High-Speed DNA Sequencing: An Approach Based Upon Fluorescence Detection of Single Molecules

Abstract

We are developing a laser based technique for the rapid sequencing of large fragments (～40 kb) of DNA based upon the detection of single, fluorescently tagged nucleotides cleaved from a single DNA fragment. We have demonstrated significant progress on several of the important steps of this technique. The projected rate of sequencing is several hundred bases per second which is orders of magnitude faster than existing methods. Once developed, this technology could be utilized by investigators for rapid sequencing of genetic material from virtually any source.     

Species identification of the psammophilous tenebrionid beetles Phaleria acuminata Küster, 1852 and Phaleria bimaculata (Linnaeus, 1767) from central Mediterranean beaches: geometric morphometrics and molecular insights from species to population level

Dominating global arid environments, from desert to coastal dunes, most Tenebrionidae are highly specific in their habitat preferences and display limited dispersal potential, thus exhibiting a remarkable degree of regional genetic and morphological differentiation. The tenebrionid genus Phaleria is speciose and widely distributed, with P. acuminata and P. bimaculata having a wide Mediterranean distribution, with numerous morphological differentiations at population level, often described as different taxa of doubtful taxonomical significance. In order to investigate the variability of the central Mediterranean populations of P. bimaculata and P. acuminata and to compare the results obtained with different identification techniques, these species were sampled on sandy beaches in Sicily (southern Italy) and on circum-Sicilian and Maltese islands. Collected samples were studied through the application of geometric morphometrics and the sequencing of a fragment of the mitochondrial COII gene. Geometric morphometrics and molecular analyses gave congruent results, allowing a sound separation of the two species. At the population level, the two species showed different patterns. P. acuminata showed a remarkable morphological and molecular homogeneity throughout the sampled area. Conversely, two well-characterized sub-clades were detected within P. bimaculata, and within the two lineages, a low-to-absent inter-populations differentiation was observed, in spite of the physical isolation of the sampled sandy beaches and of their geographical distance. These two P. bimaculata lineages, hereby named “Tyrrhenian sub-clade” and “Southern sub-clade,” might be compatible with the hypothesis of subspecific status already proposed for the populations from the Aeolian archipelago (as P. bimaculata marcuzzii Aliquò).     

Rapid sizing of individual fluorescently stained DNA fragments by flow cytometry.

Large, fluorescently stained restriction fragments of lambda phage DNA are sized by passing individual fragments through a focused continuous wave laser beam in an ultrasensitive flow cytometer at a rate of 60 fragments per second. The size of the fluorescence burst emitted by each stained DNA fragment, as it passes through the laser beam, is measured in one millisecond. One hundred sixty four seconds of fluorescence burst data allow linear sizing of DNA with an accuracy of better than two percent over a range of 10 to 50 kbp. This corresponds to analyzing less than 1 pg of DNA. Sizing of DNA fragments by this approach is much faster, requires much less DNA, and can potentially analyze large fragments with better resolution and accuracy than with gel-based electrophoresis.     

Differences in gene flow in a twofold secondary contact zone of pond turtles in southern Italy (Testudines: Emydidae: Emys orbicularis galloitalica,E. o. hellenica,E. trinacris)

Using virtually range‐wide sampling for three pond turtle taxa (Emys orbicularis galloitalica, E. o. hellenica, E. trinacris), we analyse gene flow across their southern Italian contact zone. Based on population genetic analyses of 15 highly polymorphic microsatellite loci and a mitochondrial marker, we show that the general genetic pattern matches well with the current taxon delimitation. Yet, single individuals with conflicting genetic identity suggest translocation of turtles by humans. In addition, we identify in south‐western France and the vicinity of Rome populations being heavily impacted by introduced turtles. Cline analyses reveal that the major genetic break between E. o. galloitalica and E. o. hellenica corresponds well with the currently accepted intergradation zone in southern Italy. However, introgression is largely unidirectional from E. o. galloitalica into E. o. hellenica. In the distribution range of the latter subspecies, genetic footprints of E. o. galloitalica are evident along most of the Italian east coast. Our results corroborate that E. o. galloitalica was introduced long ago in Corsica and Sardinia and naturalized there. Gene flow between E. orbicularis and E. trinacris is negligible, with the Strait of Messina matching well with the narrow cline centre between the two species. This contrasts with other Mediterranean freshwater turtle species with extensive transoceanic gene flow. Compared to the two subspecies of E. orbicularis, the Sicilian E. trinacris shows an unexpectedly strong population structuring, a finding also of some relevance for conservation. The differences between the two taxon pairs E. orbicularis/E. trinacris and E. o. galloitalica/E. o. hellenica support their current taxonomic classification and make them attractive objects for follow‐up studies to elucidate the underlying mechanisms of speciation by comparing their properties.     

Hormone stimulated steroid biosynthesis in granulosa cells studied with a fluorogenic probe for cytochrome P-450SCC.

The regulation of steroidogenesis by luteinizing hormone (LH) was studied in granulosa cells during follicular development using a fluorescent reporter assay based on the metabolism of a fluorescent probe specific for cytochrome P-450SCC (cholesterol side-chain cleavage enzyme). Intact granulosa cells or mitochondria were obtained from the first (F1) second (F2) and third (F3) largest preovulatory follicles of the hen ovary and incubated with the fluorogenic substrate. Metabolism of this substrate by cytochrome P-450SCC generates the highly fluorescent resorufin anion (the fluorescent reporter). In both mitochondria and intact granulosa cells, incubated with the fluorescent substrate, an increase in resorufin fluorescence was observed and the increase was greater in samples derived from F1 than in samples from F2 or F3. In cells, LH added simultaneously with the P-450SCC substrate significantly increased resorufin fluorescence above control values in a time- and dose-dependent manner up to 2-3 h after the incubation was initiated. Forskolin and 8-bromo-cAMP also stimulated metabolism of the P-450SCC substrate significantly by 15 min. When granulosa cells were preincubated with LH before exposure to the P-450SCC substrate resorufin fluorescence was significantly attenuated compared to controls (not exposed to LH in the preincubation period). The decrease in resorufin fluorescence observed when cells were pretreated with LH, may be due to the release of cholesterol from endogenous pools and its competition with the exogenous fluorogenic for the substrate P-450SCC enzyme. In granulosa cells that were preloaded with the P-450SCC substrate, the stimulatory effect of LH treatment remained constant from 30 min to 2 h after hormone addition. The results show that this fluorescent probe can be used in a rapid assay for the continuous measurement of the acute effects of hormone agonists on cholesterol conversion to pregnenolone in steroidogenic cells.