Effect of EPS on biofilm structure and function as revealed by an individual-based model of biofilm growth

2001 ◽  
Vol 43 (6) ◽  
pp. 135-135 ◽  
Author(s):  
J.-U. Kreft ◽  
J. W. Wimpenny
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Structure And Function ◽  
Individual Based Model ◽  
Biofilm Growth ◽  
Rate Dependent ◽  
Binding Forces ◽  
The Individual ◽  
And Function ◽  
Biofilm Structure

We have simulated a nitrifying biofilm with one ammonia and one nitrite oxidising species in order to elucidate the effect of various extracellular polymeric substance (EPS) production scenarios on biofilm structure and function. The individual-based model (IbM) BacSim simulates diffusion of all substrates on a two-dimensional lattice. Each bacterium is individually simulated as a sphere of given size in a continuous, three-dimensional space. EPS production kinetics was described by a growth rate dependent and an independent term (Luedeking-Piret equation). The structure of the biofilm was dramatically influenced by EPS production or capsule formation. EPS production decreased growth of producers and stimulated growth of non-producers because of the energy cost involved. For the same reason, EPS accumulation can fall as its rate of production increases. The patchiness and roughness of the biofilm decreased and the porosity increased due to EPS production. EPS density was maximal in the middle of the vertical profile. Introduction of binding forces between like cells increased clustering.

Clinical Biomechanics: Contributions to the Medical Treatment of Physical Abnormalities

2012 ◽  
Vol 1 (1) ◽  
pp. 17-23 ◽  
Author(s):  
Joseph Hamill ◽  
George Gorton ◽  
Peter Masso
Keyword(s):  
Cerebral Palsy ◽  
Medical Treatment ◽  
Treatment Outcomes ◽  
Clinical Assessment ◽  
Treatment Options ◽  
Three Dimensional ◽  
Structure And Function ◽  
Diverse Field ◽  
The Individual ◽  
And Function

Biomechanics is defined as the application of the laws of mechanics to the study or structure and function of movement. It is a relatively new subdiscipline to the domain of kinesiology. Biomechanics was initially closely associated with the study of sports technique. However, over the years, biomechanics has taken on a much more diverse field of study. In this paper, we will describe the contributions that biomechanics has made to the area of clinical biomechanics research in terms of clinical assessment and outcomes and the design of clinical apparatus. The first example examines a clinical assessment of a cerebral palsy child. The goals of such a clinical assessment are 1) to determine the primary problems with the locomotion capabilities of the individual, 2) to recommend treatment options, and 3) to evaluate treatment outcomes. In the second example, a procedure is described for designing braces for scoliosis patients. For this example, a three-dimensional digital twin is developed using a scanning technique. This example illustrates the research conducted on developing a technique to noninvasively and safely determine the torso deformities resulting from scoliosis. While these examples are but two of a wide variety of examples that could be used, they illustrate the contribution of biomechanics to the clinical world.

Modelling the structure and function of extracellular polymeric substances in biofilms with new numerical techniques

2001 ◽  
Vol 43 (6) ◽  
pp. 121-127 ◽  
Author(s):  
H. Horn ◽  
T. R. Neu ◽  
M. Wulkow
Keyword(s):  
Extracellular Polymeric Substances ◽  
Volume Fraction ◽  
Structure And Function ◽  
Biofilm Growth ◽  
Biofilm Model ◽  
The Matrix ◽  
Substrate Conversion ◽  
The One ◽  
And Function ◽  
Biofilm Structure

The objective of this study is the mathematical description of the structure and function of the extracellular polymeric substances (EPS) in biofilms. The basic assumptions of the EPS biofilm model are:the production of EPS in biofilms is coupled to the growth of micro-organismsthe production of EPS is additionally coupled to the substrate conditions-the EPS represent a considerable volume fraction of the matrix in biofilms and thus the density of the biofilms is strongly influenced by the EPS-sorption of biocides and pollutants in biofilms occurs mainly to EPSthe EPS can be used as an energy source during substrate limited phases. The mathematical model has been derived as a system of partial differential equations. The numerical solution of these complex balance equations has been done by a self-adaptive Galerkin-h-p-method. It can be shown, that on the one hand the simulation of substrate conversion and biofilm growth with the EPS-biofilm model yields similar results as the known biofilm models without consideration of the EPS fraction. On the other hand the advantage of the EPS-biofilm model is a better understanding of biofilm structure, which is mainly influenced by the EPS fraction in the biofilm. Furthermore, the sorption of pollutants, such as heavy metals and chlorinated organic substances, can be simulated in more detail.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

scholarly journals Impact of genetic variation on three dimensional structure and function of proteins

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0171355 ◽  
Author(s):  
Roshni Bhattacharya ◽  
Peter W. Rose ◽  
Stephen K. Burley ◽  
Andreas Prlić
Keyword(s):  
Genetic Variation ◽  
Three Dimensional ◽  
Structure And Function ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
And Function

scholarly journals Conserved Structure and Function in the Granulysin and NK-Lysin Peptide Family

2005 ◽  
Vol 73 (10) ◽  
pp. 6332-6339 ◽  
Author(s):  
Charlotte M. A. Linde ◽  
Susanna Grundström ◽  
Erik Nordling ◽  
Essam Refai ◽  
Patrick J. Brennan ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
Three Dimensional ◽  
Antimycobacterial Activity ◽  
Structure And Function ◽  
Loop Structure ◽  
E Coli ◽  
Short Loop ◽  
Peptide Family ◽  
And Function ◽  
Related Proteins

ABSTRACT Granulysin and NK-lysin are homologous bactericidal proteins with a moderate residue identity (35%), both of which have antimycobacterial activity. Short loop peptides derived from the antimycobacterial domains of granulysin, NK-lysin, and a putative chicken NK-lysin were examined and shown to have comparable antimycobacterial but variable Escherichia coli activities. The known structure of the NK-lysin loop peptide was used to predict the structure of the equivalent peptides of granulysin and chicken NK-lysin by homology modeling. The last two adopted a secondary structure almost identical to that of NK-lysin. All three peptides form very similar three-dimensional (3-D) architectures in which the important basic residues assume the same positions in space. The basic residues in granulysin are arginine, while those in NK-lysin and chicken NK-lysin are a mixture of arginine and lysine. We altered the ratio of arginine to lysine in the granulysin fragment to examine the importance of basic residues for antimycobacterial activity. The alteration of the amino acids reduced the activity against E. coli to a larger extent than that against Mycobacterium smegmatis. In granulysin, the arginines in the loop structure are not crucial for antimycobacterial activity but are important for cytotoxicity. We suggest that the antibacterial domains of the related proteins granulysin, NK-lysin, and chicken NK-lysin have conserved their 3-D structure and their function against mycobacteria.

scholarly journals Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
A.E. Naas ◽  
A.K. MacKenzie ◽  
B. Dalhus ◽  
V.G.H. Eijsink ◽  
P.B. Pope
Keyword(s):  
Active Site ◽  
Three Dimensional ◽  
Structural Features ◽  
Structure And Function ◽  
Dimensional Structure ◽  
Active Site Cleft ◽  
Polysaccharide Utilization Locus ◽  
And Function ◽  
Rumen Metagenome

Abstract Previous gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the −3 to −1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic “clamp”, potentially interacting with sugars at the +1 and +2 subsites. The enzyme’s active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft.

Individual Differences Among Users

2011 ◽  
pp. 1-24 ◽  
Author(s):  
Madeleine Keehner ◽  
Peter Khooshabeh ◽  
Mary Hegarty
Keyword(s):  
Individual Differences ◽  
Three Dimensional ◽  
Structure And Function ◽  
Science Literature ◽  
Interactive Behavior ◽  
Different Types ◽  
Interactive Visualizations ◽  
Cognitive Benefits ◽  
Sophisticated User ◽  
And Function

This chapter examines human factors associated with using interactive three-dimensional (3D) visualizations. Virtual representations of anatomical structure and function, often with sophisticated user control capabilities, are growing in popularity in medicine for education, training, and simulation. This chapter reviews the cognitive science literature and introduces issues such as theoretical ideas related to using interactive visualizations, different types and levels of interactivity, effects of different kinds of control interfaces, and potential cognitive benefits of these tools. The authors raise the question of whether all individuals are equally capable of using 3D visualizations effectively, focusing particularly on two variables: (1) individual differences in spatial abilities, and (2) individual differences in interactive behavior. The chapter draws together findings from the authors’ own studies and from the wider literature, exploring recent insights into how individual differences among users can impact the effectiveness of different types of external visualizations for different kinds of tasks. The chapter offers recommendations for design, such as providing transparent affordances to support users’ meta-cognitive understanding, and employing personalization to complement the capabilities of different individuals. Finally, the authors suggest future directions and approaches for research, including the use of methodology such as needs analysis and contextual enquiry to better understand the cognitive processes and capacities of different kinds of users.

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