Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the sequence fitness landscape of a bridge between protein folds

Most foldable protein sequences adopt only a single native fold. Recent protein design studies have, however, created protein sequences which fold into different structures apon changes of environment, or single point mutation, the best characterized example being the switch between the folds of the GA and GB binding domains of streptococcal protein G. To obtain further insight into the design of sequences which can switch folds, we have used a computational model for the fitness landscape of a single fold, built from the observed sequence variation of protein homologues. We have recently shown that such coevolutionary models can be used to design novel foldable sequences. By appropriately combining two of these models to describe the joint fitness landscape of GA and GB, we are able to describe the propensity of a given sequence for each of the two folds. We have successfully tested the combined model against the known series of designed GA/GB hybrids. Using Monte Carlo simulations on this landscape, we are able to identify pathways of mutations connecting the two folds. In the absence of a requirement for domain stability, the most frequent paths go via sequences in which neither domain is stably folded, reminiscent of the propensity for certain intrinsically disordered proteins to fold into different structures according to context. Even if the folded state is required to be stable, we find that there is nonetheless still a wide range of sequences which are close to the transition region and therefore likely fold switches, consistent with recent estimates that fold switching may be more widespread than had been thought. Author Summary While most proteins self-assemble (or “fold”) to a unique three-dimensional structure, a few have been identified that can fold into two distinct structures. These so-called “metamorphic” proteins that can switch folds have attracted a lot of recent interest, and it has been suggested that they may be much more widespread than currently appreciated. We have developed a computational model that captures the propensity of a given protein sequence to fold into either one of two specific structures (GA and GB), in order to investigate which sequences are able to fold to both GA and GB (“switch sequences”), versus just one of them. Our model predicts that there is a large number of switch sequences that could fold into both structures, but also that the most likely such sequences are those for which the folded structures have low stability, in agreement with available experimental data. This also suggests that intrinsically disordered proteins which can fold into different structures on binding may provide an evolutionary path in sequence space between protein folds.
Ramping activity in midbrain dopamine neurons signifies the use of a cognitive map

Journeys to novel and familiar destinations employ different navigational strategies. The first drive to a new restaurant relies on map-based planning, but after repeated trips the drive is automatic and guided by local environmental cues1,2. Ventral striatal dopamine rises during navigation toward goals and reflects the spatial proximity and value of goals3, but the impact of experience, the neural mechanisms, and the functional significance of dopamine ramps are unknown4,5. Here, we used fiber photometry6–8 to record the evolution of activity in midbrain dopamine neurons as mice learned a variety of reward-seeking tasks, starting recordings before training had commenced and continuing daily for weeks. When mice navigated through space toward a goal, robust ramping activity in dopamine neurons appeared immediately – after the first rewarded trial on the first training day in completely naïve animals. In this task spatial cues were available to guide behavior, and although ramps were strong at first, they gradually faded away as training progressed. If instead mice learned to run a fixed distance on a stationary wheel for reward, a task that required an internal model of progress toward the goal, strong dopamine ramps persisted indefinitely. In a passive task in which a visible cue and reward moved together toward the mouse, ramps appeared and then faded over several days, but in an otherwise identical task with a stationary cue and reward ramps never appeared. Our findings provide strong evidence that ramping activity in midbrain dopamine neurons reflects the use of a cognitive map9,10 – an internal model of the distance already covered and the remaining distance until the goal is reached. We hypothesize that dopamine ramps may be used to reinforce locations on the way to newly-discovered rewards in order to build a graded ventral striatal value landscape for guiding routine spatial behavior.
Electron microscopic observation of infected CCB and whole genome analysis of Koi herpesvirus isolate GY01

Background Cyprinid herpesvirus- 3 (CyHV-3), commonly known as Koi herpesvirus (KHV) can induce infectious and acute viremia in common/koi carp (Cyprinus carpio). In an earlier study in this laboratory a KHV isolate GY1506 (KHV GY01 in GeneBank) was isolated from diseased common carp, replicated on CCB cells and identified by PCR targeted on and phylogenetic analysis of thymidine kinase (TK) gene. Electron microscopy examination of GY01 infected CCB cell line and whole genome analysis was studied for further characteristics and epidemiological features of this strain. Results Electron microscopy examination of CCB infected with KHV GY01 strain revealed destruct of infected cells including incomplete nuclear membranes, deformed nucleus, marginalized nuclear chromosome, and the virus of different development stages and morphologies in the cytoplasm and nucleus, which resembles the herpesvirus. MEGA X and phyML were used for multiple alignment and phylogenetic analysis of whole genomes of GY01 and other 21 KHV strains available in GeneBank. analysis showed that GY01 was more close to E and KHV-I and was predicted it originated from the same ancestor as the E and KHV-I. Pairwise alignment of strain GY01 and strain E by Geneious software and YASS online version revealed that two strains had high identity(99.1%) at the nucleotide sequence level although variations and disagreement existed. The number and structure arrangement of open reading frames (orfs) or protein-encoding genes of GY01 is very similar to KHV E, and also to KHV-U but different from KHV-I. The characteristics and function of each orf need further study in the future. Conclusions Pathogenic changes of infected CCB cells and morphologies of KHV GY01 resembles the herpesvirus. Pairwise, multiple alignment and phylogenetic analysis of whole genomes of GY01 and other 21 KHV strains available in GeneBank demonstrated that the GY01 is closely related to strain KHV E and KHV-I and suggested it originated from the same ancestor as the E and KHV-I.
Belief loads of assumptions impact brain networks underlying logical reasoning: A machine learning approach

Prior knowledge and beliefs influence our reasoning in daily life and may lead us to draw unwarranted conclusions with undesirable consequences. The underlying neural correlates of the interaction between belief and logic, prior to making logical decisions, are largely unknown. In this study, we aimed to identify brain regions important in distinguishing belief load of assumptions in logical decision making. Thirty-one healthy volunteers (18-29 years old) participated in an fMRI study and were asked to respond to a series of syllogistic arguments in which assumptions were either congruent (believable) or incongruent (unbelievable) with common knowledge. An interpretable machine learning algorithm, an L1 regularized Support Vector Machine, was used to explain the discriminatory pattern of conditions given the brain activation patterns. Behavioral results confirmed that believable premises were incorrectly endorsed more than unbelievable ones. Imaging results revealed that several connectivity patterns anchored around the insula, amygdala, and IFG were important in distinguishing believable from unbelievable assumptions at different time points preceding logical decisions. Our convergent behavioral and imaging results underscore the importance of the belief loads of our assumptions for a logically sound decision. Our results provide new insights into neural and potential cognitive mechanisms underlying the interaction between belief and logic systems, with important practical implications for social, complex decisions. Highlights Belief load of premises impact logical decisions Regional importance in distinguishing belief load changes in different TRs Belief load of assumptions elicits emotional and salience responses Regional connectivity changes as the reasoning process evolves at different TRs Insula, caudate, amygdala, and IFG were among highly connected hubs during the task Significance It has been experimentally shown that decision-makers often ignore given assumptions in favor of their own beliefs, potentially leading them towards a subjective rather than a logical decision. Consider “Carbon emission tax” given the assumption of “global warming”. If a decision-maker does not believe in “global warming”, the final decision on “Carbon emission tax” is not driven by factual premises but by the personal belief of the decision-maker. Understanding neural mechanisms underlying the interaction between the decision-makers’ beliefs and factual premises sheds light on factors driving belief bias and potential interventions to circumvent it. The main contribution of this study is to investigate neural mechanisms in a logical reasoning task in which the belief load of the assumptions was manipulated.
Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation

Adult skeletal muscles are maintained during homeostasis and regenerated upon injury by muscle stem cells (MuSCs). A heterogeneity in self-renewal, differentiation and regeneration properties has been reported for MuSCs based on their anatomical location. Although MuSCs derived from extraocular muscles (EOM) have a higher regenerative capacity than those derived from limb muscles, the molecular determinants that govern these differences remain undefined. Here we show that EOM and limb MuSCs have distinct DNA methylation signatures associated with enhancers of location-specific genes, and that the EOM transcriptome is reprogrammed following transplantation into a limb muscle environment. Notably, EOM MuSCs expressed host-site specific positional Hox codes after engraftment and self-renewal within the host muscle. However, about 10% of EOM-specific genes showed engraftment-resistant expression, pointing to cell-intrinsic molecular determinants of the higher engraftment potential of EOM MuSCs. Our results underscore the molecular diversity of distinct MuSC populations and molecularly define their plasticity in response to microenvironmental cues. These findings provide insights into strategies designed to improve the functional capacity of MuSCs in the context of regenerative medicine.
Inhibitory interneurons distribute widely across the mouse thalamus and form ontogenetic spatial clusters

The proportion and distribution of local inhibitory neurons (interneurons) in the thalamus varies widely across mammals. This is reflected in the structure of thalamic local circuits, which is more complex in primates compared to smaller-brained mammals like rodents. An increase in the number of thalamic interneurons could arise from addition of novel interneuron types or from elaboration of a plesiomorphic ontogenetic program, common to all mammals. The former has been proposed for the human brain, with migration of interneurons from the ventral telencephalon into higher order thalamus as one of its unique features (Letinic and Rakic, 2001). Here, we identify a larger than expected complexity and distribution of interneurons across the mouse thalamus. All thalamic interneurons can be traced back to two developmental programs: one specified in the midbrain and the other in the forebrain. Interneurons migrate to functionally distinct thalamic nuclei, where the midbrain-derived cells populate the sensory thalamus, and forebrain-generated interneurons only the higher order regions. The latter interneuron type may be homologous to the one previously considered to be human-specific, while we also observe that markers for the midbrain-born class are abundantly expressed in the primate thalamus. These data therefore point to a shared ontogenetic organization of thalamic interneurons across mammals.
Mortalité hivernale massive dans la population de mouflons de Corse (Ovis musimon) de l’archipel subantarctique de Kerguelen

La population de moulons de Corse (Ovis musimon) introduits dans l'archipel de Kerguelen presente un cycle demographique marque par des episodes de mortalite hivernale massive survenant au plus tous les cinq ans. Cet article analyse la mortalite survenue dans cette population lors du crash de l'hiver 1988, marque par la disparition d'au moins 289 individus. Plus de 60% des cadavres ont ete retrouves sous des abris rocheux situes en pied de falaise. Ces sites sont regulierement frequentes par les moulons, ce qui leur permet de reduie les depenses energetiques imposees par la rigueur du climat subantarctique. La mortalite des agneaux a ete particulierement elevee durant le crash hivernal
Trimeric SARS-CoV-2 Spike interacts with dimeric ACE2 with limited intra-Spike avidity

A serious public health crisis is currently unfolding due to the SARS-CoV-2 pandemic. SARS-CoV-2 viral entry depends on an interaction between the receptor binding domain of the trimeric viral Spike protein (Spike-RBD) and the dimeric human angiotensin converting enzyme 2 (ACE2) receptor. While it is clear that strategies to block the Spike/ACE2 interaction are promising as anti-SARS-CoV-2 therapeutics, our current understanding is insufficient for the rational design of maximally effective therapeutic molecules. Here, we investigated the mechanism of Spike/ACE2 interaction by characterizing the binding affinity and kinetics of different multimeric forms of recombinant ACE2 and Spike-RBD domain. We also engineered ACE2 into a split Nanoluciferase-based reporter system to probe the conformational landscape of Spike-RBDs in the context of the Spike trimer. Interestingly, a dimeric form of ACE2, but not monomeric ACE2, binds with high affinity to Spike and blocks viral entry in pseudotyped virus and live SARS-CoV-2 virus neutralization assays. We show that dimeric ACE2 interacts with an RBD on Spike with limited intra-Spike avidity, which nonetheless contributes to the affinity of this interaction. Additionally, we demonstrate that a proportion of Spike can simultaneously interact with multiple ACE2 dimers, indicating that more than one RBD domain in a Spike trimer can adopt an ACE2-accessible “up” conformation. Our findings have significant implications on the design strategies of therapeutic molecules that block the Spike/ACE2 interaction. The constructs we describe are freely available to the research community as molecular tools to further our understanding of SARS-CoV-2 biology.
A process-based metacommunity framework linking local and regional scale community ecology

The metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: 1) density-independent responses to abiotic conditions, 2) density-dependent biotic interactions, and 3) dispersal. Stochasticity is incorporated in the demographic realization of each of these processes. We formalize this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning, and stability within metacommunities.This project was conceived at the sTURN working group, of which all authors are members. PLT developed the framework and model with input from all authors. PLT wrote the model code. PLT and LMG performed the simulations. PLT produced the figures and wrote the first draft with input from LMG and JMC. All authors provided feedback and edits on several versions of the manuscript.All code for running the simulation model and producing the figures is archived on Zenodo - https://doi.org/10.5281/zenodo.3833035.
Membrane bending by protein phase separation

Significance Cellular membranes take on an elaborate set of highly curved and bent shapes which are essential to diverse cellular functions from endocytosis to cell division. The prevailing view has been that membrane bending is driven by proteins with curved shapes, which assemble at the membrane surface to form solid scaffolds. In contrast, here we show that proteins which form liquid-like assemblies on membranes are also potent drivers of bending. These “liquid scaffolds” apply compressive stress to the membrane surface, generating a diverse and dynamic family of membrane shapes. These data, which come at a time when liquid-like protein assemblies are being identified throughout the cell, suggest that protein liquids may play an important role in shaping cellular membranes. Membrane bending is a ubiquitous cellular process that is required for membrane traffic, cell motility, organelle biogenesis, and cell division. Proteins that bind to membranes using specific structural features, such as wedge-like amphipathic helices and crescent-shaped scaffolds, are thought to be the primary drivers of membrane bending. However, many membrane-binding proteins have substantial regions of intrinsic disorder which lack a stable three-dimensional structure. Interestingly, many of these disordered domains have recently been found to form networks stabilized by weak, multivalent contacts, leading to assembly of protein liquid phases on membrane surfaces. Here we ask how membrane-associated protein liquids impact membrane curvature. We find that protein phase separation on the surfaces of synthetic and cell-derived membrane vesicles creates a substantial compressive stress in the plane of the membrane. This stress drives the membrane to bend inward, creating protein-lined membrane tubules. A simple mechanical model of this process accurately predicts the experimentally measured relationship between the rigidity of the membrane and the diameter of the membrane tubules. Discovery of this mechanism, which may be relevant to a broad range of cellular protrusions, illustrates that membrane remodeling is not exclusive to structured scaffolds but can also be driven by the rapidly emerging class of liquid-like protein networks that assemble at membranes.
Adaptation of tobacco plants to elevated CO2: influence of leaf age on changes in physiology, redox states and NADP-malate dehydrogenase activity

Transgenic tobacco plants (Nicotiana tabacum L. cv. Xanthi) with altered chloroplast NADP-malate dehydrogenase (NADP-MDH) content were grown under ambient or under doubled atmospheric CO 2 in order to analyse the effect of elevated CO 2 on the redox state of the chloroplasts. Since large differences exist between the individual leaves of tobacco plants, gas exchange characteristics, enzyme capacities and metabolite contents were measured separately for each leaf of the plants. Large variations between leaves of different age were found in nearly every parameter analysed, and the differences between younger and older leaves were, in most cases, larger than the differences between comparable leaves at ambient or elevated CO 2 . For all parameters (chlorophyll fluorescence, P700 reduction, NADP-MDH activation) that are indicative for the redox situation in the electron transport chains and in the chloroplast stroma, more oxidized values were determined under elevated CO 2 . The increased redox state of ferredoxin, observed at ambient conditions in the NADP-MDH-under-expressing plants, disappeared under elevated CO 2 . It was concluded that the reduced rate of photorespiration under elevated CO 2 decreases the amount of excess electrons. Interestingly, this lowered not only the activation state of NADP-MDH, but also the expression of the enzyme in the wild-type plants. The results are discussed with respect to a possible interaction between stromal reduction state and gene expression.
Synaptic polarity and sign-balance prediction using gene expression data in the Caenorhabditis elegans chemical synapse neuronal connectome network

Graph theoretical analyses of nervous systems usually omit the aspect of connection polarity, due to data insufficiency. The chemical synapse network of Caenorhabditis elegans is a well-reconstructed directed network, but the signs of its connections are yet to be elucidated. Here, we present the gene expression-based sign prediction of the C. elegans connectome, incorporating presynaptic neurotransmitter and postsynaptic receptor gene expression data (3,638 connections and 20,589 synapses total). We made successful predictions for more than two-thirds of all chemical synapses and determined a ratio of excitatory-inhibitory (E:I) interneuronal ionotropic chemical connections close to 4:1 which was found similar to that observed in many real-world networks. Our open source tool (http://EleganSign.linkgroup.hu) is simple but efficient in predicting polarities by integrating neuronal connectome and gene expression data. Author Summary The fundamental way neurons communicate is by activating or inhibiting each other via synapses. The balance between the two is crucial for the optimal functioning of a nervous system. However, whole-brain synaptic polarity information is unavailable for any species and experimental validation is challenging. The roundworm Caenorhabditis elegans possesses a fully mapped connectome with a comprehensive gene expression profile of its 302 neurons. Based on the consideration that the polarity of a synapse must be determined by the neurotransmitter(s) expressed in the presynaptic neuron and the receptors expressed in the postsynaptic neuron, we conceptualized and created a tool that predicts synaptic polarities based on connectivity and gene expression information. We were able to show for the first time that the ratio of excitatory and inhibitory synapses in C. elegans is around 4 to 1 which is in line with the balance observed in many natural systems. Our method opens a way to include spatial and temporal dynamics of synaptic polarity that would add a new dimension of plasticity in the excitatory:inhibitory balance. Our tool is freely available to be used on any network accompanied by any expression atlas.