This dissertation develops a machine learning solution for authenticating ancient mitochondrial DNA (mtDNA) using sequencederived features. While existing tools like mapDamage2 analyze postmortem degradation patterns at the read level, we demonstrate that features extracted from FASTA files (CG content, normalized relative compression, etc.) can predict ancient status with high accuracy (up to 92%) without requiring alignment files. The key innovations include a curated database of reconstructed genomes (ancient and modern) compliant with FAIR principles, a two-class XGBoost classifier (Ancient or Modern) with high accuracy, and validation using synthetic data with induced mutation rates. The method reduces computational requirements since, unlike traditional pipelines, it does not rely on read-level data. Limitations include geographic bias in the training data (predominantly European samples) and reduced accuracy for specimens older than 2,500 years. Future work will extend the model to nuclear DNA and metagenomic sources.

Several species of the genus Ceiba (Malvaceae) are ethnopharmacologically used. Thus, this study aimed to investigate the in vitro beneficial properties of the aqueous stem bark extract of Ceiba speciosa. The extract presented a great amount of phenolic compounds (117.4 ± 6.2 mg GAE/g). The antioxidant activity was assessed by DPPH (IC50 = 42.87 μg/mL), ORAC (2351.17 μmol TE/g) and FRAP (235.94 μM FeSO4/g) methods. In addition, the extract reduced MCF-7 cell viability as assessed by MTT. However, it prevented mitochondrial membrane depolarization and reduced caspase-9 activity induced by hydrogen peroxide. In conclusion, these findings indicate the extract is an excellent source of natural antioxidants and is able to protect ROS-induced cell death. Therefore, C. speciosa extract may possess beneficial properties for application in pharmaceutical industry as an antioxidant. However, further studies to better elucidate its mechanisms and to isolate its active compounds are required.

The Iberian Peninsula, in southwestern Europe, is home to a distinctive freshwater fish fauna, predominantly composed of endemic species. This is a consequence of the prolonged isolation from western Europe caused by the Pyrenees, the diverse geological and climatic gradients, and the isolation of river basins. Freshwater and diadromous fishes have diversified in the Iberian Peninsula and include 72 currently recognized native species, 50 of which are endemic to the region. Habitat loss and degradation, the introduction of invasive species, and climate change have placed Iberian freshwater and diadromous fishes among the most threatened groups of vertebrates, with some species on the brink of extinction. Here, we present 60 new complete mitochondrial genome assemblies out of the 109 freshwater and diadromous fish species found in the Iberian Peninsula, including the mitogenomes of 37 endemics. These resources are crucial for characterising the mitochondrial evolution of species, reconstructing phylogeny and paleogeography, advancing species identification, delineation, and monitoring, and ultimately supporting conservation planning.

Helicoverpa armigera, one of the world’s most destructive crop pests, was first documented in Brazil in 2013. Within a few months, this polyphagous insect had spread over the Northeast and Central-West of Brazil, causing great agricultural losses. With several reports of populations resistant to pesticides and Bt crops around the world, there is great concern about the spread of this pest in Brazil. There is confusion about the actual distribution of this species due to the high morphological similarity with the native corn earworm Helicoverpa zea, which may also coexist with H. armigera in the field. Our aims here were (i) to confirm its presence in the State of Minas Gerais, one of the most important agricultural regions in the country; and (ii) to assess the co-occurrence of this pest with the congeneric corn earworm H. zea. Using molecular screening, we confirmed the presence of H. armigera in Bt-crops of soybean and cotton, and non-Bt-crops of soybean, cotton and maize. Mixed infestations of H. armigera with H. zea were found in non-Bt maize (Viçosa, Southeastern Minas Gerais). These results highlight the need for adequate control strategies for H. armigera in Brazil, to deal with its polyphagous feeding habits, high dispersal capacity and possible risks of hybridization with congeneric species.

Recent years have seen considerable advances in our understanding of the particular physiological roles of the constituent enzymes of the tricarboxylic acid (TCA) cycle. Despite acquiring a fairly comprehensive overview of the functional importance of these proteins relatively little is known concerning how this important pathway is regulated. In this review we concentrate on the mitochondrial reactions since this organelle is the only one in which a full cycle can, at least theoretically, operate. We summarize what is known about the regulation of the enzymes of the pathway both from historical kinetic studies as well as discussing more recent transcriptional and proteomic studies and our enhanced understanding of subcellular compartmentation within the context of metabolic regulation.

It has long been recognized that photosynthesis and respiration in the plant cell must be intimately linked, given that they share carbon dioxide and oxygen as substrate and product or as product and substrate, respectively (for review, see Siedow and Day, 2000). While the core reaction schemes of the pathways of photosynthesis, respiration, and the associated process of photorespiration are well defined, it is only since the advent and widespread adoption of reverse genetic strategies that the high level of interaction between them has begun to be fully realized (Bauwe et al., 2010; Sweetlove et al., 2010). However, the exact contribution of each pathway to energy status is dependent on cell type, and fundamental questions such as the degree of inhibition of the tricarboxylic acid (TCA) cycle in the light remain somewhat controversial. Here, we will outline current understanding of the influence of mitochondrial function, focusing almost exclusively on the illuminated leaf of C3 plants and taking the majority of our case studies from tomato (Solanum lycopersicum) and Arabidopsis (Arabidopsis thaliana). We contend that, having achieved a more comprehensive understanding of the interaction between photosynthesis and respiration (and indeed also photorespiration), the manipulation of mitochondrial metabolism and machinery has recently emerged as a novel potential means to enhance photosynthesis.

Abstract Background: Although not fully understood, oxidative stress has been implicated in the pathogenesis of different autoimmune diseases such as systemic sclerosis. Accumulating evidence indicates that oxidative stress can induce mitochondrial DNA (mtDNA) damage and variations in mtDNA copy number (mtDNAcn). Objective: The aim of this study was to explore mtDNAcn and oxidative DNA damage byproducts in peripheral blood of patients with systemic sclerosis and healthy controls. Methods: Forty six patients with systemic sclerosis and forty nine healthy subjects were studied. Quantitative real-time PCR used to measure the relative mtDNAcn and the oxidative damage (oxidized purines) of each sample. Results: The mean mtDNAcn was lower in patients with systemic sclerosis than in healthy controls whereas the degree of mtDNA damage was significantly higher in cases as compared to controls. Moreover, there was a negative correlation between mtDNAcn and oxidative DNA damage. Study limitations: The lack of simultaneous analysis and quantification of DNA oxidative damage markers in serum or urine of patients with systemic sclerosis and healthy controls. Conclusion: These data suggest that alteration in mtDNAcn and increased oxidative DNA damage may be involved in the pathogenesis of systemic sclerosis.