1,721,009 research outputs found
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
Biofilm morphogenesis on soft hydrogels
No full textBacteria often colonize their environment in the form of surface attached multicellular communities called biofilms. Biofilms grow from surface-attached cells that undergo division while self-embedding in a viscoelastic matrix. Biofilms grow at the surface of biotic and abiotic materials with a wide range of mechanical properties. In particular, during infections and in microbiota, the association of the bacterial cells with the surface of soft tissues is of fundamental importance for successful colonization. For a long time, the field of microbiology has focused on biochemical aspects of infection and biofilm formation. There is now evidence that mechanical forces play critical roles in bacterial physiology and impact biofilm formation and stability. For example, evidence is emerging that fluid flow and physicochemical substrate material properties impact biofilm formation. We are however still missing a rigorous investigation of how the mechanical properties of a substrate material impacts biofilm morphogenesis and its relevance in the context of infection.
In the laboratory, bacteria are traditionally grown in liquid cultures, on agar plates or in flow cells with glass or hard plastic as a surface. However, these systems do not recapitulate the mechanical complexity of a real infection environment, where bacteria most often colonize soft tissues while experiencing flow. To solve these technical limitations, I combined synthetic PEGDA hydrogels with microfluidics which enabled high-resolution live imaging of single bacteria and biofilm formation while interacting with soft substrates in flow.
In chapter 2, I show that the pathogens Vibrio cholerae and Pseudomonas aeruginosa deform the synthetic soft gels. This behavior is the result of a buckling instability generated by the buildup of compressive mechanical stress inside the growing biofilm and its adhesion to the substrate. By using mutants in matrix components and comparing overproducer strains with wild type ones we showed that cell-cell cohesion and cell-substrate adhesion simultaneously drive deformation. In addition, we found that buckling biofilms can exert forces that compromise the integrity of soft epithelial cells monolayers, thus suggesting that biofilm can mechanically compromise host integrity.
In chapter 3, I investigated the effect of substrate mechanical properties on P. aeruginosa biofilm morphology. We showed that biofilms take different shapes as a function of substrate mesh size due to differences in exploratory twitching motility. The mechanical control of single-cell twitching speed, gives rise to a range of architectures that vary from compact, dome shaped biofilms to flat and dispersed ones, ultimately influencing both their tolerance to antibiotics and the spatial structure of different lineages.
Overall, our results show that the mechanical coupling with soft substrates impacts bacterial phenotypes such as surface motility and biofilm architecture and can play a role in the outcome of an infection both by modulating the biofilm susceptibility to antibiotics or by actively becoming a source of virulence.UPPERSA
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
Characterization of Pseudomonas aeruginosa mechanosensing through label-free imaging of type IV pili
No full textBacteria are ubiquitously found in all sorts of environment. They're found in the ocean, soil, or even in our guts or on our skin. Independently of their niche, they can transition from a planktonic state were they freely swim in an aqueous environment to a surface-associated state where they form multicellular communities known as biofilms. It is known that bacteria change their physiology when associated with surfaces. This is many times accompanied with a different transcriptional state compared to planktonic populations. Pseudomonas aeruginosa is an opportunistic pathogen often involved in nosocomial infections that can lead to chronic infection in immunocompromised patients. P. aeruginosa infections are often associated with a surface-associated biofilm lifestyle. In addition, it uses a host contact-dependent toxin secretion system during pathogenicity. It also possesses a surface-specific motility system known as twitching. These three examples are all physiological adaptation to surface contact. All these are a result of a change in gene expression upon surface contact.
To power twitching motility, P. aeruginosa uses long and thin extracellular filaments called type IV pili (TFP). P. aeruginosa extends and retracts its TFP to pull itself forward on surfaces. Beyond their function in motility, TFP extension, attachment on a solid substrate and retraction are required for a surface-specific transcriptional response in a process called mechanosensing. A chemotaxis-like two component system called the Chp system also mediates this surface-dependent response. The activated Chp system upregulates transcription of virulence related genes including genes involved in TFP biogenesis. However, little is known about how the Chp system is activated by TFP, and how TFP respond to mechanosensing.
The aim of this thesis is to characterize the mechanisms of mechanosensation in P. aeruginosa. In order to achieve this, one must first better characterize the mechanical input signal generated by TFP attachment events. This is an experimental challenge as TFP fibers cannot be imaged with conventional microscopes. In this thesis I present an approach to the investigation of P. aeruginosa mechanosensation by leveraging interferometric scattering microscopy (iSCAT) that I optimized for label-free detection of TFP during live cell imaging. I also show the power of iSCAT microscopy to detect and analyze TFP and their dynamic behavior on surfaces.
By combining iSCAT to fluorescence microscopy, I could then track intracellular regulatory proteins and simultaneous TFP activity. Combining these measurements with single cell motility assays and protein localization, I was able to highlight signaling feedback loops between TFP and the Chp chemotaxis system that are critical to motility and mechanosensing. This feedback system allows for cell-polarization that directs twitching motility, which we term mechanotaxis.
Finally, based on new biophysical and structural evidence, I propose a model for the mechanisms of mechanosensing by TFP and the Chp system. Here, my preliminary data show that the PilA monomers that are disassembled from TFP during retraction interact with the Chp chemosensor PilJ. Due to TFP attachment, the flux of PilA towards PilJ is different in liquid vs surfaces. I propose a mechanism wherein PilJ senses this flux imbalance.UPPERSA
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
Engineering synthetic adhesins for biophysical investigation and rewiring of host-microbe interactions
Full text linkHost attachment is often a critical step in the onset of pathogenesis. To attach to host cells, bacteria have evolved a range of adhesins that bind to specific receptors. Some of these adhesins have been thoroughly characterized using biochemical techniques. However, how adhesins engage with their receptors in a realistic context of host colonization remains obscure. For instance, how target cell surface properties regulate attachment has been overlooked. This hinders our understanding of pathogenicity, thereby limiting our ability to develop new therapeutic approaches.
Here, we aimed at characterizing the biophysical rules underlying bacterial attachment to live cells. In this context, we displayed synthetic adhesins on both bacterial and mammalian target cell surfaces to study how the mammalian membrane microenvironment regulates attachment. By leveraging microfluidics and high-temporal resolution confocal microscopy, we tracked the early adhesion of bacteria to target cells and compared it to abiotic surfaces. We modeled the distribution of residence times and uncovered that the binding to mammalian cells is a two-step process, as opposed to one-step binding to an abiotic surface. In particular, we highlight the impact of the mammalian cell glycocalyx and of the actin-mediated cell remodeling. Altogether, our results demonstrate that adhesin-ligand binding is not the only regulator of bacterial adhesion, due to the host mechanical microenvironment playing a critical role on the initiation of infection.
With a better knowledge of in vivo adhesion, we repurposed the synthetic adhesin system as a tool for bacterial-based therapy. Our plan consists in using adhesion to rewire host-pathogen interactions. By analogy with pathogenic viruses transformed into therapeutic gene delivery vectors, we focused on pathogenic bacteria injecting DNA to eukaryotic cells. Agrobacterium tumefaciens is a pathogen that delivers DNA to plants using its type IV secretion. It is widely used for gene editing in plants, and sometimes in yeast and fungal cells. It is therefore an attractive candidate as a human gene delivery vector. However, some cell types such as plant monocots or animal cells show extremely low transformation efficiency. Studies demonstrated a positive correlation between adhesion to recalcitrant plants and transformation efficiency. Hence, would a synthetic binding of A. tumefaciens to non-natural target cells increase delivery?
To measure the impact of adhesion on delivery efficiency, we repurposed an endogenous autotransporter of A. tumefaciens to display the previously characterized synthetic adhesin. This significantly increased the binding to yeast and mammalian cells displaying the target surface receptor. In addition, we developed a split luciferase assay to quantify the transfer of helper proteins to target mammalian cell. This allowed us to optimize A. tumefaciens-mediated delivery to mammalian cells and to refine hypotheses concerning the translocation mechanisms involved in mammalian cells. Altogether, we show that synthetic adhesins are a valuable tool to improve our understanding of host-microbe interactions and for repurposing pathogens into therapeutic tools.UPPERSA
Bacterial colonization in realistic environments: how mechanics impact biofilm formation in the wild and during infection
No full textA variety of physical inputs acts onto bacteria in nature. However, these are most often ignored in the studies of their physiology. There is now increasing evidence indicating that bacteria respond to physical stimuli, including mechanical forces. Yet, quantitative links between environmental mechanics, bacterial colonization and physiology remains to be established. For that purpose, studying bacteria in environments integrating relevant mechanical features is necessary. The constant improvement of microfabrication technologies and tissue engineering provides us with valuable tools to mimic such environments in the laboratory. In my PhD project, I will seek to engineer such environment with the goal to understand how mechanics influence bacteria in two distinct settings: 1) I will investigate how flow intensity modulates biofilm formation and architecture of the freshwater bacterium Caulobacter crescentus. To characterize this, I will use a microfluidics approach; 2) I will characterize how mucosal mechanics influence colonization of the respiratory tract by the pathogen Pseudomonas aeruginosa. I will achieve this using a tissue engineering approach. Overall, the goal of my PhD is to develop new platforms to study microbes in a more realistic physical context, and to gain knowledge on the complex interplay between physics and microbiology that determines the fate of bacteria in natural environments.UPPERSA
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