190 research outputs found
Boron isotope fractionation in soils at Shale Hills CZO
Isotope fractionation of many elements can fingerprint the biogeochemical, weathering and erosion processes that govern the evolution of the Critical Zone (CZ). This study investigates boron isotope fractionation in two soil profiles developed on the same shale bedrock at Shale Hills Critical Zone Observatory. The first soil profile, located at the valley floor, is isotopically similar to the bedrock and appears to have lost boron mostly through the loss of fine particles matter (clays) with no isotopic fractionation. The second soil profile, located at the ridge top appears to be more depleted in boron concentration and isotopically fractionated toward lower values, as expected from mineral dissolution followed by adsorption/co-precipitation processes
Boron isotope fractionation in soils at Shale Hills CZO
Isotope fractionation of many elements can fingerprint the biogeochemical, weathering and erosion processes that govern the evolution of the Critical Zone (CZ). This study investigates boron isotope fractionation in two soil profiles developed on the same shale bedrock at Shale Hills Critical Zone Observatory. The first soil profile, located at the valley floor, is isotopically similar to the bedrock and appears to have lost boron mostly through the loss of fine particles matter (clays) with no isotopic fractionation. The second soil profile, located at the ridge top appears to be more depleted in boron concentration and isotopically fractionated toward lower values, as expected from mineral dissolution followed by adsorption/co-precipitation processes
Creation and Reproduction of Model Cells with Semipermeable Membrane
A high activity of reactions can be confined in a model cell with a
semipermeable membrane in the Schl\"ogl model. It is interpreted as a model of
primitive metabolism in a cell. We study two generalized models to understand
the creation of primitive cell systems conceptually from the view point of the
nonlinear-nonequilibrium physics. In the first model, a single-cell system with
a highly active state confined by a semipermeable membrane is spontaneously
created from an inactive homogeneous state by a stochastic jump process. In the
second model, many cell structures are reproduced from a single cell, and a
multicellular system is created.Comment: 11 pages, 7 figure
Soft Listeria: actin-based propulsion of liquid drops
We study the motion of oil drops propelled by actin polymerization in cell
extracts. Drops deform and acquire a pear-like shape under the action of the
elastic stresses exerted by the actin comet. We solve this free boundary
problem and calculate the drop shape taking into account the elasticity of the
actin gel and the variation of the polymerization velocity with normal stress.
The pressure balance on the liquid drop imposes a zero propulsive force if
gradients in surface tension or internal pressure are not taken into account.
Quantitative parameters of actin polymerization are obtained by fitting theory
to experiment.Comment: 5 pages, 4 figure
Reaction-Diffusion System in a Vesicle with Semi-Permeable Membrane
We study the Schloegl model in a vesicle with semi-permeable membrane. The
diffusion constant takes a smaller value in the membrane region, which prevents
the outflow of self-catalytic product. A nonequilibrium state is stably
maintained inside of the vesicle. Nutrients are absorbed and waste materials
are exhausted through the membrane by diffusion. It is interpreted as a model
of primitive metabolism in a cell.Comment: 8 pages, 6 figure
Domain Growth Kinetics in a Cell-sized Liposome
We investigated the kinetics of domain growth on liposomes consisting of a
ternary mixture (unsaturated phospholipid, saturated phospholipid, and
cholesterol) by temperature jump. The domain growth process was monitored by
fluorescence microscopy, where the growth was mediated by the fusion of domains
through the collision. It was found that an average domain size r develops with
time t as r ~ t^0.15, indicating that the power is around a half of the
theoretical expectation deduced from a model of Brownian motion on a
2-dimensional membrane. We discuss the mechanism of the experimental scaling
behavior by considering the elasticity of the membrane
Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription Translation (TX-TL) Systems
RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or rewire existing ones. A potential strength of RNA networks is that they may be able to propagate signals on time scales that are set by the fast degradation rates of RNAs. However, a current bottleneck to verifying this potential is the slow design-build-test cycle of evaluating these networks in vivo. Here, we adapt an Escherichia coli-based cell-free transcription-translation (TX-TL) system for rapidly prototyping RNA networks. We used this system to measure the response time of an RNA transcription cascade to be approximately five minutes per step of the cascade. We also show that this response time can be adjusted with temperature and regulator threshold tuning. Finally, we use TX-TL to prototype a new RNA network, an RNA single input module, and show that this network temporally stages the expression of two genes in vivo
New Proposed Mechanism of Actin-Polymerization-Driven Motility
We present the first numerical simulation of actin-driven propulsion by
elastic filaments. Specifically, we use a Brownian dynamics formulation of the
dendritic nucleation model of actin-driven propulsion. We show that the model
leads to a self-assembled network that exerts forces on a disk and pushes it
with an average speed. This simulation approach is the first to observe a speed
that varies non-monotonically with the concentration of branching proteins
(Arp2/3), capping protein and depolymerization rate (ADF), in accord with
experimental observations. Our results suggest a new interpretation of the
origin of motility that can be tested readily by experiment.Comment: 31 pages, 5 figure
Internal lipid synthesis and vesicle growth as a step toward self-reproduction of the minimal cell
One of the major properties of the semi-synthetic minimal cell, as a model for early living cells, is the ability to self-reproduce itself, and the reproduction of the boundary layer or vesicle compartment is part of this process. A minimal bio-molecular mechanism based on the activity of one single enzyme, the FAS-B (Fatty Acid Synthase) Type I enzyme from Brevibacterium ammoniagenes, is encapsulated in 1-palmitoyl-2oleoyl-sn-glycero-3-phosphatidylcholine (POPC) liposomes to control lipid synthesis. Consequently molecules of palmitic acid released from the FAS catalysis, within the internal lumen, move toward the membrane compartment and become incorporated into the phospholipid bilayer. As a result the vesicle membranes change in lipid composition and liposome growth can be monitored. Here we report the first experiments showing vesicles growth by catalysis of one enzyme only that produces cell boundary from within. This is the prototype of the simplest autopoietic minimal cell
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