A genome sequence for the threatened whitebark pine

Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.

Intra-horn insemination in the alpaca Vicugna pacos: Copulatory wounding and deep sperm deposition

Alpacas (Vicugna pacos) are reported to be the rare mammal in which the penis enters the uterus in mating. To date, however, only circumstantial evidence supports this assertion. Using female alpacas culled for meat, we determined that the alpaca penis penetrates to the very tips of the uterine horns, abrading the tract and breaking fine blood vessels. All female alpacas sacrificed one hour or 24 hours after mating showed conspicuous bleeding in the epithelium of some region of their reproductive tract, including the hymen, cervix and the tips of each uterine horn, but typically not in the vagina. Unmated females showed no evidence of conspicuous bleeding. Histological examination of mated females revealed widespread abrasion of the cervical and endometrial epithelium, injuries absent in unmated females. Within one hour of mating, sperm were already present in the oviduct. The male alpaca's cartilaginous penis tip with a hardened urethral process is likely responsible for the copulatory abrasion. The entire female reproductive tract interacts with the penis, functioning like a vagina. Alpacas are induced ovulators, and wounding may hasten delivery of the seminal ovulation-inducing factor beta-NGF into the female's blood stream. There is no evidence of sexual conflict in copulation in alpaca, and thus wounding may also be one of a variety of mechanisms devised by mammals to induce a beneficial, short-term inflammatory response that stimulates blastocyst implantation, the uterine remodeling associated with placental development, and thus the success of early pregnancy.

Generic Air-Gen Effect in Nanoporous Materials for Sustainable Energy Harvesting from Air Humidity

Air humidity is a vast, sustainable reservoir of energy that, unlike solar and wind, is continuously available. However, previously described technologies for harvesting energy from air humidity are either not continuous or require unique material synthesis or processing, which has stymied scalability and broad deployment. Here, a generic effect for continuous energy harvesting from air humidity is reported, which can be applied to a broad range of inorganic, organic, and biological materials. The common feature of these materials is that they are engineered with appropriate nanopores to allow air water to pass through and undergo dynamic adsorption-desorption exchange at the porous interface, resulting in surface charging. The top exposed interface experiences this dynamic interaction more than the bottom sealed interface in a thin-film device structure, yielding a spontaneous and sustained charging gradient for continuous electric output. Analyses of material properties and electric outputs lead to a "leaky capacitor" model that can describe how electricity is harvested and predict current behaviors consistent with experiments. Predictions from the model guide the fabrication of devices made from heterogeneous junctions of different materials to further expand the device category. The work opens a wide door for the broad exploration of sustainable electricity from air.

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

Hypodescent or ingroup overexclusion?: Children's and adults' racial categorization of ambiguous black/white biracial faces

Two processes describe racially ambiguous Black/White Biracial categorization-the one-drop rule, or hypodescent, whereby racially ambiguous people are categorized as members of their socially subordinated racial group (i.e., Black/White Biracial faces categorized as Black) and the ingroup overexclusion effect, whereby racially ambiguous people are categorized as members of a salient outgroup, regardless of the group's status. Without developmental research with racially diverse samples, it is unclear when these categorization patterns emerge. Study 1 included White, Black, and racially diverse Biracial children (aged 3- to 7-years) and their parents to test how racial group membership and social context influence face categorization biases. To provide the clearest test of hypodescent and ingroup overexclusion, White participants came from majority White neighborhoods and Black participants from majority Black neighborhoods (with Biracial participants from more racially diverse neighborhoods)-two samples with prominent racial ingroups. Study 2 aimed to replicate the parent findings with a separate sample of White, Black, Black/White Biracial, and Asian adults. Results suggest the ingroup overexclusion effect is present across populations early in development and persists into adulthood. Additionally, categorization was meaningfully related to parental context, pinpointing a pathway that potentially contributes to ingroup overexclusion. RESEARCH HIGHLIGHTS: White, Black, and racially diverse Biracial children and adults tended to categorize racially ambiguous Black/White Biracial faces as racial outgroup members, even if the outgroup was White. This contradicts most work arguing Black/White Biracial racially ambiguous people are more often seen as Black. Children and parents' categorizations were related, though children's categorizations were not related to socialization above and beyond parents' categorizations. Children showed similar categorization patterns across dichotomous and continuous measures.

Modulation of Singlet-Triplet Gap in Atomically Precise Silver Cluster-Assembled Material

Silver cluster-based solids have garnered considerable attention owing to their tunable luminescence behavior. While surface modification has enabled the construction of stable silver clusters, controlling interactions among clusters at the molecular level has been challenging due to their tendency to aggregate. Judicious choice of stabilizing ligands becomes pivotal in crafting a desired assembly. However, detailed photophysical behavior as a function of their cluster packing remained unexplored. Here, we modulate the packing pattern of Ag12 clusters by varying the nitrogen-based ligand. CAM-1 formed through coordination of the tritopic linker molecule and NC-1 with monodentate pyridine ligand; established via non-covalent interactions. Both the assemblies show ligand-to-metal-metal charge transfer (LMMCT) based cluster-centered emission band(s). Temperature-dependent photoluminescence spectra exhibit blue shifts at higher temperatures, which is attributed to the extent of the thermal reverse population of the S1 state from the closely spaced T1 state. The difference in the energy gap (ΔEST ) dictated by their assemblies played a pivotal role in the way that Ag12 cluster assembly in CAM-1 manifests a wider ΔEST and thus requires higher temperatures for reverse intersystem crossing (RISC) than assembly of NC-1. Such assembly-defined photoluminescence properties underscore the potential toolkit to design new cluster- assemblies with tailored optoelectronic properties.

Plant-plant interactions can mitigate (or exacerbate) hot drought impacts

This article is a Commentary on Mas et al. (2024), 241: 1021–1034.

Electron and Spin Delocalization in [Co6 Se8 (PEt3 )6 ]0/+1 Superatoms

Molecular clusters can function as nanoscale atoms/superatoms, assembling into superatomic solids, a new class of solid-state materials with designable properties through modifications on superatoms. To explore possibilities on diversifying building blocks, here we thoroughly studied one representative superatom, Co6 Se8 (PEt3 )6 . We probed its structural, electronic, and magnetic properties and revealed its detailed electronic structure as valence electrons delocalize over inorganic [Co6 Se8 ] core while ligands function as an insulated shell. 59 Co SSNMR measurements on the core and 31 P, 13 C on the ligands show that the neutral Co6 Se8 (PEt3 )6 is diamagnetic and symmetric, with all ligands magnetically equivalent. Quantum computations cross-validate NMR results and reveal degenerate delocalized HOMO orbitals, indicating aromaticity. Ligand substitution keeps the inorganic core nearly intact. After losing one electron, the unpaired electron in [Co6 Se8 (PEt3 )6 ]+1 is delocalized, causing paramagnetism and a delocalized electron spin. Notably, this feature of electron/spin delocalization over a large cluster is attractive for special single-electron devices.

The (moral) language of hate

Humans use language toward hateful ends, inciting violence and genocide, intimidating and denigrating others based on their identity. Despite efforts to better address the language of hate in the public sphere, the psychological processes involved in hateful language remain unclear. In this work, we hypothesize that morality and hate are concomitant in language. In a series of studies, we find evidence in support of this hypothesis using language from a diverse array of contexts, including the use of hateful language in propaganda to inspire genocide (Study 1), hateful slurs as they occur in large text corpora across a multitude of languages (Study 2), and hate speech on social-media platforms (Study 3). In post hoc analyses focusing on particular moral concerns, we found that the type of moral content invoked through hate speech varied by context, with Purity language prominent in hateful propaganda and online hate speech and Loyalty language invoked in hateful slurs across languages. Our findings provide a new psychological lens for understanding hateful language and points to further research into the intersection of morality and hate, with practical implications for mitigating hateful rhetoric online.

Tough Hydrogel Electrolytes for Anti-Freezing Zinc-Ion Batteries

As the soaring demand for energy storage continues to grow, batteries that can cope with extreme conditions are highly desired. Yet, existing battery materials are limited by weak mechanical properties and freeze-vulnerability, prohibiting safe energy storage in devices that are exposed to low temperature and unusual mechanical impacts. Herein, a fabrication method harnessing the synergistic effect of co-nonsolvency and "salting-out" that can produce poly(vinyl alcohol) hydrogel electrolytes with unique open-cell porous structures, composed of strongly aggregated polymer chains, and containing disrupted hydrogen bonds among free water molecules, is introduced. The hydrogel electrolyte simultaneously combines high strength (tensile strength 15.6 MPa), freeze-tolerance (< -77 °C), high mass transport (10× lower overpotential), and dendrite and parasitic reactions suppression for stable performance (30 000 cycles). The high generality of this method is further demonstrated with poly(N-isopropylacrylamide) and poly(N-tertbutylacrylamide-co-acrylamide) hydrogels. This work takes a further step toward flexible battery development for harsh environments.

Enhancement of Closed-Loop Cognitive Stress Regulation using Supervised Control Architectures

Goal: We propose novel supervised control architectures to regulate the cognitive stress state and close the loop. Methods: We take information present in underlying neural impulses of skin conductance signals and employ model-based control techniques to close the loop in a state-space framework. For performance enhancement, we establish a supervised knowledge-based layer to update control system in real time. In the supervised architecture, the controller parameters are being updated in real-time. Results: Statistical analyses demonstrate the efficiency of supervised control architectures in improving the closed-loop results while maintaining stress levels within a desired range with more optimized control efforts. The model-based approaches would guarantee the control system-perspective criteria such as stability and optimality, and the proposed supervised knowledge-based layer would further enhance their efficiency. Conclusion: Outcomes in this in silico study verify the proficiency of the proposed supervised architectures to be implemented in the real world.

DIRT/3D: 3D root phenotyping for field-grown maize (Zea mays)

The development of crops with deeper roots holds substantial promise to mitigate the consequences of climate change. Deeper roots are an essential factor to improve water uptake as a way to enhance crop resilience to drought, to increase nitrogen capture, to reduce fertilizer inputs, and to increase carbon sequestration from the atmosphere to improve soil organic fertility. A major bottleneck to achieving these improvements is high-throughput phenotyping to quantify root phenotypes of field-grown roots. We address this bottleneck with Digital Imaging of Root Traits (DIRT)/3D, an image-based 3D root phenotyping platform, which measures 18 architecture traits from mature field-grown maize (Zea mays) root crowns (RCs) excavated with the Shovelomics technique. DIRT/3D reliably computed all 18 traits, including distance between whorls and the number, angles, and diameters of nodal roots, on a test panel of 12 contrasting maize genotypes. The computed results were validated through comparison with manual measurements. Overall, we observed a coefficient of determination of r2>0.84 and a high broad-sense heritability of Hmean2> 0.6 for all but one trait. The average values of the 18 traits and a developed descriptor to characterize complete root architecture distinguished all genotypes. DIRT/3D is a step toward automated quantification of highly occluded maize RCs. Therefore, DIRT/3D supports breeders and root biologists in improving carbon sequestration and food security in the face of the adverse effects of climate change.

The LINC complex, mechanotransduction, and mesenchymal stem cell function and fate

Mesenchymal stem cells (MSCs) show tremendous promise as a cell source for tissue engineering and regenerative medicine, and are understood to be mechanosensitive to external mechanical environments. In recent years, increasing evidence points to nuclear envelope proteins as a key player in sensing and relaying mechanical signals in MSCs to modulate cellular form, function, and differentiation. Of particular interest is the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex that includes nesprin and SUN. In this review, the way in which cells can sense external mechanical environments through an intact nuclear envelope and LINC complex proteins will be briefly described. Then, we will highlight the current body of literature on the role of the LINC complex in regulating MSC function and fate decision, without and with external mechanical loading conditions. Our review and suggested future perspective may provide a new insight into the understanding of MSC mechanobiology and related functional tissue engineering applications.

Engineering Immune Tolerance with Biomaterials

Autoimmune diseases, rejection of transplanted organs and grafts, chronic inflammatory diseases, and immune-mediated rejection of biologic drugs impact a large number of people across the globe. New understanding of immune function is revealing exciting opportunities to help tackle these challenges by harnessing-or correcting-the specificity of immune function. However, realizing this potential requires precision control over the interaction between regulatory immune cues, antigens attacked during inflammation, and the tissues where these processes occur. Engineered materials-such as polymeric and lipid particles, scaffolds, and inorganic materials-offer powerful features that can help to selectively regulate immune function during disease without compromising healthy immune functions. This review highlights some of the exciting developments to leverage biomaterials as carriers, depots, scaffolds-and even as agents with intrinsic immunomodulatory features-to promote immunological tolerance.

Magic angle spinning spheres

Magic angle spinning (MAS) is commonly used in nuclear magnetic resonance of solids to improve spectral resolution. Rather than using cylindrical rotors for MAS, we demonstrate that spherical rotors can be spun stably at the magic angle. Spherical rotors conserve valuable space in the probe head and simplify sample exchange and microwave coupling for dynamic nuclear polarization. In this current implementation of spherical rotors, a single gas stream provides bearing gas to reduce friction, drive propulsion to generate and maintain angular momentum, and variable temperature control for thermostating. Grooves are machined directly into zirconia spheres, thereby converting the rotor body into a robust turbine with high torque. We demonstrate that 9.5-mm-outside diameter spherical rotors can be spun at frequencies up to 4.6 kHz with N₂(g) and 10.6 kHz with He(g). Angular stability of the spinning axis is demonstrated by observation of ⁷⁹Br rotational echoes out to 10 ms from KBr packed within spherical rotors. Spinning frequency stability of ±1 Hz is achieved with resistive heating feedback control. A sample size of 36 μl can be accommodated in 9.5-mm-diameter spheres with a cylindrical hole machined along the spinning axis. We further show that spheres can be more extensively hollowed out to accommodate 161 μl of the sample, which provides superior signal-to-noise ratio compared to traditional 3.2-mm-diameter cylindrical rotors.

Influence of Substituent Chain Branching on the Transfection Efficacy of Cyclopropenium-Based Polymers

The realization of gene therapy relies on the development of delivery vectors with high efficiency and biocompatibility. With a multitude of structures accessible, the core challenge is precisely tuning vector structure to probe and optimize structure⁻property relationships. Employing a modular strategy, two pairs of cationic polymers based on the trisaminocyclopropenium (TAC) ion were synthesized where the substituents differ in the degree of alkyl chain branching. All TAC-based polymers exhibited higher transfection efficiencies than the untreated controls, with variable in vitro toxicities. Considering both cytotoxicity and transfection efficacy, an optimal nonviral vector was identified. Our studies highlight the importance of exercising precise control over polymer structure, both in terms of backbone identity and substituent nature, and the necessity of a robust, modular platform from which to study them.