scholarly journals Review and perspective on mathematical modeling of microbial ecosystems

2018 ◽  
Vol 46 (2) ◽  
pp. 403-412 ◽  
Author(s):  
Antonella Succurro ◽  
Oliver Ebenhöh
Keyword(s):  
Microbial Communities ◽  
Multiple Scales ◽  
Macroscopic Description ◽  
Modeling Methods ◽  
Societal Challenges ◽  
Microbial Ecosystems ◽  
Differential Equation Models ◽  
Spatio Temporal ◽  
Temporal Interactions ◽  
Stoichiometric Models

Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial ‘who is there?’ question. An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

scholarly journals Video action detection by learning graph-based spatio-temporal interactions

2021 ◽  
Vol 206 ◽  
pp. 103187
Author(s):  
Matteo Tomei ◽  
Lorenzo Baraldi ◽  
Simone Calderara ◽  
Simone Bronzin ◽  
Rita Cucchiara
Keyword(s):  
Action Detection ◽  
Spatio Temporal ◽  
Temporal Interactions

Spatio-temporal interactions between Northeast Atlantic Mackerel and its fishery - Simulating different futures

Marine Policy ◽  
2021 ◽  
Vol 133 ◽  
pp. 104740
Author(s):  
Sandra Rybicki ◽  
Katell G. Hamon ◽  
Sarah Simons ◽  
Axel Temming
Keyword(s):  
Northeast Atlantic ◽  
Atlantic Mackerel ◽  
Spatio Temporal ◽  
Temporal Interactions

scholarly journals Image-Based Modeling from a High -Resolution Route Panorama

2010 ◽  
Vol 9 (1) ◽  
pp. 27-35
Author(s):  
Ryuji Shibata ◽  
Hajime Nagahara
Keyword(s):  
Belief Propagation ◽  
3D Models ◽  
Single Image ◽  
Multiple Viewpoints ◽  
Modeling Methods ◽  
Image Based Modeling ◽  
Spatio Temporal ◽  
Effective Use ◽  
Scene Depth ◽  
Route Panorama

Image-based modeling methods for generating 3D models from an image sequence have been widely studied. Most of these methods, however, require huge redundant spatio-temporal images to estimate scene depth. This is not an effective use of capturing higher resolution texture. On the other hand, a route panorama, which is a continuous panoramic image along a path, is an efficient way of consolidating information from multiple viewpoints into a single image. A route panorama captured by a line camera also has the advantage of capturing higher resolution easily. In this paper, we propose a method for estimating the depth of an image from a route panorama using color drifts. The proposed method detects color drift by deformable window matching of the color channels. It also uses a hierarchical belief propagation to estimate the depth stably and decrease the computation cost thereof.

Socio-Spatial Practice and Racial Representations in a Changing South Africa

2005 ◽  
Vol 35 (3) ◽  
pp. 444-459 ◽  
Author(s):  
Kevin Durrheim
Keyword(s):  
South Africa ◽  
Spatial Practice ◽  
Running Away ◽  
Racial Representations ◽  
Blacks And Whites ◽  
Spatio Temporal ◽  
Temporal Interactions ◽  
Historical Periods

This article argues (a) that the content of racial representations in South Africa has changed historically, and (b) that these representations are grounded in concrete patterns of spatio-temporal interactions between blacks and whites that have characterised different historical epochs. These arguments are developed by means of a consideration of racial interactions and representations in four historical periods: the early Cape colony, the frontier, apartheid and the contemporary post-apartheid period. The bulk of the discussion concerns the kinds of representations that are being developed and perpetuated in the present desegregated context, where whites experience displacement at the hands of blacks, and blacks experience whites running away from them.

scholarly journals Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

2013 ◽  
Vol 16 (6) ◽  
pp. 1472-1481 ◽  
Author(s):  
Karen De Roy ◽  
Massimo Marzorati ◽  
Pieter Van den Abbeele ◽  
Tom Van de Wiele ◽  
Nico Boon
Keyword(s):  
Microbial Communities ◽  
Microbial Ecosystems
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