Momentum considerations inside near-zero index materials

Near-zero index (NZI) materials, i.e., materials having a phase refractive index close to zero, are known to enhance or inhibit light-matter interactions. Most theoretical derivations of fundamental radiative processes rely on energetic considerations and detailed balance equations, but not on momentum considerations. Because momentum exchange should also be incorporated into theoretical models, we investigate momentum inside the three categories of NZI materials, i.e., inside epsilon-and-mu-near-zero (EMNZ), epsilon-near-zero (ENZ) and mu-near-zero (MNZ) materials. In the context of Abraham-Minkowski debate in dispersive materials, we show that Minkowski-canonical momentum of light is zero inside all categories of NZI materials while Abraham-kinetic momentum of light is zero in ENZ and MNZ materials but nonzero inside EMNZ materials. We theoretically demonstrate that momentum recoil, transfer momentum from the field to the atom and Doppler shift are inhibited in NZI materials. Fundamental radiative processes inhibition is also explained due to those momentum considerations inside three-dimensional NZI materials. Absence of diffraction pattern in slits experiments is seen as a consequence of zero Minkowski momentum. Lastly, consequence on Heisenberg inequality, microscopy applications and on the canonical momentum as generator of translations are discussed. Those findings are appealing for a better understanding of fundamental light-matter interactions at the nanoscale as well as for lasing applications.

Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes

Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that produce biofilms on abiotic and biotic surfaces. While genetic and morphological diversification enables the adaptation of multicellular communities, this area remains largely unknown in the Bacillus cereus group. In this work, we dissected the experimental evolution of Bacillus thuringiensis 407 Cry- during continuous recolonization of plastic beads. We observed the evolution of a distinct colony morphotype that we named fuzzy spreader (FS) variant. Most multicellular traits of the FS variant displayed higher competitive ability versus the ancestral strain, suggesting an important role for diversification in the adaptation of B. thuringiensis to the biofilm lifestyle. Further genetic characterization of FS variant revealed the disruption of a guanylyltransferase gene by an insertion sequence (IS) element, which could be similarly observed in the genome of a natural isolate. The evolved FS and the deletion mutant in the guanylyltransferase gene (Bt407ΔrfbM) displayed similarly altered aggregation and hydrophobicity compared to the ancestor strain, suggesting that the adaptation process highly depends on the physical adhesive forces.

Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load

New lineages of SARS-CoV-2 are of potential concern due to higher transmissibility, risk of severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and risk factors, such as age of primary case and viral load remains poorly understood. Here, we used comprehensive administrative data from Denmark, comprising the full population (January 11 to February 7, 2021), to estimate household transmissibility. This study included 5,241 households with primary cases; 808 were infected with lineage B.1.1.7 and 4,433 with other lineages. Here, we report an attack rate of 38% in households with a primary case infected with B.1.1.7 and 27% in households with other lineages. Primary cases infected with B.1.1.7 had an increased transmissibility of 1.5-1.7 times that of primary cases infected with other lineages. The increased transmissibility of B.1.1.7 was multiplicative across age and viral load.

Ultra-coherent nanomechanical resonators based on inverse design

Engineered micro- and nanomechanical resonators with ultra-low dissipation constitute a promising platform for various quantum technologies and foundational research. Traditionally, the improvement of the resonator's performance through nanomechanical structural engineering has been driven by human intuition and insight. Such an approach is inefficient and leaves aside a plethora of unexplored mechanical designs that potentially achieve better performance. Here, we use a computer-aided inverse design approach known as topology optimization to structurally design mechanical resonators with optimized performance of the fundamental mechanical mode. Using the outcomes of this approach, we fabricate and characterize ultra-coherent nanomechanical resonators with, to the best of our knowledge, record-high Q ⋅ f products for their fundamental mode (where Q is the quality factor and f is the frequency). The proposed approach - which can also be used to improve phononic crystals and coupled-mode resonators - opens up a new paradigm for designing ultra-coherent micro- and nanomechanical resonators, enabling e.g. novel experiments in fundamental physics and extreme sensing.

Quantum surface-response of metals revealed by acoustic graphene plasmons

A quantitative understanding of the electromagnetic response of materials is essential for the precise engineering of maximal, versatile, and controllable light-matter interactions. Material surfaces, in particular, are prominent platforms for enhancing electromagnetic interactions and for tailoring chemical processes. However, at the deep nanoscale, the electromagnetic response of electron systems is significantly impacted by quantum surface-response at material interfaces, which is challenging to probe using standard optical techniques. Here, we show how ultraconfined acoustic graphene plasmons in graphene-dielectric-metal structures can be used to probe the quantum surface-response functions of nearby metals, here encoded through the so-called Feibelman d-parameters. Based on our theoretical formalism, we introduce a concrete proposal for experimentally inferring the low-frequency quantum response of metals from quantum shifts of the acoustic graphene plasmons dispersion, and demonstrate that the high field confinement of acoustic graphene plasmons can resolve intrinsically quantum mechanical electronic length-scales with subnanometer resolution. Our findings reveal a promising scheme to probe the quantum response of metals, and further suggest the utilization of acoustic graphene plasmons as plasmon rulers with ångström-scale accuracy.

Microthermal-induced subcellular-targeted protein damage in cells on plasmonic nanosilver-modified surfaces evokes a two-phase HSP-p97/VCP response

Despite proteotoxic stress and heat shock being implicated in diverse pathologies, currently no methodology to inflict defined, subcellular thermal damage exists. Here, we present such a single-cell method compatible with laser-scanning microscopes, adopting the plasmon resonance principle. Dose-defined heat causes protein damage in subcellular compartments, rapid heat-shock chaperone recruitment, and ensuing engagement of the ubiquitin-proteasome system, providing unprecedented insights into the spatiotemporal response to thermal damage relevant for degenerative diseases, with broad applicability in biomedicine. Using this versatile method, we discover that HSP70 chaperone and its interactors are recruited to sites of thermally damaged proteins within seconds, and we report here mechanistically important determinants of such HSP70 recruitment. Finally, we demonstrate a so-far unsuspected involvement of p97(VCP) translocase in the processing of heat-damaged proteins. Overall, we report an approach to inflict targeted thermal protein damage and its application to elucidate cellular stress-response pathways that are emerging as promising therapeutic targets.

High cell densities favor lysogeny: induction of an H20 prophage is repressed by quorum sensing and enhances biofilm formation in Vibrio anguillarum

Temperate ϕH20-like phages are repeatedly identified at geographically distinct areas as free phage particles or as prophages of the fish pathogen Vibrio anguillarum. We studied mutants of a lysogenic isolate of V. anguillarum locked in the quorum-sensing regulatory modes of low (ΔvanT) and high (ΔvanO) cell densities by in-frame deletion of key regulators of the quorum-sensing pathway. Remarkably, we find that induction of the H20-like prophage is controlled by the quorum-sensing state of the host, with an eightfold increase in phage particles per cell in high-cell-density cultures of the quorum-sensing-deficient ΔvanT mutant. Comparative studies with prophage-free strains show that biofilm formation is promoted at low cell density and that the H20-like prophage stimulates this behavior. In contrast, the high-cell-density state is associated with reduced prophage induction, increased proteolytic activity, and repression of biofilm. The proteolytic activity may dually function to disperse the biofilm and as a quorum-sensing-mediated antiphage strategy. We demonstrate an intertwined regulation of phage-host interactions and biofilm formation, which is orchestrated by host quorum-sensing signaling, suggesting that increased lysogeny at high cell density is not solely a strategy for phages to piggy-back the successful bacterial hosts but is also a host strategy evolved to take control of the lysis-lysogeny switch to promote host fitness.

A library of ab initio Raman spectra for automated identification of 2D materials

Raman spectroscopy is frequently used to identify composition, structure and layer thickness of 2D materials. Here, we describe an efficient first-principles workflow for calculating resonant first-order Raman spectra of solids within third-order perturbation theory employing a localized atomic orbital basis set. The method is used to obtain the Raman spectra of 733 different monolayers selected from the Computational 2D Materials Database (C2DB). We benchmark the computational scheme against available experimental data for 15 known monolayers. Furthermore, we propose an automatic procedure for identifying a material based on an input experimental Raman spectrum and apply it to the cases of MoS2 (H-phase) and WTe2 (T[Formula: see text]-phase). The Raman spectra of all materials at different excitation frequencies and polarization configurations are freely available from the C2DB. Our comprehensive and easily accessible library of ab initio Raman spectra should be valuable for both theoreticians and experimentalists in the field of 2D materials.

Plasma membrane H+-ATPases sustain pollen tube growth and fertilization

Pollen tubes are highly polarized tip-growing cells that depend on cytosolic pH gradients for signaling and growth. Autoinhibited plasma membrane proton (H+) ATPases (AHAs) have been proposed to energize pollen tube growth and underlie cell polarity, however, mechanistic evidence for this is lacking. Here we report that the combined loss of AHA6, AHA8, and AHA9 in Arabidopsis thaliana delays pollen germination and causes pollen tube growth defects, leading to drastically reduced fertility. Pollen tubes of aha mutants had reduced extracellular proton (H+) and anion fluxes, reduced cytosolic pH, reduced tip-to-shank proton gradients, and defects in actin organization. Furthermore, mutant pollen tubes had less negative membrane potentials, substantiating a mechanistic role for AHAs in pollen tube growth through plasma membrane hyperpolarization. Our findings define AHAs as energy transducers that sustain the ionic circuit defining the spatial and temporal profiles of cytosolic pH, thereby controlling downstream pH-dependent mechanisms essential for pollen tube elongation, and thus plant fertility.

Electrogenic sulfide oxidation mediated by cable bacteria stimulates sulfate reduction in freshwater sediments

Cable bacteria are filamentous members of the Desulfobulbaceae family that oxidize sulfide with oxygen or nitrate by transferring electrons over centimeter distances in sediments. Recent studies show that freshwater sediments can support populations of cable bacteria at densities comparable to those found in marine environments. This is surprising since sulfide availability is presumably low in freshwater sediments due to sulfate limitation of sulfate reduction. Here we show that cable bacteria stimulate sulfate reduction in freshwater sediment through promotion of sulfate availability. Comparing experimental freshwater sediments with and without active cable bacteria, we observed a three- to tenfold increase in sulfate concentrations and a 4.5-fold increase in sulfate reduction rates when cable bacteria were present, while abundance and community composition of sulfate-reducing microorganisms (SRM) were unaffected. Correlation and ANCOVA analysis supported the hypothesis that the stimulation of sulfate reduction activity was due to relieve of the kinetic limitations of the SRM community through the elevated sulfate concentrations in sediments with cable bacteria activity. The elevated sulfate concentration was caused by cable bacteria-driven sulfide oxidation, by sulfate production from an indigenous sulfide pool, likely through cable bacteria-mediated dissolution and oxidation of iron sulfides, and by enhanced retention of sulfate, triggered by an electric field generated by the cable bacteria. Cable bacteria in freshwater sediments may thus be an integral component of a cryptic sulfur cycle and provide a mechanism for recycling of the scarce resource sulfate, stimulating sulfate reduction. It is possible that this stimulation has implication for methanogenesis and greenhouse gas emissions.

Single particles as resonators for thermomechanical analysis

Thermal methods are indispensable for the characterization of most materials. However, the existing methods require bulk amounts for analysis and give an averaged response of a material. This can be especially challenging in a biomedical setting, where only very limited amounts of material are initially available. Nano- and microelectromechanical systems (NEMS/MEMS) offer the possibility of conducting thermal analysis on small amounts of materials in the nano-microgram range, but cleanroom fabricated resonators are required. Here, we report the use of single drug and collagen particles as micro mechanical resonators, thereby eliminating the need for cleanroom fabrication. Furthermore, the proposed method reveals additional thermal transitions that are undetected by standard thermal methods and provide the possibility of understanding fundamental changes in the mechanical properties of the materials during thermal cycling. This method is applicable to a variety of different materials and opens the door to fundamental mechanistic insights.

Autophagy role(s) in response to oncogenes and DNA replication stress

Autophagy is an evolutionarily conserved process that captures aberrant intracellular proteins and/or damaged organelles for delivery to lysosomes, with implications for cellular and organismal homeostasis, aging and diverse pathologies, including cancer. During cancer development, autophagy may play both tumour-supporting and tumour-suppressing roles. Any relationships of autophagy to the established oncogene-induced replication stress (RS) and the ensuing DNA damage response (DDR)-mediated anti-cancer barrier in early tumorigenesis remain to be elucidated. Here, assessing potential links between autophagy, RS and DDR, we found that autophagy is enhanced in both early and advanced stages of human urinary bladder and prostate tumorigenesis. Furthermore, a high-content, single-cell-level microscopy analysis of human cellular models exposed to diverse genotoxic insults showed that autophagy is enhanced in cells that experienced robust DNA damage, independently of the cell-cycle position. Oncogene- and drug-induced RS triggered first DDR and later autophagy. Unexpectedly, genetic inactivation of autophagy resulted in RS, despite cellular retention of functional mitochondria and normal ROS levels. Moreover, recovery from experimentally induced RS required autophagy to support DNA synthesis. Consistently, RS due to the absence of autophagy could be partly alleviated by exogenous supply of deoxynucleosides. Our results highlight the importance of autophagy for DNA synthesis, suggesting that autophagy may support cancer progression, at least in part, by facilitating tumour cell survival and fitness under replication stress, a feature shared by most malignancies. These findings have implications for better understanding of the role of autophagy in tumorigenesis, as well as for attempts to manipulate autophagy as an anti-tumour therapeutic strategy.

Nanoscopic diffusion of water on a topological insulator

The microscopic motion of water is a central question, but gaining experimental information about the interfacial dynamics of water in fields such as catalysis, biophysics and nanotribology is challenging due to its ultrafast motion, and the complex interplay of inter-molecular and molecule-surface interactions. Here we present an experimental and computational study of the nanoscale-nanosecond motion of water at the surface of a topological insulator (TI), Bi[Formula: see text]Te[Formula: see text]. Understanding the chemistry and motion of molecules on TI surfaces, while considered a key to design and manufacturing for future applications, has hitherto been hardly addressed experimentally. By combining helium spin-echo spectroscopy and density functional theory calculations, we are able to obtain a general insight into the diffusion of water on Bi[Formula: see text]Te[Formula: see text]. Instead of Brownian motion, we find an activated jump diffusion mechanism. Signatures of correlated motion suggest unusual repulsive interactions between the water molecules. From the lineshape broadening we determine the diffusion coefficient, the diffusion energy and the pre-exponential factor.

Metal ions weaken the hydrophobicity and antibiotic resistance of Bacillus subtilis NCIB 3610 biofilms

Surface superhydrophobicity makes bacterial biofilms very difficult to fight, and it is a combination of their matrix composition and complex surface roughness which synergistically protects these biomaterials from wetting. Although trying to eradicate biofilms with aqueous (antibiotic) solutions is common practice, this can be a futile approach if the biofilms have superhydrophobic properties. To date, there are not many options available to reduce the liquid repellency of biofilms or to prevent this material property from developing. Here, we present a solution to this challenge. We demonstrate how the addition of metal ions such as copper and zinc during or after biofilm formation can render the surface of otherwise superhydrophobic B. subtilis NCIB 3610 biofilms completely wettable. As a result of this procedure, these smoother, hydrophilic biofilms are more susceptible to aqueous antibiotics solutions. Our strategy proposes a scalable and widely applicable step in a multi-faceted approach to eradicate biofilms.

A combination of chitooligosaccharide and lipochitooligosaccharide recognition promotes arbuscular mycorrhizal associations in Medicago truncatula

Plants associate with beneficial arbuscular mycorrhizal fungi facilitating nutrient acquisition. Arbuscular mycorrhizal fungi produce chitooligosaccharides (COs) and lipo-chitooligosaccharides (LCOs), that promote symbiosis signalling with resultant oscillations in nuclear-associated calcium. The activation of symbiosis signalling must be balanced with activation of immunity signalling, which in fungal interactions is promoted by COs resulting from the chitinaceous fungal cell wall. Here we demonstrate that COs ranging from CO4-CO8 can induce symbiosis signalling in Medicago truncatula. CO perception is a function of the receptor-like kinases MtCERK1 and LYR4, that activate both immunity and symbiosis signalling. A combination of LCOs and COs act synergistically to enhance symbiosis signalling and suppress immunity signalling and receptors involved in both CO and LCO perception are necessary for mycorrhizal establishment. We conclude that LCOs, when present in a mix with COs, drive a symbiotic outcome and this mix of signals is essential for arbuscular mycorrhizal establishment.

Pyrolytic carbon resonators for micromechanical thermal analysis

Thermal analysis is essential for the characterization of polymers and drugs. However, the currently established methods require a large amount of sample. Here, we present pyrolytic carbon resonators as promising tools for micromechanical thermal analysis (MTA) of nanograms of polymers. Doubly clamped pre-stressed beams with a resonance frequency of 233 ± 4 kHz and a quality factor (Q factor) of 800 ± 200 were fabricated. Optimization of the electrical conductivity of the pyrolytic carbon allowed us to explore resistive heating for integrated temperature control. MTA was achieved by monitoring the resonance frequency and quality factor of the carbon resonators with and without a deposited sample as a function of temperature. To prove the potential of pyrolytic carbon resonators as thermal analysis tools, the glass transition temperature (T g) of semicrystalline poly(L-lactic acid) (PLLA) and the melting temperature (T m) of poly(caprolactone) (PCL) were determined. The results show that the T g of PLLA and T m of PCL are 61.0 ± 0.8 °C and 60.0 ± 1.0 °C, respectively, which are in excellent agreement with the values measured by differential scanning calorimetry (DSC).

Deletion of biosynthetic genes, specific SNP patterns and differences in transcript accumulation cause variation in hydroxynitrile glucoside content in barley cultivars

Barley (Hordeum vulgare L.) produces five leucine-derived hydroxynitrile glucosides, potentially involved in alleviating pathogen and environmental stresses. These compounds include the cyanogenic glucoside epiheterodendrin. The biosynthetic genes are clustered. Total hydroxynitrile glucoside contents were previously shown to vary from zero to more than 10,000 nmoles g-1 in different barley lines. To elucidate the cause of this variation, the biosynthetic genes from the high-level producer cv. Mentor, the medium-level producer cv. Pallas, and the zero-level producer cv. Emir were investigated. In cv. Emir, a major deletion in the genome spanning most of the hydroxynitrile glucoside biosynthetic gene cluster was identified and explains the complete absence of hydroxynitrile glucosides in this cultivar. The transcript levels of the biosynthetic genes were significantly higher in the high-level producer cv. Mentor compared to the medium-level producer cv. Pallas, indicating transcriptional regulation as a contributor to the variation in hydroxynitrile glucoside levels. A correlation between distinct single nucleotide polymorphism (SNP) patterns in the biosynthetic gene cluster and the hydroxynitrile glucoside levels in 227 barley lines was identified. It is remarkable that in spite of the demonstrated presence of a multitude of SNPs and differences in transcript levels, the ratio between the five hydroxynitrile glucosides is maintained across all the analysed barley lines. This implies the involvement of a stably assembled multienzyme complex.

Increased susceptibility to cortical spreading depression and epileptiform activity in a mouse model for FHM2

Migraine is a highly prevalent, debilitating, episodic headache disorder affecting roughly 15% of the population. Familial hemiplegic migraine type 2 (FHM2) is a rare subtype of migraine caused by mutations in the ATP1A2 gene, encoding the α2 isoform of the Na+/K+-ATPase, predominantly expressed in astrocytes. Differential comorbidities such as epilepsy and psychiatric disorders manifest in patients. Using a mouse model harboring the G301R disease-mutation in the α2 isoform, we set to unravel whether α2+/G301R mice show an increased susceptibility for epilepsy and cortical spreading depression (CSD). We performed in vivo experiments involving cortical application of KCl in awake head-restrained male and female mice of different age groups (adult and aged). Interestingly, α2+/G301R mice indeed showed an increased susceptibility to both CSD and epileptiform activity, closely replicating symptoms in FHM2 patients harboring the G301R and other FHM2-causing mutations. Additionally, this epileptiform activity was superimposed on CSDs. The age-related alteration towards CSD indicates the influence of female sex hormones on migraine pathophysiology. Therefore, the FHM2, α2+/G301R mouse model can be utilized to broaden our understanding of generalized epilepsy and comorbidity hereof in migraine, and may be utilized toward future selection of possible treatment options for migraine.

Direct quality control of glycoengineered erythropoietin variants

Recombinant production of glycoprotein therapeutics like erythropoietin (EPO) in mammalian CHO cells rely on the heterogeneous N-glycosylation capacity of the cell. Recently, approaches for engineering the glycosylation capacities of mammalian cells for custom designed glycoforms have been developed. With these opportunities there is an increasing need for fast, sensitive, and global analysis of the glycoproteoform landscape produced to evaluate homogeneity and consistency. Here we use high-resolution native mass spectrometry to measure the glycoproteoform profile of 24 glycoengineered variants of EPO. Based on the unique mass and intensity profiles of each variant, we classify them according to similarities in glycosylation profiles. The classification distinguishes EPO variants with varying levels of glycan branchingand sialylation, which are crucial parameters in biotherapeutic efficacy. We propose that our methods could be of great benefit in the characterization of other glycosylated biopharmaceuticals, ranging from the initial clonal selection to batch-to-batch controls, and the assessment of similarity between biosimilar/biobetter products.