DNA Content Variation and SNP Diversity Within a Single Population of Asexual Snails.

A growing body of research suggests that many clonal populations maintain genetic diversity even without occasional sexual reproduction. The purpose of our study was to document variation in single-nucleotide polymorphism (SNP) diversity, DNA content, and pathogen susceptibility in clonal lineages of the New Zealand freshwater snail, Potamopyrgus antipodarum. We studied snails that were collected from multiple field sites around a single lake (Lake Alexandrina), as well as isofemale clonal lineages that had been isolated and maintained in the laboratory. We used the kompetitive allele specific PCR (KASP) method to genotype our samples at 46 nuclear SNP sites, and we used flow cytometry to estimate DNA content. We found high levels of SNP diversity, both in our field samples and in our clonal laboratory lines. We also found evidence of high variation in DNA content among clones, even among clones with identical genotypes across all SNP sites. Controlled pathogen exposures of the laboratory populations revealed variation in susceptibility among distinct clonal genotypes, which was independent of DNA content. Taken together, these results show high levels of diversity among asexual snails, especially for DNA content, and they suggest rapid genome evolution in asexuals.

Ultralow Lattice Thermal Conductivity at Room Temperature in Cu4 TiSe4.

Ultralow thermal conductivity draws great attention in a variety of fields of applications such as thermoelectrics and thermal barrier coatings. Herein, the crystal structure and transport properties of Cu4 TiSe4 are reported. Cu4 TiSe4 is a unique example of a non-toxic and low-cost material that exhibits a lattice ultra-low thermal conductivity of 0.19 Wm-1 K-1 at room temperature. The main contribution to the unusually low thermal conductivity is connected with the atomic lattice and its dynamics. This ultralow value of lattice thermal conductivity (kL ) can be attributed to the presence of the localized modes of Cu, which partially hybridize with the Se atoms, which in turn leads to avoidance of crossing of acoustic phonon modes that reach the zone boundary with a reduced frequency. Like a phonon glass electron crystal, Cu4 TiSe4 could also open a route to efficient thermoelectric materials, even, with chalcogenides of relatively high electrical resistivity and a large band gap, provided that their structures offer a sublattice with lightly bound cations.

Evolution of increased virulence is associated with decreased spite in the insect-pathogenic bacterium Xenorhabdus nematophila.

Disease virulence may be strongly influenced by social interactions among pathogens, both during the time course of an infection and evolutionarily. Here, we examine how spiteful bacteriocin production in the insect-pathogenic bacterium Xenorhabdus nematophila is evolutionarily linked to its virulence. We expected a negative correlation between virulence and spite owing to their inverse correlations with growth. We examined bacteriocin production and growth across 14 experimentally evolved lineages that show faster host-killing relative to their ancestral population. Consistent with expectations, these more virulent lineages showed reduced bacteriocin production and faster growth relative to the ancestor. Further, bacteriocin production was negatively correlated with growth across the examined lineages. These results strongly support an evolutionary trade-off between virulence and bacteriocin production and lend credence to the view that disease management can be improved by exploiting pathogen social interactions.

Formation of Vacancies in Si- and Ge-based Clathrates: Role of Electron Localization and Symmetry Breaking.

The formation of framework vacancies in Si- and Ge-based type-I clathrates is studied using density-functional theory as a function of filling the cages with K and Ba atoms. Our analysis reveals the relevance of structural disorder, geometric relaxation, and electronic saturation as well as vibrational and configurational entropy. In the Si clathrates, we find that vacancies are unstable, but very differently, in Ge clathrates, up to three vacancies per unit cell can be stabilized. This contrasting behavior is largely driven by the different energy gain on populating the electronic vacancy states, which originates from the different degree of localization of the valence orbitals of Si and Ge. This also actuates a qualitatively different atomic relaxation of the framework.

Early stress evokes dysregulation of histone modifiers in the medial prefrontal cortex across the life span.

Early stress has been hypothesized to recruit epigenetic mechanisms to mediate persistent molecular, cellular, and behavioral changes. Here, we have examined the consequence of the early life stress of maternal separation (ES) on the gene expression of several histone modifiers that regulate histone acetylation and methylation within the medial prefrontal cortex (mPFC), a key limbic brain region that regulates stress responses and mood-related behavior. ES animals exhibit gene regulation of both writer (histone acetyltransferases and histone methyltransferases) and eraser (histone deacetylases and histone lysine demethylases) classes of histone modifiers. While specific histone modifiers (Kat2a, Smyd3, and Suv420h1) and the sirtuin, Sirt4 were downregulated across life within the mPFC of ES animals, namely at postnatal Day 21, 2 months, and 15 months of age, we also observed gene regulation restricted to these specific time points. Despite the decline noted in expression of several histone modifiers within the mPFC following ES, this was not accompanied by any change in global or residue-specific H3 acetylation and methylation. Our findings indicate that ES results in the regulation of several histone modifiers within the mPFC across life, and suggest that such perturbations may contribute to the altered prefrontal structural and functional plasticity observed following early adversity.

A first-principles study of the III-IV-V semiconductor nanosheets.

Alloying the III-V and IV-IV sheets leads to III-IV-V nano-composites, such as the BC2N sheet, having a lower band gap than their parent III-V counterparts while having higher cohesive energies. Unlike the well known BC2N sheet, the formation energy of the III-IV-V sheets with high Z atomic constituents is much low suggesting in favour of their experimental realisation. From first-principles hybrid density functional calculations, we report a family of group III-IV-V nano-sheets that have their electronic band gap lying between 0.13-1.0 eV, which is ideal for device applications. In particular, we compare the electronic, vibrational, mechanical and thermal properties of a set of III-IV-V sheets with their III-V and IV-IV counterparts. The cohesive energies of these III-IV-V sheets are found to be the intermediate of their parent III-V and IV-IV counterparts. The puckered geometry and the presence of heterogeneous bonds may result in low thermal conductivity (due to scattering of low energy phonons at the junction of the IIIV and IVIV chains) of these sheets.

Early stress evokes temporally distinct consequences on the hippocampal transcriptome, anxiety and cognitive behaviour.

The early stress of maternal separation (ES) exerts long-lasting effects on cognition and anxiety. Recent evidence indicates enhanced hippocampus-dependent spatial learning in young adult ES animals, which shifts towards a decline in long-term memory in middle-aged life. Further, we find that ES animals exhibit enhanced anxiety in young adulthood that does not persist into middle-aged life. Here, we demonstrate unique, predominantly non-overlapping, hippocampal transcriptomes in young adult and middle-aged ES animals that accompany the temporally-specific behavioural consequences. Strikingly, the extent of gene dysregulation in middle-aged ES animals was substantially higher than in young adulthood. Functional analysis revealed distinct biological processes enriched at the two ages, highlighting the temporal shift in ES-evoked gene regulation. Our results suggest that ES history interacts with aging to exacerbate age-associated transcriptional changes and cognitive decline. qPCR profiling of histone deacetylases (Hdacs) and histone methyltransferases (HMTs) revealed an age-dependent, opposing regulation with decreased expression noted in young adult ES animals (Hdac 2, 7, 8, 9 and Suv39h1) and enhanced levels in middle-aged life (Hdac 2, 6, 8 and Suv39h1). While altered expression of histone modifying enzymes did not translate into global histone acetylation or methylation changes, we noted differential enrichment of histone acetylation and methylation modifications at the promoters of multiple genes regulated in the hippocampi of young adult and middle-aged ES animals. Our results highlight the differential molecular and behavioural consequences of ES across a life-span, and suggest a possible role for epigenetic mechanisms in contributing to the temporally-specific transcriptional changes following ES.

Revealing Na-segregation at the Si/Graphene Interface and Its Implications toward the Na-storage Behavior of Si-Based Electrodes.

The feasibility of reversible alloying of Na with Si has led to Si being considered as a potential anode material for the upcoming Na-ion battery system. However, Si exhibits useful Na-storage capacity and associated electrochemical cyclic stability only in the presence of graphene-based interlayers/additives. Despite this, no knowledge exists concerning the characteristics/phenomena at the Si/graphene interface and the possible influence of the same toward Na-storage behavior/performance. Against this backdrop, a combination of first-principles-based calculations and experimental investigations has revealed here the occurrence of preferential Na-segregation at the Si/graphene interface. Bader charge analysis indicates that when positioned right at the interface, Na undergoes the greatest extent of charge transfer (to become positively charged), with electrons being transferred primarily to the more electronegative C (as compared to Si). More importantly, the binding energy of Na assumes the most negative value at the interface. Furthermore, the overall energy of the Na-Si-graphene system gets minimized to the greatest extent when the Na atom gets located at the Si/graphene interface. The abovementioned predictions have been verified by mapping the Na-concentrations from the surfaces of galvanostatically sodiated amorphous Si films down to bare Cu or graphene-coated Cu substrates (i.e., across Si film thickness) via depth profiling ToF-SIMS. Such measurements indicate that the overall Na-concentration in the sodiated Si film is considerably greater in the presence of a graphene-based interlayer between Si and Cu, thus agreeing with the as-observed enhanced Na-storage capacity. More importantly, the observation of a definite "hump" in the Na-concentration profile very close to the Si/graphene interface, in contrast to almost no Na-concentration close to the Si/Cu interface in the absence of a graphene-based interlayer, is direct evidence for preferential Na-segregation at the Si/graphene interface (unlike at the Si/Cu interface).

Disorder in the Human Skp1 Structure is the Key to its Adaptability to Bind Many Different Proteins in the SCF Complex Assembly.

Skp1(S-phase kinase-associated protein 1 - Homo sapiens) is an adapter protein of the SCF(Skp1-Cullin1-Fbox) complex, which links the constant components (Cul1-RBX) and the variable receptor (F-box proteins) in Ubiquitin E3 ligase. It is intriguing how Skp1 can recognise and bind to a variety of structurally different F-box proteins. For practical reasons, previous efforts have used truncated Skp1, and thus it has not been possible to track the crucial aspects of the substrate recognition process. In this background, we report the solution structure of the full-length Skp1 protein determined by NMR spectroscopy for the first time and investigate the sequence-dependent dynamics in the protein. The solution structure reveals that Skp1 has an architecture: ß1-ß2-H1-H2-L1-H3-L2-H4-H5-H6-H7(partially formed) and a long tail-like disordered C-terminus. Structural analysis using DALI (Distance Matrix Alignment) reveals conserved domain structure across species for Skp1. Backbone dynamics investigated using NMR relaxation suggest substantial variation in the motional timescales along the length of the protein. The loops and the C-terminal residues are highly flexible, and the (R2/R1) data suggests µs-ms timescale motions in the helices as well. Further, the dependence of amide proton chemical shift on temperature and curved profiles of their residuals indicate that the residues undergo transitions between native state and excited state. The curved profiles for several residues across the length of the protein suggest that there are native-like low-lying excited states, particularly for several C-terminal residues. Our results provide a rationale for how the protein can adapt itself, bind, and get functionally associated with other proteins in the SCF complex by utilising its flexibility and conformational sub-states.

Low Lattice Thermal Conductivity in a Wider Temperature Range for Biphasic-Quaternary (Ti,V)CoSb Half-Heusler Alloys.

Intrinsically high lattice thermal conductivity has remained a major bottleneck for achieving a high thermoelectric figure of merit (zT) in state-of-the-art ternary half-Heusler (HH) alloys. In this work, we report a stable n-type biphasic-quaternary (Ti,V)CoSb HH alloy with a low lattice thermal conductivity κL ≈ 2 W m-1 K-1 within a wide temperature range (300-873 K), which is comparable to the reported nanostructured HH alloys. A solid-state transformation driven by spinodal decomposition upon annealing is observed in Ti0.5V0.5CoSb HH alloy, which remarkably enhances phonon scattering, while electrical properties correlate well with the altering electronic band structure and valence electron count (VEC). A maximum zT ≈ 0.4 (±0.05) at 873 K was attained by substantial lowering of κL and synergistic enhancement of the power factor. We perform first-principles density functional theory calculations to investigate the structure, stability, electronic structure, and transport properties of the synthesized alloy, which rationalize the reduction in the lattice thermal conductivity to the increase in anharmonicity due to the alloying. This study upholds the new possibilities of finding biphasic-quaternary HH compositions with intrinsically reduced κL for prospective thermoelectric applications.

Self-Doping for Synergistically Tuning the Electronic and Thermal Transport Coefficients in n-Type Half-Heuslers.

Ternary intermetallic half-Heusler (HH) compounds (XYZ) with 18 valence electron count, namely, ZrCoSb, ZrNiSn, and ZrPdSn, have revealed promising thermoelectric properties. Exemplarily, it has been experimentally observed that a slight change in the content of Y site atoms (by ∼3-12.5% i.e., m = 0.03 and 0.125 in ZrY1+mZ) leads to a drastic decrease in lattice thermal conductivity κL by more than 65-80% in many of these compounds. The present work aims at exploring the possibility of maximizing the electronic transport scenario after achieving the low κL limit in these compounds. By taking into account the full anharmonicity of the lattice dynamics, Boltzmann transport calculations are performed under the framework of density functional theory. Our results show that these excess atoms present in the vacant lattice site induce scattering either by acting as a rattling mode or by hybridizing with the acoustic modes of the host depending upon their mass and bonding chemistry, respectively. Furthermore, the introduction of these scattering centers may lead either to the formation of a defect midgap state in the electronic band structure (detrimental for electronic transport) or to light doping of the host compound. The latter is found to be particularly conducive for attaining synergy in both thermal and electronic transport.

Deviation from guest dominated glass like lattice dynamics in prototypical ternary Ba8Ni x Ge[Formula: see text] clathrates.

Intermetallic guest filled clathrate cages have been identified as promising materials for thermoelectric applications. The structure, electronic structure, and phonon dynamics of type-I Ba filled Ni substituted Ge clathrates have been explored using density-functional theory. The formation energy of type-I Ba8Ni x Ge[Formula: see text] clathrates with y  vacancies [Formula: see text] in their framework is calculated as a function of concentration of Ni substitution x. Metal substitution i.e. with Ni destabilized the framework vacancies resulting in a framework devoid of vacancies beyond a particular concentration of Ni substituition (for [Formula: see text]). By tuning the concentration of Ni in the framework, n-type to p -type doping can be achieved while retaining the compositional homogeinity. Furthermore, Ni substitution in the framework lowered the thermal conductivity of these compounds. Results of molecular dynamics simulations showed that with the increase in temperature the guest, the substitutional host as well as the host atoms rattled to collectively lower the lattice thermal conductivity of these clathrates. This is found to be contradictory to the concept of guest dominated glass like phonon dynamics in these compounds.

Evolutionary consequences of feedbacks between within-host competition and disease control.

Lay Summary: Competition often occurs among diverse parasites within a single host, but control efforts could change its strength. We examined how the interplay between competition and control could shape the evolution of parasite traits like drug resistance and disease severity.

Suppression of bacteriocin resistance using live, heterospecific competitors.

Rapidly spreading antibiotic resistance has led to the need for novel alternatives and sustainable strategies for antimicrobial use. Bacteriocins are a class of proteinaceous anticompetitor toxins under consideration as novel therapeutic agents. However, bacteriocins, like other antimicrobial agents, are susceptible to resistance evolution and will require the development of sustainable strategies to prevent or decelerate the evolution of resistance. Here, we conduct proof-of-concept experiments to test whether introducing a live, heterospecific competitor along with a bacteriocin dose can effectively suppress the emergence of bacteriocin resistance in vitro. Previous work with conventional chemotherapeutic agents suggests that competition between conspecific sensitive and resistant pathogenic cells can effectively suppress the emergence of resistance in pathogenic populations. However, the threshold of sensitive cells required for such competitive suppression of resistance may often be too high to maintain host health. Therefore, here we aim to ask whether the principle of competitive suppression can be effective if a heterospecific competitor is used. Our results show that a live competitor introduced in conjunction with low bacteriocin dose can effectively control resistance and suppress sensitive cells. Further, this efficacy can be matched by using a bacteriocin-producing competitor without any additional bacteriocin. These results provide strong proof of concept for the effectiveness of competitive suppression using live, heterospecific competitors. Currently used probiotic strains or commensals may provide promising candidates for the therapeutic use of bacteriocin-mediated competitive suppression.

Compositional Tailoring for Realizing High Thermoelectric Performance in Hafnium-Free n-Type ZrNiSn Half-Heusler Alloys.

Compositional tailoring enables fine-tuning of thermoelectric (TE) transport parameters by synergistic modulation of electronic and vibrational properties. In the present work, the aspects of compositionally tailored defects have been explored in ZrNiSn-based half-Heusler (HH) TE materials to achieve high TE performance and cost effectiveness in n-type Hf-free HH alloys. In off-stoichiometric Ni-rich ZrNi1+xSn alloys in a low Ni doping limit (x < 0.1), excess Ni induces defects (Ni/vacancy antisite + interstitials), which tend to cause band structure modification. In addition, the structural similarity of HH and full-Heusler (FH) compounds and formation energetics lead to an intrinsic phase segregation of FH nanoscale precipitates that are coherently dispersed within the ZrNiSn HH matrix as nanoclusters. A consonance was achieved experimentally between these two competing mechanisms for optimal HH composition having both FH precipitates and Ni/vacancy antisite defects in the HH matrix by elevating the sintering temperature up to the solubility limit range of the ZrNiSn system. Defect-mediated optimization of electrical and thermal transport via carrier concentration tuning, energy filtering, and possibly all scale-hierarchical architecture resulted in a maximum ZT ≈ 1.1 at 873 K for the optimized ZrNi1.03Sn composition. Our findings highlight the realistic prospect of enhancing TE performance via compositional engineering approach for wide applications of TE.

Plastic responses to competition: Does bacteriocin production increase in the presence of nonself competitors?

Anticompetitor traits such as the production of allelopathic toxins can confer significant competitive benefits but are often costly to produce. Evolution of these traits may be facilitated by environment-specific induction; however, the extent to which costly anticompetitor traits are induced by competitors is not well explored. Here, we addressed this question using bacteriocins, which are highly specific, proteinaceous anticompetitor toxins, produced by most lineages of bacteria and archaea. We tested the prediction that bacteriocin production is phenotypically plastic and induced by the presence of competitors by examining bacteriocin production in the presence and absence of nonself competitors over the course of growth of a producing strain. Our results show that bacteriocin production is detectable only at high cell densities, when competition for resources is high. However, the amount of bacteriocin activity was not significantly different in the presence vs. the absence of nonself competitors. These results suggest that bacteriocin production is either (a) canalized, constitutively produced by a fixed frequency of cells in the population or (b) induced by generic cues of competition, rather than specific self/nonself discrimination. Such a nonspecific response to competition could be favored in the natural environment where competition is ubiquitous.

The origin of diverse lattice dynamics in the graphene family.

We employ first principles based density functional theory calculations to explore the lattice dynamics of members of the graphene family. We explore the changes observed in the lattice thermal conductivity via adopting physical models for estimating phonon lifetimes. This allows us to establish a connection between the parameters such as group velocity, Grüneisen parameter, and Debye temperature of the acoustic phonon modes and the lattice thermal conductivity. Our calculations show that the presence of buckling reduces the group velocity and the Debye temperature of the sheets down the group, and hence, reduces their lattice thermal conductivity. However, there is no linear dependence between the buckling height and the observed lowering. An increase in buckling height in sheets with different geometries of the same atomic species, beyond a certain limit, does not lead to change in the group velocity and the Debye temperature of the sheets.

Early emergence of altered 5-HT2A receptor-evoked behavior, neural activation and gene expression following maternal separation.

The early stress of Maternal Separation (MS) contributes to the establishment of adult psychopathology. The serotonergic (5-HT) system is implicated during this temporal window in mediating the development of mood-related behaviors. MS is reported to evoke altered 5-HT2A receptor function in adulthood. However, the ontogeny of altered 5-HT2A receptor responsivity following MS remains unknown. Here, we examined 5-HT2A receptor agonist, DOI (1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane) (2mg/kg) evoked responses, namely stereotypical head-twitch behaviors in control and MS Sprague-Dawley rat pups at postnatal day 21 (P21). MS involved a separation of pups from the dam for 3h daily from postnatal day 2-14. MS pups at P21 exhibited significantly enhanced head-twitch behaviors compared to controls. Using c-Fos cell counting we examined neural activation in control and MS pups following DOI treatment. MS pups exhibited altered DOI-evoked c-Fos expression within all mPFC subdivisions, but not in the hippocampus, lateral septum and hypothalamus, suggesting differential prefrontal neural activation upon 5-HT2A receptor stimulation following early stress. Gene profiling of 5-HT2A receptor-regulated immediate early genes (IEGs) indicated a decline in the expression of Fos, Fra1 and Egr1 mRNA under baseline conditions in the mPFC of MS pups. MS pups also showed an altered pattern in the regulation of several 5-HT2A receptor-regulated IEGs (Fos, Fra1, Bdnf, Egr1, Egr3) following DOI treatment. Collectively, these results highlight an early emergence of altered 5-HT2A receptor-evoked behavioral responses and neural activation patterns in multiple brain regions in animals with a history of MS.

Coevolutionary interactions with parasites constrain the spread of self-fertilization into outcrossing host populations.

Given the cost of sex, outcrossing populations should be susceptible to invasion and replacement by self-fertilization or parthenogenesis. However, biparental sex is common in nature, suggesting that cross-fertilization has substantial short-term benefits. The Red Queen hypothesis (RQH) suggests that coevolution with parasites can generate persistent selection favoring both recombination and outcrossing in host populations. We tested the prediction that coevolving parasites can constrain the spread of self-fertilization relative to outcrossing. We introduced wild-type Caenorhabditis elegans hermaphrodites, capable of both self-fertilization, and outcrossing, into C. elegans populations that were fixed for a mutant allele conferring obligate outcrossing. Replicate C. elegans populations were exposed to the parasite Serratia marcescens for 33 generations under three treatments: a control (avirulent) parasite treatment, a fixed (nonevolving) parasite treatment, and a copassaged (potentially coevolving) parasite treatment. Self-fertilization rapidly invaded C. elegans host populations in the control and the fixed-parasite treatments, but remained rare throughout the entire experiment in the copassaged treatment. Further, the frequency of the wild-type allele (which permits selfing) was strongly positively correlated with the frequency of self-fertilization across host populations at the end of the experiment. Hence, consistent with the RQH, coevolving parasites can limit the spread of self-fertilization in outcrossing populations.

Exploring N-Rich Phases in Li(x)N(y) Clusters for Hydrogen Storage at Nanoscale.

We have performed cascade genetic algorithm and ab initio atomistic thermodynamics under the framework of first-principles-based hybrid density functional theory to study the (meta-)stability of a wide range of Li(x)N(y) clusters. We found that hybrid xc-functional is essential to address this problem as a local/semilocal functional simply fails even to predict a qualitative prediction. Most importantly, we find that though in bulk lithium nitride, the Li-rich phase, that is, Li3N, is the stable stoichiometry; in small Li(x)N(y) clusters, N-rich phases are more stable at thermodynamic equilibrium. We further show that these N-rich clusters are promising hydrogen storage material because of their easy adsorption and desorption ability at respectively low (≤300 K) and moderately high temperature (≥600 K).