[Different active ingredients of medicinal plant based on function differentiation of homologous gene].

In the research field of quality control in Chinese medicinal materials, variation in active ingredients of medicinal plant is always the key and hot issues. With the development of high-throughput sequencing technologies and reducing cost, a large numbers of genes from medicinal plant were cloning and provide a solid foundation for further research of gene structure and its biological function, and also provides conditions for explore active ingredient variation and its quality control from the perspective of molecular pharmacognosy. This paper introduces the concept of homologous gene, gene duplication and classification. We prospect the function of duplicated genes in the role of molecular mechanism research about variation in active ingredients, aiming at providing a new way for medicinal materials quality control.

[Advances in high-throughput transcriptome research of traditional Chinese medicines].

Traditional Chinese medicine is a treasure of Chinese culture, absorbing the wisdom of the Chinese people. Continuous application of new technologies makes traditional Chinese medicine research advance with the times. After several years of development, high-throughput transcriptome study has become a mature research tool in biology. This paper reviewed the advances in medicine transcriptome study, and compared two sequencing platforms, Roche's GS FLX platform and Illumina's HiSeq 2000 platform. Moreover, this paper introduced medicine transcriptome analysis process, with Panax quinquefolius and Lonicera japonica for examples, showing the characteristics of traditional Chinese medicine transcriptome studies. High-throughput transcriptome studies facilitate traditional Chinese medicine research with overall understand of functional genes, give clear elucidation of metabolic pathways, lay molecular foundation for the traditional Chinese medicine research and offer modern interpretation for traditional Chinese medicine theory. However, the current study faces several difficulties, including weak molecular basis, high sequencing cost and staff shortages in data anaysis. In the future, with the development in sequencing technology, the combination of transcriptome and other genomics, such as proteome and metabolome, will lay a solid foundation for the new high-throughput screening and developing model for the traditional Chinese medicine industry.

Fangyukangsuan granules ameliorate hyperuricemia and modulate gut microbiota in rats.

Hyperuricaemia (HUA) is a metabolic disorder characterised by high blood uric acid (UA) levels; moreover, HUA severity is closely related to the gut microbiota. HUA is also a risk factor for renal damage, diabetes, hypertension, and dyslipidaemia; however, current treatments are associated with detrimental side effects. Alternatively, Fangyukangsuan granules are a natural product with UA-reducing properties. To examine their efficacy in HUA, the binding of small molecules in Fangyukangsuan granules to xanthine oxidase (XOD), a key factor in UA metabolism, was investigated via molecular simulation, and the effects of oral Fangyukangsuan granule administration on serum biochemical indices and intestinal microorganisms in HUA-model rats were examined. Overall, 24 small molecules in Fangyukangsuan granules could bind to XOD. Serum UA, creatinine, blood urea nitrogen, and XOD levels were decreased in rats treated with Fangyukangsuan granules compared to those in untreated HUA-model rats. Moreover, Fangyukangsuan granules restored the intestinal microbial structure in HUA-model rats. Functional analysis of the gut microbiota revealed decreased amino acid biosynthesis and increased fermentation of pyruvate into short-chain fatty acids in Fangyukangsuan granule-treated rats. Together, these findings demonstrate that Fangyukangsuan granules have anti-hyperuricaemic and regulatory effects on the gut microbiota and may be a therapeutic candidate for HUA.

Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the Miscellaneous Crenarchaeotic Group (MCG): implications for physiology and evolution of marine sedimentary archaea.

Archaea of the Miscellaneous Crenarchaeotic Group (MCG) exist widely in soil, freshwater and marine sediments of both surface and subsurface. However, current knowledge about this group is limited to its phylogenetic diversity. An archaeal 16S library was constructed from a sediment sample from the South China Sea, which was dominated by MCG and Marine Group I (MG-I). A metagenomic library was constructed from the same sediment sample, and three MCG fosmids (E6-3G, E37-7F and E48-1C) containing 16S rRNA genes were screened. Annotation showed that the three genomic fragments encode a variety of open reading frames (ORFs) that are potentially homologous to important functional genes related to lipid biosynthesis, energy metabolism, and resistance to oxidants. No colinear regions were found between MCG fosmids and reported archaeal genomic fragments or genomes, suggesting that the MCG archaea are quite different from the sequenced archaea in gene arrangement. Analyses of both the phylogenies of 16S rRNA genes and several informational processing genes and nucleotide frequencies showed that MCG archaea are distinct from MG-I plus relatives. In addition, tetranucleotide frequency analysis in combination with phylogenetic analysis suggested that some fragments in the MCG fosmids are probably derived from non-MCG or non-archaeal genomes.

[EST-SSR identification of Lonicera japonica Thunb].

Simple and effective methods are needed for the identification of Chinese medicinal material species and their variety. Lonicera japonica Thunb. is one of Chinese herbal medicines widely demanded. A total of 3 705 EST-SSRs of L. japonica and 2 818 EST-SSRs of L. japonica var. chinensis Thunb. were identified from EST database in our lab. In average, there was one EST-SSR per 4.05 kb in L. japonica ESTs and per 7.49 kb in L. japonica var. chinensis ESTs, separately. The identified SSRs in L. japonica were consisted of 51.98% dinucleotide and 34.61% trinucleotide repeats, while SSRs in L. japonica var. chinensis had 57.45% dinucleotide and 30.09% trinucleotide. The results reviewed that the classes AG/TC and GAG/TCT were predominant in the dinucleotide motifs and the trinucleotide motifs, respectively. Total 87 EST-SSRs were identified of significant difference between L. japonica and L. japonica var. chinensis. PCR products were obtained from 52 L. japonica samples in 13 out of 15 SSR markers tested. The polymorphism in L. japonica, L. japonica var. chinensis and other honeysuckles could be distinguished by three markers (jp.ssr4, jp.ssr64 and jp.ssr65) tested.

The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.

BACKGROUND: Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. RESULTS: The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. CONCLUSION: Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.

[Effects of reduced nitrogen application on yield, nitrogen utilization of spring maize and soil nitrate content in Weibei dryland, Northwest China]. / å‡é‡æ–½æ°®å¯¹æ¸­åŒ—æ—±åœ°æ˜¥çŽ‰ç±³äº§é‡ã€æ°®ç´ åˆ©ç”¨åŠåœŸå£¤ç¡æ€æ°®å«é‡çš„å½±å“.

To get a scientific pattern for nitrogen-reducing and efficiency-increasing production of spring maize in Weibei dryland, we conducted an in-situ field experiment of spring maize (Zhengdan 958 and Shaandan 8806) under dryland farming from 2016 to 2019 in Heyang County, located in Weibei dryland of Shaanxi. There were five nitrogen (N) treatments, including 360 kg·hm-2(N360, a rate commonly adopted by local farm households), 270 kg·hm-2(N270), 150-180 kg·hm-2(N150-180), 75-90 kg·hm-2(N75-90) and 0 kg·hm-2(N0). We investigated the effects of reduced nitrogen application on maize yield, nitrogen uptake and utilization of spring maize and soil nitrate residue. The results showed that: 1) Maize yield of both varieties at N150-180 was increased by 0.9%-7.1% and nitrogen uptake was decreased by 4.1%-4.6%, while average reco-very efficiency, partial-factor productivity and agronomic efficiency of N at N150-180 were increased by 79.3%-83.6%, 105.9%-157.7%, and 101.9%-114.1% compared with those at N360, respectively. 2) The contents of residual nitrate increased significantly when nitrogen application rate was more than 180 kg·hm-2, while nitrogen uptake was significantly reduced under rainfall shortage, and thus resulted in increasing soil residual nitrogen. After four-year treatments, the residual nitrate was up to 504.7-620.8 kg·hm-2 in 0-200 cm soil layer, with a peak in 80-140 cm soil layer. There was a risk of nitrate leaching. According to the comprehensive evaluation for annual yield, nitrogen use efficiency and soil nitrate residue, the optimum N application rate was recommended to be 150-180 kg N·hm-2 for spring maize in Weibei dryland.

[Establishment of lymphocyte cell lines with abnormal chromosome karyotypes and its application in external quality assesment for chromosome karyotype analysis].

OBJECTIVE: To develop chromosome abnormal karyotype quality control cell and to explore the external quality assessment (EQA) method for chromosome karyotype analysis. METHODS: The chromosome abnormal karyotype quality control cells were prepared by EB virus (EBV) transfection of human B lymphocyte strain establishment and were distributed to participating labs for EQA test of chromosome karyotype analysis project at appointed time. The evaluation results were obtained through 4 grades scoring. RESULTS: Six kinds of chromosome abnormal karyotype quality control cells were initially developed, the karyotypes of which were 46,X, t(Y;5)(q12;q21), 46, XY, 15p +, 46, XX, t(13;18)(q12;q21), 46, X, r(Xp), 46,X,t(Y;Y), 46,XX,t(9;20)(p13;p13) respectively. In the external quality assessment, feedbacks from the participating labs on the sequencing results of the six kinds of quality control cells showed that the wholly overlapping rate were 82.1%, 92.0%, 84.6%, 80.8%, 86.2%, 74.1% and the wholly deviation rate were 10.7%, 8.0%, 11.5%, 19.2%, 13.8%, 18.5%. The overall wholly overlapping rate, partial overlapping rate, partial deviation rate and wholly deviation rate turned out to be 83.2%, 0.6%, 2.5% and 13.7% respectively. CONCLUSION: The misdiagnose rate of chromosome karyotype analysis is rather high and regular external quality assessment is necessary to achieve dynamic information and improve diagnosis quality.

Complete mitochondrial genome of Costaria costata shows conservative evolution in Laminariales.

Costaria costata, with great commercial and industrial value, typically grows in low intertidal and subtidal retgions in East Asia. The complete mitochondrial genome of C. costata is determined as circular-mapping and AT-rich (65%). The 37,461 bp mitochondrial genome consists of 25 tRNAs, 38 genes (including ORFs) and 3 ribosome genes. The gene arrangement and component are identical to those of Laminaria mitochondrial genomes, which show highly conservative evolution in mitochondrial genomes within the Laminariales. Moreover, the C. costata mitogenome makes full use of nucleotide and genetic information by large amounts of gene overlappings for better adapting the evolution of small genomes.

Structures and functions of crotoxin-like heterodimers and acidic phospholipases A2 from Gloydius intermedius venom: Insights into the origin of neurotoxic-type rattlesnakes.

The cDNAs encoding four major phospholipases A2 (PLA2s) were sequenced while the expressed sequence tags of Gloydius intermedius venom glands were constructed. These PLA2s were designated as Gintexin-A precursor, Gintexin-B, Gin-E6a and Gin-E6b, respectively. The deduced amino acid sequences of the former two PLA2s are 80% and 90% identical to those of crotoxin-A-precursor and crotoxin-B1, respectively. We also purified Gintexin-A, Gintexin-B, Gin-E6a and Gin-E6b like PLA2 from the venom. The latter three PLA2s are enzymatically active but not strongly anticoagulant for human plasma. Gin-E6a and E6b-like PLA2s induced mouse platelet aggregation but inhibited rabbit platelet aggregation. The isolated Gintexin, a 1:1 complex of Gintexin-A and Gintexin-B, blocked the twitch of chick biventer cervicis tissue presynaptically. Results of N-terminal sequencing and peptide mass fingerprinting reveal that Gintexin-A undergoes proteolytic processing similar to crotoxin-A. This is the first time heterodimeric ß-neurotoxins are found in Asian pitviper venom, and incompatible neurotoxic- and hemorrhagic-type venoms are found to evolve in parallel within the genus Gloydius, like in Crotalus. Thus, G. intermedius probably is the ancestor of rattlesnakes with type-II venom, and characterization of its venomics helps us to understand the evolution of heterodimeric neurotoxic PLA2s and the paedomorphic trend observed in Neotropical rattlesnake venoms. BIOLOGICAL SIGNIFICANCE: For the first time, a heterodimeric neurotoxic PLA2 (designated as Gintexin) has been isolated from the venom of an Asian pitviper, which shows a characteristic venom gland transcriptome similar to those of the neurotoxic type rattlesnakes. The fact that the venom of G. intermedius is less hemorrhagic than those of other Gloydius species, reveals that incompatible neurotoxic- and hemorrhagic-type venoms have evolved in parallel within the genus Gloydius, like the genus Crotalus. Our findings suggest that G. intermedius is the most probable ancestor of some Neotropical rattlesnakes. The results may revolutionize the theory regarding the origin of type-II rattlesnakes and assist with the diagnosis and clinical management of G. intermedius bites. Furthermore, the possibility of using the currently available antivenoms of Neotropical rattlesnakes to treat G. intermedius bites seems feasible.