Signal-exon trap: a novel method for the identification of signal sequences from genomic DNA

We describe a genomic DNA-based signal sequence trap method, signal-exon trap (SET), for the identification of genes encoding secreted and membrane-bound proteins. SET is based on the coupling of an exon trap to the translation of captured exons, which allows screening of the exon-encoded polypeptides for signal peptide function. Since most signal sequences are expected to be located in the 5′-terminal exons of genes, we first demonstrate that trapping of these exons is feasible. To test the applicability of SET for the screening of complex genomic DNA, we evaluated two critical features of the method. Specificity was assessed by the analysis of random genomic DNA and efficiency was demonstrated by screening a 425 kb YAC known to contain the genes of four secretory or membrane-bound proteins. All trapped clones contained a translation initiation signal followed by a hydrophobic stretch of amino acids representing either a known signal peptide, transmembrane domain or novel sequence. Our results suggest that SET is a potentially useful method for the isolation of signal sequence-containing genes and may find application in the discovery of novel members of known secretory gene clusters, as well as in other positional cloning approaches.     

A method for obtaining DNA from compost

An effective cell lysis method for extraction of bacterial genomic DNA from compost was developed in this study. Enzymatic disruption method, physical–chemical combination method, and commercial kit method were used to extract DNA from compost samples and were compared by analyzing DNA yield and efficient cell lysis. The results showed that all the three methods can be used to extract high-quality DNA from compost, but the enzymatic method had better cell lysis efficiency and DNA yields than others without the use of special equipment and expensive spending. Comparison of different methods for lysing gram-positive bacteria Bacillus subtilis indicated that the enzymatic cell lysis is superior for destroying the gram-positive cell wall. Spin-bind DNA column was used for DNA purification, and the purity of the purified sample was checked by polymerase chain reaction to amplify a region of the 16S rRNA. Results indicated that the part of 16S rRNA were amplified from all the purified DNA samples, and all the amplification products could be digested by the restriction enzyme HhaI.     

SPLICE: a technique for generating in vitro spliced coding sequences from genomic DNA

We describe a rapid and cost-effective technique for the in vitro removal of introns and other unwanted regions from genomic DNA to generate a single sequence of continuous coding capacity, where tissues required for RNA extraction and complementary DNA synthesis are unavailable. Based on an overlapping fusion-PCR strategy, we name this procedure SPLICE (for swift PCR for ligating in vitro constructed exons). As proof-of-principle, we used SPLICE successfully to generate a single piece of DNA containing the coding region of a five-exon gene, the short-wavelength-sensitive 1 (SWS1) opsin gene, from genomic DNA extracted from the brown lemur, Eulemur fulvus, in only two short rounds of PCR. Where the genomic structure and sequence is known, this technique may be universally applied to any gene expressed in any organism to generate a practical unit for investigating the function of a particular gene of interest. In this report, we provide a detailed protocol, experimental considerations, and suggestions for troubleshooting.     

A fast method for high-quality genomic DNA extraction from whole human blood

A simple and fast protocol is described for the purification of genomic DNA from 0.3 ml of whole human blood. The recovery of DNA is quantitative and reproducible; the quality is such that it can be used for all relevant molecular biology techniques.     

A simple method for obtaining blood samples from mature frogs

A technique was developed for obtaining periodic blood samples from mature frogs. Up to 150 microliter of blood was collected at weekly intervals. Anesthetization was not required. The data compiled with this technique indicated that activity-induced hyperglycemia was minimal.     

Inconsistencies in Neanderthal genomic DNA sequences

Two recently published papers describe nuclear DNA sequences that were obtained from the same Neanderthal fossil. Our reanalyses of the data from these studies show that they are not consistent with each other and point to serious problems with the data quality in one of the studies, possibly due to modern human DNA contaminants and/or a high rate of sequencing errors.     

Validation of a cheap and simple nondestructive method for obtaining AFLPs and DNA sequences (mitochondrial and nuclear) in amphibians

The use of nondestructive methods for obtaining DNA from amphibians (e.g. buccal swabs) allows genetic studies to be performed without affecting the survival of the studied individuals. In this study, we compared two methods of nondestructive DNA sampling, buccal swabs and interdigital membrane or toe‐clipping, in several amphibian species of different size: Rhinella spinulosa, R. atacamensis, six species of the genus Telmatobius and Pleurodema thaul. We evaluated the integrity of the DNA extracted by sequencing fragments of mitochondrial and nuclear genes and by generating amplified fragment length polymorphisms markers (AFLPs). In all cases, we obtained an adequate amount of DNA (mean range 55–298 ng/μL). We obtained identical DNA sequences from buccal swab and interdigital membrane/toe‐clip for all individuals. The differences in the coding of AFLP markers between the tissues were similar to those reported for replicas of the same type of sample in similar analyses in other species of amphibians. In conclusion, the use of buccal swabs is a trustworthy and inexpensive method to obtain DNA for mitochondrial and nuclear sequencing and AFLP analyses. Given the types of markers evaluated, buccal swabs may be used for phylogenetic, phylogeographic and population genetic studies, even in small amphibians (<33 mm).     

A large-scale comparison of genomic sequences: one promising approach

We introduce a novel, linguistic-like method of genome analysis. We propose a natural approach to characterizing genomic sequences based on occurrences of fixed length words from a predefined, sufficiently large set of words (strings over the alphabet {A, C, G, T} ). A measure based on this approach is called compositional spectrum and is actually a histogram of imperfect word occurrences. Our results assert that the compositional spectrum is an overall characteristic of a long sequence i.e., a complete genome or an uninterrupted part of a chromosome. This attribute is manifested in the similarity of spectra obtained on different stretches of the same genome, and simultaneously in a broad range of dissimilarities between spectral representations of different genomes. High flexibility characterizes this approach due to imperfect matching and as a result sets of relatively long words can be considered. The proposed approach may have various applications in intra- and intergenomic sequence comparisons.     

An improved method for genomic DNA extraction from cyanobacteria

We present an improved method for genomic DNA extraction from cyanobacteria by updating the earlier method from our group (Sinha et al. 2001) that does not require lysozyme treatment or sonication to lyse the cells. This method use lysis buffer to lyse the cells and also skips the initial treatments to remove the exopolysaccharides or to break the clumps. To test the efficacy of the method DNA was extracted from the freshwater cyanobacteria Anabaena variabilis PCC 7937, Anabaena sp. PCC 7120, Synechocystis sp. PCC 6803, Synechococcus sp. PCC 6301 and Rivularia sp. HKAR-4 (Accession number: FJ939128). The spectrophotometric and gel electrophoresis analysis revealed high yield and high quality of genomic DNA extracted by this method. Furthermore, the RAPD resulted in the amplification of unidentified genomic regions of various lengths; however, rDNA amplification gave only one band of 1.5 kb in all studied cyanobacteria. Thymine dimer detection study revealed that thymine dimers are induced only by UV-B radiation in A. variabilis PCC 7937 and there is no effect of PAR and UV-A on its genome. Collectively, all these findings put forward the applicability of this method in different studies and purposes.     

一种粗糙脉孢霉基因组DNA的快速制备方法

粗糙脉孢霉基因组ＤＮＡ的制备方法一般很费工费时。ＷｅｎｄｌａｎｄＪＡ等人发展了一种丝状真菌的ＤＮＡ提取方法 ,应用在裂褶菌取得了良好的效果[1] 。本文基于该方法制备粗糙脉孢霉基因组ＤＮＡ也取得了成功 ,应用ＰＣＲ从基因组扩增出了一个与无机焦磷酸酶有同源性的基因。1　材料与方法1 1　菌种 :粗糙脉孢霉 (Ｎｅｕｒｏｓｐｏｒａｃｒａｓｓａ)菌种 490 7ｐｒｄ - 4 ,ｂｄＡ ,来自ＦｕｎｇａｌＧｅｎｅｔｉｃｓｓｔｏｃｋｃｅｎｔｅｒ,ＵｎｉｖｅｒｓｉｔｙｏｆＫａｎｓａｓＭｅｄｉｃａｌＣｅｎｔｅｒ,Ｋａｎｓａｓ ,ＵＳＡ。1 2…     

Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants

Extrachromosomal circular DNA (eccDNA) is one characteristic of the plasticity of the eukaryotic genome. It was found in various non-plant organisms from yeast to humans. EccDNA is heterogeneous in size and contains sequences derived primarily from repetitive chromosomal DNA. Here, we report the occurrence of eccDNA in small and large genome plant species, as identified using two-dimensional gel electrophoresis. We show that eccDNA is readily detected in both Arabidopsis thaliana and Brachycome dichromosomatica , reflecting a normal phenomenon that occurs in wild-type plants. The size of plant eccDNA ranges from > 2 kb to < 20 kb, which is similar to the sizes found in other organisms. These DNA molecules correspond to 5S ribosomal DNA (rDNA), non-coding chromosomal high-copy tandem repeats and telomeric DNA of both species. Circular multimers of the repeating unit of 5S rDNA were identified in both species. In addition, similar multimers were also demonstrated with the B. dichromosomatica repetitive element Bdm29. Such circular multimers of tandem repeats were found in animal models, suggesting a common mechanism for eccDNA formation among eukaryotes. This mechanism may involve looping-out via intrachromosomal homologous recombination. The implications of these results on genome plasticity and evolutionary processes are discussed.     

Isolation of genomic DNA from blood using a novel filter-based DNA purification technology

A novel DNA purification technology is described that enables the purification of pure dsDNA from blood. When compared to existing DNA purification methods, the Whatman BioScience Purification System (WBPS) offers a fast and convenient way to recover high yields of DNA. WBPS is based on a unique filter system that entraps DNA within a matrix. This allows the process to be performed in a single unidirectional reaction vessel, reducing user interaction and multiple centrifugation steps.     

Comparison of genomic DNA sequences: solved and unsolved problems

MOTIVATION: The DNA sequences of entire genomes are being determined at a rapid rate. Whereas initial genome sequencing efforts were for organisms chosen to be widely spaced in the tree of life, there is a growing emphasis on projects to sequence a species that is sufficiently similar to an already-sequenced species to allow direct comparison of those two DNA sequences. This and other changes in genome sequencing strategies have created a strong need for new methods to compare genomic sequences. RESULTS: We sketch the current state of software for comparing genomic DNA sequences and outline research directions that we believe are likely to result in important advances in practice.     

A strategy for producing single-stranded DNA in the polymerase chain reaction: A direct method for genomic sequecing

A strategy for synthesizing single-stranded DNA by the polymerase chain reaction method is explored and two protocols are developed. DNA produced with these methods can be sequenced using standard ³⁵S or ³²P dideoxy sequencing protocols. The methods allow rapid genetic screening and population genetic analysis of sequence variation.     

一种冬虫夏草全基因组DNA的提取方法

冬虫夏草是真菌与昆虫形成的复合生物体,本研究建立了一种可同时提取冬虫夏草真菌子座和虫体全部基因组DNA的方法。该方法稳定高效,简便易行,提取纯度高,适用于冬虫夏草多重PCR、Realtime-PCR和DNA指纹图谱等分子水平的研究。