scholarly journals Universal scaling across biochemical networks on Earth

2017 ◽  
Author(s):  
Hyunju Kim ◽  
Harrison B. Smith ◽  
Cole Mathis ◽  
Jason Raymond ◽  
Sara I. Walker
Keyword(s):  
Scaling Laws ◽  
Network Size ◽  
Biochemical Networks ◽  
Biochemical Network ◽  
Biochemical Reactions ◽  
Global Database ◽  
Planetary Scale ◽  
Domains Of Life ◽  
Global Inventory ◽  
Life On Earth

AbstractThe application of network science to biology has advanced our understanding of the metabolism of individual organisms and the organization of ecosystems but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, we constructed biochemical networks using a global database of 28,146 annotated genomes and metagenomes, and 8,658 cataloged biochemical reactions. We uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical networks to random chemical networks reveals the observed biological scaling is not solely a product of the biochemistry shared across life on Earth. Instead, it emerges due to how the global inventory of biochemical reactions is partitioned into individuals. We show the three domains of life are topologically distinguishable, with > 80% accuracy in predicting evolutionary domain based on biochemical network size and average topology. Taken together our results point to a deeper level of organization in biochemical networks than what has been understood so far.

scholarly journals Universal scaling across biochemical networks on Earth

2019 ◽  
Vol 5 (1) ◽  
pp. eaau0149 ◽  
Author(s):  
Hyunju Kim ◽  
Harrison B. Smith ◽  
Cole Mathis ◽  
Jason Raymond ◽  
Sara I. Walker
Keyword(s):  
Scaling Laws ◽  
Network Size ◽  
Biochemical Networks ◽  
Biochemical Network ◽  
Reaction Networks ◽  
Biochemical Reaction Networks ◽  
Global Database ◽  
Universal Scaling ◽  
Planetary Scale ◽  
Domains Of Life

The application of network science to biology has advanced our understanding of the metabolism of individual organisms and the organization of ecosystems but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, we constructed biochemical networks using a global database of 28,146 annotated genomes and metagenomes and 8658 cataloged biochemical reactions. We uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical reaction networks to random reaction networks reveals that the observed biological scaling is not a product of chemistry alone but instead emerges due to the particular structure of selected reactions commonly participating in living processes. We show that the topology of biochemical networks for the three domains of life is quantitatively distinguishable, with >80% accuracy in predicting evolutionary domain based on biochemical network size and average topology. Together, our results point to a deeper level of organization in biochemical networks than what has been understood so far.

scholarly journals Scarcity of scale-free topology is universal across biochemical networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Harrison B. Smith ◽  
Hyunju Kim ◽  
Sara I. Walker
Keyword(s):  
Large Body ◽  
Biochemical Networks ◽  
Biological Organization ◽  
Scale Free ◽  
Levels Of Organization ◽  
Common Structure ◽  
Domains Of Life ◽  
Ecosystem Level ◽  
Different Levels ◽  
Organizing Principles

AbstractBiochemical reactions underlie the functioning of all life. Like many examples of biology or technology, the complex set of interactions among molecules within cells and ecosystems poses a challenge for quantification within simple mathematical objects. A large body of research has indicated many real-world biological and technological systems, including biochemistry, can be described by power-law relationships between the numbers of nodes and edges, often described as “scale-free”. Recently, new statistical analyses have revealed true scale-free networks are rare. We provide a first application of these methods to data sampled from across two distinct levels of biological organization: individuals and ecosystems. We analyze a large ensemble of biochemical networks including networks generated from data of 785 metagenomes and 1082 genomes (sampled from the three domains of life). The results confirm no more than a few biochemical networks are any more than super-weakly scale-free. Additionally, we test the distinguishability of individual and ecosystem-level biochemical networks and show there is no sharp transition in the structure of biochemical networks across these levels of organization moving from individuals to ecosystems. This result holds across different network projections. Our results indicate that while biochemical networks are not scale-free, they nonetheless exhibit common structure across different levels of organization, independent of the projection chosen, suggestive of shared organizing principles across all biochemical networks.

Scaling laws for delay-sensitive traffic in Rayleigh fading networks

2008 ◽  
Vol 464 (2096) ◽  
pp. 2187-2205 ◽  
Author(s):  
Nikhil Karamchandani ◽  
Massimo Franceschetti
Keyword(s):  
Rayleigh Fading ◽  
Scaling Laws ◽  
Scaling Limit ◽  
Network Size ◽  
Upper And Lower Bounds ◽  
Destination Node ◽  
Delay Constraint ◽  
Delay Sensitive ◽  
Remote Surveillance ◽  
Emergency Scenarios

The throughput of delay-sensitive traffic in a Rayleigh fading network is studied by adopting a scaling limit approach. The case of the study is that of a pair of nodes establishing a data stream that has routing priority over all the remaining traffic in the network. For every delay constraint, upper and lower bounds on the achievable information rate between the two endpoints of the stream are obtained as the network size grows. The analysis concerns decentralized schemes , in the sense that all nodes make next-hop decisions based only on local information, namely their channel strength to other nodes in the network and the position of the destination node. This is particularly important in a fading scenario, where the channel strength varies with time and hence pre-computing routes can be of little help. Natural applications are remote surveillance using sensor networks and communication in emergency scenarios.

scholarly journals Positive Stability Analysis and Bio-Circuit Design for Nonlinear Biochemical Networks

2013 ◽  
Vol 2013 ◽  
pp. 1-8
Author(s):  
Yonghui Sun ◽  
Zhinong Wei ◽  
Guoqiang Sun
Keyword(s):  
Stability Analysis ◽  
Equilibrium Points ◽  
Sufficient Conditions ◽  
Lyapunov Stability Theory ◽  
Positive Control ◽  
Biochemical Networks ◽  
Biochemical Network ◽  
Control Input ◽  
Convex Optimization Problem ◽  
Fuzzy Interpolation

This paper is concerned with positive stability analysis and bio-circuits design for nonlinear biochemical networks. A fuzzy interpolation approach is employed to approximate nonlinear biochemical networks. Based on the Lyapunov stability theory, sufficient conditions are developed to guarantee the equilibrium points of nonlinear biochemical networks to be positive and asymptotically stable. In addition, a constrained bio-circuits design with positive control input is also considered. It is shown that the conditions can be formulated as a solution to a convex optimization problem, which can be easily facilitated by using the Matlab LMI control toolbox. Finally, a real biochemical network model is provided to illustrate the effectiveness and validity of the obtained results.

scholarly journals Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

2009 ◽  
Vol 364 (1527) ◽  
pp. 2229-2239 ◽  
Author(s):  
Gregory P. Fournier ◽  
Jinling Huang ◽  
J. Peter Gogarten
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
Gene Trees ◽  
Individual Gene ◽  
Evolution Of Life ◽  
Domains Of Life ◽  
Life On Earth ◽  
Simple Tree

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

scholarly journals Properties of a Multidimensional Landscape Model for Determining Cellular Network Thermodynamics

2019 ◽  
Author(s):  
Joseph B. Hubbard ◽  
Michael Halter ◽  
Anne L. Plant
Keyword(s):  
Steady State ◽  
Network Control ◽  
Biochemical Networks ◽  
Biochemical Network ◽  
Thermodynamic Quantities ◽  
Dissipative Heat ◽  
Landscape Gradients ◽  
Potential Landscape ◽  
Phenotypic Responses

ABSTRACTThe steady state distributions of phenotypic responses within an isogenic population of cells result from both deterministic and stochastic characteristics of biochemical networks. A biochemical network can be characterized by a multidimensional potential landscape based on the distribution of responses and a diffusion matrix of the correlated dynamic fluctuations between N-numbers of intracellular network variables. The Boltzmann H-function defines the rate of free energy dissipation of a network system and provides a framework for determining the heat associated with the nonequilibrium steady state and its network components. We conjecture that there is an upper limit to the rate of dissipative heat produced by a biological system, and we show that the dissipative heat has a lower bound. The magnitudes of the landscape gradients and the dynamic correlated fluctuations of network variables are experimentally accessible, and through an analysis that we refer to as Thermo-Fokker-Planck (Thermo-FP), provide insight into the composition of the network and the relative thermodynamic contributions from network components. We surmise that these thermodynamic quantities allow determination of the relative importance of network components to overall network control.

scholarly journals Scaling laws in enzyme function reveal a new kind of biochemical universality

2021 ◽  
Author(s):  
Dylan C. Gagler ◽  
Bradley Karas ◽  
Chris Kempes ◽  
Aaron D. Goldman ◽  
Hyunju Kim ◽  
...  
Keyword(s):  
Scaling Laws ◽  
Chemical Compounds ◽  
Last Universal Common Ancestor ◽  
Detailed Model ◽  
Shared Set ◽  
Universal Common Ancestor ◽  
Universality Classes ◽  
Synthetic Life ◽  
Life On Earth ◽  
Enzyme Functions

AbstractAll life on Earth is unified by its use of a shared set of component chemical compounds and reactions, providing a detailed model for universal biochemistry. However, this notion of universality is specific to currently observed biochemistry and does not allow quantitative predictions about examples not yet observed. Here we introduce a more generalizable concept of biochemical universality, more akin to the kind of universality discussed in physics. Using annotated genomic datasets including an ensemble of 11955 metagenomes and 1282 archaea, 11759 bacteria and 200 eukaryotic taxa, we show how four of the major enzyme functions - the oxidoreductases, transferases, hydrolases and ligases - form universality classes with common scaling behavior in their relative abundances observed across the datasets. We verify these universal scaling laws are not explained by the presence of compounds, reactions and enzyme functions shared across all known examples of life. We also demonstrate how a consensus model for the last universal common ancestor (LUCA) is consistent with predictions from these scaling laws, with the exception of ligases and transferases. Our results establish the existence of a new kind of biochemical universality, independent of the details of the component chemistry, with implications for guiding our search for missing biochemical diversity on Earth, or other for any biochemistries that might deviate from the exact chemical make-up of life as we know it, such as at the origins of life, in alien environments, or in the design of synthetic life.

scholarly journals Scaling laws predict global microbial diversity

2016 ◽  
Author(s):  
Kenneth J Locey ◽  
Jay T Lennon
Keyword(s):  
High Throughput ◽  
Scaling Laws ◽  
Scaling Law ◽  
Molecular Data ◽  
Global Scale ◽  
Microbial Biodiversity ◽  
Domains Of Life ◽  
Community Data ◽  
Animal Community ◽  
Commonness And Rarity

Scaling laws underpin unifying theories of biodiversity and are among the most predictively powerful relationships in biology. However, scaling laws developed for plants and animals often go untested or fail to hold for microorganisms. As a result, it is unclear whether scaling laws of biodiversity will span evolutionarily distant domains of life that encompass all modes of metabolism and scales of abundance. Using a global-scale compilation of ~35,000 sites and ~5.6·106 species, including the largest ever inventory of high-throughput molecular data and one of the largest compilations of plant and animal community data, we demonstrate similar rates of scaling in commonness and rarity across microorganisms and macroscopic plants and animals. We document a universal dominance scaling law that holds across 30 orders of magnitude, an unprecedented expanse that predicts the abundance of dominant ocean bacteria. In combining this scaling law with the lognormal model of biodiversity, we predict that Earth is home to upwards one trillion (1012) microbial species. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome.

scholarly journals Assessing the viability of biochemical networks across planets

2019 ◽  
Author(s):  
Harrison B. Smith ◽  
Alexa Drew ◽  
Sara I. Walker
Keyword(s):  
Quantitative Assessment ◽  
Chemical Compounds ◽  
Biochemical Networks ◽  
Geochemical Process ◽  
Computational Tools ◽  
Planetary Protection ◽  
Methodological Foundation ◽  
The Origin Of Life ◽  
Life On Earth

AbstractThe concept of the origin of life implies that initially, life emerged from a non-living medium. If this medium was Earth’s geochemistry, then that would make life, by definition, a geochemical process. The extent to which life on Earth today could subsist outside of the geochemistry from which it is embedded is poorly quantified. By leveraging large biochemical datasets in conjunction with planetary observations and computational tools, this research provides a methodological foundation for the quantitative assessment of our biology’s viability in the context of other geospheres. Investigating a case study of alkaline prokaryotes in the context of Enceladus, we find that the chemical compounds observed on Enceladus thus far would be insufficient to allow even these extremophiles to produce the compounds necessary to sustain a viable metabolism. The environmental precursors required by these organisms provides a map for the compounds which should be prioritized for detection in future planetary exploration missions. The results of this framework have further consequences in the context of planetary protection, and hint that forward contamination may prove infeasible without meticulous intent.

scholarly journals SABIO-RK: A data warehouse for biochemical reactions and their kinetics

2007 ◽  
Vol 4 (1) ◽  
pp. 22-30 ◽  
Author(s):  
Olga Krebs ◽  
Martin Golebiewski ◽  
Renate Kania ◽  
Saqib Mir ◽  
Jasmin Saric ◽  
...  
Keyword(s):  
Systems Biology ◽  
Kinetic Data ◽  
Biochemical Networks ◽  
System Level ◽  
Kinetic Properties ◽  
Biological Processes ◽  
Biochemical Reactions ◽  
Biochemical Pathways ◽  
Application Potential ◽  
Promising Application

Abstract Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics), a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.

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