一种改进的平板影印工具及其应用

[目的]建立一种简便高效的平板影印工具,克服传统影印工具的缺陷.[方法]将大量竹签按照一定方法捆扎成与平皿内盖直径相近的捆,将单根牙签转移菌落的效果进行扩大,从而实现菌落的大规模转移.[结果]本实验室使用上述工具成功地进行了平板影印和传代,并进行转化子大规模筛选.[结论]与传统工具相比,该影印工具更为经济简便,而且效果清晰,为微生物平板筛选提供新的方法和思路.国家发明专利申请号:2007100291331.     

Condensed representations of protein secondary structure sequences and their application

In this paper, we propose a nongraphical representation for protein secondary structures. By counting the frequency of occurrence of all possible four-tuples (i.e., four-letter words) of a protein secondary structure sequence, we construct a set of 3x3 matrices for the corresponding protein secondary structure sequence. Furthermore, the leading eigenvalues of these matrices are computed and considered as invariants for the protein secondary structure sequences. To illustrate the utility of our approach, we apply it to a set of real data to distinguish protein structural classes. The result indicates that it can be used to complement the classification of protein secondary structures.     

An improved culturing method for opiine fruit fly parasitoids and its application to parasitoid monitoring in the field

Good culturing methods play an important role in the study of insect behavior and its application to pest management. Here, we describe and validate a new method for rearing the parasitoid wasp, Diachasmimorpha kraussii, which attacks some of the world's worst fruit fly pests and is an internationally used biological control agent. Our method differs from standard culturing approaches by presenting adult wasps with host‐infested artificial media within a “culturing bag,” which mimics a natural (fruit) oviposition substrate. In laboratory trials using wild collected D. kraussii, the culturing bag method was compared to the use of host‐infested nectarines, and a commonly used laboratory method of presenting host‐infested artificial media within Petri dishes. The culturing bag method proved to be a significant improvement on both methods, combining the advantages of high host survival in artificial media with parasitism levels that were the equivalent to those recorded using host‐infested fruits. In our field study, culturing bags infested with the Queensland fruit fly, Bactrocera tryoni, and hung in a mixed peach and nectarine orchard proved to be effective “artificial fruits” attracting wild D. kraussii for oviposition. Significantly more adult wasps were reared from the culturing bags compared to field collected fruits. This was shown to be due to higher fruit fly larval density in the bags, as similar percentage parasitism rates were found between the culturing bags and ripe fruits. We discuss how this cheap, time‐efficient method could be applied to collecting and monitoring wild D. kraussii populations in orchards, and assist in maintaining genetic variability in parasitoid laboratory cultures.     

An improved statistical method for detecting heterotachy in nucleotide sequences

The principle of heterotachy states that the substitution rate of sites in a gene can change through time. In this article, we propose a powerful statistical test to detect sites that evolve according to the process of heterotachy. We apply this test to an alignment of 1289 eukaryotic rRNA molecules to 1) determine how widespread the phenomenon of heterotachy is in ribosomal RNA, 2) to test whether these heterotachous sites are nonrandomly distributed, that is, linked to secondary structure features of ribosomal RNA, and 3) to determine the impact of heterotachous sites on the bootstrap support of monophyletic groupings. Our study revealed that with 21 monophyletic taxa, approximately two-thirds of the sites in the considered set of sequences is heterotachous. Although the detected heterotachous sites do not appear bound to specific structural features of the small subunit rRNA, their presence is shown to have a large beneficial influence on the bootstrap support of monophyletic groups. Using extensive testing, we show that this may not be due to heterotachy itself but merely due to the increased substitution rate at the detected heterotachous sites.     

An improved method for the simultaneous demonstration of mRNA and esterase activity at the human neuromuscular junction

The aim of this study was to develop a simple means of studying the distribution of mRNA coding for post-synaptic proteins at the human neuromuscular junction. A reliable method by which to identify the junctions in tissue sections after in situ hybridization was essential. A method is described for combining the histochemical demonstration of esterase activity at the neuromuscular junction with autoradiographic localization of mRNA by in situ hybridization in the same cryostat section of skeletal muscle. The indigogenic esterase method of Strum and Hall-Craggs (1982) was modified in such a way that it is able to survive the multiple steps involved in in situ hybridization and autoradiography. The protocol is simple and reproducible and has been used successfully on sections of both rat and human skeletal muscle. To demonstrate the method, sections were reacted to reveal esterase activity and were then processed for in situ hybridization using a 35S-labelled probe specific for the -s ubunit of the acetylcholine receptor. The reaction product was retained after the lengthy in situ hybridization and autoradiographic procedures. To our knowledge, this is the first demonstration of acetylcholine receptor mRNA by in situ hybridization at human neuromuscular junctions. © Chapman & Hall     

An algorithm for discriminating sequences and its application to yeast transfer RNA

We describe an algorithm for finding nucleotide residues stronglycorrelated with the amino acid acceptor functions of transferRNAs. The algorithm exploits the fact that each tRNA acceptsonly one of 20 amino acids. The algorithm is applied to 37 Saccharomycescerevisiae transfer RNAs. Received on January 28, 1987     

A characterization of globin mRNA sequences in the nucleus of duck immature red blood cells

Studies were performed with duck immature red blood cells to identify and characterize the globin mRNA sequences in nuclear RNA. Annealing of ³H-globin cDNA to unlabeled nuclear RNA has identified three distinct size classes of nuclear RNA molecules containing globin mRNA sequences. The largest size class contained 1–2% of total nuclear globin mRNA sequences and sedimented through 85% formamide-sucrose gradients at the same rate as 28S ribosomal RNA. Chromatography on oligo(dT)-cellulose indicated that most of these molecules are not polyadenylated. The bulk of nuclear globin mRNA sequences (70%) was contained in polyadenylated RNA molecules which sedimented at 16.5S. The remainder of nuclear globin mRNA sequences (～30%) was detected in molecules sedimenting at 10S (the position of cytoplasmic globin mRNA).To determine whether a precursor-product relationship exists between these nuclear molecules and cytoplasmic globin mRNA, pulse-label and chase experiments were performed. Labeled globin mRNA sequences were assayed by annealing to globin cDNA-cellulose. Labeled 28S nuclear globin RNA sequences could not be detected, perhaps due to technical reasons. 16.5S nuclear globin RNA was labeled and chased into cytoplasmic globin mRNA sequences. The half-life of 16.5S nuclear globin RNA was estimated to be less than 30 min. These results demonstrate that in duck immature red blood cells, globin mRNA is transcribed as a larger precursor. Furthermore, size characterization of this precursor during pulse-label and chase periods suggests that it is processed within the nucleus to 10S globin RNA.     

A new method to predict the consensus secondary structure of a set of unaligned RNA sequences

MOTIVATION: To predict the consensus secondary structure, possibly including pseudoknots, of a set of RNA unaligned sequences. RESULTS: We have designed a method based on a new representation of any RNA secondary structure as a set of structural relationships between the helices of the structure. We refer to this representation as a structural pattern. In a first step, we use thermodynamic parameters to select, for each sequence, the best secondary structures according to energy minimization and we represent each of them using its corresponding structural pattern. In a second step, we search for the repeated structural patterns, i.e. the largest structural patterns that occur in at least one sequence, i.e. included in at least one of the structural patterns associated to each sequence. Thanks to an efficient encoding of structural patterns, this search comes down to identifying the largest repeated word suffixes in a dictionary. In a third step, we compute the plausibility of each repeated structural pattern by checking if it occurs more frequently in the studied sequences than in random RNA sequences. We then suppose that the consensus secondary structure corresponds to the repeated structural pattern that displays the highest plausibility. We present several experiments concerning tRNA, fragments of 16S rRNA and 10Sa RNA (including pseudoknots); in each of them, we found the putative consensus secondary structure.     

Increase in globin chains and globin mRNA in erythroleukemia cells in response to hemin.

Addition of 50 μm hemin to mouse erythroleukemia cells cultured in 0.5% dimethyl-sulfoxide (DMSO) resulted in >10-fold stimulation of globin chain synthesis as a percentage of acid precipitable protein. In cultures fully induced with 1.5% DMSO, addition of 15 mm 3-amino-1,2,4-triazole (AT), an inhibitor of heme synthesis, reduced globin chain synthesis to uninduced levels and reduced globin mRNA levels to less than 20% of induced values. The inhibition of AT was prevented by simultaneous addition of 25 μm hemin to the cultures. Using RNA-DNA hybridization analysis, the amount of globin mRNA sequences as a fraction of total cytoplasmic RNA was also increased by addition of 50 μm hemin to cultures with 0.5% DMSO. The results suggest that exogenous hemin can promote globin chain synthesis, that endogenously synthesized heme can be required for globin chain synthesis, and that hemin directly or indirectly also alters the appearance or degradation of globin mRNA sequences in the cytoplasm.     

An improved biclustering algorithm and its application to gene expression spectrum analysis

Cheng and Church algorithm is an important approach in biclustering algorithms. In this paper, the process of the extended space in the second stage of Cheng and Church algorithm is improved and the selections of two important parameters are discussed. The results of the improved algorithm used in the gene expression spectrum analysis show that, compared with Cheng and Church algorithm, the quality of clustering results is enhanced obviously, the mining expression models are better, and the data possess a strong consistency with fluctuation on the condition while the computational time does not increase significantly.     

Association of globin ribonucleic acid and its precursors with the chicken erythroblast nuclear matrix

Nuclear matrix was prepared from both erythroblasts and erythrocytes of chicken red blood cells. Greater than 90% of the globin nuclear RNA remains bound to the erythroblast nuclear matrix. There are approximately 1000 copies of globin RNA in the nucleus per cell, and most of these contain a poly(A) tail. Precursor beta globin RNA exists in four high molecular weight forms, some of which are larger than the natural beta globin gene. Most of the ribosomal RNA is lost during the preparation of an erythroblast nuclear matrix. In contrast, some of the snRNAs are specifically enriched in the erythroblast nuclear matrix. There is little or no globin nuclear RNA in the erythrocyte nuclear matrix. There appears to be no selective attachment of the globin genes to the erythroblast nuclear matrix. The nuclear matrix is postulated to be a platform for the differential processing of nuclear RNA.     

An improved method for DNA alkaline gradient analysis and its application to the effect of carcinogens on mouse liver DNA

An alkaline sodium iodide density gradient technique is described, for use in sedimentation rate centrifugation studies of in vivo induction of single strand breaks in DNA. The combination of this type of gradient with a sensitive fluorometric DNA estimation makes it possible to analyze very small amounts of DNA without any need for labeling the nucleic acid with radioactive thymidine.     

An improved direct RNA sequence method; its application to Vicia faba 5.8S ribosomal RNA.

We have developed a direct read-off sequencing procedure, based on the method of Stanley and Vassilenko using E. coli 5S ribosomal RNA as a model compound. Radioactive bands were transferred from an acrylamide gel fractionation in the first dimension onto a DEAE-cellulose thin layer plate. After in situ enzymatic digestion with RNase T2, mononucleoside 3',5'-diphosphates were separated in the second dimension by electrophoresis at pH 2.3. Using this two-dimensional procedure the entire sequence of 163 residues of the previously unknown Vicia faba (broad bean) 5.8S ribosomal RNA was deduced.