Archival single-cell genomics reveals persistent subclones during DCIS progression.

Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.

Liquid-to-solid phase transition of oskar ribonucleoprotein granules is essential for their function in Drosophila embryonic development.

Asymmetric localization of oskar ribonucleoprotein (RNP) granules to the oocyte posterior is crucial for abdominal patterning and germline formation in the Drosophila embryo. We show that oskar RNP granules in the oocyte are condensates with solid-like physical properties. Using purified oskar RNA and scaffold proteins Bruno and Hrp48, we confirm in vitro that oskar granules undergo a liquid-to-solid phase transition. Whereas the liquid phase allows RNA incorporation, the solid phase precludes incorporation of additional RNA while allowing RNA-dependent partitioning of client proteins. Genetic modification of scaffold granule proteins or tethering the intrinsically disordered region of human fused in sarcoma (FUS) to oskar mRNA allowed modulation of granule material properties in vivo. The resulting liquid-like properties impaired oskar localization and translation with severe consequences on embryonic development. Our study reflects how physiological phase transitions shape RNA-protein condensates to regulate the localization and expression of a maternal RNA that instructs germline formation.

The Centrosome Is a Selective Condensate that Nucleates Microtubules by Concentrating Tubulin.

Centrosomes are non-membrane-bound compartments that nucleate microtubule arrays. They consist of nanometer-scale centrioles surrounded by a micron-scale, dynamic assembly of protein called the pericentriolar material (PCM). To study how PCM forms a spherical compartment that nucleates microtubules, we reconstituted PCM-dependent microtubule nucleation in vitro using recombinant C. elegans proteins. We found that macromolecular crowding drives assembly of the key PCM scaffold protein SPD-5 into spherical condensates that morphologically and dynamically resemble in vivo PCM. These SPD-5 condensates recruited the microtubule polymerase ZYG-9 (XMAP215 homolog) and the microtubule-stabilizing protein TPXL-1 (TPX2 homolog). Together, these three proteins concentrated tubulin ∼4-fold over background, which was sufficient to reconstitute nucleation of microtubule asters in vitro. Our results suggest that in vivo PCM is a selective phase that organizes microtubule arrays through localized concentration of tubulin by microtubule effector proteins.

Intelligent electroactive material systems with self-adaptive mechanical memory and sequential logic.

By synthesizing the requisite functionalities of intelligence in an integrated material system, it may become possible to animate otherwise inanimate matter. A significant challenge in this vision is to continually sense, process, and memorize information in a decentralized way. Here, we introduce an approach that enables all such functionalities in a soft mechanical material system. By integrating nonvolatile memory with continuous processing, we develop a sequential logic-based material design framework. Soft, conductive networks interconnect with embedded electroactive actuators to enable self-adaptive behavior that facilitates autonomous toggling and counting. The design principles are scaled in processing complexity and memory capacity to develop a model 8-bit mechanical material that can solve linear algebraic equations based on analog mechanical inputs. The resulting material system operates continually to monitor the current mechanical configuration and to autonomously search for solutions within a desired error. The methods created in this work are a foundation for future synthetic general intelligence that can empower materials to autonomously react to diverse stimuli in their environment.

Oxygenate-induced structural evolution of high-entropy electrocatalysts for multifunctional alcohol electrooxidation integrated with hydrogen production.

High-entropy compounds have been emerging as promising candidates for electrolysis, yet their controllable electrosynthesis strategy remains a formidable challenge because of the ambiguous ionic interaction and codeposition mechanism. Herein, we report a oxygenates directionally induced electrodeposition strategy to construct high-entropy materials with amorphous features, on which the structural evolution from high-entropy phosphide to oxide is confirmed by introducing vanadate, thus realizing the simultaneous optimization of composition and structure. The representative P-CoNiMnWVOx shows excellent bifunctional catalytic performance toward alkaline hydrogen evolution reaction and ethanol oxidation reaction (EOR), with small potentials of -168 mV and 1.38 V at 100 mA cm-2, respectively. In situ spectroscopy illustrates that the electrochemical reconstruction of P-CoNiMnWVOx induces abundant Co-O species as the main catalytic active species for EOR and follows the conversion pathway of the C2 product. Theoretical calculations reveal the optimized electronic structure and adsorption free energy of reaction intermediates on P-CoNiMnWVOx, thereby resulting in a facilitated kinetic process. A membrane-free electrolyzer delivers both high Faradaic efficiencies of acetate and H2 over 95% and superior stability at100 mA cm-2 during 120 h electrolysis. In addition, the unique composition and structural advantages endow P-CoNiMnWVOx with multifunctional catalytic activity and realize multipathway electrosynthesis of formate-coupled hydrogen production.

Lack of evidence for GWAS signals of exfoliation glaucoma working via monogenic loss-of-function mutation in the nearest gene.

PURPOSE: Exfoliation syndrome (XFS) is a systemic disease of elastin-rich tissues involving a deposition of fibrillar exfoliative material (XFM) in the anterior chamber of the eye, which can promote glaucoma. The purpose of this study was to create mice with CRISPR/Cas9-induced variations in candidate genes identified from human genome-wide association studies (GWAS) and screen them for indices of XFS. METHODS: Variants predicted to be deleterious were sought in the Agpat1, Cacna1a, Loxl1, Pomp, Rbms3, Sema6a, and Tlcd5 genes of C57BL/6J mice using CRISPR/Cas9-based gene editing. Strains were phenotyped by slit-lamp, SD-OCT imaging, and fundus exams at 1-5 mos of age. Smaller cohorts of 12-mos-old mice were also studied. RESULTS: Deleterious variants were identified in six targets; Pomp was recalcitrant to targeting. Multiple alleles of some targets were isolated, yielding 12 strains. Across all genotypes and ages, 277 mice were assessed by 902 slit-lamp exams, 928 SD-OCT exams, and 358 fundus exams. Homozygosity for Agpat1 or Cacna1a mutations led to early lethality; homozygosity for Loxl1 mutations led to pelvic organ prolapse, preventing aging. Loxl1 homozygotes exhibited a conjunctival phenotype of potential relevance to XFS. Multiple other genotype-specific phenotypes were variously identified. XFM was not observed in any mice. CONCLUSIONS: This study did not detect XFM in any of the strains. This may have been due to species-specific differences, background dependence, or insufficient aging. Alternatively, it is possible that the current candidates, selected based on proximity to GWAS signals, are not effectors acting via monogenic loss-of-function mechanisms.

Excess microtubule and F-Actin formation mediates primary cilia shortening and loss in response to hyperosmotic milieu.

The primary cilium is a small organelle protruding from the cell surface and receives signals from the extracellular milieu. While dozens of studies have reported that several genetic factors impair the structure of primary cilia, evidence for environmental stimuli affecting primary cilia structures is limited. Here, we investigated an extracellular stress that affected primary cilia morphology and its underlying mechanisms. Hyperosmotic shock induced reversible shortenings and disassembly of primary cilia in murine intramedullary collecting duct cells. The primary cilia shortening caused by hyperosmotic shock followed delocalization of pericentriolar materials (PCMs). Excessive microtubule and F-actin formation in the cytoplasm coincided with those hyperosmotic shock-induced changes of primary cilia and PCMs. A microtubule-disrupting agent, Nocodazole, prevented the hyperosmotic shock-induced primary cilia disassembly partially, while preventing the delocalization of PCMs almost 100%. An actin polymerization inhibitor, Latrunculin A, also prevented partially the hyperosmotic shock-induced primary cilia shortening and disassembly, while preventing the delocalization of PCMs almost 100%. We demonstrate that hyperosmotic shock induces reversible morphological changes in primary cilia and PCMs in a manner dependent on excessive formation of microtubule and F-actin.

Shedding light on rechargeable Na/Cl2 battery.

Advancing new ideas of rechargeable batteries represents an important path to meeting the ever-increasing energy storage needs. Recently, we showed rechargeable sodium/chlorine (Na/Cl2) (or lithium/chlorine Li/Cl2) batteries that used a Na (or Li) metal negative electrode, a microporous amorphous carbon nanosphere (aCNS) positive electrode, and an electrolyte containing dissolved aluminum chloride and fluoride additives in thionyl chloride [G. Zhu et al., Nature 596, 525-530 (2021) and G. Zhu et al., J. Am. Chem. Soc. 144, 22505-22513 (2022)]. The main battery redox reaction involved conversion between NaCl and Cl2 trapped in the carbon positive electrode, delivering a cyclable capacity of up to 1,200 mAh g-1 (based on positive electrode mass) at a ~3.5 V discharge voltage [G. Zhu et al., Nature 596, 525-530 (2021) and G. Zhu et al., J. Am. Chem. Soc. 144, 22505-22513 (2022)]. Here, we identified by X-ray photoelectron spectroscopy (XPS) that upon charging a Na/Cl2 battery, chlorination of carbon in the positive electrode occurred to form carbon-chlorine (C-Cl) accompanied by molecular Cl2 infiltrating the porous aCNS, consistent with Cl2 probed by mass spectrometry. Synchrotron X-ray diffraction observed the development of graphitic ordering in the initially amorphous aCNS under battery charging when the carbon matrix was oxidized/chlorinated and infiltrated with Cl2. The C-Cl, Cl2 species and graphitic ordering were reversible upon discharge, accompanied by NaCl formation. The results revealed redox conversion between NaCl and Cl2, reversible graphitic ordering/amorphourization of carbon through battery charge/discharge, and probed trapped Cl2 in porous carbon by XPS.

Bifurcation instructed design of multistate machines.

We propose a design paradigm for multistate machines where transitions from one state to another are organized by bifurcations of multiple equilibria of the energy landscape describing the collective interactions of the machine components. This design paradigm is attractive since, near bifurcations, small variations in a few control parameters can result in large changes to the system's state providing an emergent lever mechanism. Further, the topological configuration of transitions between states near such bifurcations ensures robust operation, making the machine less sensitive to fabrication errors and noise. To design such machines, we develop and implement a new efficient algorithm that searches for interactions between the machine components that give rise to energy landscapes with these bifurcation structures. We demonstrate a proof of concept for this approach by designing magnetoelastic machines whose motions are primarily guided by their magnetic energy landscapes and show that by operating near bifurcations we can achieve multiple transition pathways between states. This proof of concept demonstration illustrates the power of this approach, which could be especially useful for soft robotics and at the microscale where typical macroscale designs are difficult to implement.

Tunable pheromone interactions among microswimmers.

Indirect interactions via shared memory deposited on the field ("field memory") play an essential role in collective motions. Some motile species, such as ants and bacteria, use attractive pheromones to complete many tasks. Mimicking these kinds of collective behavior at the laboratory scale, we present a pheromone-based autonomous agent system with tunable interactions. In this system, colloidal particles leave phase-change trails reminiscent of the process of pheromone deposition by individual ants, and the trails attract other particles and themselves. To implement this, we combine two physical phenomena: the phase change of a Ge2Sb2Te5 (GST) substrate by self-propelled Janus particles (pheromone deposition) and the AC (alternating current) electroosmotic (ACEO) flow generated by this phase change (pheromone attraction). Laser irradiation causes the GST layer to crystalize locally beneath the Janus particles, owing to the lens heating effect. Under AC field application, the high conductivity of the crystalline trail causes a field concentration and generates ACEO flow, and we introduce this flow as an attractive interaction between the Janus particles and the crystalline trail. By changing the AC frequency and voltage, we can tune the attractive flow, i.e., the sensitivity of the Janus particles to the trail, and the isolated particles undergo diverse states of motion, from self-caging to directional motion. A swarm of Janus particles also shows different states of collective motion, including colony formation and line formation. This tunability enables a reconfigurable system driven by a pheromone-like memory field.

PBE-GGA predicts the B8↔B2 phase boundary of FeO at Earth's core conditions.

FeO is a crucial component of the Earth's core, and its thermodynamic properties are essential to developing more accurate core models. It is also a notorious correlated insulator in the NaCl-type (B1) phase at ambient conditions. It undergoes two polymorphic transitions at 300 K before it becomes metallic in the NiAs-type (B8) structure at ~100 GPa. Although its phase diagram is not fully mapped, it is well established that the B8 phase transforms to the CsCl-type (B2) phase at core pressures and temperatures. Here, we report a successful ab initio calculation of the B8↔B2 phase boundary in FeO at Earth's core pressures. We show that fully anharmonic free energies computed with the Perdew-Burke-Ernzerhof-generalized gradient approximation coupled with thermal electronic excitations reproduce the experimental phase boundary within uncertainties at P > 255 GPa, including the largely negative Clapeyron slope of -52 MPa/K. This study validates the applicability of a standard density functional theory functional to FeO under Earth's core conditions and demonstrates the theoretical framework that enables complex predictive studies of this region.

Heat shock potentiates aminoglycosides against gram-negative bacteria by enhancing antibiotic uptake, protein aggregation, and ROS.

The potentiation of antibiotics is a promising strategy for combatting antibiotic-resistant/tolerant bacteria. Herein, we report that a 5-min sublethal heat shock enhances the bactericidal actions of aminoglycoside antibiotics by six orders of magnitude against both exponential- and stationary-phase Escherichia coli. This combined treatment also effectively kills various E. coli persisters, E. coli clinical isolates, and numerous gram-negative but not gram-positive bacteria and enables aminoglycosides at 5% of minimum inhibitory concentrations to eradicate multidrug-resistant pathogens Acinetobacter baumannii and Klebsiella pneumoniae. Mechanistically, the potentiation is achieved comprehensively by heat shock-enhanced proton motive force that thus promotes the bacterial uptake of aminoglycosides, as well as by increasing irreversible protein aggregation and reactive oxygen species that further augment the downstream lethality of aminoglycosides. Consistently, protonophores, chemical chaperones, antioxidants, and anaerobic culturing abolish heat shock-enhanced aminoglycoside lethality. We also demonstrate as a proof of concept that infrared irradiation- or photothermal nanosphere-induced thermal treatments potentiate aminoglycoside killing of Pseudomonas aeruginosa in a mouse acute skin wound model. Our study advances the understanding of the mechanism of actions of aminoglycosides and demonstrates a high potential for thermal ablation in curing bacterial infections when combined with aminoglycosides.

International agreements and the plant genetics research community: A guide to practice.

Plant genetic resources (PGR), including collections held in national and international gene banks, provide access to a wide array of genetic diversity and are critical to genomics research, conservation efforts, and applied breeding. Yet, there is a general lack of awareness in the research community about the rules and treaties that govern the use of PGR, about access and benefit sharing obligations contained in international treaties and/or national laws, and about how best to comply with potentially applicable requirements. This article provides a brief history and overview of three key international agreements, namely the Convention on Biological Diversity, the Nagoya Protocol, and the International Treaty on Plant Genetic Resources for Food and Agriculture, which collectively address responsibilities and obligations related to the use of much of the world's PGR. By highlighting the coverage and key considerations of each agreement, the article provides a guide for those who use PGR in plant genetics research to better understand when and how international agreements apply, and-where the rules are unclear-to suggest best practices for compliance with existing agreements.

High-performance and low-power source-gated transistors enabled by a solution-processed metal oxide homojunction.

Cost-effective fabrication of mechanically flexible low-power electronics is important for emerging applications including wearable electronics, artificial intelligence, and the Internet of Things. Here, solution-processed source-gated transistors (SGTs) with an unprecedented intrinsic gain of ~2,000, low saturation voltage of +0.8 ± 0.1 V, and a ~25.6 µW power consumption are realized using an indium oxide In2O3/In2O3:polyethylenimine (PEI) blend homojunction with Au contacts on Si/SiO2. Kelvin probe force microscopy confirms source-controlled operation of the SGT and reveals that PEI doping leads to more effective depletion of the reverse-biased Schottky contact source region. Furthermore, using a fluoride-doped AlOx gate dielectric, rigid (on a Si substrate) and flexible (on a polyimide substrate) SGTs were fabricated. These devices exhibit a low driving voltage of +2 V and power consumption of ~11.5 µW, yielding inverters with an outstanding voltage gain of >5,000. Furthermore, electrooculographic (EOG) signal monitoring can now be demonstrated using an SGT inverter, where a ~1.0 mV EOG signal is amplified to over 300 mV, indicating significant potential for applications in wearable medical sensing and human-computer interfacing.

Photoreceptor nanotubes mediate the in vivo exchange of intracellular material.

Emerging evidence suggests that intracellular molecules and organelles transfer between cells during embryonic development, tissue homeostasis and disease. We and others recently showed that transplanted and host photoreceptors engage in bidirectional transfer of intracellular material in the recipient retina, a process termed material transfer (MT). We used cell transplantation, advanced tissue imaging approaches, genetic and pharmacologic interventions and primary cell culture to characterize and elucidate the mechanism of MT. We show that MT correlates with donor cell persistence and the accumulation of donor-derived proteins, mitochondria and transcripts in acceptor cells in vivo. MT requires cell contact in vitro and is associated with the formation of stable microtubule-containing protrusions, termed photoreceptor nanotubes (Ph NTs), that connect donor and host cells in vivo and in vitro. Ph NTs mediate GFP transfer between connected cells in vitro. Furthermore, interfering with Ph NT outgrowth by targeting Rho GTPase-dependent actin remodelling inhibits MT in vivo. Collectively, our observations provide evidence for horizontal exchange of intracellular material via nanotube-like connections between neurons in vivo.

Uncovering the crystal defects within aragonite CaCO3.

Knowledge of deformation mechanisms in aragonite, one of the three crystalline polymorphs of CaCO3, is essential to understand the overall excellent mechanical performance of nacres. Dislocation slip and deformation twinning were claimed previously as plasticity carriers in aragonite, but crystallographic features of dislocations and twins have been poorly understood. Here, utilizing various transmission electron microscopy techniques, we reveal the atomic structures of twins, partial dislocations, and associated stacking faults. Combining a topological model and density functional theory calculations, we identify complete twin elements, characters of twinning disconnection, and the corresponding twin shear angle (∼8.8°) and rationalize unique partial dislocations as well. Additionally, we reveal an unreported potential energy dissipation mode within aragonite, namely, the formation of nanograins via the pile-up of partial dislocations. Based on the microstructural comparisons of biogenic and abiotic aragonite, we find that the crystallographic features of twins are the same. However, the twin density is much lower in abiotic aragonite due to the vastly different crystallization conditions, which in turn are likely due to the absence of organics, high temperature and pressure differences, the variation in inorganic impurities, or a combination thereof. Our findings enrich the knowledge of intrinsic crystal defects that accommodate plastic deformation in aragonite and provide insights into designing bioengineering materials with better strength and toughness.

High-harmonic spectroscopy of quantum phase transitions in a high-Tc superconductor.

We report on the nonlinear optical signatures of quantum phase transitions in the high-temperature superconductor YBCO, observed through high harmonic generation. While the linear optical response of the material is largely unchanged when cooling across the phase transitions, the nonlinear optical response sensitively imprints two critical points, one at the critical temperature of the cuprate with the exponential growth of the surface harmonic yield in the superconducting phase and another critical point, which marks the transition from strange metal to pseudogap phase. To reveal the underlying microscopic quantum dynamics, a strong-field quasi-Hubbard model was developed, which describes the measured optical response dependent on the formation of Cooper pairs. Further, the theory provides insight into the carrier scattering dynamics and allows us to differentiate between the superconducting, pseudogap, and strange metal phases. The direct connection between nonlinear optical response and microscopic dynamics provides a powerful methodology to study quantum phase transitions in correlated materials. Further implications are light wave control over intricate quantum phases, light-matter hybrids, and application for optical quantum computing.

Transient learning degrees of freedom for introducing function in materials.

SignificanceMany protocols used in material design and training have a common theme: they introduce new degrees of freedom, often by relaxing away existing constraints, and then evolve these degrees of freedom based on a rule that leads the material to a desired state at which point these new degrees of freedom are frozen out. By creating a unifying framework for these protocols, we can now understand that some protocols work better than others because the choice of new degrees of freedom matters. For instance, introducing particle sizes as degrees of freedom to the minimization of a jammed particle packing can lead to a highly stable state, whereas particle stiffnesses do not have nearly the same impact.

Role of smooth muscle activation in the static and dynamic mechanical characterization of human aortas.

Experimental data and a suitable material model for human aortas with smooth muscle activation are not available in the literature despite the need for developing advanced grafts; the present study closes this gap. Mechanical characterization of human descending thoracic aortas was performed with and without vascular smooth muscle (VSM) activation. Specimens were taken from 13 heart-beating donors. The aortic segments were cooled in Belzer UW solution during transport and tested within a few hours after explantation. VSM activation was achieved through the use of potassium depolarization and noradrenaline as vasoactive agents. In addition to isometric activation experiments, the quasistatic passive and active stress-strain curves were obtained for circumferential and longitudinal strips of the aortic material. This characterization made it possible to create an original mechanical model of the active aortic material that accurately fits the experimental data. The dynamic mechanical characterization was executed using cyclic strain at different frequencies of physiological interest. An initial prestretch, which corresponded to the physiological conditions, was applied before cyclic loading. Dynamic tests made it possible to identify the differences in the viscoelastic behavior of the passive and active tissue. This work illustrates the importance of VSM activation for the static and dynamic mechanical response of human aortas. Most importantly, this study provides material data and a material model for the development of a future generation of active aortic grafts that mimic natural behavior and help regulate blood pressure.

Dynamic multifunctional devices enabled by ultrathin metal nanocoatings with optical/photothermal and morphological versatility.

Inspired by the intriguing adaptivity of natural life, such as squids and flowers, we propose a series of dynamic and responsive multifunctional devices based on multiscale structural design, which contain metal nanocoating layers overlaid with other micro-/nanoscale soft or rigid layers. Since the optical/photothermal properties of a metal nanocoating are thickness dependent, metal nanocoatings with different thicknesses were chosen to integrate with other structural design elements to achieve dynamic multistimuli responses. The resultant devices demonstrate 1) strain-regulated cracked and/or wrinkled topography with tunable light-scattering properties, 2) moisture/photothermal-responsive structural color coupled with wrinkled surface, and 3) mechanically controllable light-shielding properties attributed to the strain-dependent crack width of the nanocoating. These devices can adapt external stimuli, such as mechanical strain, moisture, light, and/or heat, into corresponding changes of optical signals, such as transparency, reflectance, and/or coloration. Therefore, these devices can be applied as multistimuli-responsive encryption devices, smart windows, moisture/photothermal-responsive dynamic optics, and smartphone app-assisted pressure-mapping sensors. All the devices exhibit high reversibility and rapid responsiveness. Thus, this hybrid system containing ultrathin metal nanocoatings holds a unique design flexibility and adaptivity and is promising for developing next-generation multifunctional devices with widespread application.