HDAC6 and Ubp-M BUZ domains recognize specific C-terminal sequences of proteins.

The BUZ/Znf-UBP domain is a protein module found in the cytoplasmic deacetylase HDAC6, E3 ubiquitin ligase BRAP2/IMP, and a subfamily of ubiquitin-specific proteases. Although several BUZ domains have been shown to bind ubiquitin with high affinity by recognizing its C-terminal sequence (RLRGG-COOH), it is currently unknown whether the interaction is sequence-specific or whether the BUZ domains are capable of binding to proteins other than ubiquitin. In this work, the BUZ domains of HDAC6 and Ubp-M were subjected to screening against a one-bead-one-compound (OBOC) peptide library that exhibited random peptide sequences with free C-termini. Sequence analysis of the selected binding peptides as well as alanine scanning studies revealed that the BUZ domains require a C-terminal Gly-Gly motif for binding. At the more N-terminal positions, the two BUZ domains have distinct sequence specificities, allowing them to bind to different peptides and/or proteins. A database search of the human proteome on the basis of the BUZ domain specificities identified 11 and 24 potential partner proteins for Ubp-M and HDAC6 BUZ domains, respectively. Peptides corresponding to the C-terminal sequences of four of the predicted binding partners (FBXO11, histone H4, PTOV1, and FAT10) were synthesized and tested for binding to the BUZ domains by fluorescence polarization. All four peptides bound to the HDAC6 BUZ domain with low micromolar K(D) values and less tightly to the Ubp-M BUZ domain. Finally, in vitro pull-down assays showed that the Ubp-M BUZ domain was capable of binding to the histone H3-histone H4 tetramer protein complex. Our results suggest that BUZ domains are sequence-specific protein-binding modules, with each BUZ domain potentially binding to a different subset of proteins.

水稻花发育相关基因RA68和OsUBP1的分离与功能分析

　　　　　　　　　　　　　　　　　第一部分 利用减法杂交和RACEs从水稻中克隆了一个编码含有脯氨酸和苏氨酸丰富结构域多肽的cDNA,其相应的基因被命名为RA68。RA68由3个外显子和2个内含子组成，编码的蛋白由219个氨基酸残基组成。该蛋白由一个21个氨基酸残基组成的信号肽，一个亲水性的N－端结构域和一个疏水性的C－端结构域组成。 N端结构域是一段嵌合PTPTSYG motif的富含脯氨酸和苏氨酸的序列。 Southern杂交和序列分析结果表明RA68在水稻基因组中以单拷贝存在，定位于第2号染色体。Northern杂交结果表明RA68在幼芽和花中表达量较高，在根和叶中不表达。原位杂交分析结果表明：在幼苗期RA68 主要在幼芽胚芽鞘的内外层细胞和幼叶原基的表层细胞中表达;转入生殖生长期后，在花序分生组织、枝梗原基顶端、花器官原基、大孢子囊和花粉粒中表达。用GFP作报告基因，用洋葱表皮细胞进行的瞬间表达测试结果显示RA68蛋白定位于细胞核中。转反义RA68水稻植株抽穗期比对照野生型延迟30天左右。这些结果表明RA68可能是水稻花分生组织特征基因，在成花转变过程中起作用。 　　　　　　　　　　　　　　　　　　　第二部分 通过RACE和RT-PCR方法分离了水稻OsUBP1基因，其推测编码蛋白含有UBP结构域（Cys Box和His Box）和TopⅥA结构域。RT-PCR分析结果表明OsUBP1在转录过程中通过可变剪接产生多个不同的转录本，这些转录本在叶、根、颖花和幼芽中存在着时空调节表达模式，每种组织中的转录本是不一样的。这些转录本内含子剪切位点除了经典的GT-AG外，还有GC-AG、CT-AC、TT-GA、GT-GA和CT-GA。由于发生了GC-AG的可变剪切产生了OsUBP1的重要功能结构域Cys Box。水稻OsUBP1基因和OsSPO11-1基因位于11号染色体的同一基因座位上。原位杂交分析表明，在花中OsUBP1 mRNA 主要在药壁绒毡层、花粉粒、大孢子囊和颖花底部维管束中表达。转反义OsUBP1植株大多不能正常结实，这说明OsUBP1可能参与水稻的育性调节。 关键词

抗氧化剂对大豆下胚轴GUS基因瞬时表达率的影响

大豆是我国最重要的油料作物之一，在我国的农业乃至幽民经济中占有重要地位。但是，由于我国人豆品质较差、产量较低，严重地影响着我国的大豆牛产及其在国际市场上的竞争力。农杆菌介导的转基因方法是大豆改良的最简便和最经济的方法之一，然而大豆基因转化效率低一直是大豆基因工程的主要限制因素。本研究以含有GUS报告基因和NPT II筛选基因的农杆菌1301侵染大豆子叶节和下胚轴，并用组织化学定位法测定GUS基因在叶节和下胚轴上瞬时表达，研究了抗氧化剂对提高大豆基因转化效率的影响，为建立大豆高效基因转化体系奠定基础。 以子叶节为外植体，用农杆菌侵染和共培养后进行GUS染色，观察其瞬时表达情况。在培养基中不含抗氧化剂的情况下，子叶节上未发现染色点，仅在下胚轴侧面有极少染色点。而在培养基巾含有抗氧化剂的情况下，外植体上产生了人量GUS染色点，其中大部分位于下胚轴处，子叶节部位几乎很少被染色。这说明下胚轴比f叶节更容易接受外源基因。本论文分别以子叶节和下胚轴为外植体进行研究。 以子叶节为外植体，在抗氧化剂作用下用农杆菌侵染，诱导丛生芽，在含有潮霉素的筛选培养基上培养，以筛选抗性苗。实验只得到一株抗性幼苗。 为了进一步研究抗氧化剂对GUS暴凶在下胚轴中瞬时表达的影响，我们特别以下胚轴为外植体，测定了多种条件下的瞬时表达率情况。 我们研究了共培养时间对大豆下胚轴基因瞬时表达率的影响，通过确定合适的共培养时间以获得最佳转化率。在共培养2天后，GUS基因的表达率是8%，但是在3天后，GUS基因瞬时表达率大幅度上升，达到23.4%。随后两天GUS基因瞬时表达率没有太大变化，因此，大豆下胚轴的GUS基因瞬时表达的最适共培养时间为3天。 农杆菌再悬浮液稀释浓度对大豆下胚轴GUS基因瞬时表达也有较大影响：再悬浮培养基与农杆菌菌液等体积时，GUS基因瞬时表达率最高，随稀释浓度提高，转化效率降低。这说明随农杆菌菌液浓度提高，侵染几率增加，从而提高了GUS基因的瞬时表达率。 很多研究表明大豆基因转化存在很大的品种问差异，我们选择了四种基因型差异较大的品种在上述最佳条件下分别测定了GUS基因瞬时表达率，但没有发现品种之间存在显著差异，说明抗氧化剂在大豆下胚轴基因转化中具有品种普遍适用性。 上述研究结果表明抗氧化剂能够大大促进GUS基因在下胚轴的瞬时表达，这对于今后开展大豆基因组研究和品质改良工作具有一定意义。

Effective Cell-Centred Time-Domain Maxwell's Equations Numerical Solvers

This research work analyses techniques for implementing a cell-centred finite-volume time-domain (ccFV-TD) computational methodology for the purpose of studying microwave heating. Various state-of-the-art spatial and temporal discretisation methods employed to solve Maxwell's equations on multidimensional structured grid networks are investigated, and the dispersive and dissipative errors inherent in those techniques examined. Both staggered and unstaggered grid approaches are considered. Upwind schemes using a Riemann solver and intensity vector splitting are studied and evaluated. Staggered and unstaggered Leapfrog and Runge-Kutta time integration methods are analysed in terms of phase and amplitude error to identify which method is the most accurate and efficient for simulating microwave heating processes. The implementation and migration of typical electromagnetic boundary conditions. from staggered in space to cell-centred approaches also is deliberated. In particular, an existing perfectly matched layer absorbing boundary methodology is adapted to formulate a new cell-centred boundary implementation for the ccFV-TD solvers. Finally for microwave heating purposes, a comparison of analytical and numerical results for standard case studies in rectangular waveguides allows the accuracy of the developed methods to be assessed.