Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments

Massively-parallel measurements of dominant negative inhibition by protein fragments have been used to map protein interaction sites and discover peptide inhibitors. However, the underlying principles governing fragment-based inhibition have thus far remained unclear. Here, we adapt a high-throughput inhibitory fragment assay for use in Escherichia coli, applying it to a set of ten essential proteins. This approach yielded single amino acid resolution maps of inhibitory activity, with peaks localized to functionally important interaction sites, including oligomerization interfaces and folding contacts. Leveraging these data, we perform a systematic analysis to uncover principles of fragment-based inhibition. We determine a robust negative correlation between susceptibility to inhibition and cellular protein concentration, demonstrating that inhibitory fragments likely act primarily by titrating native protein interactions. We also characterize a series of trade-offs related to fragment length, showing that shorter peptides allow higher-resolution mapping but suffer from lower inhibitory activity. We employ an unsupervised statistical analysis to show that the inhibitory activities of protein fragments are largely driven not by generic properties such as charge, hydrophobicity, and secondary structure, but by the more specific characteristics of their bespoke macromolecular interactions. AlphaFold computational modeling of peptide complexes with one protein shows that the inhibitory activity of peptides is associated with their predicted ability to form native-like interactions. Overall, this work demonstrates fundamental characteristics of inhibitory protein fragment function and provides a foundation for understanding and controlling protein interactions in vivo.

Metapragmatics and genre: Connecting the strands

Genre analysis involves at least a foray into the social/contextual dimension framing genre-exemplars. One way to explore this dimension is drawing on the concept of metapragmatics, which is primarily associated with (American) linguistic anthropology. However, with a few exceptions, genre studies have not consistently operationalized metapragmatics, either theoretically or practically. The purpose of this article is, therefore, to explore one possible angle of such operationalization by means of studying discourse fragments reflecting on fragments of (these very or other) discourses (so-called metapragmatic discourses) vis--vis any generic properties of the reflected discourse. Specifically, we analyzed comments sections for a number of YouTube videos exemplifying several lifestyle genres. The results indicate that generic references can range from simply using a generic label to refer to the discourse in question (as a token of a certain type/genre) to actually discussing the generic characteristics of the genre it instantiates, as well as projecting certain (generic) metapragmatic stances. Another observation is that different wordings used by the discourse community to refer to generic models can be, as it were, proper generic labels, but they can also be words and phrases that would hardly qualify as proper names of genres from an analysts point of view. Both these proper and other - genre-like - labels are also often used in conjunction with or are replaced by other ways of metapragmatically referring to what the speaker does or even what they are in/by dint of using the discourse in question. This suggests that any generic labels or cues are just part of a large pool of other possible metapragmatic meanings, knowledge, and ideologies circulating in discourse communities. More broadly, the results may indicate that genre studies should see genre as an even less stabilized entity because what a genre is depends on what people who actually use it make of it, as well as augment their standard toolkits with methods aimed at exploring metapragmatic discourse.

Generic properties of free boundary problems in plasma physics*

We are concerned with the global bifurcation analysis of positive solutions to free boundary problems arising in plasma physics. We show that in general, in the sense of domain variations, the following alternative holds: either the shape of the branch of solutions resembles the monotone one of the model case of the two-dimensional disk, or it is a continuous simple curve without bifurcation points which ends up at a point where the boundary density vanishes. On the other hand, we deduce a general criterion ensuring the existence of a free boundary in the interior of the domain. Application to a classic nonlinear eigenvalue problem is also discussed.

Rotating bodies; the Kerr metric

Spacetime around a general rigidly rotating body is discussed, and the Kerr solution explored in detail. First we obtain generic properties of stationary, axisymmetric metrics. The stationary limit surface and ergoregion is defined. Then the Kerr metric is presented (without derivation) and discussed. Horizons and limit surfaces are obtained, and the overall structure of the Kerr black hole deduced. The mass and angular momentum is extracted. Equations for particle orbits are obtained, and their properties discussed.

Thermodynamic formalism for quantum channels: Entropy, pressure, Gibbs channels and generic properties

Denote [Formula: see text] the set of complex [Formula: see text] by [Formula: see text] matrices. We will analyze here quantum channels [Formula: see text] of the following kind: given a measurable function [Formula: see text] and the measure [Formula: see text] on [Formula: see text] we define the linear operator [Formula: see text], via the expression [Formula: see text]. A recent paper by T. Benoist, M. Fraas, Y. Pautrat, and C. Pellegrini is our starting point. They considered the case where [Formula: see text] was the identity. Under some mild assumptions on the quantum channel [Formula: see text] we analyze the eigenvalue property for [Formula: see text] and we define entropy for such channel. For a fixed [Formula: see text] (the a priori measure) and for a given a Hamiltonian [Formula: see text] we present a version of the Ruelle Theorem: a variational principle of pressure (associated to such [Formula: see text]) related to an eigenvalue problem for the Ruelle operator. We introduce the concept of Gibbs channel. We also show that for a fixed [Formula: see text] (with more than one point in the support) the set of [Formula: see text] such that it is [Formula: see text]-Erg (also irreducible) for [Formula: see text] is a generic set. We describe a related process [Formula: see text], [Formula: see text], taking values on the projective space [Formula: see text] and analyze the question of the existence of invariant probabilities. We also consider an associated process [Formula: see text], [Formula: see text], with values on [Formula: see text] ([Formula: see text] is the set of density operators). Via the barycenter, we associate the invariant probability mentioned above with the density operator fixed for [Formula: see text].

Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation

Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid carriage. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.

A supervised learning algorithm for interacting topological insulators based on local curvature

Topological order in solid state systems is often calculated from the integration of an appropriate curvature function over the entire Brillouin zone. At topological phase transitions where the single particle spectral gap closes, the curvature function diverges and changes sign at certain high symmetry points in the Brillouin zone. These generic properties suggest the introduction of a supervised machine learning scheme that uses only the curvature function at the high symmetry points as input data. { We apply this scheme to a variety of interacting topological insulators in different dimensions and symmetry classes. We demonstrate that an artificial neural network trained with the noninteracting data can accurately predict all topological phases in the interacting cases with very little numerical effort.} Intriguingly, the method uncovers a ubiquitous interaction-induced topological quantum multicriticality in the examples studied.

Entanglement wedge cross section in holographic excited states

We evaluate the entanglement wedge cross section (EWCS) in asymptotically AdS geometries which are dual to boundary excited states. We carry out a perturbative analysis for calculating EWCS between the vacuum and other states for a symmetric configuration consisting of two disjoint strips and obtain analytical results in the specific regimes of the parameter space. In particular, when the states described by purely gravitational excitations in the bulk we find that the leading correction to EWCS is negative and hence the correlation between the boundary subregions decreases. We also study other types of excitations upon adding the extra matter fields including current and scalar condensate. Our study reveals some generic properties of boundary information measures dual to EWCS, e.g., entanglement of purification, logarithmic negativity and reflected entropy. Finally, we discuss how these results are consistent with the behavior of other correlation measures including the holographic mutual information.