Algorithm of Regulatory Signal Recognition in DNA Sequences

An algorithm is proposed for extracting regulatory signals from DNA sequences. The algorithm complexity is nearly quadratic. The results of testing the algorithm on artificial and natural sequences are presented.     

Aryl-β-C-LNA Monomers as Universal Hybridization Probes[1] [2]

Abstract

High-affinity universal hybridization is demonstrated for oligonucleotides containing the pyrenyl-LNA monomer 6b, 2′-O-Me-RNA monomers and LNA monomers.     

A Universal Method for the Identification of Bacteria Based on General PCR Primers

The Universal Method (UM) described here will allow the detection of any bacterial rDNA leading to the identification of that bacterium. The method should allow prompt and accurate identification of bacteria. The principle of the method is simple; when a pure PCR product of the 16S gene is obtained, sequenced, and aligned against bacterial DNA data base, then the bacterium can be identified. Confirmation of identity may follow. In this work, several general 16S primers were designed, mixed and applied successfully against 101 different bacterial isolates. One mixture, the Golden mixture7 (G7) detected all tested isolates (67/67). Other golden mixtures; G11, G10, G12, and G5 were useful as well. The overall sensitivity of the UM was 100% since all 101 isolates were detected yielding intended PCR amplicons. A selected PCR band from each of 40 isolates was sequenced and the bacterium identified to species or genus level using BLAST. The results of the UM were consistent with bacterial identities as validated with other identification methods; cultural, API 20E, API 20NE, or genera and species specific PCR primers. Bacteria identified in the study, covered 34 species distributed among 24 genera. The UM should allow the identification of species, genus, novel species or genera, variations within species, and detection of bacterial DNA in otherwise sterile samples such as blood, cerebrospinal fluid, manufactured products, medical supplies, cosmetics, and other samples. Applicability of the method to identifying members of bacterial communities is discussed. The approach itself can be applied to other taxa such as protists and nematodes.     

如何提高学术论文投稿录用率

探讨了如何提高学术论文投稿录用率;从论文选题、题名、内容、格式、参考文献等方面阐述论文录用应注意的一些问题;从选刊、投稿后的注意事项等方面提出了提高投稿录用率的建议。     

A self-referential model for the formation of the genetic code

A model for the formation of the genetic code is presented where protein synthesis is directed initially by tRNA dimers. Proteins that are resistant to degradation and efficient RNA-binders protect the RNAs. Replication becomes elongational producing poly-tRNAs from which the mRNAs and ribosomes are derived. Attributions are successively fixed to tRNAs paired through the perfect palindromic anticodons, with the same bases at the extremities (5′ANA: UNU 3′; GNG: CNC; principal dinucleotides, pDiN). The 5′ degeneracy is then developed. The first pairs to be encoded correspond to the hydropathy correlation outliers (Gly-CC: Pro-GG and Ser-GA: Ser-CU) and to the sector of homogeneous pDiN, composed by two pyrimidines or two purines. These amino acids are preferred in the N-ends of proteins, stabilizers of proteins against catabolism and strong RNA-binders. The next pairs complete the sector of homogeneous pDiN (Asp, Glu-UC: Leu-AG and Asn, Lys-UU: Phe-AA). This set of nine amino acids forms the protein cores with the predominant aperiodic conformation. Next enter the pairs with mixed pDiN (one purine and one pyrimidine), the RY attributions composing the protein N-ends and the YR attributions the C-ends. The last pair contains the main punctuation signs (Ile, Met, iMet-AU: Tyr, Stop-UA). The model indicates that genetic information emerged during the process of formation of the coding/decoding system and that genes were defined by the proteins. Stable proteins constructed the nucleoprotein system by binding to the RNAs that produced them. In this circular rationale, genes are memories in a metabolic system for production of proteins that stabilize it. The simplicity and the highly deterministic character of the process suggest that the Last Universal Common Ancestor populations could be composed, in early stages, of lineages bearing similar genetic codes.     

Novel Photocleavable Universal Support for Oligonucleotide Synthesis

Abstract

A novel photocleavable universal support for the automated solid phase synthesis of oligonucleotides is described. The linker between the growing oligonucleotide chain and CPG support contains a nucleophilic amine protected with a photocleavable group. On exposure to UV light, this group is detached and the free amine affords cleavage of the oligonucleotide from the support. The use of long wavelength UV light avoids damage to the DNA.     

通用型流感疫苗的研究现状与展望

接种流感疫苗是预防和控制流感最为有效的措施。流感病毒由于其宿主多样、亚型众多,流感疫苗的有效性十分受限,同时由于其具有高度的变异性,一旦有较大的变异或新亚型的流感病毒出现,现有疫苗就会失效,因此研制能够通过免疫交叉反应对变异较大或多种亚型的流感病毒提供广泛保护的通用型流感疫苗迫在眉睫。     

具偏差变元的偏微分方程组的振动性定理

获得了一类具偏差变元的偶数阶偏微分方程组解振动的若干充分条件。     

USLE/RUSLE中植被覆盖与管理因子研究进展

通用土壤流失方程(USLE)及修正通用土壤流失方程(RUSLE)是世界范围内应用最广泛的土壤侵蚀预报模型,模型中C因子表示植被覆盖和管理措施对土壤侵蚀的作用,是人为控制土壤侵蚀的重要因子。回溯了C因子发展演变历程,依据国内外最新研究成果,系统阐述了不同尺度C因子估算方法。在小区、坡面、小流域尺度上,C因子确定主要依赖于野外实验观测,研究条件的一致性尤其是标准小区的统一是C因子值可比性的前提。流域、区域尺度C因子确定通常需要利用遥感影像,遥感技术的发展促进了流域、区域尺度C因子估算方法的进步,使提取的C因子图更加精细、准确,但是使用遥感数据全面刻画C因子含义仍然是一大挑战,因此仍需加强C因子相关研究。共归纳了10种确定C因子的方法,介绍了不同方法的优缺点及适用条件,提出了我国C因子研究应加强的工作,希望为相关领域研究者提供参考。     

Examination of the effect of structural variation on the N-glycosidic torsion (ΦN) among N-(β-d-glycopyranosyl)acetamido and propionamido derivatives of monosaccharides based on crystallography and quantum chemical calculations

GlcNAcβAsn linkage is conserved in the N-glycoproteins of all eukaryotes. l-Glutamine (Gln), which is a one carbon higher homolog of Asn, is never glycosylated. X-ray crystallographic study of several β-1-N-acetamido- and propionamido derivatives of monosaccharides has earlier shown that the N-glycosidic torsion, Φ_N, is influenced to a larger extent by the structural variation of the sugar part than that of the aglycon moiety. In order to examine the influence of the carbohydrate pendent groups on the conformational preference of the N-glycosidic linkage with respect to Φ_N, several models and analogs with gluco and manno configuration have been studied in the present work by computational chemistry. The crystal structure of XylβNHPr is reported here and its molecular packing compared with related analogs. The conjunction of combining Crystallographic and computational studies allows to demonstrate the strong influence that the group at C2, and environmental factors particularly inter- and intramolecular interactions involving regular hydrogen bonds and the weak C-H···O contacts, have on the energy preference of the Φ_N torsion angle.     

图论在RNA二级结构中的应用

图论是以图为研究对象的数学分支,是一门研究事物对象在图表示法中的特征与性质的学科。鉴于RNA二级结构在功能基因组研究中的重要地位,已发展了用二维图解表示法描述RNA二级结构。文章介绍了用于RNA二级结构图解表示法的两种图,即树图和对偶图的构造规则。并在树图表示基础上产生Laplacian矩阵和相应本征值谱。以有害突变预测和类RNA模体设计的例子,说明图论在RNA二级结构中的应用,同时对可能存在的一些问题做了讨论。