1,720,959 research outputs found
The spatial ecology of microbes
No full textTesis (Doctoral of Philosophy degree in Biological Sciences : Ecology)--Pontificia Universidad Católica de Chile, 2021Guided by cell biophysics experimentation and equipped with toolsets from theoretical ecology,
the aim of my thesis is to explore the ways in which spatial structure influences the dynamics and
distributions of microbial cells, populations and communities.
In my first project, we highlighted range expansion experiments of a colicin producing-colicin
sensitive E.coli community on solid agar; The process of colony formation is driven by colicin
production, cell lysis and division all driving the dynamical structure and ecological composition of
the colony. Making analogies to percolation theory from statistical physics, we were able to develop
a spatial model to quantify regimes of strain coexistence, competitive exclusion and extinction.
Next we aimed to understand the spatial conditions under which microbial common goods games
could persist. A particular bacterial system motivating this study was Pseudomonas aeruginosa,
which excretes a costly ‘iron-scavenging’ compound (siderophore) in order to bind and transport
iron across the cell membrane. This compound represents a common-pool resource, susceptible to
exploitation by nearby bacteria free from producing this metabolically costly resource. With this
system in mind we asked the following question: what spatial conditions permit these common-pool
resources to be monopolized by a cooperator strategy in competition with an exploiter strategy?
By developing a stochastic spatial model, we quantified the phase transition from monopolized
to exploited and predicted which circumstances to expect coexistence between niche constructing
and exploiter strategies as a result of differences in niche monopolization and colonization rates,
respectively, and when to expect a collapse of the niche and a ‘tragedy of the commons’.
Following this work, I began to apply newly acquired expertise in microfluidics, microfabrication
techniques, microscopy and experimental cell biophysics in order to observe and study the spatial
colonization dynamics of E.coli and P.aeruginosa in structured microfabricated landscapes. We showed how these two bacterial species enact a competition-colonization tradeoff where the faster
colonizing E.coli can be overwhelmed locally by the slower but superior competitor, P.aeruginosa.
This work constituted the first evidence of an abstract ecological theory in a spatial bacterial
community. Furthermore, these results showed the importance of spatial structure in leading to
coexistence as E.coli is able to effectively localize P.aeruginosa populations when competing in a
patchy landscape via priority-effects. Conversely, in well-mixed ‘mean-field’ conditions the superior competitor always wins. In order to address the priority effects observed by E.coli, we made
analogies to the Kronig-Penny model of solid state physics to our patchy landscape. To help understand the role habitat structure plays in the process of ecological colonization via invading wave
populations, we represented our patchy landscapes as a periodic potential. An interesting result of
such interpretation is the opening for the possibility of Anderson localization phenomena to take
place; whereby species modulate each other’s dynamic habitat landscape. In this scenario E. coli
cells modulate the potential seen by P.aeruginosa and introduce randomness to ecological corridors.
In this way E. coli can induce strong localization in the spatial distribution of the P.aeruginosa
metapopulation. This work highlights the importance of invisible corridor interactions and their
potential to determine patterns of patch occupancy.
Building on these results we next made an explicit connection between the topological properties
of spatially structured microbial landscapes and Taylor’s Law, which asserts that the fluctuations
within a metapopulation is a power law function of the mean. This statistical phenomena of populations, while well-documented in both the macro- and microscopic world, has yet to be connected
to processes shaping spatially structured microbial populations and communities. Pursuing this
analogy from solid state physics further we generated different degrees of randomness in the patchconnecting ecological corridor widths within a microfabricated microfluidics landscape, we found
that a critical level of randomness leads to a qualitative transition in the fluctuation scaling of an
Escherichia coli metapopulation. That induced randomness leads to such a result is neither expected experimentally nor completely understood theoretically. Nevertheless, these results bring a
landscape perspective to Taylor’s law and the desire to connect this phenomena to ecological processes. Furthermore, bridging Taylor’s Law with other ecological scaling laws is an ongoing effort
in the field of macroecology and one which we think would benefit from collaborations between
theoreticians and experimental cell biophysics techniques like the one implemented here.
Finally, given the unique perspective of this collaborative effort between cell biophysics and
theoretical ecology, we conclude this thesis with a review of the literature in the field. Primarily, we
focus on the necessary theoretical ecology needed for cell biophysicists to interpret their experimental
results. In particular, we review landmark experimental cell biophysics discoveries from the past 15
years ranging from single-cell, population and community/biofilm studies, as well as following-up
with newer findings all of which we discuss from an ecological viewpoint.2021-10-0
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Expansion, Exploitation and Extinction: Niche Construction in Ephemeral Landscapes
Full text linkWe aim to understand general consequences of niche construction on metapopulation dynamics in ephemeral landscapes. To this effect, a contact process-like stochastic spatial model is introduced where local populations colonize and go extinct on a dynamic landscape of habitable and destroyed patches. In contrast to previous models, where the extinction threshold is a consequence of available niche rendered by global rates of patch destruction/renewal, here we investigate how the metapopulation persists when they are the sole generators of their own niche. Niche construction is full-filled by localized populations through the transformation of destroyed patches in their neighborhood to viable habitat for future colonization. With this theoretical framework we are able to address the dual nature of niche construction by investigating the ephemerality of the landscape (destruction rate) and the continuum of population level strategies, where construction comes at a cost to colonization. Using mean field theory and Monte Carlo simulations of the model, we are able to quantify optimal population level strategies in a wide range of ephemeral landscapes. Interestingly, we observe qualitative differences at the extinction threshold between analytic and numeric results. Investigating this discrepancy further, we find that increasing niche construction neighborhood in the spatial model leads to two interrelated effects i) an increased rate in range expansion ii) a loss in resiliency and return of the discontinuous transition at the extinction threshold. Furthermore, in the discontinuous regime of the model, spatial clustering prior to a critical transition disappears. This is a significant finding as spatial clustering has been considered to be an early warning signal before ecosystems reach their 'tipping point'. In addition to maintaining stability, we find local niche construction strategies have an advantage when in scramble competition with an exploiter strategy because of their ability to monopolize the constructed niche due to spatial adjacency. As the niche construction neighborhood expands this advantage disappears and the exploiter strategy out-competes the niche constructor. In some cases the exploiter pushes the niche constructor to extinction, thus a tragedy of the commons ensues leading to 'ecological suicide' and a collapse of the niche
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