Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions

The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand the interplay of resonant and nonresonant charge carrier transport mechanisms. This study reports STM break junction measurements of peptide nucleic acids (PNAs) with a G-block structure and contrasts the findings with previous results for DNA duplexes. The conductance of G-block PNA duplexes is much higher than that of the corresponding DNA duplexes of the same sequence; however, they do not display the strong even-odd dependence conductance oscillations found in G-block DNA. Theoretical analysis finds that the conductance oscillation magnitude in PNA is suppressed because of the increased level of electronic coupling interaction between G-blocks in PNA and the stronger PNA-electrode interaction compared to that in DNA duplexes. The strong interactions in the G-block PNA duplexes produce molecular conductances as high as 3% G₀, where G₀ is the quantum of conductance, for 5 nm duplexes.

Effects of the Backbone and Chemical Linker on the Molecular Conductance of Nucleic Acid Duplexes

Scanning tunneling microscope break junction measurements are used to examine how the molecular conductance of nucleic acids depends on the composition of their backbone and the linker group to the electrodes. Molecular conductances of 10 base pair long homoduplexes of DNA, aeg-PNA, γ-PNA, and a heteroduplex of DNA/aeg-PNA with identical nucleobase sequence were measured. The molecular conductance was found to vary by 12 to 13 times with the change in backbone. Computational studies show that the molecular conductance differences between nucleic acids of different backbones correlate with differences in backbone structural flexibility. The molecular conductance was also measured for duplexes connected to the electrode through two different linkers, one directly to the backbone and one directly to the nucleobase stack. While the linker causes an order-of-magnitude increase in the overall conductance for a particular duplex, the differences in the electrical conductance with backbone composition are preserved. The highest molecular conductance value, 0.06G₀, was measured for aeg-PNA duplexes with a base stack linker. These findings reveal an important new strategy for creating longer and more complex electroactive, nucleic acid assemblies.

A scanning tunneling microscope break junction method with continuous bias modulation

Single molecule conductance measurements on 1,8-octanedithiol were performed using the scanning tunneling microscope break junction method with an externally controlled modulation of the bias voltage. Application of an AC voltage is shown to improve the signal to noise ratio of low current (low conductance) measurements as compared to the DC bias method. The experimental results show that the current response of the molecule(s) trapped in the junction and the solvent media to the bias modulation can be qualitatively different. A model RC circuit which accommodates both the molecule and the solvent is proposed to analyze the data and extract a conductance for the molecule.

Invasion dynamics of a fish-free landscape by brown trout (Salmo trutta)

Metapopulation dynamics over the course of an invasion are usually difficult to grasp because they require large and reliable data collection, often unavailable. The invasion of the fish-free freshwater ecosystems of the remote sub-Antarctic Kerguelen Islands following man-made introductions of brown trout (Salmo trutta) in the 1950's is an exception to this rule. Benefiting from a full long term environmental research monitoring of the invasion, we built a Bayesian dynamic metapopulation model to analyze the invasion dynamics of 85 river systems over 51 years. The model accounted for patch size (river length and connections to lakes), alternative dispersal pathways between rivers, temporal trends in dynamics, and uncertainty in colonization date. The results show that the model correctly represents the observed pattern of invasion, especially if we assume a coastal dispersal pathway between patches. Landscape attributes such as patch size influenced the colonization function, but had no effect on propagule pressure. Independently from patch size and distance between patches, propagule pressure and colonization function were not constant through time. Propagule pressure increased over the course of colonization, whereas the colonization function decreased, conditional on propagule pressure. The resulting pattern of this antagonistic interplay is an initial rapid invasion phase followed by a strong decrease in the invasion rate. These temporal trends may be due to either adaptive processes or environmental gradients encountered along the colonization front. It was not possible to distinguish these two hypotheses. Because invasibility of Kerguelen Is. freshwater ecosystems is very high due to the lack of a pre-existing fish fauna and minimal human interference, our estimates of invasion dynamics represent a blueprint for the potential of brown trout invasiveness in pristine environments. Our conclusions shed light on the future of polar regions where, because of climate change, fish-free ecosystems become increasingly accessible to invasion by fish species.

Polychlorinated biphenyls in freshwater salmonids from the Kerguelen Islands in the Southern Ocean

The Subantarctic Kerguelen Islands (49°S, 70°E) contain freshwater ecosystems among the most isolated in the world. Concentrations of polychlorinated biphenyls (PCBs) were assessed in the muscle of 48 brook trout and 38 brown trout caught during summer and spring 2006 in the rivers, lakes and ponds of Kerguelen. The sum of 29 PCBs averaged 404 and 358 ng g(-1) lipid, and dioxin-like PCB was 19 and 69 ng g(-1) lipid, in brook and brown trout, respectively. The values showed a high variability and some fish accumulated PCBs at levels similar to those of fish from impacted areas. While inter-sex differences were limited, the season and the morphotype appeared to have the most influence. Fish captured in summer had muscle PCB concentrations about three times higher than those caught in spring and the 'river' morphotype of brook trout showed the highest PCB levels.

Effects of habitat on individual reproductive success of mature male parr of Atlantic salmon Salmo salar

The effect of the presence of stone blocks in the spawning habitat on the reproductive success of mature male parr of Atlantic salmon Salmo salar of various sizes and ages was tested in an artificial channel. Shelters allowed smaller individuals to contribute to egg fertilization as much as large parr, suggesting that the size-based dominance observed in a shelterless habitat was not maintained in a more complex habitat.

Introgression in the genus Salmo via allotriploids

Hybridization between sympatric species is not uncommon in the wild. Wild allotriploids (individuals with two chromosome sets from a species + one chromosome set from another species) are generally the result of a backcross between interspecific hybrids that produce unreduced gametes and one of the parental species. In animals, allotriploids are commonly sterile, except for some vertebrate species complexes in which allotriploids reproduce by parthenogenesis, gynogenesis and/or hybridogenesis, producing generally clonal or hemiclonal gametes; nuclear DNA introgression between hybridizing species is considered to be extremely rare. Employing species-specific molecular markers, we show genetic introgression between the chromosomally well-differentiated salmonids Atlantic salmon (2n = 58) and brown trout (2n = 80) through spontaneous bisexual reproduction of allotriploids leading to salmon-like offspring bearing some brown trout genes. Although introgression between these Salmo species can occur via allotriploids, we hypothesize that extinction of parental species can be discarded based on very low survival of allotriploid offspring.

Observation of muon neutrino disappearance with the MINOS detectors in the NuMI neutrino beam

This Letter reports results from the MINOS experiment based on its initial exposure to neutrinos from the Fermilab NuMI beam. The rates and energy spectra of charged current nu(mu) interactions are compared in two detectors located along the beam axis at distances of 1 and 735 km. With 1.27 x 10(20) 120 GeV protons incident on the NuMI target, 215 events with energies below 30 GeV are observed at the Far Detector, compared to an expectation of 336+/-14 events. The data are consistent with nu(mu) disappearance via oscillations with |Delta(m)2/32|=2.74 +0.44/-0.26 x10(-3)eV(2) and sin(2)(2theta(23))>0.87 (68% C.L.).

Dispersal and rapid evolution in brown trout colonizing virgin Subantarctic ecosystems

Two brown trout Salmo trutta stocks of different origin (wild Polish, domestic commercial) came into secondary contact after deliberate releases conducted in virgin rivers systems of the Subantarctic Kerguelen Islands (70 degrees E 49 degrees S). Samples obtained in 2001-2003 and a historical sample from 1993 were analysed for genetic variation at seven microsatellite loci and one allozyme locus (LDH-C1*). Bayesian clustering analysis demonstrated that rapid genetic differentiation formed separate genetic units in neighbouring rivers in less than 20 years. These genetic units were characterized by a large proportion of Polish genotypes mixed with some genomes of domestic origin (up to 30%). A different colonization strategy of the naturalized stocks, likely related with differential performance, was identified as a cause of rapid population differentiation in this area.

Interspecific barriers between salmonids when hybridisation is due to sneak mating

Male sneaking behaviour can lead to interspecific hybridisation if sneakers attempt to fertilise ova in heterospecific mating, contributing to break down of interspecific barriers. In south European rivers, sneaking Atlantic salmon males fertilise an important proportion of ova from adult females in heterospecific crosses, up to 65%. In a south French flow-controlled stream, we found that they were able to naturally fertilise brown trout ova in absence of brown trout males. Aggressiveness of brown trout males towards sneaking salmon males and low survival of hybrids issued from salmon sneakers are found to be interspecific barriers.

Alternative mating strategies in Atlantic salmon and brown trout

By screening variable number of tandem repeat (VNTR) loci, multiple paternity within clutches has been found in wild populations of southern European Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). For Atlantic salmon, we determined the relative contribution of alternative male phenotypes to the next generation. Individual males that are morphologically juvenile yet sexually mature fertilized a large proportion of eggs, and they thereby contributed to an increase of genetic variability in wild populations via (1) balancing the sex ratio, (2) increasing outbreeding, and (3) enlarging the effective population size, in part a consequence of (1) and (2). In addition, these precocious males ensured that interspecific spawns involving Atlantic salmon females and brown trout males (a fairly common occurrence in southern Europe where the two species are sympatric) resulted mostly in Atlantic salmon progeny. For brown trout, preliminary genetic results indicated that multiple paternity, when present, was not due to alternative mating strategies by males, but rather to successive fertilizations by adult suitors.

Multiple paternity increases effective size of southern Atlantic salmon populations

Genetic analyses were performed on the progeny of Atlantic salmon (Salmo salar L.) sampled in natural redds of three rivers flowing into the Bay of Biscay, the Nivelle, the Mandeo and the Sella. These rivers are at the southern limit of the European distribution of the species and their populations are small and endangered by human activities. Nine variable number of tandem repeat (VNTR) loci (five minisatellites and four microsatellites) were used for parentage analysis. Multiple male participation was recognized in the fertilization of eggs. A large proportion was fertilized by precociously mature parr. We demonstrate that multiple paternity derived from mature parr is crucial for the conservation of genetic variability in small populations of Atlantic salmon.

Reproductive behavioural sequences of single pairs of Atlantic salmon in an experimental stream

We studied 12 size-matched pairs of Atlantic salmon, Salmo salar, in an experimental stream in southwest France, to determine whether fish activity and motivation changed during the course of reproduction. The absolute weight of spawners did not affect their spawning activity. On average, females deposited their eggs within 3 days in nine nests. Male and female breeding behaviours changed throughout the reproductive period. This cyclic variation in behaviour appeared to be determined in part by the activity of the other sex, as a consequence of complex interplay between the sexes, but also largely by the stage of the spawning period. During the first three ovipositions, male-female stimulus-reaction chaining became more consistent just before spawning, which may help synchronize gamete release for successful fertilization. During the last three ovipositions, sequence chaining between the sexes was less coherent, possibly as a result of reduced mate attractiveness and/or physiological limitations. Copyright 1999 The Association for the Study of Animal Behaviour.

Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region

Hepatitis C virus (HCV) showed substantial nucleotide sequence diversity distributed throughout the viral genome, with many variants showing only 68 to 79% overall sequence similarity to one another. Phylogenetic analysis of nucleotide sequences derived from part of the gene encoding a non-structural protein (NS-5) has provided evidence for six major genotypes of HCV amongst a worldwide collection of 76 samples from HCV-infected blood donors and patients with chronic hepatitis. Many of these HCV types comprised a number of more closely related subtypes, leading to a current total of 11 genetically distinct viral populations. Phylogenetic analysis of other regions of the viral genome produced relationships between published sequences equivalent to those found in NS-5, apart from the more highly conserved 5' non-coding region in which only the six major HCV types, but not subtypes, could be differentiated. A new nomenclature for HCV variants is proposed in this communication that reflects the two-tiered nature of sequence differences between different viral isolates. The scheme classifies all known HCV variants to date, and describes criteria that would enable new variants to be assigned within the classification as they are discovered.

At least five related, but distinct, hepatitis C viral genotypes exist

Hepatitis C virus, the major causative agent of blood-borne non-A, non-B hepatitis in the world, has been the subject of considerable nucleic acid sequence analysis. Although all reported hepatitis C sequences from the United States have been represented by the prototype hepatitis C virus type 1 sequence, two groups of variant sequences have been reported in Japan. However, we have noted five distinct, but related, genotypes (I-V) throughout the world, based on detailed sequence determination and analysis of the first 1700 nucleotides and part of the nonstructural region 5 at the C terminus of the open reading frame. The nucleotide sequence for a large number of hepatitis C virus isolates spanning six continents was obtained by direct sequence analysis of PCR products after reverse transcription. Genotype was classified by using several distinct sequence motifs. We observed that most genotypes coexist in several geographic regions, including the United States, Japan, Germany, and Italy. So far, genotype V has been found only in South Africa. Interestingly, each distinct genotype seems to be maintained throughout the genome in the segments studied. These genotype distinctions should be considered when designing specific diagnostic tests, developing potential vaccines, and studying viral transmission.

Comparison of hepatitis C virus markers in patients with NANB hepatitis

10 different HCV-specific assays and RT-PCR of the 5' untranslated region of HCV RNA were used to analyze sixty-four patients with chronic NANB liver disease. Po, CP-9 and C22 antigens are located in the putative core; C33c in the putative NS3; C100-3 in the putative NS3/4; KCL in the putative NS4/5 and C825 is located in the putative NS5. GOR protein is not part of the HCV genome, but antibodies to it appear to be present in response to a hepatitis C infection. Positive rates were 91% for Po, 89% for CP-9, 94% for C22, 97% for C33c, 88% for C100-3 (Ortho, EIA), 86% for C100-3 (Abbott, EIA), 84% for C100-3 (Ohtsuka, RIA), 88% for KCL, 59% for C825, 58% for GOR, and 83% for RT-PCR. There were 8 cases which were negative by all anti-C100 tests. 7 of these cases were positive by other anti-HCV markers and/or PCR suggesting the need for improved blood screening assays. There is a variation in the relative reactivity for different markers with different samples. Of the tests employed, anti C33c shows the highest positivity rate.

Use of a signature nucleotide sequence of hepatitis C virus for detection of viral RNA in human serum and plasma

The nucleic acid sequence of the putative 5'-untranslated (5PUT) region of hepatitis C virus (HCV), determined for samples obtained from a variety of geographic origins, was found to be over 98% conserved among all isolates. On the basis of this signature sequence for HCV, a viral RNA assay was developed by using cDNA synthesis with reverse transcriptase, followed by polymerase chain reaction (PCR). The new assay was compared with the Ortho-Chiron C100-3 HCV enzyme-linked immunosorbent assay to research radioimmunoassays for antibodies to the C33c and C22 HCV antigens and to the first reported set of HCV PCR primers designed from the NS3 domain. Plasma samples from 16 Japanese patients with non-A, non-B hepatitis (NANBH) and 16 immunoassay-positive blood donors from the United States were investigated. The 5PUT PCR primers were found to be superior to the NS3 primers in sensitivity and specificity (15 of 25 versus 3 of 25 of the C100 enzyme-linked immunosorbent assay-positive samples, respectively). Samples from two C100-negative patients with acute NANBH were found to react with the 5PUT primers but not with the NS3 primers. Also, two of three patients with chronic NANBH converted from reverse transcriptase PCR positive to negative after interferon treatment. Although the clinical significance of the presence or absence of HCV RNA in samples from patients is not fully understood, the use of probes and primers from the 5PUT region (as opposed to primers from other segments) should not lead to false-negative results due to nucleic acid sequence variations in viral isolates.

Structure-function analysis of the histidine permease and comparison with cystic fibrosis mutations

Traffic ATPases constitute a superfamily of transporters that include prokaryotic permeases and medically important eukaryotic proteins, such as the multidrug resistance P-glycoprotein and the cystic fibrosis gene product. We present a structure-function analysis of a member of this superfamily, the prokaryotic histidine permease, using mutations generated both in vitro and in vivo, and assaying several biochemical functions. The analysis supports a previously predicted structural model and allows the assignment of specific functions to several predicted structural features. Mutations in the secondary structure features which form the nucleotide-binding pocket in general cause the loss of ATP binding activity. Mutations in the helical domain retain ATP binding activity. Several mutations have been identified which may affect the signaling mechanism between ATP hydrolysis and membrane translocation. We relate our findings to those emerging from the recent biochemical and genetic analyses of cystic fibrosis mutations.