In transcription antitermination by Q[lambda], NusA induces refolding of Q[lambda] to form a nozzle
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Yin, Zhou↗
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Inhibition of FOXP3 by stapled alpha-helical peptides dampens regulatory T cell function
Despite continuing advances in the development of novel cellular-, antibody-, and chemotherapeutic-based strategies to enhance immune reactivity, the presence of regulatory T cells (Treg cells) remains a complicating factor for their clinical efficacy. To overcome dosing limitations and off-target effects from antibody-based Treg cell deletional strategies or small molecule drugging, we investigated the ability of hydrocarbon stapled alpha-helical (SAH) peptides to target FOXP3, the master transcription factor regulator of Treg cell development, maintenance, and suppressive function. Using the crystal structure of the FOXP3 homodimer as a guide, we developed SAHs in the likeness of a portion of the native FOXP3 antiparallel coiled-coil homodimerization domain (SAH-FOXP3) to block this key FOXP3 protein-protein interaction (PPI) through molecular mimicry. We describe the design, synthesis, and biochemical evaluation of single- and double-stapled SAHs covering the entire coiled-coil expanse. We show that lead SAH-FOXP3s bind FOXP3, are cell permeable and nontoxic to T cells, induce dose-dependent transcript and protein level alterations of FOXP3 target genes, impede Treg cell function, and lead to Treg cell gene expression changes in vivo consistent with FOXP3 dysfunction. These results demonstrate a proof of concept for rationally designed FOXP3-directed peptide therapeutics that could be used as approaches to amplify endogenous immune responsiveness.
60 APPLIED LIFE SCIENCES↗
Perpendicular crossing chains enable high mobility in a noncrystalline conjugated polymer
The nature of interchain π-system contacts, and their relationship to hole transport, are elucidated for the high-mobility, noncrystalline conjugated polymer C16-IDTBT by the application of scanning tunneling microscopy, molecular dynamics, and quantum chemical calculations. The microstructure is shown to favor an unusual packing motif in which paired chains cross-over one another at near-perpendicular angles. By linking to mesoscale microstructural features, revealed by coarse-grained molecular dynamics and previous studies, and performing simulations of charge transport, it is demonstrated that the high mobility of C16-IDTBT can be explained by the promotion of a highly interconnected transport network, stemming from the adoption of perpendicular contacts at the nanoscale, in combination with fast intrachain transport.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Polarons are probes of the dynamic nanoscale environments found in electrochemically doped π-conjugated polymers
Charge carriers (i.e., polarons) in electrochemically doped organic (semi)conductors are proposed to be regulated by several physicochemical features, including the chemical compositions and structures of the π-conjugated frameworks of the semiconductor building blocks, the chemistry of the electrolyte (considering both the salt and solvent), multiscale and time-dependent morphology variations across the material as a function of electrochemical processes, and assorted permutations of these and other factors. To address these hypotheses, we investigate the energetic, optoelectronic, chemical, and local structural properties of negative polarons (radical anions) as a function of electrochemical doping in the donor–acceptor, π-conjugated redox copolymer P(NDI2OD-T2), also referred to as N2200. A critical finding is that there is not just “one type” of polaron in electrochemically doped P(NDI2OD-T2). Rather, an ensemble of polarons exists, with the polarons having optoelectronic signatures that are defined by their nanoscale environments. Importantly, the polaron optical signatures serve as local probes for how the operando electrochemical environments are dynamically working in concert to facilitate charge transport. Collectively, the distinctive and extensive integration of theory and measurement science presented here establishes a baseline for the roles that semiconductor and electrolyte chemistries and dynamic structural features have on polarons in electrochemically doped organic semiconductors and how these factors influence the energetics and rates of polaron transport.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Covalent 2D Cr 2 Te 3 ferromagnet
To broaden the scope of van der Waals 2D magnets, we report the synthesis and magnetism of covalent 2D magnetic Cr 2 Te 3 with a thickness down to one-unit-cell. The 2D Cr 2 Te 3 crystals exhibit robust ferromagnetism with a Curie temperature of 180 K, a large perpendicular anisotropy of 7 × 10 5 J m -3 , and a high coercivity of ~4.6 kG at 20 K. First principles calculations further show a transition from canted to collinear ferromagnetism, a transition from perpendicular to in-plane anisotropy, and emergent half-metallic behavior in atomically-thin Cr 2 Te 3 , suggesting its potential application for injecting carriers with high spin polarization into spintronic devices.
2D magnets↗
Future of condensed matter physics for the next 10 years
This perspective outlines a selection of research directions that members of the JPCM editorial board anticipate may shape the frontier of condensed matter physics over the next decade. Rather than a comprehensive review or formal roadmap, this perspective reflects a set of informed views drawn from diverse areas of expertise. Our intention is to spark curiosity, provoke discussion, and encourage readers to imagine—and pursue—the exciting possibilities that lie ahead.
chemical physics↗
Massive neutrinos and degeneracies in Lyman-alpha forest simulations
Using a suite of hydrodynamical simulations with cold dark matter, baryons, and neutrinos, we present a detailed study of the effect of massive neutrinos on the 1-D and 3-D flux power spectra of the Lyman-α (Lyα) forest. The presence of massive neutrinos in cosmology induces a scale- and time-dependent suppression of structure formation that is strongest on small scales. Measuring this suppression is a key method for inferring neutrino masses from cosmological data, and is one of the main goals of ongoing and future surveys like eBOSS, DES, LSST, Euclid or DESI . The clustering in the Lyα forest traces the quasi-linear power at late times and on small scales. In combination with observations of the cosmic microwave background, the forest therefore provides some of the tightest constraints on the sum of the neutrino masses. However there is a well-known degeneracy between Σmν and the amplitude of perturbations in the linear matter power spectrum. We study the corresponding degeneracy in the 1-D flux power spectrum of the Lyα forest, and for the first time also study this degeneracy in the 3-D flux power spectrum. We show that the non-linear effects of massive neutrinos on the Lyα forest, beyond the effect of linear power amplitude suppression, are negligible, and this degeneracy persists in the Lyα forest observables to a high precision. Here, we discuss the implications of this degeneracy for choosing parametrisations of the Lyα forest for cosmological analysis.
79 ASTRONOMY AND ASTROPHYSICS↗
Assessing variation in faecal glucocorticoid concentrations in gray whales exposed to anthropogenic stressors
Understanding how individual animals respond to stressors behaviourally and physiologically is a critical step towards quantifying long-term population consequences and informing management efforts. Glucocorticoid (GC) metabolite accumulation in various matrices provides an integrated measure of adrenal activation in baleen whales and could thus be used to investigate physiological changes following exposure to stressors. In this study, we measured GC concentrations in faecal samples of Pacific Coast Feeding Group (PCFG) gray whales (Eschrichtius robustus) collected over seven consecutive years to assess the association between GC content and metrics of exposure to sound levels and vessel traffic at different temporal scales, while controlling for contextual variables such as sex, reproductive status, age, body condition, year, time of year and location. We develop a Bayesian Generalized Additive Modelling approach that accommodates the many complexities of these data, including non-linear variation in hormone concentrations, missing covariate values, repeated samples, sampling variability and some hormone concentrations below the limit of detection. Estimated relationships showed large variability, but emerging patterns indicate a strong context-dependency of physiological variation, depending on sex, body condition and proximity to a port. Our results highlight the need to control for baseline hormone variation related to context, which otherwise can obscure the functional relationship between faecal GCs and stressor exposure. Therefore, extensive data collection to determine sources of baseline variation in well-studied populations, such as PCFG gray whales, could shed light on cetacean stress physiology and be used to extend applicability to less-well-studied taxa. GC analyses may offer greatest utility when employed as part of a suite of markers that, in aggregate, provide a multivariate measure of physiological status, better informing estimates of individuals’ health and ultimately the consequences of anthropogenic stressors on populations.
59 BASIC BIOLOGICAL SCIENCES↗
Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid Camelina sativa : implications for future breeding and research studies
Abstract Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, “alongside an understanding of the genetic diversity” and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified 13 distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported and may not be universal across all organ types. From a global analysis, SG3 “was only significant higher expressed” in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.
Agriculture↗
The Deeper, Wider, Faster programme: exploring stellar flare activity with deep, fast cadenced DECam imaging via machine learning
ABSTRACT We present our 500 pc distance-limited study of stellar flares using the Dark Energy Camera as part of the Deeper, Wider, Faster programme. The data were collected via continuous 20-s cadence g-band imaging and we identify 19 914 sources with precise distances from Gaia DR2 within 12, ∼3 deg2, fields over a range of Galactic latitudes. An average of ∼74 min is spent on each field per visit. All light curves were accessed through a novel unsupervised machine learning techniques designed for anomaly detection. We identify 96 flare events occurring across 80 stars, the majority of which are M dwarfs. Integrated flare energies range from ∼1031–1037 erg, with a proportional relationship existing between increased flare energy with increased distance from the Galactic plane, representative of stellar age leading to declining yet more energetic flare events. In agreement with previous studies we observe an increase in flaring fraction from M0 to M6 spectral types. Furthermore, we find a decrease in the flaring fraction of stars as vertical distance from the galactic plane is increased, with a steep decline present around ∼100 pc. We find that $\sim 70{{\ \rm per\ cent}}$ of identified flares occur on short time-scales of <8 min. Finally, we present our associated flare rates, finding a volumetric rate of 2.9 ± 0.3 × 10−6 flares pc−3 h−1.
Webb, S.↗
Stellar migration and chemical enrichment in the milky way disc: a hybrid model
ABSTRACT We develop a hybrid model of galactic chemical evolution that combines a multiring computation of chemical enrichment with a prescription for stellar migration and the vertical distribution of stellar populations informed by a cosmological hydrodynamic disc galaxy simulation. Our fiducial model adopts empirically motivated forms of the star formation law and star formation history, with a gradient in outflow mass loading tuned to reproduce the observed metallicity gradient. With this approach, the model reproduces many of the striking qualitative features of the Milky Way disc’s abundance structure: (i) the dependence of the [O/Fe]–[Fe/H] distribution on radius Rgal and mid-plane distance |z|; (ii) the changing shapes of the [O/H] and [Fe/H] distributions with Rgal and |z|; (iii) a broad distribution of [O/Fe] at sub-solar metallicity and changes in the [O/Fe] distribution with Rgal, |z|, and [Fe/H]; (iv) a tight correlation between [O/Fe] and stellar age for [O/Fe] > 0.1; (v) a population of young and intermediate-age α-enhanced stars caused by migration-induced variability in the Type Ia supernova rate; (vi) non-monotonic age–[O/H] and age–[Fe/H] relations, with large scatter and a median age of ∼4 Gyr near solar metallicity. Observationally motivated models with an enhanced star formation rate ∼2 Gyr ago improve agreement with the observed age–[Fe/H] and age–[O/H] relations, but worsen agreement with the observed age–[O/Fe] relation. None of our models predict an [O/Fe] distribution with the distinct bimodality seen in the observations, suggesting that more dramatic evolutionary pathways are required. All code and tables used for our models are publicly available through the Versatile Integrator for Chemical Evolution (VICE; https://pypi.org/project/vice).
79 ASTRONOMY AND ASTROPHYSICS↗
The Milky Way tomography with APOGEE: intrinsic density distribution and structure of mono-abundance populations
ABSTRACT The spatial distribution of mono-abundance populations (MAPs, selected in [Fe/H] and [Mg/Fe]) reflect the chemical and structural evolution in a galaxy and impose strong constraints on galaxy formation models. In this paper, we use APOGEE data to derive the intrinsic density distribution of MAPs in the Milky Way, after carefully considering the survey selection function. We find that a single exponential profile is not a sufficient description of the Milky Way’s disc. Both the individual MAPs and the integrated disc exhibit a broken radial density distribution; densities are relatively constant with radius in the inner Galaxy and rapidly decrease beyond the break radius. We fit the intrinsic density distribution as a function of radius and vertical height with a 2D density model that considers both a broken radial profile and radial variation of scale height (i.e. flaring). There is a large variety of structural parameters between different MAPs, indicative of strong structure evolution of the Milky Way. One surprising result is that high-α MAPs show the strongest flaring. The young, solar-abundance MAPs present the shortest scale height and least flaring, suggesting recent and ongoing star formation confined to the disc plane. Finally we derive the intrinsic density distribution and corresponding structural parameters of the chemically defined thin and thick discs. The chemical thick and thin discs have local surface mass densities of 5.62 ± 0.08 and 15.69 ± 0.32 M⊙pc−2, respectively, suggesting a massive thick disc with a local surface mass density ratio between thick to thin disc of 36 per cent.
79 ASTRONOMY AND ASTROPHYSICS↗
A forecast for large-scale structure constraints on Horndeski gravity with CO line intensity mapping
Here we consider the potential for line intensity mapping (LIM) of the rotational CO(1-0), CO(2-1), and CO(3-2) transitions to detect deviations from General Relativity from 0 < z < 3 within the framework of a very general class of modified gravity models, called Horndeski’s theories. Our forecast assumes a multitracer analysis separately obtaining information from the matter power spectrum and the first two multipoles of the redshift space distortion power spectrum. To achieve ±0.1 level constraints on the slope of the kinetic gravity braiding and Planck mass evolution parameters, a mm-wave LIM experiment would need to accumulate ≈10 8 –10 9 spectrometre-hours, feasible with instruments that could be deployed in the 2030s. Such a measurement would constrain the parameters of Horndeski’s theory at a level at worst competitive to and at best an order of magnitude tighter than existing constraints from the CMB and LSS. Our modelling code is publicly available.
79 ASTRONOMY AND ASTROPHYSICS↗
Brassica rapa Domestication: Untangling Wild and Feral Forms and Convergence of Crop Morphotypes
The study of domestication contributes to our knowledge of evolution and crop genetic resources. Human selection has shaped wild Brassica rapa into diverse turnip, leafy, and oilseed crops. Despite its worldwide economic importance and potential as a model for understanding diversification under domestication, insights into the number of domestication events and initial crop(s) domesticated in B. rapa have been limited due to a lack of clarity about the wild or feral status of conspecific noncrop relatives. To address this gap and reconstruct the domestication history of B. rapa, we analyzed 68,468 genotyping-by-sequencing-derived single nucleotide polymorphisms for 416 samples in the largest diversity panel of domesticated and weedy B. rapa to date. To further understand the center of origin, we modeled the potential range of wild B. rapa during the mid-Holocene. Our analyses of genetic diversity across B. rapa morphotypes suggest that noncrop samples from the Caucasus, Siberia, and Italy may be truly wild, whereas those occurring in the Americas and much of Europe are feral. Clustering, tree-based analyses, and parameterized demographic inference further indicate that turnips were likely the first crop type domesticated, from which leafy types in East Asia and Europe were selected from distinct lineages. These findings clarify the domestication history and nature of wild crop genetic resources for B. rapa, which provides the first step toward investigating cases of possible parallel selection, the domestication and feralization syndrome, and novel germplasm for Brassica crop improvement.
59 BASIC BIOLOGICAL SCIENCES↗
The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome
Abstract Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.
Biochemistry & Molecular Biology↗
Wealth inequality in the prehispanic northern US Southwest: from Malthus to Tyche
Persistent differences in wealth and power among prehispanic Pueblo societies are visible from the late AD 800s through the late 1200s, after which large portions of the northern US Southwest were depopulated. In this paper we measure these differences in wealth using Gini coefficients based on house size, and show that high Ginis (large wealth differences) are positively related to persistence in settlements and inversely related to an annual measure of the size of the unoccupied dry-farming niche. We argue that wealth inequality in this record is due first to processes inherent in village life which have internally different distributions of the most productive maize fields, exacerbated by the dynamics of systems of balanced reciprocity; and second to decreasing ability to escape village life owing to shrinking availability of unoccupied places within the maize dry-farming niche as villages get enmeshed in regional systems of tribute or taxation. We embed this analytical reconstruction in the model of an ‘Abrupt imposition of Malthusian equilibrium in a natural-fertility, agrarian society’ proposed by Puleston et al. (Puleston C, Tuljapurkar S, Winterhalder B. 2014 PLoS ONE 9, e87541 (doi:10.1371/journal.pone.0087541)), but show that the transition to Malthusian dynamics in this area is not abrupt but extends over centuries. This article is part of the theme issue ‘Evolutionary ecology of inequality’.
99 GENERAL AND MISCELLANEOUS↗
Cosmic filaments from cosmic strings
Cosmic strings are generically predicted in many extensions of the Standard Model of particle physics. In this work, we propose a new avenue for detecting cosmic strings through their effect on the filamentary structure in the cosmic web. Using cosmological simulations of the density wake from a cosmic string, we examine a variety of filament structure probes. We show that the largest effect of the cosmic string is an overdensity in the filament distribution around the string wake. The signal from the overdensity is stronger at higher redshift and more robust with a wider field. We analyze the spatial distribution of filaments from a publicly available catalog of filaments built from Sloan digital sky survey galaxies. With existing data, we find no evidence for the presence of a cosmic string wake with string tension parameter $\textit{Gμ}$ above 5 × 10 –6 . However, we project WFIRST will be able to detect a signal from such a wake at the 99% confidence level at redshift $\textit{z}$ = 2, with significantly higher confidence and the possibility of probing lower tensions ($\textit{Gμ}$ ~ 10 –6 ), at $\textit{z}$ = 10. The sensitivity of this method is not competitive with constraints derived from the cosmic microwave background. However, it provides an independent discovery channel at low redshift, which could be a smoking gun in scenarios in which the cosmic microwave background bound can be weakened.
79 ASTRONOMY AND ASTROPHYSICS↗