An oligonucleotide hybridization approach to DNA sequencing

We have proposed a DNA sequencing method based on hybridization of a DNA fragment to be sequenced with the complete set of fixed-length oligonucleotides (e.g., 4(8) = 65,536 possible 8-mers) immobilized individually as dots of a 2-D matrix [(1989) Dokl. Akad. Nauk SSSR 303, 1508-1511]. It was shown that the list of hybridizing octanucleotides is sufficient for the computer-assisted reconstruction of the structures for 80% of random-sequence fragments up to 200 bases long, based on the analysis of the octanucleotide overlapping. Here a refinement of the method and some experimental data are presented. We have performed hybridizations with oligonucleotides immobilized on a glass plate, and obtained their dissociation curves down to heptanucleotides. Other approaches, e.g., an additional hybridization of short oligonucleotides which continuously extend duplexes formed between the fragment and immobilized oligonucleotides, should considerably increase either the probability of unambiguous reconstruction, or the length of reconstructed sequences, or decrease the size of immobilized oligonucleotides.     

An integrative approach for the optical sequencing of single DNA molecules

A new approach for optically sequencing ensembles of single DNA molecules using DNA polymerase to mediate the consecutive incorporation of fluorochrome-labeled nucleotides into an array of large single DNA molecules is presented. The approach utilizes cycles of labeled fluorochrome addition, detection to count incorporations, and bleaching to reset the counter. These additions are imaged and analyzed to estimate the number of labeled additions and to correlate them on a per-locus basis along DNA backbones. Initial studies used precisely labeled polymerase chain reaction products to aid the development and validation of simple models of fluorochrome point spread functions within the imaging system. In complementary studies, nucleotides labeled with the fluorochrome R110 were incorporated into surface-elongated lambda DNA, and fluorescent signals corresponding to the addition of R110-dUTP were counted and assigned precise loci along DNA backbones. The labeled DNAs were then subjected to photobleaching and to a second cycle of addition of R110-labeled nucleotides-a second round of additions was correlated with the first to establish strings of addition histories among the ensemble of largely double-stranded templates. These results confirm the basic operational validity of this approach and point the way to the development of a practical system for optical sequencing.     

The use of stable isotopes to study ecosystem gas exchange

Stable isotopes are a powerful research tool in environmental sciences and their use in ecosystem research is increasing. In this review we introduce and discuss the relevant details underlying the use of carbon and oxygen isotopic compositions in ecosystem gas exchange research. The current use and potential developments of stable isotope measurements together with concentration and flux measurements of CO₂ and water vapor are emphasized. For these applications it is critical to know the isotopic identity of specific ecosystem components such as the isotopic composition of CO₂, organic matter, liquid water, and water vapor, as well as the associated isotopic fractionations, in the soil-plant- atmosphere system. Combining stable isotopes and concentration measurements is very effective through the use of ”Keeling plots.” This approach allows the identification of the isotopic composition and the contribution of ecosystem, or ecosystem components, to the exchange fluxes with the atmosphere. It also allows the estimation of net ecosystem discrimination and soil disequilibrium effects. Recent modifications of the Keeling plot approach permit examination of CO₂ recycling in ecosystems. Combining stable isotopes with dynamic flux measurements requires precision in isotopic sampling and analysis, which is currently at the limit of detection. Combined with the micrometeorological gradient approach (applicable mostly in grasslands and crop fields), stable isotope measurements allow separation of net CO₂ exchange into photosynthetic and soil respiration components, and the evapotranspiration flux into soil evaporation and leaf transpiration. Similar applications in conjunction with eddy correlation techniques (applicable to forests, in addition to grasslands and crop fields) are more demanding, but can potentially be applied in combination with the Keeling plot relationship. The advance and potential in using stable isotope measurements should make their use a standard component in the limited arsenal of ecosystem-scale research tools. Received: 8 July 1999 / Accepted: 10 January 2000     

An approach for the stable immobilization of proteins

An approach is presented for the stable covalent immobilization of proteins with a high retention of biological activity. First, chemical modification studies were used to establish enzyme structural and functional properties relevant to the covalent immobilization of an enzyme to agarose based supports. Heparinase was used as a model enzyme in this set of studies. Amine modifications result in 75-100% activity loss, but the effect is moderated by a reduction in the degree of derivatization. N-hydroxysuccinimide, 1,1,1-trifluoroethanesulfonic acid, and epoxide activated agarose were utilized to determine the effect of amine reactive supports on immobilized enzyme activity retention. Cysteine modifications resulted in 25-50% loss in activity, but free cysteines were inaccessible to either immobilized bromoacetyl or p-chloromercuribenzoyl groups. Amine reactive coupling chemistries were therefore utilized for the covalent immobilization of heparinase. Second, to ensure maximal stability of the immobile protein-support linkage, the identification and subsequent elimination of the principal sources of protein detachment were systematically investigated. By using high-performance liquid chromatography (HPLC), electrophoresis, and radiolabeling techniques, the relative contributions of four potential detachment mechanisms-support degradation, proteolytic degradation, desorption of noncovalently bound protein, and bond solvolysis-were quantified. The mechanisms of lysozyme, bovine serum albumin, and heparinase leakage from N-hydroxysuccinimide or 1,1,1-trifluoroethanesulfonic acid activated agarose were elucidated. By use of stringent postimmobilization support wash procedures, noncovalently bound protein loss. An effective postimmobilization washing procedure is presented for the removal of adsorbed protein and the complete elimination of immobilized protein loss.     

The use of stable isotopes to trace small-scale movements by small fish species

Valuable biological information can be obtained by monitoring the movement of organisms. However, the choice of monitoring method becomes highly restricted when following small organisms (<100 mm), especially in aquatic ecosystems. Stable isotopes are being increasingly used in this respect but rarely at the local spatial scale, i.e. 10–1000 s of metres. We sought to identify movement of small fishes between a main river channel and its tributary. Little overlap in isotope baseline was detected between the two channels despite some temporal variability in δ¹⁵N of baseline indicator organisms in the main river. The individuals of two small cyprinid fish species (Leuciscus souffia and Alburnoides bipunctatus) of all the size classes (40–100 mm) caught within the tributary showed considerable heterogeneity in δ¹⁵N values. Classification and discriminant analysis on isotope-derived data distinguished two significantly different groups. Moreover, this result was supported by further sampling of fish caught in the main river (in May and December 2006). Alternative hypotheses, such as dietary differences, biological factors, temporal shifts and spatial differences in diet, did not explain δ¹⁵N variability. This application of stable isotopes at a relatively small spatial and temporal scales further demonstrates its potential as a tool for ecologists.     

Strategy for DNA sequencing: use of transposing elements

A variety of approaches to determine the complete sequence of large DNA fragments is summarized. Main attention is paid to a transposon-based DNA sequencing strategy.     

Single-molecule detection as an approach to rapid DNA sequencing.

Current sequencing technologies are insufficient to cope with large-scale projects such as sequencing the human genome and genomes of model organisms. In addition, as genetic lesions associated with specific human diseases are identified, DNA sequencing will be used increasingly for clinical applications. Thus, new approaches are needed to combine high-throughput with accuracy for both research and diagnostic purposes. A novel technology based on detection of individual fluorescent nucleotides in a flowing sample stream is under development.     

The use of stable isotopes and spectroscopy to investigate the energy transducing function of cytochrome c oxidase

We have used EPR and FTIR spectroscopy in combination with (17)O and (15)N stable isotopes to investigate the mechanism of cytochrome c oxidase (CcO). A high-spin state of heme a(3) was found in high yield by EPR, achieved upon turning over the enzyme until it was anaerobic, and shown to be a mixture of heme with a coordinated oxygen-based ligand and five-coordinate heme. Allowing the enzyme to consume (17)O(2) for a few milliseconds before freezing, we also showed that the product H(2)(17)O exits toward the external side of the enzyme, binding to the nonredox active Mg/Mn site en route. Specific (15)N labeling of histidine, in comparison with global (15)N labeling and unlabeled samples, allowed us to more definitively assign heme and histidine peaks in the electrochemically induced FTIR difference spectrum. Additionally, the assignment of heme bands affords a reliable method of spectrum normalization between samples, providing a more accurate comparison of the spectral features of bovine with bacterial cytochrome oxidase and revealing multiple differences between the two species.     

An automated instrument for the performance of enzymatic DNA sequencing reactions

An instrument has been developed for the automation of enzymatic DNA sequencing reactions. Up to 96 DNA templates contained in a microtiter plate can be processed for either radioactive or fluorescence-based sequence analysis in a three-hour period. The quality of the resultant data is comparable to that obtained manually. The system is simple, flexible and is readily adapted to the use of new polymerases or modified experimental protocols.     

Production of single-stranded DNA for sequencing: an alternative approach.

We describe a simple procedure for the direct sequencing of single-stranded, PCR-amplified, target regions of human genomic DNA. At variance with previously reported procedures, purification of the desired double-stranded DNA was introduced. This additional step allowed the single-stranded amplification and sequencing of the target gene. This step is required for direct sequencing of some amplified regions of human genomic DNA. However, no individual technique seems suitable to generate and sequence all single-stranded DNA.     

Scope for use of stable carbon isotopes in discerning the incorporation of forest detritus into aquatic foodwebs

Stable isotope analysis of carbon has been proposed as a means for discerning the incorporation of terrestrial forest detritus into aquatic foodwebs, and as such, has the potential to be used as a biomonitor of the aquatic effects of riparian deforestation. A synthesis of ¹³C/¹²C data from the literature indicates, however, that the scope for successful use of carbon isotope analysis in separating allochthonous and autochthonous food provenance is much more limited than was once thought. This occurs due the overlap in carbon isotope ratios between terrestrial forest detritus and those of both lotic attached algae and lentic filamentous attached algae. Only within rockyshored, oligotrophic lakes without macrophytes, and forest-fringed estuaries and lagoons, where the carbon isotope ratios for attached algae and forest detritus are significantly different, is there any likelihood of discerning the incorporation of allochthonous carbon into aquatic foodwebs using ¹³C/¹²C values alone.     

A distance-type measure approach to the analysis of copy number variation in DNA sequencing data

Background

The next generation sequencing technology allows us to obtain a large amount of short DNA sequence (DNA-seq) reads at a genome-wide level. DNA-seq data have been increasingly collected during the recent years. Count-type data analysis is a widely used approach for DNA-seq data. However, the related data pre-processing is based on the moving window method, in which a window size need to be defined in order to obtain count-type data. Furthermore, useful information can be reduced after data pre-processing for count-type data.

Results

In this study, we propose to analyze DNA-seq data based on the related distance-type measure. Distances are measured in base pairs (bps) between two adjacent alignments of short reads mapped to a reference genome. Our experimental data based simulation study confirms the advantages of distance-type measure approach in both detection power and detection accuracy. Furthermore, we propose artificial censoring for the distance data so that distances larger than a given value are considered potential outliers. Our purpose is to simplify the pre-processing of DNA-seq data. Statistically, we consider a mixture of right censored geometric distributions to model the distance data. Additionally, to reduce the GC-content bias, we extend the mixture model to a mixture of generalized linear models (GLMs). The estimation of model can be achieved by the Newton-Raphson algorithm as well as the Expectation-Maximization (E-M) algorithm. We have conducted simulations to evaluate the performance of our approach. Based on the rank based inverse normal transformation of distance data, we can obtain the related z-values for a follow-up analysis. For an illustration, an application to the DNA-seq data from a pair of normal and tumor cell lines is presented with a change-point analysis of z-values to detect DNA copy number alterations.

Conclusion

Our distance-type measure approach is novel. It does not require either a fixed or a sliding window procedure for generating count-type data. Its advantages have been demonstrated by our simulation studies and its practical usefulness has been illustrated by an experimental data application.

     

An illustration of the use of isotopes: the biosynthesis of porphyrins

In this article, David Shemin, who is now in retirement, describes how in 1944 he ingested 66 g of 15N-labeled glycine in order to determine the half-life of hemoglobin and other blood proteins. The ramifications of the experiment led to the unravelling of the biosynthesis of porphyrins and the role of glycine and alpha-aminolevulinic acid in heme, vitamin B12 and chlorophyll synthesis.     

Biosynthesis in opisthobranch molluscs: General outline in the light of recent use of stable isotopes

The use of stable isotopes has been recently introduced in the biosynthetic studies of metabolites produced by opisthobranch molluscs. This methodology offers numerous advantages since it avoids the complex and tedious manipulations of potentially dangerous radioactive compounds and gives unequivocal evidence for the incorporation. In these studies, high field NMR spectroscopy is a particularly useful tool to localize the labeled atoms in the molecule. This chapter updates the biosynthetic studies on opisthobranch molluscs with particular attention to the recent experiments with precursors labeled with stable isotopes. Opisthobranchs are able to biosynthesize de novo a wide array of chemical skeletons including polyketides, polypropionates, acetogenins, and terpenoids. The studies regarding this latter class is proposed in the light of the recent debate about classical and independent mevalonate pathway.The content of the present review is part of the plenary lecture presented at International Symposium Chemistry & Biology of Marine Organisms, September 21–26, 2003 – Kolympari, Crete, Greece.