蛋白质二组结构由氨基酸和mRNA序列编码

据氨基酸序列，密码子序列和蛋白质二组结构序列的比较，指出约18%的两肽的密码子具有反常的蛋白质结构偏好性，并且这种反常不能用随机涨落解释，因而关于蛋白质折迭的Anfinsen原理可能需要作适当修正。

HSF2 mRNA 在热应激和大剂量11酸睾酮诱导恒河猴生精细胞凋亡中的表达变化

为了探讨 HSF2 mRNA 在热应激和超生理剂量睾酮诱导恒河猴生精细胞凋亡中的表达变化, 作者建立了手术诱导单侧隐睾和注射大剂量11酸睾酮(TU)恒河猴动物模型, 应用3′末端标记分析(TUNEL)和原位杂交方法, 检测睾丸细胞的凋亡信号和 HSF2的表达变化. TUNEL 结果显示热应激和超生理剂量睾酮能够诱导生精细胞出现凋亡信号, 它分别于处理后第5天和第30天达到最强, 表明热应激和睾酮干扰精子发生可能是通过生精细胞凋亡的方式来实现的. HSF2 mRNA 水平在生精细胞凋亡早期(凋亡信号达到最强以前)略有降低, 而在凋亡高峰期之后其表达急剧下降. Hsf2基因与作者以前研究的 Hsp70-2基因的表达具有时间上的相关性, 表明 HSF2蛋白可能调控 Hsp70-2基因的表达, 而且 HSF2可能通过多种方式影响精子的发生以及抑制生精细胞的凋亡。

翻译过程中mRNA的拓扑形态及其链构象分析

对mRNA发夹结构和单链结构的理论模型构建,以及基于对X射线晶体衍射和NMR实验数据的模拟研究显示,在翻译过程中,核糖体上mRNA解折叠后的单链拓扑形态,与mRNA本身的发夹结构密切相关,均呈现为不同程度的螺旋与卷曲相间的构象。通过包括翻译速度在内的调节作用,这种构象可能会影响到新生肽链的折叠。

Is there a genetic relationship between mRNA and the encoded protein at three-dimensional level?

A comparative study on the structures of some mRNAs and their encoded proteins shows an intriguing correlation between the two foldings. Non-random distribution of codons in the secondary structures of mRNAs is also shown, which appears to be in accordance with the conformational properties of amino acids in protein structures to some extent. These results seem to suggest that there may be a kind of genetic relationship between mRNA and protein at three-dimensional level.

Expression and regulation of orphan receptor TR2 mRNA in germ cells of cryptorchid testis in rat and rhesus monkey

Expression and cellular localization of orphan receptor TR2 mRNA in relation to germ cell apoptosis in cryptorchid testes of rat and rhesus monkey have been studied by using in situ hybridization and in situ 3'-end labeling of DNA fragments (TUNEL). The results show that: (i) TR2 mRNA is specifically expressed in the germ cells, mainly in the spermatocytes, round and elongated spermatids. The expression level of TR2 mRNA varies with the seminiferous cycle, (ii) In the rat cryptorchid testes on days 3 and 5 after the surgery, the germ cells began to undergo apoptosis with no evident decrease in TR2 mRNA level. On day 7.5, however, most germ cells underwent apoptosis, while the expression level of TR2 mRNA declined markedly, and TR2 mRNA was rarely expressed on day 10 thereafter. (iii) On days 15 and 20 of the cryptorchid testes of rhesus monkey, TR2 mRNA was only expressed in a few of primary spermatocytes and the mRNA was almost undetectable on days 30, 45, 60. These results suggest that TR2 mRNA probably plays an important role in spermatogenesis and germ cell apoptosis.

The topological configuration and conformational analysis of mRNA in translation

The theoretical model construction of mRNA hairpin structure and single-stranded structure as well as the simulation studies on RNA structure determined by the X-ray crystal diffraction and nuclear magnetic resonance revealed that in translation, after mRNA being unfolded into single-stranded structure, its topological configuration was closely correlative with the original hairpin structure. The conformational features of single-stranded mRNA appeared as helical regions alternating with curly regions to different extents, which might exert the influence on the folding of nascent polypeptide by various regulating effects including different translational rates.

Stable RNA hairpins in 88 coding regions of human mRNA

RNA hairpins containing UNCG, GNRA, CUUG (N = A, U, C or G, R = G or A) loops are unusually thermodynamic stable and conserved structures. The structural features of these hairpin loops are very special, and they play very important roles in vivo. They are prevalent in rRNA, catalytic RNA and non-coding mRNA. However, the 5' C(UUCG)G 3' hairpin is not found in the folding structure of 88 human mRNA coding regions. It is also different from rRNA in that there is no preference for certain sequences among tetraloops in these 88 mRNA folding structures.

The identification and quantification of highly stable 'common hairpin' in the dynamic process of co-transcriptional mRNA folding

In our studies, 88 human mRNA samples were collected from the Integrated Sequence-Structure database and then the dynamic process in co-transcriptional mRNA folding was simulated using the RNAstructure version 4.1 program. Through statistical analyses of the frequencies of occurrence of hairpins, a group of special folding structures-the 'common hairpins'-were identified. These 'common hairpins' have lower energies and occur in all the subsequent folding units that formed in the dynamic folding process. By applying the formulas (1)-(4) of the 'common hairpins' statistical model, 163 'common hairpins' were found, to make up about 7% of the total of 2286 hairpins. Classified studies further show that the 'common hairpins' that were studied may oscillate in the dynamic folding process. However, the hairpin loops of the 'common hairpins' and stems proximal to those 'common hairpins' loops maintain topologically stable structures, while other loops and stems distal to the 'common hairpins' loops are shown to be alterable structures. Strikingly, further studies indicate that the stable structures of these 'common hairpins' may have unbeknown effects on controlling the formation of protein structures in the translation process (unpublished results). (c) 2005 Elsevier B.V. All rights reserved.

Exploring consensus mRNA secondary (folding) structure units by stochastic sampling and folding simulation

It is extremely difficult to explore mRNA folding structure by biological experiments. In this report, we use stochastic sampling and folding simulation to test the existence of the stable secondary structural units of-mRNA, look for the folding units, and explore the probabilistic stabilization of the units. Using this method, We made simulations for all possible local optimum secondary structures of a single strand mRNA within a certain range, and searched for the common parts of the secondary structures. The consensus secondary structure units (CSSUs) extracted from the above method are mainly hairpins, with a few single strands. These CSSUs suggest that the mRNA folding units could be relatively stable and could perform specific biological function. The significance of these observations for the mRNA folding problem in general is also discussed. (c) 2004 Elsevier B.V. All rights reserved.

不同纬度螅状独缩虫耐热能力及Hsp70 mRNA表达水平的比较

本文以游泳体的形成作为虫体对热激响应的指征,比较了不同纬度(西安:东经108°98′,北纬34°25′;武汉:东经114°34′,北纬30°57′)两地螅状独缩虫(Carchesium polypinum)的耐热能力,发现武汉地区螅状独缩虫(WH株)形成游泳体的热激温度(36℃)高于西安地区(XA株)的33℃,说明前者的耐热能力较强;进一步利用实时PCR技术分析不同热激温度下两地螅状独缩虫热休克蛋白Hsp70mRNA的表达变化发现,XA株Hsp70mRNA热激后高表达水平的阈值温度为28℃,而WH株的为3

Molecular cloning of growth hormone receptor (GHR) from common carp (Cyprinus carpio L.) and identification of its two forms of mRNA transcripts

The cDNA of growth hormone receptor (GHR) was cloned from the liver of 2-year common carp (Cyprinus carpio L.) by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA end (RACE). Its open reading frame (ORF) of 1806 nucleotides is translated into a putative peptide of 602 amino acids, including an extracellular ligand-binding domain of 244 amino acids (aa), a single transmembrane domain of 24 aa and an intracellular signal-transduction domain of 334 aa. Sequence analysis indicated that common carp GHR is highly homologous to goldfish (Carassius auratus) GHR at both gene and protein levels. Using a pair of gene-specific primers, a GHR fragment was amplified from the cDNA of 2-year common carp, a 224 bp product was identified in liver and a 321 bp product in other tissues. The sequencing of the products and the partial genomic DNA indicated that the difference in product size was the result of a 97 bp intron that alternatively spliced. In addition, the 321 bp fragment could be amplified from all the tissues of 4-month common carp including liver, demonstrating the occurrence of the alternative splicing of this intron during the development of common carp. Moreover, a semi-quantitative RT-PCR was performed to analyze the expression level of GHR in tissues of 2-year common carp and 4-month common carp. The result revealed that in the tissues of gill, thymus and brain, the expression level of GHR in 2-year common carp was significantly tower than that of 4-month common carp.

树突状细胞体外分化成熟的时程、mi/mRNA 表达谱分析和共生菌影响的研究

树突状细胞（dendritic cells, DC）作为机体天然免疫和获得性免疫反应的桥梁和枢纽，发挥着重要的启动和调控作用。随着体外诱导方法的建立和生物学技术的进步，有关DC 的基础生物学研究得到了快速的发展，在诱导方法、个体发生及基因表达和调控等方面，涌现出很多新的、未解的关键问题。同时，随着对粘膜免疫机理研究的深入，DC 在粘膜生态环境中的功能和影响，渐已成为免疫学研究前沿领域中的热点和要点。在本研究中，为了确定DC 体外分化成熟的最短时程，同时为了研究DC 分化成熟相关的基因表达调控，我们建立了快速的DC 体外诱导方法，分析了体外快速诱导 DC 的mi/mRNA 表达谱。此外，在原始分离的女性生殖道共生乳酸杆菌的基础上，以THP-1作为DC 前体细胞的细胞系模型，开展了女性生殖道共生乳酸杆菌刺激活化 THP-1 的研究，希望能够为乳酸杆菌作为生殖道粘膜免疫疫苗的应用提供理论基础。首先，采用外周血单个核细胞（peripheral blood mononuclear cells, PBMC）来源的CD14+细胞为DC 前体，经过GM-CSF 和IL-4 的刺激，1-6 天后得到未成熟DC （immature dendritic cells, iDC），并经成熟因子（TNF-α, IL-1β, IL-6 与PGE2）诱导 1-2 天后，获得成熟DC（mature dendritic cells, mDC）。经过比较和分析，明确了完全分化和成熟各2 天，即“2+2”，为DC 诱导分化的最佳和最短时程，从而证实和建立了DC 体外快速诱导的体系和方法。该方法获得的iDC 与mDC，具有与传统的“6+2” 方法获得的DC 相同的形态与表型，而且，利用该方法获得的DC 总数高于“1+1”， “1+2”与“6+2”的方法，为DC 的生物学研究提供了基础数据。我们进而采用芯片技术，对体外快速分化成熟的DC 进行了mi/mRNA 表达谱分析，确定了DC 不同分化发育阶段特征性的mi/mRNA 表达差异。结果发现，与CD14+ 单核细胞即DC 前体相比，iDC 与mDC 之间具有更加相近的mi/mRNA 表达方式。 miRNA 表达谱分析则表明，不同的miRNA 表达与DC 的不同分化和发育阶段相关。而且，位于同一基因簇内的miRNA，呈现协同表达的情况。特别值得注意的是，本研究发现了在DC 的某些发育阶段特异表达的miRNA，它们在DC 发育过程中的功能，还未得到诠释，它们在DC 某些分化阶段的特异表达，提示了DC 各分化阶段的相关性与特异性。结合mRNA 表达谱分析，我们发现miRNA 的表达与其目的基因的表达在mRNA 水平呈现负相关的特性。同时，免疫相关mRNA 与miRNA 在DC 体外不同发育阶段的表达亦呈现差异，其中，miRNA（如hsa-miR-181a, hsa-miR-223, hsa-miR-155, hsa-miR-146, hsa-miR-106a 与hsa-miR-20a 等）与mRNA（如ALM1 等）参与了特定的与免疫相关的GO（Gene Ontology）与通路（Pathway），提示这些miRNA 与mRNA 可能通过不同的方式调节控制着DC 的体外诱导过程。在有关粘膜生态环境中DC 的分化、成熟及其功能影响的研究中，我们首先通过各种乳酸杆菌鉴定方法的综合应用，确定了6 种原始分离的女性生殖道主要共生乳酸杆菌：发酵乳酸杆菌（L.Fermentum）、约氏乳酸杆菌（L.Johnsonni）、卷曲乳酸杆菌（L.Crispatus）、革氏乳酸杆菌（L.Gasseri）、詹氏乳酸杆菌（L.Jensenii）与德氏乳酸杆菌（L.Delbrueckii ）。其中，德氏乳酸杆菌（L.Delbrueckii）和发酵乳酸杆菌（L.Fermentum）具有较高的产H2O2 的能力。在此基础上，我们在与THP-1 的共同培养体系中，将乳酸杆菌对DC 前体的作用和影响进行了比较和研究。结果发现，L.Crispatus 在分离的各原始菌株中，具有最强的刺激THP-1 活化的能力，而且，在相同刺激比例下，L.Crispatus 活菌具有比死菌更强的免疫刺激能力，表现为明显上调THP-1 细胞表面标志CD40、CD80、CD86、 CD1a、CCR6 与CD324 的表达水平，同时可诱导活化THP-1 上调表达Th1 型细胞因子。通过FITC-Dextran 吞噬实验，我们发现，经过L.Crispatus 刺激的THP-1 细胞，其吞噬外来抗原的能力明显下降，但尚未检测到经过活化的THP-1 细胞刺激T 细胞增殖的能力。通过流式细胞术分析的方法，我们检测了TLR1、TLR2、TLR4 与TLR6 在不同的刺激分化阶段的表达水平，结果表明，THP-1 主要通过TLR2 与TLR6 识别女性生殖道L.Crispatus。综上所述，本研究首先通过对DC 体外分化成熟的最短时程的分析，确立了快速诱导DC 的最佳方法，进而利用芯片技术，研究了快速诱导DC 的mi/mRNA 表达谱，揭示了DC 体外分化发育过程中可能的调控途径，为进一步研究DC 的基础生物学提供了恰当的模型和具有指向性的线索。同时，通过与DC 前体THP-1 的共同培养体系，证实了生殖道共生乳酸杆菌的免疫调节作用，为以乳酸杆菌为载体的生殖道粘膜免疫疫苗的研究和应用提供了实验依据

大肠杆菌的mRNA翻译效率决定于Shine-Dalgarno的局部结构(英文)

在大肠杆菌中,多胺对mRNA翻译的影响程度决定于Shine-Dalgarno(SD)序列局部结构.与信使RNA其他区域松散配对的SD序列的局部结构受多胺的扰动较大,其局部解链的概率也较大,因而SD序列结合到核糖体RNA上并启动蛋白质翻译的概率也较大,相反,则启动mRNA翻译的概率就会较小.基于此,建立一个简单数学模型来描述这一现象,即蛋白质的表达水平是与由多胺刺激而引起mRNA的SD序列局部暴露的概率相关的.结果显示,模型与实验结果相符的很好.