Named entity recognition of rice genes and phenotypes based on BiGRU neural networks.

Named Entity Recognition (NER) is a fundamental but crucial task in natural language processing (NLP) and big data analysis, with wide application range. NER for rice genes and phenotypes is a technique to identify genes and phenotypes from a large amount of text. NER for rice genes and phenotypes can facilitate the acquisition of information in the field of crops and provide references for our research on higher quality crops. At the same time, named entity recognition still faces many challenges. In this paper, we propose an improved bidirectional gated recurrent unit neural network (BI-GRU) method, which is used to automatically identify the required entities (i.e. gene names, rice phenotypes) from relevant rice literature and patents. The neural network model is combined with the Softmax function to directly output the probabilities of labels, forming the BI-GRU-SF model. With the ability of deep learning methods, the semantic information in the context can be learned without the need for feature engineering. Finally, we conducted experiments, and the results showed that our proposed model provided better performance compared to other models. All datasets and resource codes of BI-GRU-SF are available at https://github.com/qqeeqq/NER for academic use.

Whole-Genome Resequencing Reveals the Diversity of Patchouli Germplasm.

As an important medicinal and aromatic plant, patchouli is distributed throughout most of Asia. However, current research on patchouli's genetic diversity is limited and lacks genome-wide studies. Here, we have collected seven representative patchouli accessions from different localities and performed whole-genome resequencing on them. In total, 402,650 single nucleotide polymorphisms (SNPs) and 153,233 insertions/deletions (INDELs) were detected. Based on these abundant genetic variants, patchouli accessions were primarily classified into the Chinese group and the Southeast Asian group. However, the accession SP (Shipai) collected from China formed a distinct subgroup within the Southeast Asian group. As SP has been used as a genuine herb in traditional Chinese medicine, its unique molecular markers have been subsequently screened and verified. For 26,144 specific SNPs and 16,289 specific INDELs in SP, 10 of them were validated using Polymerase Chain Reaction (PCR) following three different approaches. Further, we analyzed the effects of total genetic variants on genes involved in the sesquiterpene synthesis pathway, which produce the primary phytochemical compounds found in patchouli. Eight genes were ultimately investigated and a gene encoding nerolidol synthetase (PatNES) was chosen and confirmed through biochemical assay. In accession YN, genetic variants in PatNES led to a loss of synthetase activity. Our results provide valuable information for understanding the diversity of patchouli germplasm resources.

Global dissection of R2R3-MYB in Pogostemon cablin uncovers a species-specific R2R3-MYB clade.

MYB family is one of the largest transcription factor families in plants and plays a crucial role in regulating plant biochemical and physiological processes. However, R2R3-MYBs in patchouli have not been systematically investigated. Here, based on the gene annotation of patchouli genome sequence, 484 R2R3-MYB transcripts were detected. Further in-depth analysis of the gene structure and expression of R2R3-MYBs supported the tetraploid hybrid origin of patchouli. When combined with R2R3-MYBs from Arabidopsis, a phylogenetic tree of patchouli R2R3-MYBs was constructed and divided into 31 clades. Interestingly, a patchouli-specific R2R3-MYB clade was found and confirmed by homologous from other Lamiaceae species. The syntenic analysis demonstrated that tandem duplication contributed to its evolution. This study systematically analysed the R2R3-MYB family in patchouli, providing information on its gene characterization, functional prediction, and species evolution.

Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli.

Patchouli (Pogostemon cablin (Blanco) Benth.), a member of the Lamiaceae family, is an important aromatic plant that has been widely used in medicine and perfumery. Here, we report a 1.94 Gb chromosome-scale assembly of the patchouli genome (contig N50 = 7.97 Mb). The gene annotation reveals that tandem duplication of sesquiterpene biosynthetic genes may be a major contributor to the biosynthesis of patchouli bioactivity components. We further phase the genome into two distinct subgenomes (A and B), and identify a chromosome substitution event that have occurred between them. Further investigations show that a burst of universal LTR-RTs in the A subgenome lead to the divergence between two subgenomes. However, no significant subgenome dominance is detected. Finally, we track the evolutionary scenario of patchouli including whole genome tetraploidization, subgenome divergency, hybridization, and chromosome substitution, which are the key forces to determine the complexity of patchouli genome. Our work sheds light on the evolutionary history of patchouli and offers unprecedented genomic resources for fundamental patchouli research and elite germplasm development.

RicENN: Prediction of Rice Enhancers with Neural Network Based on DNA Sequences.

Enhancers are the primary cis-elements of transcriptional regulation and play a vital role in gene expression at different stages of plant growth and development. Having high locational variation and free scattering in non-encoding genomes, identification of enhancers is a crucial, but challenging work in understanding the biological mechanism of model plants. Recently, applications of neural network models are gaining increasing popularity in predicting the function of genomic elements. Although several computational models have shown great advantages to tackle this challenge, a further study of the identification of rice enhancers from DNA sequences is still lacking. We present RicENN, a novel deep learning framework capable of accurately identifying enhancers of rice, integrating convolution neural networks (CNNs), bi-directional recurrent neural networks (RNNs), and attention mechanisms. A combined-feature representation method was designed to extract the sequence features from original DNA sequences using six types of autocorrelation encodings. Moreover, we verified that the integrated model achieves the best performance by an ablation study. Finally, our deep learning framework realized a reliable prediction of the rice enhancers. The results show RicENN outperforms available alternative approaches in rice species, achieving the area under the receiver operating characteristic curve (AUROC) and the area under the precision-recall curve (AUPRC) of 0.960 and 0.960 on cross-validation, and 0.879 and 0.877 during independent tests, respectively. This study develops a hybrid model to combine the merits of different neural network architectures, which shows the potential ability to apply deep learning in bioinformatic sequences and contributes to the acceleration of functional genomic studies of rice. RicENN and its code are freely accessible at http://bioinfor.aielab.cc/RicENN/ .

Towards highly specific aptamer-affinity monolithic column by efficient UV light-initiated polymerization in "one-pot".

Time-consuming or tedious operation in multiple-step process might is the obstacle for efficiently preparing aptamer-affinity monolithic column. Here, a new and facile strategy to prepare aptamer-based hybrid affinity monolith in "one-pot" at room temperature was exploited, in which UV light-initiated free-radical polymerization and "thiol-ene" click reaction were implemented simultaneously. Only 7 min was cost for finishing the polymerization reaction, which was only 1/100 of that for the traditional thermal polymerization. Using ochratoxin A (OTA) as the model analyte, the recipe for photo-initiated polymerization was optimized, and SEM morphology, FTIR, EDS, pore size distribution and specific recognition performance were also studied. Compared with traditional thermal polymerization, the resultant monolith was achieved more facilely and displayed better results such as more homogeneous skeleton structure, higher reaction efficiency of aptamer (>88.2%) and better specific selectivity to OTA. Besides, an extremely low nonspecific adsorption of analogues was obtained and showed a level at only 1/25 of that in the similar aptamer-affinity monolith prepared by thermal polymerization. Applied to beer and red wine samples, good recovery yields about 99.7 ± 4.0% -101.2 ± 2.3% (n = 3)was achieved with the acceptable RSDs. It would open up a rapid and promising access to efficiently preparing high-performance aptamer-based affinity monolithic columns for online specific recognition.

Online specific recognition of mycotoxins using aptamer-grafted ionic affinity monolith with mixed-mode mechanism.

Herein, a facile and practical aptamer-grafted ionic affinity monolith with mixed-mode mechanism was explored as a versatile platform for online specific recognition of polar and non-polar mycotoxins. The mixed-mode mechanism including molecular affinity adsorption (between aptamers and targets), hydrophilic interaction and ionic interaction (between stationary phase and targets) were adopted and provided a better flexibility in adjusting separation selectivity to reduce nonspecific adsorption with respect to the single mode. Preparation and characterization of aptamer-based affinity monoliths were investigated, The characterization of pore size distribution, Brunauer-Emmett-Teller (BET) surface area and the specificity and cross-reaction were also evaluated. As a result, the hydrophilic nature and negative charge on affinity monolith were obtained. Multiple interactions including aptamer affinity binding, hydrophilic interaction (HI) and ion exchange (IE) could be adopted for online selective extraction. Specific recognitions of polar ochratoxin A (OTA), non-polar zearalenone (ZEN) and aflatoxin B1 (AFB1) was fulfilled with LODs as 0.03, 0.05 and 0.05 µg/L, respectively. Applied to real cereals, good recoveries of the fortified OTA, AFB1 and ZEN were achieved as 92.6 ± 1.3% ~ 95.6 ± 1.3% (n=3), 93.9 ± 2.3% ~ 98.2 ± 3.4% (n=3) and 92.7 ± 2.0% ~ 96.9 ± 3.5% (n=3) in corn, wheat and rice, respectively. The results displayed that Apt-MCs with hydrophilic and ionic interaction mixed-mode mechanism were efficient enough and competent for the online recognition of mycotoxins in cereals.

Preparation and evaluation of highly hydrophilic aptamer-based hybrid affinity monolith for on-column specific discrimination of ochratoxin A.

Nonspecific adsorption is a challenge of specific recognition on aptamer-based affinity monoliths. Here, a novel highly hydrophilic polyhedral oligomeric silsesquioxane (POSS)-containing aptamer-based hybrid-silica affinity monolith with a good recognition nature was prepared and used for specific discrimination of ochratoxin A (OTA). A homogeneous polymerization mixture consisted of POSS chemicals, hydrophilic monomers and aptamer solution was directly polymerized via the "one-pot" method. Preparation and characterization of the resultant affinity monolith were studied in detail. A highly hydrophilic nature was obtained and the typical hydrophilic interaction liquid chromatography (HILIC) was observed when acetonitrile (ACN) content in mobile phase was 25%, which reached the highest hydrophilicity of POSS-based hybrid monoliths. By using OTA as model analyte, the nonspecific adsorption was effectively suppressed. The recovery of the analogue ochratoxin B (OTB) was only about 0.1% even if the content of OTB was 50 times more than OTA, which was much better than other POSS-containing monoliths and polar siloxane-based hybrid monoliths. Applied to beer samples, the adsorption of background materials was drastically resisted, and efficient recognition of OTA was obtained with the recoveries of 94.9-99.8%. Much less disturbance was observed than that occurred in hydrophobic POSS-based affinity monolith. It lights an attractive implement with high hydrophilicity and specificity for online selective recognition of OTA.

Preparation of aptamer-bound polyamine affinity monolithic column via a facile triazine-bridged strategy and application to on-column specific discrimination of ochratoxin A.

Developing a high-performance modification protocol is critical for efficiently fabricating affinity monolith. Herein, by using 2,4,6-trichloro-1,3,5-triazine as the linker, a simple triazine-bridged approach was proposed for efficiently fabricating aptamer-grafted polyhedral oligomeric silsesquioxane-polyethyleneimine affinity monolith with high specificity toward ochratoxin A. Experimental parameters, column characteristics and specificity performances of the resultant affinity monolith were investigated in detail. Under the optimal conditions, 2,4,6-trichloro-1,3,5-triazine was rapidly grafted on the polyamine matrix, and effectively applied to the subsequent bridge linkage of aptamers. It was simple and effective, which resulted in a significant decrease of modification time, excellent properties including the high coverage density of aptamer up to 1799 pmol/µL and sensitive detection of ochratoxin A as low as 10 pg/mL in beer samples. This protocol provides a facile approach for fabricating aptamer-grafted polyamine affinity monoliths with highly selective discrimination performance.

Highly hydrophilic polyhedral oligomeric silsesquioxane (POSS)-containing aptamer-modified affinity hybrid monolith for efficient on-column discrimination with low nonspecific adsorption.

A novel polyhedral oligomeric silsesquioxane (POSS)-containing aptamer-modified hybrid affinity monolith with excellent hydrophilicity and unique architecture without Si-OH groups is presented herein, and the nonspecific adsorption caused by the hydrophobic nature of the monolithic column or polar interaction with silanol groups is minimized. Via a simple "one-pot" procedure, hydrophilic monomers were facilely polymerized with the POSS-methacryl substituted (POSS-MA) and aptamer; a highly hydrophilic nature was obtained and the lowest contact angle of 11° was achieved. By using ochratoxin A (OTA) as the model analyte, highly selective recognition of OTA in the mixture was achieved and the control of nonspecific interactions and the cross-reactivity of OTB and AFB1 were significantly improved. The recovery yield of OTB caused by nonspecific adsorption in the resultant monolith was only about 0.1% and remained steady even with the coexistence of a high OTB content (OTA : OTB = 1 : 50), which reached the best level to date and was obviously less than the 6.1% occurring in the hydrophobic POSS-containing control monolith, 8.3% in the POSS-PEI@AuNPs@aptamer affinity monolith and 18.7% in the silica-hybrid affinity monolith. When applied to wine and wheat samples, the nonspecific adsorption was significantly reduced and efficient discrimination of OTA was obtained with better results than that of the hydrophobic POSS-containing affinity column. This provides an attractive tool for minimizing the nonspecific adsorption for highly selective on-column recognition.

Aptamer-based polyhedral oligomeric silsesquioxane (POSS)-containing hybrid affinity monolith prepared via a "one-pot" process for selective extraction of ochratoxin A.

A novel aptamer-based polyhedral oligomeric silsesquioxane (POSS)-containing hybrid affinity monolith has been prepared with a facile "one-pot" process simultaneously via "free radical polymerization" and "thiol-ene" click reaction, and used for on-line selective extraction and practical analysis to trace ochratoxin A (OTA). By using the ternary porogenic mixture composed of water/DMF/PEG, a homogeneous polymerization mixture with POSS chemicals, acrylate-based monomers and aptamer aqueous solution was obtained, and the copolymerization of POSS chemicals, polymer monomers and aptamer aqueous solution was systematically studied. Characterizations such as the morphology, FT-IR and fluorescence spectra, mechanical stability, dynamic binding capacity, cross-reactivity and selectivity of the resultant affinity monolith were also evaluated. Attributed to the porous monolithic structure and aptamer-based affinity interaction, acceptable selective recognition and recovery yields towards trace OTA were obtained. With a 5-fold volume enrichment, the limit of detection (LOD) and limit of quantitation (LOQ) of OTA in fortified beer samples were gained at 0.025 ng/mL (S/N = 3) and 0.045 ng/mL (S/N = 10), respectively. It could be competent for the sensitive measure of actual OTA residues in real beer samples. In comparison with the previously reported strategies containing common "sol-gel" chemistry, the proposed protocol to fabricating aptamer-modified POSS-containing hybrid affinity monolith showed a simpler preparation with acceptable selectivity and higher recovery to trace OTA.

[Water intake and its influencing factors of children and adolescents in Shanghai].

OBJECTIVE: To describe the total drinking water intake and its influencing factors among children and adolescents in Shanghai, and to accumulate basis for developing adequate water intakes for children and adolescents in China. METHODS: A total of 1454 children and adolescents aged 8-17 years from two districts of Shanghai was selected by using stratified random sampling method. The information on amounts and types of daily drinking water was recorded by subjects for seven consecutive days using a quantitative measurement. Total drinking water was the sum of plain water and beverages. RESULTS: The median of total drinking water of subjects was 1014 ml/d, and the median of plain water and beverages was 580 and 339 ml/d, respectively. The consumption of total drinking water, plain water, and beverages in boys was significantly higher than that in girls, was increasing with aging and in urban was significantly higher than that in suburbs (P < 0.05). The obese drank more beverages (P < 0.05). CONCLUSION: The total drinking water of children and adolescents in Shanghai was less. To establish adequate intake of water, the comprehensive effect of gender, age, BMI and region when should be considered.

Circulating CD4+ CD25+ regulatory T cells correlate with chronic hepatitis B infection.

Circulating CD4+ CD25+ regulatory T cells (Tregs) have been demonstrated to maintain immunotolerance and suppress the antigen-specific or antigen-non-specific T-cell responses, but their role in chronic hepatitis B (CHB) infection in humans has not been well characterized. In this study, we analysed the frequency and phenotypic characteristics of CD4+ CD25+ Tregs in patients of different hepatitis B virus (HBV) infection status, and investigated the effect of Tregs on antiviral immune responses in CHB patients, and the mechanism of this effect. A total of 137 subjects, including 79 CHB patients, 26 asymptomatic HBV carriers (ASCs), 12 acute hepatitis B (AHB) patients and 20 healthy controls, were enrolled in the study. We found that the frequency of CD4+ CD25(high) Tregs in AHB patients was comparable to that in healthy controls, while it was significantly increased in CHB patients. CD4+ CD25+ Tregs produced interleukin (IL)-10 but little or no interferon (IFN)-gamma under anti-CD3 stimulation. In CHB patients, the frequency of CD4+ CD25(high) Tregs positively correlated with serum viral load, and the Tregs were capable of suppressing the proliferation and IFN-gamma production of autologous peripheral blood mononuclear cells (PBMC) mediated by HBV antigen stimulation in vitro. However, combined administration of anti-programmed death-1 (PD-1) and anti-cytotoxic lymphocyte antigen-4 (CTLA-4) monoclonal antibody slightly enhanced the cellular proliferation and significantly increased the IFN-gamma production of PBMC cocultured with Tregs at a ratio of 2:1. Thus, the frequency of circulating CD4+ CD25+ Tregs is increased in patients with CHB, and this may play an important role in viral persistence by modulating virus-specific immune responses.

PD-1 upregulation is associated with HBV-specific T cell dysfunction in chronic hepatitis B patients.

Programmed death-1 (PD-1) is demonstrated to have an increased expression on antigen-specific T cells during chronic virus infections, and the blockage of PD-1/PD-ligand (PD-L1) pathway could restore the function of exhausted T cells. We measured the PD-1 expression levels on HBV-specific CD8 T cells and investigated the role of PD-1/PD-L1 pathway in T-cell responses of patients with different HBV infection statuses. Compared to the patients with convalescent acute hepatitis B, PD-1 expression on total CD8 T cells from chronic hepatitis B (CHB) patients was significantly upregulated, especially on the HBV pentamer-positive CD8 T cells. And PD-L1, but not PD-L2, was also significantly upregulated on PBMC from CHB patients. In CHB patients, HBV-specific T cells and cellular proliferation could be observed under the recombinant HBV-Ag stimulation in vitro, and blockade of PD-1 pathway significantly enhanced the IFN-gamma production and cellular proliferation of PBMC. Furthermore, PD-1 expression level on HBV-pentamers positive CD8 T cells was positively associated with plasma viral load in CHB patients. Thus, PD-1 upregulation on HBV-specific CD8 T cells is engaged in the dysfunction of T cells and high viraemia in CHB patients, and the antiviral T-cell responses could be improved by the blockade of this inhibitory PD-1/PD-L1 pathway.

Preparation and characterization of a novel exendin-4 human serum albumin fusion protein expressed in Pichia pastoris.

A novel recombinant exendin-4 human serum albumin fusion protein (rEx-4/HSA) expressed in Pichia pastoris was prepared and characterized. Ex-4 is a 39-amino acid peptide isolated from the salivary gland of the lizard Heloderma suspectum and is thought to be a novel therapeutic agent for type 2 diabetes. But to gain a continued effect, the peptide has to be injected twice a day owing to its short plasma half-life (t(1/2) = 2.4 h). To extend the half-life of Ex-4 molecule in vivo, we designed a genetically engineered Ex-4/HSA fusion protein. Between Ex-4 and HSA, a peptide linker GGGGS was inserted and the fusion protein was expressed in methylotrophic yeast P. pastoris with native HSA secretion signal sequence. The recombinant protein was secreted correctly and was obtained with high purity (typically > 98%) by a three-step purification procedure. cAMP assay demonstrated that the fusion protein had a bioactivity similar to Ex-4 for interaction with GLP-1 receptors in vitro. Results from oral glucose tolerance test indicated that rEx-4/HSA could effectively improve glucose tolerance in diabetic db/db mice. Pharmacokinetics studies in cynomologus monkeys also showed that rEx-4/HSA had a much longer plasma half-life. Therefore, rEx-4/HSA fusion protein could potentially be used as a new recombinant biodrug for type 2 diabetes therapy.