Miracle-dz/UniFAR-FTUs huggingface dataset:
Sodium ion regulates liquidity of biomolecular condensates in hyperosmotic stress response

Biomolecular condensates are membraneless structures formed through phase separation. Recent studies have demonstrated that the material properties of biomolecular condensates are crucial for their biological functions and pathogenicity. However, the phase maintenance of biomolecular condensates in cells remains elusive. Here, we show that sodium ion (Na+) influx regulates the condensate liquidity under hyperosmotic stress. The fluidity of ASK3 condensates increases at the high intracellular Na+ concentration derived from extracellular hyperosmotic solution. Moreover, we identified TRPM4 as a cation channel that allows Na+ influx under hyperosmotic stress. TRPM4 inhibition causes the liquid-to-solid phase transition of ASK3 condensates, leading to impairment of the ASK3 osmoresponse. In addition to ASK3 condensates, intracellular Na+ widely regulates the condensate liquidity and aggregate formation of biomolecules, including DCP1A, TAZ and polyQ-protein, under hyperosmotic stress. Our findings demonstrate that changes in Na+ contribute to the cellular stress response via liquidity maintenance of biomolecular condensates.
Nanobody‐mediated complement activation to kill HIV‐infected cells

The complement system which is part of the innate immune response against invading pathogens, represents a powerful mechanism for killing of infected cells. Utilizing direct complement recruitment for complement-mediated elimination of HIV-1-infected cells is underexplored. We developed a novel therapeutic modality to direct complement activity to the surface of HIV-1-infected cells. This bispecific complement engager (BiCE) is comprised of a nanobody recruiting the complement-initiating protein C1q, and single-chain variable fragments of broadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope (Env) protein. Here, we show that two anti-HIV BiCEs targeting the V3 loop and the CD4 binding site, respectively, increase C3 deposition and mediate complement-dependent cytotoxicity (CDC) of HIV-1 Env expressing Raji cells. Furthermore, anti-HIV BiCEs trigger complement activation on primary CD4 T cells infected with laboratory-adapted HIV-1 strain and facilitates elimination of HIV-1-infected cells over time. In summary, we present a novel approach to direct complement deposition to the surface of HIV-1-infected cells leading to complement-mediated killing of these cells.
Gait Abnormalities and Aberrant D2 Receptor Expression and Signaling in a Mouse Model of the Human Pathogenic Mutation DRD2I212F

A dopamine D2 receptor mutation was recently identified in a family with a novel hyperkinetic movement disorder (Mov Disord 36: 729-739, 2021). That allelic variant D2-I212F is a constitutively active and G protein-biased receptor. We now describe mice engineered to carry the D2-I212F variant, Drd2I212F. The mice exhibited gait abnormalities resembling those in other mouse models of chorea and/or dystonia, and had decreased striatal D2 receptor expression. Electrically evoked IPSCs in midbrain dopamine neurons and striatum from Drd2I212F mice exhibited slow onset and decay compared to wild type mice. In the presence of dopamine, current decay initiated by photolytic release of sulpiride from CyHQ-sulpiride was slower in midbrain slices from Drd2I212F mice than Drd2+/+ mice. Furthermore, in contrast to wild type mice in which dopamine is more potent at neurons in the nucleus accumbens than in the dorsal striatum, reflecting activation of Gαo vs. Gαi1, dopamine had similar potencies in those two brain regions of Drd2I212F mice. Repeated cocaine treatment, which decreases dopamine potency in the nucleus accumbens of wild type mice, had no effect on dopamine potency in Drd2I212F mice. The results demonstrate the utility of this mouse model for investigating the role of pathogenic DRD2 variants in early-onset hyperkinetic movement disorders.
Lipid Transport by Candida albicans Dnf2 Is Required for Hyphal Growth and Virulence

Candida albicans is a common cause of human mucosal yeast infections, and invasive candidiasis can be fatal. Antifungal medications are limited, but those targeting the pathogen cell wall or plasma membrane have been effective. ABSTRACT Candida albicans is a common cause of human mucosal yeast infections, and invasive candidiasis can be fatal. Antifungal medications are limited, but those targeting the pathogen cell wall or plasma membrane have been effective. Therefore, virulence factors controlling membrane biogenesis are potential targets for drug development. P4-ATPases contribute to membrane biogenesis by selecting and transporting specific lipids from the extracellular leaflet to the cytoplasmic leaflet of the bilayer to generate lipid asymmetry. A subset of heterodimeric P4-ATPases, including Dnf1-Lem3 and Dnf2-Lem3 from Saccharomyces cerevisiae, transport phosphatidylcholine (PC), phosphatidylethanolamine (PE), and the sphingolipid glucosylceramide (GlcCer). GlcCer is a critical lipid for Candida albicans polarized growth and virulence, but the role of GlcCer transporters in virulence has not been explored. Here, we show that the Candida albicans Dnf2 (CaDnf2) requires association with CaLem3 to form a functional transporter and flip fluorescent derivatives of GlcCer, PC, and PE across the plasma membrane. Mutation of conserved substrate-selective residues in the membrane domain strongly abrogates GlcCer transport and partially disrupts PC transport by CaDnf2. Candida strains harboring dnf2-null alleles (dnf2ΔΔ) or point mutations that disrupt substrate recognition exhibit defects in yeast-to-hypha growth transition, filamentous growth, and virulence in systemically infected mice. The influence of CaDNF1 deletion on the morphological phenotypes is negligible, although the dnf1ΔΔ dnf2ΔΔ strain was less virulent than the dnf2ΔΔ strain. These results indicate that the transport of GlcCer and/or PC by plasma membrane P4-ATPases is important for the pathogenicity of Candida albicans.
Peroxiredoxin 5 regulates osteogenic differentiation via interaction with hnRNPK during bone regeneration

Peroxiredoxin 5 (Prdx5) is involved in pathophysiological regulation via the stress-induced cellular response. However, the function of Prdx5 in the bone remains largely unknown. Here, we show that Prdx5 is involved in osteoclast and osteoblast differentiation, resulting in osteoporotic phenotypes in Prdx5 knockout (Prdx5Ko) mice. Through immunoprecipitation and liquid chromatography combined with tandem mass spectrometry analysis, heterogeneous nuclear ribonucleoprotein K (hnRNPK) was identified as a potential binding partner of Prdx5 during osteoblast differentiation in vitro. We found that Prdx5 acts as a negative regulator of hnRNPK-mediated osteocalcin (Ocn) expression. In addition, transcriptomic analysis revealed that in vitro differentiated osteoclasts from the bone marrow-derived macrophages of Prdx5Ko mice showed enhanced expression of several osteoclast-related genes. These findings indicate that Prdx5 might contribute to the maintenance of bone homeostasis by regulating osteoblast differentiation. This study proposes a new function of Prdx5 in bone remodeling that may be used in developing therapeutic strategies for bone diseases.
Effects of habitat management on rodent diversity, abundance, and virus infection dynamics

Biodiversity is necessary for healthy ecosystem functioning. As anthropogenic factors continue to degrade natural areas, habitat management is needed to restore and maintain biodiversity. However, the impacts of different habitat management regimes on ecosystems have largely focused on vegetation analyses, with limited evaluation of downstream effects on wildlife. We compared the effects of prairie management regimes (controlled burning, cutting/haying, or no active management) on rodent communities and the viruses they hosted. Rodents were trapped in 13 existing prairie sites in Northwest Arkansas, USA during 2020 and 2021. Rodent blood samples were screened for antibodies against three common rodent-borne virus groups: orthohantaviruses, arenaviruses, and orthopoxviruses. We captured 616 rodents across 5953 trap nights. Burned and unmanaged sites had similarly high abundance and diversity (H), but burned sites had a greater proportion of grassland specialists than control sites; cut sites had the highest proportion of grassland specialist species but the lowest rodent abundance and diversity. A total of 38 rodents were seropositive for one of the three virus groups (34 orthohantavirus, three arenavirus, and one orthopoxvirus). Thirty-six seropositive individuals were found in burned sites, and two orthohantavirus-seropositive individuals were found in cut sites. Cotton rats and prairie voles, two grassland specialists, accounted for 97% of the rodents seropositive for orthohantavirus, and heavier individuals were more likely to be seropositive than lighter individuals. Policy implications: Our study indicates that controlled burns lead to a diverse and abundant community of grassland rodent species when compared to other management regimes; as keystone taxa, these results also have important implications for many other species in food webs. Higher prevalence of antibodies against rodent-borne viruses in burned prairies shows an unexpected consequence likely resulting from these community structures. Ultimately, these results provide empirical evidence that can inform prairie grassland restoration and ongoing management strategies.
A Study of Creativity and Innovation Support Within an Agile Context : Applied on a Scrum Team

The objective of the master thesis was to extend and evaluate a management system to support creativity for an agile team, with the aim to secure innovation at Alten. The thesis was divided into a literature study and a case study. The literature study focused on determining internal innovation determinants and analysing the interplay between creativity, innovation and agility. The case study included multiple methods and had a quasi-experimental approach. The work was limited to software development and a time period of twenty weeks. Several shared success factors between creativity, innovation and agile principles emerged from the literature study. There were also discovered contradictions betweenthe three concepts. Guidelines were extracted from the literature and supported the design of the new dimension in the management system. The main part of the implementation of the management system was to evaluate the requirements in relation to the Scrum team. Two workshops were held, primarily to establish an action plan. The result showed that nine requirements were fulfilled by agile practices. The empirical findings strengthened ten success factors that were derived from research. Also, three new success factors emerged; diverse insight, communication channels and reflection. External pressure was the only strengthened contradictionin relation to the literature. Two new contradictions emerged; ’documentation’, ’processes and tools’.
A Legionella toxin mimics tRNA and glycosylates the translation machinery to trigger a ribotoxic stress response

Pathogens often secrete proteins or nucleic acids that mimic the structure and/or function of molecules expressed in their hosts. Molecular mimicry empowers pathogens to subvert critical host processes and establish infection. We report that the intracellular bacterium Legionella pneumophila secretes the toxin SidI (substrate of icm/dot transporter I), which possesses a transfer RNA (tRNA)-like shape and functions as a mannosyl transferase. The 3.1 Å cryo-EM structure of SidI reveals an N-terminal domain that exhibits a characteristic ‘inverted L-shape’ and charge distribution that is present in two other known protein mimics of tRNAs, the bacterial elongation factor EF-G and the mammalian release factor eRF1. In addition, we show that SidI’s C-terminal domain adopts a glycosyl transferase B fold similar to a mannosyl transferase. This molecular coupling of the protein’s fold and enzymatic function allows SidI to bind and glycosylate components of the host translation apparatus, including the ribosome, resulting in a robust block of protein synthesis that is comparable in potency to ricin, one of the most powerful toxins known. Additionally, we find that translational pausing activated by SidI elicits a stress response signature reminiscent of the ribotoxic stress response that is activated by elongation inhibitors that induce ribosome collisions. SidI-mediated effects on the ribosome activate the stress kinases ZAKα and p38, which in turn drive an accumulation of the protein activating transcription factor 3 (ATF3). Intriguingly, ATF3 escapes the translation block imposed by SidI, translocates to the nucleus, and orchestrates the transcription of stress-inducible genes that promote cell death. Thus, using Legionella and its effectors as tools, we have unravelled the role of a ribosome-to-nuclear signalling pathway that regulates cell fate.
Regulated extracellular matrix trafficking shapes cell growth during cartilage morphogenesis

Craniofacial malformations are present in more than one third of all congenital syndromes, but the pathogenesis of skeletal dysmorphology is poorly understood. Here, using an unbiased forward genetics approach in zebrafish, we identified a mutation in erc1b that leads to craniofacial defects, including micrognathia and hypertelorism caused by impaired cartilage and bone growth. To date, ERC1 has not been considered a candidate gene for craniofacial syndromes. Using live in vivo imaging, genetic depletion and replacement experiments, and transgenic approaches, we interrogated erc1b function. We found that Erc1b regulates extracellular matrix (ECM) trafficking required for the highly conserved “stack of coins” organization of chondrocytes in cartilage that is essential for skeletal growth and integrity. Erc1b functions cellautonomously at the chondrocyte cell cortex to regulate traffic of ECM and plasma membrane expansion in a microtubule dependent manner during isometric cell growth. Disruption of Erc1-Rab8-Kinesin-1 axis leads to failure of cartilage maturation, endochondral bone formation and ultimately chondrocyte cell death. Our study identifies Erc1b as a candidate genetic factor for craniofacial syndromes.
Exogenous NaV1.1 activity in excitatory and inhibitory neurons reverts Dravet syndrome comorbidities when delivered post-symptom onset in mice with Dravet

Dravet syndrome (DS), an intractable childhood epileptic encephalopathy with a high fatality rate, is caused by loss-of-function mutations in one allele of SCN1A, which encodes NaV1.1. In contrast to other epilepsies, pharmaceutical treatment for DS is limited. Here, we demonstrate that viral vector-mediated delivery of a codon-modified SCN1A cDNA improves DS comorbidities in juvenile and adolescent DS mice (Scn1aA1783V/WT). Notably, bilateral vector injections into the hippocampus or thalamus of DS mice improved the survival of the mice, reduced the occurrence of epileptic spikes, provided protection from thermally-induced seizures, and corrected background electrocorticography activity. Together, our results provide a proof-of-concept for the potential of SCN1A delivery as a therapeutic approach for infants and adolescents with DS-associated comorbidities.
Modulation of multiple gene clusters expression by a single PAS-LuxR transcriptional regulator

PAS-LuxR transcriptional regulators are highly conserved enzymes governing polyene macrolide antifungal biosynthesis. PteF is one of such regulators, situated in the polyene macrolide filipin gene cluster from Streptomyces avermitilis. Its mutation leads to a drastic filipin production decline, but also to a severe loss of oligomycin production, an ATP-synthase inhibitor of macrolide structure, and a delay in sporulation, thus it has been considered as a transcriptional activator. Transcriptomic analyses were carried out in S. avermitilis ΔpteF and its parental strain S. avermitilis NRRL 8165 as control. Both strains were grown in YEME medium without sucrose, and samples were taken in the exponential and stationary growth phases. 257 genes showed altered expression in the PteF-deleted mutant, most of them in the exponential phase of growth. Surprisingly, despite PteF being an activator of filipin biosynthesis, a majority of the genes affected upon mutation showed overexpression thus suggesting a negative modulation of those genes. Genes affected were related to various metabolic processes, including genetic information processing; DNA, energy, carbohydrate, and lipid metabolism; morphological differentiation; and transcriptional regulation; among others, but particularly to secondary metabolite biosynthesis. Notably, ten secondary metabolite gene clusters out of 38 encoded by the genome, some of them encoding cryptic compounds, showed altered expression profiles in the mutant, suggesting a regulatory role for PteF wider than expected. Transcriptomic results were validated by quantitative reverse transcription polymerase chain reaction. These findings provide important clues to understand the intertwined regulatory machinery that modulates antibiotic biosynthesis in Streptomyces.
Temporally robust occupancy frequency distributions in riverine metacommunities explained by local biodiversity regulation

The mechanisms determining the distribution of the number of sites species occupy—the occupancy frequency distribution (OFD)—remain incompletely understood despite decades of research. Here we study OFD in fresh-water metacommunities in England. We show that OFD are largely time invariant despite continuous turnover in community composition and well described by log-series distributions. Both shape and temporal robustness are readily explained by a simple patch occupancy model with intrinsic regulation of local richness. The model is mathematically analogous to classical neutral theory, but concerns numbers of patches occupied instead of individuals present. The precise shape of the model’s log-series OFD is determined by a parameter representing the rate of colonisation from adjacent sites, which we estimate for the data. Our results support the view that meta-community structure reflects a dynamic steady state controlled by local ecological constraints. Interspecific trait differences underlie these constraints, but are unlikely to determine macroecological structure.
Doing what’s not wanted: conflict in incentives and misallocation of behavioural control lead to drug-seeking despite adverse outcomes

Despite being aware of negative consequences and wanting to quit, long-term addicts find it difficult to quit seeking and consuming drugs. This inconsistency between the (often compulsive) behavioural patterns and the explicit knowledge of negative consequences represents a cognitive conflict which is a central characteristic of addiction. Neurobiologically, differential cue-induced activity in distinct striatal subregions, as well as the dopamine connectivity spiraling from ventral striatal regions to the dorsal regions, play critical roles in compulsive drug seeking. The focus of this work is to illustrate the mechanisms that lead to a cognitive conflict and it’s impact on actions taken i.e. addictive choices. We propose an algorithmic model that captures how the action choices that the agent makes when reinforced with drug-rewards become incongruent with the presence of negative consequences that often follow those choices. We advance the understanding of having a decision hierarchy in representing “cognitive control” and how lack of such control at higher-level in the hierarchy could potentially lead to consolidated drug-seeking habits. We further propose a cost-benefit based arbitration scheme, which mediates the allocation of control across different levels of the decision-making hierarchy. Lastly, we discuss how our work on extending a computational model to an algorithmic one, could in turn also helps us improve the understanding of how drugs hijack the dopamine-spiralling circuit at an implementation level.
Modelling the mechanical cross-talk between cells and fibrous extracellular matrix using hybrid cellular Potts and molecular dynamics methods

The mechanical interaction between cells and the extracellular matrix (ECM) is fundamental to coordinate collective cell behavior in multicellular tissues. Relating individual cell-level mechanics to tissue-scale collective behavior is an outstanding challenge which cell-based models such as the cellular Potts model (CPM) are well-positioned to address. These models generally represent the ECM with mean-field approaches, which assume substrate homogeneity. This assumption breaks down with fibrous ECM, which has non-trivial structure and mechanics. Here, we extend the CPM with a bead-spring chain model of ECM fiber networks modelled using molecular dynamics. We model contractile cells pulling with discrete focal adhesion-like sites on the ECM fiber network, and demonstrate agreement with experimental spatiotemporal fiber densification and displacement. We show that contractile cell forces propagate over multiple cell radii scaling with power law exponent of ≈ −0.5 typical of viscoelastic ECM. Further, we use in silico atomic force microscopy to measure local cell-induced network stiffening consistent with experiments. Our model lays the foundation to investigate how local and long-ranged cell-ECM mechanobiology contributes to multicellular morphogenesis.