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Abstract Genomes record past climatic impact on species’ range shifts, admixture, refugial isolation, and adaptative evolution. However, these processes are poorly understood in perennial herbaceous species forming a dominant group of temperate flora. We present a demographic history of the perennial herb woodland strawberry (Fragaria vescaL.) reconstructed from 200 genomes spanning most of its European range. Temporal population structure reveals a strong division into western and eastern genetic clusters along a longitudinal climatic gradient, with eastern core populations showing greater resilience during glaciations. Divergence patterns indicate that postglacial recolonization of western and eastern Europe occurred from distinct refugia in multiple waves. The current largest, admixed populations from the Mediterranean to northern Europe form a continuous chain maintained by east–west gene flow through Central Europe, with historical migration patterns indicating comparable connections during earlier interglacials. Our reconstruction of woodland strawberry’s climatic history with high temporal resolution reveals how the late Pleistocene core-periphery dynamics shaped its survival and genome evolution under climate change. The data points to populations that are essential for maintaining the long term genetic diversity of the species and opens new avenues to understand climatic adaptation of temperate flora. 

Fluorescent biosensors are a valuable means to report the spatiotemporal dynamics of protein activities in live cells and animals. However, biosensors affect the activities they are reporting. This can be ameliorated by increasing sensitivity, to use lower biosensor concentrations, or by choosing designs that minimize undesirable interactions. For biosensors in which fluorescent components interact to produce Forster Resonance Energy Transfer (FRET), perturbation is often due to interaction of biosensor components with nonfluorescent, endogenous proteins, rather than productive interactions that lead to FRET. Here we engineer the interface between biosensor components using charge swap and ‘knob into hole’ mutations to reduce all but desired interactions. Novel biosensors for Rac1 and Cdc42 showed reduced interactions with endogenous GTPases and effectors, normal activation by guanine nucleotide exchange factors (GEFs), and correctly reproduced previous reports of GTPase activation dynamics. Assaying concentration-dependent effects on cell motility showed substantially reduced perturbation of normal cell behavior. Computational models indicated that minimal perturbation could be achieved over a broader range of concentrations using the new ‘orthogonal’ biosensors. 

Nontrivial geometry of electronic Bloch states gives rise to topological insulators which are robust against sufficiently weak randomness inevitably present in any quantum material. However, increasing disorder triggers a quantum phase transition into a featureless normal insulator. As the underlying quantum critical point is approached from the topological side, small scattered droplets of normal insulators start to develop in the system and their coherent nucleation causes ultimate condensation into a trivial insulator. Unless disorder is too strong, the normal insulator accommodates disjoint tiny topological puddles. Furthermore, in the close vicinity of such a transition the emergent islands of topological and trivial insulators display spatial fractal structures, a feature that is revealed only by local topological markers. Here, we showcase this (possibly) generic phenomenon that should be apposite to dirty topological crystals of any symmetry class in any dimension from the Bott index and local Chern marker for a square-lattice-based disordered Chern insulator model. 

Abstract Regulatory networks coordinate metabolism to control how plants adapt to biotic and abiotic stresses. This coordination can align transcriptional shifts across metabolic pathways using cis-regulatory elements shared across the enzyme genes within these pathways. While the role of transcription factors (TFs) in controlling this process across pathways is well known, less is known regarding the role of shared cis-regulatory elements across the genes in a pathway. Sharing cis-regulatory elements across the genes in an enzyme complex or pathway, can create coordinated regulation of the pathway by a TF. However, it is unclear if all the genes in a pathway or enzyme complex need to be fully coordinated for maximal function. For example, if one gene in an enzyme complex loses a cis-regulatory element, it may not alter the function of the enzyme complexes function if post-transcriptional or compensatory transcriptional changes are sufficient to balance the complex. To test how cis-modular membership shapes the function of an enzyme complex, we used CRISPR/Cas9 to abolish a common cis-regulatory element across the promoters of nine genes required for the mitochondrial pyruvate dehydrogenase complex (mtPDC). This complex is composed of three apoenzymes and is a central hub coordinating carbon flow between glycolysis and the tricarboxylic acid (TCA) cycle. Different combinations of these cis-element mutations were tested across the genes in the complex inArabidopsis thalianaand the created genotypes were phenotyped for altered enzyme function using digital growth analysis, disease assays, metabolomics, and transcriptomics. This analysis revealed that mutating cis-element motifs of genes in this enzyme complex produced distinct phenotypes, displaying promoter-specific buffering and modularity. 

A series of 1,3,5,7-tetraphenyl-aza-BODIPY dyes functionalized with electron-donating or withdrawing groups at the para-positions of the phenyl rings on either the 1,7- or 3,5-positions were synthesized and characterized. The electron-donating group selected was –NH2, while the electron-withdrawing groups spanned a range of strengths, from strong (-NO2) to moderate (-NH3+) and mild (-Ndouble bondCdouble bondS). The structural modifications were strategically implemented to investigate their impact on the dyes photophysical properties. Spectroscopic studies revealed that these dyes exhibit intense absorption and emission in the near-infrared (NIR) region (678–855 nm). The photophysical properties, including molar absorptivity, fluorescence quantum yield, and Stokes shift were found to depend significantly on both the electronic nature (donating/withdrawing) and positioning (1,7- vs. 3,5-) of the substituents. Complementary computational studies provided insights into the electronic structures and excited-state dynamics, corroborating experimental observations. Time-dependent density functional theory (TD-DFT) calculations revealed that the electron density distribution and the frontier orbitals’ energies and shapes were significantly influenced by the electronic effects of the substituent groups. This study underscores the tunability of aza-BODIPY dyes through rational molecular design, enabling precise control over their optical properties for tailored NIR applications. 

Orthopoxviruses (OPVs), including the causative agents of smallpox and mpox have led to devastating outbreaks in human populations worldwide. However, the discontinuation of smallpox vaccination, which also provides cross-protection against related OPVs, has diminished global immunity to OPVs more broadly. We apply machine learning models incorporating both host ecological and viral genomic features to predict likely reservoirs of OPVs.Wedemonstrate that incorporating viral genomic features in addition to host ecological traits enhanced the accuracy of potential OPV host predictions, highlighting the importance of host-virus molecular interactions in predicting potential host species. We identify hotspots for geographic regions rich with potential OPV hosts in parts of southeast Asia, equatorial Africa, and the Amazon, revealing high overlap between regions predicted to have a high number of potential OPV host species and those with the lowest smallpox vaccination coverage, indicating a heightened risk for the emergence or establishment of zoonotic OPVs. Our findings can be used to target wildlife surveillance, particularly related to concerns about mpox establishment beyond its historical range.