A cellular mechanism for multi-robot construction via evolutionary multi-objective optimization of a gene regulatory network

A major research challenge of multi-robot systems is to predict the emerging behaviors from the local interactions of the individual agents. Biological systems can generate robust and complex behaviors through relatively simple local interactions in a world characterized by rapid changes, high uncertainty, infinite richness, and limited availability of information. Gene Regulatory Networks (GRNs) play a central role in understanding natural evolution and development of biological organisms from cells. In this paper, inspired by biological organisms, we propose a distributed GRN-based algorithm for a multi-robot construction task. Through this algorithm, multiple robots can self-organize autonomously into different predefined shapes, and self-reorganize adaptively under dynamic environments. This developmental process is evolved using a multi-objective optimization algorithm to achieve a shorter travel distance and less convergence time. Furthermore, a theoretical proof of the system's convergence is also provided. Various case studies have been conducted in the simulation, and the results show the efficiency and convergence of the proposed method.     

Phenotypic expression of ADH regulatory genes inDrosophila melanogaster: a comparative study between a paleartic and a tropical population

In vitro ADH activity was studied inD. melanogaster males from two sets of third chromosome substitution lines, one from a paleartic population (Gigean, France), the other from a tropical population (Brazzaville, Congo). As a linear model with raw ADH activity dependent on fresh weight was significant in both sets of lines, the raw activity was adjusted by regression on weight. Two main results were found: (a) the well-known substantial intrapopulation variability; and (b) third chromosome geographical origin did not affect the mean ADH activity. Unlike the structuralAdh gene polymorphism which allows the two populations to be distinguished, the polymorphism of the third chromosome ADH regulatory genes (or more exactly their phenotypic expression) does not allow to discriminate between them. These results are discussed in the context of the adaptation ofD. melanogaster to the alcoholic substrates in light of a model proposed by Hedrick and McDonald (1980) in order to interpret variations in both structural and regulatory gene polymorphisms.     

Evolutionary pattern of the regulatory network for flower development:Insights gained from a comparison of two Arabidopsis species

Previous studies on Arabidopsis thaliana and other model plants have indicated that the development of a flower is controlled by a regulatory network composed of genes and the interactions among them.Studies on the evolution of this network will therefore help understand the genetic basis that underlies flower evolution.In this study,by reviewing the most recent published work,we added 31 genes into the previously proposed regulatory network for flower development.Thus,the number of genes reached 60.We then compared the composition,structure,and evolutionary rate of these genes between A.thaliana and one of its allies,A.lyrata.We found that two genes (FLC and MAF2) show 1∶ 2 and 2∶ 2 relationships between the two species,suggesting that they have experienced independent,post-speciation duplications.Of the remaining 58 genes,35 (60.3％) have diverged in exon-intron structure and,consequently,code for proteins with different sequence features and functions.Molecular evolutionary analyses further revealed that,although most floral genes have evolved under strong purifying selection,some have evolved under relaxed or changed constraints,as evidenced by the elevation of nonsynonymous substitution rates and/or the presence of positively selected sites.Taken together,these results suggest that the regulatory network for flower development has evolved rather rapidly,with changes in the composition,structure,and functional constraint of genes,as well as the interactions among them,being the most important contributors.     

Evolutionary pattern of the regulatory network for flower development: Insights gained from a comparison of two Arabidopsis species

Abstract Previous studies on Arabidopsis thaliana and other model plants have indicated that the development of a flower is controlled by a regulatory network composed of genes and the interactions among them. Studies on the evolution of this network will therefore help understand the genetic basis that underlies flower evolution. In this study, by reviewing the most recent published work, we added 31 genes into the previously proposed regulatory network for flower development. Thus, the number of genes reached 60. We then compared the composition, structure, and evolutionary rate of these genes between A. thaliana and one of its allies, A. lyrata. We found that two genes (FLC and MAF2) show 1: 2 and 2: 2 relationships between the two species, suggesting that they have experienced independent, post‐speciation duplications. Of the remaining 58 genes, 35 (60.3%) have diverged in exon–intron structure and, consequently, code for proteins with different sequence features and functions. Molecular evolutionary analyses further revealed that, although most floral genes have evolved under strong purifying selection, some have evolved under relaxed or changed constraints, as evidenced by the elevation of nonsynonymous substitution rates and/or the presence of positively selected sites. Taken together, these results suggest that the regulatory network for flower development has evolved rather rapidly, with changes in the composition, structure, and functional constraint of genes, as well as the interactions among them, being the most important contributors.     

Gene regulatory network from microarray data of colon cancer patients using TSK-type recurrent neural fuzzy network

In this work we applied a TSK-type recurrent neural fuzzy approach to extract regulatory relationship among genes and reconstruct gene regulatory network from microarray data. The identified signature has captured the regulatory relationship among 27 differentially expressed genes from microarray dataset. We applied three different methods viz., feed forward neural fuzzy, modified genetic algorithm and recurrent neural fuzzy, on the same data set for the inference of GRNs and the results obtained are almost comparable. In all tested cases, TRNFN identified more biologically meaningful relations. We found that 87.8% of the total interactions extracted by TRNFN are correct in accordance with the biological knowledge. Our analysis resulted in 2 major outcomes. First, upregulated genes are regulated by more genes than downregulated genes. Second, tumor activators activate other tumor activators and suppress tumor suppressers strongly in the disease environment. These findings will help to elucidate the common molecular mechanism of colon cancer, and provide new insights into cancer diagnostics, prognostics and therapy.     

Matrix metalloproteinases as target genes for gene regulatory networks driving molecular and cellular pathways related to a multistep pathogenesis of cerebrovascular disease

The present study investigated a joint contribution of matrix metalloproteinases (MMPs) genes to ischemic stroke (IS) development and analyzed interactions between MMP genes and genome-wide associated loci for IS. A total of 1288 unrelated Russians (600 IS patients and 688 healthy individuals) from Central Russia were recruited for the study. Genotyping of seven single nucleotide polymorphisms (SNPs) of MMP genes (rs1799750, rs243865, rs3025058, rs11225395, rs17576, rs486055, and rs2276109) and eight genome-wide associated loci for IS were done using Taq-Man–based assays and MALDI-TOF mass spectrometry iPLEX platform, respectively. Allele − 799T at rs11225395 of the MMP8 gene was significantly associated with a decreased risk of IS after adjustment for sex and age (OR = 0.82; 95%CI, 0.70-0.96; P = 0.016). The model-based multifactor dimensionality reduction method has revealed 21 two-order, 124 three-order, and 474 four-order gene-gene (G×G) interactions models meaningfully (P_perm < 0.05) associated with the IS risk. The bioinformatic analysis enabled establishing the studied MMP gene polymorphisms possess a clear regulatory potential and may be targeted by gene regulatory networks driving molecular and cellular pathways related to the pathogenesis of IS. In conclusion, the present study was the first to identify an association between polymorphism rs11225395 of the MMP8 gene and IS risk. The study findings also indicate that MMPs deserve special attention as a potential class of genes influencing the multistep mechanisms of cerebrovascular disease including atherosclerosis in cerebral arteries, acute cerebral artery occlusion as well as the ischemic injury of the brain and its recovery.     

Transplantation of a polyembryonic wasp embryo: a technique for transferring endoparasitic embryo into the host egg

Concealed development of many animal embryos prevents examination of development and limits the application of embryo manipulation techniques aimed at understanding developmental processes. In embryos developing in utero, such as in mammals, it is necessary to dissect embryos from the mother and, upon manipulative intervention, to implant them back into the recipient. Parasitic wasps present a promising system for understanding the evolution of early developmental processes. In basal ectoparasitic species that lay eggs on the surface of the host, it is possible to adapt embryo manipulation techniques developed in Drosophila. However, their derived endoparasitic relatives, which exhibit various modifications of developmental programs, undergo concealed development within the host body. For example, the parasitic polyembryonic wasp Copidosoma floridanum oviposits an egg into the egg of the host moth Trichoplusia ni. The host larva emerges and the parasite undergoes development within the host body, preventing embryo manipulation as a means of examining developmental regulation. Here we present a protocol for embryo transfer that allows the transplantation of C. floridanum egg into the host egg. This approach opens a new avenue in the application of various embryo manipulation techniques aimed at understanding the evolution of embryogenesis in endoparasitic Hymenoptera. In addition, this approach has potential for the development of other tools in C. floridanum, such as transgenesis and reverse genetics, which can also be extended to other endoparasitic species.     

Mutated polyadenylation signals for controlling expression levels of multiple genes in mammalian cells

A set of mutated SV40 early polyadenylation signals (SV40pA) with varying strengths is generated by mutating the AATAAA sequence in the wild-type SV40pA. They are shown to control the expression level of a gene over a 10-fold range using luciferase reporter genes in transient transfection assays. The relative strength of these SV40pA variants remains similar under three commonly used mammalian promoters and in five mammalian cell lines. Application of SV40pA variants for controlling expression level of multiple genes is demonstrated in a study of monoclonal antibody (mAb) synthesis in mammalian cells. By using SV40pA variants of different strengths, the expression of light chain (LC) and heavy chain (HC) genes encoded in a single vector is independently altered which results in different ratios of LC to HC expression spanning a range from 0.24 to 16.42. The changes in gene expression are determined by measuring mRNA levels and intracellular LC and HC polypeptides. It is found that a substantial decrease of HC expression, which increases the LC/HC mRNA ratio, only slightly reduces mAb production. However, reducing the LC expression by a similar magnitude, which decreases the LC/HC mRNA ratio results in a sharp decline of mAb production to trace amounts. This set of SV40pA variants offers a new tool for accurate control of the relative expression levels of multiple genes. It will have wide-ranging applications in fields related to the study of biosynthesis of multi-subunit proteins, proteomic research on protein interactions, and multi-gene metabolic engineering.     

Simultaneous expression of glutaryl-7-aminocephalosporanic acid acylase gene and lysis genes of phage λ in a recombinant E. coli

Glutaryl-7-aminocephalosporanic acid acylase (GLA), recommended for use in the form of immobilized-enzyme, is one of the two key enzymes in the two-step synthesis of 7-aminocephalosporanic acid. For simplifying the process of cell disruption and immobilization, the lysis genes of phage λ (S⁻RRz) with the S amber mutation were designed to introduce into the over-expression system of GLA. A novel recombinant strain, E. coli TB1/pMKC-AS, simultaneously containing the maltose binding protein gene (malE), the lysis genes (S⁻RRz) and the target GLA gene (Acy) in a same operon, was successfully constructed. Under neutral pH conditions, cell growth and GLA activity of TB1/pMKC-AS was not affected by the presence of the lysis genes, however, autolysis phenomenon was observed under weak alkaline conditions. Through pH control and fed-batch culture, the GLA activity of TB1/pMKC-AS reached as high as 6810 U/L with 24.8 g/L dry cell density (OD₆₀₀ = 67.9) in a 5 L fermentor. In contrast to the cells of E. coli TB1/pMKC-Acy without the lysis genes, the mild EDTA/Tris buffer (pH 8.0) can cause the lysis of the cells of TB1/pMKC-AS containing the lysis genes. Correspondingly, a mild pH 9.0/42 °C incubation method was developed for conveniently degrading the recombinant cells of TB1/pMKC-AS, based on the expression of the lysis genes. Further experiments showed that the cell lysate after the mild incubation disruption can be directly immobilized by 10% polyacrylamide to make the immobilized enzymes. In comparison with the immobilized GLA from TB1/pMKC-Acy, the immobilized cell lysate of TB1/pMKC-AS has the similar characteristics of catalysis stability, implying a great potential for industrial application of the lysis genes-assisted cell disruption.     

Regulation of interlocking gene regulatory network subcircuits by a small molecule inhibitor of retinoblastoma protein (RB) phosphorylation: Cancer cell expression of HLA-DR

The induction of the major histocompatibility (MHC), antigen-presenting class II molecules by interferon-gamma, in solid tumor cells, requires the retinoblastoma tumor suppressor protein (Rb). In the absence of Rb, a repressosome blocks the access of positive-acting, promoter binding proteins to the MHC class II promoter. However, a complete molecular linkage between Rb expression and the disassembly of the MHC class II repressosome has been lacking. By treating A549 lung carcinoma cells with a novel small molecule that prevents phosphorylation-mediated, Rb inactivation, we demonstrate that Rb represses the synthesis of an MHC class II repressosome component, YY1. The reduction in YY1 synthesis correlates with the advent of MHC class II inducibility; with loss of YY1 binding to the promoter of the HLA–DRA gene, the canonical human MHC class II gene; and with increased Rb binding to the YY1 promoter. These results support the concept that the Rb gene regulatory network (GRN) subcircuit that regulates cell proliferation is linked to a GRN subcircuit regulating a tumor cell immune function.     

The genes and enzymes for the catabolism of galactitol,D-tagatose,and related carbohydrates in<Emphasis Type="Italic"> Klebsiella oxytoca</Emphasis> M5a1 and other enteric bacteria display convergent evolution

Enteric bacteria (Enteriobacteriaceae) carry on their single chromosome about 4000 genes that all strains have in common (referred to here as obligatory genes), and up to 1300 facultative genes that vary from strain to strain and from species to species. In closely related species, obligatory and facultative genes are orthologous genes that are found at similar loci. We have analyzed a set of facultative genes involved in the degradation of the carbohydrates galactitol, D-tagatose, D-galactosamine and N-acetyl-galactosamine in various pathogenic and non-pathogenic strains of these bacteria. The four carbohydrates are transported into the cell by phosphotransferase (PTS) uptake systems, and are metabolized by closely related or even identical catabolic enzymes via pathways that share several intermediates. In about 60% of Escherichia coli strains the genes for galactitol degradation map to a gat operon at 46.8 min. In strains of Salmonella enterica, Klebsiella pneumoniae and K. oxytoca, the corresponding gat genes, although orthologous to their E. coli counterparts, are found at 70.7 min, clustered in a regulon together with three tag genes for the degradation of D-tagatose, an isomer of D-fructose. In contrast, in all the E. coli strains tested, this chromosomal site was found to be occupied by an aga/kba gene cluster for the degradation of D-galactosamine and N-acetyl-galactosamine. The aga/kba and the tag genes were paralogous either to the gat cluster or to the fru genes for degradation of D-fructose. Finally, in more then 90% of strains of both Klebsiella species, and in about 5% of the E. coli strains, two operons were found at 46.8 min that comprise paralogous genes for catabolism of the isomers D-arabinitol (genes atl or dal) and ribitol (genes rtl or rbt). In these strains gat genes were invariably absent from this location, and they were totally absent in S. enterica. These results strongly indicate that these various gene clusters and metabolic pathways have been subject to convergent evolution among the Enterobacteriaceae. This apparently involved recent horizontal gene transfer and recombination events, as indicated by major chromosomal rearrangements found in their immediate vicinity.Communicated by A. Kondorosi