祁连山高寒草原碱性土壤固氮微生物数量及固氮基因(nifH)群落结构研究

对祁连山高寒草原碱性土壤可培养固氮菌数量、 固氮基因(nifH)群落结构及其理化性质进行了研究. 结果表明: 固氮菌数量在土层0~40 cm处于3.6×10⁵~0.21×10⁵CFUs·g^-1之间, 除了海拔3 001 m的土样AQ4外, 其他3个土样固氮菌数量随着土壤深度的加深而减小. 固氮菌数量与地下生物量呈显著正相关性, 与有机碳、 可溶有机氮、 速效磷和速效钾呈正相关性, 而与pH值和全盐呈负相关性. 通过基因测序得到的37个固氮基因nifH克隆中, 蓝藻门占41%, 变形菌门占8%, 厚壁菌门占14%, 未知菌株占37%; 蓝藻门在除了AQ4外的土样中普遍存在, 并且是AQ1的优势固氮菌群. 此外, 还发现了4个新的nifH基因, 分别是AQ1-12(KC412109)、 AQ4-3(KC412133)、 AQ4-4(KC412133)、 AQ4-5(KC412133), 其中后三者是土样AQ4的优势种群.     

长牡蛎两个Dmrt家族基因的时空表达

本文以长牡蛎27个幼虫发育阶段个体以及成体的5个组织织作为实验材料,采用实时荧光定量PCR技术对Dmrt家族中的2个基因（CgDsx和CgDmrtA2）的主要对长牡蛎Dmrt家族中的2个基因（CgDsx和CgDmrtA2）在幼虫时期和成体组织中的表达模式以及在性别决定中可能发挥的作用进行了研究。采用实时荧光定量PCR技术对幼虫27个发育阶段以及成体5个组织的表达进行了测定。结果表明,长牡蛎CgDsx基因在胚胎发育初期有大量表达,其中囊胚期到担轮幼虫初期表达量最高从囊胚期到担轮幼虫初期表达量最高,其后之后表达量开始降低,在D形幼虫后期之后一直维持在极低的表达水平,此后仅在成体的雄性性腺中具有高度表达。该结果表明由此可见,CgDsx 可能也对早期胚胎发育起一定调控作用,除了同时参与了性别决定外,可能也对早期胚胎发育起一定调控作用。CgDmrtA2在长牡蛎所有组织中均有表达,各组织间表达差异不显著,在长牡蛎D形幼虫至壳顶后期表达量较高,表明其参与了胚胎中后期的发育过程说明它参与了胚胎中后期的发育过程,可能与神经的形成相关,但是其具体功能还需要进一步研究。     

二、三倍体牙鲆肌肉和脑组织实时定量PCR内参基因的筛选及鉴定

多倍体诱导会造成物种中不同基因的表达水平变化不同,以内参基因作为对照的相对实时定量PCR是检测基因表达水平变化的一种高效方法,这就需要对多倍体中的内参基因进行筛选以获得较适宜的参比基因.本研究以二倍体和三倍体牙鲆肌肉和脑组织为对象,以绝对定量及2-ΔCt等方法分析管家基因18S rRNA、β-肌动蛋白基因(β-acti...     

传统聚落景观基因的识别与提取方法研究

近年来,由中国学者提出的传统聚落景观基因理论在传统聚落区划、特征识别和旅游规划等领域得到了广泛的应用。然而,该理论还缺乏有效的景观基因识别方法。针对前述问题,结合实践探讨了传统聚落景观基因的特征解构提取方法和识别模式。首先,分析了传统聚落景观基因的分类方法并结合面向对象的思想提出了面向对象的景观基因分类模式（OOCPLG）,这为构建特征解构提取方法奠定了理论基础。其次,通过分析景观识别的要求,结合现有的元素提取、图案提取、结构提取和含义提取的不足与优点,建立了特征解构的基因提取方法。最后,总结了景观基因的识别模式和基本操作流程。     

基于鳃的microRNA转录组研究中国蛤蜊对重金属镉的响应

中国蛤蜊（Mactra chinensis）是一种重要的经济贝类,分布于我国的辽宁和山东。近年来,生境恶化和过度捕捞导致我国蛤蜊资源量减少。我们利用Illumina Hiseq-2500平台对中国蛤蜊鳃的microRNA转录组进行测序,运用差异表达寻找对镉刺激有响应的功能microRNA。结果显示对照组获得了14 415 256条clean reads,实验组获得了15 570 111条clean reads。在这些reads中一共存在14 584 077小RNA,包括1 898 035条unique小RNA,其中对照组和实验组共有187 859条unique小RNA。两个组的小RNA文库的片段长度分布是相似的,大部分小RNA长度分布在26~27 nt。在对照组文库中最丰富的片段长度是27 nt,其次是28 nt、26 nt和23 nt。在实验组文库中,数量最丰富的片段长度是26 nt,其次是27 nt、28 nt和23 nt。经过对序列前体以及结构特征的分析,发现这两个组中一共有50个microRNA,其中已知的是38个,新发现的是12个。对照组和实验组microRNA含量最丰富的片段长度是23 nt。通过差异表达分析,5个microRNA基因具有显著性差异且从对照组到实验组的表达量是上调的,其余45个没有显著性的差异。把这50个序列与中国蛤蜊转录组进行比对,一共找到了542个靶基因。5个具有表达差异的基因一共比对到11个靶基因。把这11个靶基因与NCBI数据库比对,4个靶基因在COG中得到注释,1个靶基因在GO中得到注释,6个靶基因在KEGG中得到注释,11个靶基因在nr数据库中得到注释,注释到的基因有泛素蛋白连接酶E3,Wnt信号通路,G蛋白信号调控等。     

漂白粉消毒后对虾养殖源水细菌群落的响应特征研究

漂白粉消毒是凡纳滨对虾养殖源水常见的管控措施, 可有效控制病原菌传播; 然而,消毒会强烈扰动水体微生物群落,但源水细菌群落对漂白粉消毒的响应特征尚未阐明。在室内条件下, 设置高浓度(60 mg/L)和低浓度(20 mg/L)漂白粉消毒源水, 通过高通量测序及荧光定量PCR技术探究消毒后源水细菌群落、病原菌及抗生素抗性基因(ARGs)的动态响应规律。结果显示, 消毒后, 拟杆菌门(Bacteroidota)丰度上升, 高浓度组变形菌门(Proteobacteria)的丰度显著降低; 至第3天, 两组源水的细菌群落组成趋于一致。此外, 漂白粉消毒显著改变了源水的细菌群落结构及共现网络的复杂性。在控制水体病原菌方面, 消毒后病原菌的总丰度降低, 但种类增加, 高浓度漂白粉消毒对病原菌的抑制作用更加显著。漂白粉消毒对ARGs的去除具有选择性, 仅对sul1、floR、cfr、tetQ有一定的去除作用, 且高、低浓度对ARGs的去除无差异。综上, 60 mg/L可以作为漂白粉消毒养殖源水的更好浓度选择。研究结果从微生物生态视角评价了不同浓度漂白粉的消毒作用, 可为对虾养殖生产中的源水管控提供理论支撑。     

Spatial and diel variations of the prokaryotic community in the Phaeocystis globosa blooms area of Beibu Gulf,China

While prokaryotes play key roles in nutrient cycling and energy flow during Phaeocystis globosa blooms, the information on the spatial and diel temporal distribution of the prokaryotic community during Phaeocystis blooms remains scarce. In January 2019, we used high-throughput sequencing of the 16S rRNA gene to explore the spatial and diel variations of particle-attached (PA) and free-living (FL) prokaryotic communities during the blooming phase of P. globosa in Beibu Gulf, Guangxi, China. The results suggested a significant spatial variation pattern in the horizontal distribution of prokaryotic communities, while there was no significant difference in the vertical direction. Both spatial distance and environmental variables shaped the horizontal distribution of the prokaryotic community structure, while environmental variables, particularly the abundance of P. globosa colony and Chl a, showed more significant influence and were closely related to the structure and variation of the prokaryotic community. Strong vertical mixing of the water column disrupted the vertical structure heterogeneity of the prokaryotic community in winter. There were significant differences in the diel samples of PA prokaryotic communities, but not in the FL prokaryotic communities. Nitrate, ammonium and the abundance of P. globosa colony were the key environmental variables impacting the diel variations of prokaryotic communities over the sampling period. The present study provided valuable information to depict the spatial-temporal variations of the microbial community and its association with environmental parameters during P. globosa bloom in the tropical gulf.     

Construction of cDNA library from intestine, mesentery and coelomocyte of Apostichopus japonicus Selenka infected with Vibrio sp. and a preliminary analysis of immunity-related genes

The aquaculture of sea cucumber Apostichopus japonicus (Echinodermata, Holothuroidea) has grown rapidly during recent years and has become an important sector of the marine industry in Northern China. However, with the rapid growth of the industry and the use of non-standard culture techniques, epidemic diseases of A. japonicus now pose increasing problems to the industry. To screen the genes with stress response to bacterial infection in sea cucumber at a genome wide level, we constructed a cDNA library from A. japonicus Selenka (Aspidochirotida: Stichopodidae) after infecting them with Vibrio sp. for 48 h. Total RNA was extracted from the intestine, mesentery and coelomocyte of infected sea cucumber using Trizol and mRNA was isolated by Oligotex mRNA Kits. The ligated cDNAs were transformed into DH5α, and a library of 3.24×105 clones (3.24×105 cfu mL-1) was obtained with the sizes of inserted fragments ranging from 0.8 to 2.5 kb. Sequencing the cDNA clones resulted in a total of 1106 ESTs that passed the quality control. BlastX and BlastN searches have identified 168 (31.5%) ESTs sharing significant homology with known sequences in NCBI protein or nucleotide databases. Among a panel of 25 putative immunity-related genes, serum lectin isoform, complement component 3, complement component 3-like genes were further studied by real-time PCR and they all increased more than 5 fold in response to Vibrio sp. challenge. Our library provides a valuable molecular tool for future study of invertebrate immunity against bacterial infection and our gene expression data indicates the importance of the immune system in the evolution and development of sea cucumber.     

Essential cellular modules for the proliferation of the primitive cell

Bacteria appeared early in the evolution of cellular life on planet Earth, and therefore the universally essential genes or biological pathways found across bacterial domains may represent fundamental genetic or cellular systems used in early life. The essential genes and the minimal gene set required to support bacterial life have recently been experimentally and computationally identified. It is, however,still hard to estimate the ancient genes present in primitive cells compared to the essential genes in contemporary bacteria, because we do not know how ancestral primitive cells lived and proliferated, and therefore cannot directly evaluate the essentiality of the genes in ancestral primitive cells. The cell wall is normally essential for bacterial proliferation and cellular division of walled bacterial cells is normally highly controlled by the essential FtsZ cell division machinery. But, bacteria are capable of reverting to their cell wall deficient ancestral form, called the "L-form". Unlike "normal" cells, L-forms divide by a simple physical mechanism based on the effects of membrane dynamics, suggesting a mode of primitive proliferation before the appearance of the cell wall. In this review, we summarize the experimental and computational investigations of minimal gene sets and discuss the minimal cellular modules required to support the proliferation of primitive cells, based on L-form proliferation.