PSMD: An extensive database for pan‐species microsatellite investigation and marker development

Microsatellites are widely distributed throughout nearly all genomes which have been extensively exploited as powerful genetic markers for diverse applications due to their high polymorphisms. Their length variations are involved in gene regulation and implicated in numerous genetic diseases even in cancers. Although much effort has been devoted in microsatellite database construction, the existing microsatellite databases still had some drawbacks, such as limited number of species, unfriendly export format, missing marker development, lack of compound microsatellites and absence of gene annotation, which seriously restricted researchers to perform downstream analysis. In order to overcome the above limitations, we developed PSMD (Pan‐Species Microsatellite Database, http://big.cdu.edu.cn/psmd/ ) as a web‐based database to facilitate researchers to easily identify microsatellites, exploit reliable molecular markers and compare microsatellite distribution pattern on genome‐wide scale. In current release, PSMD comprises 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms, which covered almost all species with available genomic data. In addition to interactive browse interface, PSMD also offers a flexible filter function for users to quickly gain desired microsatellites from large data sets. PSMD allows users to export GFF3 formatted file and CSV formatted statistical file for downstream analysis. We also implemented an online tool for analysing occurrence of microsatellites with user‐defined parameters. Furthermore, Primer3 was embedded to help users to design high‐quality primers with customizable settings. To our knowledge, PSMD is the most extensive resource which is likely to be adopted by scientists engaged in biological, medical, environmental and agricultural research.     

Substrate availability regulates the suppressive effects of Canada goldenrod invasion on soil respiration

基质有效性调节加拿大一枝黄花入侵对土壤呼吸的抑制作用 外来植物入侵不仅会降低河边近岸湿地生态系统植被多样性,而且会改变湿地生态系统的地下碳过程。外来入侵植物加拿大一枝黄花(Solidago canadensis L.)已广泛入侵我国东南部地区,但加拿大一枝黄花入侵对入侵地生态系统地下土壤碳循环过程的影响却知之甚少。本研究通过野外原位观测实验和温室模拟入侵实验,探究外来植物加拿大一枝黄花入侵对入侵地土壤呼吸的影响规律及其驱动因素。野 外原位观测实验开展于2018年7月21日至12月15日,期间每周测定样地土壤呼吸。温室模拟入侵实验开展于2019年7月15日至12月15日,期间每月1日与15日上午测定土壤呼吸、自养呼吸和异养呼吸。土壤呼吸、自养呼吸和异养呼吸通过静态箱结合深埋根系隔离法测定。野外原位观测实验和温室模拟入侵实验结果均显示,加拿大一枝黄花的入侵降低了土壤二氧化碳的排放通量。加拿大一枝黄花入侵对土壤呼吸的抑制作用可能归因于其入侵引起的土壤可利用底物质量与数量的变化,表明外来入侵植物加拿大一枝黄花可通过改变植物释放基质以及与本地植物和/或土壤微生物争夺土壤有效基质而影响土壤碳循环。这些研究结果对于评估外来入侵植物对入侵地地下碳动态的影响以及对全球变暖的贡献具有重要意义。     

褶纹冠蚌珍珠囊发育的研究

以褶纹冠蚌(Cristaria plicata Leach)为实验对象,应用光学显微技术和扫描电子显微技术研究珍珠囊的发育,结果表明在水温16℃左右时约需30d形成具有单层上皮细胞的珍珠囊,6个月后稳定分泌珍珠质。构成珍珠囊的上皮细胞从高柱状逐渐变成扁平状或立方形,细胞的碳酸酐酶污性也日益增强。大部分移植细胞小片的结缔组织与母蚌的结缔组织共同成层排列在珍珠囊腔外围。游走细胞在珍珠囊的早期发育阶段十分活跃。本文还阐明了珍珠囊液是存在于上皮细胞与珍珠表面之间的一薄层流体状物质。碳酸钙结晶的核化(nucleation)和初期生长都发生在珍珠囊液中。     

我国汉族人群的乙二醛酶Ⅰ遗传多态性

用琼脂糖平板凝胶电泳技术分析了我国六个城市的汉族共1238人的红细胞乙二醛酶I的遗传多态性。每个汉族人群的受检人数和GLO1*1基因频率分别为:郑州200人(0.1023),哈尔滨195人(0.1103),呼和浩特210人(0.1259),贵阳204人(0.1373),兰州210人(0.1476),西安199人(0.1508)。中国不同地区汉族人群之间的GLOI基因频率分布存在显著性差异,但这种差异明显小于中国不同少数民族之间的差异。     

In vivo intranasal anti-CD23 treatment inhibits allergic responses in a murine model of allergic rhinitis

Although CD23-dependent transcytosis of IgE and IgE-derived immune complexes across respiratory epithelial cells is likely to play a pivotal role in the initiation and development of airway allergic inflammation, there is currently a lack of physiological support for this phenomena to suggest that the targeting of CD23 could be used as a means of therapeutic intervention. The present study was designed to detect the CD23 expression in the nasal mucosa of allergic rhinitis (AR) murine model by immunohistochemistry and western blotting, and to investigate whether intranasal anti-CD23 treatment could inhibit allergen-induced upper airway inflammation in the AR model. This is the first report to show that CD23 was constitutively expressed in murine nasal epithelial cells, and its expression was significantly up-regulated in the AR murine model. In vivo, the up-regulation of CD23 expression was correlated with increased serum IL-4 levels. Following intranasal anti-CD23 treatment, nasal symptoms were alleviated and histopathologic examination showed a significant decrease in eosinophilic infiltration. Meanwhile, ELISA analysis showed levels of serum leukotriene C4 (LTC4), eosinophil cation protein (ECP), ovalbumin (OVA)-specific IgE and IL-4 also significantly decreased, as were LTC4 and OVA-specific IgE in the nasal lavage fluid. Furthermore, Western blotting analysis showed that ECP expression in the nasal mucosa was down-regulated. Finally, flow cytometric analysis revealed anti-CD23 treatment inhibited Th2 cell responses. These results indicate that intranasal anti-CD23 treatment can reduce allergic responses in a murine model of allergic rhinitis.     

Development and Application of Microsatellites in Candidate Genes Related to Wood Properties in the Chinese White Poplar (Populus tomentosa Carr.)

Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2–7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.     

Fungal Diversity in Deep Sea Sediments from East Yap Trench and Their Denitrification Potential

Abstract

In recent years, the hadal trenches have been recognized as biological hot spots for deep sea researchers. Due to high hydrostatic pressure, low temperatures, high salinity and low nutrients, the microorganisms in hadal trenches may have unique community structure with potential for biotechnical application. Compared with bacteria and archaea, the diversity and ecological roles of fungi in hadal trenches remain largely unknown. The purpose of this study was to explore fungal diversity in deep-sea sediments of the Yap trench and their denitrification potential. In the present study, a total of 106 fungal strains were isolated from six sediment samples collected in the East Yap Trench. These fungi belonged to five classes (Dothideomycetes, Eurotiomycetes, Sordariomycetes, Cystobasidiomycetes, and Microbotryomycetes), thirteen genera (Acremonium, Alternaria, Aureobasidium, Aspergillus, Cladosporium, Cystobasidium, Engyodontium, Gliomastix, Lecanicillium, Penicillium, Phoma, Rhodotorula and Trichoderma) and eighteen species, based on morphological identification and ITS-rDNA sequence analysis. Among them, the dominant genus is Cladosporium, which accounting for 42.45% of the total fungal strains. Meanwhile, the denitrification potential of the fungal strains was also examined with two different denitrifying media (nitrate and nitrite as sole substrate, respectively). Two fungal strains (Acremonium sp. and Aspergillus versicolor), were found to be able to produce N₂O ex situ in the presence of nitrite. No fungus was found to produce N₂O by using nitrate. Our results suggest that fungi in hadal sediments, play important roles in nitrogen cycles.     

Functional analysis of slow myosin heavy chain 1 and myomesin-3 in sarcomere organization in zebrafish embryonic slow muscles

Myofibrillogenesis, the process of sarcomere formation, requires close interactions of sarcomeric proteins and various components of sarcomere structures. The myosin thick filaments and M-lines are two key components of the sarcomere. It has been suggested that myomesin proteins of M-lines interact with myosin and titin proteins and keep the thick and titin filaments in order. However, the function of myomesin in myofibrillogenesis and sarcomere organization remained largely enigmatic. No knockout or knockdown animal models have been reported to elucidate the role of myomesin in sarcomere organization in vivo. In this study, by using the gene-specific knockdown approach in zebrafish embryos, we carried out a loss-of-function analysis of myomesin-3 and slow myosin heavy chain 1 (smyhc1) expressed specifically in slow muscles. We demonstrated that knockdown of smyhc1 abolished the sarcomeric localization of myomesin-3 in slow muscles. In contrast, loss of myomesin-3 had no effect on the sarcomeric organization of thick and thin filaments as well as M- and Z-line structures. Together, these studies indicate that myosin thick filaments are required for M-line organization and M-line localization of myomesin-3. In contrast, myomesin-3 is dispensable for sarcomere organization in slow muscles.     

The complete mitochondrial genomes of largemouth bass of the northern subspecies (Micropterus salmoides salmoides) and Florida subspecies (Micropterus salmoides floridanus) and their applications in the identification of largemouth bass species

The largemouth bass belongs to the family Centrarchidae, which includes two subspecies: the northern subspecies, Micropterus salmoides salmoides, and the Florida subspecies, Micropterus salmoides floridanus. In this study, the complete mitochondrial genomes of the two subspecies were sequenced, and their genetic differences were identified. The mitogenomes of M. s. salmoides and M. s. floridanus are 16,486 and 16,479?bp in length, respectively. The two subspecies consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA), which are typical for vertebrate mtDNA. Phylogenetic analysis provided statistical support for the monophyly of the family Centrarchidae. Comparison of the two subspecies' mitogenomes revealed a relatively high number (450) of single nucleotide polymorphisms (SNPs) in protein-coding genes. We characterized SNPs in the partial cytochrome c oxidase subunit 1 gene of different individuals from three cultured populations, one wild northern subspecies population, and one wild Florida subspecies population. Twenty-eight SNPs were fixed with alternative nucleotides in the two subspecies, which could be used for differentiating them. Based on this gene, phylogenetic tree and genetic distance analyses supported that cultured largemouth bass in China belongs to the northern subspecies.