Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

Transcription factor is a key trans-acting factor to mediate stress response by regulating gene expression. Plants have developed a series of mechanisms to modulate development, stress response, signaling and disease resistance at transcription level. DNA binding with one finger (DOF), containing one C₂-C₂ zinc finger domain, is a special plant transcription factor. Specifically, the conserved domain at N-terminus of DOF has multiple functions, including interacting with DNA and protein, which could be involved in plant development and stress response. Although many DOF family genes are characterized in plant stress response, it is not clear if DOF genes have functions in cereal plants. In the present paper, the role of DOF family genes on cereal plants were discussed based on a comprehensive phylogenetic relationship analysis, expression profiles in different tissues and various environmental conditions. The results obtained here will provide an important reference for further understanding the mechanism of gramineous crops in stress resistance.
DNA-Binding Proteins ; metabolism ; Gene Expression Regulation, Plant ; Phylogeny ; Plant Proteins ; metabolism ; Plants ; genetics ; Transcription Factors ; metabolism ; Zinc Fingers

In order to investigate the enzyme production mechanism of yak rumen-derived anaerobic fungus Orpinomyces sp. YF3 under the induction of different carbon sources, anaerobic culture tubes were used for in vitro fermentation. 8 g/L of glucose (Glu), filter paper (Flp) and avicel (Avi) were respectively added to 10 mL of basic culture medium as the sole carbon source. The activity of fiber-degrading enzyme and the concentration of volatile fatty acid in the fermentation liquid were detected, and the enzyme producing mechanism of Orpinomyces sp. YF3 was explored by transcriptomics. It was found that, in glucose-induced fermentation solution, the activities of carboxymethyl cellulase, microcrystalline cellulase, filter paper enzyme, xylanase and the proportion of acetate were significantly increased (P < 0.05), the proportion of propionate, butyrate, isobutyrate were significantly decreased (P < 0.05). The results of transcriptome analysis showed that there were 5 949 differentially expressed genes (DEGs) between the Glu group and the Flp group, 10 970 DEGs between the Glu group and the Avi group, and 6 057 DEGs between the Flp group and the Avi group. It was found that the DEGs associated with fiber degrading enzymes were significantly up-regulated in the Glu group. Gene ontology (GO) function enrichment analysis identified that DEGs were mainly associated with the xylan catabolic process, hemicellulose metabolic process, β-glucan metabolic process, cellulase activity, endo-1,4-β-xylanase activity, cell wall polysaccharide metabolic process, carbohydrate catabolic process, glucan catabolic process and carbohydrate metabolic process. Moreover, the differentially expressed pathways associated with fiber degrading enzymes enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were mainly starch and sucrose metabolic pathways and other glycan degradation pathways. In conclusion, Orpinomyces sp. YF3 with glucose as carbon source substrate significantly increased the activity of cellulose degrading enzyme and the proportion of acetate, decreased the proportion of propionate, butyrate and isobutyrate. Furthermore, the degradation ability and energy utilization efficiency of fungus in the presence of glucose were improved by means of regulating the expression of cellulose degrading enzyme gene and participating in starch and sucrose metabolism pathway, and other glycan degradation pathways, which provides a theoretical basis for the application of Orpinomyces sp. YF3 in practical production and facilitates the application of Orpinomyces sp. YF3 in the future.
Animals ; Cattle ; Neocallimastigales/metabolism* ; Anaerobiosis ; Rumen/microbiology* ; Propionates/metabolism* ; Isobutyrates/metabolism* ; Cellulose/metabolism* ; Fungi ; Starch/metabolism* ; Glucose/metabolism* ; Acetates ; Sucrose/metabolism* ; Cellulases ; Cellulase

Gibberellin is an essential plant hormone that plays an important regulatory role throughout the life cycle of higher plants. A total of 23 genes involved in gibberellin action were identified from Phyllostachys edulis genome, including 8 GA20ox and 1 GA3ox genes involved in the gibberellin biosynthesis, 8 GA2ox genes involved in the metabolism of gibberellin, 2 GID1 genes involved in gibberellin perception, 2 GID2 genes and 2 DELLA genes involved in gibberellin signal transduction. Phylogenetic analysis of these genes from Arabidopsis, Oryza sativa and Phyllostachys edulis revealed that gibberellin biosynthesis, metabolism, and signaling pathways are conserved in these species. Treatment of seeds and seedlings of bamboo with exogenous gibberellin revealed that gibberellin significantly increased seed germination rate and stem elongation of seedlings, and had the best concentration of action. The expression levels of GA20ox and GA3ox genes in the bamboo seedlings were down-regulated and the expression of the active gibberellin-degrading gene GA2ox was up-regulated after GA3 treatment, and the transcriptional level of the gibberellin receptor GID1 and the positive regulatory gene GID2 was significantly increased while the expression of the negative regulatory gene DELLA was decreased. These genes have significant differences in the expression of different spatial locations of bamboo shoot stems, GA20ox, GA3ox, GA2ox, GID1 and GID2 are all expressed in the upper part of bamboo shoots, while the repressor gene DELLA accumulates at the bottom of the shoots and is hardly expressed at the top.
Arabidopsis ; Gene Expression Regulation, Plant ; Gibberellins ; biosynthesis ; Phylogeny ; Plant Growth Regulators ; Plant Proteins ; Poaceae

Long terminal repeat (LTR) retrotransposons are mobile DNA sequences that ubiquitously exist in eukaryotic genomes. They replicate themselves in the genome by copy-paste mechanism with RNA as medium. In higher plants, many active LTR retrotransposons have been applied to analyze molecular marker technology, genetic tagging, insertion mutation and gene function. Here, we systematically review the characteristics of plant active LTR retrotransposons, including their structures, copy numbers and distributions. We further analyzed the gag (group-specific antigen) and pol (polymerase) sequence features of different plants active LTR retrotransposons and the distribution patterns of the cis-acting elements in LTR regions. The results show that autonomous active LTR retrotransposons must contain LTR regions and code Gag, Pr, Int, Rt, Rh proteins. Both LTR regions are highly homologous with each other and contain many cis-regulatory elements; RVT and RNase_H1_RT domain are essential for Rt and Rh protein respectively. These results provide the basis for subsequent identification of plant active LTR retrotransposons and their functional analysis.
Genome, Plant ; Mutagenesis, Insertional ; Plants ; genetics ; Retroelements ; Terminal Repeat Sequences

Objective: To understand the epidemiological and etiological characteristics of mumps in Fujian province, 2005-2017. Methods: All the reported mumps cases were collected through the National Notifiable Disease Information Management System, 2005-2017. Active search and interviews were conducted to collect the information on vaccination of mumps. Throat swab specimens were collected for cells culture, genotyping and gene sequence analysis on mumps virus (MuV). Results: A total of 83 959 cases of mumps were reported in Fujian province from 2005 to 2017, with an average annual incidence of 17.6 per 100 000. Since 2007, the incidence appeared increasing but then decreasing, reaching the lowest level (7.5 per 100 000), after the setup of a monitoring program. Annually, the onset time of mumps showed an obvious two seasonal peaks, one from April to July, with a weakening trend, and the other from October to January with a rising trend. Most of the mumps cases occurred among students, kindergarten and scattered children (89.2%, 5 814/6 517), children aged 5-9 years (38.8%, 2 527/6 517), with cases reported from every region. Program from the pathogen surveillance showed that the transmission chain of G genotype mumps virus did exist in Fujian. Data from the sequence analysis revealed that mutations in the nucleotide of G genotype strain in 2015 had led to mutation of 6 amino acid sites in the SH gene coding region, resulting in the differences appearing in both nucleotide and amino acid homology with type A vaccine strain. Conclusions: The incidence of mumps decreased annually, in Fujian. Prevention programs should focus on primary and secondary school students. In Fujian province, we also noticed the transmission chain of mumps G genotype with some amino acid mutations in the SH gene coding region. Monitor programs on both epidemiologic and etiology, should be strengthened.
Child ; Child, Preschool ; China/epidemiology* ; Genotype ; Humans ; Incidence ; Mumps/epidemiology* ; Mumps virus/pathogenicity* ; Phylogeny ; Sequence Analysis

To research the expression of key enzymes in saikosaponin biosynthesis and the content of saikosaponin under the drought stress, the study focused on the gene-level and the end product responses to environmental change. Taking the five months of Bupleurum chinense as research materials, the contents of saikosaponin A and saikosaponin D under different stress levels were measured by HPLC. The drought was simulated by poly ethylene glycol. The real-time fluorescence quantitative PCR was used to analyze the expression of four key enzymes genes HMGR, IPPI, FPS, β-AS and the expression of β-tubulin was set as a reference gene. The results showed that drought stress significantly improved the content of saikosaponin. The contents of SSa and SSd were highest researching 0.648% and 0.781%, respectively when the concentration of PEG was 10%. Meanwhile, the results reflected that the expression of four key enzymes had risen differently and FPS, β-AS raised significantly(P<0.01). In addition, the results of correlation analysis showed that there was a significant positive correlation between the expression of the four key enzymes genes and the content of saikosaponin. In a word, the contents of secondary metabolites were regulated by the expression of key enzymes genes under the drought stress in B. chinense.

To develop more active LTR retrotransposons in Phyllostachys edulis, a Ph. edulis LTR retrotransposon (Ph-LTR2) was identified, and the expression pattern of the transposon under stress was systematically analyzed. Ph-LTR2 transposon is 6 030 bp in length and belongs to the Reina subfamily in the Ty3-Gypsy family. With the similarity of 96.41% of both LTR sequences, the Ph-LTR2 transposon inserted the moso bamboo genome about 61.92 thousand years ago. There are 5 copies identified in the genome. The Ph-LTR2 transposon domain includes GAG (gag protein) protein domain, PR (Proteases) protein domain, RT (Reverse transcriptase) protein domain, RH (Ribonuclease H) protein domain, INT (Integrase) protein domain and CHR (Chromatin organization modifier) protein domain. The expression patterns of INT, RT and RH were detected by real-time quantitative PCR. The three domains were found to have specific expression patterns at different tissues of the bamboo. Under the conditions of low/high temperature, methylation inhibitors treatments, irradiation and high salt stress, transcription levels of the three domains of the Ph-LTR2 transposon increased with different degrees. Specifically, after treatment with low/high temperature and methylation inhibitors, the transcription level was up-regulated; after low dose radiation treatment and low concentration of salt solution treatment, the transcription level was also increased, but the expression level decreased with increasing dose of radiation and concentration of salt solution. These results indicate that the expression pattern of the Ph-LTR2 transposon responds to the changes of the external environment, but the exact mechanism is not yet known. The results of this study laid a certain theoretical foundation for the development of the genetic tool based on Ph-LTR2 transposons.
Genome ; Phylogeny ; Poaceae ; Retroelements

Headspace-solid phase microextraction/gas chromatography-mass spectrometry (HS-SPME/GC-MS) were used to analyze the interaction between the β-lactoglobulin (β-LG) and the botany volatile organic compounds (BVOCs) from pomelo peel to screen out the pharmacodynamic active BVOCs substance group. The selective binding effect between β-LG and BVOCs was analyzed by quantitative recovery of BVOCs, and the binding parameters were calculated. Then, the molecular model of BVOCs binding with β-LG was established by molecular docking and spectroscopic method, and the molecular mechanism of interaction between pharmacodynamic active BVOCs and β-LG was discussed from the perspective of omics. The results showed that dipentene (Dt), linalylacetate (La) and nootkatone (Nt) of BVOCs were selected by HS-SPME/GC-MS by the interaction of β-LG and BVOCs substance group. Parameter calculation showed that β-LG had the strongest affinity with Nt, but the binding force was not strong, and the affinity for La was the weakest. The affinity of β-LG to Dt was weak, but the binding force was the strongest, with a binding rate of 54. 66%, indicating that the selective binding strength of β-LG with the pharmacodynamic active BVOCs depended on the chemical structure of BVOCs molecules. The β-LG preferred to bind to the aldehyde and ketone BVOCs molecules containing carbonyl oxygen structure. The molecular model of β-LG and BVOCs group (Dt, La, Nt) was established to evaluate the binding position of BVOCs group (Dt, La, Nt) on β-LG. The loosening, extension and conformational change of β-LG secondary structure caused by the introduction of BVOCs are the result of van der Waals force, hydro-phobicity and hydrogen bonding. This study provides a new method for screening pharmacodynamic active BVOCs from the perspective of whole substance group of BVOCs, and provides a useful reference for investigating the binding mechanism between pharmacodynamic active BVOCs and functional protein molecules from the perspective of omics.

BACKGROUNDElective radiation of lower neck is controversial for nasopharyngeal carcinoma (NPC) without lymph node metastasis (N0 disease). Tumor volume is an important prognostic indicator. The objective of this study is to explore the potential impact of tumor volume on the indication of the lower neck irradiation for N0-NPC, by a qualitative evaluation of the relationship between tumor volume and nodal metastasis.

METHODSMagnetic resonance (MR) images of 99 consecutive patients with NPC who underwent treatment were retrospectively reviewed. Primary tumor volumes of NPC were semi-automatically measured, nodal metastases were N-classified and neck level involvements were examined. Distributions of tumor volumes among N-category-based groups and distributions of N-categories among tumor volume-based groups were analyzed, respectively.

RESULTSThe numbers of patients with N0 to N3 disease were 12, 39, 32, and 16, respectively. The volumes of primary tumor were from 3.3 to 89.6 ml, with a median of 17.1 ml. For patients with nodal metastasis, tumor volume did not increase significantly with the advancing of N-category (P > 0.05). No significant difference was found for the distribution of N1, N2, and N3 categories among tumor volume-based groups (P > 0.05). Nevertheless patients with nodal metastasis had significantly larger tumor volumes than those without metastasis (P < 0.05). Patients with larger tumor volumes were associated with an increased incidence of nodal metastasis.

CONCLUSIONSCertain positive correlations existed between tumor volume and the presence of nodal metastasis. The tumor volume (>10 ml) is a potential indicator for the lower neck irradiation for N0-NPC.

Adolescent ; Adult ; Aged ; Carcinoma ; Female ; Humans ; Lymphatic Metastasis ; Male ; Middle Aged ; Nasopharyngeal Neoplasms ; pathology ; radiotherapy ; Neck ; radiation effects ; Retrospective Studies ; Tumor Burden