Biology subjects

Buckley, H.

Publications and source records attributed to Buckley, H..

6 recordsLinked to original sources

bioRxiv2023

Exploring archaeogenetic studies of dental calculus to shed light on past human migrations in Oceania

The Pacific islands have experienced multiple waves of human migrations, providing a case study for exploring the potential of using the microbiome to study human migration. We performed a metagenomic study of archaeological dental calculus from 103 ancient individuals, originating from 12 Pacific islands and spanning a time range of [~]3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone from the Pacific, and comparable to that seen in calculus from temperate regions. Variation in the microbial community composition was minimally driven by time period and geography within the Pacific, while comparison with samples from Europe, Africa, and Asia reveal the microbial communities of Pacific calculus samples to be distinctive. Phylogenies of individual bacterial species in Pacific calculus reflect geography. Archaeological dental calculus shows potential to yield information about past human migrations, complementing studies of the human genome.

microbiology↗

bioRxiv2022

The heterogeneous distribution of extracellular adenosine reveals a myeloid-dependent axis, shaping the immunosuppressive microenvironment in pancreatic ductal adenocarcinoma

The prognosis for patients with pancreatic ductal adenocarcinoma (PDAC) remains extremely poor. It has been suggested that the adenosine pathway contributes to the ability of PDAC to evade the immune system and its resistance to immunotherapies (Immuno-Oncology Therapy, IOT), by generating extracellular adenosine (eAdo). Using genetically engineered allograft models of PDAC in syngeneic mice with differential immune infiltration and response to IOT, we showed enrichment of the adenosine pathway in tumour-infiltrating immune cells (in particular, myeloid populations). Using MS-Imaging, we showed that extracellular adenosine distribution is heterogeneous in tumours, with high concentrations in hypoxic margins that surround necrotic areas, associated with a rich myeloid infiltration, demonstrated using Imaging Mass Cytometry (IMC). Pro-tumorigenic M2 macrophages express high levels of the Adora2a receptor; particularly in the IOT resistant model. Blocking the in vivo formation and function of eAdo (Adoi), using a combination of anti-CD73 antibody and an Adora2a inhibitor slowed tumour growth and reduced metastatic burden. In addition, blocking the adenosine pathway improved the efficacy of combinations of cytotoxic agents or immunotherapy. Finally, Adoi remodelled the tumour microenvironment (TME), as evidenced by reduced infiltration of M2 macrophages and Tregs. RNAseq analysis showed that genes related to immune modulation, hypoxia and tumour stroma were downregulated following Adoi and a specific adenosine signature derived from this is associated with a poorer prognosis in patients with PDAC. The formation of eAdo appears to promote the development of the immunosuppressive TME in PDAC, contributing to its resistance to conventional and novel therapies. Therefore, inhibition of the adenosine pathway may represent a strategy to modulate the stroma and improve therapy response in patients with PDAC.

cancer biology↗

bioRxiv2021

LOTVS: a global collection of permanent vegetation plots

Analysing temporal patterns in plant communities is extremely important to quantify the extent and the consequences of ecological changes, especially considering the current biodiversity crisis. Long-term data collected through the regular sampling of permanent plots represent the most accurate resource to study ecological succession, analyse the stability of a community over time and understand the mechanisms driving vegetation change. We hereby present the LOng-Term Vegetation Sampling (LOTVS) initiative, a global collection of vegetation time-series derived from the regular monitoring of vascular plants in permanent plots. With 79 datasets from five continents and 7789 vegetation time-series monitored for at least six years and mostly on an annual basis, LOTVS possibly represents the largest collection of temporally fine-grained vegetation time-series derived from permanent plots and made accessible to the research community. As such, it has an outstanding potential to support innovative research in the fields of vegetation science, plant ecology and temporal ecology.

ecology↗

bioRxiv2018

Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from thirteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100-1700 years ago). Early agriculturalists from Man Bac in Vietnam possessed a mixture of East Asian (southern Chinese farmer) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. In a striking parallel with Europe, later sites from across the region show closer connections to present-day majority groups, reflecting a second major influx of migrants by the time of the Bronze Age.

genetics↗

bioRxiv2018

Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

evolutionary biology↗

bioRxiv2018

Population Turnover in Remote Oceania Shortly After Initial Settlement

Ancient DNA analysis of three individuals dated to ~3000 years before present (BP) from Vanuatu and one ~2600 BP individual from Tonga has revealed that the first inhabitants of Remote Oceania (\"First Remote Oceanians\") were almost entirely of East Asian ancestry, and thus their ancestors passed New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture with the Papuan groups they encountered [1]. However, all present-day populations in Near and Remote Oceania harbor 25-100% Papuan ancestry, implying that there must have been at least one later stream of migration eastward from Near Oceania. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu ranging from 3,000-150 BP, along with 185 present-day Vanuatu individuals from 18 islands. We show that people of almost entirely Papuan ancestry had arrived in Vanuatu by 2400 BP, an event that coincided with the end of the Lapita cultural period, changes in skeletal morphology, and the cessation of long-distance trade between Near and Remote Oceania [2]. First Remote Oceanian ancestry subsequently increased via admixture but remains at 10-20% in most islands. Through a fine-grained comparison of ancestry profiles in Vanuatu and Polynesia with diverse groups in Near Oceania, we find that Papuan ancestry in Vanuatu is consistent with deriving from the Bismarck Archipelago instead of the geographically closer Solomon Islands. Papuan ancestry in Polynesia also shows connections to the ancestry profiles present in the Bismarck Archipelago but is more similar to Tolai from New Britain and Tutuba from Vanuatu than to the ancient Vanuatu individuals and the great majority of present-day Vanuatu populations. This suggests a third eastward stream of migration from Near to Remote Oceania bringing a different type of Papuan ancestry.

genetics↗