Browse Articles

Experimental and theoretical evidence of universality in superfluid vortex reconnections

The minimum separation between reconnecting vortices in fluids and superfluids obeys a universal scaling law with respect to time. The prereconnection and the postreconnection prefactors of this scaling law are different, a property related to irreversibility and to energy transfer and dissipation mechanisms. In the present work, we determine the temperature dependence of these prefactors in superfluid helium from experiments and a numeric model which fully accounts for the coupled dynamics of the superfluid vortex lines and the thermal normal fluid component. At all temperatures, we observe a pre- and postreconnection asymmetry similar to that observed in other superfluids and in classical viscous fluids, indicating that vortex reconnections display a universal behavior independent of the small-scale regularizing dynamics. We also numerically show that each vortex reconnection event represents a sudden injection of energy in the normal fluid. Finally we argue that in a turbulent flow, these punctuated energy injections can sustain the normal fluid in a perturbed state, provided that the density of superfluid vortices is large enough.

Multiparametric functional characterization of individual lipid nanoparticles using surface-sensitive light-scattering microscopy

The most efficient lipid nanoparticles (LNPs) for gene therapeutics rely on specific lipids that protect the oligonucleotide cargo and aid cellular uptake and subsequent endosomal escape. Yet, the efficacy of current state-of-the-art LNP formulations remains low, a few percent at best. A deeper understanding of how LNP cargo, lipid composition, stoichiometry, size, structure, and pH-induced conformational changes influence their efficiency is therefore necessary for improved design. Given the variability of these properties, preferred screening methods should offer single-particle-resolved multiparametric characterization. In this work, we employ combined surface-sensitive fluorescence and label-free scattering microscopy with single LNP resolution, which when integrated with microfluidics for liquid exchange between media of varying refractive index, enables quantification of LNP size, refractive index, and cargo content. We investigate two LNP formulations that, while similar in size and mRNA content, exhibit differences in functional mRNA delivery. Correlating size with the content of Cy5-labeled mRNA revealed that the cargo scaled with LNP volume for both types of LNPs, while the refractive index varied marginally across LNP size. While this multiparametric fingerprinting alone could not distinguish the two LNP formulations, we use the same experimental platform to show that their difference in fusogenicity to a supporting lipid bilayer under early endosomal conditions (drop in pH from 7.4 to 6.0) correlates with observed differences in in vitro cellular data. This highlights a limitation of the current state-of-the-art toolbox for in situ LNP characterization, which generally focuses on structural properties of suspended LNPs, which may not adequately capture functional performance.

The white lupin CCR1 receptor-like kinase controls systemic Autoregulation of Cluster Root and Nodule Development

Root development is tightly regulated in plants to optimize nutrient acquisition and interactions with soil microorganisms. In legumes, the Autoregulation of Nodulation (AoN) pathway systemically controls the proliferation of root nodules, which are energy-intensive organs. Mutations affecting the AoN pathway result in a hypernodulation phenotype accompanied by altered root development. However, it remains unclear whether this modification of root development is also systemic and coordinated with nodulation. In this study, we report the identification of the constitutive cluster root 1 (ccr1) mutant in white lupin ( Lupinus albus ), which exhibits constitutive production of an excessive number of cluster roots. We demonstrate that CCR1 is an ortholog of HAR1/SUNN/NARK leucin-rich repeat-receptor like kinases (LRR-RLKs), which are key regulators of the AoN pathway. Furthermore, we show that CCR1 negatively regulates both nodule and cluster root development. Interspecific grafting experiments between white and narrow-leaved lupin ( Lupinus angustifolius ), a species incapable of producing cluster roots, show that ccr1 shoots can induce the formation of cluster-like roots in narrow-leaved lupin rootstocks. This highlights the conservation of a CCR1-dependent signaling cascade. Transcriptome analyses reveal that CCR1 targets the conserved NIN/LBD16-NFYA regulatory module, which connects nodule and lateral root development through a shared inhibitory systemic pathway. We propose that this pathway represents a broader developmental control mechanism of root organogenesis, termed Autoregulation of Cluster Root and Nodule Development (AoDev).

Cancer-associated fibroblast-derived SEMA3C facilitates colorectal cancer liver metastasis via NRP2-mediated MAPK activation

Liver metastasis remains the predominant cause of mortality in patients with colorectal cancer (CRC). Nevertheless, the mechanisms underlying the initiation of colorectal cancer liver metastasis remain poorly elucidated. During the metastatic process of CRC cells from the primary site to the liver, we performed time-resolved analyses and identified a subset of tumor cells spatially located in the primary tumor and temporally distributed in the early stages of liver metastasis. These cells were termed liver metastasis-initiating cells (LMICs). LMICs exhibit high stemness, low proliferation, active interaction with surrounding stromal components, and a close association with liver metastasis. Notably, we found significant interactions between cancer-associated fibroblasts (CAFs) and LMICs via the SEMA3C–NRP2 receptor–ligand pair. Further in vivo and in vitro experiments confirmed that CAF-secreted SEMA3C could bind to the NRP2 receptor, which activates the MAPK pathway and promotes colorectal cancer liver metastasis. Our findings suggest potential therapeutic strategies for the early prevention of colorectal cancer liver metastasis.

Correction for Masliah et al., β-Amyloid peptides enhance α-synuclein accumulation and neuronal deficits in a transgenic mouse model linking Alzheimer’s disease and Parkinson’s disease

Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles

Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike–antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.

Correction for Garaizar et al., Toward understanding lipid reorganization in RNA lipid nanoparticles in acidic environments

CD83 suppresses endogenous March-I-dependent MHC class II ubiquitination, endocytosis, and degradation

MHC class II glycoproteins (MHC-II) bind peptides derived from exogenous antigens and dendritic cells (DCs) present these peptide MHC-II (pMHC-II) complexes to antigen-specific CD4 T cells during immune responses. The turnover of surface pMHC-II on antigen-presenting cells (APCs) is controlled by ubiquitin-mediated degradation of pMHC-II by the E3 ubiquitin ligase March-I. To study March-I protein expression, we have generated a mouse in which a V5 epitope-tag was knocked-in to the endogenous March-I gene, thereby allowing us to follow the fate of March-I using high-affinity anti-V5 antibodies. Quantitative analysis revealed that resting spleen DCs and B cells express only ~500 and 125 March-I molecules/cell, respectively. Endogenous March-I protein has a very short half-life in DCs and March-I mRNA, March-I protein, and MHC-II ubiquitination are rapidly terminated upon activation of both DCs and B cells. Like March-I, CD83 is a known regulator of MHC-II expression in APCs and we also show that CD83 suppresses endogenous March-I-dependent MHC-II ubiquitination, endocytosis, and degradation in mouse spleen DCs. Thus, our study reveals molecular mechanisms for both March-I- and CD83-dependent regulation of MHC-II expression in APCs.

Correction for Christos et al., A model of <i>d</i> -wave superconductivity, antiferromagnetism, and charge order on the square lattice

The diet crazes of the nineteenth century

Mechanisms of photoreceptor protection upon targeting the <i>Nrl–Nr2e3</i> pathway

Acute knockout of the rod photoreceptor transcription factor Nrl delays retinal degeneration in multiple mouse models of blindness, but the downstream transcriptomic changes that mediate these therapeutic effects are unknown. Here, we show that acute Nrl knockout causes upregulation of a subset of cone genes in rods as well as downregulation of rod genes, including the rod-specific transcriptional repressor Nr2e3 . We hypothesized that Nr2e3 downregulation might mediate some of the therapeutic effects of Nrl knockout. Indeed, acute knockout of Nr2e3 prevents photoreceptor degeneration and preserves visual function in mice with mutations in the catalytic subunit of the rod-specific phosphodiesterase ( Pde6b rd10/rd10 ). Upregulation of Pde6c , the cone-specific paralog of Pde6b , in Nr2e3 -knockout rods is required to prevent degeneration in Pde6b rd10/rd10 mice, suggesting that this therapeutic effect is mediated, at least in part, by a gene-replacement mechanism. In contrast, acute Nr2e3 knockout fails to prevent degeneration caused by loss- or gain-of-function mutations in Rhodopsin ( Rho −/− and Rho P23H/P23H ), whereas acute Nrl knockout delays degeneration in both models. Surprisingly, the therapeutic effect of acute Nrl knockout in Pde6b rd10/rd10 mice does not depend on Pde6c upregulation. These results suggest that acute Nrl knockout may exert its therapeutic effects via a mechanism independent of Nr2e3 downregulation, perhaps by downregulating other rod genes. We conclude that acute NRL knockout may be a promising gene-independent strategy for preventing photoreceptor degeneration in human patients.

Time-management skills I honed as a PhD student now serve me well in industry

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Inhibiting 15-PGDH blocks blood–brain barrier deterioration and protects mice from Alzheimer’s disease and traumatic brain injury

Alzheimer’s disease (AD) and traumatic brain injury (TBI) are currently untreatable neurodegenerative disorders afflicting millions of people worldwide. These conditions are pathologically related, and TBI is one of the greatest risk factors for AD. Although blood–brain barrier (BBB) disruption drives progression of both AD and TBI, strategies to preserve BBB integrity have been hindered by lack of actionable targets. Here, we identify 15-hydroxyprostaglandin dehydrogenase (15-PGDH), an enzyme that catabolizes eicosanoids and other anti-inflammatory mediators, as a therapeutic candidate that protects the BBB. We demonstrate that 15-PGDH is enriched in BBB-associated myeloid cells and becomes markedly elevated in human and mouse models of AD and TBI, as well as aging, another major risk factor for AD. Pathological increase in 15-PGDH correlates with pronounced oxidative stress, neuroinflammation, and neurodegeneration, alongside profound BBB structural degeneration characterized by astrocytic endfeet swelling and functional impairment. Pharmacologic inhibition or genetic reduction of 15-PGDH in AD and TBI models strikingly mitigates oxidative damage, suppresses neuroinflammation, and restores BBB integrity. Most notably, inhibiting 15-PGDH not only halts neurodegeneration but also preserves cognitive function at levels indistinguishable from healthy controls. Remarkably, these neuroprotective effects in AD are achieved without affecting amyloid pathology, underscoring a noncanonical mechanism for treating AD. In a murine microglia cell line exposed to amyloid beta oligomer, major protection was demonstrated by multiple anti-inflammatory substrates that 15-PGDH degrades. Thus, our findings position 15-PGDH inhibition as a broad-spectrum strategy to protect the BBB and thereby preserve brain health and cognition in AD and TBI.

Activation dynamics of ubiquitin-specific protease 7

Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme that plays a crucial role in cellular processes, including the maintenance of genome stability and regulation of antiviral and immune responses. Its dysfunction is linked to various cancers and neurodevelopmental disorders such as Hao-Fountain syndrome. Unlike other USP-family enzymes, the triad of catalytic residues in USP7 adopts an inactive conformation and undergoes rearrangement into the active state upon substrate binding. Despite its potential importance for regulating the enzyme’s activity, the dynamics of USP7 have not been explored. In this study, we combine advanced CPMG NMR relaxation dispersion measurements with the analysis of enzyme kinetics to investigate the conformational dynamics of USP7 in solution and its role in enzyme activation. Our results suggest that apo-USP7 exists in a dynamic equilibrium, transiently switching between inactive and low-populated active conformations, indicating that enzyme activation can occur spontaneously, even in the absence of a substrate. Furthermore, we show that the Hao-Fountain syndrome-associated variant G392D enhances the conformational dynamics of the enzyme, leading to a significant increase in its catalytic activity. This study captures the sparsely populated, "invisible" active conformation of USP7 and demonstrates how changes in enzyme dynamics can contribute to activity, offering broader insights into enzyme function and disease mechanisms.

A direct computational assessment of vinculin–actin unbinding kinetics reveals catch-bonding behavior

Vinculin forms a catch bond with the cytoskeletal polymer actin, displaying an increased bond lifetime upon force application. Notably, this behavior depends on the direction of the applied force, which has significant implications for cellular mechanotransduction. In this work, we present a comprehensive molecular dynamics simulation study, employing enhanced sampling techniques to investigate the thermodynamic, kinetic, and mechanistic aspects of this phenomenon at physiologically relevant forces. We dissect a catch bond mechanism in which force shifts vinculin between either a weakly or strongly bound state. Our results demonstrate that models for these states have unbinding times consistent with those from single-molecule studies, and suggest that both have some intrinsic catch-bonding behavior. We provide atomistic insight into this behavior, and show how a directional pulling force can promote the strong or weak state. Crucially, our strategy can be extended to measure the difficult-to-capture effects of small mechanical forces on biomolecular systems in general, and those involved in mechanotransduction more specifically.

Fake AI images will cause headaches for journals

Nonenzymatic RNA copying with a potentially primordial genetic alphabet

Nonenzymatic RNA copying is thought to have been responsible for the replication of genetic information during the origin of life. However, chemical copying with the canonical nucleotides (A, U, G, and C) strongly favors the incorporation of G and C and disfavors the incorporation of A and especially U because of the stronger G:C vs. A:U base pair and the weaker stacking interactions of U. Recent advances in prebiotic chemistry suggest that the 2-thiopyrimidines were precursors to the canonical pyrimidines, raising the possibility that they may have played an important early role in RNA copying chemistry. Furthermore, 2-thiouridine (s 2 U) and inosine (I) form by deamination of 2-thiocytidine (s 2 C) and A, respectively. We used thermodynamic and crystallographic analyses to compare the I:s 2 C and A:s 2 U base pairs. We find that the I:s 2 C base pair is isomorphic and isoenergetic with the A:s 2 U base pair. The I:s 2 C base pair is weaker than a canonical G:C base pair, while the A:s 2 U base pair is stronger than the canonical A:U base pair, so that a genetic alphabet consisting of s 2 U, s 2 C, I, and A generates RNA duplexes with uniform base pairing energies. Consistent with these results, kinetic analysis of nonenzymatic template-directed primer extension reactions reveals that s 2 C and s 2 U substrates bind similarly to I and A in the template, and vice versa. Our work supports the plausibility of a potentially primordial genetic alphabet consisting of s 2 U, s 2 C, I, and A and offers a potential solution to the long-standing problem of biased nucleotide incorporation during nonenzymatic template copying.

Engineering spin coherence in core-shell diamond nanocrystals

Fluorescent diamond nanocrystals can host spin qubit sensors capable of probing the physical properties of biological systems with nanoscale spatial resolution. Sub-100 nm diamond nanosensors can readily be delivered into intact cells and even living organisms. However, applications beyond current proof-of-principle experiments require a substantial increase in sensitivity, which is limited by surface induced charge instability and electron-spin dephasing. In this work, we utilize engineered core-shell structures to achieve a drastic increase in qubit coherence times ( T 2 ) from 1.1 to 35 μs in bare nanodiamonds to upward of 52 to 87 μs. We use electron-paramagnetic-resonance results to present a band bending model and connect silica encapsulation to the removal of deleterious mid-gap surface states that are negatively affecting the qubit’s spin properties. Combined with a 1.9-fold increase in particle luminescence these advances correspond to up to two-order-of-magnitude reduction in integration time. Probing qubit dynamics at a single particle level further reveals that the noise characteristics fundamentally change from a bath with spins that rearrange their spatial configuration during the course of an experiment to a more dilute static bath. The observed results shed light on the underlying mechanisms governing fluorescence and spin properties in diamond nanocrystals and offer an effective noise mitigation strategy based on engineered core-shell structures.

Daily briefing: Harvard has had nearly 1,000 research grants cancelled