Complex networks: the key to systems biology

Costa, Luciano da Fontoura; Rodrigues, Francisco A.; Cristino, Alexandre S.

doi:10.1590/s1415-47572008000400001

Cited by 77 publications

(48 citation statements)

References 81 publications

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“…Only the alignments passing a threshold of 70% identity for each PSSM were considered as significant matches. We used concepts of graph theory and complex networks [39]. …”

Section: Methodsmentioning

confidence: 99%

Genes involved in thoracic exoskeleton formation during the pupal-to-adult molt in a social insect model, Apis mellifera

et al. 2013

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BackgroundThe insect exoskeleton provides shape, waterproofing, and locomotion via attached somatic muscles. The exoskeleton is renewed during molting, a process regulated by ecdysteroid hormones. The holometabolous pupa transforms into an adult during the imaginal molt, when the epidermis synthe3sizes the definitive exoskeleton that then differentiates progressively. An important issue in insect development concerns how the exoskeletal regions are constructed to provide their morphological, physiological and mechanical functions. We used whole-genome oligonucleotide microarrays to screen for genes involved in exoskeletal formation in the honeybee thoracic dorsum. Our analysis included three sampling times during the pupal-to-adult molt, i.e., before, during and after the ecdysteroid-induced apolysis that triggers synthesis of the adult exoskeleton.ResultsGene ontology annotation based on orthologous relationships with Drosophila melanogaster genes placed the honeybee differentially expressed genes (DEGs) into distinct categories of Biological Process and Molecular Function, depending on developmental time, revealing the functional elements required for adult exoskeleton formation. Of the 1,253 unique DEGs, 547 were upregulated in the thoracic dorsum after apolysis, suggesting induction by the ecdysteroid pulse. The upregulated gene set included 20 of the 47 cuticular protein (CP) genes that were previously identified in the honeybee genome, and three novel putative CP genes that do not belong to a known CP family. In situ hybridization showed that two of the novel genes were abundantly expressed in the epidermis during adult exoskeleton formation, strongly implicating them as genuine CP genes. Conserved sequence motifs identified the CP genes as members of the CPR, Tweedle, Apidermin, CPF, CPLCP1 and Analogous-to-Peritrophins families. Furthermore, 28 of the 36 muscle-related DEGs were upregulated during the de novo formation of striated fibers attached to the exoskeleton. A search for cis-regulatory motifs in the 5′-untranslated region of the DEGs revealed potential binding sites for known transcription factors. Construction of a regulatory network showed that various upregulated CP- and muscle-related genes (15 and 21 genes, respectively) share common elements, suggesting co-regulation during thoracic exoskeleton formation.ConclusionsThese findings help reveal molecular aspects of rigid thoracic exoskeleton formation during the ecdysteroid-coordinated pupal-to-adult molt in the honeybee.

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“…Only the alignments passing a threshold of 70% identity for each PSSM were considered as significant matches. We used concepts of graph theory and complex networks [39]. …”

Section: Methodsmentioning

confidence: 99%

Genes involved in thoracic exoskeleton formation during the pupal-to-adult molt in a social insect model, Apis mellifera

et al. 2013

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“…3 In the present work, we study this system for parameter and state estimation along with structure identification with a 5-variable S-system in-lieu of the model Eq. (18) .…”

Section: Circadian Oscillations Of Period Protein In Drosophilamentioning

confidence: 99%

“…Complex behavior observed in biological systems are manifested through interaction networks of biomolecules in the form of gene regulatory networks, metabolic pathways and signaling cascades [1][2][3] . The presence of highly nonlinear interactions makes mathematical modeling of such systems a difficult task.…”

Section: Introductionmentioning

confidence: 99%

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Inverse problem studies of biochemical systems with structure identification of S-systems by embedding training functions in a genetic algorithm

Sarode

Kumar

Kulkarni

2016

Mathematical Biosciences

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“…Application of the CNT has been increasing since the twentieth century, with extensive studies in social sciences [6], computer science [7], transport [8], and biological sciences [9]. In particular, the CNT has been increasingly accepted in ecological studies over the last 17 years, and its development is fast and consistent [10], being a robust tool for ecosystem stability analysis, with possible applications in biodiversity and conservation [11], and as an indicator of the ecosystem health [1].…”

Section: Introductionmentioning

confidence: 99%

Heavy metal biomagnification and genotoxic damage in two trophic levels exposed to mine tailings: a network theory approach

Cervantes-Ramírez¹,

Ramírez-López²,

Mussali-Galante³

et al. 2018

Rev. Chil. de Hist. Nat.

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Background: The analysis of the negative effects of environmental metal pollution is complex and difficult to assess, because the great number of variables and levels of biological organization involved. Therefore, an integral interpretation of the structure of ecological interactions from the multifactorial toxicological vision can be achieved by the use of new analysis tools, such as the complex network theory analysis (CNT). Results: Our results demonstrated that the trophic level has an effect on metal enrichment, being the detritivores who presented the highest bioaccumulation levels in comparison to plants, as well as higher biomagnification levels in the soil-plant-detritivores relationship. Also, Vachellia farnesiana displayed greater sensitivity to genotoxic damage than Eisenia fetida. Finally, the analysis of complex networks showed that detritivores are the key link in this dynamics, on which the interactions between heavy metals, plant and detritivores depend. Conclusions: This study shows that there is an effect of the study site on heavy metal bioaccumulation and DNA damage induction, and that these responses are particular to each species and to each bioaccumulated metal, which in turn reveals specific sensitivity for each trophic level. Moreover, the application of CNT methodology allowed us to clarify in this particular system, the interaction types and the principal components of the trophic structure.

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Complex networks: the key to systems biology

Cited by 77 publications

References 81 publications

Genes involved in thoracic exoskeleton formation during the pupal-to-adult molt in a social insect model, Apis mellifera

Genes involved in thoracic exoskeleton formation during the pupal-to-adult molt in a social insect model, Apis mellifera

Inverse problem studies of biochemical systems with structure identification of S-systems by embedding training functions in a genetic algorithm

Heavy metal biomagnification and genotoxic damage in two trophic levels exposed to mine tailings: a network theory approach

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