Gut content metabarcoding reveals potential importance of fisheries discards consumption in marine fauna

Fisheries discards have become a source of concern for the perennation of marine resources. To reduce discards, the European Union adopted a Landing Obligation under the reform of its Common Fisheries Policy. However, food web consequences of reducing discards remain uncertain since their degree and pathway of reintegration are understudied. We used multi-marker DNA metabarcoding of gut contents and an ecological network approach to quantify marine fauna reliance on discarded fish and functional importance of discard consumers in coastal fishing grounds. We show that potential discard consumption is widespread across fish and invertebrates, but particularly important for decapods which were also pinpointed as functionally important. Potential discard consumption may represent up to 66% of all interactions involving fish prey in the reconstructed network. We highlight that discard reliance may be more important than previously assessed in some fishing areas and support functionally important taxa. While reducing discarding remains a conservation priority, it is crucial to understand discards reintegration in marine food webs to anticipate changes in the context of an ecosystem approach to fisheries management.

More Tolerant Reconstructed Networks Using Self-Healing against Attacks in Saving Resource

Complex network infrastructure systems for power supply, communication, and transportation support our economic and social activities; however, they are extremely vulnerable to frequently increasing large disasters or attacks. Thus, the reconstruction of a damaged network is more advisable than an empirically performed recovery of the original vulnerable one. To reconstruct a sustainable network, we focus on enhancing loops so that they are not trees, which is made possible by node removal. Although this optimization corresponds with an intractable combinatorial problem, we propose self-healing methods based on enhancing loops when applying an approximate calculation inspired by statistical physics. We show that both higher robustness and efficiency are obtained in our proposed methods by saving the resources of links and ports when compared to ones in conventional healing methods. Moreover, the reconstructed network can become more tolerant than the original when some damaged links are reusable or compensated for as an investment of resource. These results present the potential of network reconstruction using self-healing with adaptive capacity in terms of resilience.

Systemic Risk Contagion in Reconstructed Financial Credit Network within Banking and Firm Sectors on DebtRank Based Model

This paper is dedicated to building a multilayer financial network within banking sectors and firm sectors (nonbanking) on the balance sheet of two types of agents and to assessing systemic risk contagion in the reconstructed network. Two propagation channels due to interbank credit and counterparty risk via banks’ loans to firms are comprehensively taken into account in systemic risk contagion assessment, which is based on the DebtRank model by analyzing the relative loss of each bank’s equity and the vulnerability of the network. The computational simulation on how systemic risk contagious process evolves has been conducted, where the possible influential factors of network structure, agent’s initial risk status, external shock ratio, liquidity flow rate, and different layers of the network are considered. The findings show that the reconstructed network is absolutely vulnerable under the assumed market circumstance without any bailouts and the risk contagion process shows nonlinear behavior. Specifically, when the average degree of the network and the external shock ratio increases, the risk contagion speed becomes relatively high and the resulting negative effects on the network are more intense. Besides, risks originating from the failed firms in bank-firm layer should place more negative effect on the financial system than that only happening in interbank market. Different liquidity rates in financial market could lead to obvious discrepancy of the risk contagion speed and the extent of asset loss. Additionally, the two layers of the network have diverse influences on risk contagious process resulting in totally different banks’ status in each layer.

The First Reconstruction of Intercellular Interaction Network in Mus musculus Immune System

Intercellular interactions play an important role in regulating communications of cells with each other. So far, many studies have been done with both experimental and computational approaches in this field. Therefore, in order to investigate and analyze the intercellular interactions, use of network reconstruction has attracted the attention of many researchers recently. The intercellular interaction network was reconstructed using receptor and ligand interaction dataset and gene expression data of the first phase of the immunological genome project. In the reconstructed network, there are 9271 communications between 162 cells which were created through 460 receptor-ligand interactions. The results indicate that cells of hematopoietic lineages use fewer communication pathways for interacting with each other and the most network communications belong to non-hematopoietic stromal cells and macrophages. The results indicated the importance of the communication of stromal cells with immune cells and also high specificity of genes expression in these cells. The stromal cells have the most autocrine communication, and interactions between the wnt5a with the Ror1/2 and Fzd5a among the stromal lineage cells are abundant.

Whole-transcriptome causal network inference with genomic and transcriptomic data

Reconstruction of causal gene networks can distinguish regulators from targets and reduce false positives by integrating genetic variations. Its recent developments in speed and accuracy have enabled whole-transcriptome causal network inference on a personal computer. Here we demonstrate this technique with program Findr on 3,000 genes from the Geuvadis dataset. Subsequent analysis reveals major hub genes in the reconstructed network.

miRNA–mRNA network involved in folliculogenesis interactome: systems biology approach

At later phases of folliculogenesis, the mammalian ovarian follicle contains layers of granulosa cells surrounding an antral cavity. To better understand the molecular basis of follicular growth and granulosa cell maturation, we study transcriptome profiling of granulosa cells from small (<5 mm) and large (>10 mm) bovine follicles using simultaneous method of Affymetrix microarrays (24,128 probe sets) and RNA-Seq data sets. This study proposes a computational method to discover the functional miRNA–mRNA regulatory modules, that is, groups of miRNAs and their target mRNAs that are believed to take part cooperatively in post-transcriptional gene regulation under specific conditions. The reconstructed network was named Integrated miRNA–mRNA Bipartite Network. 277 genes and 6 key modules were disclosed through clustering for mRNA master list. The 66 genes are among the genes that belong to at least two modules. All these genes, being involved in at least one of the phenomena, namely cell survival, proliferation, metastasis and apoptosis, have an overexpression pattern (P < 0.01). For miRNA master list, a total of 172 sequences were differentially expressed (P < 0.01) between dominant (large) and each of subordinate (small) follicles. Within the follicle, these miRNAs were predominantly expressed in mural granulosa cells. Finally, predicted and validated targets of these miRNAs enriched in dominant (large) follicles were identified, which are mapped to signaling pathways involved in follicular cell proliferation, steroidogenesis, PI3K/AKT/mTOR and Ras/Raf/MEK/ERK. The identification of miRNAs and their target mRNAs and the construction of their regulatory networks may give new insights into biological procedures.