493,960 research outputs found
Optimal localization patterns in bacterial protein synthesis
In bacterium, the molecular compounds involved in
protein synthesis, messenger RNAs (mRNAs) and ribosomes, show marked
intracellular localization patterns. Yet a quantitative understanding of the
physical principles which would allow one to control protein synthesis by
designing, bioengineering, and optimizing these localization patterns is still
lacking. In this study, we consider a scenario where a synthetic modification
of mRNA reaction-diffusion properties allows for controlling the localization
and stoichiometry of mRNAs and polysomescomplexes of multiple
ribosomes bound to mRNAs. Our analysis demonstrates that protein synthesis can
be controlled, e.g., optimally enhanced or inhibited, by leveraging mRNA
spatial localization and stoichiometry only, without resorting to alterations
of mRNA expression levels. We identify the physical mechanisms that control the
protein-synthesis rate, highlighting the importance of colocalization between
mRNAs and freely diffusing ribosomes, and the interplay between polysome
stoichiometry and excluded-volume effects due to the DNA nucleoid. The
genome-wide, quantitative predictions of our work may allow for a direct
verification and implementation in cell-biology experiments, where localization
patterns and protein-synthesis rates may be monitored by fluorescence
microscopy in single cells and populations
Declining Volatility, a General Property of Disparate Systems: From Fossils, to Stocks, to the Stars
There may be structural principles pertaining to the general behavior of
systems that lead to similarities in a variety of different contexts. Classic
examples include the descriptive power of fractals, the importance of surface
area to volume constraints, the universality of entropy in systems, and
mathematical rules of growth and form. Documenting such overarching principles
may represent a rejoinder to the Neodarwinian synthesis that emphasizes
adaptation and competition. Instead, these principles could indicate the
importance of constraint and structure on form and evolution. Here we document
a potential example of a phenomenon suggesting congruent behavior of very
different systems. We focus on the notion that universally there has been a
tendency for more volatile entities to disappear from systems such that the net
volatility in these systems tends to decline. We specifically focus on
origination and extinction rates in the marine animal fossil record, the
performance of stocks in the stock market, and the characters of stars and
stellar systems. We consider the evidence that each is experiencing declining
volatility, and also consider the broader significance of this.Comment: Accepted for publication in Palaeontology. 13 pages, 3 figure
Recommended from our members
Precise multimodal optical control of neural ensemble activity.
Understanding brain function requires technologies that can control the activity of large populations of neurons with high fidelity in space and time. We developed a multiphoton holographic approach to activate or suppress the activity of ensembles of cortical neurons with cellular resolution and sub-millisecond precision. Since existing opsins were inadequate, we engineered new soma-targeted (ST) optogenetic tools, ST-ChroME and IRES-ST-eGtACR1, optimized for multiphoton activation and suppression. Employing a three-dimensional all-optical read-write interface, we demonstrate the ability to simultaneously photostimulate up to 50 neurons distributed in three dimensions in a 550 × 550 × 100-µm3 volume of brain tissue. This approach allows the synthesis and editing of complex neural activity patterns needed to gain insight into the principles of neural codes
Production of high yield gold/gold-sulfide nanoparticles via cellulose membrane.
The properties of gold nanoparticles (GNP) holds promising potential for drug delivery, diagnostics, plasmonic photothermal therapy of diseases, electronics, catalysis, and photovoltaics (Liu et al., 2006; Huang et al., 2003; Thompson, 2007; Atwater and Polman, 2010). This field is growing at a fast pace with the demand for GNPs ever increasing with slow progress on development of synthesis techniques. The objective of this study was to develop a new synthesis technique that produces gold/gold sulfide (GGS) nanoparticles with a high yield. This process can control the equilibrium shift of the surface plasmon resonance (SPR) of the nanoparticles (Patel, 2012). The goal of this research is to increase the total volume of GGS nanoparticles to be synthesized while keeping their tunability for the SPR absorption peak. This research has demonstrated the ability of cellulose membrane to reduce the need for purification steps, which are associated with traditional synthesis techniques for removing small colloidal gold (\u3c 10 nm). It was found that controlling the surface area to volume ratio (SA/Vol) of the cellulose to GGS solution and temperature of the synthesis process, would provide, greater control over the SPR peak. Using these principles allows for larger volume synthesis to be performed while still retaining the ability to tune the SPR peak. It was also discovered that dialyzing out ions during the synthesis process makes bare GGS nanoparticles more stable over time. The time for the reaction to reach equilibrium was observed and showed an increase in temperature and/or SA/Vol reduces the reaction time. In conclusion, this study demonstrated how increasing the temperature and SA/Vol shifts the SPR peak and reduces the time for the reaction to reach equilibrium
Nano-enabled synthetic biology: A cell mimic based sensing platform for exploiting biochemical networks
Exploring and understanding how the smallest scale features of a cell affect biochemical reactions has always been a challenge. Nanoscale fabrication advancements have allowed scientists to create small volume reaction containers that resemble the physical scale of cell membranes. Engineers seek to use biological design principles to manipulate information and import new functionality to such synthetic devices, which in turn, play a crucial role in allowing them to explore the effects of physical transport and extreme conditions of temperature and pH on reaction systems. Engineered reaction containers can be physically and chemically defined to control the flux of molecules of different sizes and charge. The design and testing of such a container is described here. It has a volume of 19 pL and has defined slits of 10-200 nm. The device successfully contains DNA and protein molecules and has been used to conduct and analyze enzyme reactions under different substrate concentrations and a continuous cell-free protein synthesis. The effect of DNA concentration and slit size on protein yield is also discussed.
Glucose oxidase and horseradish peroxidase were loaded in the small volume container and fed with a solution containing glucose and Amplex Red™ to produce Resorufin. Fluorescent microscopy was used to monitor the reaction, which was carried out under microfluidic control. Enzyme kinetics were characterized and compared with conventional scale results.
Continuous cell free protein synthesis in arrays of nanoporous, picoliter volume containers has also been achieved. A multiscale fabrication process allows for the monolithic integration of the containers and an addressable microfluidic network. Synthesis of enhanced green fluorescent protein (eGFP) in the nanoporous containers continues beyond 24 hours and yields more than twice the amount of protein, on a per volume basis, than conventional scale batch reactions. These picoliter, nanoporous containers provide new ways for quick determination of enzyme kinetics and continuous protein synthesis in microfluidic systems. They can be used in a wide variety of applications such as drug discovery, clinical diagnostics and high-throughput screening
Kant on Perception, Experience and Judgements Thereof
It is commonly thought that the distinction between subjectively valid
judgements of perception and objectively valid judgements of experience
in the Prolegomena is not consistent with the account of judgement Kant
offers in the B Deduction, according to which a judgement is ‘nothing
other than the way to bring given cognitions to the objective unity of
apperception’. Contrary to this view, I argue that the Prolegomena
distinction maps closely onto that drawn between the mathematical and
dynamical principles in the System of Principles: Kant’s account of the
Prolegomena distinction strongly suggests that it is the Analogies of
Experience that make it possible for judgements of perception to give rise
to judgements of experience. This means that judgements of perception are
objectively valid with regard to the quantity and quality of objects, and
subjectively valid with regard to the relation they posit between objects.
If that is the case, then the notion of a judgement of perception is consistent
with the B Deduction account of judgement
Control of multiscale systems with constraints. 1. Basic principles of the concept of evolution of systems with varying constraints
Physical fundamentals of the self-organizing theory for the system with
varying constraints are considered. A variation principle, specifically the
principle of dynamic harmonization as a generalization of the Gauss-Hertz
principle for the systems with varying internal structure is formulated. In
compliance with this principle the system evolves through dynamics of the
processes leading to harmonization of the internal multiscale structure of the
system and its connections with external actions as a result of minimizing the
dynamic harmonization function. Main principles of the shell model of
self-organization under the action of the dominating entropic disturbance are
formulated.Comment: First par
Are there Many Philosophies or is there Just ‘Doing Philosophy’?
The term ‘philosophy’ may be used in more than one sense to refer to both the subjective human activity of ‘doing philosophy’ and its result, namely the production of systems of thought – philosophical theories – which history demonstrates as many and various. It will be argued that there is only one way of doing philosophy and that this is proceeding from the common principles of the human mind in the search for truth of what is real. The mark of true philosophy is unity. A unity of true philosophy may be sought from what seems disparate: Aquinas embodies this effort towards synthesis, convinced that reality is unified and ordered. ‘Just doing philosophy’ is what Thomism embodies
Recommended from our members
Computational predictions of energy materials using density functional theory
In the search for new functional materials, quantum mechanics is an exciting starting point. The fundamental laws that govern the behaviour of electrons have the possibility, at the other end of the scale, to predict the performance of a material for a targeted application. In some cases, this is achievable using density functional theory (DFT). In this Review, we highlight DFT studies predicting energy-related materials that were subsequently confirmed experimentally. The attributes and limitations of DFT for the computational design of materials for lithium-ion batteries, hydrogen production and storage materials, superconductors, photovoltaics and thermoelectric materials are discussed. In the future, we expect that the accuracy of DFT-based methods will continue to improve and that growth in computing power will enable millions of materials to be virtually screened for specific applications. Thus, these examples represent a first glimpse of what may become a routine and integral step in materials discovery
- …