University of Liverpool

About: University of Liverpool is a education organization based out in Liverpool, United Kingdom. It is known for research contribution in the topics: Population & Context (language use). The organization has 40406 authors who have published 94388 publications receiving 3188970 citations. The organization is also known as: Liverpool University & The University of Liverpool.

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

Abstract: Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidron cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidron Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein.

Abstract: SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this novel coronavirus to provide a fundamental description of the virus’s genomic and proteomic potential. We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. Allied to this, we used tandem mass spectrometry to investigate the proteome and phosphoproteome of the same virally infected cells. Our integrated analysis revealed that the viral transcripts (i.e. subgenomic mRNAs) generally fitted the expected transcription model for coronaviruses. Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein and was predicted to remove a proposed furin cleavage site from the S glycoprotein. Tandem mass spectrometry identified over 500 viral peptides and 44 phosphopeptides in virus-infected cells, covering almost all proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. The furin site directs cleavage of the S glycoprotein into functional subunits during virus entry or exit and likely contributes strongly to the pathogenesis and zoonosis of this virus. Our data emphasises that the viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.

Patients' perceptions of medical explanations for somatisation disorders: qualitative analysis.

Abstract: Objectives: To describe, from the perspective of patients, distinguishing features of doctors9 attempts to explain the symptoms of somatisation disorders. Design: Qualitative analysis of verbatim records of interviews in which patients recounted doctors9 explanations of their symptoms. Setting: Patients with persistent somatising symptoms referred from general practices in Liverpool and St Helens and Knowsley were interviewed before entry into a treatment programme. Subjects: 228 of 324 patients referred were interviewed. Initial interviews were used to develop the process and technique, and the final analysis was based on a subsample of 68 records, randomly chosen from the transcripts of 188 subjects who were interviewed subsequently. Results: Doctors9 explanations were often at odds with the patients9 own thinking. Analysis showed that medical explanations could be grouped into one of three categories, defined by the patients9 perceptions. Most explanations were experienced as rejecting the reality of the symptoms. An intermediate category comprised explanations that were viewed as colluding, in which the doctor acquiesced with the patients9 own biomedical theories. However, a few explanations were perceived by patients as tangible, exculpating, and involving. These explanations were experienced by patients as satisfying and empowering. Conclusions: Patients with somatisation disorders feel satisfied and empowered by medical explanations that are tangible, exculpating, and involving. Empowering explanations could improve these patients9 wellbeing and help to reduce the high demands they make on health services.

The industrial melanism mutation in British peppered moths is a transposable element

Abstract: Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example of a visible evolutionary response is industrial melanism in the peppered moth (Biston betularia): the replacement, during the Industrial Revolution, of the common pale typica form by a previously unknown black (carbonaria) form, driven by the interaction between bird predation and coal pollution. The carbonaria locus has been coarsely localized to a 200-kilobase region, but the specific identity and nature of the sequence difference controlling the carbonaria-typica polymorphism, and the gene it influences, are unknown. Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element into the first intron of the gene cortex. Statistical inference based on the distribution of recombined carbonaria haplotypes indicates that this transposition event occurred around 1819, consistent with the historical record. We have begun to dissect the mode of action of the carbonaria transposable element by showing that it increases the abundance of a cortex transcript, the protein product of which plays an important role in cell-cycle regulation, during early wing disc development. Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of 'jumping genes' as a source of major phenotypic novelty.

New method to evaluate the therapeutic value of lymph node dissection for gastric cancer

Abstract: The results of 1281 potentially curative resections for advanced gastric cancer performed at the National Cancer Center Hospital between 1972 and 1986 were studied using a novel approach which circumvents the stage migration phenomenon. The incidence of metastasis and the 5-year survival rate of patients with positive nodes were calculated independently for each lymph node 'station', without any reference to overall pathological nodal stage. The therapeutic value of extended lymph node dissection was estimated by multiplication of incidence of metastasis and percentage 5-year survival rate of patients with metastasis for each station. The incidence of metastasis ranged from 2.4 per cent to 66 per cent and the 5-year survival rate of affected patients from 0 to 58.7 per cent in perigastric stations, depending on the site of the primary tumour. The incidence of metastasis was between 3.0 per cent and 44.4 per cent in the second tier of nodes (n2), and the 5-year survival rate ranged from 0 per cent to 47.5 per cent. The majority of second-tier stations showed evidence of benefit from node dissection.