A Tale of Two Theories: Using an Engineered Strain of E. coli to Bridge the Gap Between Quorum Sensing and Diffusion Sensing

Cooperation is a trait that is found at all levels of biological organization. Interestingly, cooperation appears to occur in bacteria that produce small, easily diffusible molecules called autoinducers. To understand why bacteria produce these autoinducers, the scientific community has focused on one predominant theory called quorum sensing. Under this theory, bacteria produce autoinducers so they can sense the density of the population. Once a sufficiently high population density is reached, autoinducers initiate the production of a costly gene product that serves to benefit the population. In contrast, a competing theory called diffusion sensing suggests that autoinducers are used by the individual cells and are not used for cooperation. Here, the production of the autoinducer serves as a mechanism to sense environmental conditions. If the environmental conditions are favorable, a costly gene product is produced. To what extent, and under what conditions, are each of these opposing theories valid remains to be identified. In this thesis, an engineered strain of Escherichia coli was used to identify the conditions under which quorum sensing and diffusing sensing can be observed. It was discovered that, depending upon the frequency at which the spatial distribution of the autoinducer and bacteria was disrupted, the population of engineered bacteria displayed hallmarks of either quorum sensing or diffusion sensing. Specifically, when the spatial distribution was disturbed at high or low frequency, quorum sensing was observed. However, when spatial distribution was disturbed at an intermediate frequency, diffusion sensing was observed. Understanding how these disturbances affect survival in bacteria may result in novel treatments for bacterial infections. In more general applications, it may be exploited in the development of alternative mechanisms for controlling invasive species or aid in species reintroduction

Cooperation and Competition Shape Ecological Resistance During Periodic Spatial Disturbance of Engineered Bacteria

Cooperation is fundamental to the survival of many bacterial species. Previous studies have shown that spatial structure can both promote and suppress cooperation. Most environments where bacteria are found are periodically disturbed, which can affect the spatial structure of the population. Despite the important role that spatial disturbances play in maintaining ecological relationships, it remains unclear as to how periodic spatial disturbances affect bacteria dependent on cooperation for survival. Here, we use bacteria engineered with a strong Allee effect to investigate how the frequency of periodic spatial disturbances affects cooperation. We show that at intermediate frequencies of spatial disturbance, the ability of the bacterial population to cooperate is perturbed. A mathematical model demonstrates that periodic spatial disturbance leads to a tradeoff between accessing an autoinducer and accessing nutrients, which determines the ability of the bacteria to cooperate. Based on this relationship, we alter the ability of the bacteria to access an autoinducer. We show that increased access to an autoinducer can enhance cooperation, but can also reduce ecological resistance, defined as the ability of a population to resist changes due to disturbance. Our results may have implications in maintaining stability of microbial communities and in the treatment of infectious diseases

Marine mammal hotspots across the circumpolar Arctic

Aim: Identify hotspots and areas of high species richness for Arctic marine mammals. Location: Circumpolar Arctic. Methods: A total of 2115 biologging devices were deployed on marine mammals from 13 species in the Arctic from 2005 to 2019. Getis-Ord Gi* hotspots were calculated based on the number of individuals in grid cells for each species and for phyloge-netic groups (nine pinnipeds, three cetaceans, all species) and areas with high spe-cies richness were identified for summer (Jun-Nov), winter (Dec-May) and the entire year. Seasonal habitat differences among species’ hotspots were investigated using Principal Component Analysis. Results: Hotspots and areas with high species richness occurred within the Arctic continental-shelf seas and within the marginal ice zone, particularly in the “Arctic gateways” of the north Atlantic and Pacific oceans. Summer hotspots were generally found further north than winter hotspots, but there were exceptions to this pattern, including bowhead whales in the Greenland-Barents Seas and species with coastal distributions in Svalbard, Norway and East Greenland. Areas with high species rich-ness generally overlapped high-density hotspots. Large regional and seasonal dif-ferences in habitat features of hotspots were found among species but also within species from different regions. Gap analysis (discrepancy between hotspots and IUCN ranges) identified species and regions where more research is required. Main conclusions: This study identified important areas (and habitat types) for Arctic marine mammals using available biotelemetry data. The results herein serve as a benchmark to measure future distributional shifts. Expanded monitoring and teleme-try studies are needed on Arctic species to understand the impacts of climate change and concomitant ecosystem changes (synergistic effects of multiple stressors). While efforts should be made to fill knowledge gaps, including regional gaps and more com-plete sex and age coverage, hotspots identified herein can inform management ef-forts to mitigate the impacts of human activities and ecological changes, including creation of protected areas

Measurement of the F2 structure function in deep inelastic e+^{+}p scattering using 1994 data from the ZEUS detector at HERA

We present measurements of the structure function \Ft\ in e^+p scattering at HERA in the range 3.5\;\Gevsq < \qsd < 5000\;\Gevsq. A new reconstruction method has allowed a significant improvement in the resolution of the kinematic variables and an extension of the kinematic region covered by the experiment. At \qsd < 35 \;\Gevsq the range in x now spans 6.3\cdot 10^{-5} < x < 0.08 providing overlap with measurements from fixed target experiments. At values of Q^2 above 1000 GeV^2 the x range extends to 0.5. Systematic errors below 5\perc\ have been achieved for most of the kinematic urray, W

Comparison of ZEUS data with standard model predictions for e+p→e+Xe^+ p \rightarrow e^+ X scattering at high xx and Q2Q^2

Using the ZEUS detector at HERA, we have studied the reaction e(+)p --> e(+)X for Q(2) > 5000 GeV2 with a 20.1 pb(-1) data sample collected during the years 1993 to 1996. For Q(2) below 15000 GeV2, the data are in good agreement with Standard Model expectations. For Q(2) > 35000 GeV2. two events are observed while 0.145 +/- 0.013 events are expected, A statistical analysis of a large ensemble of simulated Standard Model experiments indicates that with probability 6.0%, an excess at least as unlikely as that observed would occur above some Q(2) cut. For x > 0.55 and y > 0.75, four events are observed where 0.91 +/- 0.08 events are expected, A statistical analysis of the two-dimensional distribution of the events in x and y yields a probability of 0.72% for the region x > 0.55 and y > 0.25 and a probability of 7.8% for the entire Q(2) > 5000 GeV2 data sample. The observed excess above Standard Model expectations is particularly interesting because it occurs in a previously unexplored kinematic region

Measurement of Elastic ϕ\phi Photoproduction at HERA

The production of $\phi$ mesons in the reaction $e^{+}p \rightarrow e^{+} \phi p$ ($\phi \rightarrow K^{+}K^{-}$) at a median $Q^{2}$ of $10^{-4} \ \rm{GeV^2}$has been studied with the ZEUS detector at HERA. The differential$\phi$photoproduction cross section$d\sigma/dt$has an exponential shape and has been determined in the kinematic range$0.1<|t|<0.5 \ \rm{GeV^2}$and$60 < W < 80 \ \rm{GeV}$. An integrated cross section of$\sigma_{\gamma p \rightarrow \phi p} = 0.96 \pm 0.19^{+0.21}_{-0.18}$$\rm{\mu b}$has been obtained by extrapolating to {\it t} = 0. When compared to lower energy data, the results show a weak energy dependence of both$\sigma_{\gamma p \rightarrow \phi p}$and the slope of the$t$distribution. The$\phi$decay angular distributions are consistent with$s$-channel helicity conservation. From lower energies to HERA energies, the features of$\phi$ photoproduction are compatible with those of a soft diffractive process.Comment: 23 pages, including 6 post script figure

Linoleate-Enrichment of Mitochondrial Cardiolipin Molecular Species Is Developmentally Regulated and a Determinant of Metabolic Phenotype

Cardiolipin (CL), the major mitochondrial phospholipid, regulates the activity of many mitochondrial membrane proteins. CL composition is shifted in heart failure with decreases in linoleate and increases in oleate side chains, but whether cardiolipin composition directly regulates metabolism is unknown. This study defines cardiolipin composition in rat heart and liver at three distinct ages to determine the influence of CL composition on beta-oxidation (ß-OX). CL species, expression of ß-OX and glycolytic genes, and carnitine palmitoyltransferase (CPT) activity were characterized in heart and liver from neonatal, juvenile, and adult rats. Ventricular myocytes were cultured from neonatal, juvenile, and adult rats and cardiolipin composition and CPT activity were measured. Cardiolipin composition in neonatal rat ventricular cardiomyocytes (NRVMs) was experimentally altered and mitochondrial respiration was assessed. Linoleate-enrichment of CL was observed in rat heart, but not liver, with increasing age. ß-OX genes and CPT activity were generally higher in adult heart and glycolytic genes lower, as a function of age, in contrast to liver. Palmitate oxidation increased in NRVMs when CL was enriched with linoleate. Our results indicate (1) CL is developmentally regulated, (2) linoleate-enrichment is associated with increased ß-OX and a more oxidative mitochondrial phenotype, and (3) experimentally induced linoleate-enriched CL in ventricular myocytes promotes a shift from pyruvate metabolism to fatty acid ß-OX

HDAC6 modulates myofibril stiffness and diastolic function of the heart

Passive stiffness of the heart is determined largely by extracellular matrix and titin, which functions as a molecular spring within sarcomeres. Titin stiffening is associated with the development of diastolic dysfunction (DD), while augmented titin compliance appears to impair systolic performance in dilated cardiomyopathy. We found that myofibril stiffness was elevated in mice lacking histone deacetylase 6 (HDAC6). Cultured adult murine ventricular myocytes treated with a selective HDAC6 inhibitor also exhibited increased myofibril stiffness. Conversely, HDAC6 overexpression in cardiomyocytes led to decreased myofibril stiffness, as did ex vivo treatment of mouse, rat, and human myofibrils with recombinant HDAC6. Modulation of myofibril stiffness by HDAC6 was dependent on 282 amino acids encompassing a portion of the PEVK element of titin. HDAC6 colocalized with Z-disks, and proteomics analysis suggested that HDAC6 functions as a sarcomeric protein deacetylase. Finally, increased myofibril stiffness in HDAC6-deficient mice was associated with exacerbated DD in response to hypertension or aging. These findings define a role for a deacetylase in the control of myofibril function and myocardial passive stiffness, suggest that reversible acetylation alters titin compliance, and reveal the potential of targeting HDAC6 to manipulate the elastic properties of the heart to treat cardiac diseases