Patterns and drivers of tetrapod diversity and biogeography in the late Palaeozoic and early Mesozoic

Tetrapods (four-limbed vertebrates) invaded the land more than 370 million years ago and began to diversify into a spectacular range of morphologies and life modes, rapidly achieving a global distribution. However, due to the inherent temporal and spatial bias of the fossil record, global patterns of tetrapod diversity and biogeography during critical intervals of the group’s evolution remain unresolved. This thesis focuses on examining the patterns and drivers of tetrapod diversity during two of these key intervals. Firstly, advanced statistical, phylogenetic, and modelling approaches were used to examine the impact of major environmental change on the first tetrapods to emerge onto land during the late Palaeozoic (358–272 million years ago). Next, these approaches were combined with palaeoclimatic reconstructions to examine the influence of climate on tetrapod diversity during the early Mesozoic (237–174 million years ago), when modern vertebrate groups, including the dinosaurs, were originating. Together, the results provide a comprehensive assessment of the impact of sampling biases on estimates of past diversity, as well as providing greater insights into the role of environmental and climate change on tetrapod diversity and biogeography

Rise and diversification of chondrichthyans in the Paleozoic

The Paleozoic represents a key time interval in the origins and early diversification of chondrichthyans (cartilaginous fishes), but their diversity and macroevolution are largely obscured by heterogenous spatial and temporal sampling. The predominantly cartilaginous skeletons of chondrichthyans pose an additional limitation on their preservation potential and hence on the quality of their fossil record. Here, we use a newly compiled genus-level dataset and the application of sampling standardization methods to analyze global total-chondrichthyan diversity dynamics through time from their first appearance in the Ordovician through to the end of the Permian. Subsampled estimates of chondrichthyan genus richness were initially low in the Ordovician and Silurian but increased substantially in the Early Devonian. Richness reached its maximum in the middle Carboniferous before dropping across the Carboniferous/Permian boundary and gradually decreasing throughout the Permian. Sampling is higher in both the Devonian and Carboniferous compared with the Silurian and most of the Permian stages. Shark-like scales from the Ordovician are too limited to allow for some of the subsampling techniques. Our results detect two Paleozoic radiations in chondrichthyan diversity: the first in the earliest Devonian, led by acanthodians (stem-group chondrichthyans), which then decline rapidly by the Late Devonian, and the second in the earliest Carboniferous, led by holocephalans, which increase greatly in richness across the Devonian/Carboniferous boundary. Dispersal of chondrichthyans, specifically holocephalans, into deeper-water environments may reflect a niche expansion following the faunal displacement in the aftermath of the Hangenberg extinction event at the end of the Devonian

Supporting Women In Engineering and Technology Through A Collaborative Practice And Support Network Using Targeted Interventions

Despite ongoing efforts to recruit and retain women in third level engineering programmes in Ireland, there is still a lack of diversity in these programmes with typically fewer than 20% of students being female. This paper will describe the evolution of a female focused university wide network called WITU (Women in Technology United), which aims to retain female students in engineering and technology programmes, and to increase the number of gender minorities coming onto these programmes. It is also a response to the Sustainable Development Goals, particularly, SDG 4 (quality education), and SDG 5 (gender equality), and addresses actions highlighted in a recent Athena Swan review in our University. The network was formed in 2020 and extended to become University wide during lockdown, which in itself presented specific challenges. This paper describes the activities of the WITU network which runs events and celebrations for female students on our engineering and technology programmes such as ‘Meet & Greet’ events for incoming year one students, scholarship workshops, coding camps and International Women’s Day celebrations. The events are run collaboratively with students, academics and employer networks, with participation from recent female graduate role models, who are contributing to the wider engineering community. This paper describes these events and their impact on participants. Outcomes and feedback from participants show the critical role of these types of targeted interventions in supporting women and gender minorities and address some of the most pressing global challenges relating to the abovementioned SDGs

Scleromochlus and the early evolution of Pterosauromorpha

Pterosaurs, the first vertebrates to evolve powered flight, were key components of Mesozoic terrestrial ecosystems from their sudden appearance in the Late Triassic until their demise at the end of the Cretaceous1,2,3,4,5,6. However, the origin and early evolution of pterosaurs are poorly understood owing to a substantial stratigraphic and morphological gap between these reptiles and their closest relatives6, Lagerpetidae7. Scleromochlus taylori, a tiny reptile from the early Late Triassic of Scotland discovered over a century ago, was hypothesized to be a key taxon closely related to pterosaurs8, but its poor preservation has limited previous studies and resulted in controversy over its phylogenetic position, with some even doubting its identification as an archosaur9. Here we use microcomputed tomographic scans to provide the first accurate whole-skeletal reconstruction and a revised diagnosis of Scleromochlus, revealing new anatomical details that conclusively identify it as a close pterosaur relative1 within Pterosauromorpha (the lagerpetid + pterosaur clade). Scleromochlus is anatomically more similar to lagerpetids than to pterosaurs and retains numerous features that were probably present in very early diverging members of Avemetatarsalia (bird-line archosaurs). These results support the hypothesis that the first flying reptiles evolved from tiny, probably facultatively bipedal, cursorial ancestors1

Raman Spectroscopy of Lymphocytes for the Identification of Prostate Cancer Patients with Late Radiation Toxicity Following Radiotherapy

The success of radiotherapy in tumour control depends on the total dose given. However, the tolerance of the normal tissues surrounding the tumour limits this dose. It is not known why some patients develop radiation toxicity and, currently, it is not possible to predict before treatment which patients will experience adverse effects. Thus, there is an unmet clinical need for a new test to identify patients at risk of radiation toxicity. Here, we report a new approach based on Raman spectroscopy.Blood samples were collected from 42 patients who had undergone radiotherapy for prostate cancer and had shown either severe or no/minimal late radiation toxicity in follow up. Radiation response was assessed following in vitro irradiation using Raman spectroscopy in addition to the G2 chromosomal radiosensitivity assay and the H2AX DNA damage assay.A Partial Least Squares Discriminant Analysis model was developed to classify patients using known radiation toxicity scores. A sensitivity of 95%, specificity of 92% and overall accuracy of 93% was achieved. In the future, this technology may have potential to lead to individualised patient radiotherapy by identifying which patients are at risk of radiation toxicity

Vibrational Spectroscopy of Liquid Biopsies for Prostate Cancer Diagnosis

Background: Screening for prostate cancer with prostate specific antigen and digital rectal examination allows early diagnosis of prostate malignancy but has been associated with poor sensitivity and specificity. There is also a considerable risk of over-diagnosis and overtreatment, which highlights the need for better tools for diagnosis of prostate cancer. This study investigates the potential of high throughput Raman and Fourier Transform Infrared (FTIR) spectroscopy of liquid biopsies for rapid and accurate diagnosis of prostate cancer. Methods: Blood samples (plasma and lymphocytes) were obtained from healthy control subjects and prostate cancer patients. FTIR and Raman spectra were recorded from plasma samples, while Raman spectra were recorded from the lymphocytes. The acquired spectral data was analysed with various multivariate statistical methods, principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and classical least squares (CLS) fitting analysis. Results: Discrimination was observed between the infrared and Raman spectra of plasma and lymphocytes from healthy donors and prostate cancer patients using PCA. In addition, plasma and lymphocytes displayed differentiating signatures in patients exhibiting different Gleason scores. A PLS-DA model was able to discriminate these groups with sensitivity and specificity rates ranging from 90% to 99%. CLS fitting analysis identified key analytes that are involved in the development and progression of prostate cancer. Conclusions: This technology may have potential as an alternative first stage diagnostic triage for prostate cancer. This technology can be easily adaptable to many other bodily fluids and could be useful for translation of liquid biopsy-based diagnostics into the clinic

Effect of hemolysis on Fourier transform infrared and Raman spectra of blood plasma

Hemolysis is a very common phenomenon and is referred as the release of intracellular components from red blood cells to the extracellular fluid. Hemolyzed samples are often rejected in clinics due to the interference of hemoglobin and intracellular components in laboratory measurements. Plasma and serum based vibrational spectroscopy studies are extensively applied to generate spectral biomarkers for various diseases. However, no studies have reported the effect of hemolysis in blood based vibrational spectroscopy studies. This study was undertaken to evaluate the effect of hemolysis on infrared and Raman spectra of blood plasma. In this study, prostate cancer plasma samples (n = 30) were divided into three groups (nonhemolyzed, mildly hemolyzed, and moderately hemolyzed) based on the degree of hemolysis and FTIR and Raman spectra were recorded using high throughput (HT)-FTIR and HT-Raman spectroscopy. Discrimination was observed between the infrared and Raman spectra of nonhemolyzed and hemolyzed plasma samples using principal component analysis. A classical least square fitting analysis showed differences in the weighting of pure components in nonhemolyzed and hemolyzed plasma samples. Therefore, it is worth to consider the changes in spectral features due to hemolysis when comparing the results within and between experiments

Prediction of DNA Damage and G2 Chromosomal Radio-Sensitivity Ex-vivo in Peripheral Blood Mononuclear Cells with Label-Free Raman Microspectroscopy

Liquid biopsies are a potentially rich store of biochemical information that can be linked to an individual’s response to therapeutic treatments, including radiotherapy, and which may ultimately play a role in the individualization of treatment regimens. Peripheral blood mononuclear cells (PBMCs) can be used for the biochemical profiling of the individual, but also, being living cells, can provide insights into the individuals response to ionizing radiation exposure