect, i.e. a change in the perceived size of an object, could be observed in these altered stimuli. In four conditions, we created stimuli that either had a high or low frequency surround in addition to being presented with a proximal thin surround or a distal thick surround. We found a significant difference in perceived object size for all four conditions compared to control indicating the presence of an illusion, and we discuss these findings in relation to existing literature from electrophysiological animal studies.
Mark-release-recapture of male Aedes aegypti (Diptera: Culicidae): Use of rhodamine B to estimate movement, mating and population parameters in preparation for an incompatible male program

Rapid advances in biological and digital technologies are revolutionizing the population control of invasive disease vectors such as Aedes aegypti. Methods such as the sterile and incompatible insect techniques (SIT/IIT) rely on modified males to seek out and successfully mate with females, and in doing so outcompete the wild male population for mates. Currently, these interventions infer the success of mating interactions between male and female insects through area-wide population surveillance and observations of mating competitiveness are rare. Furthermore, little is known about male Ae. aegypti behaviours and biology in field settings. In preparation for a large, community scale IIT program, we undertook a series of mark-release-recapture experiments using rhodamine B to mark male Ae. aegypti sperm and measure mating interactions with females. We also developed the Spatial and Temporally Evolving Isotropic Kernel (STEIK) framework to assist researchers to estimate the movement of individuals through space and time. Results showed that ~40% of daily females captured were unmated, suggesting interventions will need to release males regularly to be effective at suppressing Ae. aegypti populations. Males moved rapidly through the landscape, particularly when released during the night. Although males moved further than what is typically observed in females of the species, survival was considerably lower. These unique insights will lead to a greater understanding of mating interactions in wild insect populations and lay the foundation for robust suppression strategies in the future. Author Summary Modern scientific techniques for controlling populations of the dengue vector, Aedes aegypti, utilize the mating biology of adult male mosquitoes to achieve suppression through a sterilization process. As the study of Ae. aegypti control has typically focused on adult female mosquitoes, knowledge on male movement, survival and mating interactions in the field is lacking. Here we undertook several mark-release-recapture experiments on adult male Ae. aegypti in Innisfail, Australia, and measured important biological parameters. For the first time in large field experiments, we employed rhodamine B as a marker that when fed to adult males, identified both marked males and the wild females they mated with. We observed males moving further through the landscape, but surviving for a shorter period, than previous measurements undertaken on females in a field setting. A high proportion (~40%) of unmated females suggests individuals are constantly available for mating. As such, sterile male strategies may need to release at regular intervals to achieve effective population suppression. The unique insights provided by this study will assist in designing future sterile male field interventions.
Evolution of mushroom body inversion and associated gyriform neuropils parallel the evolved transposition of the mammalian hippocampus

1 Neural organization of mushroom bodies (MB) is largely consistent across insects, whereas 2 across malacostracan crustaceans the ancestral ground pattern diverges broadly, resulting in 3 successive loss of lobes and acquisition of domed MBs retaining ancestral Hebbian-like 4 networks and aminergic connections. We demonstrate here a radical departure from this 5 evolutionary trend in the recent malacostracan lineage Brachyura. In the shore crab, 6 Hemigrapsus nudus, MBs are entirely inverted. Instead of their expected location at the brain’s 7 rostral surface, inverted calyces are buried deep within it, extending columns (lobes) outwards to 8 an expansive system of cortex-like gyri. This elaborate ensemble is DC0-immunoreactive, 9 indicating extensive circuits for cognition. MB inversion and association with overlying gyri is 10 an evolutionary novelty comparable to transposition of mammalian hippocampus to a location 11 beneath multistratified cortices. We propose the brachyuran’s unique MB and its associated 12 gyriform centers have enabled its successful exploitation of topographically challenging habitats 13 in water and on land. 14
Geographic variation in the seed mycobiome of Pseudotsuga menziesii var. menziesii across the Pacific Northwest, USA

Fungal symbionts occur in all plant tissues, and many aid their host plants with critical functions, including nutrient acquisition, defense against pathogens, and tolerance of abiotic stress. “Core” taxa in the plant mycobiome, defined as fungi present across individuals, populations, or time, may be particularly crucial to plant survival during the challenging seedling stage. However, studies on core seed fungi are limited to individual sampling sites, raising the question of whether core taxa exist across large geographic scales. We addressed this question using both culture-based and culture-free techniques to identify the fungi found in individual seeds collected from nine provenances across the range of Coastal Douglas-fir (Pseudotsuga menziesii var. menziesii), a foundation tree species in the Pacific Northwest and a globally important timber crop that is propagated commercially by seed. Two key findings emerged: 1) Seed mycobiome composition differed among seed provenances. 2) Despite spatial variation in the seed mycobiome, we detected four core members, none of which is a known pathogen of Douglas-fir: Trichoderma spp. , Hormonema macrosporum, Mucor plumbeus and Talaromyces rugulosus. Our results support the concept of a core seed microbiome, yet additional work is needed to determine the functional consequences of core taxa for seedling germination, growth, survival and competition.