Bipartite partial duals and circuits in medial graphs

It is well known that a plane graph is Eulerian if and only if its geometric dual is bipartite. We extend this result to partial duals of plane graphs. We then characterize all bipartite partial duals of a plane graph in terms of oriented circuits in its medial graph.Comment: v2: minor changes. To appear in Combinatoric

Expansions for the Bollobas-Riordan polynomial of separable ribbon graphs

We define 2-decompositions of ribbon graphs, which generalise 2-sums and tensor products of graphs. We give formulae for the Bollobas-Riordan polynomial of such a 2-decomposition, and derive the classical Brylawski formula for the Tutte polynomial of a tensor product as a (very) special case. This study was initially motivated from knot theory, and we include an application of our formulae to mutation in knot diagrams.Comment: Version 2 has minor changes. To appear in Annals of Combinatoric

Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade

SAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world’s oceans, where they play a major role in the ocean carbon cycle. Correlations between the phylogenetic branching order and spatiotemporal patterns in cell distributions from planktonic ocean environments indicate that SAR11 has evolved into perhaps a dozen or more specialized ecotypes that span evolutionary distances equivalent to a bacterial order. We isolated and sequenced genomes from diverse SAR11 cultures that represent three major lineages and encompass the full breadth of the clade. The new data expand observations about genome evolution and gene content that previously had been restricted to the SAR11 Ia subclade, providing a much broader perspective on the clade’s origins, evolution, and ecology. We found small genomes throughout the clade and a very high proportion of core genome genes (48 to 56%), indicating that small genome size is probably an ancestral characteristic. In their level of core genome conservation, the members of SAR11 are outliers, the most conserved free-living bacteria known. Shared features of the clade include low GC content, high gene synteny, a large hypervariable region bounded by rRNA genes, and low numbers of paralogs. Variation among the genomes included genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important to niche partitioning and ecotype divergence within the clade. These data provide support for the conclusion that streamlining selection for efficient cell replication in the planktonic habitat has occurred throughout the evolution and diversification of this clade

Safety Study of Photodynamic Therapy Using Talaporfin Sodium in the Pancreas and Surrounding Tissues in the Syrian Golden Hamster

Aim. To assess the safety of photodynamic therapy (PDT) using talaporfin sodium on the pancreas and surrounding organs in normal hamsters. Methods. Fluorescence microscopy documented talaporfin levels in liver, duodenum, and pancreas up to 24 hours after photosensitisation. Lesion size in liver 3 days after PDT (50 J, 5 mg/kg, variable drug-light interval (DLI)) was documented to optimise the DLI. Using optimum DLI, pancreas and surrounding organs were treated with laser fibre touching the surface and animals were killed at 3 or 21 days. Results. Peak fluorescence was seen in duodenum and pancreas at 15 mins (second lower peak at 2 hours). Liver fluorescence was consistently high (peak 1 hour) until after 4 hours. Optimum DLI was seen at 15 minutes. The pancreas was relatively resistant to direct PDT injury (small lesions at high doses) but surrounding stomach, duodenum, and liver were more susceptible with evidence of adhesions and full thickness damage (localised peritonitis and duodenal perforation at highest doses). Conclusion. The safety profile is similar to PDT with longer acting photosensitisers. The pancreas appears safe to treat, but care is required to avoid high light doses to the intestinal tract, particularly the duodenum

Palynological, geochemical, and mineralogical characteristics of the Early Jurassic Liasidium Event in the Cleveland Basin, Yorkshire, UK

A previously proposed hyperthermal episode in the Early Jurassic (mid-Sinemurian) is investigated from the shallow marine succession at Robin Hood’s Bay, Cleveland Basin, Yorkshire, UK. Palynological study confirms that the stratigraphical extent of the distinctive dinoflagellate cyst Liasidium variabile corresponds very closely to the oxynotum Zone. The range of Liasidium variabile also corresponds to an overall negative excursion in carbon-isotopes measured in bulk organic matter, which here exhibits a double spike in the middle oxynotum Zone. Additionally, Liasidium variabile abundances track overall transgressive-regressive facies trends with peak abundance of dinoflagellate cysts corresponding to deepest water facies and maximum flooding. Lithological cycles (parasequences), defined by visual description and hand-held X-ray fluorescence analysis of powdered samples, match previously suggested short eccentricity cycles, and allow a total duration for the event of at least one million years to be suggested. Changes in clay mineralogy throughout the section determined by whole rock X-ray diffraction and scanning electron microscopy are shown to be largely related to authigenic processes, and neither support nor refute the proposition of coeval palaeoclimate changes. The combined characteristics of the Liasidium Event described from Robin Hood’s Bay are similar to, but much less extreme than, the Early Jurassic Toarcian Oceanic Anoxic Event albeit, at this locality, there is no evidence for the development of significant bottom water deoxygenation

MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments

The conclusions of thousands of peer-reviewed publications rely on data obtained using fluorescence-based quantitative real-time PCR technology. However, the inadequate reporting of experimental detail, combined with the frequent use of flawed protocols is leading to the publication of papers that may not be technically appropriate. We take the view that this problem requires the delineation of a more transparent and comprehensive reporting policy from scientific journals. This editorial aims to provide practical guidance for the incorporation of absolute minimum standards encompassing the key assay parameters for accurate design, documentation and reporting of qPCR experiments (MIQE précis) and guidance on the publication of pure 'reference gene' articles

Projection Methods

Natural Resource Ecology & Mgm

RT-qPCR Diagnostics: The “Drosten” SARS-CoV-2 Assay Paradigm

The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is an established tool for the diagnosis of RNA pathogens. Its potential for automation has caused it to be used as a presence/absence diagnostic tool even when RNA quantification is not required. This technology has been pushed to the forefront of public awareness by the COVID-19 pandemic, as its global application has enabled rapid and analytically sensitive mass testing, with the first assays targeting three viral genes published within days of the publication of the SARS-CoV-2 genomic sequence. One of those, targeting the RNA-dependent RNA polymerase gene, has been heavily criticised for supposed scientific flaws at the molecular and methodological level, and this criticism has been extrapolated to doubts about the validity of RT-qPCR for COVID-19 testing in general. We have analysed this assay in detail, and our findings reveal some limitations but also highlight the robustness of the RT-qPCR methodology for SARS-CoV-2 detection. Nevertheless, whilst our data show that some errors can be tolerated, it is always prudent to confirm that the primer and probe sequences complement their intended target, since, when errors do occur, they may result in a reduction in the analytical sensitivity. However, in this case, it is unlikely that a mismatch will result in poor specificity or a significant number of false-positive SARS-CoV-2 diagnoses, especially as this is routinely checked by diagnostic laboratories as part of their quality assurance

Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon

PCR inhibition by nucleic acid extracts is a well known yet poorly described phenomenon. Inhibition assessment generally depends on the assumption that inhibitors affect all PCR reactions to the same extent; i.e. that the reaction of interest and the control reaction are equally susceptible to inhibition. To test this assumption we performed inhibition assessment on DNA extracts from human urine samples, fresh urine and EDTA using different PCR reactions