Topology-Driven Discovery of Transmembrane Protein S-Palmitoylation.

Protein S-palmitoylation is a reversible lipophilic posttranslational modification regulating a diverse number of signaling pathways. Within transmembrane proteins (TMPs), S-palmitoylation is implicated in conditions from inflammatory disorders to respiratory viral infections. Many small-scale experiments have observed S-palmitoylation at juxtamembrane Cys residues. However, most large-scale S-palmitoyl discovery efforts rely on trypsin-based proteomics within which hydrophobic juxtamembrane regions are likely underrepresented. Machine learning- by virtue of its freedom from experimental constraints - is particularly well suited to address this discovery gap surrounding TMP S-palmitoylation. Utilizing a UniProt-derived feature set, a gradient boosted machine learning tool (TopoPalmTree) was constructed and applied to a holdout dataset of viral S-palmitoylated proteins. Upon application to the mouse TMP proteome, 1591 putative S-palmitoyl sites (i.e. not listed in SwissPalm or UniProt) were identified. Two lung-expressed S-palmitoyl candidates (synaptobrevin Vamp5 and water channel Aquaporin-5) were experimentally assessed. Finally, TopoPalmTree was used for rational design of an S-palmitoyl site on KDEL-Receptor 2. This readily interpretable model aligns the innumerable small-scale experiments observing juxtamembrane S-palmitoylation into a proteomic tool for TMP S-palmitoyl discovery and design, thus facilitating future investigations of this important modification.

Accelerated discovery of perovskite solid solutions through automated materials synthesis and characterization.

Accelerating perovskite solid solution discovery and sustainable synthesis is crucial for addressing challenges in wireless communication and biosensors. However, the vast array of chemical compositions and their dependence on factors such as crystal structure, and sintering temperature require time-consuming manual processes. To overcome these constraints, we introduce an automated materials discovery approach encompassing machine learning (ML) assisted material screening, robotic synthesis, and high-throughput characterization. Our proposed platform for rapid sintering and dielectric analysis streamlines the characterization of perovskites and the discovery of disordered materials. The setup has been successfully validated, demonstrating processing materials within minutes, in stark contrast to conventional procedures that can take hours or days. Following setup validation with established samples, we showcase synthesizing single-phase solid solutions within the barium family, such as (BaxSr1-x)CeO3, identified through ML-guided chemistry.

Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap).

Proteins undergo reversible S-acylation via a thioester linkage in vivo. S-palmitoylation, modification by C16:0 fatty acid, is a common S-acylation that mediates critical protein-membrane and protein-protein interactions. The most widely used S-acylation assays, including acyl-biotin exchange and acyl resin-assisted capture, utilize blocking of free Cys thiols, hydroxylamine-dependent cleavage of the thioester and subsequent labeling of nascent thiol. These assays generally require >500 µg of protein input material per sample and numerous reagent removal and washing steps, making them laborious and ill-suited for high throughput and low input applications. To overcome these limitations, we devised "Acyl-Trap", a suspension trap-based assay that utilizes a thiol-reactive quartz to enable buffer exchange and hydroxylamine-mediated S-acyl enrichment. We show that the method is compatible with protein-level detection of S-acylated proteins (e.g., H-Ras) as well as S-acyl site identification and quantification using "on trap" isobaric labeling and LC-MS/MS from as little as 20 µg of protein input. In mouse brain, Acyl-Trap identified 279 reported sites of S-acylation and 1298 previously unreported putative sites. Also described are conditions for long-term hydroxylamine storage, which streamline the assay. More generally, Acyl-Trap serves as a proof-of-concept for PTM-tailored suspension traps suitable for both traditional protein detection and chemoproteomic workflows.

Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap).

Proteins undergo reversible S-acylation via a thioester linkage in vivo. S-palmitoylation, modification by C16:0 fatty acid, is a common S-acylation that mediates critical protein-membrane and protein-protein interactions. The most widely used S-acylation assays, including acyl-biotin exchange and acyl resin-assisted capture, utilize blocking of free Cys thiols, hydroxylamine-dependent cleavage of the thioester and subsequent labeling of nascent thiol. These assays generally require >500 micrograms of protein input material per sample and numerous reagent removal and washing steps, making them laborious and ill-suited for high throughput and low input applications. To overcome these limitations, we devised "Acyl-Trap", a suspension trap-based assay that utilizes a thiol-reactive quartz to enable buffer exchange and hydroxylamine-mediated S-acyl enrichment. We show that the method is compatible with protein-level detection of S-acylated proteins (e.g. H-Ras) as well as S-acyl site identification and quantification using "on trap" isobaric labeling and LC-MS/MS from as little as 20 micrograms of protein input. In mouse brain, Acyl-Trap identified 279 reported sites of S-acylation and 1298 previously unreported putative sites. Also described are conditions for long-term hydroxylamine storage, which streamlines the assay. More generally, Acyl-Trap serves as a proof-of-concept for PTM-tailored suspension traps suitable for both traditional protein detection and chemoproteomic workflows.

An integrated experimental and theoretical approach to probe Cr(vi) uptake using decorated halloysite nanotubes for efficient water treatment.

Halloysite nanotubes (HNTs) were surface functionalized using four distinct chemical moieties (amidoxime, hydrazone, ethylenediamine (EDA), and diethylenetriamine (DETA)), producing modified HNTs (H1-H4) capable of binding with Cr(vi) ions. Advanced techniques like FTIR, XRD, SEM, and EDX provided evidence of the successful functionalization of these HNTs. Notably, the functionalization occurred on the surface of HNTs, rather than within the interlayer or lumen. These decorated HNTs were effective in capturing Cr(vi) ions at optimized sorption parameters, with adsorption rates ranging between 58-94%, as confirmed by atomic absorption spectroscopy (AAS). The mechanism of adsorption was further scrutinized through the Freundlich and Langmuir isotherms. Langmuir isotherms revealed the nearest fit to the data suggesting the monolayer adsorption of Cr(vi) ions onto the nanotubes, indicating a favorable adsorption process. It was hypothesized that Cr(vi) ions are primarily attracted to the amine groups on the modified nanotubes. Quantum chemical calculations further revealed that HNTs functionalized with hydrazone structures (H2) demonstrated a higher affinity (interaction energy -26.33 kcal mol-1) for the Cr(vi) ions. This can be explained by the formation of stronger hydrogen bonds with the NH moieties of the hydrazone moiety, than those established by the OH of oxime (H1) and longer amine chains (H3 and H4), respectively. Overall, the findings suggest that these decorated HNTs could serve as an effective and cost-efficient solution for treating water pollution.

Dihydroxyterephthalate-A Trojan Horse PET Counit for Facile Chemical Recycling.

Here, low-energy poly(ethylene terephthalate) (PET) chemical recycling in water: PET copolymers with diethyl 2,5-dihydroxyterephthalate (DHTE) undergo selective hydrolysis at DHTE sites, autocatalyzed by neighboring group participation, is demonstrated. Liberated oligomeric subchains further hydrolyze until only small molecules remain. Poly(ethylene terephthalate-stat-2,5-dihydroxyterephthalate) copolymers were synthesized via melt polycondensation and then hydrolyzed in 150-200 °C water with 0-1 wt% ZnCl2 , or alternatively in simulated sea water. Degradation progress follows pseudo-first order kinetics. With increasing DHTE loading, the rate constant increases monotonically while the thermal activation barrier decreases. The depolymerization products are ethylene glycol, terephthalic acid, 2,5-dihydroxyterephthalic acid, and bis(2-hydroxyethyl) terephthalate dimer, which could be used to regenerate virgin polymer. Composition-optimized copolymers show a decrease of nearly 50% in the Arrhenius activation energy, suggesting a 6-order reduction in depolymerization time under ambient conditions compared to that of PET homopolymer. This study provides new insight to the design of polymers for end-of-life while maintaining key properties like service temperature and mechanical properties. Moreover, this chemical recycling procedure is more environmentally friendly compared to traditional approaches since water is the only needed material, which is green, sustainable, and cheap.

Cavitation-Mediated Fracture Energy Dissipation in Polylactide at Rubbery Soybean Oil-Based Block Copolymer Interfaces Formed via Reactive Extrusion.

Here, we spearhead a new approach to biopolymer impact modification that demonstrates superior performance while maintaining greater than 99% compostability. Using soybean-based monomers, a virtually untapped resource in terms of commercial volume and overall cost, a series of hyperbranched block copolymers were synthesized and melt-processed with poly(l-lactide) (PLA) to yield impact resistant all-polymer composites. Although PLA impact modification has been treated extensively, to date, the only practical solutions have relied on non-compostable petroleum-based rubbers. This study illustrates the activity of energy dissipation mechanisms such as cavitation, classically relegated to well-entangled petroleum-based rubbers, in poorly entangled hyperbranched soybean-based rubbers. Furthermore, we present a complete study of the mechanical performance and morphology of these impact modified PLA composites. The significance of combining deformation theory with a scalable green alternative to petroleum-based rubbers opens up a potential avenue for cheap compostable engineering thermoplastics.

Structure-function clustering in weighted brain networks.

Functional networks, which typically describe patterns of activity taking place across the cerebral cortex, are widely studied in neuroscience. The dynamical features of these networks, and in particular their deviation from the relatively static structural network, are thought to be key to higher brain function. The interactions between such structural networks and emergent function, and the multimodal neuroimaging approaches and common analysis according to frequency band motivate a multilayer network approach. However, many such investigations rely on arbitrary threshold choices that convert dense, weighted networks to sparse, binary structures. Here, we generalise a measure of multiplex clustering to describe weighted multiplexes with arbitrarily-many layers. Moreover, we extend a recently-developed measure of structure-function clustering (that describes the disparity between anatomical connectivity and functional networks) to the weighted case. To demonstrate its utility we combine human connectome data with simulated neural activity and bifurcation analysis. Our results indicate that this new measure can extract neurologically relevant features not readily apparent in analogous single-layer analyses. In particular, we are able to deduce dynamical regimes under which multistable patterns of neural activity emerge. Importantly, these findings suggest a role for brain operation just beyond criticality to promote cognitive flexibility.

Bioenabled Platform to Access Polyamides with Built-In Target Properties.

The diversification of platform chemicals is key to today's petroleum industry. Likewise, the flourishing of tomorrow's biorefineries will rely on molecules with next-generation properties from biomass. Herein, we explore this opportunity with a novel approach to monomers with custom property enhancements. Cyclic diacids with alkyl and aromatic decorations were synthesized from muconic acid by Diels-Alder cycloaddition, and copolymerized with hexamethylenediamine and adipic acid to yield polyamides with built-in hydrophobicity and flame retardancy. Testing shows a 70% reduction in water uptake and doubling of char production while largely retaining other key properties of the parent Nylon-6,6. The present approach can be generalized to access a wide range of performance-advantaged polyamides.

The role of node dynamics in shaping emergent functional connectivity patterns in the brain.

The contribution of structural connectivity to functional brain states remains poorly understood. We present a mathematical and computational study suited to assess the structure-function issue, treating a system of Jansen-Rit neural mass nodes with heterogeneous structural connections estimated from diffusion MRI data provided by the Human Connectome Project. Via direct simulations we determine the similarity of functional (inferred from correlated activity between nodes) and structural connectivity matrices under variation of the parameters controlling single-node dynamics, highlighting a nontrivial structure-function relationship in regimes that support limit cycle oscillations. To determine their relationship, we firstly calculate network instabilities giving rise to oscillations, and the so-called 'false bifurcations' (for which a significant qualitative change in the orbit is observed, without a change of stability) occurring beyond this onset. We highlight that functional connectivity (FC) is inherited robustly from structure when node dynamics are poised near a Hopf bifurcation, whilst near false bifurcations, and structure only weakly influences FC. Secondly, we develop a weakly coupled oscillator description to analyse oscillatory phase-locked states and, furthermore, show how the modular structure of FC matrices can be predicted via linear stability analysis. This study thereby emphasises the substantial role that local dynamics can have in shaping large-scale functional brain states.

Next-generation neural mass and field modeling.

The Wilson-Cowan population model of neural activity has greatly influenced our understanding of the mechanisms for the generation of brain rhythms and the emergence of structured brain activity. As well as the many insights that have been obtained from its mathematical analysis, it is now widely used in the computational neuroscience community for building large-scale in silico brain networks that can incorporate the increasing amount of knowledge from the Human Connectome Project. Here, we consider a neural population model in the spirit of that originally developed by Wilson and Cowan, albeit with the added advantage that it can account for the phenomena of event-related synchronization and desynchronization. This derived mean-field model provides a dynamic description for the evolution of synchrony, as measured by the Kuramoto order parameter, in a large population of quadratic integrate-and-fire model neurons. As in the original Wilson-Cowan framework, the population firing rate is at the heart of our new model; however, in a significant departure from the sigmoidal firing rate function approach, the population firing rate is now obtained as a real-valued function of the complex-valued population synchrony measure. To highlight the usefulness of this next-generation Wilson-Cowan style model, we deploy it in a number of neurobiological contexts, providing understanding of the changes in power spectra observed in electro- and magnetoencephalography neuroimaging studies of motor cortex during movement, insights into patterns of functional connectivity observed during rest and their disruption by transcranial magnetic stimulation, and to describe wave propagation across cortex.

Psychoanalytic Underpinnings of Socially-Shared Normativity.

Alongside social anthropology and discursive psychology, conversation analysis has highlighted numerous ways in which cultural forms of perceiving and acting in the world are primarily rooted in socially shared normativity. However, when consideration turns to the origins and purposes of human affect and emotion, ethnomethodology, and conversation analysis appear to face particular difficulties that arise from the over-arching focus on sense-making practices. This article considers the proposal that psychoanalytic thinking might inform our understanding of how socially shared normativity emerges during infancy and early childhood. First, a framework is sketched out that highlights the fact that from the beginning, an infant's earliest experience is bound up with those procedures, practices, and social actions that make up what conversation analysts call members' methods. Second, comparisons are drawn between conversation analysis and psychoanalytic accounts of early experience for infants during the first years of life. Discussion then moves to the Kleinian notion of object relations and the concept of projective identification. Essentially, this is a theoretical account of how "what-was-once-one" (the mother-infant unit) somehow differentiates resulting in the gradual emergence of the "individuated being." What is often glossed over in this account is the discursively embedded nature of projective identification; a process that is itself interdependent with the embodiment that makes up the infant's lived engagement with the world. Whatever might constitute consciousness emerges from somatic, embodied, material-physical, tactile/affective experience - that is, a fundamentally social milieu. Ultimately, this raises the question of how transformation (i.e., from the social to the individual) occurs. One answer may be Winnicott's idea of the transitional space, where the "good-enough" parent is said to be somebody, who can "contain" both negative and positive identifications coming from the infant, transform and re-project such identifications, but in modified form. In this way, the infant begins to recognize/experience what it is they are "feeling." Such projective identifications are conveyed within and through the prevailing discourses that constitute all social practices. Concluding comments note that conversation analysis may find in psychoanalytic thinking a framework for understanding the interdependence between affect and action, given that in psychoanalytic thought, we find a thoroughly relational conception of human nature.

ERK-dependent proteasome degradation of Txnip regulates thioredoxin oxidoreductase activity.

Dynamic control of thioredoxin (Trx) oxidoreductase activity is essential for balancing the need of cells to rapidly respond to oxidative/nitrosative stress and to temporally regulate thiol-based redox signaling. We have previously shown that cytokine stimulation of the respiratory epithelium induces a precipitous decline in cell S-nitrosothiol, which depends upon enhanced Trx activity and proteasome-mediated degradation of Txnip (thioredoxin-interacting protein). We now show that tumor necrosis factor-α-induced Txnip degradation in A549 respiratory epithelial cells is regulated by the extracellular signal-regulated protein kinase (ERK) mitogen-activated protein kinase pathway and that ERK inhibition augments both intracellular reactive oxygen species and S-nitrosothiol. ERK-dependent Txnip ubiquitination and proteasome degradation depended upon phosphorylation of a PXTP motif threonine (Thr349) located within the C-terminal α-arrestin domain and proximal to a previously characterized E3 ubiquitin ligase-binding site. Collectively, these findings demonstrate the ERK mitogen-activated protein kinase pathway to be integrally involved in regulating Trx oxidoreductase activity and that the regulation of Txnip lifetime via ERK-dependent phosphorylation is an important mediator of this effect.

Self-assembly of Janus Dumbbell Nanocrystals and Their Enhanced Surface Plasmon Resonance.

Self-assembly is a critical process that can greatly expand the existing structures and lead to new functionality of nanoparticle systems. Multicomponent superstructures self-assembled from nanocrystals have shown promise as multifunctional materials for various applications. Despite recent progress in assembly of homogeneous nanocrystals, synthesis and self-assembly of Janus nanocrystals with contrasting surface chemistry remains a significant challenge. Herein, we designed a novel Janus nanocrystal platform to control the self-assembly of nanoparticles in aqueous solutions by balancing the hydrophobic and hydrophilic moieties. A series of superstructures have been assembled by systematically varying the Janus balance and assembly conditions. Janus Au-Fe3O4 dumbbell nanocrystals (<20 nm) were synthesized with the hydrophobic ligands coated on the Au lobe and negatively charged hydrophilic ligands coated on the Fe3O4 lobe. We systematically fine-tune the lobe size ratio, surface coating, external conditions, and even additional growth of Au nanocrystal domains on the Au lobe of dumbbell nanoparticles (Au-Au-Fe3O4) to harvest self-assembly structures including clusters, chains, vesicles, and capsules. It was discovered that in all these assemblies the hydrophobic Au lobes preferred to stay together. In addition, these superstructures clearly demonstrated different levels of enhanced surface plasmon resonance that is directly correlated with the Au coupling in the assembly structure. The strong interparticle plasmonic coupling displayed a red-shift in surface plasmon resonance, with larger structures formed by Au-Au-Fe3O4 assembly extending into the near-infrared region. Self-assembly of Janus dumbbell nanocrystals can also be reversible under different pH values. The biphasic Janus dumbbell nanocrystals offer a platform for studying the novel interparticle coupling and open up opportunities in applications including sensing, disease diagnoses, and therapy.

How children aged 2;6 tailor verbal expressions to interlocutor informational needs.

Although preschoolers are pervasively underinformative in their actual usage of verbal reference, a number of studies have shown that they nonetheless demonstrate sensitivity to listener informational needs, at least when environmental cues to this are obvious. We investigated two issues. The first concerned the types of visual cues to interlocutor informational needs which children aged 2;6 can process whilst producing complex referring expressions. The second was whether performance in experimental tasks related to naturalistic conversational proficiency. We found that 2;6-year-olds used fewer complex expressions when the objects were dissimilar compared to highly similar objects, indicating that they tailor their verbal expressions to the informational needs of another person, even when the cue to the informational need is relatively opaque. We also found a correlation between conversational skills as rated by the parents and the degree to which 2;6-year-olds could learn from feedback to produce complex referring expressions.

Cohort Profile: The Barwon Infant Study.

The modern environment is associated with an increasing burden of non-communicable diseases (NCDs). Mounting evidence implicates environmental exposures, experienced early in life (including in utero), in the aetiology of many NCDs, though the cellular/molecular mechanism(s) underlying this elevated risk across the life course remain unclear. Epigenetic variation has emerged as a candidate mediator of such effects. The Barwon Infant Study (BIS) is a population-derived birth cohort study (n = 1074 infants) with antenatal recruitment, conducted in the south-east of Australia (Victoria). BIS has been designed to facilitate a detailed mechanistic investigation of development within an epidemiological framework. The broad objectives are to investigate the role of specific environmental factors, gut microbiota and epigenetic variation in early-life development, and subsequent immune, allergic, cardiovascular, respiratory and neurodevelopmental outcomes. Participants have been reviewed at birth and at 1, 6, 9 and 12 months, with 2- and 4-year reviews under way. Biological samples and measures include: maternal blood, faeces and urine during pregnancy; infant urine, faeces and blood at regular intervals during the first 4 years; lung function at 1 month and 4 years; cardiovascular assessment at 1 month and 4 years; skin-prick allergy testing and food challenge at 1 year; and neurodevelopmental assessment at 9 months, 2 and 4 years. Data access enquiries can be made at [www.barwoninfantstudy.org.au] or via [peter.vuillermin@deakin.edu.au].

Ex Vivo Culture of Primary Intestinal Stem Cells in Collagen Gels and Foams.

Three-dimensional ex vivo cell culture systems have been of great interest to tissue engineering and regenerative medicine. In vitro intestinal epithelium culture models are normally employed to mimics the physiological realistic environment for the study of normal and aberrant intestinal epithelium. In this study, we demonstrated the applicability to use collagen I based gels for the culture of primary intestinal stem cells. The resulting three-dimensional cell culture systems supported the long-term proliferation and differentiation of encapsulated intestinal stem cells. We further confirmed the feasibility of collagen I foams as cell carriers for the delivery of intestinal stem cells. These ex vivo systems will facilitate the research of intestinal stem-cell-based regenerative therapy for enteric disorders and diseases.

Thioredoxin-mediated denitrosylation regulates cytokine-induced nuclear factor κB (NF-κB) activation.

S-nitrosylation of nuclear factor κB (NF-κB) on the p65 subunit of the p50/p65 heterodimer inhibits NF-κB DNA binding activity. We have recently shown that p65 is constitutively S-nitrosylated in the lung and that LPS-induced injury elicits a decrease in SNO-p65 levels concomitant with NF-κB activation in the respiratory epithelium and initiation of the inflammatory response. Here, we demonstrate that TNFα-mediated activation of NF-κB in the respiratory epithelium similarly induces p65 denitrosylation. This process is mediated by the denitrosylase thioredoxin (Trx), which becomes activated upon cytokine-induced degradation of thioredoxin-interacting protein (Txnip). Similarly, inhibition of Trx activity in the lung attenuates LPS-induced SNO-p65 denitrosylation, NF-κB activation, and airway inflammation, supporting a pathophysiological role for this mechanism in lung injury. These data thus link stimulus-coupled activation of NF-κB to a specific, protein-targeted denitrosylation mechanism and further highlight the importance of S-nitrosylation in the regulation of the immune response.