785 research outputs found
Dynamics-dependent density distribution in active suspensions
No full textDataset for the manuscript entitled 'Dynamics-dependent density distribution in active suspensions': Self-propelled colloids constitute an important class of intrinsically non-equilibrium matter. Typically, such a particle moves ballistically at short times, but eventually changes its orientation, and displays random-walk behaviour in the long-time limit. Theory predicts that if the velocity of non-interacting swimmers varies spatially in 1D, v(x), then their density ρ(x) satisfies ρ(x) = ρ(0)v(0)/v(x), where x = 0 is an arbitrary reference point. Such a dependence of steady-state ρ(x) on the particle dynamics, which was the qualitative basis of recent work demonstrating how to ‘paint’ with bacteria, is forbidden in thermal equilibrium. We verify this prediction quantitatively by constructing bacteria that swim with an intensity-dependent speed when illuminated and implementing spatially-resolved differential dynamic microscopy (sDDM) for quantitative analysis over ∼ mm length-scales. A spatial light pattern therefore creates a speed profile, along which we find that, indeed, ρ(x)v(x) = constant, provided that steady state is reached
Dataset for "High-throughput characterisation of bull semen motility using differential dynamic microscopy"
No full textDataset supporting the manuscript "High-throughput characterisation of bull semen motility using differential dynamic microscopy" published in PLOSone.Jepson, Alys; Arlt, Jochen; Martinez, Vincent. (2019). Dataset for "High-throughput characterisation of bull semen motility using differential dynamic microscopy", [dataset]. University of Edinburgh. School of Physics & Astronomy. Institute for Condensed Matter and Complex Systems. https://doi.org/10.7488/ds/2492
Probing the dynamics of turbid colloidal suspensions using Differential Dynamic Microscopy
No full textDataset for the manuscript entitled 'Probing the dynamics of turbid colloidal suspensions using Differential Dynamic Microscopy': Few techniques can reliably measure the dynamics of colloidal suspensions or other soft materials over a wide range of turbidities. Here we systematically investigate the capability of Differential Dynamic Microscopy (DDM) to characterise particle dynamics in turbid colloidal suspensions based on brightfield optical microscopy. We measure the Intermediate Scattering Function (ISF) of polystyrene microspheres suspended in water over a range of concentrations, turbidities, and up to 4 orders of magnitude in time-scales. These DDM results are compared to data obtained from both Dynamic Light Scattering (DLS) and Two-colour Dynamic Light Scattering (TCDLS). The latter allows for suppression of multiple scattering for moderately turbid suspensions. We find that DDM can obtain reliable diffusion coefficients at up to 10 and 1000 times higher particle concentrations than TCDLS and standard DLS, respectively. Additionally, we investigate the roles of the four length-scales relevant when imaging a suspension: the sample thickness , the imaging depth , the imaging depth of field DoF, and the photon mean free path . More detailed experiments and analysis reveal the appearance of a short-time process as turbidity is increased, which we associate with multiple scattering events within the imaging depth of field. The long-time process corresponds to the particle dynamics from which particle-size can be estimated in the case of non-interacting particles. Finally, we provide a simple theoretical framework, ms-DDM, for turbid samples, which accounts for multiple scattering
Experimental study of swimming flagellated bacteria and their collective behaviour in concentrated suspensions
Full text linkThis thesis investigates bacterial motility from the mechanism permitting individual selfpropulsion
to the complex collective flocking motility in Escherichia coli and Bacillus subtilis
cells. Understanding bacterial swimming has intrigued scientists for decades and recently there
has been a growing interest in collective swimming behaviour. The first part of this thesis
reviews the characteristics of E. coli and B. subtilis cells subsequently describing the governing
physics and constraints of self-propulsion in the low Reynolds regime. The second part of this
thesis presents three self-contained experimental sections, examining individual swimming in
non-conventional body shaped cells and subsequently focusing on concentrated bacterial
swimming in normal cells.
We first investigated motility in mutant spherical E. coli cells KJB24 motivated by simulations,
which often model bacteria as self-propelled spheres. Somewhat unexpectedly these spherical
cells do not exhibit runs and tumbles but diffuse slower than expected. As an introduction to
working with microbiology and to familiarise with microbiology techniques we investigated why
these spherical cells do not swim. Secondly we investigated how cellular motility varies as a
function of body length by inhibiting cell division in wild-type E. coli with cephalexin; which
remained motile despite body elongation. Fluorescent flagella visualization provided evidence of
multiple bundle formations along the lateral walls as a mechanism to sustain motility. The
average swimming velocity, body and flagella rotation rates, the number of flagella and number
of flagella bundles were extracted experimentally as a function of length. The extracted
experimental parameters for normal sized cells were consistent with Purcell’s model. We
explored simple adaptations and scaling of this model to describe motility for filamentous cells,
which agrees with experimental values.
The main focus is on collective behaviour of B. subtilis by examining the onset from individual
swimming to collective motility using time-lapse microscopy. Results demonstrated a smooth
transition where cells self-organize into domains expanding rapidly by recruiting cells. We
present advancements in B. subtilis fluorescent flagella staining which revealed unexpected
multiple flagella bundle arrangements during runs, contradictory to general conjectures. Novel
visualisation of flagella filaments during reversal events is presented in both E. coli and B.
subtilis cells, providing experimental evidence for complex flagella ‘flipping’. Cellular reversal
is hypothesized as a mechanism for quorum polarity facilitating collective swimming. We
present novel flagella imaging in the setting of collective behaviour showing evidence to support
quorum polarity. Subsequently we extracted the run length distributions of cells as a function of
concentration, yielding a decreasing trend with increasing concentration. Using particle tracking
we quantitatively extracted the mean squared displacement of swimming cells versus passive
tracers at different concentrations during collective swimming, these novel results are discussed
in respect to recent simulations. These presented experiments provide new insights into
collective behaviour improving current understanding of this phenomenon
Painting with bacteria: Smart templated self assembly using motile bacteria
No full textDataset supporting the manuscript entitled 'Painting with bacteria: Smart templated self assembly using motile
bacteria':
External control of the swimming speed of ‘active particles’ can be used to self assemble designer structures in situ on the µm to mm scale. We demonstrate such reconfigurable templated active self assembly in a fluid environment using light powered strains of Escherichia coli. The physics and biology controlling the sharpness and formation speed of patterns is investigated using a bespoke fast-responding strain
Self-diffusion in Isotropic and Liquid Crystalline Phases of fd Virus Colloidal Rods: a Combined Single Particle Tracking and Differential Dynamic Microscopy Study
No full textDataset for the manuscript entitled 'Self-diffusion in Isotropic and Liquid Crystalline Phases of fd Virus Colloidal Rods: a Combined Single Particle Tracking and Differential Dynamic Microscopy Study':
In this study, we investigate the dynamics of self-organised suspensions formed by rod-like fd virus colloids. Two methods have been employed for analysing fluorescence microscopy movies: single particle tracking (SPT) in direct space and differential dynamic microscopy (DDM) in reciprocal space. We perform a quantitative analysis on this anisotropic system with complex diffusion across different self-assembled states, ranging from dilute and semi-dilute liquids to nematic and smectic organisations. By leveraging the complementary strengths of SPT and DDM, we provide new insights in the dynamics of viral colloidal rods, such as long time diffusion coefficients in the smectic phase. We further discuss the advantages and limitations of both methods for studying the intricate dynamics of anisotropic colloidal systems
Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex
Full text linkCampylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation
Investigation of the interactions between fluorescent base analogues and the natural DNA bases
Full text linkDNA and RNA are integral to all life on Earth, and yet their physical properties
and behaviour in their native environment are still only imperfectly understood. Using
fluorescent analogues of natural DNA bases (FBAs) as a probe of local inter-base
interactions is a widely employed solution-phase technique to obtain information
about DNA conformation and its response to enzyme activity. Work presented in this
thesis aims to show that free FBAs in solution with the natural DNA bases is a useful
model of the inter-base interactions of FBAs in oligonucleotides, and that the effect of
substituting DNA bases with fluorescent analogues on DNA conformation can be
predicted computationally. Some results from fluorescence spectroscopy to gain
further insights into the effect of conformation on electronic energy transfer will also
be discussed.
2-aminopurine (2AP) is a responsive fluorescent base analogue that is widely
used as a probe of the local molecular environment in DNA. However, the mechanism
of this inter-base quenching remains imperfectly understood. Two previous studies of
collisional quenching of 2AP by the natural nucleotides presented conflicting results.
A comprehensive investigation of inter-base quenching of 2AP by the natural bases in
solution is presented here, reproducing the buffer conditions used in the previous
studies. Time-resolved fluorescence measurements are used to provide insight into
both dynamic and static quenching, showing consistent trends across both buffer
systems, and the results support a charge transfer mechanism. Time-resolved
fluorescence data also provide evidence for formation of 2AP-nucleotide ground-state
complexes in solution, the fluorescence lifetimes of which are comparable to that seen
in 2AP-containing oligonucleotides.
Collisional quenching studies were extended to a recently reported FBA,
pentacyclic adenine (pA), which has red-shifted emission relative to 2AP, as well as
increased brightness. However, rapid photobleaching of pA makes it difficult to use
steady-state fluorescence measurements to calculate quenching efficiencies; in
consequence time-resolved fluorescence data was obtained to quantify the effect of
the natural monophosphate nucleotides on the fluorescence of pA. It was found that
collisional interaction of pA with the purine bases increased its fluorescence lifetime
(the inverse of a quenching effect), while interaction with the pyrimidine bases shortened the lifetime. These observations were consistent with previous studies of the
effect of the base sequence surrounding pA in oligonucleotides. The results of these
collisional quenching experiments for 2AP and pA show that measuring the
fluorescence of free FBAs in solution in the presence of the natural bases is a valid
technique for predicting the behaviour of FBAs in oligonucleotide strands.
In order to complement the spectroscopic studies, computational techniques
were employed to examine the structural impact of substituting a natural base with a
base analogue in oligonucleotide sequences. Geometry optimisations of dinucleotides
containing pA were carried out, using the DFT functional M06-2X, which accounts
for dispersion, to model the effect of this novel FBA on inter-base stacking in DNA.
DNA base-step and backbone structural parameters were extracted from the optimised
structures and used to show that the substituted dinucleotides adopt conformations
similar to that associated with B-form DNA.
Previous studies have shown that, in 2AP-containing dinucleotides, electronic
energy transfer occurs from the natural base to 2AP, on excitation of the natural base
at 260 nm. It was found that there was a substantial increase in energy transfer
efficiency in frozen solution at 77 K compared to room temperature. In the present
study, the energy transfer process was investigated as a function of temperature over
the range 5-25 °C, to examine the effect of reducing temperature while maintaining
fluid conditions. A trend of decreasing quenching efficiency with increasing
temperature was found, which is consistent with the previous findings. The results of
this work also show that energy transfer is conformationally selective over this
temperature range, as can be inferred from decay parameters obtained using time-resolved fluorescence measurements.
In summary, this thesis yields deeper understanding of the effect of interactions
with natural DNA bases on the photophysics of two FBAs, pA and 2AP, and presents
a method for predicting the behaviour of novel FBAs without a priori preparing
substituted dinucleotides
Real-time fluorescence lifetime imaging system with a 32 × 32 0.13?m CMOS low dark-count single-photon avalanche diode array
No full textA compact real-time fluorescence lifetime imaging microscopy (FLIM) system based on an array of low dark count 0.13?m CMOS singlephoton avalanche diodes (SPADs) is demonstrated. Fast background-insensitive fluorescence lifetime determination is achieved by use of a recently proposed algorithm called ‘Integration for Extraction Method’ (IEM) [J. Opt. Soc. Am. A 25, 1190 (2008)]. Here, IEM is modified for a wider resolvability range and implemented on the FPGA of the new SPAD array imager. We experimentally demonstrate that the dynamic range and accuracy of calculated lifetimes of this new camera is suitable for widefield FLIM applications by imaging a variety of test samples, including various standard fluorophores covering a lifetime range from 1.6ns to 16ns, microfluidic mixing of fluorophore solutions, and living fungal spores of Neurospora Crassa. The calculated lifetimes are in a good agreement with literature values. Real-time fluorescence lifetime imaging is also achieved, by performing parallel 32 × 16 lifetime calculations, realizing a compact and low-cost FLIM camera and promising for bigger detector arrays.Micro ElectronicsElectrical Engineering, Mathematics and Computer Scienc
Die Römische Republik /
No full textWer sich für antike Geschichte interessiert, greift zu dieser knappen und gut lesbaren Geschichte der Römischen Republik, geschrieben von einem der bekanntesten Althistoriker Deutschlands. Jochen Bleicken (1926-2005) führt den Leser von der Zeit der Etrusker bis zum Ende der Republik, das die Herrschaft Caesars besiegelte. Alle wichtigen Phasen der republikanischen Geschichte entfalten sich: die Ständekämpfe, Aufstieg Roms zur Weltherrschaft - und die zugehörigen ungeheuren kriegerischen Auseinandersetzungen -, Ursachen und Beginn der inneren Krise seit den Gracchen, die Restauration unter Sulla und schließlich: die Auflösung der Republik und die Begründung der Monarchie. Aloys Winterling Jochen Bleicken, 1926-2005, war Professor für Alte Geschichte an der Universität Göttingen und u.a. Mitherausgeber von "Oldenbourg Grundriss der Geschichte" und der HISTORISCHEN ZEITSCHRIFT.Wer sich für antike Geschichte interessiert, greift zu dieser knappen und gut lesbaren Geschichte der Römischen Republik, geschrieben von einem der bekanntesten Althistoriker Deutschlands. Jochen Bleicken (1926-2005) führt den Leser von der Zeit der Etrusker bis zum Ende der Republik, das die Herrschaft Caesars besiegelte. Alle wichtigen Phasen der republikanischen Geschichte entfalten sich: die Ständekämpfe, Aufstieg Roms zur Weltherrschaft - und die zugehörigen ungeheuren kriegerischen Auseinandersetzungen -, Ursachen und Beginn der inneren Krise seit den Gracchen, die Restauration unter Sulla und schließlich: die Auflösung der Republik und die Begründung der Monarchie. Aloys Winterling Jochen Bleicken, 1926-2005, war Professor für Alte Geschichte an der Universität Göttingen und u.a. Mitherausgeber von "Oldenbourg Grundriss der Geschichte" und der HISTORISCHEN ZEITSCHRIFT.Mode of access: Internet via World Wide Web.Description based on online resource; title from PDF title page (publisher's Web site, viewed 08. Jul 2019
- …
