Self-Sterilizing Inoculating Loop

A self-sterilizing inoculating loop consisting of a step-down transformer and an adjustable timing circuit are described.     

Loop energy in DNA

The loop function ?(N), representing the statistical weight of N complementary residues in a closed ring, has been determined by analysis of high-resolution melting curves of a series of recombinant homopoly(A · T)_N inserts in pBR322 DNA, where 150 > N > 50 base pairs (bp). Loops are found more stable and therefore presumably less elastic than expected for an ideal, freely jointed chain. A value of 97 ± 2 bp is obtained for the empirical orientation-stiffness parameter D in the expression for nonideal chains, ?(N) = (N + D)^?1.7. The 10% increase in apparent stiffness over that of an ideal chain closely coincides with the extent of residual stacking in the loop. It is thus concluded that the more favorable loop energy, such as expected of smaller loops, is due to the incipient helical orientation of some residues, predisposing the loop to reclosure. A quantitative loop function is essential for the prediction and assignment of domains in DNA.     

Many Ways to Loop DNA

In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered.     

生态系统的环分析方法

生态系统的环分析方法郭中伟，李典谟（中国科学院动物研究所，北京１０００８０）ＬｏｏｐＡｎａｌｙｓｉｓｉｎＥｃｏｓｙｓｔｅｍＳｔｕｄｙ．￥ＧｕｏＺｈｏｎｇｗｅｉ；ＬｉＤｉａｎｍｏ（ＩｎｓｔｉｔｕｔｅｏｆＺｏｏｌｏｇｙ，，ＡｃａｄｅｍｉａＳｉｎｉｃａ，Ｂ...     

Coarse-Grained Prediction of RNA Loop Structures

One of the key issues in the theoretical prediction of RNA folding is the prediction of loop structure from the sequence. RNA loop free energies are dependent on the loop sequence content. However, most current models account only for the loop length-dependence. The previously developed “Vfold” model (a coarse-grained RNA folding model) provides an effective method to generate the complete ensemble of coarse-grained RNA loop and junction conformations. However, due to the lack of sequence-dependent scoring parameters, the method is unable to identify the native and near-native structures from the sequence. In this study, using a previously developed iterative method for extracting the knowledge-based potential parameters from the known structures, we derive a set of dinucleotide-based statistical potentials for RNA loops and junctions. A unique advantage of the approach is its ability to go beyond the the (known) native structures by accounting for the full free energy landscape, including all the nonnative folds. The benchmark tests indicate that for given loop/junction sequences, the statistical potentials enable successful predictions for the coarse-grained 3D structures from the complete conformational ensemble generated by the Vfold model. The predicted coarse-grained structures can provide useful initial folds for further detailed structural refinement.     

Chemical Scale Studies of the Phe-Pro Conserved Motif in the Cys Loop of Cys Loop Receptors

The functions of two conserved residues, Phe¹³⁵ and Pro¹³⁶, located at the apex of the Cys loop of the nicotinic acetylcholine receptor are investigated. Both residues were substituted with natural and unnatural amino acids, focusing on the role of aromaticity at Phe¹³⁵, backbone conformation at Pro¹³⁶, side chain polarity and volume, and the specific interaction between the aromatic side chain and the proline. NMR spectroscopy studies of model peptides containing proline and unnatural proline analogues following a Phe show a consistent increase in the population of the cis conformer relative to peptides lacking the Phe. In the receptor, a strong interaction between the Phe and Pro residues is evident, as is a strong preference for aromaticity and hydrophobicity at the Phe site. A similar influence of hydrophobicity is observed at the proline site. In addition, across a simple homologous series of proline analogues, the results reveal a correlation between receptor function and cis bias at the proline backbone. This could suggest a significant role for the cis proline conformer at this site in receptor function.     

Loop size in newt lampbrush chromosomes

Lampbrush chromosome 11 from the newtTaricha granulosa was studied by scanning electron microscopy (SEM) to determine the size of all loops in this bivalent. Measurements with an XY digitizer revealed a mean loop length of 14.9 µm, with a large standard deviation and a skewed distribution toward higher values. The size of the loops at this stage of diplotene extension is similar to that reported in other eukaryotes studies with different approaches. We estimated, from the DNA content of chromosome 11, that between 0.4% and 2.2% of the DNA is found in the loops while the rest of the DNA must remain in the compact chromomeres.     

Loop fold nature of globular proteins

Protein chains make numerous returns in globules, thus forming loops, closed by tight residue-to-residue contacts-closed loops. Previous statistical analysis of the sizes and locations of the closed loops in all major protein folds revealed that the loops have an almost standard contour length of 25-30 amino acid residues and follow one after another along the chain. In this work the closed loops of the major folds are presented in three dimensions. A special image filtering procedure is introduced that allows one to visualize the standard size closed loops for the first time. The loop positions along the sequences are verified by detection of loop-end clusters.     

犬传染性肝炎病毒Hexon蛋白Loop1、Loop2基因的克隆与表达

犬传染性肝炎病毒（ICHV）主要的中和抗原表位位于六邻体蛋白Loop1、Loop2上。本次研究参考Genebank发表的基因序列设计引物,提取ICHV基因组DNA,,分别PCR扩增六邻体蛋白（Hexon）的Loop1、Loop2基因片段,用T4酶连接在一起,克隆入原核表达载体pET28a中,测序显示本室保存病毒分离株Loop1与CLL株、RI261株和Toronto A26/61株核苷酸序列同源性分别为100%、100%和83.8%;Loop2与CLL株、RI261株和Toronto A26/61株核苷酸序列同源性分别为88.1%、88.1%和99.3%,推导的氨基酸序列同源性分别为93.6%、93.6%和98.6%。转化BL21工程菌,实现了重组Loop蛋白在大肠杆菌中的高效表达,其表达的重组蛋白以包涵体形式存在,分子量约为36kDa,并且利用镍柱纯化重组蛋白,纯度达95%以上。本实验为建立新的犬传染性肝炎病毒基因工程产品奠定了良好的基础。     

Loop stereochemistry and dynamics in transfer RNA

The stereochemistry and the dynamics of two loops of yeast tRNA-asp, the thymine loop and the anticodon loop, are compared in the hope of a better understanding of the relationships between loop sequence and loop topology. Both loops are seven residues long and both present sharp turns after the second residue, U33 and psi 55, stabilized by hydrogen bonds between N3-H of the pyrimidine and the phosphates of C36 and A58 and stacking interactions of the pyrimidine ring with the phosphates of U35 and A57, respectively. In the thymine loop, the two purines following C56, A57 and A58, open up to leave space for the intercalation of the first invariant guanine residue of the D-loop, while the two pyrimidine bases, which follow A58, turn away from the stacking pattern of the thymine arm and stack instead with the last base pair of the dihydrouridine arm A15-U48. In the anticodon loop, however, the bases G34 to C38 form an helical stack in continuity with the anticodon stem on the 3'-end. At the same time C36 forms Watson-Crick hydrogen bonds with G34 of a twofold symmetrically related molecule. The anticodon-anticodon base pairing interactions between symmetrically-related molecules are stabilized by stacking with the modified base G37 on both sides of the triplet. Some comparisons are made with the structure of yeast tRNA-phe and some implications about the structure of mitochondrial tRNAs are discussed.