On the Origin of Biomolecular Networks

Janwa, Heeralal; Massey, Steven E.; Velev, Julian P.; Mishra, Bud

doi:10.3389/fgene.2019.00240

Cited by 20 publications

(25 citation statements)

References 127 publications

(193 reference statements)

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Section: Resultsmentioning

confidence: 99%

“…This model of a bio-molecular signaling game implies that the first signaling games were played between bio-molecules in the earliest life forms, once the bio-molecules were large enough to exert specificity [ 33 ] [ 14 ] [ 34 ]. This in turn implies that ‘meaning’ first arose from the primordial soup, as the first signal was strategically sent, between a pair of replicating macro-molecules.…”

Section: Resultsmentioning

confidence: 99%

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How Signaling Games Explain Mimicry at Many Levels: From Viral Epidemiology to Human Sociology

Casey¹,

Massey²,

Mishra³

2020

Preprint

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Mimicry is exhibited in multiple scales, ranging from molecular, to organismal, and then to human society. ‘Batesian’ type mimicry entails a conflict of interest between sender and receiver, reflected in a deceptive mimic signal. ‘Mullerian’ type mimicry occurs when there is perfect common interest between sender and receiver, manifested by an honest co-mimic signal. Using a signaling games approach, simulations show that invasion by Batesian mimics will make Mullerian mimicry unstable, in a coevolutionary chase. We use these results to better understand the deceptive strategies of SARS-CoV-2 and their key role in the COVID-19 pandemic. At the biomolecular level, we explain how cellularization promotes Mullerian molecular mimicry, and discourages Batesian molecular mimicry. A wide range of processes analogous to cellularization are presented; these might represent a manner of reducing oscillatory instabilities. Lastly, we identify examples of mimicry in human society, that might be addressed using a signaling game approach.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

How Signaling Games Explain Mimicry at Many Levels: From Viral Epidemiology to Human Sociology

Casey¹,

Massey²,

Mishra³

2020

Preprint

Self Cite

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“…The weighted HITS algorithm has yielded important information about biomolecular networks [37][38][39][40][41][42][43][44][45]. For network topology, we refer to [46], and for the latest on the origin of biomolecular networks, topological, combinatorial, and spectral methods, we refer to [47].…”

Section: Sparse Network and The Weighted Hits Algorithmmentioning

confidence: 99%

Network Analysis of Gene Transcriptions of Arabidopsis thaliana in Spaceflight Microgravity

Manian

Orozco-Sandoval

Gangapuram

et al. 2021

Genes

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The transcriptomic datasets of the plant model organism Arabidopsis thaliana grown in the International Space Station provided by GeneLab have been mined to isolate the impact of spaceflight microgravity on gene expressions related to root growth. A set of computational tools is used to identify the hub genes that respond differently in spaceflight with controlled lighting compared to on the ground. These computational tools based on graph-theoretic approaches are used to infer gene regulatory networks from the transcriptomic datasets. The three main algorithms used for network analyses are LASSO, Pearson correlation, and the HITS algorithm. Graph-based spectral analyses reveal distinct properties of the spaceflight microgravity networks for the WS, Col-0, and mutant phyD ecotypes. The set of hub genes that are significantly altered in spaceflight microgravity are mainly involved in cell wall synthesis, protein transport, response to auxin, stress responses, and catabolic processes. Network analysis highlights five important root growth-regulating hub genes that have the highest outdegree distribution in spaceflight microgravity networks. These concerned genes coding for proteins are identified from the Gene Regulatory Networks (GRNs) corresponding to spaceflight total light environment. Furthermore, network analysis uncovers genes that encode nucleotide-diphospho-sugar interconversion enzymes that have higher transcriptional regulation in spaceflight microgravity and are involved in cell wall biosynthesis.

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“…Network tree analysis is a new approach for examining relationships between empirical networks 4,60,61 . In the context of this study, the approach may help to reveal the dynamics of pathway loss during genome reduction.…”

Section: Network Tree Analysismentioning

confidence: 99%

Synergism between the Black Queen effect and the proteomic constraint on genome size reduction in the photosynthetic picoeukaryotes

Derilus¹,

Rahman²,

Piñero³

et al. 2020

Sci Rep

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The photosynthetic picoeukaryotes (PPEs) comprise a rare example of free-living eukaryotes that have undergone genome reduction. Here, we examine a duality in the process; the proposed driver of genome reduction (the Black Queen hypothesis, BQH), and the resultant impact of genome information loss (the Proteomic Constraint hypothesis, PCH). The BQH predicts that some metabolites may be shared in the open ocean, thus driving loss of redundant metabolic pathways in individual genomes. In contrast, the PCH predicts that as the information content of a genome is reduced, the total mutation load is also reduced, leading to loss of DNA repair genes due to the resulting reduction in selective constraint. Consistent with the BQH, we observe that biosynthetic pathways involved with soluble metabolites such as amino acids and carotenoids are preferentially lost from the PPEs, in contrast to biosynthetic pathways involved with insoluble metabolites, such as lipids, which are retained. Consistent with the PCH, a correlation between proteome size and the number of DNA repair genes, and numerous other informational categories, is observed. While elevated mutation rates resulting from the loss of DNA repair genes have been linked to reduced effective population sizes in intracellular bacteria, this remains to be established. This study shows that in microbial species with large population sizes, an underlying factor in modulating their DNA repair capacity appears to be information content. Photosynthetic picoeukaryotes (PPEs) are single celled eukaryotic algae of cell size less than 3 µm in diameter 1. Their individual cell size is much reduced compared to other eukaryotes, and comparable to Prochlorococcus and Synechococcus picocyanobacteria, which have also undergone cell size reduction (cell size <2 µm 2 ,). They are typically motile and found in the oceanic euphotic zone 3,4. Molecular 5 and metagenomic 6-9 analyses show that PPEs possess a global distribution. While factors which affect the distribution of PPEs are not well understood 3 , temperature and dissolved oxygen appear to have a role 8. There is evidence of the importance of PPEs in biogeochemical processes such as carbon fixation 6,10 , despite their low numerical abundance compared to cyanobacteria 10. The reduction in cell size of both marine PPEs and picocyanobacteria has occurred concomitantly with a reduction in genome size. These two groups of photosynthetic microbes represent rare examples of free-living organisms that have undergone reduction in genome size, however the evolutionary forces and environmental factors leading to genome reduction in these two lineages are not well understood 11,12. While these forces may be similar given their common habitat, it is unclear if they represent a case of convergent evolution, until the imperatives behind cell and genome size reduction have been determined in both groups. One potential explanation is that the cell surface/volume ratio is increased upon reduction in cell size, which enhances nutrient uptake 13. Thi...

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On the Origin of Biomolecular Networks

Cited by 20 publications

References 127 publications

How Signaling Games Explain Mimicry at Many Levels: From Viral Epidemiology to Human Sociology

How Signaling Games Explain Mimicry at Many Levels: From Viral Epidemiology to Human Sociology

Network Analysis of Gene Transcriptions of Arabidopsis thaliana in Spaceflight Microgravity

Synergism between the Black Queen effect and the proteomic constraint on genome size reduction in the photosynthetic picoeukaryotes

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