Life-history traits of the marbled electric ray,Torpedo marmorata Risso, 1810, from the Greek Seas,north-eastern Mediterranean Sea

Environmental Biology of Fishes - This work presents new information on the morphological aspects, reproductive biology and diet of the marbled electric ray Torpedo marmorata Risso 1810, in the...     

Principal component analysis: Development of a multivariate index for assessing eutrophication according to the European water framework directive

The discriminating power of eutrophication assessment schemes is often affected by the intercorrelation between cause (nutrient concentrations) and response (phytoplankton biomass and diversity) variables. Principal component analysis, a multivariate data reduction technique producing new sets of uncorrelated variables, was applied on nitrate, nitrite, ammonia, phosphate and chlorophyll α concentrations from coastal waters in the Aegean Sea, Eastern Mediterranean, and the first principal component was derived and evaluated as a eutrophication index on an independent dataset. The index, a linear combination of the five variables with almost equal weights, was found efficient in discriminating levels of eutrophication and critical thresholds characterizing oligotrophy, mesotrophy and eutrophication were set. The applicability of these thresholds for the implementation of the European Water Framework Directive was also examined thereof a five-level water quality classification scheme was developed.     

The Influence of Dopaminergic Striatal Innervation on Upper Limb Locomotor Synergies

To determine the role of striatal dopaminergic innervation on upper limb synergies during walking, we measured arm kinematics in 13 subjects with Parkinson disease. Patients were recruited according to several inclusion criteria to represent the best possible in vivo model of dopaminergic denervation. Of relevance, we included only subjects with normal spatio-temporal parameters of the stride and gait speed to avoid an impairment of upper limbs locomotor synergies as a consequence of gait impairment per se. Dopaminergic innervation of the striatum was measured by FP-CIT and SPECT. All patients showed a reduction of gait-associated arms movement. No linear correlation was found between arm ROM reduction and contralateral dopaminergic putaminal innervation loss. Still, a partition analysis revealed a 80% chance of reduced arm ROM when putaminal dopamine content loss was >47%. A significant correlation was described between the asymmetry indices of the swinging of the two arms and dopaminergic striatal innervation. When arm ROM was reduced, we found a positive correlation between upper-lower limb phase shift modulation (at different gait velocities) and striatal dopaminergic innervation. These findings are preliminary evidence that dopaminergic striatal tone plays a modulatory role in upper-limb locomotor synergies and upper-lower limb coupling while walking at different velocities.     

Use of internally nuclease‐protected single‐strand DNA oligonucleotides and silencing of the mismatch repair protein,MSH2, enhances the replication of corrected cells following gene editing

Background

Gene editing is potentially a powerful technology for introducing genetic changes by using short single‐stranded DNA oligonucleotides (ssODNs). However, their efficiency is reduced by the mismatch repair system, especially MSH2, which may suppress gene editing, although findings vary depending on readout and type of oligonucleotide used. Additionally, successfully edited cells are reported to arrest at the S‐ or G2‐phase. In the present study, we evaluate whether a novel ssODN design and down‐regulation of MSH2 expression allows the isolation of replicating gene‐edited cells.

Methods

Cultured Chinese hamster ovary cells expressing mutated enhanced green fluorescent protein were targeted with ssODNs of varying design, all capable of restoring fluorescence, which allows the monitoring of correction events by flow cytometry. Converted cells were isolated by cell sorting and grown to determine colony formation efficiencies. MSH2 expression was suppressed with small interfering RNA and the cell cycle distribution of cells transfected with ssODN was quantified by flow cytometry, following propidium iodide or DRAQ5 staining.

Results

Although efficiency was higher using ssODN end‐protected with phosphorothioate, the potential of edited cells to form colonies was lower than those targeted with unmodified ssODN. We established that ssODN transfection itself perturbs the cell cycle and that MSH2 gene silencing increases correction efficiency. In both cases, however, the effect was dependent on the positioning of the protected nucleotides. Importantly, when internally protected ssODN was used in combination with MSH2 suppression, a higher proportion of G1‐phase corrected cells was observed 48–64 h after transfection.

Conclusions

Use of internally protected ssODN and downregulating cellular MSH2 activity may facilitate isolation of viable, actively replicating gene‐edited cells. Copyright © 2009 John Wiley & Sons, Ltd.     

On the presence of short-range periodicities in protein structures that are not related to established secondary structure elements

Standard secondary structure elements such as α-helices or β-sheets, are characterized by repeating backbone torsion angles (φ,ψ) at the single residue level. Two-residue motifs of the type (φ,ψ)₂ are also observed in nonlinear conformations, mainly turns. Taking these observations a step further, it can be argued that there is no a priori reason why the presence of higher order periodicities can not be envisioned in protein structures, such as, for example, periodic transitions between successive residues of the type (…-α-β-α-β-α-…), or (…-β-α_L-β-α_L-β-…), or (…-α-β-α_L-α-β-α_L-…), and so forth, where the symbols (α,β,α_L) refer to the established Ramachandran-based residue conformations. From all such possible higher order periodicities, here we examine the deposited (with the PDB) protein structures for the presence of short-range periodical conformations comprising five consecutive residues alternating between two (and only two) distinct Ramachandran regions, for example, conformations of the type (α-β-α-β-α) or (β-α_L-β-α_L-β), and so forth. Using a probabilistic approach, we have located several thousands of such peptapeptides, and these were clustered and analyzed in terms of their structural characteristics, their sequences, and their putative functional correlations using a gene ontology-based approach. We show that such nonstandard short-range periodicities are present in a large and functionally diverse sample of proteins, and can be grouped into two structurally conserved major types. Examination of the structural context in which these peptapeptides are observed gave no conclusive evidence for the presence of a persistent structural or functional role of these higher order periodic conformations.     

Quantum transport in the FMO photosynthetic light-harvesting complex

The very high light-harvesting efficiency of natural photosynthetic systems in conjunction with recent experiments, which showed quantum-coherent energy transfer in photosynthetic complexes, raised questions regarding the presence of non-trivial quantum effects in photosynthesis. Grover quantum search, quantum walks, and entanglement have been investigated as possible effects that lead to this efficiency. Here we explain the near-unit photosynthetic efficiency without invoking non-trivial quantum effects. Instead, we use non-equilibrium Green’s functions, a mesoscopic method used to study transport in nano-conductors to compute the transmission function of the Fenna–Matthews–Olson (FMO) complex using an experimentally derived exciton Hamiltonian. The chlorosome antenna and the reaction center play the role of input and output contacts, connected to the FMO complex. We show that there are two channels for which the transmission is almost unity. Our analysis also revealed a dephasing-driven regulation mechanism that maintains the efficiency in the presence of varying dephasing potentials.     

Changes in Organic Carbon and Trace Elements in the Soil of Willow Short-Rotation Coppice Plantations

Short rotation coppice (SRC) is a biomass production system for energy usually grown on former agricultural land with fast-growing tree species. In Sweden, willow SRC has been grown since the late 1980s. SRC on arable soils may induce changes in some soil quality parameters due to differences in crop characteristics and management practices. In this study, pH, organic carbon (C), and trace element concentrations in the soil of 14 long-term (10–20 years) commercial willow SRC fields in Sweden were compared with those in adjacent, conventionally managed arable soils. The results showed that organic C concentrations in the topsoil and subsoil of SRC fields were, on average, significantly higher (9 % in topsoil, 27 % in subsoil) than in the reference fields. When comparisons were made only for the ten sites where the reference field had a crop rotation dominated by cereal crops, the corresponding figures were 10 % and 22 %. The average concentration of cadmium (Cd), which is considered the most hazardous trace element for human health in the food chain, was 12 % lower in the topsoil of SRC fields than in the reference fields. In the corresponding comparison of subsoils, no such difference was found. For chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), and zinc (Zn), there were no significant differences in concentrations between SRC fields and the reference fields in either topsoil or subsoil. Negligible differences in pH in the same comparisons were found.