Table of Content

18 August 2020, Volume 37 Issue 4 Previous Issue   

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Machine learning-assisted enzyme directed evolution JIANG Ying-ying, QU Ge, SUN Zhou-tong 2020, 37 (4):  1.  doi: 10.3969/j.issn.2095-1736.2020.04.001 Abstract ( 1288 )   PDF   Save Directed evolution plays a central role in the fields of biocatalysis, biomedicine and biotechnology, etc. Taking advantages of increasingly computer performance and numerous datasets, artificial intelligence has rapidly developed. Recently, machine learning algorithms have also been applied to protein engineering, especially in helping prediction of protein structures, improving enzyme stability / selectivity / solubility, and guiding rational protein design as well as other functions. This paper reviews the state of the art in algorithms and descriptors used in enzyme engineering. Related Articles | Metrics

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Research on the formation of intermolecular G-quadruplex complexes by telomeric DNA and non-coding telomeric RNA TERRA in vitro HE Miao, WANG Tao 2020, 37 (4):  12.  Abstract ( 303 )   PDF   Save Telomeric DNA and TERRA(Telomeric repeat-containing RNA, a non-coding telomeric RNA) are consisted of tandem repeats rich in successive guanines, both can form G-quadruplex structures to inhibit the telomere extension by the telomerase and prevent the infinite proliferation of cancer cells. An intermolecular G-quadruplex complex can be formed between telomeric DNA and TERRA and has some functions, but little has been reported about this. Nuclear magnetic resonance(NMR) experiment showed that both human and Giardia lamblia telomeres formed DNA-RNA intermolecular G-quadruplex complexes. Based on the circular dichroism(CD) spectrum and NMR titration, it was found that, due to sharing the same sequence, a short sequence of TERRA was able to compete with and eventually replace the corresponding short telomeric DNA sequence within a DNA-DNA parallel-antiparallel hybrid intermolecular G-quadruplex complex. The resulting DNA-RNA G-quadruplex complex is induced into a full parallel conformation. In addition, the DNA-RNA G-quadruplex complex is more stable than the DNA-DNA G-quadruplex complex. Study on the structure and properties of telomeric DNA-RNA G-quadruplex complex can provide new insights into the interacting mode between TERRA and telomeric DNA and the way to maintain telomeric stability by TERRA. Related Articles | Metrics

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Studies on interaction between erianin and its potential target protein， pyruvate carboxylase #br# XIE Ze-yu, CHEN Shui-ling, YANG Zhi-hua, RUAN Zi-jing, HUANG Xin-he 2020, 37 (4):  17.  doi: 10.3969/j.issn.2095-1736.2020.04.017 Abstract ( 377 )   PDF   Save This study aimed to investigate the interaction between erianin and human pyruvate carboxylase(hPC), and thus lay a foundation for elucidating its pharmacology and toxicology. Computer molecular simulation docking was employed to predict the binding and interaction intensity of erianin and hPC, furthermore, mitochondrial protein incubation system was used to verify the effect of erianin on hPC activity in vitro. Molecular docking results showed that erianin could bind to hPC at multiple sites. The best binding poses were AD interface and BC interface of the tetramer protein, the trimethoxyphenyl group of erianin interacted with the hPC methionine(B: 804) residue via a π-sulfur and a π-alkyl interaction, the main benzene ring interacted with the aspartic acid(C: 774) residue of hPC through hydrogen bonding and π-anion interaction, and there were also multiple methoxy groups that had a hydrocarbon-non-bond interaction with hPC. Consistently, In vitro inhibition experiments showed that erianin had a significant inhibitory effect on hPC in a dose-dependent manner. Collectively, the experiments showed that the binding of erianin and hPC, and also erianin treatment inhibited the enzyme activity of hPC. Related Articles | Metrics

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Study on the effect of different types of bovine serum on the cultivation of MDCK cell LI Zi-liang, WANG Jia-min, ZHAO Cai-hong, WANG Mei-hao, LI Zhuo, QIAO Zi-lin, MA Zhong-ren 2020, 37 (4):  21.  doi: 10.3969/j.issn.2095-1736.2020.04.021 Abstract ( 294 )   PDF   Save In order to establish a rapid screening method for optimal serum of adherent culture cells, MDCK cells were serially subcultured in DMEM containing 10% different types of bovine serum, and observed by passage stability, growth curve and growth kinetics were analyzed. The method of learning and adherence rate was used to evaluate the effect of different types of bovine serum on the growth-promoting effect of MDCK adherent cells, and further expanded culture verification in cell factories. The results showed that all three types of serum could promote cell growth and proliferation and the cell growth curve was "S" type. MDCK cell growth kinetics analysis found that the average specific growth rate of the three types of serum was not significantly different (P>0.05); the maximum proliferation density and doubling time fetal bovine serum were superior to newborn bovine serum; the average colony formation rate analysis showed that, compared with the domestic fetal bovine serum(FBS), imported FBS made slightly difference (P=0.02), and the domestic newborn bovine serum was significantly lower than that of domestic and imported fetal bovine serum (P<0.0001). The domestic newborn bovine serum was used in subcultured MDCK cells in the 1st and 10th layer cell factories, the cells grew well, and the cell growth was stable during the passage. Studying the effects of different types of bovine serum on the culture of MDCK cells would provide a scientific basis for the expansion of MDCK cells in vaccine production and successful screening the best serum for MDCK cells in a short period of time. Related Articles | Metrics

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Construction and application of structural model of alanine aminotransferase in soybean LIN Shen, ZHONG Rong-hua, MENG Fan-mei, ZHENG Xiao-ru, WU Jian-er, ZHANG Shang-hong 2020, 37 (4):  26.  doi: 10.3969/j.issn.2095-1736.2020.04.026 Abstract ( 304 )   PDF   Save Soybean is an important nitrogen-fixing crop having strong amino acid metabolism and high activity of alanine aminotransferase during seed germination. Alanine aminotransferase can catalyze the reversible reaction of glutamic acid and pyruvate to produce alpha-ketoglutarate and alanine. This reaction is essential in the metabolism of amino acid in organisms. In this study, the possible sequence of Glycine max glutamic-alanine aminotransferase was obtained through database. We built a 3-D homology model of the protein sequence of Glycine max alanine aminotransferase (NP_001237567.2) with Discovery Studio, explored the conditions of the model in different concentrations of buffers with molecular dynamic, and obtained a stable model of solution state. The modification and optimization of the three-dimensional structure model of alanine aminotransferase prove the feasibility of adding histidine labelling to Glycine max alanine aminotransferase and make a theoretical preparation for the expression and separation of Glycine max alanine transaminase later. Related Articles | Metrics

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Identification of high-yielding strain Halomonas sp. XH26  for producing ectoine and UV mutagenesis breeding #br# IAN Lei, ZHANG Fang, SHEN Guo-ping, GAO Xiang, LONG Qi-fu, ZHU De-rui 2020, 37 (4):  31.  doi: 10.3969/j.issn.2095-1736.2020.04.031 Abstract ( 223 )   PDF   Save In order to provide an excellent source of fermentation bacteria for engineering production of ectoine, Halomonas sp. XH26 from the Xiao Chaidan Saline lake, was mutated by UV radiation to obtain the mutant strain with high yield of ectoine. Morphological observation, physiological and biochemical test and 16S rRNA gene sequencing were used to determine the classification status of the strain. The positive mutant strain was screened by UV mutagenesis with ectoine yield more than twice that of the original strain, intracellular ectoine production was determined by HPLC, and the mutant strain was subcultured to study the yield stability of ectoine. The experimental results showed that the original strain XH26 (optimal yield of ectoine 456.82 mg/L±15.72 mg/L, CDW 0.71 g/g±0.04 g/g) was treated with 9 rounds of UV mutagenesis, and 7 strains with high-yielding mutant ectoine were obtained, and the yield of ectoine was significantly increased (about 200%). Among them, the strain HU09-32 with the largest accumulation amount had a yield up to 1351.09 mg/L±17.69 mg/L (an increase of 290%), and it was continuously subcultured for 40 days (inoculated for 2 days/time). The intracellular ectoine yield was stable, and the growth characteristics, proliferation speed and accumulation amount were significantly better than the original strain XH26, with good fermentation production and industrial application potential. Related Articles | Metrics

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Functional study of a small non-coding RNA, sR082, of Edwardsiella piscicida ZHOU Hai-zhen, LI Mo-fei 2020, 37 (4):  36.  doi: 10.3969/j.issn.2095-1736.2020.04.036 Abstract ( 291 )   PDF   Save Edwardsiella piscicida is a major pathogen of marine fish in aquaculture, leading to severe economic loss. The mechanisms underline E. piscicida infection is yet to be fully understood. In our previous work, we identified multiple sRNAs with differential transcription levels under various conditions, including a sRNA termed sR082. The present study analyzed the transcription levels of sR082 of E. piscicida strain TXD1 upon acid stress. Further, with a sR082 knock-out strain designated TXΔsR082, we investigated the impacts of sR082 on the infective capacities to fish cell line, tissues and individuals, respectively. The results indicated that the transcription of sRNA was significantly upregulated under acidic condition. Compared to TXD1, the mutant strain TXΔsR082 exhibited significantly lower capacities on infecting and replicating in flounder FG cells, decreased dissemination in multiple flounder tissues, and attenuated lethality to fish. These observations suggested that sR082 likely plays important roles in response to acid stress and virulence of E. piscicida. Related Articles | Metrics

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Study on stress granules of zebrafish embryo fibroblasts cell (ZF4) under cold stress CHENG Peng-li, HU Rui-qin, LI Gen-fang, CHEN Liang-biao 2020, 37 (4):  40.  doi: 10.3969/j.issn.2095-1736.2020.04.040 Abstract ( 323 )   PDF   Save To investigate the formation and depolymerization of stress granules in zebrafish embryonic fibroblasts cell (ZF4) under cold stress, 18 ℃, 13 ℃ and 10 ℃ were selected as the cold stress temperature, and the low temperature treatment was carried out at different times； and then TIAL1 and G3BP1 (marker of stress granules) were used to conduct cellular immunofluorescence experiments and RT-qPCR experiments； finally, the temperature and time of stress recovery were selected to investigate the depolymerization of stress granules (SG). The results showed that under cold stress at different temperatures, stress granules were formed at different time in ZF4 cells， and the stress granules had different sizes, with the increase of low temperature treatment time. The stress granules of ZF4 cells were formed when treated at 18 ℃ for 24 h, 13 ℃ for 4 h and 10 ℃ for 1 h. As the temperature decreased, the rate of formation of stress granules also accelerated. The formation of stress granules is manifested by a gradual increase in stress granules and an increase in the size of the diameter. When ZF4 cells were treated at 13 ℃ for 4 h and then the temperature was restored to the optimum growth temperature (28 ℃), it was found that the stress granules depolymerized rapidly in about ten minutes. Depolymerization of stress granules is manifested by the rapid dissolution of stress granules. This paper firstly found that fish cells form stress granules at low temperature, and the main components are similar to mammalian cells, indicating that stress granules are the general response mechanism of animal cells to cold stress. Related Articles | Metrics

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Phylogeography of Populus cathayana from the Qinghai-Tibetan Plateau based on cpDNA sequence #br# ZHANG Yu, WANG Jiu-li, XIA Ming-ze, ZHANG Fa-qi 2020, 37 (4):  45.  doi: 10.3969/j.issn.2095-1736.2020.04.045 Abstract ( 328 )   PDF   Save Phylogeography study of P. cathayana′ 14 wild populations in Qinghai-Tibet Plateau was developed by using chloroplast DNA markers. The genetic structure and population dynamics were analyzed in order to reveal its evolutionary history during the Quaternary Glaciation to provide theoretical basis for germplasm resource evaluation and genetic protection strategy formulation. The genomic DNA of P. cathayana was extracted, then the atpH-atpI and rbcL fragments of non-coding region were amplified, detected, purified and sequenced. The mutation sites of the combined sequence of cpDNA were counted and 13 haplotypes were identified. Molecular variation analysis showed that genetic variation mainly existed among populations rather than within populations. There was no phylogenetic relationship between haplotypes in this study, and no recent population expansion was detected by bifurcation analysis and neutral detection. There is no significant correlation between genetic distribution and geographical distribution of P. cathayana. This may be due to the existence of multiple micro-shelters in the study area. For example, the Qilian and Hengduan Mountains may be micro-shelters for P.cathayana during the glacial period, and these areas are also the origin centers of population migration and diffusion after the glacial period. Related Articles | Metrics

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Response of radial growth of Populus euphratica Oliv. to extreme low temperature in the lower reaches of Tarim River DU Heng-wen, YE Mao 2020, 37 (4):  50.  doi: 10.3969/j.issn.2095-1736.2020.04.050 Abstract ( 124 )   PDF   Save Taking the Populus euphratica forest in the lower reaches of the Tarim River as the object, three typical sections of the downstream rivers, Yingsu, Kardaiyi and Arakan, were selected to analyze the radial growth of the P. euphratica in the lower of the Tarim River, based on the weather station near the section. The average minimum temperature and extreme low temperature data of long time series were analyzed by correlation analysis method to study the radial growth of P. euphratica in the lower reaches of the Tarim River and the response of the P. euphratica index to the average minimum temperature and extreme low temperature dynamics. The results showed that the radial growth of P. euphratica in three typical samples in the lower reaches of the Tarim River showed a decreasing trend. There was a significant negative correlation between radial growth and temperature of P. euphratica along the rivers in the lower reaches of the Tarim River, and the radial growth of P. euphratica in the Yingsu section was positively correlated with temperature, despite not obvious. The annual growth index of P. euphratica in three sections showed a downward trend and the mid-wheel index of the three samples showed a negative correlation with the average minimum temperature and the extreme minimum temperature. Related Articles | Metrics

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Mixotrophic cultivation of Phaeodactylum tricornutum with mannitol to produce polyunsaturated fatty acids and fucoxanthin DING Xiao-ting, WANG Li-juan, FAN Yong, ZHANG Pei-yu, LI Fu-li 2020, 37 (4):  54.  doi: 10.3969/j.issn.2095-1736.2020.04.054 Abstract ( 265 )   PDF   Save In this study, mannitol was used as organic carbon source to investigate its effects on the accumulation of biomass, polyunsaturated fatty acids and fucoxanthin of Phaeodactylum tricornutum under this mixtrophic condition. The concentration of mannitol at 2 g/L was finally selected for the cultivation. Furthermore, tea polyphenols at 0.2 g/L could effectively promote the utilization of mannitol. Compared with that of autotrophic culture, the final biomass was increased by 63%, and the yield of fucoxanthin reached to 75.3 mg/L, increased by 90%; EPA（Eicosapentaenoic acid） accounted for 36% of the total lipid, increased by 35%. This study provided a potential mixtrophic carbon source and antioxidant for improving production of EPA and fucoxanthin by P. tricornutum. Related Articles | Metrics

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Characteristics and influencing factors of diatom bloom in Lin Hekou Reservoir HU En, WANG Wen-ke, ZHANG Zhen-wen, SUN Chang-shun, SU Ya-ling 2020, 37 (4):  58.  doi: 10.3969/j.issn.2095-1736.2020.04.058 Abstract ( 274 )   PDF   Save In April 2017, there was been an abnormal phenomenon of the “dark brown-water” in Lin Hekou Reservoir of Lanhe River, a tributary of the Hanjiang river basin, which caused panic within local residents. The water quality and the algae community structure were investigated to explore the mechanism for the “dark brown-water” in the reservoir. It was shown that the reservoir was eutrophicated and reached a heavy extent of algae bloom, and the dominating species were Bacillariophyta, Cyanophyta and Cryptophyta, of which, Bacillariophyta accounted for 90.4% of the total phytoplankton in terms of density; with respect to biomass, Bacillariophyta, Cryptophyta and Pyrrophyta were the top three phylum, and Bacillariophyta accounted for 92% of the total phytoplankton biomass. The predominant genera of diatom were Achnanthes exigua and Synedra spp., among which, Achnanthes exigua (98.2%) showed the highest abundance of dominance. Being eutrophic state of the Lin Hekou Reservoir, diatom blooms may be the main cause of “dark brown-water” and the diatom blooms are related to the factors of nutrient level, weather and hydrology conditions. With the aim of water safety of Central Line Project of South-to-North Water Diversion, catchment management and reduction of nutrients into reservoir are crucial for decreasing the risk of algae blooms in the channel-reservoir of Hanjiang river basin. Related Articles | Metrics

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Influencing factors of sexual harassment in adult female Tibetan macaques (Macaca thibetana) PANG Kui-hai, WANG Xi, LI Jin-hua 2020, 37 (4):  62.  doi: 10.3969/j.issn.2095-1736.2020.04.062 Abstract ( 221 )   PDF   Save  In non-human primates, sexual harassment behavior has been defined as any response from non-copulatory individuals to ongoing copulatory individuals. However, the motivation of adult females′ sexual harassment remains obscure. In this study, we analyzed the variation in patterns and factors of sexual harassment in Tibetan macaques (Macaca thibetana) at Mt. Huangshan, China from August 2016 to May 2017, using all occurrence sampling method. The results showed that the frequency of non-contact harassment was higher compared to the contact harassment (P<0.05); the frequency of sexual harassment among adult females was not significantly influenced by age-class (P>0.05); sexual harassment was positively correlated to social rank (P<0.05); adult females harassed toward kinship than non-kinship individuals more frequently (P<0.05). Our results suggested sexual harassment among adult females in Tibetan macaques is influenced by kinship or social rank. This study will provide some explanations about motivation of sexual harassment by adult females. Related Articles | Metrics

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Seasonal dynamics of bird community in Lhalu watland National Nature Reserve, Tibet, China ZHOU Sheng-ling, YANG Le, LIU Shan-si, YANG Zheng, WENG Shi-yang 2020, 37 (4):  66.  doi: 10.3969/j.issn.2095-1736.2020.04.066 Abstract ( 260 )   PDF   Save From May 2014 to April 2015, we investigated the diversity of birds in the Lhalu wetland, Lhasa， using line transect method. A total of 69 species were recorded, belonging to 26 families, 12 orders, accounting for 11.5% of( more than 600 specie) birds in Tibet of which one species(Grus nigricollis) of I national protection bird and one species of Ⅱ national protection bird were found. The geographic region system was dominated by Palearctic species with 39 species, accounting for 56.52%, including 17 species of Oriental birds and 13 species of widespread species. Resident was in the majority with 28(40.58%) species, followed 24(34.78%) species of migratory bird, 13 winter visitor and 11 summer visitor, and 17(24.64%) species of passage migrant or vagrant visitor. The similarity of birds in different seasons was the highest between spring and summer, and the lowest between winter and summer. In spring and autumn, the number of species was abundant, but the population was small,and in winter the number of species was low, but the population was large. Compared with each month, it could be seen that the population in January was the highest, the number of species in May was the highest, and the population and number of species in July were both the lowest. Bird diversity showed two small peaks in May and November, and the values of Simpson and Pielou were stable throughout the year. Related Articles | Metrics

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Establishment of a model of two-head planarian XI Xing-zi, WANG Hong-liang, MA Ke-xue 2020, 37 (4):  72.  doi: 10.3969/j.issn.2095-1736.2020.04.072 Abstract ( 395 )   PDF   Save How animals establish the anterior-posterior (AP) polarity of body is one of the most fundamental problems in biology. The positional distribution of Hox genes along the AP polarity of body may be important for primary axis patterning during animal development. Observations have revealed that Wnt/β-catenin signaling controls the AP axis patterning in most animals and is indispensable for posterior formation. Planarians possess AP polarity of body, the anterior part of the body is head and the posterior part of the body is tail. Interference of β-catenin-1 expression can reverse the AP polarity, which induce two-head planarian phenotype. However, it is an unsolved question that how the disturbance of β-catenin-1 affects the Hox genes arrangements in planarians. To answer this question, it is essential to establish a model of two-head planarian. In this work, double-stranded RNA (dsRNA) of β-catenin-1 was transcribed in vitro and was fed to planarians by mixing with liver paste, resulting in two-head phenotype. The ratio of two-head planarian phenotype could reach 100% under our experimental condition. Compared with ingestion of bacterially expression dsRNA and injection of dsRNA, the major advantage of feeding in vitro synthesized dsRNA is that it provides a simple, quantity-controllable, easily-practical method for RNA interference (RNAi) in planarians. Related Articles | Metrics

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Research on the complex of horseradish peroxidase with fluorescent carbon dots LIU Li, DING Hai-zhen, FANG Wei, BI Hong 2020, 37 (4):  75.  doi: 10.3969/j.issn.2095-1736.2020.04.075 Abstract ( 239 )   PDF   Save Horseradish peroxidase (HRP) is a glycoprotein containing iron ions derived from horseradish that can be used for biochemical analysis, and catalyze the phenol in the presence of hydrogen peroxide. HRP can be combined with many substances to improve its performance and application. This work used a one-step hydrothermal method to easily synthesize fluorine-doped fluorescent carbon dots (F-CDs) with an average size of 2 nm. The as-synthesized F-CDs had obvious excitation light dependence, showing yellow-green fluorescence under ultraviolet light, and concentration dependence. The relative quantum yield was calculated to be as high as 45.6% with the quinoline sulfate as a reference. The results indicated that F-CDs have better fluorescence imaging performance in Hela cells, and F-CDs can form stable complexes (F-CDs/HRP) with HRP. The F-CDs/HRP complex not only preserved the ability of the enzyme to oxidize 2,2′-diazide-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS), but also retained the excellent fluorescence performance of F-CDs. Moreover, the added hydrogen peroxide concentration will affect the ability of F-CDs/HRP to catalyze the oxidation of ABTS. At the temperature as low as 4 ℃, HRP still kept the activity to catalyze the oxidation of ABTS. Therefore, the catalytic activity of HRP in the obtained F-CDs/HRP could be analyzed qualitatively by the degree of chromogenic reaction. Therefore, the F-CDs/HRP complex has potential for application in immunofluorescence analysis. Related Articles | Metrics

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The influence of naringenin on acute radiation-induced skin reaction ZHANG Qian-yu, XU Bin, JIN Wei, ZHOU Shou-bin, LI Wen-juan, ZHANG Qiu-jun, HU Dan-dan, LI Wen-yu, LIU Hu 2020, 37 (4):  79.  doi: 10.3969/j.issn.2095-1736.2020.04.079 Abstract ( 316 )   PDF   Save Acute radiation-induced skin reaction is a common complication during radiation therapy and no standard and effective therapy is available currently. Naringenin is a flavonoid compound rich in fruits. In order to evaluate whether naringenin ameliorates acute radiation skin dermatitis and relative mechanism, forty male rats were divided into 5 groups randomly, including external naringenin scream prophylactically group, external naringenin cream therapeutically group, intragastrical naringenin group, irradiation model group and control group. The cutaneous damage to the rats was assessed after irradiation, the serum IL-6 and MCP-1 of the rats were also detected, the pathological change of skin structure under microscope was observed, and the local macrophage expression was analyzed. To further explore whether naringenin has a protective effect on patients suffering from radiation, eleven patients with bilateral neck radiotherapy due to head and neck tumors were enrolled. Before radiotherapy, one side was applied naringenin cream and the other side was used as a control. The results showed that the use of naringenin significantly reduced the severity of radiation dermatitis in rats, reduced the concentration of serum IL-6 and MCP-1 and local macrophage infiltration, and improved the epidermal and dermal structural disorders caused by radiotherapy. Among the 11 patients, 2 patients had better dermatitis on the medication side than the control side. Therefore, this study showed that naringenin could improve radiation dermatitis in rats by reducing macrophage infiltration and inflammatory factor levels. Although the effectiveness is limite, it is safe clinically. Related Articles | Metrics

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Review on the synthesis and function of 1-methylguanosine on transfer RNAs ZHANG Tao, LIU Xue, CHEN Peng 2020, 37 (4):  85.  doi: 10.3969/j.issn.2095-1736.2020.04.085 Abstract ( 419 )   PDF   Save Many nucleosides in transfer RNAs are modified. Modified nucleosides play important roles in the structure and function of tRNAs. Up to now, more than 108 kinds of modified nucleosides have been identified, and methylation is one of most commonly found post-transcriptional modification on tRNA molecules. Methylation and N1 position of guanosine, or 1-methylguanosine (m1G), is presented on different tRNAs. Studies have shown that the presence of m1G at those locations are good for stabilizing tRNA tertiary structure, correct folding and preventing translational error. In this review, we discussed the location and functionality of m1G, summarized enzymes found for m1G, and compard their biochemical activity and biological roles in different organisms, with highlight on the mechanism difference on the synthesis and difference on substrate recognition by protein domains for each of the activity. we hope to provide a reference for the study of m1G nucleoside modification and its related proteins, and to give insight for future research in related area. Related Articles | Metrics

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Research progress on key metabolic enzymes in de novo synthesis pathway of ceramide LI Yu-hui, CHEN Cheng 2020, 37 (4):  90.  doi: 10.3969/j.issn.2095-1736.2020.04.090 Abstract ( 1318 )   PDF   Save Ceramide is an important active lipid that regulates cell differentiation, proliferation, apoptosis, aging, tumor immunity and other vital life activities, and it is also a universal precursor for a series of important physiological sphingolipids such as glycosphingolipids. As the center of sphingolipid metabolism, the syntheses and degradations of ceramide in the body are strictly regulated. Its syntheses include de novo synthesis pathway, sphingomyelinase pathway and remedy pathway. Although de novo synthesis pathway contributes only 5%-10% to the synthesis of ceramide in the body, recent studies on key metabolic enzymes in this pathway have shown that they are closely related to many diseases, which also illustrates the complexity and importance of this pathway in the life of the organism. The purpose of this article is to systematically review the research progress of key metabolic enzymes in de novo synthesis, in order to provide a theoretical reference for further understanding of this pathway and the functions of key metabolic enzymes, and also lay an foundation for the development of personalized medicine for this pathway in the future. Related Articles | Metrics

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Application of the different models of GWAS on Sclerotinia sclerotiorum resistance in soybean ZHANG Yu, ZHOU Wan-ying, FRANOIS Belzile 2020, 37 (4):  96.  doi: 10.3969/j.issn.2095-1736.2020.04.096 Abstract ( 261 )   PDF   Save SNP results that had been previously obtained via Illumina Hiseq2000 sequencing of 126 soybean strains were analyzed using two methods (using all 126 samples and using only extreme phenotypes) for association with stem lesion length data that had been collected subsequent to inoculation with Sclerotinia sclerotiorum. The association analysis, based on both single SNPs and haplotypes, was performed. When α≤0.05, MAF values of 0.01, 0.05, and 0.1 yielded the same loci; however, a more restrictive MAF threshold of 0.25 resulted in relatively different association loci, with the exception of only a single chromosome. Furthermore, peak SNPs also appeared in their corresponding haplotypes. The analysis based on the association of all samples and extreme phenotypes in PLINK v1.07 and HAPLOVIEW4.2 showed little difference. The results of significant correlation by SNP-Trait association locus were significantly different from those of Haplotype-Trait association, However, there is less difference in stronger correlations. Some potential significant SNP loci and related genes related to soybean Sclerotinia sclerotiorum resistance were found. Related Articles | Metrics

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Medium optimization of cold-active amylase by Pseudomonas sp. using response surface methodology WANG Ji-lian, REN Yu, LI Ming-yuan 2020, 37 (4):  101.  doi: 10.3969/j.issn.2095-1736.2020.04.101 Abstract ( 236 )   PDF   Save The fermentation medium for the clutivation of cold-active amylase producing strain Pseudomonas sp. D5-2, which was isolated in previous studies, was optimized to improve its enzyme production capacity. The effect of medium factor was determined by single factor test. Then, base on surface methodology, a Box-Benhnken design was used to identify the optimal level and interaction of significant factors to obtain the best combination. The results revealed that lactose, peptone and Cu2+were important factors affecting fermentation. The optimal conditions for producing of the maximal amylase activity by strain pseudomones sp. were as follows: 19.715 g/L lactose, 14.191 g/L peptone and 2.417 g/L CuSO4. Under the conditions, the highest amylase activity was predicted to be 98.876 U/mL, and the actual value was 99.2 U /mL, which was highly consistent with the theoretical model. The Box-Benhnken response surface method is feasible to optimize the fermentation medium of D5-2, which can provide guidance for the explanation of catalytic mechanism and industrial application of cold-active enzyme. Related Articles | Metrics

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Optimization of Escherichia coli CRISPR/Cas9 gene editing system and its application SHAO Meng-yao, LU Fu-ping, ZHU Xin-na, ZHANG Xue-Li 2020, 37 (4):  106.  doi: 10.3969/j.issn.2095-1736.2020.04.106 Abstract ( 652 )   PDF   Save CRISPR/Cas9 gene editing system has been widely used in the construction of Escherichia coli engineering strains. If a continuous gene editing-based CRISPR/Cas9 system can be constructed, the construction efficiency of E. coli engineering strains will be greatly improved. In this study, a donor plasmid pV4, with self-cutting function was constructed to optimize the existing double plasmid CRISPR/Cas9 gene editing system in the laboratory, and to realize the continuous knockout or integration of the gene. Three elements were added to the skeleton region of the original donor plasmid placZ: the N20-gRNA sequence of chloramphenicol gene(Cat) on the donor plasmid; Ptrc promoter; lacIq sequence. After gene editing with pV4 series plasmids(knockout or integration), these elements were induced by IPTG and with the help of Cas9 protein to achieve self-cutting of donor plasmids. The optimized pV4 series plasmids(knockout or integration) were used to engineer a strain to produce itaconic, and the result showed that this new CRISPR/Cas9 gene editing system can quickly perform continuous knockout or integration of genes, which is a broad prospect of construction and application of engineering strains. Related Articles | Metrics

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Micro lesson design: from base to artificial life—De novo synthesis of genome WANG Dong-mei, HONG Jiong 2020, 37 (4):  111.  doi: 10.3969/j.issn.2095-1736.2020.04.111 Abstract ( 286 )   PDF   Save As a supplementary way, micro lesson has been applied widely in teaching activities. DNA chemical synthesis of large scale and high throughput is a key technique in the study of synthetic biology. Here we designed a micro lesson to introduce this knowledge. The teaching background, learning objective, teaching content were introduced. The key points and difficulties were analyzed. The learning activities were outlined, and finally, the knowledge points were summarized. We also introduced the teaching characteristics, teaching effects and evaluation of this micro lesson. And finally we shared some experience of making this micro lesson. The results showed that this teaching practice stimulated the learning interests of students and improved the teaching efficiency. Related Articles | Metrics

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Project-based assignments connecting classroom teaching with scientific frontiers in a zoology course LEI Lei, JIANG Xiao-dong 2020, 37 (4):  115.  doi: 10.3969/j.issn.2095-1736.2020.04.115 Abstract ( 291 )   PDF   Save The project-based assignments connecting classroom teaching with scientific frontiers were designed in a zoology course by using related Nature and Science papers in order to cultivate self-learning ability and critical thinking in students, and to modify the unfavorable situation stressing on memory but ignoring creativity. The project-based assignments were implemented through group cooperation, including literature retrieval, paper selection, reading comprehension, content presentation, online discussion, teaching feedback, and works archiving. The project-based assignments guided an early leading in academic reading, enhanced enthusiasm for active learning, and promoted communication. The project-based assignments were based on an online course platform, and combined modern technology with classroom teaching to achieve online and offline blended teaching. Related Articles | Metrics

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Application of bilingual teaching in oncology LYU Yin 2020, 37 (4):  120.  doi: 10.3969/j.issn.2095-1736.2020.04.120 Abstract ( 205 )   PDF   Save The morbidity and mortality of malignant tumors continue to rise, becoming the biggest threat to the lives and health of Chinese residents today. Oncology is developing rapidly, and cooperation and communication with the international are increasing. The cultivation of high-quality medical personnel in line with international standards needs urgent attention. Bilingual education with Chinese and English is an important way of providing medical students with high-quality training and education, as well as a globalized perspective. It has been recognized as an important measure of improving the quality of medical education in China. In recent years, many medical schools in China have made continuous progress and achievements in the implementation of bilingual teaching, but some problems also need to be resolved. Promoting the organic integration of bilingual teaching with China′s medical education deserves attention.This paper will discuss the effect and significance of applying the bilingual education strategy in clinical oncology in Anhui Medical University as a reference for further development of bilingual teaching in clinical medicine in China. Related Articles | Metrics

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Exploration for the laboratory rotation tutor system in all-round practice teaching system of the undergraduate HE Jie, NIE Huan, SHI Ming, WEI Li-jun, MA Wen-jun, LI Yu 2020, 37 (4):  124.  doi: 10.3969/j.issn.2095-1736.2020.04.124 Abstract ( 234 )   PDF   Save In the process of cultivating undergraduate students in universities, a very significant purpose is to improve students′ scientific research and innovation ability and to realize the cultivation of all-round talents. The cultivation of practical operation ability is an important part of the practical teaching of undergraduates. However, a considerable number of colleges and universities currently are facing the problems such as the large number of students, limited experimental hours, and lack of practical opportunities. In view of the problems above, combined with the "strive to improve the whole staff, the whole process and the all-round education system" put forward by our Institute, this paper explicited the implementation scheme of the laboratory rotation tutor system in the cultivation of undergraduate students majoring in biology，and determined the cycle and requirements of the laboratory rotation, improved the experimental content of the laboratory rotation, and established the evaluation method of the system. After more than two years′ practice, it showed that the system made full use of students′ initiative, helped students to choose their favorite research direction, trained students′ comprehensive quality and creative thinking of scientific research and further improved the quality of undergraduate practice teaching. Related Articles | Metrics

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he application of MATLAB software in the teaching process of biostatistics——a case study of sampling distribution YING Zhi-xia, ZHANG Huan, GE Gang, ZOU Zhi-wen 2020, 37 (4):  127.  doi: 10.3969/j.issn.2095-1736.2020.04.127 Abstract ( 311 )   PDF   Save Biostatistics, as an indispensable tool in modern agricultural scientific and production, is a compulsory basic course for undergraduates in the field of life sciences. In biostatistics, sampling distribution serves as the basis of statistical inference theory and plays a linking role in probability theory and inference statistics. However, the abstraction and complexity of the theory causes the difficulty for beginners′ understanding which may further lead to a poor teaching effect. Therefore, it is imperative to apply MATLAB software in the teaching process to enhance students′ learning interest and understanding ability via real-time simulation and display in classroom teaching, and thus improve the teaching effect. In this study, the MATLAB software is introduced to design and compile the simulation of several common sampling distributions, i.e., the u distribution, the t distribution and the χ2 distribution from a normal distribution population. The simulation results that intuitively describe the sampling distribution deepen students′ understanding and mastery of the relationship between the population parameters and sample statistics, and sampling distribution which provides an auxiliary tool for the theoretical teaching process of biostatistics. Related Articles | Metrics