Biology subjects

Emonet, T.

Publications and source records attributed to Emonet, T..

23 records · Page 2Linked to original sources

bioRxiv2019

Controlling and measuring dynamic odorant stimuli in the laboratory

Animals experience complex odorant stimuli that vary widely in composition, intensity and temporal properties. However, stimuli used to study olfaction in the laboratory are much simpler. This mismatch arises from the challenges in measuring and controlling them precisely and accurately. Even simple pulses can have diverse kinetics that depend on their molecular identity. Here, we introduce a model to describe how stimulus kinetics depend on the molecular identity of the odorant and the geometry of the delivery system. We describe methods to deliver dynamic odorant stimuli of several types, including broadly distributed stimuli that reproduce some of the statistics of naturalistic plumes, in a reproducible and precise manner. Finally, we introduce a method to calibrate a Photo-Ionization Detector to any odorant it can detect, using no additional components. Our approaches are affordable and flexible and can be used to advance our understanding of how olfactory neurons encode real-world odor signals.

neuroscience↗

bioRxiv2019

Modulation of Flagellar Rotation in Surface-Attached Bacteria: A Circuit for Rapid Surface-Sensing

Attachment is a necessary first step in bacterial commitment to surface-associated behaviors that include colonization, biofilm formation, and host-directed virulence. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa can initially attach to surfaces via its single polar flagellum. Although many bacteria quickly detach, some become irreversibly attached and express surface-associated structures, such as Type IV pili, and behaviors, including twitching motility and biofilm initiation. P. aeruginosa that lack the GTPase FlhF assemble a randomly placed flagellum that is motile; however, we observed that these mutant bacteria show defects in biofilm formation comparable to those seen for non-motile, aflagellate bacteria. This phenotype was associated with altered behavior of {Delta}flhF bacteria immediately following surface-attachment. Forward and reverse genetic screens led to the discovery that FlhF interacts with FimV to control flagellar rotation at a surface, and implicated cAMP signaling in this pathway. Although cAMP controls many transcriptional programs in P. aeruginosa, the known targets of this second messenger were not required to modulate flagellar rotation in surface-attached bacteria. Instead, alterations in switching behavior of the motor appear to result from previously undescribed effects of cAMP on switch complex proteins and/or the motor-stators associated with them.\n\nAuthor SummaryAttachment to a surface often triggers programs of gene expression that alter the behavior, virulence and fitness of bacteria. Initial contact is usually mediated by surface exposed adhesins, such as flagella or pili/fimbriae, and there is much interest in how these structures might sense and respond to surface attachment. The human bacterial pathogen Pseudomonas aeruginosa usually contacts surfaces via its polar flagellum, the rotary motor that also powers bacterial swimming. We observed that wild-type bacteria quickly stopped rotating their flagellum after surface attachment, but that a mutant lacking the flagellar-associated protein FlhF did not. Using a combination of genetic approaches, we demonstrated that FlhF interacts with a component of the flagellar rotor (FliG) and with a polar scaffolding protein that positively regulates cAMP production (FimV) to stop flagellar rotation and thereby favor bacterial persistence at a surface. We provide evidence that the second messenger cAMP is the likely signal generated by flagellar-mediated surface attachment and show that cAMP is sufficient to alter the behavior of the flagellar motor.

microbiology↗

bioRxiv2018

Front-end Weber-Fechner gain control enhances the fidelity of combinatorial odor coding

Odor identity is encoded by spatiotemporal patterns of activity in olfactory receptor neurons (ORNs). In natural environments, the intensity and timescales of odor signals can span several orders of magnitude, and odors can mix with one another, potentially scrambling the combinatorial code mapping neural activity to odor identity. Recent studies have shown that in Drosophila melanogaster the ORNs that express the olfactory co-receptor Orco scale their gain inversely with mean odor concentration according to the Weber-Fechner Law of psychophysics. Here we use a minimal biophysical model of signal transduction, ORN firing, and signal decoding to investigate the implications of this front-end scaling law for the neural representations of odor identity. We find that Weber-Fechner scaling enhances coding capacity and promotes the reconstruction of odor identity from dynamic odor signals, even in the presence of confounding background odors and rapid intensity fluctuations. We show that these enhancements are further aided by downstream transformations in the antennal lobe and mushroom body. Thus, despite the broad overlap between individual ORN tuning curves, a mechanism of front-end adaptation, when endowed with Weber-Fechner scaling, may play a vital role in preserving representations of odor identity in naturalistic odor landscapes.

neuroscience↗

bioRxiv2018

Spatial Self-Organization Resolves Conflicts Between Individuality and Collective Migration

Collective behavior can spontaneously emerge when individuals follow common rules of interaction. However, the behavior of each individual will differ due to existing genetic and non-genetic variation within the population. It remains unclear how this individuality is managed to achieve collective behavior. We quantified individuality in bands of clonal Escherichia coli cells that migrate collectively along a channel by following a self-generated gradient of attractant. We discovered that despite substantial differences in individual chemotactic abilities, the cells are able to migrate as a coherent group by spontaneously sorting themselves within the moving band. This sorting mechanism ensures that differences between individual chemotactic abilities are compensated by differences in the local steepness of the traveling gradient each individual must navigate, and determines the minimum performance required to travel with the band. By resolving conflicts between individuality and collective migration, this mechanism enables populations to maintain advantageous diversity while on the move.

biophysics↗

bioRxiv2017

Generation And Attenuation Of Variability In A Bacterial Signalling Network Revealed By Single-Cell FRET

We present in vivo single-cell FRET measurements in the Escherichia coli chemotaxis system that reveal pervasive signaling variability, both across cells in isogenic populations and within individual cells over time. We quantify cell-to-cell variability of adaptation, ligand response, as well as steady-state output level, and analyze the role of network design in shaping this diversity from gene expression noise. In the absence of changes in gene expression, we find that single cells demonstrate strong temporal fluctuations. We provide evidence that such signaling noise can arise from at least two sources: (i) stochastic activities of adaptation enzymes, and (ii) receptor-kinase dynamics in the absence of adaptation. We demonstrate that under certain conditions, (ii) can generate giant fluctuations that drive signaling activity of the entire cell into a stochastic two-state switching regime. Our findings underscore the importance of molecular noise, arising not only in gene expression but also in protein networks.

systems biology↗