Super Resolution Fluorescence Microscopy and Tracking of Bacterial Flotillin (Reggie) Paralogs Provide Evidence for Defined-Sized Protein Microdomains within the Bacterial Membrane but Absence of Clusters Containing Detergent-Resistant Proteins

Biological membranes have been proposed to contain microdomains of a specific lipid composition, in which distinct groups of proteins are clustered. Flotillin-like proteins are conserved between pro—and eukaryotes, play an important function in several eukaryotic and bacterial cells, and define in vertebrates a type of so-called detergent-resistant microdomains. Using STED microscopy, we show that two bacterial flotillins, FloA and FloT, form defined assemblies with an average diameter of 85 to 110 nm in the model bacterium Bacillus subtilis. Interestingly, flotillin microdomains are of similar size in eukaryotic cells. The soluble domains of FloA form higher order oligomers of up to several hundred kDa in vitro, showing that like eukaryotic flotillins, bacterial assemblies are based in part on their ability to self-oligomerize. However, B. subtilis paralogs show significantly different diffusion rates, and consequently do not colocalize into a common microdomain. Dual colour time lapse experiments of flotillins together with other detergent-resistant proteins in bacteria show that proteins colocalize for no longer than a few hundred milliseconds, and do not move together. Our data reveal that the bacterial membrane contains defined-sized protein domains rather than functional microdomains dependent on flotillins. Based on their distinct dynamics, FloA and FloT confer spatially distinguishable activities, but do not serve as molecular scaffolds

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

Tight Lower Bounds for Testing Linear Isomorphism

We study lower bounds for testing membership in families of linear/affine-invariant Boolean functions over the hypercube. A family of functions P ⊆ {{0, 1} n → {0, 1}} is linear/affine invariant if for any f ∈ P, it is the case that f ◦ L ∈ P for any linear/affine transformation L of the domain. Motivated by the recent resurgence of attention to the permutation isomorphism problem, we first focus on families that are linearly/affinely isomorphic to some fixed function. A function f: {0, 1} n → {0, 1} is called linear isomorphic to a fixed Boolean function g if f = g ◦ A for some non-singular transformation A. Our main result is a tight adaptive, two-sided Ω(n2) lower bound for testing linear isomorphism to the inner-product function. This is the first lower bound for testing linear isomorphism to a specific function that matches the trivial upper bound. Our proof exploits the elegant connection between testing and communication complexity discovered by Blais et al. (Computational Complexity, 2012.) Our results are also the first instance of this connection that gives better than Ω(n) lower bound for any property of Boolean functions. These results extend to testing linear isomorphism to any fixed function in the larger class of so-called Maiorana-McFarland bent functions. Our second result shows an Ω(2n/4) query lower bound for any adaptive, two-sided tester for membership in the Maiorana-McFarland class of bent functions. This class of Boolean functions is also affine-invariant and its rich structure and pseudorandom properties have been well-studied in mathematics, coding theory and cryptography

Dynamics of <i>Bacillus</i> flotillin structures.

<p>A) overlay of a bright field image of a single <i>Bacillus</i> cells with the first frame of fluorescence (green signals) and of 9 trajectories, each having a different colour, of YFP tagged protein FloA, displayed over a time course of 8 seconds. B) individual mean squared displacement curves of the 9 particles observed (in corresponding colours) C) Example of about 50 tracks in 2 <i>Bacillus</i> cells, which are analysed in D) MSD curves for FloA; E) MSD curves of FloT for an experiment analogous to that shown in A) and C). F) weighted mean over all tracked MSD curves of FloA (3152 tracks, red curve) and of FloT (N = 1024, black curve). Error bars indicate the confidence of the mean values, (given by the weighted standard deviation, divided by the number of degrees of freedom). Dotted lines show the fits to the diffusion constants. G) Plot like in panel F), but differentiated into movement in the y-direction or in the x-direction for FloA-YFP; H) distribution of instantaneous velocities of FloA and along the perpendicular (v_x, blue bars) and longitudinal (v_y, red bars) cell axis, No = number. I) same as H) for FloT. For FloA, the tails of the distribution are visibly broader than for FloT, indicating a higher variance and therefore a higher diffusion constant of FloA.</p