2,969 research outputs found
Lambda-prophage induction modeled as a cooperative failure mode of lytic repression
We analyze a system-level model for lytic repression of lambda-phage in E.
coli using reliability theory, showing that the repressor circuit comprises 4
redundant components whose failure mode is prophage induction. Our model
reflects the specific biochemical mechanisms involved in regulation, including
long-range cooperative binding, and its detailed predictions for prophage
induction in E. coli under ultra-violet radiation are in good agreement with
experimental data.Comment: added referenc
Evolutionary game theory in growing populations
Existing theoretical models of evolution focus on the relative fitness
advantages of different mutants in a population while the dynamic behavior of
the population size is mostly left unconsidered. We here present a generic
stochastic model which combines the growth dynamics of the population and its
internal evolution. Our model thereby accounts for the fact that both
evolutionary and growth dynamics are based on individual reproduction events
and hence are highly coupled and stochastic in nature. We exemplify our
approach by studying the dilemma of cooperation in growing populations and show
that genuinely stochastic events can ease the dilemma by leading to a transient
but robust increase in cooperationComment: 4 pages, 2 figures and 2 pages supplementary informatio
Observation of Quantum Effects in sub Kelvin Cold Reactions
There has been a long-standing quest to observe chemical reactions at low
temperatures where reaction rates and pathways are governed by quantum
mechanical effects. So far this field of Quantum Chemistry has been dominated
by theory. The difficulty has been to realize in the laboratory low enough
collisional velocities between neutral reactants, so that the quantum wave
nature could be observed. We report here the first realization of merged
neutral supersonic beams, and the observation of clear quantum effects in the
resulting reactions. We observe orbiting resonances in the Penning ionization
reaction of argon and molecular hydrogen with metastable helium leading to a
sharp increase in the absolute reaction rate in the energy range corresponding
to a few degrees kelvin down to 10 mK. Our method is widely applicable to many
canonical chemical reactions, and will enable a breakthrough in the
experimental study of Quantum Chemistry
Why do we talk to ourselves?
Human beings talk to themselves; sometimes out-loud, other times in inner speech. In this paper, I present a resolution to the following dilemma that arises from self-talk. If self-talk exists then either, (i) we know what we are going to say and self-talk serves no communicative purpose, and must serve some other purpose, or (ii) we don’t know what we are going to say, and self-talk does serve a communicative purpose, namely, it is an instance of us communicating with ourselves. Adopting (i) was the strategy taken by Bart Geurts, who claims that the primary purpose of self-talk is to entrain commitments, and is not (primarily) communicative. While accepting that self-talk can usefully play this role, I criticise the view that entraining commitments is self-talk’s fundamental role. I argue that adopting the view that we are self-blind, at least to a significant degree, means that we can accept that self-talk does play a communicative role
Aquisição da linguagem escrita e intervenções pedagógicas: uma abordagem histórico-cultural
Conformational changes and loose packing promote E. coli Tryptophanase cold lability
<p>Abstract</p> <p>Background</p> <p>Oligomeric enzymes can undergo a reversible loss of activity at low temperatures. One such enzyme is tryptophanase (Trpase) from <it>Escherichia coli</it>. Trpase is a pyridoxal phosphate (PLP)-dependent tetrameric enzyme with a Mw of 210 kD. PLP is covalently bound through an enamine bond to Lys270 at the active site. The incubation of holo <it>E. coli </it>Trpases at 2°C for 20 h results in breaking this enamine bond and PLP release, as well as a reversible loss of activity and dissociation into dimers. This sequence of events is termed cold lability and its understanding bears relevance to protein stability and shelf life.</p> <p>Results</p> <p>We studied the reversible cold lability of <it>E. coli </it>Trpase and its Y74F, C298S and W330F mutants. In contrast to the holo <it>E. coli </it>Trpase all apo forms of Trpase dissociated into dimers already at 25°C and even further upon cooling to 2°C. The crystal structures of the two mutants, Y74F and C298S in their apo form were determined at 1.9Å resolution. These apo mutants were found in an open conformation compared to the closed conformation found for <it>P. vulgaris </it>in its holo form. This conformational change is further supported by a high pressure study.</p> <p>Conclusion</p> <p>We suggest that cold lability of <it>E. coli </it>Trpases is primarily affected by PLP release. The enhanced loss of activity of the three mutants is presumably due to the reduced size of the side chain of the amino acids. This prevents the tight assembly of the active tetramer, making it more susceptible to the cold driven changes in hydrophobic interactions which facilitate PLP release. The hydrophobic interactions along the non catalytic interface overshadow the effect of point mutations and may account for the differences in the dissociation of <it>E. coli </it>Trpase to dimers and <it>P. vulgaris </it>Trpase to monomers.</p
Estrogen-Receptor Expression and Function in Thymocytes in Relation to Gender and Age
The expression of estrogen receptor (ER) in thymocytes was studied in young, middle-aged, and
old (2, 12, and 24 months, respectively) female and male C57BL/6J mice. Western immunoblots
prepared from the thymocytes of females of all age groups showed the presence of a 67-kD
protein band, which has been associated with the apparent MW of denatured ER. Flow cytometry
analysis o,f cells stained with a monoclonal anti-ER antibody (clone 13H2) disclosed ER
expression in both females and males of all age groups. In vivo treatment with estradiol (E2) led
to an increase in the specific activity of thymic creatine kinase (CK) in the female mice, whereas
the male thymocytes responded with an increase in CK activity only on treatment with
dihydrotestosterone (DHT). The data show no differences in ER expression between male and
females, but the receptor appears not to be functional in males. Interestingly, when estradiol was
applied to co-cultures of lymphoid-depleted fetal thymus (FT) explants and bone-marrow cells,
or thymocytes, from young and old females, it resulted in increased cellularity of cultures
containing cells of the young, and not those of the old. The proportion of CD4/CD8 phenotypes
of the developing cells in these cultures was not affected by E2 treatment. These observations
provide a new insight into ER expression and function in T-cell development in relation to
gender and age
How brains make decisions
This chapter, dedicated to the memory of Mino Freund, summarizes the Quantum
Decision Theory (QDT) that we have developed in a series of publications since
2008. We formulate a general mathematical scheme of how decisions are taken,
using the point of view of psychological and cognitive sciences, without
touching physiological aspects. The basic principles of how intelligence acts
are discussed. The human brain processes involved in decisions are argued to be
principally different from straightforward computer operations. The difference
lies in the conscious-subconscious duality of the decision making process and
the role of emotions that compete with utility optimization. The most general
approach for characterizing the process of decision making, taking into account
the conscious-subconscious duality, uses the framework of functional analysis
in Hilbert spaces, similarly to that used in the quantum theory of
measurements. This does not imply that the brain is a quantum system, but just
allows for the simplest and most general extension of classical decision
theory. The resulting theory of quantum decision making, based on the rules of
quantum measurements, solves all paradoxes of classical decision making,
allowing for quantitative predictions that are in excellent agreement with
experiments. Finally, we provide a novel application by comparing the
predictions of QDT with experiments on the prisoner dilemma game. The developed
theory can serve as a guide for creating artificial intelligence acting by
quantum rules.Comment: Latex file, 20 pages, 3 figure
The role of input noise in transcriptional regulation
Even under constant external conditions, the expression levels of genes
fluctuate. Much emphasis has been placed on the components of this noise that
are due to randomness in transcription and translation; here we analyze the
role of noise associated with the inputs to transcriptional regulation, the
random arrival and binding of transcription factors to their target sites along
the genome. This noise sets a fundamental physical limit to the reliability of
genetic control, and has clear signatures, but we show that these are easily
obscured by experimental limitations and even by conventional methods for
plotting the variance vs. mean expression level. We argue that simple, global
models of noise dominated by transcription and translation are inconsistent
with the embedding of gene expression in a network of regulatory interactions.
Analysis of recent experiments on transcriptional control in the early
Drosophila embryo shows that these results are quantitatively consistent with
the predicted signatures of input noise, and we discuss the experiments needed
to test the importance of input noise more generally.Comment: 11 pages, 5 figures minor correction
Exact, time-independent estimation of clone size distributions in normal and mutated cells
Biological tools such as genetic lineage tracing, three dimensional confocal microscopy and next generation DNA sequencing are providing new ways to quantify the distribution of clones of normal and mutated cells. Population-wide clone size distributions in vivo are complicated by multiple cell types, and overlapping birth and death processes. This has led to the increased need for mathematically informed models to understand their biological significance. Standard approaches usually require knowledge of clonal age. We show that modelling on clone size independent of time is an alternative method that offers certain analytical advantages; it can help parameterize these models, and obtain distributions for counts of mutated or proliferating cells, for example. When applied to a general birth-death process common in epithelial progenitors this takes the form of a gamblers ruin problem, the solution of which relates to counting Motzkin lattice paths. Applying this approach to mutational processes, an alternative, exact, formulation of the classic Luria Delbruck problem emerges. This approach can be extended beyond neutral models of mutant clonal evolution, and also describe some distributions relating to sub-clones within a tumour. The approaches above are generally applicable to any Markovian branching process where the dynamics of different "coloured" daughter branches are of interest
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