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bioRxiv2016

Immunoecology of species with alternative reproductive tactics and strategies

Alternative reproductive tactics and strategies (ARTS) refer to polymorphic reproductive behaviours in which in addition to the usual two sexes, there are one or more alternative morphs, usually male, that have evolved the ability to circumvent direct intra-sexual competition. Each morph has its own morphological, ecological, developmental, behavioural, life-history, and physiological profile that shifts the balance between reproduction and self-maintenance, one aspect being immunity. Immunoecological work on species with ARTS, which is the topic of this review, is particularly interesting because the alternative morphs make it possible to separate the effects of sex, per se, from other factors that in other species are inextricably linked with sex. We first summarize the evolution, development and maintenance of ARTS. We then review immunoecological hypotheses relevant to species with ARTS, dividing them into physiological, life-history, and ecological hypotheses. In context of these hypotheses, we critically review in detail all immunoecological studies we could find on species with ARTS. Several interesting patterns emerge. Oddly, there is a paucity of studies on insects, despite the many benefits that arise from working with insects: larger sample sizes, simple immune systems, and countless forms of alternative reproductive strategies and tactics. Of all the hypotheses considered, the immunocompetence handicap hypothesis has generated the greatest amount of work, but not necessarily the greatest level of understanding. Unfortunately, it is often used as a general guiding principle rather than a source of explicitly articulated predictions. Other hypotheses are usually considered a posteriori, but it is perhaps time that they take centre stage. Whereas blanket concepts such as "immunocompetence" and "androgens" might useful to develop a rationale, predictions need to be far more explicitly articulated. Integration so far has been a one-way street, with ecologists delving deeper into physiology, seemingly at the cost of ignoring their organisms evolutionary history and ecology. One possible useful framework is to divide ecological and evolutionary factors affecting immunity into those that stimulate the immune system, and those that depress it. Finally, the contributions of genomics to ecology are being increasingly recognized, including in species with ARTS, but we must ensure that evolutionary and ecological hypotheses drive the effort, as there is no grandeur in the strict reductionist view of life.

Evolutionary Biology↗

bioRxiv2016

De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)

Background: Spiny mice of the genus Acomys are small desert-dwelling rodents that display physiological characteristics not typically found in rodents. Recent investigations have reported a menstrual cycle and scar free-wound healing in this species; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique physiological traits, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research. However, little genetic information is currently available for Acomys, limiting the application of some modern investigative techniques. This project aimed to generate a reference transcriptome assembly for the common spiny mouse (Acomys cahirinus).\n\nResults: Illumina RNA sequencing of male and female spiny mice produced 451 million, 150bp paired-end reads from 15 organ types. An extensive survey of de novo transcriptome assembly approaches of high-quality reads using Trinity, SOAPdenovo-Trans, and Velvet/Oases at multiple kmer lengths was conducted with 49 single-kmer assemblies generated from this dataset, with and without in silico normalization and probabilistic error correction. Merging transcripts from 49 individual single-kmer assemblies into a single meta-assembly of non-redundant transcripts using the EvidentialGene tr2aacds pipeline produced the highest quality transcriptome assembly, comprised of 880,080 contigs, of which 189,925 transcripts were annotated using the SwissProt/Uniprot database.\n\nConclusions: This study provides the first detailed characterization of the spiny mouse transcriptome. It validates the application of the EvidentialGene tr2aacds pipeline to generate a high-quality reference transcriptome assembly in a mammalian species, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys.

Bioinformatics↗

bioRxiv2016

Spatially periodic calcium profiles around single channels

The concept of calcium nanodomains established around the sites of calcium entry into the cell is fundamental for mechanistic consideration of key physiological responses. It stems from linear models of calcium diffusion from single channel into the cytoplasm, but is only valid for calcium increases smaller than the concentration of calcium-binding species. Recent experiments indicate much higher calcium levels in the vicinity of channel exit that should cause buffer saturation. I here derive explicit solutions of respective non-linear reaction-diffusion problem and found dichotomous solution - for small fluxes the steady state calcium profiles have quasi-exponential form, whereas in the case of buffer saturation calcium distributions show spatial periodicity. These non-trivial and novel spatial calcium profiles are supported by Monte-Carlo simulations. Imaging of 1D- and radial distributions around single -synuclein channels measured in cell-free conditions supports the theory. I suggest that periodic patterns may arise under different physiological conditions and play specific role in cell physiology.

Biophysics↗

bioRxiv2016

Can we test the influence of prosociality on high frequency heart rate variability? A double-blind sham-controlled approach.

The polyvagal theory (Porges, 2007) proposes that physiological flexibility dependent on heart- brain interactions is associated with prosociality. So far, whether prosociality has a causal effect on physiological flexibility is unknown. Previous studies present mitigated results on this matter. In a randomized double-blind protocol, we used a generation of social closeness procedure against a standardized control condition in order to manipulate social affiliation as a prosocial interaction factor. High frequency heart rate variability (HF-HRV, indexing physiological flexibility), electromyographical activity of the corrugator supercilii (sensitive to the valence of the interaction) and self-reported measure of social closeness were monitored before, during, and after experimental manipulation. Cooperation was measured after the experimental manipulation as an index of behavioral prosociality. Data reveal no evidence toward and effect of the experimental manipulation on these measures. We discuss methodological aspects related to the experimental constraints observed in social psychophysiology. Implications for the experimental test of the polyvagal theory are approached within alternative theoretical frameworks.

Neuroscience↗

bioRxiv2017

Cyclic-di-GMP is required for corneal infection by Pseudomonas aeruginosa and modulates host immunity

Biofilms are extremely tolerant toward antimicrobial treatment and host immune clearance due to their distinct physiology and protection by extracellular polymeric substances. Bis-(3{acute}-5{acute})-cyclic dimeric guanosine monophosphate (c-di-GMP) is an essential messenger that regulates biofilm formation by a wide range of bacteria. However, there is a lack of physiological characterization of biofilms in vivo as well as the roles of c-di-GMP signaling in mediating host-biofilm interactions. Here, we employed dual RNA-Seq to characterize the host and pathogen transcriptomes during Pseudomonas aeruginosa infection using a mouse keratitis model. In vivo P. aeruginosa biofilms maintained a distinct physiology compared with in vitro P. aeruginosa biofilms, with enhanced virulence and iron uptake capacity. C-di-GMP synthesis was enhanced in P. aeruginosa cells in vivo, potentially due to down-regulation of the expression of several phosphodiesterases (e.g., DipA, NbdA). Increased intracellular c-di-GMP levels were required for long-term ocular colonization of P. aeruginosa and impaired host innate immunity.

microbiology↗

bioRxiv2017

Deciphering the combinatorial influence of diet and the microbiota on experimental colitis

Background & AimsThe complex interactions between diet and the microbiota that influence mucosal inflammation and inflammatory bowel disease are poorly understood. Experimental colitis models provide the opportunity to control and systematically perturb diet and the microbiota in parallel to quantify the contributions between multiple dietary ingredients and the microbiota on host physiology and colitis.\n\nMethodsTo examine the interplay of diet and the gut microbiota on host health and colitis, we fed over 40 different diets with varied macronutrient sources and concentrations to specific pathogen free or germ free mice either in the context of healthy, unchallenged animals or colitis models (dextran sodium sulfate (DSS) and T cell transfer).\n\nResultsDiet influenced physiology in both health and colitis across all models, with the concentration of protein and psyllium fiber having the most profound effects. Increasing dietary protein elevated gut microbial density and worsened DSS colitis severity. Depleting gut microbial density by using germ-free animals or antibiotics negated the effect of a high protein diet. Psyllium fiber influenced host physiology and attenuated colitis severity through microbiota-dependent and microbiota-independent mechanisms. Combinatorial perturbations to dietary protein and psyllium fiber in parallel explain most variation in gut microbial density, intestinal permeability, and DSS colitis severity, and changes in one ingredient can be offset by changes in the other.\n\nConclusionsOur results demonstrate the importance of examining complex mixtures of nutrients to understand the role of diet in intestinal inflammation.

microbiology↗

bioRxiv2017

Could Plants Be Sentient?

Feelings in humans are mental states representing groups of physiological functions that usually have defined behavioural objectives or purpose. Feelings are thought to be coordinated in the brain stem of animals and are evolutionarily ancient. One function of the brain is to prioritise between competing mental states, and thus groups of physiological functions and in turn behaviour. Anger, fear or pain call for immediate action whereas hunger, or thirst, signify longer term needs and a requirement for search. Plants use groups of coordinated physiological activities to deal with defined environmental situations but currently have no known mental state to prioritise any order of response. Plants do have a nervous system based on phloem which is highly cross linked. Its potential for forming a mental state is unknown but it could be used to distinguish between different and even contradictory signals and thus determine a priority of response. The vascular nervous system stretches throughout the whole plant providing the potential for assessment in all parts and commensurate with its self-organising, phenotypically plastic behaviour.

plant biology↗

bioRxiv2017

Worldwide Population Structure Of Escherichia coli Reveals Two Major Subspecies

Recombination is one of the most important mechanisms of prokaryotic species evolution but its exact roles are still in debate. Here we try to infer genome-wide recombination events within a species uti-lizing a dataset of 104 complete genomes of Escherichia coli from diverse origins, among which 45 from world-wide animal-hosts are in-house sequenced using SMRT (single-molecular real time) technology.Two major clades are identified based on evidences of ecological and physiological characteristics, as well as distinct genomic features implying scarce inter-clade genetic exchange. By comparing the synteny of identical fragments genome-widely searched for each genome pair, we achieve a fine-scale map of re-combination within the population. The recombination is rather extensive within clade, which is able to break linkages between genes but does not interrupt core genome framework and primary metabolic port-folios possibly due to natural selection for physiological compatibility and ecological fitness. Meanwhile,the recombination between clades declines drastically as the phylogenetic distance increases, generally 10-fold reduced than those of the intra-clade, which establishes genetic barrier between clades. These empirical data of recombination suggest its critical role in the early stage of speciation, where recombina-tion rate differs according to phylogentic distance. The extensive intra-clade recombination coheres sister strains into a quasi-sexual group and optimizes genes or alleles to streamline physiological activities,whereas shapely declined inter-clade recombination split the population into clades adaptive to divergent ecological niches.\n\nSignificance StatementRoles of recombination in species evolution have been debated for decades due to difficulties in inferring recombination events during the early stage of speciation, especially when recombination is always complicated by frequent gene transfer events of bacterial genomes. Based on 104 high-quality complete E. coli genomes, we infer gene-centric dynamics of recombination in the formation of two E. coli clades or subpopulations, and recombination is found to be rather intensive in a within-clade fashion, which forces them to be quasi-sexual. The recombination events can be mapped among individual genomes in the context of genes and their variations; decreased between-clade and increased intra-claderecombination engender a genetic barrier that further encourages clade-specific secondary metabolic portfolios for better environmental adaptation. Recombination is thus a major force that accelerates bacterial evolution to fit ecological diversity.

microbiology↗

bioRxiv2017

Artificial pseudoneglect: Connectional constraints leading to the emergence of spatial bias in neurorobots

Most people tend to bisect horizontal lines slightly to the left of their true center (pseudoneglect), and start visual search from left-sided items. This physiological leftward spatial bias may depend on hemispheric asymmetries in the organization of attentional networks, but the precise mechanisms are unknown. Here we modeled relevant aspects of the ventral and dorsal attentional networks (VAN and DAN) of the human brain. First, we demonstrated pseudoneglect in visual search in 101 right-handed psychology students. Participants consistently tended to start the task from a left-sided item, thus showing pseudoneglect. Second, we trained populations of simulated neurorobots to perform a similar task, by using a genetic algorithm. The neurorobots behavior was controlled by artificial neural networks, which simulated the human VAN and DAN in the two brain hemispheres. Neurorobots differed in the connectional constraints that were applied to the anatomy and function of the attention networks. Results indicated that (1) neurorobots provided with a biologically plausible hemispheric asymmetry of the VAN-DAN connections, as well as with inter-hemispheric inhibition, displayed the best match with human data; however, (2) anatomical asymmetry per se was not sufficient to generate pseudoneglect; in addition, the VAN must have an excitatory influence on the ipsilateral DAN; (3) neurorobots provided with bilateral competence in the VAN but without inter-hemispheric inhibition failed to display pseudoneglect. These findings provide a proof of concept of the causal link between connectional asymmetries and pseudoneglect, and specify important biological constraints that result in physiological asymmetries of human behavior.\n\nSignificance statementMost of us start our exploration of the environment from the left side. Here we demonstrated this tendency in undergraduate students, and trained artificial agents (neurorobots) to perform a similar visual search task. The neurorobots behavior was controlled by artificial neural networks, inspired by the human fronto-parietal attentional system. In seven distinct populations of neurorobots, different constraints were applied on the network connections within and between the brain hemispheres. Only one of the artificial populations behaved in a similar way to the human participants. The connectional constraints applied to this population included known characteristics of the human fronto-parietal networks, but had also additional properties not previously described. Thus, our findings specify biological constraints that induce physiological asymmetries of human behavior.

neuroscience↗

bioRxiv2017

Intercellular communication via the comX-Inducing Peptide (XIP) of Streptococcus mutans

Gram-positive bacteria utilize exported peptides to coordinate genetic and physiological processes required for biofilm formation, stress responses and ecological competitiveness. One example is activation of natural genetic competence by ComR and the comX-inducing peptide (XIP) in Streptococcus mutans. Although the competence pathway can be activated by addition of synthetic XIP in defined medium, the hypothesis that XIP is able to function as an intercellular signal molecule has not been rigorously tested. Co-culture model systems were developed that included a \"sender\" strain that overexpressed the XIP precursor (ComS) and a \"responder\" strain harboring a GFP reporter fusion to a ComR-activated gene (comX) promoter. The ability of the sender strain to provide a signal to activate GFP expression was monitored at the individual cell and population levels using i) planktonic culture systems, ii) cells suspended in an agarose matrix or iii) cells growing in biofilms. XIP was shown to be freely diffusible and XIP signaling between the S. mutans sender and responder strains did not require cell-to-cell contact. The presence of a sucrose-derived exopolysaccharide matrix diminished the efficiency of XIP signaling in biofilms, possibly by affecting spatial distribution of XIP senders and potential responders. Intercellular signaling was greatly impaired in a strain lacking the primary autolysin, AtlA, and was substantially greater when the sender strain underwent lysis. Collectively, these data provide evidence that S. mutans XIP can indeed function as a peptide signal between cells and highlight the importance of studying signaling with endogenously-produced peptide(s) in populations in various environments and physiologic states.\n\nIMPORTANCEThe comX-inducing peptide (XIP) of Streptococcus mutans is a key regulatory element in the activation of genetic competence, which allows cells to take up extracellular DNA. XIP has been found in cell culture fluids and addition of synthetic XIP to physiologically receptive cells can robustly induce competence gene expression. However, there is a lack of consensus as to whether XIP can function as an intercellular communication signal. Here, we show that XIP indeed signals between cells in S. mutans, but that cell lysis may be a critical factor, as opposed to a dedicated secretion/processing system, in allowing for release of XIP into the environment. The results have important implications in the context of the ecology, virulence and evolution of a ubiquitous human pathogen and related organisms.

microbiology↗

bioRxiv2017

A transgenic toolkit for visualizing and perturbing microtubules reveals unexpected functions in the epidermis

Differentiation induces reorganization of microtubules (MTs) into non-centrosomal arrays in a variety of tissues. The physiological functions of these microtubule arrays are just beginning to be understood as few tools currently exist to genetically perturb microtubule organization in vivo, particularly in mammals. We developed a genetic toolkit that can be broadly applied to the study of microtubule dynamics and function in many cell types. Using a TRE-EB1-GFP mouse we demonstrate that distinct differentiation transitions in the epidermis cause a decrease in microtubule growth rates and microtubule growth lifetimes, resulting in strong suppression of dynamics. To understand the physiological functions of these stable, non-centrosomal microtubules, we generated a TRE-spastin mouse, which can be used to perturb microtubule organization in a wide-variety of tissues in vivo. Unexpectedly, microtubule perturbation exclusively in post-mitotic keratinocytes had profound consequences on epidermal morphogenesis. We uncoupled novel cell-autonomous roles for MTs in differentiation-driven cell flattening from non-cell autonomous functions in regulating proliferation, differentiation, and tissue architecture. Taken together, we have created tools that will be broadly useful for the study of microtubule dynamics and function in mammalian tissue physiology and have used them to uncover previously unknown functions for non-centrosomal microtubules during mammalian epidermal development.

cell biology↗

bioRxiv2017

A Mixed Periodic Paralysis & Myotonia Mutant, P1158S, Imparts pH Sensitivity in Skeletal Muscle Voltage-gated Sodium Channels

Skeletal muscle channelopathies, many of which are inherited as autosomal dominant mutations, include both myotonia and periodic paralysis. Myotonia is defined by a delayed relaxation after muscular contraction, whereas periodic paralysis is defined by episodic attacks of weakness. One sub-type of periodic paralysis, known as hypokalemic periodic paralysis (hypoPP), is associated with low potassium levels. Interestingly, the P1158S missense mutant, located in the third domain S4-S5 linker of the skeletal muscle voltage-gated sodium channel, Nav1.4, has been implicated in causing both myotonia and hypoPP. A common trigger for these conditions is physical activity. We previously reported that Nav1.4 is relatively insensitive to changes in extracellular pH compared to Nav1.2 and Nav1.5. Given that intense exercise is often accompanied by blood acidosis, we decided to test whether changes in pH would push gating in P1158S towards either phenotype. Our results indicate that, unlike in WT Nav1.4, low pH depolarizes the voltage-dependence of activation and steady-state fast inactivation, decreases current density, and increases late currents in P1185S. Thus, P1185S turns the normally pH-insensitive Nav1.4 into a proton-sensitive channel. Using action potential modeling we also predict a pH-to-phenotype correlation in patients with P1158S. We conclude that activities which alter blood pH may trigger myotonia or periodic paralysis in P1158S patients.\n\nSIGNIFICANCE STATEMENTVoltage-gated sodium channels (Nav) contribute to the physiology and pathophysiology of electrical signaling in excitable cells. Nav subtypes are expressed in a tissue-specific manner, thus they respond differently to physiological modulators. For instance, the cardiac subtype, Nav1.5, can be modified by changes in blood pH; however, the skeletal muscle subtype, Nav1.4, is mostly pH-insensitive. Nav1.4 mutants can mostly cause either hyper-or hypo-excitability in skeletal muscles, leading to conditions such as myotonia or periodic paralysis. P1158S uniquely causes both phenotypes. This study investigates pH-sensitivity in P1158S, and describes how physiological pH changes can push P1158S to cause myotonia and periodic paralysis.

biophysics↗

bioRxiv2017

Large scale in vivo recording of sensory neuron activity with GCaMP6

Greater emphasis on the study of intact cellular networks in their physiological environment has led to rapid advances in intravital imaging in the central nervous system, while the peripheral system remains largely unexplored. To assess large networks of sensory neurons we selectively label primary afferents with GCaMP6s and visualise their functional responses in vivo to peripheral stimulation. We show that we are able to monitor simultaneously the activity of hundreds of sensory neurons with sensitivity sufficient to detect, in most cases, single action potentials with a typical rise time of around 200 milliseconds, and an exponential decay with a time constant of approximately 700 milliseconds. Using this sensitive technique we are able to show that large scale recordings demonstrate the recently disputed polymodality of nociceptive primary afferents with between 40-80% of thermally sensitive DRG neurons responding also to noxious mechanical stimulation. We also specifically assess the small population of peripheral cold fibres and demonstrate significant sensitisation to cooling after a model of sterile and persistent inflammation, with significantly increased sensitivity already at decreases of 5{degrees}C when compared to uninflamed responses. This not only reveals interesting new insights into the (patho)physiology of the peripheral nervous system but also demonstrates the sensitivity of this imaging technique to physiological changes in primary afferents.\n\nSignificance StatementMost of our functional understanding of the peripheral nervous system has come from single unit recordings. However, the acquisition of such data is labour-intensive and usually low yield. Moreover, some questions are best addressed by studying populations of neurons. To this end we report on a system that monitors activity in hundreds of single sensory neurons simultaneously, with sufficient sensitivity to detect in most cases single action potentials. We use this technique to characterise nociceptor properties and demonstrate polymodality in the majority of neurons and their sensitization under inflammatory conditions. We therefore believe this approach will be very useful for the studies of the somatosensory system in general and pain in particular.

neuroscience↗

bioRxiv2017

Polymodal Allosteric Regulation of Type 1 Serine/Threonine Kinase Receptors via a Conserved Electrostatic Lock

Type 1 Serine/Threonine Kinase Receptors (STKR1) transduce a wide spectrum of biological signals mediated by TGF-{beta} superfamily members. The STKR1 activity is tightly controlled by their regulatory glycine-serine rich (GS) domain adjacent to the kinase domain. Despite decades of studies, it remains unknown how physiological or pathological GS domain modifications are coupled to STKR1 kinase activity. Here, by performing molecular dynamics simulations and free energy calculation of Activin-Like Kinase 2 (ALK2), we found that GS domain phosphorylation, FKBP12 dissociation, and disease mutations all destabilize a D354-R375 salt-bridge, which normally acts as an electrostatic lock to prevent coordination of adenosine triphosphate (ATP) to the catalytic site. We developed a WAFEX-guided principal analysis and unraveled how phosphorylation destabilizes this highly conserved salt-bridge in temporal and physical space. Using current-flow betweenness scores, we identified an allosteric network of residue-residue contacts between the GS domain and the catalytic site that controls the formation and disruption of this salt bridge. Importantly, our novel network analysis approach revealed how certain disease-causing mutations bypass FKBP12-mediated kinase inhibition to produce leaky signaling in the absence of ligand. We further provide experimental evidence that this salt-bridge lock exists in other STKR1s, and acts as a general safety mechanism in STKR1 to prevent pathological leaky signaling. In summary, our study provides a compelling and unifying allosteric activation mechanism in STKR1 kinases that reconciles a large number of experimental studies and sheds light on a novel therapeutic avenue to target disease-related STKR1 mutants.\n\nAUTHOR SUMMARYKinases play central role in essential physiological process and are attractive therapeutic drug targets. One of the important kinase families is Type 1 Serine/Threonine Kinase Receptors (STKR1), which control gene expression in response to extracellular growth factors. The activities of STKR1 are tightly controlled by their regulatory domain, which is distant from the kinase catalytic site. The underlying molecular mechanism is elucidated here. We identified that formation or disruption of a highly conserved charge-charge interaction located near the ATP binding site, mediates the physiological inhibition or activation of STKR1. We find that the stability of this charge-charge interaction is remotely controlled by interactions propagated from the distant regulatory domain. Several disease-causing mutations are located at the regulatory domain. We demonstrate how those mutations bypass these endogenous STKR1 inhibition mechanisms to produce pathological phenotypes. This study provides a general activation mechanism in STKR1 kinases, thus may benefit understanding the molecular mechanism of diseases and drug development.

biophysics↗

bioRxiv2017

Alpha oscillations control cortical gain by modulating excitatory-inhibitory background activity.

The first recordings of human brain activity in 1929 revealed a striking 8-12 Hz oscillation in the visual cortex. During the intervening 90 years, these alpha oscillations have been linked to numerous physiological and cognitive processes. However, because of the vast and seemingly contradictory cognitive and physiological processes to which it has been related, the physiological function of alpha remains unclear. We identify a novel neural circuit mechanism--the modulation of both excitatory and inhibitory neurons in a balanced configuration--by which alpha can modulate gain. We find that this model naturally unifies the prior, highly diverse reports on alpha dynamics, while making the novel prediction that alpha rhythms have two functional roles: a sustained high-power mode that suppresses scortical gain and a weak, bursting mode that enhances gain.

neuroscience↗

bioRxiv2017

Genetic and metabolic regulation of Mycobacterium tuberculosis acid growth arrest

Mycobacterium tuberculosis (Mtb) senses and adapts to acidic environments during the course of infection. Acidic pH-dependent adaptations include the induction of metabolic genes associated with anaplerosis and growth arrest on specific carbon sources. In this study, reverse and forward genetic studies were undertaken to define new mechanisms underlying pH-dependent adaptations. Here we report that deletion of isocitrate lyase (icl1/2) or phosphoenolpyruvate carboxykinase (pckA) results in reduced growth at acidic pH and altered metabolite profiles, supporting that remodeling of anaplerotic metabolism is required for pH-dependent adaptation. Mtb cultured at pH 5.7 in minimal medium containing glycerol as a single carbon source exhibits an acid growth arrest phenotype, where the bacterium is non-replicating but viable and metabolically active. The bacterium uptakes and metabolizes glycerol and maintains ATP pools during acid growth arrest and becomes tolerant to detergent stress and the antibiotics isoniazid and rifampin. A forward genetic screen identified mutants that do not arrest their growth at acidic pH, including four enhanced acid growth (eag) mutants with three distinct mutations in the PPE gene MT3221. Overexpression of the MT3221(S211R) variant protein in wild type Mtb results in enhanced acid growth and reduced drug tolerance. Together, these findings provide new evidence for a genetic and physiological basis for acid growth arrest and support that growth arrest is an adaptive process and not simply a physiological limitation associated with acidic pH.\n\nAuthor SummaryThe bacterium Mycobacterium tuberculosis (Mtb) causes the disease tuberculosis in humans. During infection Mtb colonizes a variety of environments that have acidic environments and Mtb must adapt to these environments to cause disease. One of these adaptations is that Mtb slows and arrests its growth at acidic pH, and the goal of this study was to examine the genetics and physiology of these pH-dependent adaptations. We found that Mtb modifies its metabolism at acidic pH and that these adaptations are required for optimal growth. We also found that acidic pH and specific nutrient sources can promote the bacterium to enter a state of dormancy, called acid growth arrest, where the bacterium becomes tolerant to antibiotics. Mutants were identified that do not arrest their growth at acidic, revealing that acid growth arrest is a genetically controlled process. Overall, understanding how Mtb adapts to acidic pH has revealed pathway that are required for virulence and drug tolerance and thus may identify new targets for drug development that may function to shorten the course of TB therapy.

microbiology↗

bioRxiv2017

Non-Elastic Remodeling of the 3D Extracellular Matrix by Cell-Generated Forces

The mechanical properties of the extracellular matrix (ECM) - a complex, 3D, fibrillar scaffold of cells in physiological environments - modulate cell behavior and can drive tissue morphogenesis, regeneration, and disease progression. For simplicity, it is often convenient to assume these properties to be time-invariant. In living systems, however, cells dynamically remodel the ECM and create time-dependent local environments. Here, we demonstrate that cell generated contractile forces are capable of producing substantial irreversible changes to the density and architecture of physiologically relevant ECMs - collagen I and fibrin - in a matter of minutes. We measure the 3D mechanical deformation profiles of the ECM surrounding cancer and endothelial cells during stages when force generation is active or inactive. We further correlate these measurements to both discrete fiber simulations that incorporate fiber crosslink unbinding kinetics and continuum-scale modeling. Our findings reveal that plasticity, as a mechanical law in these networks, is fundamentally related to the force-driven unbinding of fiber crosslinks. These results illustrate the dynamic nature of the mechanical environment of physiologically mimicking cell-in-gel systems.

bioengineering↗

bioRxiv2017

Assessing the quality of supplementary sensory feedback using a crossmodal congruency task

Peripheral nerve interfaces show promise in making prosthetic limbs more biomimetic and ultimately more intuitive and useful for patients. However, approaches to assess these emerging technologies are limited in their scope and the insight they provide. When outfitting a prosthesis with a new feedback system it would be helpful to quantify its physiological correspondence, i.e. how well the experimental feedback mimics the perceived feedback in an intact limb. Here we present an approach to quantify physiological correspondence using a modified crossmodal congruency task. We trained 60 able-bodied subjects to control a bypass prosthesis under different feedback conditions and training durations. We find that the crossmodal congruency effect (CCE) score is sensitive to changes in feedback modality (multi-way ANOVA; F(2,48) = 6.02, p<0.05). After extended training, the CCE score increased as the spatial separation between expected and perceived feedback decreased (unpaired t-test, p<0.05). We present a model that can quantitatively estimate physiological correspondence given the CCE result and the measured spatial separation of the feedback. This quantification approach gives researchers a tool to assess an aspect of emerging augmented feedback systems that is not measurable with current motor assessments.

neuroscience↗