280 research outputs found
Asymptotic Analysis of Microtubule-Based Transport by Multiple Identical Molecular Motors
We describe a system of stochastic differential equations (SDEs) which model
the interaction between processive molecular motors, such as kinesin and
dynein, and the biomolecular cargo they tow as part of microtubule-based
intracellular transport. We show that the classical experimental environment
fits within a parameter regime which is qualitatively distinct from conditions
one expects to find in living cells. Through an asymptotic analysis of our
system of SDEs, we develop a means for applying in vitro observations of the
nonlinear response by motors to forces induced on the attached cargo to make
analytical predictions for two parameter regimes that have thus far eluded
direct experimental observation: 1) highly viscous in vivo transport and 2)
dynamics when multiple identical motors are attached to the cargo and
microtubule
Renewal reward perspective on linear switching diffusion systems
In many biological systems, the movement of individual agents is commonly
characterized as having multiple qualitatively distinct behaviors that arise
from various biophysical states. This is true for vesicles in intracellular
transport, micro-organisms like bacteria, or animals moving within and
responding to their environment. For example, in cells the movement of
vesicles, organelles and other cargo are affected by their binding to and
unbinding from cytoskeletal filaments such as microtubules through molecular
motor proteins. A typical goal of theoretical or numerical analysis of models
of such systems is to investigate the effective transport properties and their
dependence on model parameters. While the effective velocity of particles
undergoing switching diffusion is often easily characterized in terms of the
long-time fraction of time that particles spend in each state, the calculation
of the effective diffusivity is more complicated because it cannot be expressed
simply in terms of a statistical average of the particle transport state at one
moment of time. However, it is common that these systems are regenerative, in
the sense that they can be decomposed into independent cycles marked by returns
to a base state. Using decompositions of this kind, we calculate effective
transport properties by computing the moments of the dynamics within each cycle
and then applying renewal-reward theory. This method provides a useful
alternative large-time analysis to direct homogenization for linear
advection-reaction-diffusion partial differential equation models. Moreover, it
applies to a general class of semi-Markov processes and certain stochastic
differential equations that arise in models of intracellular transport.
Applications of the proposed framework are illustrated for case studies such as
mRNA transport in developing oocytes and processive cargo movement by teams of
motor proteins.Comment: 35 pages, 6 figure
Maximum Likelihood Estimation for Single Particle, Passive Microrheology Data with Drift
Volume limitations and low yield thresholds of biological fluids have led to
widespread use of passive microparticle rheology. The mean-squared-displacement
(MSD) statistics of bead position time series (bead paths) are either applied
directly to determine the creep compliance [Xu et al (1998)] or transformed to
determine dynamic storage and loss moduli [Mason & Weitz (1995)]. A prevalent
hurdle arises when there is a non-diffusive experimental drift in the data.
Commensurate with the magnitude of drift relative to diffusive mobility,
quantified by a P\'eclet number, the MSD statistics are distorted, and thus the
path data must be "corrected" for drift. The standard approach is to estimate
and subtract the drift from particle paths, and then calculate MSD statistics.
We present an alternative, parametric approach using maximum likelihood
estimation that simultaneously fits drift and diffusive model parameters from
the path data; the MSD statistics (and consequently the compliance and dynamic
moduli) then follow directly from the best-fit model. We illustrate and compare
both methods on simulated path data over a range of P\'eclet numbers, where
exact answers are known. We choose fractional Brownian motion as the numerical
model because it affords tunable, sub-diffusive MSD statistics consistent with
typical 30 second long, experimental observations of microbeads in several
biological fluids. Finally, we apply and compare both methods on data from
human bronchial epithelial cell culture mucus.Comment: 29 pages, 12 figure
Spectrum of antibacterial activity and mode of action of a novel tris-stilbene bacteriostatic compound
The spectrum of activity and mode of action of a novel antibacterial agent, 135C, was investigated using a range of microbiological and genomic approaches. Compound 135C was active against Gram-positive bacteria with MICs for Staphylococcus aureus ranging from 0.12-0.5 μg/ml. It was largely inactive against Gram-negative bacteria. The compound showed bacteriostatic activity in time-kill studies and did not elicit bacterial cell leakage or cell lysis. Checkerboard assays showed no synergy or antagonism when 135C was combined with a range of other antibacterials. Multi-step serial passage of four S. aureus isolates with increasing concentrations of 135C showed that resistance developed rapidly and was stable after drug-free passages. Minor differences in the fitness of 135C-resistant strains and parent wildtypes were evident by growth curves, but 135C-resistant strains did not show cross-resistance to other antibacterial agents. Genomic comparison of resistant and wildtype parent strains showed changes in genes encoding cell wall teichoic acids. 135C shows promising activity against Gram-positive bacteria but is currently limited by the rapid resistance development. Further studies are required to investigate the effects on cell wall teichoic acids and to determine whether the issue of resistance development can be overcome
Two rapid assays for screening of patulin biodegradation
ArtÃculo sobre distintos ensayos para comprobar la biodegradación de la patulinaThe mycotoxin patulin is produced by the blue
mould pathogen Penicillium expansum in rotting apples
during postharvest storage. Patulin is toxic to a wide range
of organisms, including humans, animals, fungi and bacteria.
Wash water from apple packing and processing
houses often harbours patulin and fungal spores, which can
contaminate the environment. Ubiquitous epiphytic yeasts,
such as Rhodosporidium kratochvilovae strain LS11 which
is a biocontrol agent of P. expansum in apples, have the
capacity to resist the toxicity of patulin and to biodegrade
it. Two non-toxic products are formed. One is desoxypatulinic
acid. The aim of the work was to develop rapid,
high-throughput bioassays for monitoring patulin degradation
in multiple samples. Escherichia coli was highly
sensitive to patulin, but insensitive to desoxypatulinic acid.
This was utilized to develop a detection test for patulin,
replacing time-consuming thin layer chromatography or
high-performance liquid chromatography. Two assays for patulin degradation were developed, one in liquid medium
and the other in semi-solid medium. Both assays allow the
contemporary screening of a large number of samples. The
liquid medium assay utilizes 96-well microtiter plates and
was optimized for using a minimum of patulin. The semisolid
medium assay has the added advantage of slowing
down the biodegradation, which allows the study and isolation
of transient degradation products. The two assays are
complementary and have several areas of utilization, from
screening a bank of microorganisms for biodegradation
ability to the study of biodegradation pathways
Genetic versus Rearing-Environment Effects on Phenotype: Hatchery and Natural Rearing Effects on Hatchery- and Wild-Born Coho Salmon
With the current trends in climate and fisheries, well-designed mitigative strategies for conserving fish stocks may become increasingly necessary. The poor post-release survival of hatchery-reared Pacific salmon indicates that salmon enhancement programs require assessment. The objective of this study was to determine the relative roles that genotype and rearing environment play in the phenotypic expression of young salmon, including their survival, growth, physiology, swimming endurance, predator avoidance and migratory behaviour. Wild- and hatchery-born coho salmon adults (Oncorhynchus kisutch) returning to the Chehalis River in British Columbia, Canada, were crossed to create pure hatchery, pure wild, and hybrid offspring. A proportion of the progeny from each cross was reared in a traditional hatchery environment, whereas the remaining fry were reared naturally in a contained side channel. The resulting phenotypic differences between replicates, between rearing environments, and between cross types were compared. While there were few phenotypic differences noted between genetic groups reared in the same habitat, rearing environment played a significant role in smolt size, survival, swimming endurance, predator avoidance and migratory behaviour. The lack of any observed genetic differences between wild- and hatchery-born salmon may be due to the long-term mixing of these genotypes from hatchery introgression into wild populations, or conversely, due to strong selection in nature—capable of maintaining highly fit genotypes whether or not fish have experienced part of their life history under cultured conditions
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