Insights into the genome of the 'Loco' Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae.

BACKGROUND: The Peruvian 'chanque' or Chilean 'loco' Concholepas concholepas is an economically, ecologically, and culturally important muricid gastropod heavily exploited by artisanal fisheries in the temperate southeastern Pacific Ocean. In this study, we have profited from a set of bioinformatics tools to recover important biological information of C. concholepas from low-coverage short-read NGS datasets. Specifically, we calculated the size of the nuclear genome, ploidy, and estimated transposable elements content using an in silico k-mer approach, we discovered, annotated, and quantified those transposable elements, we assembled and annotated the 45S rDNA RNA operon and mitochondrial genome, and we confirmed the phylogenetic position of C. concholepas within the muricid subfamily Rapaninae based on translated protein coding genes. RESULTS: Using a k-mer approach, the haploid genome size estimated for the predicted diploid genome of C. concholepas varied between 1.83 Gbp (with kmer = 24) and 2.32 Gbp (with kmer = 36). Between half and two thirds of the nuclear genome of C. concholepas was composed of transposable elements. The most common transposable elements were classified as Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements, which were more abundant than DNA transposons, simple repeats, and Long Terminal Repeats. Less abundant repeat elements included Helitron mobile elements, 45S rRNA DNA, and Satellite DNA, among a few others.The 45S rRNA DNA operon of C. concholepas that encodes for the ssrRNA, 5.8S rRNA, and lsrRNA genes was assembled into a single contig 8,090 bp long. The assembled mitochondrial genome of C. concholepas is 15,449 bp long and encodes 13 protein coding genes, two ribosomal genes, and 22 transfer RNAs. CONCLUSION: The information gained by this study will inform the assembly of a high quality nuclear genome for C. concholepas and will support bioprospecting and biomonitoring using environmental DNA to advance development of conservation and management plans in this overexploited marine snail.

Ballistic Conductance through Porphyrin Nanoribbons.

The search for long molecular wires that can transport charge with maximum efficiency over many nanometers has driven molecular electronics since its inception. Single-molecule conductance normally decays with length and is typically far below the theoretical limit of G0 (77.5 µS). Here, we measure the conductances of a family of edge-fused porphyrin ribbons (lengths 1-7 nm) that display remarkable behavior. The low-bias conductance is high across the whole series. Charging the molecules in situ results in a dramatic realignment of the frontier orbitals, increasing the conductance to 1 G0 (corresponding to a current of 20 µA). This behavior is most pronounced in the longer molecules due to their smaller HOMO-LUMO gaps. The conductance-voltage traces frequently exhibit peaks at zero bias, showing that a molecular energy level is in resonance with the Fermi level. This work lays the foundations for long, perfectly transmissive, molecular wires with technological potential.

Low-lying LUMO Boosts Conductance in Antiaromatic Dibenzopentalene Versus Aromatic Analogues.

Antiaromaticity is a fundamental concept in chemistry, but the study of molecular wires incorporating antiaromatic units is limited. Despite initial predictions, very few studies show that antiaromaticity has a beneficial effect on electron transport. Dibenzo[a,e]pentalene (DBP) is a stable structure that displays appreciable antiaromaticity within the five-membered rings of the pentalene core. We have investigated derivatives of DBP furnished with pyridyl (Py) and F4-pyridyl (PyF4) anchor groups, and compared the conductance with purely aromatic phenyl and anthracene analogues. We find that the low-bias conductance of DBP-Py is approximately 60 % larger than that of the anthracene analogue Anth-Py and 250 % larger compared to the phenyl derivative Ph-Py. This is due to a better alignment of the LUMO with the gold Fermi level, which we confirm by conductance-voltage spectroscopy where the conductance of DBP-Py shows the greatest voltage-dependence. The F4-pyridyl compounds, which have lower LUMO energies compared to the pyridyl analogues, did not, however, form detectable molecular junctions. The strongly electron-withdrawing fluorine atoms reduce the donor capability of the nitrogen lone-pair to the point where stable N-Au bonds no longer form.

Enhanced Thermoelectricity in Metal-[60]Fullerene-Graphene Molecular Junctions.

The thermoelectric properties of molecular junctions consisting of a metal Pt electrode contacting [60]fullerene derivatives covalently bound to a graphene electrode have been studied by using a conducting-probe atomic force microscope (c-AFM). The [60]fullerene derivatives are covalently linked to the graphene via two meta-connected phenyl rings, two para-connected phenyl rings, or a single phenyl ring. We find that the magnitude of the Seebeck coefficient is up to nine times larger than that of Au-C60-Pt molecular junctions. Moreover, the sign of the thermopower can be either positive or negative depending on the details of the binding geometry and on the local value of the Fermi energy. Our results demonstrate the potential of using graphene electrodes for controlling and enhancing the thermoelectric properties of molecular junctions and confirm the outstanding performance of [60]fullerene derivatives.

Chiral Single-Molecule Potentiometers Based on Stapled ortho- Oligo(phenylene)ethynylenes.

We report on the chemical design of chiral molecular junctions with stress-dependent conductance, whose helicity is maintained during the stretching of a single molecule junction due to the stapling of both ends of the inner helix. In the reported compounds, different conductive pathways are observed, with clearly different conductance values and plateau-length distributions, attributed to different conformations of the helical structures. The large chiro-optical responses and the potential use of these molecules as unimolecular spin filters have been theoretically proved using state-of-the-art Density Functional Theory (DFT) calculations, including a fully ab-initio estimation of the CISS-originating spin polarization which is done, for the first time, for a realistic molecular system.

A Peierls Transition in Long Polymethine Molecular Wires: Evolution of Molecular Geometry and Single-Molecule Conductance.

Molecules capable of mediating charge transport over several nanometers with minimal decay in conductance have fundamental and technological implications. Polymethine cyanine dyes are fascinating molecular wires because up to a critical length, they have no bond-length alternation (BLA) and their electronic structure resembles a one-dimensional free-electron gas. Beyond this threshold, they undergo a symmetry-breaking Peierls transition, which increases the HOMO-LUMO gap. We have investigated cationic cyanines with central polymethine chains of 5-13 carbon atoms (Cy3+-Cy11+). The absorption spectra and crystal structures show that symmetry breaking is sensitive to the polarity of the medium and the size of the counterion. X-ray crystallography reveals that Cy9·PF6 and Cy11·B(C6F5)4 are Peierls distorted, with high BLA at one end of the π-system, away from the partially delocalized positive charge. This pattern of BLA distribution resembles that of solitons in polyacetylene. The single-molecule conductance is essentially independent of molecular length for the polymethine salts of Cy3+-Cy11+ with the large B(C6F5)4- counterion, but with the PF6- counterion, the conductance decreases for the longer molecules, Cy7+-Cy11+, because this smaller anion polarizes the π-system, inducing a symmetry-breaking transition. At higher bias (0.9 V), the conductance of the shorter chains, Cy3+-Cy7+, increases with length (negative attenuation factor, ß = -1.6 nm-1), but the conductance still drops in Cy9+ and Cy11+ with the small polarizing PF6- counteranion.

Single-Molecule Conductance of 1,4-Azaborine Derivatives as Models of BN-doped PAHs.

The single-molecule conductance of a series of BN-acene-like derivatives has been measured by using scanning tunneling break-junction techniques. A strategic design of the target molecules has allowed us to include azaborine units in positions that unambiguously ensure electron transport through both heteroatoms, which is relevant for the development of customized BN-doped nanographenes. We show that the conductance of the anthracene azaborine derivative is comparable to that of the pristine all-carbon anthracene compound. Notably, this heteroatom substitution has also allowed us to perform similar measurements on the corresponding pentacene-like compound, which is found to have a similar conductance, thus evidencing that B-N doping could also be used to stabilize and characterize larger acenes for molecular electronics applications. Our conclusions are supported by state-of-the-art transport calculations.

Testing for deterministic succession in metazoan parasite communities of marine fish.

Parasite communities are similar to free-living communities; decay of similarity over geographic distance, theory of island biogeography, species-area relationships and nestedness have been documented in both communities. Ecological succession has been studied in free-living communities but has rarely been examined in parasite communities. We use seriation with replication to test the hypothesis that succession of parasite community structure is deterministic, thus developing throughout consecutive changes along the fish ontogeny, via a seriated pattern. 12 306 marine fishes (95 species) were studied. In 40 species, a seriated pattern was detected; 25 had a tendency towards a seriated pattern, and for 31 species, succession was at random. Age-classes for each host species explained deterministic successional patterns for whole parasite communities and ectoparasites. Richness and number of age-classes explained this pattern for endoparasites. Seriated successional pattern was evident for parasite communities of long-lived marine fish, indicating that parasite communities follow sequential changes over time, like many free-living communities.

Description of Echthrogaleus spinulus n. sp. (Copepoda: Pandaridae) parasitic on a torpedo ray from the central Pacific Ocean utilising a morphological and molecular approach.

A new species of parasitic copepod, Echthrogaleus spinulus n. sp. (Pandaridae), is described from the torpedo ray Tetronarce tokionis (Tanaka) (Torpedinidae) captured in pelagic Hawaiian waters. The new species has pediger 4 bearing large dorsal plates with denticles on posterior margin, genital complex with posterolateral lobes widely curved medially and overlapping, leg 4 exopod incompletely 3-segmented, and the largest body size (maximum length 16 mm from anterior rim of frontal plates to tip of caudal rami, excluding setae). This morphology does not match any of the seven valid species of Echthrogaleus Steenstrup & Lütken, 1861. Analysis of 28S rDNA sequences separated the new material from the Central Pacific from samples of E. coleoptratus in the Atlantic and Eastern Pacific Oceans. However, due to the lack of DNA sequences in the databases, the new 28S rDNA sequence cannot used to confirm the species identity. The unique morphological characteristics of the Central Pacific female copepods combined with 28S rDNA sequencing was used as a basis to validate the new species.

Unusual Length Dependence of the Conductance in Cumulene Molecular Wires.

Cumulenes are sometimes described as "metallic" because an infinitely long cumulene would have the band structure of a metal. Herein, we report the single-molecule conductance of a series of cumulenes and cumulene analogues, where the number of consecutive C=C bonds in the core is n=1, 2, 3, and 5. The [n]cumulenes with n=3 and 5 have almost the same conductance, and they are both more conductive than the alkene (n=1). This is remarkable because molecular conductance normally falls exponentially with length. The conductance of the allene (n=2) is much lower, because of its twisted geometry. Computational simulations predict a similar trend to the experimental results and indicate that the low conductance of the allene is a general feature of [n]cumulenes where n is even. The lack of length dependence in the conductance of [3] and [5]cumulenes is attributed to the strong decrease in the HOMO-LUMO gap with increasing length.

Bias-Driven Conductance Increase with Length in Porphyrin Tapes.

A key goal in molecular electronics has been to find molecules that facilitate efficient charge transport over long distances. Normally, molecular wires become less conductive with increasing length. Here, we report a series of fused porphyrin oligomers for which the conductance increases substantially with length by >10-fold at a bias of 0.7 V. This exceptional behavior can be attributed to the rapid decrease of the HOMO-LUMO gap with the length of fused porphyrins. In contrast, for butadiyne-linked porphyrin oligomers with moderate inter-ring coupling, a normal conductance decrease with length is found for all bias voltages explored (±1 V), although the attenuation factor (ß) decreases from ca. 2 nm-1 at low bias to <1 nm-1 at 0.9 V, highlighting that ß is not an intrinsic molecular property. Further theoretical analysis using density functional theory underlines the role of intersite coupling and indicates that this large increase in conductance with length at increasing voltages can be generalized to other molecular oligomers.

Detecting Mechanochemical Atropisomerization within an STM Break Junction.

We have employed the scanning tunneling microscope break-junction technique to investigate the single-molecule conductance of a family of 5,15-diaryl porphyrins bearing thioacetyl (SAc) or methylsulfide (SMe) binding groups at the ortho position of the phenyl rings (S2 compounds). These ortho substituents lead to two atropisomers, cis and trans, for each compound, which do not interconvert in solution under ambient conditions; even at high temperatures, isomerization takes several hours (half-life 15 h at 140 °C for SAc in C2Cl4D2). All the S2 compounds exhibit two conductance groups, and comparison with a monothiolated (S1) compound shows the higher group arises from a direct Au-porphyrin interaction. The lower conductance group is associated with the S-to-S pathway. When the binding group is SMe, the difference in junction length distribution reflects the difference in S-S distance (0.3 nm) between the two isomers. In the case of SAc, there are no significant differences between the plateau length distributions of the two isomers, and both show maximal stretching distances well exceeding their calculated junction lengths. Contact deformation accounts for part of the extra length, but the results indicate that cis-to-trans conversion takes place in the junction for the cis isomer. The barrier to atropisomerization is lower than the strength of the thiolate Au-S and Au-Au bonds, but higher than that of the Au-SMe bond, which explains why the strain in the junction only induces isomerization in the SAc compound.

Incorporating single molecules into electrical circuits. The role of the chemical anchoring group.

Constructing electronic circuits containing singly wired molecules is at the frontier of electrical device miniaturisation. When a molecule is wired between a pair of electrodes, the two points of contact are determined by the chemical anchoring groups, located at the ends of the molecule. At this point, when a bias is applied, electrons are channelled from a metallic environment through an extremely narrow constriction, essentially a single atom, into the molecule. The fact that this is such an abrupt change in the electron pathway makes the nature of the chemical anchoring groups critically important regarding the propagation of electrons from the electrode across the molecule. A delicate interplay of phenomena can occur when a molecule binds to the electrodes, which can produce profound differences in conductance properties depending on the anchoring group. This makes answering the question "what is the best anchoring group for single molecule studies" far from straight forward. In this review, we firstly take a look at techniques developed to 'wire-up' single molecules, as understanding their limitations is key when assessing a molecular wire's performance. We then analyse the various chemical anchoring groups, and discuss their merits and disadvantages. Finally we discuss some theoretical concepts of molecular junctions to understand how transport is affected by the nature of the chemical anchor group.

Toward Multiple Conductance Pathways with Heterocycle-Based Oligo(phenyleneethynylene) Derivatives.

In this paper, we have systematically studied how the replacement of a benzene ring by a heterocyclic compound in oligo(phenyleneethynylene) (OPE) derivatives affects the conductance of a molecular wire using the scanning tunneling microscope-based break junction technique. We describe for the first time how OPE derivatives with a central pyrimidine ring can efficiently link to the gold electrode by two pathways presenting two different conductance G values. We have demonstrated that this effect is associated with the presence of two efficient conductive pathways of different length: the conventional end-to-end configuration, and another with one of the electrodes linked directly to the central ring. This represents one of the few examples in which two defined conductive states can be set up in a single molecule without the aid of an external stimulus. Moreover, we have observed that the conductance through the full length of the heterocycle-based OPEs is basically unaffected by the presence of the heterocycle. All these results and the simplicity of the proposed molecules push forward the development of compounds with multiple conductance pathways, which would be a breakthrough in the field of molecular electronics.

An optimized method for (15)N R(1) relaxation rate measurements in non-deuterated proteins.

(15)N longitudinal relaxation rates are extensively used for the characterization of protein dynamics; however, their accurate measurement is hindered by systematic errors. (15)N CSA/(1)H-(15)N dipolar cross-correlated relaxation (CC) and amide proton exchange saturation transfer from water protons are the two main sources of systematic errors in the determination of (15)N R1 rates through (1)H-(15)N HSQC-based experiments. CC is usually suppressed through a train of 180° proton pulses applied during the variable (15)N relaxation period (T), which can perturb water magnetization. Thus CC cancellation is required in such a way as to minimize water saturation effects. Here we examined the level of water saturation during the T period caused by various types of inversion proton pulses to suppress CC: (I) amide-selective IBURP-2; (II) cosine-modulated IBURP-2; (III) Watergate-like blocks; and (IV) non-selective hard. We additionally demonstrate the effect of uncontrolled saturation of aliphatic protons on (15)N R1 rates. In this paper we present an optimized pulse sequence that takes into account the crucial effect of controlling also the saturation of the aliphatic protons during (15)N R1 measurements in non-deuterated proteins. We show that using cosine-modulated IBURP-2 pulses spaced 40 ms to cancel CC in this optimized pulse program is the method of choice to minimize systematic errors coming from water and aliphatic protons saturation effects.

Single-molecule conductance of a chemically modified, π-extended tetrathiafulvalene and its charge-transfer complex with F4TCNQ.

We describe the synthesis and single-molecule electrical transport properties of a molecular wire containing a π-extended tetrathiafulvalene (exTTF) group and its charge-transfer complex with F4TCNQ. We form single-molecule junctions using the in situ break junction technique using a homebuilt scanning tunneling microscope with a range of conductance between 10 G0 down to 10(-7) G0. Within this range we do not observe a clear conductance signature of the neutral parent molecule, suggesting either that its conductance is too low or that it does not form a stable junction. Conversely, we do find a clear conductance signature in the experiments carried out on the charge-transfer complex. Due to the fact we expected this species to have a higher conductance than the neutral molecule, we believe this supports the idea that the conductance of the neutral molecule is very low, below our measurement sensitivity. This idea is further supported by theoretical calculations. To the best of our knowledge, these are the first reported single-molecule conductance measurements on a molecular charge-transfer species.

Parapedocotyle prolatili gen. n. et sp. n., a representative of a new subfamily of the Diclidophoridae (Monogenea), a gill parasite of Prolatilus jugularis (Teleostei: Pinguipedidae) from Chile.

Parapedocotylinae, a new subfamily, is proposed to accommodate the gen. n. et sp. n. Parapedocotyle prolatili (Monogenea: Diclidophoridae), a gill parasite of the Pacific sandperch, Prolatilus jugularis (Valenciennes) (Pinguipedidae) from northern Chile (30 degrees 56'S; 71 degrees 20'W). Among the Diclidophoridae Cerfontaine, 1895, the species of the Pedocotylinae Yamaguti, 1963 are unique by bearing the first pair of clamps (most posteriorly) in a haptoral projection. Pedocotyle MacCallum, 1913, the only genus in the Pedocotylinae, is characterised by the first pair of clamps non-pedunculate, modified and non-functional, without accessory suckers, and clamps of pairs 2-4 being pedunculate and functional. In contrast, the first pair of clamps in Parapedocotyle is well developed and functional at the terminal end of a long haptoral appendix and having clamp pairs 2-4 pedunculated, modified and apparently not functional. Seminal receptacle is preovarian in Parapedocotyle in opposition to its postovarian position in Pedocotyle. These differences justified the erection of the new subfamily Parapedocotylinae. The new subfamily is also supported by genetic analyses (18S rDNA, 28S rDNA and cox1 sequences) demonstrating that the Pedocotylinae and Parapedocotylinae belong to different clades in the Diclidophoridae.

Engineering the thermopower of C60 molecular junctions.

We report the measurement of conductance and thermopower of C60 molecular junctions using a scanning tunneling microscope (STM). In contrast to previous measurements, we use the imaging capability of the STM to determine precisely the number of molecules in the junction and measure thermopower and conductance continuously and simultaneously during formation and breaking of the molecular junction, achieving a complete characterization at the single-molecule level. We find that the thermopower of C60 dimers formed by trapping a C60 on the tip and contacting an isolated C60 almost doubles with respect to that of a single C60 and is among the highest values measured to date for organic materials. Density functional theory calculations show that the thermopower and the figure of merit continue increasing with the number of C60 molecules, demonstrating the enhancement of thermoelectric preformance by manipulation of intermolecular interactions.

Patterns of variation in parasite component communities and infracommunities of a littoral fish species from the northern coast of Chile.

The structure and similarity of the parasite communities of fish can be evaluated at the component community (CC) and infracommunity (IC) levels. Both hierarchical levels have been used to assess parasite variations in fish at large (biogeographic) scales. However, studies evaluating the consistency between these two hierarchical levels at smaller geographical scales are scarce. In this study, the parasite assemblages of 124 Paralabrax humeralis collected by local fishermen by spear fishing at four sites (El Fierro, EF; P. Angamos, PA; Santa María, ISM; San Jorge, BSJ) in northern Chile were compared to assess the variability (or similarity) of their CCs and ICs at a limited geographical scale using multivariate analysis. At the IC level, discriminant analyses showed that P. humeralis parasite communities varied significantly among sites; 70% of ectoparasite ICs were correctly assigned to each site, but only 55% of helminth parasite ICs were correctly classified. At the CC level, the composition of parasite communities as assessed by correspondence analyses varied significantly between sites. Tagia sp., Neobenedenia sp. and Philometra sp. were associated with BSJ, ISM and PA, respectively; Corynosoma sp. and most digeneans were associated with both ISM and EF. Analysis of similarities (ANOSIM) showed significant variations in the degree of similarity between P. humeralis CCs from different sites, but not between ICs. Variations between CCs from different sites reflect fish population processes (e.g., population age, reproductive segregation) and the particular conditions of their respective habitats, whereas ICs reflect individual host movements. This study demonstrated that, when examined at a limited geographical scale, IC is better than CC at capturing the local pool of parasite assemblages when host populations are spatially segregated. Therefore, in this study, it is demonstrated that at a small geographic scale, CC variations are not reflected by IC, when host population is spatially segregated.