U-Th dating, taphonomy, and taxonomy of shell middens at Klasies River main site indicate stable and systematic coastal exploitation by MIS 5c-d

The archaeological record, particularly of shellfish, from the Klasies River main site (KRM) is important in understanding the fluctuating nature of coastal occupational patterns and changing coastal ecologies. In this paper, we provide new uranium–thorium (U-Th) dates for one of the earlier phases of coastal exploitation at KRM, and the microstratigraphic analyses generate novel information about the taphonomy of shell-bearing deposits from the Later Stone Age (LSA) to the MSA I period that, in turn, provide a broader context for middening at the site. A wide range of syndepositional taphonomic processes related to human activities and post-depositional effects include burning, fragmentation and compaction, chemical alteration, and cementation. Despite such issues influencing recovery, shellfish data are informative and are presented from three layers of the Witness Baulk: Shell Midden One (SMONE), Black Occupational Soils (BOS), and Silty Black Soils (SBLS). These coarse shell midden deposits exhibit visible decalcification coupled with cementation with secondary carbonate formation in association with conditions of high moisture and soft sedimentation deformation of the underlying sediments of SBLS. This stratigraphy section is chronologically anchored for the first time using U-Th dating of speleothems associated with a hiatus after the deposition of BOS. The three ages, 110,060 ± 1,100, 109,800 ± 970, and 106,000 ± 2,100 years, place the BOS layer as the base of the SASL sub-member at over 110 ka, making the underlying middens from the LBS member even older. The zooarchaeological analyses of the three layers indicate coastal ecological changes from more sheltered conditions prior to the hiatus, with the exploitation of alikreukel and brown mussels predominating. Before 110 ka, in BOS and SBLS, more exposed coastal conditions occurred, and the diversity of exploited shellfish increased. SMONE and BOS are associated with MSA II/Mossel Bay lower lithic technology and SBLS with MSA I technology, indicating asynchronous coastal ecological and technological changes. The MIS 5c-d evidence for early coastal occupation at KRM provides details on the period during which coastal occupation became stable and systematic on the South African coast and puts the KRM amongst the handful of sites with shell-bearing deposits, occurring prior to 110 ka in South Africa.publishedVersio

Geoarchaeological investigation of occupation deposits in Blombos Cave in South Africa indicate changes in site use and settlement dynamics in the southern Cape during MIS 5b-4

The archaeological assemblage recovered from the Middle Stone Age (MSA) levels in Blombos Cave, South Africa, is central to our understanding of the development of early modern humans. Here, we demonstrate that the cultural and technological innovations inferred from the Blombos Cave MSA record also correlate with significant shifts in site use and occupational intensity. Through a comprehensive geoarchaeological investigation of three MSA occupation phases, we identified distinct diachronic trends in the frequency of visits and the modes of occupation. During the earliest phases (ca. 88–82 ka), humans inhabited the cave for more extended periods, but cave visits were not frequent. During the later phases (ca. 77–72 ka), the cave was more regularly visited but for shorter periods each time. We argue that these changes in local occupational intensity, which also coincide with shifts in vegetation, sea levels, and subsistence, can best be explained by broader changes in hunter-gatherer mobility strategies and occupation patterns. Fundamental changes in regional settlement dynamics during Marine Oxygen Isotope Stages 5b-4 would have significantly affected the nature and frequency of social interaction within and between prehistoric populations living in the southern Cape, a scenario that ultimately may explain some of the social and technological advances that occurred there during this time frame.publishedVersio

Reconstructing formation processes at the Canary Islands indigenous site of Belmaco Cave (La Palma, Spain) through a multiproxy geoarchaeological approach

The indigenous populations of La Palma (Canary Islands), who arrived on the island from Northwest Africa ca. 2000 years B.P., were predominantly pastoralists. Yet, many aspects of their subsistence economy such as the procurement, management, and use of wild plant resources remain largely unknown. To explore this, we studied the 600–1100-year-old archaeological site of Belmaco Cave, which comprises a stratified sedimentary deposit representative of a fumier. Here, we present a high-resolution, multiproxy geoarchaeological study combining soil micromorphology, lipid biomarker analysis, X-ray diffraction, μ-X-ray diffraction, μ-X-ray fluorescence, Fourier transform infrared spectroscopy, and μ-Fourier transform infrared spectroscopy, to characterize formation processes and explore plant sources. Recurrent goat/sheep habitation and maintenance activities are represented by interstratified layers of unburned dung, charcoal-rich sediment, and dung ash. Lipid biomarker data show a herd diet mainly composed of herbaceous plants, which is key to understanding the mobility of indigenous shepherds. Our results also revealed an unusual suite of authigenic minerals including hazenite, aragonite, and sylvite, possibly formed through diagenetic processes involving interaction between ash, dung, urine, volcanogenic components, and bacterial activity, coupled with arid and alkaline conditions. Our study shows the potential of a multiproxy approach to a fumier deposit in a volcanogenic sedimentary context.publishedVersio

Hunter-gatherer environments at the Late Pleistocene sites of Mwanganda's Village and Bruce, northern Malawi

Mwanganda's Village (MGD) and Bruce (BRU) are two open-air site complexes in northern Malawi with deposits dating to between 15 and 58 thousand years ago (ka) and containing Middle Stone Age (MSA) lithic assemblages. The sites have been known since 1966 and 1965, respectively, but lacked chronometric and site formation data necessary for their interpretation. The area hosts a rich stone artifact record, eroding from and found within alluvial fan deposits exhibiting poor preservation of organic materials. Although this generally limits opportunities for site-based environmental reconstructions, MGD and BRU are located at the distal margins of the alluvial fan, where lacustrine lagoonal deposits were overprinted by a calcrete paleosol. This has created locally improved organic preservation and allowed us to obtain ecological data from pollen, phytoliths, and pedogenic carbonates, producing a regional- to site-scale environmental context for periods of site use and abandonment. Here, we integrate the ecological data into a detailed site formation history, based on field observations and micromorphology, supplemented by cathodoluminescence microscopy and μ-XRF. By comparing local, on-site environmental proxies with more regional indicators, we can better evaluate how MSA hunter-gatherers made decisions about the use of resources across the landscape. Our data indicate that while tree cover similar to modern miombo woodland and evergreen gallery forest prevailed at most times, MSA hunter-gatherers chose more locally open environments for activities that resulted in a lithic artifact record at multiple locations between 51 and 15 ka.publishedVersio

Early human impacts and ecosystem reorganization in southern-central Africa

Modern Homo sapiens engage in substantial ecosystem modification, but it is difficult to detect the origins or early consequences of these behaviors. Archaeological, geochronological, geomorphological, and paleoenvironmental data from northern Malawi document a changing relationship between forager presence, ecosystem organization, and alluvial fan formation in the Late Pleistocene. Dense concentrations of Middle Stone Age artifacts and alluvial fan systems formed after ca. 92 thousand years ago, within a paleoecological context with no analog in the preceding half-million-year record. Archaeological data and principal coordinates analysis indicate that early anthropogenic fire relaxed seasonal constraints on ignitions, influencing vegetation composition and erosion. This operated in tandem with climate-driven changes in precipitation to culminate in an ecological transition to an early, pre-agricultural anthropogenic landscape.info:eu-repo/semantics/publishedVersio

Evolution of long-term vaccine-induced and hybrid immunity in healthcare workers after different COVID-19 vaccine regimens

BACKGROUND: Both infection and vaccination, alone or in combination, generate antibody and T cell responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the maintenance of such responses-and hence protection from disease-requires careful characterization. In a large prospective study of UK healthcare workers (HCWs) (Protective Immunity from T Cells in Healthcare Workers [PITCH], within the larger SARS-CoV-2 Immunity and Reinfection Evaluation [SIREN] study), we previously observed that prior infection strongly affected subsequent cellular and humoral immunity induced after long and short dosing intervals of BNT162b2 (Pfizer/BioNTech) vaccination. METHODS: Here, we report longer follow-up of 684 HCWs in this cohort over 6-9 months following two doses of BNT162b2 or AZD1222 (Oxford/AstraZeneca) vaccination and up to 6 months following a subsequent mRNA booster vaccination. FINDINGS: We make three observations: first, the dynamics of humoral and cellular responses differ; binding and neutralizing antibodies declined, whereas T and memory B cell responses were maintained after the second vaccine dose. Second, vaccine boosting restored immunoglobulin (Ig) G levels; broadened neutralizing activity against variants of concern, including Omicron BA.1, BA.2, and BA.5; and boosted T cell responses above the 6-month level after dose 2. Third, prior infection maintained its impact driving larger and broader T cell responses compared with never-infected people, a feature maintained until 6 months after the third dose. CONCLUSIONS: Broadly cross-reactive T cell responses are well maintained over time-especially in those with combined vaccine and infection-induced immunity ("hybrid" immunity)-and may contribute to continued protection against severe disease

Secretion of Genome-Free Hepatitis B Virus – Single Strand Blocking Model for Virion Morphogenesis of Para-retrovirus

As a para-retrovirus, hepatitis B virus (HBV) is an enveloped virus with a double-stranded (DS) DNA genome that is replicated by reverse transcription of an RNA intermediate, the pregenomic RNA or pgRNA. HBV assembly begins with the formation of an “immature” nucleocapsid (NC) incorporating pgRNA, which is converted via reverse transcription within the maturing NC to the DS DNA genome. Only the mature, DS DNA-containing NCs are enveloped and secreted as virions whereas immature NCs containing RNA or single-stranded (SS) DNA are not enveloped. The current model for selective virion morphogenesis postulates that accumulation of DS DNA within the NC induces a “maturation signal” that, in turn, triggers its envelopment and secretion. However, we have found, by careful quantification of viral DNA and NCs in HBV virions secreted in vitro and in vivo, that the vast majority of HBV virions (over 90%) contained no DNA at all, indicating that NCs with no genome were enveloped and secreted as empty virions (i.e., enveloped NCs with no DNA). Furthermore, viral mutants bearing mutations precluding any DNA synthesis secreted exclusively empty virions. Thus, viral DNA synthesis is not required for HBV virion morphogenesis. On the other hand, NCs containing RNA or SS DNA were excluded from virion formation. The secretion of DS DNA-containing as well as empty virions on one hand, and the lack of secretion of virions containing single-stranded (SS) DNA or RNA on the other, prompted us to propose an alternative, “Single Strand Blocking” model to explain selective HBV morphogenesis whereby SS nucleic acid within the NC negatively regulates NC envelopment, which is relieved upon second strand DNA synthesis

Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep (Ovis aries)

Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations

Quantifying neutralising antibody responses against SARS-CoV-2 in dried blood spots (DBS) and paired sera

The ongoing SARS-CoV-2 pandemic was initially managed by non-pharmaceutical interventions such as diagnostic testing, isolation of positive cases, physical distancing and lockdowns. The advent of vaccines has provided crucial protection against SARS-CoV-2. Neutralising antibody (nAb) responses are a key correlate of protection, and therefore measuring nAb responses is essential for monitoring vaccine efficacy. Fingerstick dried blood spots (DBS) are ideal for use in large-scale sero-surveillance because they are inexpensive, offer the option of self-collection and can be transported and stored at ambient temperatures. Such advantages also make DBS appealing to use in resource-limited settings and in potential future pandemics. In this study, nAb responses in sera, venous blood and fingerstick blood stored on filter paper were measured. Samples were collected from SARS-CoV-2 acutely infected individuals, SARS-CoV-2 convalescent individuals and SARS-CoV-2 vaccinated individuals. Good agreement was observed between the nAb responses measured in eluted DBS and paired sera. Stability of nAb responses was also observed in sera stored on filter paper at room temperature for 28 days. Overall, this study provides support for the use of filter paper as a viable sample collection method to study nAb responses.</p

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice