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Glutathione peroxidase (GPx) has been the focus of increased research because of its important role as an antioxidant and in reactive oxygen species (ROS) induced damage repair. Studies on GPxs have relevance with Macrobrachium nipponense because it has poor tolerance to hypoxia in Macrobrachium nipponense. The two subunits named as MnGPx-3 and MnGPx-4 according to the glutathione peroxidase nomenclature system. Both full-length cDNAs were cloned from the hepatopancreas. In this study, we analyzed the expression of two GPxs in Macrobrachium nipponense in response to changes in environmental oxygen. Expression levels of MnGPx-3 and MnGPx-4 indicated that both have strong responses to hypoxia. In situ hybridization showed that MnGPx-3 and MnGPx-4 were located in secretory and storage cells in hepatopancreas. These results suggest that GPx gene is expressed and released by secretory cells and released response to hypoxia. In the gill tissue, however, GPxs are located in blood cells, suggesting that they perform different functions in different tissues or organs. The results of in situ hybridization were consistent with those of quantitative Real-time PCR. This study provides a basis for understanding the oxidative stress response in M. nipponense under hypoxia.

FimA is an important virulence factor of Porphyromonas gingivalis (P. gingivalis). According to its DNA sequence, the fimA genotype of P. gingivalis can be divided into six categories (I, Ib, Ⅱ, III, IV, V). The fimA gene may be a key factor in the diversity of virulence found in P. gingivalis. Moreover, the role fimA plays in the pathogenesis of P. gingivalis is closely associated with periodontitis, making it an important factor of study for disease prevention and treatment. In this study, the prevalence of fimA genotypes of P. gingivalis in patients with periodontal diseases was evaluated by meta-analysis. The Embase and PubMed databases were searched for articles from 1999 to 2019 using the following search terms: Porphyromonas gingivalis or P. gingivalis; periodontitis or chronic periodontal disease; fimA or fimA genotype. The reference lists of relevant published articles were searched manually. A total of 17 studies were included in this report. A statistical software package (Stata, version 11.0/mp, StataCorp) was utilized to calculate and analyze the P. gingivalis fimA genotypes for each combined incidence estimate. The pooled rates of fimA Ⅰ, fimA Ib, fimA Ⅱ, fimA Ⅲ, fimA Ⅳ and fimA Ⅴ genotypes of P. gingivalis were 8.4% (95% CI: 5.7-11.1), 11.7% (95% CI: 7.4-16), 42.9% (95% CI: 34.2-51.7), 6.5% (95% CI: 5.1-7.9), 17.8% (95% CI: 9.0-26.5), and 3.2% (95% CI: 1.6-4.9), respectively. This study showed that the fimA Ⅱ and fimA Ⅳ genotypes of P. gingivalis are highly present in patients with periodontal disease. Therefore, these two genotypes may be related to the pathogenesis and progress of periodontal disease, one of the main risk factors of periodontitis.

The normal studies on air traffic departure scheduling problem (DSP) mainly deal with an independent airport in which the departure traffic is not affected by surrounded airports, which, however, is not a consistent case. In reality, there still exist cases where several commercial airports are closely located and one of them possesses a higher priority. During the peak hours, the departure activities of the lower-priority airports are usually required to give way to those of higher-priority airport. These giving-way requirements can inflict a set of changes on the modeling of departure scheduling problem with respect to the lower-priority airports. To the best of our knowledge, studies on DSP under this condition are scarce. Accordingly, this paper develops a bi-objective integer programming model to address the flight departure scheduling of the partly-restricted (e.g., lower-priority) one among several adjacent airports. An adapted tabu search algorithm is designed to solve the current problem. It is demonstrated from the case study of Tianjin Binhai International Airport in China that the proposed method can obviously improve the operation efficiency, while still realizing superior equity and regularity among restricted flows.

White spot syndrome virus (WSSV) is one of the most devastating pathogens of cultured shrimp, responsible for massive loss of its commercial products worldwide. The oriental river prawn Macrobrachium nipponense is an economically important species that is widely farmed in China and adult prawns can be infected by WSSV. However, the molecular mechanisms of the host pathogen interaction remain unknown. There is an urgent need to learn the host pathogen interaction between M. nipponense and WSSV which will be able to offer a solution in controlling the spread of WSSV. Next Generation Sequencing (NGS) was used in this study to determin the transcriptome differences by the comparison of control and WSSV-challenged moribund samples, control and WSSV-challenged survived samples of hepatopancreas in M. nipponense. A total of 64,049 predicted unigenes were obtained and classified into 63 functional groups. Approximately, 4,311 differential expression genes were identified with 3,308 genes were up-regulated when comparing the survived samples with the control. In the comparison of moribund samples with control, 1,960 differential expression genes were identified with 764 genes were up-regulated. In the contrast of two comparison libraries, 300 mutual DEGs with 95 up-regulated genes and 205 down-regulated genes. All the DEGs were performed GO and KEGG analysis, overall a total of 85 immune-related genes were obtained and these gene were groups into 13 functions and 4 KEGG pathways, such as protease inhibitors, heat shock proteins, oxidative stress, pathogen recognition immune receptors, PI3K/AKT/mTOR pathway, MAPK signaling pathway and Ubiquitin Proteasome Pathway. Ten genes that valuable in immune responses against WSSV were selected from those DEGs to furture discuss the response of host to WSSV. Results from this study contribute to a better understanding of the immune response of M. nipponense to WSSV, provide information for identifying novel genes in the absence of genome of M. nipponense. Furthermore, large number of transcripts obtained from this study could provide a strong basis for future genomic research on M. nipponense.

The oriental river prawn, Macrobrachium nipponense, is an important commercial aquaculture resource in China. In order to overwinter, M. nipponense displays decreased physiological activity and less consumption of energy. Sudden warming would trigger molting and cause an extensive death, resulting in huge economic losses. Therefore, it is of great practical significance to study the molting mechanism of oriental river prawns. Molt-inhibiting hormone gene (MIH) plays a major role in regulating molting in crustaceans. In this study, a full length MIH cDNA of M. nipponense (Mn-MIH) was cloned from the eyestalk. The total length of the Mn-MIH was 925 bp, encoding a protein of 119 amino acids. Tissue distribution analysis showed that Mn-MIH was highly expressed in the eyestalk, and that it had relatively low expression in gill, ovary, and abdominal ganglion. Mn-MIH was detected in all developmental stages, and changed regularly in line with the molting cycle of the embryo and larva. Mn-MIH varied in response to the molting cycle, suggesting that Mn-MIH negatively regulates ecdysteroidogenesis. Mn-MIH inhibition by RNAi resulted in a significant acceleration of molting cycles in both males and females, confirming the inhibitory role of MIH in molting. After long-term RNAi males, but not females had significant weight gain, confirming that Mn-MIH plays an important role in growth of M. nipponense. Our work contributes to a better understanding of the role of Mn-MIH in crustacean molting and growth.

This paper suggests a probability-dominant user equilibrium (PdUE) model to describe the selfish routing equilibrium in a stochastic traffic network. At PdUE, travel demands are only assigned to the most dominant routes in the same origin-destination pair. A probability-dominant rerouting dynamic model is proposed to explain the behavioral mechanism of PdUE. To facilitate applications, the logit formula of PdUE is developed, of which a well-designed route set is not indispensable and the equivalent varitional inequality formation is simple. Two routing strategies, i.e., the probability-dominant strategy (PDS) and the dominant probability strategy (DPS), are discussed through a hypothetical experiment. It is found that, whether out of insurance or striving for perfection, PDS is a better choice than DPS. For more general cases, the conducted numerical tests lead to the same conclusion. These imply that PdUE (rather than the conventional stochastic user equilibrium) is a desirable selfish routing equilibrium for a stochastic network, given that the probability distributions of travel time are available to travelers.

The mobility of modern metropolises strongly relies on urban rail transit (URT) systems, and such a heavy dependence causes that even minor service interruptions would make the URT systems unsustainable. This study aims at optimally dispatching the ground feeder-bus to coordinate with the urban rails' operation for eliminating the effect of unexpected service interruptions in URT corridors. A feeder-bus dispatch planning model was proposed for the collaborative optimization of URT and feeder-bus cooperation under emergency situations and minimizing the total evacuation cost of the feeder-buses. To solve the model, a concept of dummy feeder-bus system is proposed to transform the non-linear model into traditional linear programming (ILP) model, i.e., traditional transportation problem. The case study of Line #2 of Nanjing URT in China was adopted to illustrate the model application and sensitivity analyses of the key variables. The modeling results show that as the evacuation time window increases, the total evacuation cost as well as the number of dispatched feeder-buses decrease, and the dispatched feeder-buses need operate for more times along the feeder-bus line. The number of dispatched feeder-buses does not show an obvious change with the increase of parking spot capacity and time window, indicating that simply increasing the parking spot capacity would cause huge waste for the emergent bus utilization. When the unbalanced evacuation demand exists between stations, the more feeder-buses are needed. The method of this study will contribute to improving transportation emergency management and resource allocation for URT systems.

Bifidobacteria are well known for their human health-promoting effects and are therefore widely applied in the food industry. Members of the Bifidobacterium genus were first identified from the human gastrointestinal tract and were then found to be widely distributed across various ecological niches. Although the genetic diversity of Bifidobacterium has been determined based on several marker genes or a few genomes, the global diversity and evolution scenario for the entire genus remain unresolved. The present study comparatively analyzed the genomes of 45 type strains. We built a robust genealogy for Bifidobacterium based on 402 core genes and defined its root according to the phylogeny of the tree of bacteria. Our results support that all human isolates are of younger lineages, and although species isolated from bees dominate the more ancient lineages, the bee was not necessarily the original host for bifidobacteria. Moreover, the species isolated from different hosts are enriched with specific gene sets, suggesting host-specific adaptation. Notably, bee-specific genes are strongly associated with respiratory metabolism and are potential in helping those bacteria adapt to the oxygen-rich gut environment in bees. This study provides a snapshot of the genetic diversity and evolution of Bifidobacterium, paving the way for future studies on the taxonomy and functional genomics of the genus.

BACKGROUND: The oriental river prawn, Macrobrachium nipponense, is an important aquaculture species in China, even in whole of Asia. The androgenic gland produces hormones that play crucial roles in sexual differentiation to maleness. This study is the first de novo M. nipponense transcriptome analysis using cDNA prepared from mRNA isolated from the androgenic gland. Illumina/Solexa was used for sequencing. METHODOLOGY AND PRINCIPAL FINDING: The total volume of RNA sample was more than 5 ug. We generated 70,853,361 high quality reads after eliminating adapter sequences and filtering out low-quality reads. A total of 78,408 isosequences were obtained by clustering and assembly of the clean reads, producing 57,619 non-redundant transcripts with an average length of 1244.19 bp. In total 70,702 isosequences were matched to the Nr database, additional analyses were performed by GO (33,203), KEGG (17,868), and COG analyses (13,817), identifying the potential genes and their functions. A total of 47 sex-determination related gene families were identified from the M. nipponense androgenic gland transcriptome based on the functional annotation of non-redundant transcripts and comparisons with the published literature. Furthermore, a total of 40 candidate novel genes were found, that may contribute to sex-determination based on their extremely high expression levels in the androgenic compared to other sex glands,. Further, 437 SSRs and 65,535 high-confidence SNPs were identified in this EST dataset from which 14 EST-SSR markers have been isolated. CONCLUSION: Our study provides new sequence information for M. nipponense, which will be the basis for further genetic studies on decapods crustaceans. More importantly, this study dramatically improves understanding of sex-determination mechanisms, and advances sex-determination research in all crustacean species. The huge number of potential SSR and SNP markers isolated from the transcriptome may shed the lights on research in many fields, including the evolution and molecular ecology of Macrobrachium species.

As one of the most widespread protein post-translational modifications, phosphorylation is involved in many biological processes such as cell cycle, apoptosis. Identification of phosphorylated substrates and their corresponding sites will facilitate the understanding of the molecular mechanism of phosphorylation. Comparing with the labor-intensive and time-consuming experiment approaches, computational prediction of phosphorylation sites is much desirable due to their convenience and fast speed. In this paper, a new bioinformatics tool named CKSAAP_PhSite was developed that ignored the kinase information and only used the primary sequence information to predict protein phosphorylation sites. The highlight of CKSAAP_PhSite was to utilize the composition of k-spaced amino acid pairs as the encoding scheme, and then the support vector machine was used as the predictor. The performance of CKSAAP_PhSite was measured with a sensitivity of 84.81%, a specificity of 86.07% and an accuracy of 85.43% for serine, a sensitivity of 78.59%, a specificity of 82.26% and an accuracy of 80.31% for threonine as well as a sensitivity of 74.44%, a specificity of 78.03% and an accuracy of 76.21% for tyrosine. Experimental results obtained from cross validation and independent benchmark suggested that our method was very promising to predict phosphorylation sites and can be served as a useful supplement tool to the community. For public access, CKSAAP_PhSite is available at http://59.73.198.144/cksaap_phsite/.