Between the Danube and the Deep Blue Sea : zooarchaeological meta-analysis reveals variability in the spread and development of Neolithic farming across the western Balkans

The first spread of farming practices into Europe in the Neolithic period involves two distinct 'streams', respectively around the Mediterranean littoral and along the Danube corridor to central Europe. In this paper we explore variation in Neolithic animal use practices within and between these streams, focusing on the first region in which they are clearly distinct (and yet still in close proximity): the western Balkans. We employ rigorous and reproducible meta-analysis of all available zooarchaeological data from the region to test hypotheses (a) that each stream featured a coherent 'package' of herding and hunting practices in the earliest Neolithic, and (b) that these subsequently diverged in response to local conditions and changing cultural preferences. The results partially uphold these hypotheses, while underlining that Neolithisation was a complex and varied process. A coherent, stable, caprine-based 'package' is seen in the coastal stream, albeit with some diversification linked to expansion northwards and inland. Accounting for a severe, systematic bias in bone recovery methodology between streams, we show that sheep and goats also played a major role across the continental stream in the earliest Neolithic (c.6100-5800 BC). This was followed by a geographically staggered transition over c.500 years to an economy focused on cattle, with significant levels of hunting in some areas – a pattern we interpret in terms of gradual adaptation to local conditions, perhaps mediated by varying degrees of cultural conservatism. Subsequent westward expansion carried with it elements of this new pattern, which persisted through the middle and late Neolithic

Animal bones [from Nebelivka]

In this book, a team of international authors examines the hypothesis of independent Eastern European urbanism using the evidence gathered from the multi-disciplinary investigation of the Trypillia megasite of Nebelivka

Recording the Heart Beat of Cattle using a Gradiometer System of Optically Pumped Magnetometers

Monitoring of heart rate has the potential to provide excellent data for the remote monitoring of animals, and heart rate has been associated with stress, pyrexia, pain and illness in animals. However monitoring of heart rate in domesticated animals is difficult as it entails the restraint of the animal (which may in turn affect heart rate), and the application of complex monitoring equipment that is either invasive or not practical to implement under commercial farm conditions. Therefore accurate non-invasive automated remote monitoring of heart rate has not been possible in domesticated animals. Biomagnetism associated with muscle and nerve action provides a promising emerging field in medical sensing, but it is currently confined to magnetically-shielded clinical environments. In this study, we use biomagnetic sensing on commercial dairy cattle under farm conditions as a model system to show proof-of-principle for non-contact magnetocardiography (MCG) outside a controlled laboratory environment. By arranging magnetometers in a differential set-up and using purpose-built low-noise electronics, we are able to suppress common mode noise and successfully record the heart rate, the heart beat intervals and the heart beat amplitude. Comparing the MCG signal with simultaneous data recorded using a conventional electrocardiogram (ECG) allowed alignment of the two signals, and was able to match features of the ECG including the P-wave, the QRS complex and the T-wave. This study has shown the potential for MCG to be developed as a non-contact method for the assessment of heart rate and other cardiac attributes in adult dairy cattle. Whilst this study using an animal model showed the capabilities of un-shielded MCG, these techniques also suggest potentially exciting opportunities in human cardiac medicine outside hospital environments

Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers

The analysis of lipids (fats, oils and waxes) absorbed within archaeological pottery has revolutionized the study of past dietary diets and culinary practices. However, this technique can lack taxonomic and tissue specificity and is often unable to disentangle signatures resulting from the mixing of different food products. Here, we extract ancient proteins from ceramic vessels from the West Mound of the key early farming site of Çatalhöyük in Anatolia, revealing that this community processed mixes of cereals, pulses, dairy and meat products, and that particular vessels may have been reserved for specialized foods (e.g., cow milk and milk whey). Moreover, we demonstrate that dietary proteins can persist on archaeological artefacts for at least 8000 years, and that this approach can reveal past culinary practices with more taxonomic and tissue-specific clarity than has been possible with previous bio-molecular techniques

Heat inactivation of clinical COVID-19 samples on an industrial scale for low risk and efficient high-throughput qRT-PCR diagnostic testing.

We report the development of a large scale process for heat inactivation of clinical COVID-19 samples prior to laboratory processing for detection of SARS-CoV-2 by RT-qPCR. With more than 266 million confirmed cases, over 5.26 million deaths already recorded at the time of writing, COVID-19 continues to spread in many parts of the world. Consequently, mass testing for SARS-CoV-2 will remain at the forefront of the COVID-19 response and prevention for the near future. Due to biosafety considerations the standard testing process requires a significant amount of manual handling of patient samples within calibrated microbiological safety cabinets. This makes the process expensive, effects operator ergonomics and restricts testing to higher containment level laboratories. We have successfully modified the process by using industrial catering ovens for bulk heat inactivation of oropharyngeal/nasopharyngeal swab samples within their secondary containment packaging before processing in the lab to enable all subsequent activities to be performed in the open laboratory. As part of a validation process, we tested greater than 1200 clinical COVID-19 samples and showed less than 1 Cq loss in RT-qPCR test sensitivity. We also demonstrate the bulk heat inactivation protocol inactivates a murine surrogate of human SARS-CoV-2. Using bulk heat inactivation, the assay is no longer reliant on containment level 2 facilities and practices, which reduces cost, improves operator safety and ergonomics and makes the process scalable. In addition, heating as the sole method of virus inactivation is ideally suited to streamlined and more rapid workflows such as 'direct to PCR' assays that do not involve RNA extraction or chemical neutralisation methods

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Improving the efficiency and effectiveness of an industrial SARS-CoV-2 diagnostic facility.

On 11th March 2020, the UK government announced plans for the scaling of COVID-19 testing, and on 27th March 2020 it was announced that a new alliance of private sector and academic collaborative laboratories were being created to generate the testing capacity required. The Cambridge COVID-19 Testing Centre (CCTC) was established during April 2020 through collaboration between AstraZeneca, GlaxoSmithKline, and the University of Cambridge, with Charles River Laboratories joining the collaboration at the end of July 2020. The CCTC lab operation focussed on the optimised use of automation, introduction of novel technologies and process modelling to enable a testing capacity of 22,000 tests per day. Here we describe the optimisation of the laboratory process through the continued exploitation of internal performance metrics, while introducing new technologies including the Heat Inactivation of clinical samples upon receipt into the laboratory and a Direct to PCR protocol that removed the requirement for the RNA extraction step. We anticipate that these methods will have value in driving continued efficiency and effectiveness within all large scale viral diagnostic testing laboratories

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pig domestication had begun by ~10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ~8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic con-tribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process