Intron existence predated the divergence of eukaryotes and prokaryotes

Nucleotide sequences for the nuclear genes encoding chloroplast (GapA and GapB) and cytosolic (GapC) glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) from Arabidopsis thaliana were determined. Comparison of nucleotide sequences indicates that the divergence of chloroplast and cytosolic GAPDH genes preceded the divergence of prokaryotes and eukaryotes. In addition, some intron-exon junctions are conserved among GapB, GapC, and chicken GAPDH genes. These results provide evidence at the molecular level to support the idea that introns existed before the divergence of prokaryotes and eukaryotes.     

Atomically resolved single-walled carbon nanotube intramolecular junctions

Intramolecular junctions in single-walled carbon nanotubes are potentially ideal structures for building robust, molecular-scale electronics but have only been studied theoretically at the atomic level. Scanning tunneling microscopy was used to determine the atomic structure and electronic properties of such junctions in single-walled nanotube samples. Metal-semiconductor junctions are found to exhibit an electronically sharp interface without localized junction states, whereas a more diffuse interface and low-energy states are found in metal-metal junctions. Tight-binding calculations for models based on observed atomic structures show good agreement with spectroscopy and provide insight into the topological defects forming intramolecular junctions. These studies have important implications for applications of present materials and provide a means for assessing efforts designed to tailor intramolecular junctions for nanoelectronics.     

鱼类胰岛素样生长因子Ⅰ的生物信息学分析

对NCBI已登记的5种鱼IGFⅠ-的氨基酸序列进行生物信息学方法分析,对其组分、理化性质、跨膜结构域、二级结构、功能结构域、亚细胞定位、同源建模及分子进化进行预测和推断。结果表明,IGⅠF-定位于胞外,是一种存在信号肽的分泌性蛋白,伸展片段和自由卷曲是成熟IGFⅠ-的主要结构元件,而α-螺旋则分布于分子表面。     

Retroviral DNA integration directed by HIV integration protein in vitro

Efficient retroviral growth requires integration of a DNA copy of the viral RNA genome into a chromosome of the host. As a first step in analyzing the mechanism of integration of human immunodeficiency virus (HIV) DNA, a cell-free system was established that models the integration reaction. The in vitro system depends on the HIV integration (IN) protein, which was partially purified from insect cells engineered to express IN protein in large quantities. Integration was detected in a biological assay that scores the insertion of a linear DNA containing HIV terminal sequences into a lambda DNA target. Some integration products generated in this assay contained five-base pair duplications of the target DNA at the recombination junctions, a characteristic of HIV integration in vivo; the remaining products contained aberrant junctional sequences that may have been produced in a variation of the normal reaction. These results indicate that HIV IN protein is the only viral protein required to insert model HIV DNA sequences into a target DNA in vitro.     

Molecular architecture and evolution of a modular spider silk protein gene

Spider flagelliform silk is one of the most elastic natural materials known. Extensive sequencing of spider silk genes has shown that the exons and introns of the flagelliform gene underwent intragenic concerted evolution. The intron sequences are more homogenized within a species than are the exons. This pattern can be explained by extreme mutation and recombination pressures on the internally repetitive exons. The iterated sequences within exons encode protein structures that are critical to the function of silks. Therefore, attributes that make silks exceptional biomaterials may also hinder the fixation of optimally adapted protein sequences.     

Intron-Targeted Intron-Exon Splice Conjunction （IT-ISJ） Marker and Its Application in Construction of Upland Cotton Linkage Map

To develop a new DNA maker, which could be used in genetic diversity analysis and genetic map construction in plants, IT-ISJ （intron targeted intron-exon splice junction） primer combinations, which were designed according to the intronexon splice junction conserved sequences, were used to construct cotton genetic linkage map in the present study. 49 out of 704 IT-ISJ primer combinations showed polymorphism between upland cotton high quality cultivar Yumian 1 and multiple dominant gene line T586, and the polymorphic primer combinations accounted for 7.0% of total primer combinations. 49 IT-ISJ primer combinations were used to genotype 270 F2：7 recombinant inbred lines developed from （Yumian 1 × T586） F2, and 58 IT-ISJ loci were obtained. 58 IT-ISJ, together with 150 SSR and 8 morphological loci, were used to conduct linkage analysis, and a linkage map including 22 linkage groups and 113 loci （49 IT-ISJ, 62 SSR, and 2 morphological loci） was constructed. The linkage map covered 714.5 cM with an average interval of 6.3 cM between two markers, accounting for 16.1% of cotton genome. The present study demonstrated that the polymorphism of IT-ISJ marker is high, and it could be effectively applied in plant genetic map construction.     

植物ASK1-D3(MAX2)-D14蛋白复合体互作区特征与演化分析

ASK1-D3-D14复合体作为E3泛素连接酶的一部分,调控水稻的形态发生等生理反应.为了揭示该复合体互作区的结构特征和演化关系,通过对不同物种中D3直系蛋白间的系统进化进行分析,发现D3基因在不同物种中表现出不同的演化进程;而对ASK1-D3和D3-D14互作面的序列和空间结构分析,揭示D3直系同源蛋白质以及已知的F-box-like结构域间的序列同源性较低,而空间结构相似性较高,暗示F-box-like与ASK1类蛋白质之间的互作,空间结构的相似性重于序列的相似性.涉及D3和D14互作面的氨基酸在直系同源蛋白序列间的同源性很高,而形成互作面疏水内核的氨基酸保守性更高.这为D3复合体的进一步研究提供了依据.     

不同植物查尔酮合成酶CHS基因的生物信息学分析

采用生物信息学方法对GenBank中已登录的10种不同植物中的查尔酮合成酶基因的核苷酸序列及所推测的氨基酸序列的理化性质、信号肽、跨膜结构、亲/疏水性、功能结构域以及其二级结构进行了详细的分析,构建了不同植物CHS的系统进化树。结果表明,10种植物中CHS基因的开放阅读框的全长在1.2 kb左右,大约编码399个氨基酸;不同植物中的CHS的氨基酸序列均包括1个N-糖基化位点(32NMSS),4个蛋白激酶c磷酸化位点(69TIR、158SVK、202TFR、359SAK)和1个查尔酮合成酶活性位点(161RLMMYQQGCFAGGTVLR),均不存在信号肽、无跨膜结构域,是一个疏水性蛋白。     

Genomic structure and sequence polymorphism of E,E-alpha-farnesene synthase gene in apples (Malus domestica Borkh.)

Primer pairs were designed to amplify the genomic DNA sequence of the alpha-farnesene synthase (AFS) gene by PCR. The PCR products were sequenced, spliced and compared to cDNA sequences in the GenBank (accession No. AY182241). The genomic sequence and intron-exon organization of the AFS gene were thus obtained. The AFS genomic sequence has been registered in the GenBank (accession No. DQ901739). It has 6 introns and 7 exons, encoding a protein of 576 amino acids. The sizes of the 6 introns were 108 bp, 113 bp, > 1000 bp, 125 bp, 220 bp and 88 bp, and their phases were 0, 1, 2, 2, 0, 0, respectively. The sizes of the deduced amino acids of the 7 exons were 57, 89, 127, 73, 48, 83 and 99, respectively. The AFS protein contained three motifs: the RR(X8)W motif encoded by a sequence in exon 1, and the RxR motif and DDxxD motif encoded by two sequences in exon 4. After comparing the AFS genomic sequence (accession No. DQ901739) to the cDNA sequence (accession No. AY523409) in the GenBank, it was found that there were 6 single-nucleotide polymorphisms between the two sequences, four of which caused mutations at the amino acid level. Interestingly, one amino acid mutation (291R → RG) was found in the RxR motif, and further investigation is needed to determine whether the alpha-farnesene synthesis ability and superficial scald susceptibility of apples are influenced by this amino acid mutation and other mutations. __________ Translated from Acta Horticulturae Sinica, 2007, 34(4): 1003–1006[译自: 园艺学报]     

Templating three-dimensional self-assembled structures in bilayer block copolymer films

The registration and alignment of a monolayer of microdomains in a self-assembled block copolymer thin film can be controlled by chemical or physical templating methods. Although planar patterns are useful for nanoscale device fabrication, three-dimensional multilevel structures are required for some applications. We found that a bilayer film of a cylindrical-morphology block copolymer, templated by an array of posts functionalized with a brush attractive to the majority block, can form a rich variety of three-dimensional structures consisting of cylinder arrays with controllable angles, bends, and junctions whose geometry is controlled by the template periodicity and arrangement. This technique allows control of microdomain patterns and the ability to route and connect microdomains in specific directions.     

苹果SBP基因家族生物信息学分析

首先利用生物信息学方法对苹果42条SBP蛋白序列的系统发生和SBP基因组定位进行分析,然后对其氨基酸组成成分、理化性质以及二级和三级结构进行预测和分析,同时还分析了苹果与拟南芥的SBP基因家族之间的联系。结果显示着42条蛋白序列与拟南芥16条SBP蛋白序列一起被分成了7个亚族,拟南芥与苹果SBP基因间具有较高的保守性。基因组定位结果显示42条SBP基因分布在12条染色体上。研究还发现不同亚族间氨基酸数目、氨基酸序列疏水性存在一定的差异;二级结构预测分析发现,42条氨基酸序列以随机卷曲和α-螺旋为主要组成部分,而且42条氨基酸序列三维结构相似。     

利用重叠延伸PCR技术进行DNA的人工合成

重叠延伸PCR技术是一种通过寡聚核苷酸链之间重叠的部分互相搭桥、互为模板进行PCR扩增,从而获得目的DNA基因片段的方法。该技术在目的基因的人工合成及外源蛋白在宿主中的高效表达等方面显示出良好的应用前景。综述了重叠延伸PCR技术的原理、反应条件的优化及其应用。     

Detection, stimulation, and inhibition of neuronal signals with high-density nanowire transistor arrays

We report electrical properties of hybrid structures consisting of arrays of nanowire field-effect transistors integrated with the individual axons and dendrites of live mammalian neurons, where each nanoscale junction can be used for spatially resolved, highly sensitive detection, stimulation, and/or inhibition of neuronal signal propagation. Arrays of nanowire-neuron junctions enable simultaneous measurement of the rate, amplitude, and shape of signals propagating along individual axons and dendrites. The configuration of nanowire-axon junctions in arrays, as both inputs and outputs, makes possible controlled studies of partial to complete inhibition of signal propagation by both local electrical and chemical stimuli. In addition, nanowire-axon junction arrays were integrated and tested at a level of at least 50 "artificial synapses" per neuron.     

Room-Temperature, Electric Field-Induced Creation of Stable Devices in CulnSe2 Crystals

Multiple-junction structures were formed, on a microscopic scale, at room temperature, by the application of a strong electric field across originally homogeneous crystals of the ternary chalcopyrite semiconductor CulnSe(2). After removal of the electric field, the structures were examined with electron beam-induced current microscopy and their current-voltage characteristics were measured. Bipolar transistor action was observed, indicating that sharp bulk junctions can form in this way at low ambient temperatures. The devices are stable under normal (low-voltage) operating conditions. Possible causes for this effect, including electromigration and electric field-assisted defect reactions, are suggested.     

Electron transport in molecular wire junctions

Molecular conductance junctions are structures in which single molecules or small groups of molecules conduct electrical current between two electrodes. In such junctions, the connection between the molecule and the electrodes greatly affects the current-voltage characteristics. Despite several experimental and theoretical advances, including the understanding of simple systems, there is still limited correspondence between experimental and theoretical studies of these systems.     

Protein structure prediction and structural genomics

Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information about a subset of the proteins, computational structure prediction methods will provide valuable information for the large fraction of sequences whose structures will not be determined experimentally. The first class of protein structure prediction methods, including threading and comparative modeling, rely on detectable similarity spanning most of the modeled sequence and at least one known structure. The second class of methods, de novo or ab initio methods, predict the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures. In this Viewpoint, we begin by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes. We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics.     

牦牛和犏牛Dmrt7基因序列分析及其 在睾丸组织中的表达水平

【目的】研究牦牛和犏牛Dmrt7基因编码区序列和编码蛋白的结构,以及在睾丸组织中mRNA及其蛋白表达水平,探讨Dmrt7与犏牛雄性不育的关系,为揭示犏牛雄性不育的分子机理提供依据。【方法】利用分子克隆技术获得牦牛和犏牛Dmrt7基因编码区序列,并采用生物信息学方法对该基因及其编码蛋白的功能位点和二级结构等方面进行了预测和分析;通过半定量PCR技术检测Dmrt7基因mRNA在牦牛各组织器官中的表达水平;利用实时荧光定量PCR技术检测牦牛和犏牛睾丸组织中Dmrt7基因mRNA表达水平;并通过western blotting检测牦牛和犏牛睾丸组织中Dmrt7蛋白的表达水平。【结果】牦牛和犏牛Dmrt7基因cDNA序列一致,包含一个长度为1 113 bp的开放阅读框,编码370个氨基酸,具有完整的DM功能域,二级结构主要以无规则卷曲、α螺旋和延伸链为主。在牦牛各组织器官中,Dmrt7基因mRNA仅在睾丸组织中特异性表达。牦牛睾丸组织中Dmrt7mRNA和蛋白的表达水平极显著高于犏牛（P＜0.01）。【结论】牦牛睾丸组织中Dmrt7基因mRNA和蛋白表达水平明显高于犏牛,且Dmrt7蛋白表达水平与其mRNA表达水平相一致。     

A poliovirus neutralization epitope expressed on hybrid hepatitis B surface antigen particles

The hepatitis B virus (HBV) envelope protein carrying the surface antigen (HBsAg) is assembled with cellular lipids in mammalian cells into empty viral envelopes. In a study to evaluate the capacity of such particles to present foreign peptide sequences in a biologically active form, in-phase insertions were created in the S gene encoding the major envelope protein. One of the sequences inserted was a synthetic DNA fragment encoding a poliovirus neutralization epitope. Mammalian cells expressing the modified gene secreted hybrid particles closely resembling authentic 22-nanometer HBsAg particles. These particles reacted with a poliovirus-specific monoclonal antibody and induced neutralizing antibodies against poliovirus. The results indicate that empty viral envelopes of HBV may provide a means for the presentation of peptide sequences and for their export from mammalian cells.