Single-molecule real-time sequencing of the full-length transcriptome of Portunus pelagicus

Reconstruction and annotation of transcripts, particularly for a species without reference genome, plays a critical role in gene discovery, investigation of genomic signatures, and genome annotation in the pre-genomic era. This is the first study to use Single-molecule real-time (SMRT) sequencing for reporting the full-length transcriptome of Portunus pelagicus. Overall, 16.26 Gb of raw reads were obtained, including 7,068,387 subreads, with average length of 2,300 bp and N50 length of 3,594 bp. In total, 351,870 circular consensus sequences (CCS) reads were extracted, including 255,378 full-length non-chimeric (FLNC) reads with mean length of 3,423 bp.70,407 genes were obtained after eliminating redundant sequences, and 56,557 (80.33%) genes were annotated in at least one database, 17,267 (24.52%) genes were annotated in all of the seven databases. Further, 68,797 coding sequences (CDS) were identified, including 36,848 complete CDS. A total of 1,730 unigenes were predicted to be transcription factors (TFs). Finally, 11,894 long noncoding RNA (lncRNA) transcripts were predicted by different computational approaches and 147,262 single sequence repeat (SSR)s were obtained. The transcriptome data reported herein are bound to serve as a basis for future studies on P. pelagicus

Improvement of Teaching-Learning-Based-Optimization

Teaching-Learning-Based-Optimization is an optimization algorithm that simulates the teaching process. In the standard Teaching-Learning-Based-Optimization there are some problems such as precocity and low optimization accuracy. Through daily discovery, students’ learning effect is better when there are exercise lessons than when there are no exercise lessons. Students who study toward teacher on one’s own learn better than students who do not. Therefore, this paper proposes a teaching mode that combines exercise lessons and one-to-one to improve the Teaching-Learning-Based-Optimization

20(S)-Ginsenoside Rh2 Induce the Apoptosis and Autophagy in U937 and K562 Cells

Acute myeloid leukemia (AML) and Chronic myelogenous leukemia (CML) are common leukemia in adults. 20(S)-GRh2 is an important bioactive substance that is present in Panax ginseng. However, there are no investigations that deal with the comparison of apoptosis, the occurrence of autophagy, and the relationship between apoptosis and autophagy after being treated with 20(S)-GRh2 in AML and CML. In this study, we explored the effect of 20(S)-GRh2 on the AML and CML (U937 and K562). Fluorescence microscopy, CCK-8, Quantitative realtime PCR, Western blot, transmission electron microscopy (TEM), and flow cytometric analysis were used to detect the occurrence of cell proliferation inhibition, apoptosis, and autophagy. By using the above methods, it was determined that apoptosis induced by 20(S)-GRh2 was more obvious in K562 than U937 cells and 20(S)-GRh2 could generate autophagy in K562 and U937 cells. When pretreated by a specific inhibitor of autophagy, (3-methyladenine), the 20(S)-GRh2-induced apoptosis was enhanced, which indicated that 20(S)-GRh2-induced autophagy may protect U937 and K562 cells from undergoing apoptotic cell death. On the other hand, pretreated by an apoptosis suppressor (Z-VAD-FMK), it greatly induced the autophagy and partially prevented 20(S)-GRh2 induced apoptosis. This phenomenon indicated that 20(S)-GRh2-induced autophagy may serve as a survival mechanism and apoptosis and autophagy could act as partners to induce cell death in a cooperative manner. These findings may provide a rationale for future clinical application by using 20(S)-GRh2 combined autophagy inhibitors for AML and CML

Proteomic Analysis Associated with the Immune Response in Hemocytes of <i>Portunus trituberculatus</i> Challenged with <i>Vibrio parahaemolyticus</i>

Vibrio parahaemolyticus belongs to an expanding group of aquatic pathogens that are widely distributed in aquatic environments. This species is a lethal pathogen for a number of economically important marine crabs. However, studies exploring host–vibrio interactions between V. parahaemolyticus and crabs are scarce, and therefore, the underlying molecular mechanisms are unclear. Herein, we performed a comprehensive proteomic analysis to investigate the immune response of Portunus trituberculatus hemocytes to V. parahaemolyticus infection. A total of 4433 proteins were identified using isobaric tags for relative and absolute quantitation (iTRAQ), and 526 differentially expressed proteins (DEPs) were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, with six DEPs further subjected to quantitative real-time PCR. Several identified DEPs were found to be mainly involved in the immune defense of the crustacean, such as a hemocyanin subunit, C-type lectin, α-2-macroglobulin, Cu/Zn-superoxide dismutase, and heat shock protein 70, playing a key role in the response to V. parahaemolyticus infection. Moreover, many immune-related KEGG pathways were markedly altered, such as cell adhesion molecules, complement and coagulation cascades, and phagosomes. Our results provide insights into how V. parahaemolyticus overcomes the innate immunity of P. trituberculatus to induce pathological alterations in affected tissues. We report the first iTRAQ-based proteomic analysis and highlight the key pathways and proteins involved in the host–vibrio interactions between P. trituberculatus and V. parahaemolyticus. These findings should enhance our understanding of the molecular mechanisms underlying such interactions

Simulation of the Effect of Artificial Water Transfer on Carbon Stock of Phragmites australis in the Baiyangdian Wetland, China

How to explain the effect of seasonal water transfer on the carbon stocks of Baiyangdian wetland is studied. The ecological model of the relationship between the carbon stocks and water depth fluctuation of the reed was established by using STELLA software. For the first time the Michaelis-Menten equation (1) introduced the relation function between the water depth and reed environmental carrying capacity, (2) introduced the concept of suitable growth water depth, and (3) simulated the variation rules of water and reed carbon stocks of artificial adjustment. The model could be used to carry out the research on the optimization design of the ecological service function of the damaged wetland

Transcriptomic variation of eyestalk reveals the genes and biological processes associated with molting in <i>Portunus trituberculatus</i>

<div><p>Background</p><p>Molting is an essential biological process throughout the life history of crustaceans, which is regulated by many neuropeptide hormones expressed in the eyestalk. To better understand the molting mechanism in <i>Portunus trituberculatus</i>, we used digital gene expression (DGE) to analyze single eyestalk samples during the molting cycle by high-throughput sequencing.</p><p>Results</p><p>We obtained 14,387,942, 12,631,508 and 13,060,062 clean sequence reads from inter-molt (InM), pre-molt (PrM) and post-molt (PoM) cDNA libraries, respectively. A total of 1,394 molt-related differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analysis identified some important processes and pathways with key roles in molting regulation, such as chitin metabolism, peptidase inhibitor activity, and the ribosome. We first observed a pattern associated with the neuromodulator-related pathways during the molting cycle, which were up-regulated in PrM and down-regulated in PoM. Four categories of important molting-related transcripts were clustered and most of them had similar expression patterns, which suggests that there is a connection between these genes throughout the molt cycle.</p><p>Conclusion</p><p>Our work is the first molt-related investigation of <i>P</i>. <i>trituberculatus</i> focusing on the eyestalk at the whole transcriptome level. Together, our results, including DEGs, identification of molting-related biological processes and pathways, and observed expression patterns of important genes, provide a novel insight into the function of the eyestalk in molting regulation.</p></div

Study on the Correlation between Gene Expression and Enzyme Activity of Seven Key Enzymes and Ginsenoside Content in Ginseng in Over Time in Ji’an, China

Panax ginseng is a traditional medicine. Fresh ginseng is one of the most important industries related to ginseng development, and fresh ginseng of varying ages has different medicinal properties. Previous research has not systematically reported the correlation between changes in key enzyme activity with changes in ginsenoside content in fresh ginseng over time. In this study, for the first time, we use ginseng samples of varying ages in Ji’an and systematically reported the changes in the activity of seven key enzymes (HMGR, FPS, SS, SE, DS, CYP450, and GT). We investigated the content of ginsenoside and gene expression of these key enzymes. Ginsenoside content was measured using HPLC. HPLC, GC-MS, and LC-MS were combined to measure the enzyme activity of the key enzymes. Quantitative PCR was used in the investigation of gene expression. By analyzing the correlation between the enzyme activity and the transcription level of the key enzymes with ginsenoside content, we found that DS and GT enzyme activities are significantly correlated with the ginsenoside content in different ages of ginseng. Our findings might provide a new strategy to discriminate between ginseng of different years. Meanwhile, this research provides important information for the in-depth study of ginsenoside biosynthesis

Study on slope stability of waste dump with a weak layer using finite element limit analysis method

Slope stability is generally paid more attention to in slope protection works, especially for slope containing weak layers. Two indexes of safety factor and failure model are selected to perform slope stability. Moreover, the finite element limit analysis method comprehensively combines the advantage of the limit analysis method and the finite element method obtaining the upper and lower bounds of the safety factor and the failure mode under the slope stability limit state. In this study, taking a waste dump containing a weak layer as an engineering background, the finite element limit analysis method is adopted to explore the potential failure mode. Meanwhile, the sensitivity analysis of slope stability is performed on geometrical and geotechnical parameters of the waste dump. The results show that the failure mode of the waste dump slope is two wedges if the weak layer is located on the ground surface (Model A), while the slope can be observed as three wedges failure if the weak layer is below the ground surface (Model B). In addition, both failure modes are highly sensitive to the friction angle of the weak layer and the shear strength of waste disposal, and moderately sensitive to the heap height, the dip angle and cohesion of the weak layer, while the toe cutting has limited effect on the slope stability. Moreover, the sensitivity to the excavation of the ground depends on the location of the weak layer and failure mode

Proteomic Analysis Associated with the Immune Response in Hemocytes of Portunus trituberculatus Challenged with Vibrio parahaemolyticus

Vibrio parahaemolyticus belongs to an expanding group of aquatic pathogens that are widely distributed in aquatic environments. This species is a lethal pathogen for a number of economically important marine crabs. However, studies exploring host&ndash;vibrio interactions between V. parahaemolyticus and crabs are scarce, and therefore, the underlying molecular mechanisms are unclear. Herein, we performed a comprehensive proteomic analysis to investigate the immune response of Portunus trituberculatus hemocytes to V. parahaemolyticus infection. A total of 4433 proteins were identified using isobaric tags for relative and absolute quantitation (iTRAQ), and 526 differentially expressed proteins (DEPs) were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, with six DEPs further subjected to quantitative real-time PCR. Several identified DEPs were found to be mainly involved in the immune defense of the crustacean, such as a hemocyanin subunit, C-type lectin, &alpha;-2-macroglobulin, Cu/Zn-superoxide dismutase, and heat shock protein 70, playing a key role in the response to V. parahaemolyticus infection. Moreover, many immune-related KEGG pathways were markedly altered, such as cell adhesion molecules, complement and coagulation cascades, and phagosomes. Our results provide insights into how V. parahaemolyticus overcomes the innate immunity of P. trituberculatus to induce pathological alterations in affected tissues. We report the first iTRAQ-based proteomic analysis and highlight the key pathways and proteins involved in the host&ndash;vibrio interactions between P. trituberculatus and V. parahaemolyticus. These findings should enhance our understanding of the molecular mechanisms underlying such interactions