216 research outputs found
Structural responses of model biomembranes to Mars-relevant salts
No full textLipid membranes are a key component of contemporary living systems and are thought to have been essential to the origin of life. Most research on membranes has focused on situations restricted to ambient physiological or benchtop conditions. However, the influence of more extreme conditions, such as the deep subsurface on Earth or extraterrestrial environments are less well understood. The deep subsurface environments of Mars, for instance, may harbor high concentrations of chaotropic salts in brines, yet we know little about how these conditions would influence the habitability of such environments for cellular life. Here, we investigated the combined effects of high concentrations of salts, including sodium and magnesium perchlorate and sulfate, and high hydrostatic pressure on the stability and structure of model biomembranes of varying complexity. To this end, a variety of biophysical techniques have been applied, which include calorimetry, fluorescence spectroscopies, small-angle X-ray scattering, dynamic light scattering, and microscopy techniques. We show that the structure and phase behavior of lipid membranes is sensitively dictated by the nature of the salt, in particular its anion and its concentration. We demonstrate that, with the exception of magnesium perchlorate, which can also induce cubic lipid arrangements, long-chain saturated lipid bilayer structures can still persist at high salt concentrations across a range of pressures. The lateral organization of complex heterogeneous raft-like membranes is affected by all salts. For simple, in particular bacterial membrane-type bilayer systems with unsaturated chains, vesicular structures are still stable at Martian brine conditions, also up to the kbar pressure range, demonstrating the potential compatibility of environments containing such ionic and pressure extremes to lipid-encapsulated life
Diffusion-limited evaporation of polymer solutions
No full textIn many processes in nature and industry, water evaporates from polymer
solutions. When the evaporation is fast, a polymer layer can form at the water-air interface resulting in a diffusive mass transfer resistance inside the solution, in a process termed diffusion-limited evaporation (DLE). DLE has been observed in solutions containing lipids or microgels, that often have a specific structural complexity. To understand the generality of the physical mechanisms in DLE, it is highly relevant to study DLE of polymer solutions.
In this thesis, we study the evaporation of water from solutions containing
structurally simple polymers, with the aim of improving the fundamental
understanding of DLE. We first present experimental data, where a polymerwater solution evaporates unidirectionally from rectangular capillaries. The evaporation rate settles according to the predicted diffusive scaling m˙ (t) ∼ t−1/2, but surprisingly does not settle with m˙ (t) → 0 at late times, which would be expected at thermodynamic equilibrium with the environment. The steady state evaporation dynamics in our experiments is explained as resulting from the buildup of a tensile stress in a glassy polymer layer at the interface, resulting from the compression by the evaporation flux, that offsets the water activity at the interface ai from thermodynamic equilibrium with the environment. We furthermore show how DLE can result in evaporation from polymer solutions that is insensitive to the ambient humidity, which sets the driving force for
evaporation. Importantly, we find that for certain polymers evaporation is also humidity-insensitive at early times, without becoming diffusion-limited. This effect is caused by the rapid adsorption of polymers at the solution-air interface, with the interfacial polymer layer setting the early-times evaporation rate.
In the second part of this thesis we show DLE from polyelectrolyte solutions, that is similar to the neutral polymer at late times as a result of increased counterion condensation at high polyelectrolyte concentrations. The polymers we tested also approach a similar non-zero steady state evaporation rate m˙ (t), which suggests similar contributions from the mixing energy and mechanical response to the evaporative driving force.
The final part of this thesis presents a phase field model which allows us to
establish the ubiquitous nature of DLE, independent of polymer properties. For a one-dimensional geometry, results from the model clearly show how DLE with m˙ (t) ∼ t−1/2 occupies a large region in the evaporation phase space, which also includes pure solvent-like (m˙ (t) ∼ const.) and arrested (m˙ (t) ∼ 0) evaporative regions. Finally, we show how the model can be extended to more complicated systems, like droplets or materials with heterogeneous internal structuring, which is important to translating our results to many practical applications
Aplip1 - a potential scaffold protein of Drosophila melanogaster may be involved in facilitating signal transduction
No full textEThOS - Electronic Theses Online ServiceGBUnited Kingdo
Three Steps to Heaven: Semantic Publishing in a Real World Workflow
No full textSemantic publishing offers the promise of computable papers, enrichedvisualisation and a realisation of the linked data ideal. In reality, however, the publicationprocess contrives to prevent richer semantics while culminating in a "lumpen" PDF. In thispaper, we discuss a web-first approach to publication, and describe a three-tiered approachthat integrates with the existing authoring tooling. Critically, although it adds limitedsemantics, it does provide value to all the participants in the process: the author, the readerand the machine.&#160
Three steps to heaven: Semantic publishing in a real world workflow
No full textSemantic publishing offers the promise of computable papers, enriched visualisation and a realisation of the linked data ideal. In reality, however, the publication process contrives to prevent richer semantics while culminating in a 'lumpen' PDF. In this paper, we discuss a web-first approach to publication, and describe a three-tiered approach which integrates with the existing authoring tooling. Critically, although it adds limited semantics, it does provide value to all the participants in the process: the author, the reader and the machine
Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View
No full text: Elucidating the details of the formation, stability, interactions, and reactivity of biomolecular systems under extreme environmental conditions, including high salt concentrations in brines and high osmotic and high hydrostatic pressures, is of fundamental biological, astrobiological, and biotechnological importance. Bacteria and archaea are able to survive in the deep ocean or subsurface of Earth, where pressures of up to 1 kbar are reached. The deep subsurface of Mars may host high concentrations of ions in brines, such as perchlorates, but we know little about how these conditions and the resulting osmotic stress conditions would affect the habitability of such environments for cellular life. We discuss the combined effects of osmotic (salts, organic cosolvents) and hydrostatic pressures on the structure, stability, and reactivity of biomolecular systems, including membranes, proteins, and nucleic acids. To this end, a variety of biophysical techniques have been applied, including calorimetry, UV/vis, FTIR and fluorescence spectroscopy, and neutron and X-ray scattering, in conjunction with high pressure techniques. Knowledge of these effects is essential to our understanding of life exposed to such harsh conditions, and of the physical limits of life in general. Finally, we discuss strategies that not only help us understand the adaptive mechanisms of organisms that thrive in such harsh geological settings but could also have important ramifications in biotechnological and pharmaceutical applications
Three Steps to Heaven: Semantic Publishing in a Real World Workow
No full textAbstract. Semantic publishing offers the promise of computable pa-pers, enriched visualisation and a realisation of the linked data ideal. In reality, however, the publication process contrives to prevent richer se-mantics while culminating in a ‘lumpen ’ PDF. In this paper, we discuss a web-first approach to publication, and describe a three-tiered approach which integrates with the existing authoring tooling. Critically, although it adds limited semantics, it does provide value to all the participants in the process: the author, the reader and the machine. License: This work is licensed under a Creative Commons Attributio
Integration of probabilistic functional networks without an external Gold Standard
No full textBackground: Probabilistic functional integrated networks (PFINs) are designed to aid our understanding of cellular biology and can be used to generate testable hypotheses about protein function. PFINs are generally created by scoring the quality of interaction datasets against a Gold Standard dataset, usually chosen from a separate high-quality data source, prior to their integration. Use of an external Gold Standard has several drawbacks, including data redundancy, data loss and the need for identifier mapping, which can complicate the network build and impact on PFIN performance. Additionally, there typically are no Gold Standard data for non-model organisms. Results: We describe the development of an integration technique, ssNet, that scores and integrates both high-throughput and low-throughout data from a single source database in a consistent manner without the need for an external Gold Standard dataset. Using data from Saccharomyces cerevisiae we show that ssNet is easier and faster, overcoming the challenges of data redundancy, Gold Standard bias and ID mapping. In addition ssNet results in less loss of data and produces a more complete network. Conclusions: The ssNet method allows PFINs to be built successfully from a single database, while producing comparable network performance to networks scored using an external Gold Standard source and with reduced data loss
Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics
No full textThe identification of the protein-coding regions of a genome is straightforward due to the universality of start and stop codons. However, the boundaries of the transcribed regions, conditional operon structures, non-coding RNAs and the dynamics of transcription, such as pausing of elongation, are non-trivial to identify, even in the comparatively simple genomes of prokaryotes. Traditional methods for the study of these areas, such as tiling arrays, are noisy, labour-intensive and lack the resolution required for densely-packed bacterial genomes. Recently, deep sequencing has become increasingly popular for the study of the transcriptome due to its lower costs, higher accuracy and single nucleotide resolution. These methods have revolutionised our understanding of prokaryotic transcriptional dynamics. Here, we review the deep sequencing and data analysis techniques that are available for the study of transcription in prokaryotes, and discuss the bioinformatic considerations of these analyses
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