Structural basis for stabilisation of the RAD51 nucleoprotein filament by BRCA2.

The BRCA2 tumour suppressor protein preserves genomic integrity via interactions with the DNA-strand exchange RAD51 protein in homology-directed repair. The RAD51-binding TR2 motif at the BRCA2 C-terminus is essential for protection and restart of stalled replication forks. Biochemical evidence shows that TR2 recognises filamentous RAD51, but existing models of TR2 binding to RAD51 lack a structural basis. Here we used cryo-electron microscopy and structure-guided mutagenesis to elucidate the mechanism of TR2 binding to nucleoprotein filaments of human RAD51. We find that TR2 binds across the protomer interface in the filament, acting as a brace for adjacent RAD51 molecules. TR2 targets an acidic-patch motif on human RAD51 that serves as a recruitment hub in fission yeast Rad51 for recombination mediators Rad52 and Rad55-Rad57. Our findings provide a structural rationale for RAD51 filament stabilisation by BRCA2 and reveal a common recruitment mechanism of recombination mediators to the RAD51 filament.

A metal ion-dependent mechanism of RAD51 nucleoprotein filament disassembly.

The RAD51 ATPase polymerizes on single-stranded DNA to form nucleoprotein filaments (NPFs) that are critical intermediates in the reaction of homologous recombination. ATP binding maintains the NPF in a competent conformation for strand pairing and exchange. Once strand exchange is completed, ATP hydrolysis licenses the filament for disassembly. Here we show that the ATP-binding site of the RAD51 NPF contains a second metal ion. In the presence of ATP, the metal ion promotes the local folding of RAD51 into the conformation required for DNA binding. The metal ion is absent in the ADP-bound RAD51 filament, that rearranges in a conformation incompatible with DNA binding. The presence of the second metal ion explains how RAD51 couples the nucleotide state of the filament to DNA binding. We propose that loss of the second metal ion upon ATP hydrolysis drives RAD51 dissociation from the DNA and weakens filament stability, contributing to NPF disassembly.

Large-area periodically-poled lithium niobate wafer stacks optimized for high-energy narrowband terahertz generation.

Periodically-poled lithium niobate (PPLN) sources consisting of custom-built stacks of large-area wafers provide a unique opportunity to systematically study the multi-cycle terahertz (THz) generation mechanism as they are assembled layer-by-layer. Here we investigate and optimize the THz emission from PPLN wafer stacks as a function of wafer number, pump fluence, pulse duration and chirp, wafer separation, and pump focusing. Using 135 µm-thick, 2"-diameter wafers we generate high-energy, narrowband THz pulses with central frequencies up to 0.39 THz, directly suitable for THz-driven particle acceleration applications. We explore the multi-cycle pulse build-up with increasing wafer numbers using electro-optic sampling measurements, achieving THz conversion efficiencies up to 0.17%, while demonstrating unique control over the pulse length and bandwidth these sources offer. Guided by simulations, observed frequency-dependence on both stack-mounting and pump focusing conditions have been attributed to inter-wafer etalon and Gouy phase-shifts respectively, revealing subtle features that are critical to the understanding and performance of PPLN wafer-stack sources for optimal narrowband THz generation.

Stages, scaffolds and strings in the spatial organisation of non-homologous end joining: Insights from X-ray diffraction and Cryo-EM.

Non-homologous end joining (NHEJ) is the preferred pathway for the repair of DNA double-strand breaks in humans. Here we describe three structural aspects of the repair pathway: stages, scaffolds and strings. We discuss the orchestration of DNA repair to guarantee robust and efficient NHEJ. We focus on structural studies over the past two decades, not only using X-ray diffraction, but also increasingly exploiting cryo-EM to investigate the macromolecular assemblies.

Druggable binding sites in the multicomponent assemblies that characterise DNA double-strand-break repair through non-homologous end joining.

Non-homologous end joining (NHEJ) is one of the two principal damage repair pathways for DNA double-strand breaks in cells. In this review, we give a brief overview of the system including a discussion of the effects of deregulation of NHEJ components in carcinogenesis and resistance to cancer therapy. We then discuss the relevance of targeting NHEJ components pharmacologically as a potential cancer therapy and review previous approaches to orthosteric regulation of NHEJ factors. Given the limited success of previous investigations to develop inhibitors against individual components, we give a brief discussion of the recent advances in computational and structural biology that allow us to explore different targets, with a particular focus on modulating protein-protein interaction interfaces. We illustrate this discussion with three examples showcasing some current approaches to developing protein-protein interaction inhibitors to modulate the assembly of NHEJ multiprotein complexes in space and time.

Addressing inequality and intolerance in human-wildlife coexistence.

Millennia of human conflict with wildlife have built a culture of intolerance toward wildlife among some stakeholders. We explored 2 key obstacles to improved human-wildlife coexistence: coexistence inequality (how the costs and benefits of coexisting with wildlife are unequally shared) and intolerance. The costs of coexisting with wildlife are often disproportionately borne by the so-called global south and rural communities, and the benefits often flow to the global north and urban dwellers. Attitudes and behaviors toward wildlife (tolerance versus intolerance) vary with social and cultural norms. We suggest more empathetic advocacy is needed that, for example, promotes conservation while appropriately considering those who bear the costs of conflict with wildlife. To achieve more equitable cost-sharing, we suggest limiting the costs incurred by those most affected or by sharing those costs more widely. For example, we advocate for the development of improved wildlife compensation schemes, increasing the scale of rewilding efforts, and preventing wildlife-derived revenue leaching out of the local communities bearing the costs of coexistence.

Soluciones para la Desigualdad y la Intolerancia en la Coexistencia Humano - Fauna Resumen Los milenios de conflicto entre los humanos y la fauna han construido una cultura de intolerancia hacia la fauna entre algunos actores. Exploramos dos obstáculos importantes para la mejora de la coexistencia humano - fauna: la desigualdad de coexistencia (cómo los costos y los beneficios de la coexistencia con la fauna están compartidos de una manera desigual) y la intolerancia. Los costos de coexistir con la fauna generalmente están asumidos de manera desproporcional por las llamadas comunidades del sur global o rurales, y los beneficios de convivir con la fauna generalmente fluyen hacia el norte mundial y hacia los habitantes de zonas urbanas. Las actitudes y comportamientos hacia la fauna (tolerancia versus intolerancia) varían con las normas culturales y sociales. Sugerimos la necesidad de una defensa más empática que, por ejemplo, promueva la conservación a la vez que considera de manera apropiada a aquellos que asumen los costos del conflicto con la fauna. Para lograr costos compartidos más equitativos sugerimos limitar los costos incurridos por aquellos más afectados o compartir los costos de manera más amplia. Por ejemplo, abogamos por el desarrollo de esquemas mejorados de compensación de fauna, el incremento de la escala de los esfuerzos por el retorno a la vida silvestre y la prevención del secuestro de ingresos derivados de la fauna fuera de las comunidades locales que asumen los costos de la coexistencia.

Taxonomic status of the Australian dingo: the case for Canis dingo Meyer, 1793.

The taxonomic status and systematic nomenclature of the Australian dingo remain contentious, resulting in decades of inconsistent applications in the scientific literature and in policy. Prompted by a recent publication calling for dingoes to be considered taxonomically as domestic dogs (Jackson et al. 2017, Zootaxa 4317, 201-224), we review the issues of the taxonomy applied to canids, and summarise the main differences between dingoes and other canids. We conclude that (1) the Australian dingo is a geographically isolated (allopatric) species from all other Canis, and is genetically, phenotypically, ecologically, and behaviourally distinct; and (2) the dingo appears largely devoid of many of the signs of domestication, including surviving largely as a wild animal in Australia for millennia. The case of defining dingo taxonomy provides a quintessential example of the disagreements between species concepts (e.g., biological, phylogenetic, ecological, morphological). Applying the biological species concept sensu stricto to the dingo as suggested by Jackson et al. (2017) and consistently across the Canidae would lead to an aggregation of all Canis populations, implying for example that dogs and wolves are the same species. Such an aggregation would have substantial implications for taxonomic clarity, biological research, and wildlife conservation. Any changes to the current nomen of the dingo (currently Canis dingo Meyer, 1793), must therefore offer a strong, evidence-based argument in favour of it being recognised as a subspecies of Canis lupus Linnaeus, 1758, or as Canis familiaris Linnaeus, 1758, and a successful application to the International Commission for Zoological Nomenclature - neither of which can be adequately supported. Although there are many species concepts, the sum of the evidence presented in this paper affirms the classification of the dingo as a distinct taxon, namely Canis dingo.

A basal thunnosaurian from Iraq reveals disparate phylogenetic origins for Cretaceous ichthyosaurs.

Cretaceous ichthyosaurs have typically been considered a small, homogeneous assemblage sharing a common Late Jurassic ancestor. Their low diversity and disparity have been interpreted as indicative of a decline leading to their Cenomanian extinction. We describe the first post-Triassic ichthyosaur from the Middle East, Malawania anachronus gen. et sp. nov. from the Early Cretaceous of Iraq, and re-evaluate the evolutionary history of parvipelvian ichthyosaurs via phylogenetic and cladogenesis rate analyses. Malawania represents a basal grade in thunnosaurian evolution that arose during a major Late Triassic radiation event and was previously thought to have gone extinct during the Early Jurassic. Its pectoral morphology appears surprisingly archaic, retaining a forefin architecture similar to that of its Early Jurassic relatives. After the initial latest Triassic radiation of early thunnosaurians, two subsequent large radiations produced lineages with Cretaceous representatives, but the radiation events themselves are pre-Cretaceous. Cretaceous ichthyosaurs therefore include distantly related lineages, with contrasting evolutionary histories, and appear more diverse and disparate than previously supposed.

New ophthalmosaurid ichthyosaurs from the European Lower Cretaceous demonstrate extensive ichthyosaur survival across the Jurassic-Cretaceous boundary.

BACKGROUND: Ichthyosauria is a diverse clade of marine amniotes that spanned most of the Mesozoic. Until recently, most authors interpreted the fossil record as showing that three major extinction events affected this group during its history: one during the latest Triassic, one at the Jurassic-Cretaceous boundary (JCB), and one (resulting in total extinction) at the Cenomanian-Turonian boundary. The JCB was believed to eradicate most of the peculiar morphotypes found in the Late Jurassic, in favor of apparently less specialized forms in the Cretaceous. However, the record of ichthyosaurs from the Berriasian-Barremian interval is extremely limited, and the effects of the end-Jurassic extinction event on ichthyosaurs remains poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: Based on new material from the Hauterivian of England and Germany and on abundant material from the Cambridge Greensand Formation, we name a new ophthalmosaurid, Acamptonectes densus gen. et sp. nov. This taxon shares numerous features with Ophthalmosaurus, a genus now restricted to the Callovian-Berriasian interval. Our phylogenetic analysis indicates that Ophthalmosauridae diverged early in its history into two markedly distinct clades, Ophthalmosaurinae and Platypterygiinae, both of which cross the JCB and persist to the late Albian at least. To evaluate the effect of the JCB extinction event on ichthyosaurs, we calculated cladogenesis, extinction, and survival rates for each stage of the Oxfordian-Barremian interval, under different scenarios. The extinction rate during the JCB never surpasses the background extinction rate for the Oxfordian-Barremian interval and the JCB records one of the highest survival rates of the interval. CONCLUSIONS/SIGNIFICANCE: There is currently no evidence that ichthyosaurs were affected by the JCB extinction event, in contrast to many other marine groups. Ophthalmosaurid ichthyosaurs remained diverse from their rapid radiation in the Middle Jurassic to their total extinction at the beginning of the Late Cretaceous.

Spontaneous tool-use: an observation of a dingo (Canis dingo) using a table to access an out-of-reach food reward.

Opportunities to observe non-human animals exhibiting naturalistic 'high-order' behaviour are rare. Examples featuring canids, although often anecdotal and involving captive animals are potentially valuable, as they may provide an opportunity to examine complex problem-solving behaviour not easily observed in free-ranging settings. This paper describes observations of two captive male dingoes (Canis dingo), representing possible examples of high-order behaviour. The first set of observations involved a sub-adult male that spontaneously (i.e., without training) learned to move objects around his enclosure, apparently to multiple ends, such as in an effort to gain the additional height required to attain objects otherwise out of reach, or to attain a better view of his surroundings. The second set of observations involved an adult male that learned to open a gate, possibly in an effort to gain access to a female. These observations add to the small number of anecdotal accounts offering a window into the cognitive abilities of canids, and the observations involving the sub-adult male appear to be the first documented cases of tool-use in a canid.