Design principles for cyclin K molecular glue degraders

Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12-cyclin K to the DDB1-CUL4-RBX1 E3 ligase. Here, to investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure-activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.

Non-equilibrium dynamics of spin-lattice coupling

Quantifying the dynamics of normal modes and how they interact with other excitations is of central importance in condensed matter. Spin-lattice coupling is relevant to several sub-fields of condensed matter physics; examples include spintronics, high-Tc superconductivity, and topological materials. However, experimental approaches that can directly measure it are rare and incomplete. Here we use time-resolved X-ray diffraction to directly access the ultrafast motion of atoms and spins following the coherent excitation of an electromagnon in a multiferroic hexaferrite. One striking outcome is the different phase shifts relative to the driving field of the two different components. This phase shift provides insight into the excitation process of such a coupled mode. This direct observation of combined lattice and magnetization dynamics paves the way to access the mode-selective spin-lattice coupling strength, which remains a missing fundamental parameter for ultrafast control of magnetism and is relevant to a wide variety of materials.

Th17-associated cytokines IL-17 and IL-23 in inflamed skin of Darier disease patients as potential therapeutic targets

Darier disease (DD) is a rare, inherited multi-organ disorder associated with mutations in the ATP2A2 gene. DD patients often have skin involvement characterized by malodorous, inflamed skin and recurrent, severe infections. Therapeutic options are limited and inadequate for the long-term management of this chronic disease. The aim of this study was to characterize the cutaneous immune infiltrate in DD skin lesions in detail and to identify new therapeutic targets. Using gene and protein expression profiling assays including scRNA sequencing, we demonstrate enhanced expression of Th17-related genes and cytokines and increased numbers of Th17 cells in six DD patients. We provide evidence that targeting the IL-17/IL-23 axis in a case series of three DD patients with monoclonal antibodies is efficacious with significant clinical improvement. As DD is a chronic, relapsing disease, our findings might pave the way toward additional options for the long-term management of skin inflammation in patients with DD.

Infrared-active phonons in one-dimensional materials and their spectroscopic signatures

Dimensionality provides a clear fingerprint on the dispersion of infrared-active, polar-optical phonons. For these phonons, the local dipoles parametrized by the Born effective charges drive the LO-TO splitting of bulk materials; this splitting actually breaks down in two-dimensional materials. Here, we develop the theory for one-dimensional (1D) systems-nanowires, nanotubes, and atomic and polymeric chains. Combining an analytical model with the implementation of density-functional perturbation theory in 1D boundary conditions, we show that the dielectric splitting in the dispersion relations collapses as x 2 log ( x ) at the zone center. The dielectric properties and the radius of the 1D materials are linked by the present work to these red shifts, opening infrared and Raman characterization avenues.

Fast viral dynamics revealed by microsecond time-resolved cryo-EM

Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incomplete. To enable such observations, we have recently proposed a technique that improves the time resolution of cryo-electron microscopy (cryo-EM) to microseconds. Here, we demonstrate that microsecond time-resolved cryo-EM enables observations of fast protein dynamics. We use our approach to elucidate the mechanics of the capsid of cowpea chlorotic mottle virus (CCMV), whose large-amplitude motions play a crucial role in the viral life cycle. We observe that a pH jump causes the extended configuration of the capsid to contract on the microsecond timescale. While this is a concerted process, the motions of the capsid proteins involve different timescales, leading to a curved reaction path. It is difficult to conceive how such a detailed picture of the dynamics could have been obtained with any other method, which highlights the potential of our technique. Crucially, our experiments pave the way for microsecond time-resolved cryo-EM to be applied to a broad range of protein dynamics that previously could not have been observed. This promises to fundamentally advance our understanding of protein function.

Topological invariance in whiteness optimisation

Maximizing the scattering of visible light within disordered nano-structured materials is essential for commercial applications such as brighteners, while also testing our fundamental understanding of light-matter interactions. The progress in the research field has been hindered by the lack of understanding how different structural features contribute to the scattering properties. Here we undertake a systematic investigation of light scattering in correlated disordered structures. We demonstrate that the scattering efficiency of disordered systems is mainly determined by topologically invariant features, such as the filling fraction and correlation length, and residual variations are largely accounted by the surface-averaged mean curvature of the systems. Optimal scattering efficiency can thus be obtained from a broad range of disordered structures, especially when structural anisotropy is included as a parameter. These results suggest that any disordered system can be optimised for whiteness and give comparable performance, which has far-reaching consequences for the industrial use of low-index materials for optical scattering.

Brilliant whiteness in shrimp from ultra-thin layers of birefringent nanospheres

A fundamental question regarding light scattering is how whiteness, generated from multiple scattering, can be obtained from thin layers of materials. This challenge arises from the phenomenon of optical crowding, whereby, for scatterers packed with filling fractions higher than ~30%, reflectance is drastically reduced due to near-field coupling between the scatterers. Here we show that the extreme birefringence of isoxanthopterin nanospheres overcomes optical crowding effects, enabling multiple scattering and brilliant whiteness from ultra-thin chromatophore cells in shrimp. Strikingly, numerical simulations reveal that birefringence, originating from the spherulitic arrangement of isoxanthopterin molecules, enables intense broadband scattering almost up to the maximal packing for random spheres. This reduces the thickness of material required to produce brilliant whiteness, resulting in a photonic system that is more efficient than other biogenic or biomimetic white materials which operate in the lower refractive index medium of air. These results highlight the importance of birefringence as a structural variable to enhance the performance of such materials and could contribute to the design of biologically inspired replacements for artificial scatterers like titanium dioxide.

An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Polymorphisms have fascinated biologists for a long time, but their genetic underpinnings often remain elusive. Here, we aim to uncover the genetic basis of the gold/dark polymorphism that is eponymous of Midas cichlid fish (Amphilophus spp.) adaptive radiations in Nicaraguan crater lakes. While most Midas cichlids are of the melanic "dark morph", about 10% of individuals lose their melanic pigmentation during their ontogeny and transition into a conspicuous "gold morph". Using a new haplotype-resolved long-read assembly we discover an 8.2 kb, transposon-derived inverted repeat in an intron of an undescribed gene, which we term goldentouch in reference to the Greek myth of King Midas. The gene goldentouch is differentially expressed between morphs, presumably due to structural implications of inverted repeats in both DNA and/or RNA (cruciform and hairpin formation). The near-perfect association of the insertion with the phenotype across independent populations suggests that it likely underlies this trans-specific, stable polymorphism.

Chronic, cortex-wide imaging of specific cell populations during behavior

Measurements of neuronal activity across brain areas are important for understanding the neural correlates of cognitive and motor processes such as attention, decision-making and action selection. However, techniques that allow cellular resolution measurements are expensive and require a high degree of technical expertise, which limits their broad use. Wide-field imaging of genetically encoded indicators is a high-throughput, cost-effective and flexible approach to measure activity of specific cell populations with high temporal resolution and a cortex-wide field of view. Here we outline our protocol for assembling a wide-field macroscope setup, performing surgery to prepare the intact skull and imaging neural activity chronically in behaving, transgenic mice. Further, we highlight a processing pipeline that leverages novel, cloud-based methods to analyze large-scale imaging datasets. The protocol targets laboratories that are seeking to build macroscopes, optimize surgical procedures for long-term chronic imaging and/or analyze cortex-wide neuronal recordings. The entire protocol, including steps for assembly and calibration of the macroscope, surgical preparation, imaging and data analysis, requires a total of 8 h. It is designed to be accessible to laboratories with limited expertise in imaging methods or interest in high-throughput imaging during behavior.

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network

The exclusive presence of β-D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fraction at temperatures higher than about 50 °C is still lacking. Here, we employ a combination of NMR measurements and statistical mechanics modelling to predict a population inversion between furanose and pyranose at equilibrium at high temperatures. More importantly, we show that a steady temperature gradient may steer an open isomerisation network into a non-equilibrium steady state where furanose is boosted beyond the limits set by equilibrium thermodynamics. Moreover, we demonstrate that nonequilibrium selection of furanose is maximum at optimal dissipation, as gauged by the temperature gradient and energy barriers for isomerisation. The predicted optimum is compatible with temperature drops found in hydrothermal vents associated with extremely fresh lava flows on the seafloor.

High-resolution mapping of mitotic DNA synthesis regions and common fragile sites in the human genome through direct sequencing

DNA replication stress, a feature of human cancers, often leads to instability at specific genomic loci, such as the common fragile sites (CFSs). Cells experiencing DNA replication stress may also exhibit mitotic DNA synthesis (MiDAS). To understand the physiological function of MiDAS and its relationship to CFSs, we mapped, at high resolution, the genomic sites of MiDAS in cells treated with the DNA polymerase inhibitor aphidicolin. Sites of MiDAS were evident as well-defined peaks that were largely conserved between cell lines and encompassed all known CFSs. The MiDAS peaks mapped within large, transcribed, origin-poor genomic regions. In cells that had been treated with aphidicolin, these regions remained unreplicated even in late S phase; MiDAS then served to complete their replication after the cells entered mitosis. Interestingly, leading and lagging strand synthesis were uncoupled in MiDAS, consistent with MiDAS being a form of break-induced replication, a repair mechanism for collapsed DNA replication forks. Our results provide a better understanding of the mechanisms leading to genomic instability at CFSs and in cancer cells.

Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes

Rapidly increasing availability of genomic data and ensuing identification of disease associated mutations allows for an unbiased insight into genetic drivers of disease development. However, determination of molecular mechanisms by which individual genomic changes affect biochemical processes remains a major challenge. Here, we develop a multilayered proteomic workflow to explore how genetic lesions modulate the proteome and are translated into molecular phenotypes. Using this workflow we determine how expression of a panel of disease-associated mutations in the Dyrk2 protein kinase alter the composition, topology and activity of this kinase complex as well as the phosphoproteomic state of the cell. The data show that altered protein-protein interactions caused by the mutations are associated with topological changes and affected phosphorylation of known cancer driver proteins, thus linking Dyrk2 mutations with cancer-related biochemical processes. Overall, we discover multiple mutation-specific functionally relevant changes, thus highlighting the extensive plasticity of molecular responses to genetic lesions.

Coevolution of male and female mate choice can destabilize reproductive isolation

Sexual interactions play an important role in the evolution of reproductive isolation, with important consequences for speciation. Theoretical studies have focused on the evolution of mate preferences in each sex separately. However, mounting empirical evidence suggests that premating isolation often involves mutual mate choice. Here, using a population genetic model, we investigate how female and male mate choice coevolve under a phenotype matching rule and how this affects reproductive isolation. We show that the evolution of female preferences increases the mating success of males with reciprocal preferences, favouring mutual mate choice. However, the evolution of male preferences weakens indirect selection on female preferences and, with weak genetic drift, the coevolution of female and male mate choice leads to periodic episodes of random mating with increased hybridization (deterministic 'preference cycling' triggered by stochasticity). Thus, counterintuitively, the process of establishing premating isolation proves rather fragile if both male and female mate choice contribute to assortative mating.

Achievement motivation modulates Pavlovian aversive conditioning to goal-relevant stimuli

Pavlovian aversive conditioning is a fundamental form of learning helping organisms survive in their environment. Previous research has suggested that organisms are prepared to preferentially learn to fear stimuli that have posed threats to survival across evolution. Here, we examined whether enhanced Pavlovian aversive conditioning can occur to stimuli that are relevant to the organism's concerns beyond biological and evolutionary considerations, and whether such preferential learning is modulated by inter-individual differences in affect and motivation. Seventy-two human participants performed a spatial cueing task where the goal-relevance of initially neutral stimuli was experimentally manipulated. They subsequently underwent a differential Pavlovian aversive conditioning paradigm, in which the goal-relevant and goal-irrelevant stimuli served as conditioned stimuli. Skin conductance response was recorded as an index of the conditioned response and participants' achievement motivation was measured to examine its impact thereon. Results show that achievement motivation modulated Pavlovian aversive learning to goal-relevant vs. goal-irrelevant stimuli. Participants with high achievement motivation more readily acquired a conditioned response to goal-relevant compared with goal-irrelevant stimuli than did participants with lower achievement motivation. However, no difference was found between goal-relevant and goal-irrelevant stimuli during extinction. These findings suggest that stimuli that are detected as relevant to the organism can induce facilitated Pavlovian aversive conditioning even though they hold no inherent threat value and no biological evolutionary significance, and that the occurrence of such learning bias is critically dependent on inter-individual differences in the organism's concerns, such as achievement motivation.