Predictions from a stochastic polymer model for the MinDE dynamics in E.coli

The spatiotemporal oscillations of the Min proteins in the bacterium Escherichia coli play an important role in cell division. A number of different models have been proposed to explain the dynamics from the underlying biochemistry. Here, we extend a previously described discrete polymer model from a deterministic to a stochastic formulation. We express the stochastic evolution of the oscillatory system as a map from the probability distribution of maximum polymer length in one period of the oscillation to the probability distribution of maximum polymer length half a period later and solve for the fixed point of the map with a combined analytical and numerical technique. This solution gives a theoretical prediction of the distributions of both lengths of the polar MinD zones and periods of oscillations -- both of which are experimentally measurable. The model provides an interesting example of a stochastic hybrid system that is, in some limits, analytically tractable.Comment: 16 page

Tracing nutrient inputs into a eutrophic lake using nitrogen isotopes, Wilgreen Lake, Madison County, Kentucky

Wilgreen Lake is a dammed lake that has been classified as nutrient-impaired (303d list) by the EPA and State of Kentucky. The lake is moderately-sized covering 169 acres (0.7 km2), and drains a watershed with residential developments, cattle pasture, modified woodlands, and some industrial/urban usage in the city of Richmond. The principal tributaries are Taylor Fork and Old Town Branch that meet to form the trunk of the lake approximately one mile in length. The upper reaches of Taylor Fork are adjacent to a densely-packed (quarter-acre lots) housing development with septic systems. Old Town Branch drains cattle pasture and residential areas. Residences within these developments, while also served by septic systems, are more sparsely distributed than residences within developments adjacent to those of Taylor Fork. An ancillary tributary flowing into Pond Cove is intermittent, and drains cattle pasture and one small housing development. Recognizing and quantifying potential nutrient sources is critical to any remediation efforts in decreasing nutrient input to the lake. We hypothesize that significant nutrient input occurs from the septic systems adjacent to the shallow lake waters of Taylor Fork. We use stable nitrogen isotopes (14N and 15N) as a tracer in characterizing organic sources of nitrogen entering lake waters, and in characterizing organic sinks of nitrogen residing in the lake system. We measure the carbon-to-nitrogen ratio, carbon isotopic composition (d13C), and nitrogen isotopic composition (d15N) of organic matter held within potential nutrient sources and sinks within the Wilgreen Lake system. Potential sources include fertilizers, bovine fecal matter, human effluent from septic systems, and “natural” organic material. Sinks include plankton, macroalgae, macrophyta, and organic matter within sediments. Our samples are being measured at press time. The fundamental assumption of the test of our hypothesis is that d15N values of nitrogen sinks should reflect that of their source. With knowledge of the nitrogen isotopic composition of nitrogen sources, we may be able to recognize gradients within the nitrogen sinks of the system. Consequently, our samples of plankton, macroalgae, macrophyta, and sedimentary organic matter are taken over the entire expanse of lake

Characterizing mixed mode oscillations shaped by noise and bifurcation structure

Many neuronal systems and models display a certain class of mixed mode oscillations (MMOs) consisting of periods of small amplitude oscillations interspersed with spikes. Various models with different underlying mechanisms have been proposed to generate this type of behavior. Stochastic versions of these models can produce similarly looking time series, often with noise-driven mechanisms different from those of the deterministic models. We present a suite of measures which, when applied to the time series, serves to distinguish models and classify routes to producing MMOs, such as noise-induced oscillations or delay bifurcation. By focusing on the subthreshold oscillations, we analyze the interspike interval density, trends in the amplitude and a coherence measure. We develop these measures on a biophysical model for stellate cells and a phenomenological FitzHugh-Nagumo-type model and apply them on related models. The analysis highlights the influence of model parameters and reset and return mechanisms in the context of a novel approach using noise level to distinguish model types and MMO mechanisms. Ultimately, we indicate how the suite of measures can be applied to experimental time series to reveal the underlying dynamical structure, while exploiting either the intrinsic noise of the system or tunable extrinsic noise.Comment: 22 page

Fecal microbe distribution and abundance used as a possible proxy for nutrient source identification in eutrophic Wilgreen Lake, Madison County, Kentucky

Wilgreen Lake is a eutrophic lake that has been listed on the EPA’s 303d list as nutrient impaired. Potential sources of this impairment are from humans, cattle manure and fertilizers. We suspect that the majority of nutrients originate from human sources. As a possible proxy for nutrient input, we test our hypothesis by examining fecal microbe distribution and abundance in the lake. We took water samples at 19 sampling locations on 4 occasions. Sampling spanned 26 June to 15 August with the last 3 sampling events occurring at roughly two-week intervals. These samples were then processed using IDEXX methods, which count total coliform and Escherichia coli colonies. For sampling localities with microbial abundance that exceeded maximum sensitivity (\u3e2419 cfu/100ml), we performed dilutions of 1:4 or 1:10. Both total coliform and E. coli levels are elevated at sites adjacent to septic tank clusters. There is a gradual decline in microbial abundance distal to these populated areas and microbe levels are low in the third lake tributary that drains only cattle pasture. This strongly suggests that the source of microbial input is from septic systems; however, we cannot eliminate the possibility that fecal microbes are introduced into the lake via inflows, because of high microbial abundance in their waters. We plan on using Reverse-Transcription Polymer Chain Reaction (RT-PCR) techniques to distinguish between human and cattle sources of Bacteroides to potentially eliminate the inflows as a microbial source

Localisation of the human hSuv3p helicase in the mitochondrial matrix and its preferential unwinding of dsDNA

We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryos. Using immunofluorescence analysis, an in vitro mitochondrial uptake assay and sub‐fractionation of human mitochondria we show hSuv3p to be a soluble protein localised in the mitochondrial matrix. We expressed and purified recombinant hSuv3p protein from a bacterial expression system. The purified enzyme was capable of hydrolysing ATP with a Km of 41.9 µM and the activity was only modestly stimulated by polynucleotides. hSuv3p unwound partly hybridised dsRNA and dsDNA structures with a very strong preference for the latter. The presented analysis of the hSuv3p NTPase/helicase suggests that new functions of the protein have been acquired in the course of evolution

"2001: A Space Odyssey" Revisited--The Feasibility of 24 Hour Commuter Flights to the Moon Using NTR Propulsion with LUNOX Afterburners

The prospects for "24 hour" commuter flights to the Moon, similar to that portrayed in 2001: A Space Odyssey but on a more Spartan scale, are examined using two near term, "high leverage" technologies--liquid oxygen (LOX)-augmented nuclear thermal rocket (NTR) propulsion and "lunar-derived" oxygen (LUNOX) production. Ironrich volcanic glass, or "orange soil," discovered during the Apollo 17 mission to Taurus-Littrow, has produced a 4% oxygen yield in recent NASA experiments using hydrogen reduction. LUNOX development and utilization would eliminate the need to transport oxygen supplies from Earth and is expected to dramatically reduce the size, cost and complexity of space transportation systems. The LOX-augmented NTR concept (LANTR) exploits the high performance capability of the conventional liquid hydrogen (LH2)-cooled NTR and the mission leverage provided by LUNOX in a unique way, LANTR utilizes the large divergent section of its nozzle as an "afterburner" into which oxygen is injected and supersonically combusted with nuclear preheated hydrogen emerging front the engine's choked sonic throat--essentially "scramjet propulsion in reverse." By varying the oxygen-to-hydrogen mixture ratio, the LANTR engine can operate over a wide range of thrust and specific impulse (Isp) values while the reactor core power level remains relatively constant. The thrust augmentation feature of LANTR means that "big engine" performance can be obtained using smaller, more affordable, easier to test NTR engines. The use of high-density LOX in place of low-density LH2 also reduces hydrogen mass and tank volume resulting in smaller space vehicles. An implementation strategy and evolutionary lunar mission architecture is outlined which requires only Shuttle C or "in-line" Shuttle-derived launch vehicles, and utilizes conventional NTR-powered lunar transfer vehicles (LTVs), operating in an "expendable mode" initially, to maximize delivered surface payload on each mission. The increased payload is dedicated to installing "modular" LUNOX production units with the intent of supplying LUNOX to lunar landing vehicles (LLVS) and then LTVs at the earliest possible opportunity. Once LUNOX becomes available in low lunar orbit (LLO), monopropellant NTRs would be outfitted with an oxygen propellant module, feed system and afterburner nozzle for "bipropellant" operation. Transition to a "reusable" mission architecture now occurs with smaller, LANTR-powered LTVs delivering approximately 400% more payload on each piloted round trip mission than earlier expendable "all LH2" NTR systems. As initial lunar outposts grow to eventual lunar settlements and LUNOX production capacity increases, the LANTR concept can enable a rapid "commuter" shuttle capable of 24 hour "one way" trips to and from the Moon, A vast deposit of"iron-rich" volcanic glass beads identified at just one candidate site--located at the southeastern edge of Mare Serenitatis--could supply, sufficient LUNOX to support daily commuter flights to the Moon for the next 9000 years

High Leverage Space Transportation System Technologies for Human Exploration Missions to the Moon and Beyond

The feasibility of returning humans to the Moon by 2004, the 35th anniversary of the Apollo 11 landing, is examined assuming the use of existing launch vehicles (the Space Shuttle and Titan 4B), a near term, advanced technology space transportation system, and extraterrestrial propellant--specifically 'lunar-derived' liquid oxygen or LUNOX. The lunar transportation system (LTS) elements consist of an expendable, nuclear thermal rocket (NTR)-powered translunar injection (TLI) stage and a combination lunar lander/Earth return vehicle (LERV) using cryogenic liquid oxygen and hydrogen (LOX/LH2) chemical propulsion. The 'wet' LERV, carrying a crew of 2, is configured to fit within the Shuttle orbiter cargo bay and requires only modest assembly in low Earth orbit. After Earth orbit rendezvous and docking of the LERV with the Titan 4B-launched NTR TLI stage, the initial mass in low Earth orbit (IMLEO) is approx. 40 t. To maximize mission performance at minimum mass, the LERV carries no return LOX but uses approx. 7 t of LUNOX to 'reoxidize' itself for a 'direct return' flight to Earth followed by an 'Apollo-style' capsule recovery. Without LUNOX, mission capability is constrained and the total LTS mass approaches the combined Shuttle-Titan 4B IMLEO limit of approx. 45 t even with enhanced NTR and chemical engine performance. Key technologies are discussed, lunar mission scenarios described, and LTS vehicle designs and characteristics are presented. Mission versatility provided by using a small 'all LH2' NTR engine or a 'LOX-augmented' derivative, either individually or in clusters, for outer planet robotic orbiter, small Mars cargo, lunar 'commuter', and human Mars exploration class missions is also briefly discussed

Shift from widespread symbiont infection of host tissues to specific colonization of gills in juvenile deep-sea mussels

The deep-sea mussel Bathymodiolus harbors chemosynthetic bacteria in its gills that provide it with nutrition. Symbiont colonization is assumed to occur in early life stages by uptake from the environment, but little is known about this process. In this study, we used fluorescence in situ hybridization to examine symbiont distribution and the specificity of the infection process in juvenile B. azoricus and B. puteoserpentis (4-21 mm). In the smallest juveniles, we observed symbionts, but no other bacteria, in a wide range of epithelial tissues. This suggests that despite the widespread distribution of symbionts in many different juvenile organs, the infection process is highly specific and limited to the symbiotic bacteria. Juveniles >= 9mm only had symbionts in their gills, indicating an ontogenetic shift in symbiont colonization from indiscriminate infection of almost all epithelia in early life stages to spatially restricted colonization of gills in later developmental stages

Using E. coli and Bacteroides distribution and abundance in a eutrophic lake as a tracer for nutrient inputs, Wilgreen Lake, Madison County, Kentucky

Wilgreen Lake is a eutrophic lake that has been listed on the EPA’s 303d list as nutrient impaired. Potential sources of this impairment are likely from humans, cattle manure, and fertilizers. We suspect that the majority of nutrients originate from human sources, namely from septic tank effluent emanating from key housing developments ringing the lakeshore. We test our hypothesis with conventional microbial assays (Escherichia coli) and RT-PCR techniques (Bacteroides). We took water samples at 19 sampling locations on 4 occasions, and measured the abundance of Escherichia coli using IDEXX methods. Corresponding sub-samples slated for potential PCR analysis were stored at -40oC. We chose PCR assay candidates on the basis of elevated E. coli levels, and the probability of differing source contributions. There is a systematic decline in E. coli microbial abundance distal to developments with closely-spaced septic units. This suggests that the principal source of microbial input is from septic systems; however, we cannot eliminate the possibility that fecal microbes are introduced into the lake via inflows. We used quantitative PCR analysis to measure Bacteroides abundance, and to distinguish between human and cattle sources. We measured 14 samples and found total fecal microbe concentrations in all samples targeting all Bacteroides species ranged from 45 mg/L to 142 mg/L. Unlike other studies, there was no apparent relationship between the concentration of all Bacteroides species and that of E. coli. We also attempted to quantitatively determine the proportion of Bacteroides contributions from specific sources, namely human and bovine fecal matter. Although fecal contamination was measured in all 14 samples, only 1 sample had significant amounts of human fecal contamination (21%) as measured by the human-associated Bacteroides assay. None of the samples had significant amounts bovine fecal concentration as measured by the bovine-associated Bacteroides assay. These inconclusive results suggest that either there are other unidentified sources of fecal contamination by Bacteroides and/or E. coli, or that the prevailing drought conditions skewed our results by not capturing fecal transport effects due to lack of surface and/or groundwater flow