Search

One of the deepest branches in the tree of life separates the Archaea from the Bacteria. These prokaryotic groups have distinct cellular systems including fundamentally different phospholipid membrane bilayers. This dichotomy has been termed the lipid divide and possibly bestows different biophysical and biochemical characteristics on each cell type. Classic experiments suggest that bacterial membranes (formed from lipids extracted from Escherichia coli, for example) show permeability to key metabolites comparable to archaeal membranes (formed from lipids extracted from Halobacterium salinarum), yet systematic analyses based on direct measurements of membrane permeability are absent. Here, we develop a new approach for assessing the membrane permeability of approximately 10 μm unilamellar vesicles, consisting of an aqueous medium enclosed by a single lipid bilayer. Comparing the permeability of 18 metabolites demonstrates that diether glycerol-1-phosphate lipids with methyl branches, often the most abundant membrane lipids of sampled archaea, are permeable to a wide range of compounds useful for core metabolic networks, including amino acids, sugars, and nucleobases. Permeability is significantly lower in diester glycerol-3-phosphate lipids without methyl branches, the common building block of bacterial membranes. To identify the membrane characteristics that determine permeability, we use this experimental platform to test a variety of lipid forms bearing a diversity of intermediate characteristics. We found that increased membrane permeability is dependent on both the methyl branches on the lipid tails and the ether bond between the tails and the head group, both of which are present on the archaeal phospholipids. These permeability differences must have had profound effects on the cell physiology and proteome evolution of early prokaryotic forms. To explore this further, we compare the abundance and distribution of transmembrane transporter-encoding protein families present on genomes sampled from across the prokaryotic tree of life. These data demonstrate that archaea tend to have a reduced repertoire of transporter gene families, consistent with increased membrane permeation. These results demonstrate that the lipid divide demarcates a clear difference in permeability function with implications for understanding some of the earliest transitions in cell origins and evolution.

Transporter proteins are a vital interface between cells and their environment. In nutrient-limited environments, microbes with transporters that are effective at bringing substrates into their cells will gain a competitive advantage over variants with reduced transport function. Microbial ammonium transporters (Amt) bring ammonium into the cytoplasm from the surrounding periplasm space, but diagnosing Amt adaptations to low nutrient environments solely from sequence data has been elusive. Here, we report altered Amt sequence amino acid distribution from deep marine samples compared to variants sampled from shallow water in two important microbial lineages of the marine water column community-Marine Group I Archaea (Thermoproteota) and the uncultivated gammaproteobacterial lineage SAR86. This pattern indicates an evolutionary pressure towards an increasing dipole in Amt for these clades in deep ocean environments and is predicted to generate stronger electric fields facilitating ammonium acquisition. This pattern of increasing dipole charge with depth was not observed in lineages capable of accessing alternative nitrogen sources, including the abundant alphaproteobacterial clade SAR11. We speculate that competition for ammonium in the deep ocean drives transporter sequence evolution. The low concentration of ammonium in the deep ocean is therefore likely due to rapid uptake by Amts concurrent with decreasing nutrient flux.

Despite its widespread appearance, the scour of cohesive materials has received relatively less attention than the granular counterpart. In particular, the different modes of erosion of cohesive soils, its long-term temporal evolution, and the effect of the impinging angle and jet regime on scour features still represent open questions. To shed light on these aspects, a series of long-term experiments were conducted involving a circular jet impinging on a clay bed at angles of 45°, 60°, 75°, and 90°. Experimental evidence allowed us to provide unprecedented insights into the peculiar evolution of the scour process, as well as empirical formulas to estimate the main geometrical features of the scour hole. Scour evolution is distinguished between continuous or discontinuous. These two modes differ for scour evolution kinetics and scour profile similitude. Distinct erosion mechanisms are documented, including the formation of a peculiar ring scour shape. The transition between strongly and weakly deflected jet regimes is investigated and, for the first time, related to the soil friction angle. Overall, the analysis of physical evidence allowed us to reach the following main conclusions: (1) the inclination of the jet and the tailwater depth affect the scour process and its evolution and (2) the long-term scour behavior should not be disregarded to provide trustable predicting tools. [ABSTRACT FROM AUTHOR]

The interactions between a virus and its host vary in space and time and are affected by the presence of molecules that alter the physiology of either the host or the virus. Determining the molecular mechanisms at the basis of these interactions is paramount for predicting the fate of bacterial and phage populations and for designing rational phage-antibiotic therapies. We study the interactions between stationary phase Burkholderia thailandensis and the phage ΦBp-AMP1. Although heterogeneous genetic resistance to phage rapidly emerges in B. thailandensis, the presence of phage enhances the efficacy of three major antibiotic classes, the quinolones, the beta-lactams and the tetracyclines, but antagonizes tetrahydrofolate synthesis inhibitors. We discovered that enhanced antibiotic efficacy is facilitated by reduced antibiotic efflux in the presence of phage. This new phage-antibiotic therapy allows for eradication of stationary phase bacteria, whilst requiring reduced antibiotic concentrations, which is crucial for treating infections in sites where it is difficult to achieve high antibiotic concentrations. Author summary: Bacteriophages are viruses that infect and kill bacteria and therefore are considered to be a very valuable alternative to the antibiotic molecules that are currently employed in the clinic but towards which bacteria are becoming increasingly resistant. Here we show that when infected with a bacteriophage termed ΦBp-AMP1, the bacterium Burkholderia thailandensis becomes more susceptible to three major antibiotic classes routinely employed to treat infections caused by Burkholderia. We discovered that enhanced antibiotic efficacy in the presence of this bacteriophage is due to a decreased capability of the bacterium to expel antibiotics when it is infected with this bacteriophage. Understanding how bacteriophages and antibiotic molecules interact with each other is essential for optimizing bacteriophage-antibiotic therapy against bacterial infections. [ABSTRACT FROM AUTHOR]

Integrating miniature pumps within microfluidic devices is crucial for advancing point-of-care diagnostics. Understanding the emergence of flow from novel integrated pumping systems is the first step in their successful implementation. A Purcell-like elasto-magnetic integrated microfluidic pump has been simulated in COMSOL Multiphysics and its performance has been investigated and evaluated. An elastic, cilia-like element contains an embedded magnet, which allows for actuation via a weak, uniaxial, sinusoidally oscillating, external magnetic field. Pumping performance is correlated against a number of variables, such as the frequency of the driving field and the proximity of the pump to the channel walls, in order to understand the emergence of the pumping behavior. Crucially, these simulations capture many of the trends observed experimentally and shed light on the key interactions. The proximity of the channel walls in the in-plane direction strongly determines the direction of net fluid flow. This characterization has important implications for the design and optimization of this pump in practical applications. [ABSTRACT FROM AUTHOR]