Miracle-dz/UniFAR-FTUs huggingface dataset:
Allelic compatibility in plant immune receptors facilitates engineering of new effector recognition specificities

Engineering expanded effector recognition in plant immune receptors is a promising prospect for generating new disease resistant crop varieties. However, modification of plant NLR receptors has proven challenging due to the lack of understanding of their context as part of complex immune systems. Here, we demonstrate a new avenue for NLR-mediated engineering that exploits the allelic diversity in the Pik NLR pair to allow for the generation of receptors with expanded recognition specificities, which would otherwise result in constitutive cell death. This work lays the foundation for the incorporation of new effector recognition motifs into the Pik system and advances the development of designer NLRs that can be tailored to specific secreted pathogen signatures. Abstract Engineering the plant immune system offers genetic solutions to mitigate crop diseases caused by diverse agriculturally significant pathogens and pests. Modification of intracellular plant immune receptors of the nucleotide-binding leucine rich repeat (NLRs) superfamily for expanded recognition of pathogen virulence proteins (effectors) is a promising approach for engineering novel disease resistance. However, engineering can cause NLR autoactivation, resulting in constitutive defence responses that are deleterious to the plant. This may be due to plant NLRs associating in highly complex signalling networks that co-evolve together, and changes through breeding or genetic modification can generate incompatible combinations, resulting in autoimmune phenotypes. We have previously shown how alleles of the rice NLR pair Pik have differentially co-evolved, and how sensor/helper mismatching between non-co-evolved alleles triggers constitutive activation and cell death (De la Concepcion et al., 2021b). Here, we dissect incompatibility determinants in the Pik pair and found that HMA domains integrated in Pik-1 not only evolved to bind pathogen effectors but also likely co-evolved with other NLR domains to maintain immune homeostasis. This explains why changes in integrated domains can lead to autoactivation. We then used this knowledge to facilitate engineering of new effector recognition specificities overcoming initial autoimmune penalties. We show that by mismatching alleles of the rice sensor and helper NLRs Pik-1 and Pik-2, we can enable the integration of synthetic HMA domains with novel and enhanced recognition of an effector from the rice blast fungus. Taken together, our results reveal a new strategy for engineering NLRs, which has the potential to allow an expanded set of integrations and therefore new disease resistance specificities in plants.
A concerted mechanism involving ACAT and SREBPs by which oxysterols deplete accessible cholesterol to restrict microbial infection

Most of the cholesterol in the plasma membranes (PMs) of animal cells is sequestered through interactions with phospholipids and transmembrane domains of proteins. However, as cholesterol concentration rises above the PM’s sequestration capacity, a new pool of cholesterol, called accessible cholesterol, emerges. The transport of accessible cholesterol between the PM and the endoplasmic reticulum (ER) is critical to maintain cholesterol homeostasis. This pathway has also been implicated in the suppression of both bacterial and viral pathogens by immunomodulatory oxysterols. Here, we describe a mechanism of depletion of accessible cholesterol from PMs by the oxysterol 25-hydroxycholesterol (25HC). We show that 25HC-mediated activation of acyl coenzyme A: cholesterol acyltransferase (ACAT) in the ER creates an imbalance in the equilibrium distribution of accessible cholesterol between the ER and PM. This imbalance triggers the rapid internalization of accessible cholesterol from the PM, which is sustained for long periods of time through 25HC-mediated suppression of SREBPs. In support of a physiological role for this mechanism, 25HC failed to suppress Zika virus and human coronavirus infection in ACAT-deficient cells, and Listeria monocytogenes infection in ACAT-deficient cells and mice. We propose that selective depletion of accessible PM cholesterol triggered by ACAT activation and sustained through SREBP suppression underpins the immunological activities of 25HC and a functionally related class of oxysterols.
Generalized habitual tendencies in alcohol dependent rats

Habitual responses and ultimately compulsive behavior are thought to be at the core of addiction including alcohol use disorder (AUD). Little is known whether the habitization concerns exclusively the response towards alcohol or generalizes to other daily activities. Here, we address this question in a well-established animal model of AUD – the postdependent rat model – by testing habitual responses towards a sweet palatable reward in two striatal learning paradigms: spatial navigation and reward conditioning. For the spatial navigation task, alcohol-dependent and control rats were tested on a sequential decision-making test after short and prolonged T-Maze training; for the reward conditioning task, rats were trained under a random interval schedule for a short and prolonged period and tested in a satiety devaluation test at each time point. Another cohort of alcohol-naive rats was trained and tested on both paradigms under DREADD (designer receptors exclusively activated by designer drugs)-mediated inactivation of the dorsomedial striatum (DMS) which controls goal-directed behavior. Our results show that alcohol-dependent rats displayed increased habitual behavior to obtain saccharin reward on both paradigms, with overall more habitual choices after prolonged training on the spatial navigation task, and increased habitual responses already after short training on the reward conditioning task. Finally, DREADD-mediated inactivation of the DMS increased habitual behavior in non-dependent rats on both paradigms. Our results provide evidence that a history of alcohol dependence produces a bias towards habitual responding that generalizes to a natural reward in rats. Similarly, a habitual bias was induced in non-dependent rats after inactivation of the DMS, thus confirming the critical role of this region in maintaining goal-directed behavior and suggesting its diminished control in AUD.
METTL7A and METTL7B are responsible for S-thiol methyl transferase activity in liver

S-Methylation of drugs containing thiol-moieties often alters their activity and results in detoxification. Historically, scientists attributed methylation of exogenous aliphatic and phenolic thiols to a putative S-adenosyl-L-methionine dependent membrane-associated phase II enzyme known as thiol methyltransferase (TMT). TMT has a broad substrate specificity and methylates the thiol metabolite of spironolactone, mertansine, ziprasidone, captopril, and the active metabolites of the thienopyridine pro-drugs, clopidogrel, and prasugrel. Despite TMT’s role in the S-methylation of clinically relevant drugs, the enzyme(s) responsible for this activity remained unknown. We recently identified methyltransferase-like protein 7B (METTL7B) as an alkyl thiol-methyltransferase. METTL7B is an endoplasmic-reticulum-associated protein with similar biochemical properties and substrate specificity to TMT. Yet, the historic TMT inhibitor, 2,3-dichloro-α-methylbenzylamine (DCMB), has no effect on the activity of METTL7B, indicating that multiple enzymes contribute to TMT activity. Here we report that methyltransferase-like protein 7A (METTL7A), an uncharacterized member of the METTL7 family, also acts as a thiolmethyltransferase. METTL7A exhibits similar biochemical properties to TMT, including inhibition by DCMB (IC50 1.2 µM). Applying quantitative proteomics to human liver microsomes and gene modulation experiments in HepG2 and HeLa cells, we determined that TMT activity correlates closely with METTL7A and METTL7B protein levels. Furthermore, purification of a novel His-GST-tagged recombinant protein and subsequent activity experiments prove that METTL7A can selectively methylate exogenous thiol-containing substrates, including 7α-thiospironolactone, dithiothreitol, 4-chlorothiophenol, and mertansine. We conclude that the METTL7 family encodes for two enzymes, METTL7A and METTL7B, which we have renamed TMT1A1 and TMT1B1, respectively, that are responsible for TMT activity in liver microsomes. Significance Statement We identified METTL7A (TMT1A1) and METTL7B (TMT1B1) as the enzymes responsible for the microsomal alkyl thiol methyltransferase activity. These are the first two enzymes directly associated with microsomal TMT activity. S-Methylation of many commonly prescribed thiol-containing drugs alters their pharmacological activity and/or toxicity, and identifying the enzymes responsible, will improve our understanding of the DMPK properties of alkyl- or phenolic-thiol-containing therapeutics. Visual Abstract
Gut Microbial Disruption in Critically Ill Patients with COVID-19-Associated Pulmonary Aspergillosis

Objectives COVID-19 disease can be exacerbated by Aspergillus superinfection (CAPA). The causes of CAPA are not yet fully understood. Recently, alterations in the gut microbiome have been associated with a complicating course and increasing severity of COVID-19 disease, most likely via immunological mechanisms. Aim of this study was to investigate a potential association between severe CAPA and alterations in the gut and bronchial microbiota. Methods We performed 16S rRNA gene amplicon sequencing of stool and bronchial samples from a total of 16 COVID-19 patients with CAPA and 26 patients without CAPA. All patients were admitted to the intensive care unit. Results were carefully tested for potential influences on the microbiome during hospitalization. Results We found that late in COVID-19 disease, CAPA patients exhibited a trend towards reduced gut microbial diversity. Furthermore, late stage CAPA disease showed an increased presence of Staphylococcus epidermidis in the gut. This is not found in late non-CAPA cases or early disease. The analysis of bronchial samples did not show significant results. Conclusions This is the first study showing alterations in the gut microbiome accompany severe CAPA and possibly influence the host’s immunological response. In particular, an increase of Staphylococcus epidermidis in the intestine could be of importance. Summary The composition of intestinal bacteria in severe CAPA disease is altered with an increase in Staphylococcus epidermidis in the gut. Alterations in the composition of intestinal bacteria in severe CAPA may indicate immunologic involvement of the gut in the disease.
Deep Local Analysis estimates effects of mutations on protein-protein interactions

The spectacular advances in protein and protein complex structure prediction hold promises for the reconstruction of interactomes at large scale at the residue resolution. Beyond determining the 3D arrangement of interacting partners, modeling approaches should be able to sense the impact of sequence variations such as point mutations on the strength of the association. In this work, we report on DLA-mutation, a novel and efficient deep learning framework for accurately predicting mutation-induced binding affinity changes. It relies on a 3D-invariant description of local 3D environments at protein interfaces and leverages the large amounts of available protein complex structures through self-supervised learning. It combines the learnt representations with evolutionary information, and a description of interface structural regions, in a siamese architecture. DLA-mutation achieves a Pearson correlation coefficient of 0.81 on a large collection of more than 2000 mutations, and its generalization capability to unseen complexes is higher than state-of-the-art methods.
Modeling supernova remnants: effects of diffusive cosmic-ray acceleration on the evolution and application to observations

We present numerical models for supernova remnant evolution, using a new version of the hydrodynamical code SUPREMNA. We added a cosmic-ray diffusion equation to the code scheme, employing a two-fluid approximation. We investigate the dynamics of the simulated supernova remnants with different values of the cosmic-ray acceleration efficiency and the diffusion coefficient. We compare the numerical models with observational data of Tycho’s and SN1006 supernova remnants. We find models that reproduce the observed locations of the blast wave, contact discontinuity, and reverse shock for both remnants, thus allowing us to estimate the contribution of cosmic-ray particles to total pressure and cosmic-ray energy losses in these supernova remnants. We evaluate the energy losses due to cosmic rays escape in Tycho’s supernova remnant to be 10−20% of the kinetic energy flux and 20−50% in SN1006.
Characterization of the HHV-6 U20 immunoevasin

Roseoloviruses (HHV-6A, -6B, and -7) infect >90% of the human population during early childhood, and are thought to remain latent or persistent throughout the life of the host. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet very little is known about how these viruses so successfully escape host defenses. Herein, we characterize the HHV6A and HHV6B U20 gene products, which are encoded within a block of genes unique to the roseoloviruses, and therefore of particular interest. Despite 92% amino acid identity, U20 proteins from HHV6A and 6B have been shown to possess different host evasion functions. Here we characterize expression, trafficking, and post-translational modifications of U20 during HHV6A infection. While U20 localized to lysosomes in HHV-6A-infected cells, HHV-6B U20 trafficked to the cell surface and was rapidly internalized. HHV-6B U20 trafficked slowly through the secretory system, receiving several post translational modifications to its N-linked glycans indicative of surface expressed glycoproteins. Interestingly, U20 is also phosphorylated on at least one Ser, Thr, or Tyr residue. These results provide a framework to understand the role(s) of U20 in evading host defenses. Importance HHV6A and HHV6B U20 proteins are virus-encoded integral membrane glycoproteins possessing class I MHC-like folds. As such, it is tempting to speculate that they are involved in host evasion. Indeed, although they share 92% identity, HHV6A U20 has been shown to target NK activating ligands (1) and HHV6B U20 has been shown to inhibit TNF receptor signaling and apoptosis (2). Here, we have performed cell biological and biochemical characterization of the trafficking, glycosylation, and post-translational modifications occurring on HHV6A and -6B U20, and we demonstrate U20 expression in the context of HHV6 infection.
Complex Intracellular Mechanisms of TBK1 Kinase Activation Revealed by a Specific Small Molecule Inhibitor

TANK-binding kinase 1 (TBK1), a dimeric serine/threonine protein kinase, plays a critical role in multiple signaling pathways including innate immunity, autophagy and cell death. TBK1 is activated by the phosphorylation of an essential serine residue 172 (S172) within the activation loop of the kinase domain, and this phosphorylation can occur by trans-autophosphorylation: one TBK1 dimer phosphorylates a second dimer at S172. Here we show that phosphorylation of TBK1 S172 in cultured human cells in response to multiple inducers is reduced, but not abolished by the highly specific and potent TBK1 small molecule inhibitor GSK8612. Thus, upstream kinase(s) must phosphorylate TBK1 in response to inducers in cultured cells. We show that distinct upstream kinases are recruited for the activation of TBK1 in response to different inducers. We also identify extensive crosstalk among TBK1, IKKβ and IKKε kinases in the cellular response to various inducers. In addition, we show that dsDNA and dsRNA trigger dynamic intracellular translocation of TBK1, leading to its localization and activation on the Golgi apparatus or mitochondria, respectively. GSK8612 does not block the intracellular localization of TBK1. We conclude that TBK1 is activated by both upstream kinase phosphorylation and by trans-autophosphorylation, and the signal-dependent spatial engagement of TBK1 with other signaling molecules is a fundamental mechanism for its specific activation by multiple inducers.
Neural dynamics and geometry for transitive inference

The ability to make inferences using abstract rules and relations has long been understood to be a hallmark of human intelligence, as evidenced in logic, mathematics, and language. Intriguingly, modern work in animal cognition has established that this ability is evolutionarily widespread, indicating an ancient and possibly foun-dational role in natural intelligence. Despite this importance, it remains an open question how inference using abstract rules is implemented in the brain — possibly due to a lack of competing hypotheses at the level of collective neural activity and of behavior. Here we report the generation and analysis of a collection of neural networks (NNs) that perform transitive inference (TI), a classical cognitive task that requires inference of a single abstract relation between novel combinations of inputs (if A > B and B > C, then A > C). We found that NNs generated using standard training methods (i) generalize fully (i.e. to all novel combinations of inputs), (ii) generalize when inference requires working memory (WM), a capacity thought to be essential for inference in living subjects, (iii) express multiple emergent behaviors long documented in humans and animals, in addition to novel behaviors not previously studied, and (iv) adopt diﬀerent solutions that yield alternative predictions for both behavior and collective neural activity. Further, a subset of NNs expressed a “subtractive” solution that was characterized in neural activity space by a simple dynamical pattern (an oscillation) and geometric arrangement (ordered collinearity). Together, these ﬁndings show how collective neural activity can accomplish generalization according to an abstract rule, and provide a series of testable hypotheses not previously established in the study of TI. More broadly, these ﬁndings suggest new ways to understand how neural systems realize abstract rules and relations.
Anterograde Trafficking of Toll-Like Receptors Requires the Cargo Sorting Adaptors TMED-2 and 7 and specific N-glycans

Toll-Like Receptors (TLRs) play a pivotal role in immunity by recognizing conserved structural features of pathogens and initiating the innate immune response. TLR signaling is subject to complex regulation that remains poorly understood. Here we show that two small type I transmembrane receptors, TMED2 and 7, that function as cargo sorting adaptors in the early secretory pathway are required for transport of TLRs from the ER to Golgi. Protein interaction studies reveal that TMED7 interacts with TLR2, TLR4, and TLR5 but not with TLR3 and TLR9. On the other hand, TMED2 interacts with TLR2, TLR4 and TLR3. Dominant negative forms of TMED7 suppress the export of cell surface TLRs from the ER to the Golgi. By contrast TMED2 is required for the ER-export of both plasma membrane and endosomal TLRs. We also find that a specific N-linked glycan of TLR2 is required for anterograde trafficking and may be directly recognised by TMEDs. Together, these findings suggest that association of TMED2 and TMED7 with TLRs facilitates anterograde transport from the ER to the Golgi.
Dopamine depletion leads to pathological synchronization of distinct basal ganglia loops in the beta band

Motor symptoms of Parkinson’s Disease (PD) are associated with dopamine deficits and pathological oscillation of basal ganglia (BG) neurons in the β range ([12-30] Hz). However, how the dopamine depletion affects the oscillation dynamics of BG nuclei is still unclear. With a spiking neurons model, we here captured the features of BG nuclei interactions leading to oscillations in dopamine-depleted condition. We found that both the loop between subthalamic nucleus and Globus Pallidus pars externa (GPe) and the loop between striatal fast spiking and medium spiny neurons and GPe displayed resonances in the β range, and synchronized to a common β frequency through interaction. Crucially, the synchronization depends on dopamine depletion: the two loops were largely independent for high levels of dopamine, but progressively synchronized as dopamine was depleted due to the increased strength of the striatal loop. Our results highlight the role of the interplay between the GPe-STN and the GPe-striatum loop in generating sustained β oscillations in PD subjects, and explain how this interplay depends on the level of dopamine. This paves the way to the design of therapies specifically addressing the onset of pathological β oscillations. Author summary Parkinson’s Disease is associated to the death of neurons generating a particular neurotransmitter: the dopamine. Motor symptoms of PD, on the other hand, are known to be due to dysfunctions in a particular subcortical area of the brain, the BG network. In particular, the BG network develops pathological oscillations in a specific frequency range (β: [12-30] Hz). What is unclear is how dopamine depletion leads to these oscillations. In this work we developed a BG network model and we found the actual reason for these abnormal oscillations is the synchronization of two loops within the network that are individually oscillating in the β range. For healthy level of dopamine the two loops are decoupled and the oscillation power is low. When dopamine is depleted (as in PD) the two loops synchronize and originate the pathological oscillations associated with motor symptoms.
The fundamental role of symmetry in nuclear models

The purpose of these lectures is to illustrate how symmetry and pattern recognition play essential roles in the progression from experimental observation to an understanding of nuclear phenomena in terms of interacting neutrons and protons. We do not discuss weak interactions nor relativistic and sub-nucleon degrees of freedom. The explicit use of symmetry and the power of algebraic methods, in combination with analytical and geometrical methods are illustrated by their use in deriving a shell-model description of nuclear rotational dynamics and the structure of deformed nuclei.
Magnetic Stability of Massive Star-forming Clumps in RCW 106

The RCW 106 molecular cloud complex is an active massive star-forming region where a ministarburst is taking place. We examined its magnetic structure by near-IR polarimetric observations with the imaging polarimeter SIRPOL on the IRSF 1.4 m telescope. The global magnetic field is nearly parallel to the direction of the Galactic plane and the cloud elongation. We derived the magnetic field strength of ∼100–1600 μG for 71 clumps with the Davis–Chandrasekhar–Fermi method. We also evaluated the magnetic stability of these clumps and found that massive star-forming clumps tend to be magnetically unstable and gravitationally unstable. Therefore, we propose a new criterion to search for massive star-forming clumps. These details suggest that the process enhancing the clump density without an increase of the magnetic flux is essential for the formation of massive stars and the necessity for accreting mass along the magnetic field lines.