Framework for quantification of the dynamics of root colonization by pseudomonas fluorescens isolate SBW25

Colonization of the root surface, or rhizoplane, is one of the first steps for soil-borne bacteria to become established in the plant microbiome. However, the relative contributions of processes, such as bacterial attachment and proliferation is not well characterized, and this limits our ability to comprehend the complex dynamics of microbial communities in the rhizosphere. The work presented here addresses this knowledge gap. A model system was developed to acquire quantitative data on the colonization process of lettuce (Lactuca sativa L. cultivar. All Year Round) roots by Pseudomonas fluorescens isolate SBW25. A theoretical framework is proposed to calculate attachment rate and quantify the relative contribution of bacterial attachment to colonization. This allows the assessment of attachment rates on the root surface beyond the short time period during which it can be quantified experimentally. All techniques proposed are generic and similar analyses could be applied to study various combinations of plants and bacteria, or to assess competition between species. In the future this could allow for selection of microbial traits that improve early colonization and maintenance of targeted isolates in cropping systems, with potential applications for the development of biological fertilizers

The impact of injury on apparent survival of whale sharks (Rhincodon typus) in South Ari Atoll Marine Protected Area, Maldives

The whale shark (Rhincodon typus) is an endangered species with a declining global population. The South Ari Atoll Marine Protected Area (SAMPA), Maldives, is one of few locations globally where year-long residency of individuals occurs. This SAMPA aggregation appears to consist almost exclusively of immature males. Due to its year-round residency, this local aggregation is subjected to a high degree of tourism pressure. This ecotourism contributes to the high level of interest and protection offered to whale sharks by the local community. Unfortunately, if regulations are not followed or enforced, tourism can bring with it major stressors, such as accidental injuries. We used POPAN capture-mark-recapture models and lagged identification rate analysis to assess the effect of major injuries on whale shark residency within SAMPA. Injuries may be obtained outside SAMPA. We found individuals with major injuries had a higher apparent survival in the area than those without. Lagged identification rates also demonstrated that sharks with major injuries are more likely to return to the area. We suggest that major injuries result in sharks prolonging their time in the developmental habitat. These findings have implications for individual fitness and the population viability of this endangered species. We propose targeted conservation strategies be considered to protect sharks from further injury. Based on the presented spatio-temporal distributions of sharks, and current local knowledge of sighting patterns, speed limit zones and propeller-exclusion zones should be implemented and enforced. If carried out alongside tourist education, these measures will contribute to the protection of whale sharks within SAMPA and beyond. Furthermore, our results can aid research direction, alongside regulation and enforcement development, at similar sites worldwide.Publisher PDFPeer reviewe

A quantitative framework for studying bacterial colonisation of the rhizoplane

Colonisation of the root surface, or rhizoplane, is one of the first steps for microorganisms within soil to become established in the plant microbiome. However, the timing and relative contributions of processes, such as microbial movement, attachment, and proliferation to colonisation are not well characterized. This limits our ability to comprehend the complex dynamics of microbial communities in soil. The aim of this thesis was to develop a set of experimental and theoretical frameworks that can be used to isolate and quantify key microbial processes involved in rhizoplane colonisation. A model plant and bacterial system, consisting of Pseudomonas fluorescens isolate SBW25, transformed with a fluorescent marker plasmid, and Lettuce (Lactuca sativa) was selected for characterisation. A liquid microcosm system was developed which enabled inoculation of plants with bacterial suspensions and manipulation of the plant following treatment. Using this system, a framework for the independent quantification of bacterial attachment and proliferation on the root surface was developed. This allowed previously indistinguishable components of the colonisation process to be independently quantified. The timing and spatial distribution of colonisation in a granular environment was further analysed through the live imaging of plants grown in transparent soil. A chemotaxis assay was developed for the measurement of bacterial movement in transparent soil in response to plant root exudate. Data from chemotaxis assays was used to construct a model of bacterial diffusion and convection in soil. These novel characterisations of bacterial movement, attachment to the root surface, and proliferation offers new insight into the timing of rhizoplane colonisation by Pseudomonas fluorescens SBW25. The techniques and analyses developed in this thesis could be applied to many different combinations of plants and microorganisms. Potential applications include the selection of microbial traits which improve maintenance of targeted isolates in agricultural systems, and the development of biological fertilizers

An automated work-flow for pinniped surveys : A new tool for monitoring population dynamics

Detecting changes in population trends depends on the accuracy of estimated mean population growth rates and thus the quality of input data. However, monitoring wildlife populations poses economic and logistic challenges especially in complex and remote habitats. Declines in wildlife populations can remain undetected for years unless effective monitoring techniques are developed, guiding appropriate management actions. We developed an automated survey workflow using unmanned aerial vehicles (drones) to quantify the number and size of individual animals, using the well-studied Scandinavian harbour seal (Phoca vitulina) as a model species. We compared ground-based counts using telescopes with manual flights, using a zoom photo/video, and pre-programmed flights producing orthomosaic photo maps. We used machine learning to identify and count both pups and older seals and we present a new method for measuring body size automatically. We evaluate the population’s reproductive success using drone data, historical counts and predictions from a Leslie matrix population model. The most accurate and time-efficient results were achieved by performing pre-programmed flights where individual seals are identified by machine learning and their body sizes are measured automatically. The accuracy of the machine learning detector was 95–97% and the classification error was 4.6 ± 2.9 for pups and 3.1 ± 2.1 for older seals during good light conditions. There was a clear distinction between the body sizes of pups and older seals during breeding time. We estimated 320 pups in the breeding season 2021 with the drone, which is well beyond the expected number, based on historical data on pup production. The new high quality data from the drone survey confirms earlier indications of a deteriorating reproductive rate in this important harbour seal colony. We show that aerial drones and machine learning are powerful tools for monitoring wildlife in inaccessible areas which can be used to assess annual recruitment and seasonal variations in body condition

Novel large-range mitochondrial DNA deletions and fatal multisystemic disorder with prominent hepatopathy

► Expanded array of mtDNA deletions. ► Pearson syndrome with prominent hepatopathy associated with single mtDNA deletions. ► Detection of deletions in fibroblasts and blood avoids muscle and liver biopsy. ► Look for mtDNA deletions before to study nuclear genes related to mtDNA depletion

Mutations in the NHEJ component XRCC4 cause primordial dwarfism

Non-homologous end joining (NHEJ) is a key cellular process ensuring genome integrity. Mutations in several components of the NHEJ pathway have been identified, often associated with severe combined immunodeficiency (SCID), consistent with the requirement for NHEJ during V(D)J recombination to ensure diversity of the adaptive immune system. In contrast, we have recently found that biallelic mutations in LIG4 are a common cause of microcephalic primordial dwarfism (MPD), a phenotype characterized by prenatal-onset extreme global growth failure. Here we provide definitive molecular genetic evidence supported by biochemical, cellular, and immunological data for mutations in XRCC4, encoding the obligate binding partner of LIG4, causing MPD. We report the identification of biallelic mutations in XRCC4 in five families. Biochemical and cellular studies demonstrate that these alterations substantially decrease XRCC4 protein levels leading to reduced cellular ligase IV activity. Consequently, NHEJ-dependent repair of ionizing-radiation-induced DNA double-strand breaks is compromised in XRCC4 cells. Similarly, immunoglobulin junctional diversification is impaired in cells. However, immunoglobulin levels are normal, and individuals lack overt signs of immunodeficiency. Additionally, in contrast to individuals with LIG4 mutations, pancytopenia leading to bone marrow failure has not bee

Electrochemical, Magnetic, and Electrical Properties of α,ω-Capped Sexithiophene Films. 1. Neutral−Polaron and Polaron−Bipolaron Conductivities

Thin solid films of 14 sexithiophenes variously substituted at the terminal alpha,omega-positions were electrochemically deposited on electrodes by anodic coupling of the corresponding half-capped terthiophenes. Sexithiophene films were investigated by cyclic voltammetry, EQCM, in situ ESR, and in situ conductivity. Reversible oxidation is composed by two separate one-electron steps, the first of which is split into two 0.5-electron steps for most 3,4-ethylenedioxy-substituted terthiophenes. ESR indicates strong magnetic dimerization for the one-electron oxidized species. Conductivity (in the range 10(-4)-10(-1) S cm(-1)) is redox type and develops at the neutral-cation (neutral - polaron) and cation-dication (polaron-bipolaron) levels with values 5-10 times higher for the latter. The influence of steric, electron donor-acceptor, and conjugative effects on conductivity was evaluated by a suitable choice of endcapping substituents.Fundação para a Ciência e a Tecnologia (FCT