A Minimal Model of Metabolism Based Chemotaxis

Since the pioneering work by Julius Adler in the 1960's, bacterial chemotaxis has been predominantly studied as metabolism-independent. All available simulation models of bacterial chemotaxis endorse this assumption. Recent studies have shown, however, that many metabolism-dependent chemotactic patterns occur in bacteria. We hereby present the simplest artificial protocell model capable of performing metabolism-based chemotaxis. The model serves as a proof of concept to show how even the simplest metabolism can sustain chemotactic patterns of varying sophistication. It also reproduces a set of phenomena that have recently attracted attention on bacterial chemotaxis and provides insights about alternative mechanisms that could instantiate them. We conclude that relaxing the metabolism-independent assumption provides important theoretical advances, forces us to rethink some established pre-conceptions and may help us better understand unexplored and poorly understood aspects of bacterial chemotaxis

Chemotaxis of Escherichia coli to compounds present in human gut

Microorganisms of the gastrointestinal (GI) tract were recently shown to communicate and consequently influence the metabolism, immunity, and behavior of animal hosts. Increasing evidence suggest that communication can also occur in the opposite direction, with hormones and other host-secreted compounds being sensed by microorganisms. Here, we addressed one key aspect of the host-microbe communication by studying a very‐well known system that senses external stimulus, the chemotaxis system. We analyzed the chemotactic response of a model commensal bacterium, Escherichia coli, to several compounds that accumulate in the GI tract, namely the catecholamines 3,4-dihydroxyphenylalanine, dopamine, norepinephrine, epinephrine and 3,4-dihydroxymandelic acid; the thyroid hormones serotonin and melatonin; the sex hormones β-estradiol and testosterone; insulin; and the polyamines putrescine and spermidine. Melatonin, testosterone and spermidine were shown to be chemorepellents, with the strongest repellent response observed for spermidine, and epinephrine showed an attractant response. Biphasic responses were observed to dopamine, norepinephrine, 3,4-dihydroxymandelic acid and insulin. To determine the underlying sensing mechanism of these compounds, we investigated the chemotactic responses of strains expressing hybrid receptors that combine domains of each of the two most abundant receptors in E. coli, Tar and Tsr. We also studied the responses of mutated Tar receptors that show inverted chemotactic responses, which enable us to identify regions of receptors that sense individual compounds. While the hormones are sensed indirectly, mainly perturbing the signaling domain of Tar and Tsr, the response to spermidine involves the low-abundant chemoreceptor Trg and the periplasmic binding protein PotD, of the spermidine uptake system. Finally, to determine the physiological importance of these compounds to E. coli, we studied their effects on bacterial growth. The chemotactic effects of the tested compounds apparently correlate with their influence on growth and with their stability in the GI tract, pointing to the specificity of the observed behavior. We hypothesize that the repellent responses observed at high concentrations of chemoeffective compounds might enable bacteria to avoid harmful levels of hormones and polyamines in the gut

Frontiers in microfluidics, a teaching resource review

This is a literature teaching resource review for biologically inspired microfluidics courses or exploring the diverse applications of microfluidics. The structure is around key papers and model organisms. While courses gradually change over time, a focus remains on understanding how microfluidics has developed as well as what it can and cannot do for researchers. As a primary starting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety of applications are discussed using model prokaryotic and eukaryotic organisms from the set of bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae), slime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster), plants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and biochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics, biotic games, and diagnostics. While we have not yet reached the end-all lab on a chip, microfluidics can still be used effectively for specific applications

The Uropathogenic Escherichia coli Effector YbcL Modulates the Innate Immune Response in the Urinary Tract

Uropathogenic Escherichia coli (UPEC) are the primary etiology of urinary tract infections (UTIs), one of the most common bacterial infections afflicting the human population. While UPEC cause disease throughout the urinary tract, bladder infection, or cystitis, is most prevalent. A key aspect of UPEC pathogenesis in the bladder is the modulation of the host inflammatory response. At acute time points, UPEC delay the arrival of immune cells, such as neutrophils, to the bladder. The lack of neutrophils in the bladder lumen enables UPEC to replicate freely in the urine and invade the bladder epithelium, a requirement for bacterial persistence, in the absence of immune pressure. The UPEC products responsible for delaying the arrival of immune cells to the bladder had not been identified. This thesis work identified a bacterial protein, YbcL, that was modestly up-regulated upon UPEC exposure to either cultured bladder epithelial cells or human neutrophils. We demonstrated that YbcL suppressed the migration of neutrophils across bladder epithelia in an in vitro model of transuroepithelial neutrophil migration and an in vivo murine model of cystitis. Suppression of PMN migration by YbcL was dependent upon the presence of threonine at position 78 (T78). In fact, T78 in YbcL is highly conserved in clinical UPEC isolates, suggesting that inhibition of neutrophil migration across epithelial barriers by YbcL is a conserved mechanism of immune modulation among UPEC. Using a number of complementary approaches, we demonstrated that liberation of YbcL from the bacterial periplasm was required for suppression of neutrophil migration across a bladder epithelium. YbcL was detected in the supernatant and in association with bladder epithelial cells and neutrophils. Release of YbcL from the periplasm occurred in a manner that was dependent upon the concentration of YbcL in the periplasm, the duration of the infection and the presence of bladder epithelial cells. Although YbcL was soluble in the supernatant, we demonstrated that YbcL was not secreted from the periplasm by a canonical secretion system. Despite the apparent absence of a dedicated secretion system, these findings demonstrate that YbcL functions as an exoprotein. Investigations into the mechanism underlying suppression of neutrophil migration by YbcL revealed that YbcL did not influence the production of chemoattractant molecules by bladder epithelial cells or bacteria or the ability of neutrophils to chemotax in response to stimuli, requirements for neutrophils to traverse epithelial barriers. This work identified and began the characterization of a bacterial protein, YbcL, that contributes to modulation of the innate immune response by UPEC. Additional experimentation is required to elucidate the importance of T78, the mode of delivery of YbcL from the periplasm, and the mechanism of action of YbcL. By delaying the arrival of immune cells, the activity of YbcL likely facilitates formation of the acute intracellular niche occupied by UPEC and required for persistence in the urinary tract

Biospectroscopy diagnosis of bacterial interaction with environmental molecules

Aims: Bacteria are universal micro-organisms that can be found in almost all aquatic and terrestrial environments and strongly affect ecological systems at different spatial scales. The activities of bacteria are profound on the physicochemical features of natural environments, while natural environments shape bacterial behaviours through physical and chemical alterations. Different molecules present in the environment produce significant effects on bacteria. Therefore, it is required to study the rich and complementary interactions between bacteria and molecules. In this thesis, four research studies were conducted to investigate the interactions between bacteria and nanoparticles or carbonaceous substrates, deploying state-of-the-art techniques which can yield new insights. Methods: Raman micro-spectroscopy was employed in this thesis as a diagnostic tool to detect the biochemical alterations of bacteria post-exposure to different chemical molecules. Unlike conventional methods, such as light/electron microscopy, molecular analysis techniques and bacterial behaviour assays, Raman spectroscopy provides detailed information of biological constituents of bacteria that interact with diverse molecules. In addition, computational analysis including principal component analysis and linear discriminant analysis (PCA and LDA) was used to process the Raman spectral data. Results and Discussion: Raman spectra characterize the interaction between bacteria with different molecules. Spectral characterization showed the specific binding of nanoparticles with nucleic acids and amino acids in bacteria, and the different chemotactic behaviours of bacteria towards carbohydrates, organic acids and alkanes. Distinct spectral alterations allowed the evaluation of the alkane affinity in bacteria, and enabled quantification of the concentrations of glucose or organic acids in the aquatic phase. Furthermore, computational analysis of spectral alterations illustrated the effects of nutrient cations on alkane affinity in bacteria, and indicated the selective affinity of bacteria towards different organic carbonaceous molecules in the mixture of carbonaceous substances. Findings from this thesis showed that Raman spectroscopy is a rapid, reliable and non-destructive approach to investigate the interaction of bacterial cells with diverse molecules, which implies techniques involved in Raman spectroscopy can diagnose subcellular changes both in situ and in vivo post-exposure to different natural conditions or chemical molecules