Nonlinear Relationship and Its Evolutionary Trace between Node Degree and Average Path Length of China Aviation Network Based on Complex Network

In order to reveal the complex network characteristics and evolution principle of China aviation network,the relationship between the node degree and the average path length of China aviation network in 1988,1994,2001,2008 and 2015 was studied.According to the theory and method of complex network,the network system was constructed with the city where the airport was located as the network node and the airline as the edge of the network.On the basis of the statistical data,the node average path length of China aviation network in 1988,1994,2001,2008 and 2015 was calculated.Through regression analysis,it was found that the node degree had a logarithmic relationship with the average length of node path,and the two parameters of the logarithmic relationship had linear evolutionary trace.Key word:China aviation network,complex network,node degree,average length of node path,logarithmic relationship,evolutionary trace.

Nonlinear Relationship and Its Evolutionary Trace between Average Degree and Average Path Length of Edge Vertices of China Aviation Network Based on Complex Network

In order to reveal the complex network characteristics and evolution principle of China aviation network,the relationship between the average degree and the average path length of edge vertices of China aviation network in 1988,1994,2001,2008 and 2015 was studied.According to the theory and method of complex network,the network system was constructed with the city where the airport was located as the network node and the airline as the edge of the network.On the basis of the statistical data,the average degree and average path length of edge vertices of China aviation network in 1988,1994,2001,2008 and 2015 were calculated.Through regression analysis,it was found that the average degree had a logarithmic relationship with the average path length of edge vertices and the two parameters of the logarithmic relationship had linear evolutionary trace.

Homology modeling and evolutionary trace analysis of superoxide dismutase from extremophile Acidithiobacillus ferrooxidans

The gene sod in Acidithiobacillusferrooxidans may play a crucial role in its tolerance to the extremely acidic, toxic and oxidative environment of bioleaching. For insight into the anti-toxic mechanism of the bacteria, a three-dimensional （3D） molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and its key residues were further detected by evolutionary trace analysis. Through these procedures, some trace residues were identified and spatially clustered. Among them, the residues of Asn38, Glyl03 and Glul61 are randomly scattered throughout the mapped structure; interestingly, the other residues are all distinctly clustered in a subgroup near Fe atom. From these results, this gene can be confirmed at 3D level to encode the Fe-depending superoxide dismutase and subsequently play an anti-toxic role. Furthermore, the detected key residues around Fe binding site can be conjectured to be directly responsible for Fe binding and catalytic function.

Evolutionary trace analysis of eukaryotic DNA topoisomerase I superfamily:Identification of novel antitumor drug binding site

The studies of novel inhibitors of DNA topoisomerase I(Topo I)have already be-come very promising in cancer chemotherapy.Identifying the new drug-binding residues is playing an important role in the design and optimization of Topo I inhibitors.The designed com-pounds may have novel scaffolds,thus will be helpful to overcome the toxicities of current camptothecin(CPT)drugs and may provide a solution to cross resistance with these drugs.Mul-tiple sequence alignments were performed on eukaryotic DNA topoisomerase I superfamily and thus the evolutionary tree was constructed.The Evolutionary Trace method was applied to iden-tify functionally important residues of human Topo I.It has been demonstrated that class-specific hydrophobic residues Ala351,Met428,Pro431 are located around the 7,9-position of CPT,indi-cating suitable substitution of hydrophobic group on CPT will increase antitumor activity.The conservative residue Lys436 in the superfamily is of particular interest and new CPT derivatives designed based on this residue may greatly increase water solubility of such drugs.It has also been demonstrated that the residues Asn352 and Arg364 were conservative in the superfamily,whose mutation will render CPT resistance.As our molecular docking studies demonstrated they did not make any direct interaction with CPT,they are important drug-binding site residues for future design of novel non-camptothecin lead compounds.This work provided a strong basis for the design and synthesis of novel highly potent CPT derivatives and virtual screening for novel lead compounds.

Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes

Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging.In this study,we developed a sequence-based functional metagenomics procedure for mining the diversity of copper(Cu)resistance gene copA in global microbiomes,by combining the metagenomic assembly technology,local BLAST,evolutionary trace analysis(ETA),chemical synthesis,and conventional functional genomics.In total,87 metagenomes were collected from a public database and subjected to copA detection,resulting in 93,899 hits.Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates,which were further subjected to ETA.Eventually,175 novel copA sequences of high quality were discovered.Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins,with 55 sequences from totally unknown species.Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli(DcopA).The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake.One recombinant harboring copA-like 15(copAL15)successfully restored Cu resistance of the host with a substantially enhanced Cu uptake.Two novel copA genes were fused with the gfp gene and expressed in E.coli for microscopic observation.Imaging results showed that they were successfully expressed and their proteins were localized to the membrane.The results here greatly expand the diversity of known CopA proteins,and the sequence-based procedure developed overcomes biases in length,screening methods,and abundance of conventional functional metagenomics.