Encoding of low-quality DNA profiles as genotype probability matrices for improved profile comparisons, relatedness evaluation and database searches

Many DNA profiles recovered from crime scene samples are of a quality that does not allow them to be searched against, nor entered into, databases. We propose a method for the comparison of profiles arising from two DNA samples, one or both of which can have multiple donors and be affected by low DNA template or degraded DNA. We compute likelihood ratios to evaluate the hypothesis that the two samples have a common DNA donor, and hypotheses specifying the relatedness of two donors. Our method uses a probability distribution for the genotype of the donor of interest in each sample. This distribution can be obtained from a statistical model, or we can exploit the ability of trained human experts to assess genotype probabilities, thus extracting much information that would be discarded by standard interpretation rules. Our method is compatible with established methods in simple settings, but is more widely applicable and can make better use of information than many current methods for the analysis of mixed-source, low-template DNA profiles. It can accommodate uncertainty arising from relatedness instead of or in addition to uncertainty arising from noisy genotyping. We describe a computer program GPMDNA, available under an open source license, to calculate LRs using the method presented in this paper.Comment: 28 pages. Accepted for publication 2-Sep-2016 - Forensic Science International: Genetic

Recently published papers: Novel therapies in chronic obstructive pulmonary disease, cardiac chemicals and intensive care outcomes

The burden of chronic obstructive pulmonary disease on intensive care is heavy, but newer modalities of treatment are now available to improve outcomes. Cardiac-based research continues to generate new drugs and tests to better outcome and aid in early diagnosis. And how do various intensive care interventions compare in improving clinical and functional outcomes

Natural bounds on herbivorous coral reef fishes

Humans are an increasingly dominant driver of Earth's biological communities, but differentiating human impacts from natural drivers of ecosystem state is crucial. Herbivorous fish play a key role in maintaining coral dominance on coral reefs, and are widely affected by human activities, principally fishing. We assess the relative importance of human and biophysical (habitat and oceanographic) drivers on the biomass of five herbivorous functional groups among 33 islands in the central and western Pacific Ocean. Human impacts were clear for some, but not all, herbivore groups. Biomass of browsers, large excavators, and of all herbivores combined declined rapidly with increasing human population density, whereas grazers, scrapers, and detritivores displayed no relationship. Sea-surface temperature had significant but opposing effects on the biomass of detritivores (positive) and browsers (negative). Similarly, the biomass of scrapers, grazers, and detritivores correlated with habitat structural complexity; however, relationships were group specific. Finally, the biomass of browsers and large excavators was related to island geomorphology, both peaking on low-lying islands and atolls. The substantial variability in herbivore populations explained by natural biophysical drivers highlights the need for locally appropriate management targets on coral reefs

Brightly Luminescent Platinum Complexes of N∧C–∧N Ligands Forming Six-Membered Chelate Rings: Offsetting Deleterious Ring Size Effects Using Site-Selective Benzannulation

Brightly emissive platinum(II) complexes (λemission,max = 607–612 nm) of the type RLPtCl are reported, where RL is a cyclometalated N∧C–∧N-coordinating ligand derived from 1,3-di(2-trifluoromethyl-4-phenanthridinyl)benzene (CF3LH) or 1,3-di(2-tert-butyl-4-phenanthridinyl)benzene (tBuLH). Metathesis of the chlorido ligand can be achieved under mild conditions, enabling isolation of ionic compounds with the formula [CF3LPtL′]PF6 where L′ = pyridine or (4-dimethylamino)pyridine (DMAP), as well as the charge-neutral species tBuLPt(C≡C─C6H4─tBu) (C≡C─C6H4─tBu = 4-tert-butylphenylacetylido). Compared with N∧N∧N-ligated Pt(II) complexes that form 5-membered chelates, these compounds all contain 6-membered rings. Expanding the chelate ring size from 5 to 6 has been previously demonstrated to enhance emission in some N∧N∧N-coordinated Pt(II) species─for example, in complexes of 2,6-di(8-quinolinyl)pyridine vs those of 2,2′:6′,2″-terpyridine─but in related N∧C–∧N-coordinated species, luminescence quantum yields are significantly lower for the 6-membered chelate ring complexes. Here, we demonstrate that site-selective benzannulation of the quinolinyl side-arms can offset the deleterious effect of changing the chelate ring-size and boost photophysical properties such as the quantum yield. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations suggest that benzannulation counterintuitively destabilizes the emissive triplet states compared to the smaller π-system, with the “imine-bridged biphenyl” form of the phenanthridinyl arm helping to buffer against larger molecular distortions, enhancing photoluminescence quantum yields up to 0.09 ± 0.02. The spontaneous formation under aerated conditions of a Pt(IV) derivative (CF3LPtCl3) is also reported, together with its molecular structure in the solid state

Introduction and spread of non-native parasites with Silurus glanis L. (Teleostei: Siluridae) in UK fisheries

Despite growing concern of the ecological risks posed by the European catfish Siluris glanis L. in freshwater fisheries, little information exists on the parasite fauna of this silurid catfish in Britain. Parasitological examinations of released S. glanis from four still-water fisheries in England revealed the presence of Thaparocleidus vistulensis (Siwak, 1932) and Ergasilus sieboldi (Nordmann, 1832), both non-native parasites, the latter known to be an important fish pathogen. This represents the first record of T. vistulensis from British freshwater fish. The human-assisted movement of S. glanis between UK recreational still-water fisheries provides a clear avenue for the introduction and spread of non-native parasites

A survey of low-velocity collisional features in Saturn's F ring

Small (~50km scale), irregular features seen in Cassini images to be emanating from Saturn's F ring have been termed mini-jets by Attree et al. (2012). One particular mini-jet was tracked over half an orbital period, revealing its evolution with time and suggesting a collision with a local moonlet as its origin. In addition to these data we present here a much more detailed analysis of the full catalogue of over 800 F ring mini-jets, examining their distribution, morphology and lifetimes in order to place constraints on the underlying moonlet population. We find mini-jets randomly located in longitude around the ring, with little correlation to the moon Prometheus, and randomly distributed in time, over the full Cassini tour to date. They have a tendency to cluster together, forming complicated `multiple' structures, and have typical lifetimes of ~1d. Repeated observations of some features show significant evolution, including the creation of new mini-jets, implying repeated collisions by the same object. This suggests a population of <~1km radius objects with some internal strength and orbits spread over 100km in semi-major axis relative to the F ring but with the majority within 20km. These objects likely formed in the ring under, and were subsequently scattered onto differing orbits by, the perturbing action of Prometheus. This reinforces the idea of the F ring as a region with a complex balance between collisions, disruption and accretion.Comment: 21 pages, 12 figures. Accepted for publication in Icarus. Supplementary information available at http://www.maths.qmul.ac.uk/~attree/mini-jets

Synthesis and Coordination Chemistry of a Benzannulated Bipyridine: 6,6′-Biphenanthridine

The synthesis, characterization, and coordination chemistry of a doubly π-extended bipyridine analogue, 6,6′-biphenanthridine (biphe), is presented. The structure of the molecule has been determined in the solid state by X-ray diffraction, showing an angle of 72.6° between the phenanthridine planes. The free, uncoordinated organic molecule displays blue fluorescence in solution. It can be singly protonated with strong acids, and the protonated form displays more intense yellow emission. The effect of acid on the excited states is interpreted with the aid of TDDFT calculations. Two Ru(II) coordination complexes, tris(6,6′-biphenanthridine)ruthenium(II) dichloride, [Ru(biphe)3]Cl2, and bis(2,2′-bipyridine)(6,6′-biphenanthridine)ruthenium(II) tetraphenylborate, [Ru(bpy)2(biphe)](BPh4)2, are also reported and their structures determined in the solid state by X-ray diffraction. Both complexes display emission at 77 K that is strongly bathochromically shifted by almost 200 nm compared to that of the archetypal 3MLCT emitter [Ru(bpy)3]2+. Such a red shift is consistent with the more extended conjugation and lower-energy π* orbitals associated with the biphe ligand, lowering the energy of the 3MLCT excited state, as revealed by TDDFT calculations. The efficient non-radiative decay that is typical of such low-energy emitters renders the phosphorescence extremely weak and short-lived at ambient temperature, and rapid ligand photodissociation also competes with radiative decay, especially in the heteroleptic complex. Electrochemical analysis illustrates the effect of biphe’s stabilized vacant π* manifold, with multiple reversible reductions evident at much less negative potentials than those observed for [Ru(bpy)3]2+