Optimization models for high-speed train unit routing problems

Train unit routing problem determines the number of train units needed to carry out involved trips, which is a significant part of railway operation cost. In this paper, we focus on high-speed train unit routing problems, in which maintenance resource constraints both on time and distance are taken into account. Based on a connection network, this paper first proposes a general train unit routing model. Then, the general model is specialized to meet the circulation and maintenance conditions of high-speed train units in China, which is based on a special connection network with a two-day time horizon. A strategy is proposed to reduce the scale of the connection network, which improves the model's solvability. Furthermore, an extension on multi-depot train unit routing problem is discussed. Finally, numerical experiments based on the real data of Chinese high-speed railway are carried out to verify the effectiveness and efficiency of the proposed mode and method.Accepted Author ManuscriptTransport and Plannin

Investigation of the Rheological Properties and Chemical Structure of Asphalt under Multiple Aging Conditions of Heat, UV and Aqueous Solution

During the service period, asphalt materials are affected by various natural factors, including heat, ultraviolet light, oxygen and moisture, etc., resulting in the reduction of pavement performance, the increase of pavement distress and shortening of service life. This study aims to investigate the aging performance of asphalt under multiple aging conditions of heat, UV and aqueous solution. Thermal-oxygen aging, UV aging and hydrostatic erosion tests were carried out sequentially on asphalt. The rheological properties, chemical structure and element composition of asphalt were characterized before and after aging, and the effect mechanism of multiple conditions was discussed. The results show that the multiple conditions of heat and UV can increase the rutting resistance and weaken the cracking resistance of asphalt. However, the effect degree of UV decreases gradually with the deepening of aging degree. Additionally, the effect of water on the physicochemical properties is less than that of UV; however, water can increase the sensitivity of physicochemical properties to UV. In summary, this study explored the short-term cycling effect of heat, light and water on asphalt and provided an idea for simulation test of asphalt under multiple aging condition.Materials and Environmen

A P450 gene associated with robust resistance to DDT in ciliated protozoan, Tetrahymena thermophila by efficient degradation

Analysis of metabolic mechanisms of dichlorodiphenyltrichloroethane (DDT) accumulation and degradation in microorganisms, which could be used to reduce its hazard to higher organisms at the higher in the food chain, have not been investigated. Robust resistance to DDT (grows well in 256 mg/L DDT) and a surprising ability to degrade DDT (more than 70% DDT within 4 h) were found in the ciliated protozoan Tetrahymena thermophila. A P450 gene (CYP5013C2) was found to respond specifically to DDT treatment. In the presence of 256 mg/L DDT, cells with overexpressing CYP5013C2 (p450-OE) grew faster and degraded DDT more efficiently than wild-type (WT) cells, while cells with CYP5013C2 partially knocked down (p450-KD) grew slower and exhibited reduced ability to degrade DDT compared to \NT cells. Both dichlorodiphenyldichloroethylene (DDE) and dichlorodiphenyldichloroethane (DOD) were detected in cells after exposure to DDT, and the concentration of ODD in the p450-OE strain gradually decreased from 0.5 to 4h. Thus, we argue that this P450 gene (CYP5013C2), by efficiently degrading DDT to DDD, is associated with robust resistance to DDT in Tetrahymena, and that a strain overexpressing this gene has the potential to serve as bioreactor that degrades environmental DDT. (C) 2014 Elsevier B.V. All rights reserved.Analysis of metabolic mechanisms of dichlorodiphenyltrichloroethane (DDT) accumulation and degradation in microorganisms, which could be used to reduce its hazard to higher organisms at the higher in the food chain, have not been investigated. Robust resistance to DDT (grows well in 256 mg/L DDT) and a surprising ability to degrade DDT (more than 70% DDT within 4 h) were found in the ciliated protozoan Tetrahymena thermophila. A P450 gene (CYP5013C2) was found to respond specifically to DDT treatment. In the presence of 256 mg/L DDT, cells with overexpressing CYP5013C2 (p450-OE) grew faster and degraded DDT more efficiently than wild-type (WT) cells, while cells with CYP5013C2 partially knocked down (p450-KD) grew slower and exhibited reduced ability to degrade DDT compared to \NT cells. Both dichlorodiphenyldichloroethylene (DDE) and dichlorodiphenyldichloroethane (DOD) were detected in cells after exposure to DDT, and the concentration of ODD in the p450-OE strain gradually decreased from 0.5 to 4h. Thus, we argue that this P450 gene (CYP5013C2), by efficiently degrading DDT to DDD, is associated with robust resistance to DDT in Tetrahymena, and that a strain overexpressing this gene has the potential to serve as bioreactor that degrades environmental DDT. (C) 2014 Elsevier B.V. All rights reserved

Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics

The ciliated protozoan Tetrahymena thermophila is a useful unicellular model organism for studies of eukaryotic cellular and molecular biology. Researches on T. thermophila have contributed to a series of remarkable basic biological principles. After the macronuclear genome was sequenced, substantial progress has been made in functional genomics research on T. thermophila, including genome-wide microarray analysis of the T. thermophila life cycle, a T. thermophila gene network analysis based on the microarray data and transcriptome analysis by deep RNA sequencing. To meet the growing demands for the Tetrahymena research community, we integrated these data to provide a public access database: Tetrahymena functional genomics database (TetraFGD). TetraFGD contains three major resources, including the RNA-Seq transcriptome, microarray and gene networks. The RNA-Seq data define gene structures and transcriptome, with special emphasis on exon-intron boundaries; the microarray data describe gene expression of 20 time points during three major stages of the T. thermophila life cycle; the gene network data identify potential gene-gene interactions of 15 049 genes. The TetraFGD provides user-friendly search functions that assist researchers in accessing gene models, transcripts, gene expression data and gene-gene relationships. In conclusion, the TetraFGD is an important functional genomic resource for researchers who focus on the Tetrahymena or other ciliates.The ciliated protozoan Tetrahymena thermophila is a useful unicellular model organism for studies of eukaryotic cellular and molecular biology. Researches on T. thermophila have contributed to a series of remarkable basic biological principles. After the macronuclear genome was sequenced, substantial progress has been made in functional genomics research on T. thermophila, including genome-wide microarray analysis of the T. thermophila life cycle, a T. thermophila gene network analysis based on the microarray data and transcriptome analysis by deep RNA sequencing. To meet the growing demands for the Tetrahymena research community, we integrated these data to provide a public access database: Tetrahymena functional genomics database (TetraFGD). TetraFGD contains three major resources, including the RNA-Seq transcriptome, microarray and gene networks. The RNA-Seq data define gene structures and transcriptome, with special emphasis on exon-intron boundaries; the microarray data describe gene expression of 20 time points during three major stages of the T. thermophila life cycle; the gene network data identify potential gene-gene interactions of 15 049 genes. The TetraFGD provides user-friendly search functions that assist researchers in accessing gene models, transcripts, gene expression data and gene-gene relationships. In conclusion, the TetraFGD is an important functional genomic resource for researchers who focus on the Tetrahymena or other ciliates

Identification and characterization of the arsenite methyltransferase from a protozoan, Tetrahyrnena pyriformis

Arsenic (As) methylation in aquatic microbes plays a major role in the biogeochemistry of As. Protozoa, especially the free-living freshwater species, are important players in aquatic ecological health. In this study, an arsenite (As(III)) methyltransferase, TpyArsM, was identified and characterized in a free-living protozoan, Tetrahymena pyriformis. In order to confirm its function, TpyarsM gene was knocked-out in Tetrahymena and was also heterologously expressed in hypersensitive E. coil; these events resulted in expected decreases in As tolerance and methylation ability, respectively. In-vitro tests revealed that purified TpyArsM protein methylated inorganic As to mono- and di- methylarsenate, and also had the novel property of producing trimethylarsenite (TMA(III)) and dimethylarsine (Me2AsH) gases. This new methyltransferase gene, identified in a species near the base of the food web, has enriched our knowledge of As methyltransferases and has great potential for bioremediation of As-contaminated environments. (C) 2014 Elsevier B.V. All rights reserved.Arsenic (As) methylation in aquatic microbes plays a major role in the biogeochemistry of As. Protozoa, especially the free-living freshwater species, are important players in aquatic ecological health. In this study, an arsenite (As(III)) methyltransferase, TpyArsM, was identified and characterized in a free-living protozoan, Tetrahymena pyriformis. In order to confirm its function, TpyarsM gene was knocked-out in Tetrahymena and was also heterologously expressed in hypersensitive E. coli; these events resulted in expected decreases in As tolerance and methylation ability, respectively. In-vitro tests revealed that purified TpyArsM protein methylated inorganic As to mono- and di- methylarsenate, and also had the novel property of producing trimethylarsenite (TMA(III)) and dimethylarsine (Me2AsH) gases. This new methyltransferase gene, identified in a species near the base of the food web, has enriched our knowledge of As methyltransferases and has great potential for bioremediation of As-contaminated environments. (C) 2014 Elsevier B.V. All rights reserved

ATP-binding cassette transporter enhances tolerance to DDT in Tetrahymena

The reuse of dichlorodiphenyltrichloroethane (DDT) as an indoor residual spray was permitted by the World Health Organization in 2007, and approximately 14 countries still use DDT to control disease vectors. The extensive exposure of insects to DDT has resulted in the emergence of DDT resistance, especially in mosquitoes, and the mechanism for this resistance in mosquitoes has been widely reported. Spraying can also introduce DDT directly into surface water, and DDT can subsequently accumulate in microorganisms, but the mechanism for the resistance to DDT degradation in microorganisms is unclear. Using whole-genome microarray analysis, we detected an abcb15 gene that was up-regulated in a specific manner by DDT treatment in T. thermophile. The deduced ABCB15 peptide sequence had two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs) to form the structure TMD-NBD-TMD-NBD, and each NBD contained three conserved motifs: Walker-A, C-loop, and Walker-B, which indicated the T. thermophila abcb15 was a typical ABC transporter gene. The expression of ABCB15 fused with a C-terminal green fluorescent protein was found to be on the periphery of the cell, suggesting that ABCB15 was a membrane pump protein. In addition, cells with abcb15 partially knocked down (abcb15-KD) grew slower than wild-type cells in the presence of 256 mg L-1 DDT, indicating the tolerance of abcb15-KD strain to DDT exposure was decreased. Thus, we suggest that in Tetrahymena, the membrane pump protein encoded by ABCT gene abcb15 can enhance the tolerance to DDT and protect cells from this exogenous toxin by efficiently pumping it to the extracellular space

Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila

The unicellular eukaryote Tetrahymena thermophila has seven mating types. Cells can mate only when they recognize cells of a different mating type as non-self. As a ciliate, Tetrahymena separates its germline and soma into two nuclei. During growth the somatic nucleus is responsible for all gene transcription while the germline nucleus remains silent. During mating, a new somatic nucleus is differentiated from a germline nucleus and mating type is decided by a stochastic process. We report here that the somatic mating type locus contains a pair of genes arranged head-to-head. Each gene encodes a mating type-specific segment and a transmembrane domain that is shared by all mating types. Somatic gene knockouts showed both genes are required for efficient non-self recognition and successful mating, as assessed by pair formation and progeny production. The germline mating type locus consists of a tandem array of incomplete gene pairs representing each potential mating type. During mating, a complete new gene pair is assembled at the somatic mating type locus; the incomplete genes of one gene pair are completed by joining to gene segments at each end of germline array. All other germline gene pairs are deleted in the process. These programmed DNA rearrangements make this a fascinating system of mating type determination.The unicellular eukaryote Tetrahymena thermophila has seven mating types. Cells can mate only when they recognize cells of a different mating type as non-self. As a ciliate, Tetrahymena separates its germline and soma into two nuclei. During growth the somatic nucleus is responsible for all gene transcription while the germline nucleus remains silent. During mating, a new somatic nucleus is differentiated from a germline nucleus and mating type is decided by a stochastic process. We report here that the somatic mating type locus contains a pair of genes arranged head-to-head. Each gene encodes a mating type-specific segment and a transmembrane domain that is shared by all mating types. Somatic gene knockouts showed both genes are required for efficient non-self recognition and successful mating, as assessed by pair formation and progeny production. The germline mating type locus consists of a tandem array of incomplete gene pairs representing each potential mating type. During mating, a complete new gene pair is assembled at the somatic mating type locus; the incomplete genes of one gene pair are completed by joining to gene segments at each end of germline array. All other germline gene pairs are deleted in the process. These programmed DNA rearrangements make this a fascinating system of mating type determination

Gene Network Landscape of the Ciliate Tetrahymena thermophila

Background: Genome-wide expression data of gene microarrays can be used to infer gene networks. At a cellular level, a gene network provides a picture of the modules in which genes are densely connected, and of the hub genes, which are highly connected with other genes. A gene network is useful to identify the genes involved in the same pathway, in a protein complex or that are co-regulated. In this study, we used different methods to find gene networks in the ciliate Tetrahymena thermophila, and describe some important properties of this network, such as modules and hubs. Methodology/Principal Findings: Using 67 single channel microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient (PCC), the Spearman correlation coefficient (SCC) and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast. The CLR network with a Z-score threshold 3.49 was determined to be the most robust. The TGN was partitioned, and 55 modules were found. In addition, analysis of the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to their expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and provide evidence indicating that some of these are involved in the same process in Tetrahymena as in human. Conclusions/Significance: This study constructed a Tetrahymena gene network, provided new insights to the properties of this biological network, and presents an important resource to study Tetrahymena genes at the pathway level