The Mechanism For Inhibition Of Vibrio Cholerae Virulence Gene Expression By Bile And Its Fatty Acid Components

Vibrio cholerae is responsible for the diarrheal disease cholera by producing two major virulence factors: cholera toxin (CT) and toxin-coregulated pilus (TCP). During infection, V. cholerae downregulates its motility genes, which are actively expressed in the environment, and upregulates its virulence genes, which are inactive in the environment. Virulence gene transcription is regulated by the major transcriptional activator, ToxT. ToxT is regulated, in part, by host signals, which in turn, make ToxT active or inactive in respect to virulence gene expression. Host signals include temperature and pH as well as the chemical molecules bicarbonate and bile, which are positive and negative effectors of virulence, respectively. Bile is a heterogeneous mixture that includes unsaturated fatty acids (UFAs) that have been directly implicated in virulence gene downregulation. Another small molecule, virstatin, has also been shown to cause virulence gene downregulation. This dissertation focuses on the mechanism by which bile and its UFA components, specifically linoleic acid, downregulate virulence gene expression. The first chapter focuses on the decreased binding affinity of ToxT for various virulence gene promoters at the ToxT binding sites, termed toxboxes. These toxboxes come in different configurations and orientations, and while most promoters have two toxboxes, aldA only has one. I showed that linoleic acid can enter the cell where it can go into the cytoplasm and then interact with ToxT. It has been hypothesized that UFAs cause decreased dimerization; however at PaldA, linoleic acid still had an effect. Virstatin, which has been shown directly to decrease dimerization of ToxT, did not have an effect on ToxT DNA binding at PaldA. This suggests a mechanism in which UFAs do not affect dimerization but can affect monomeric ToxT binding to DNA. In chapter two, we characterize an unstructured region of the N-terminal domain of ToxT in response to bile and UFAs. By mutating each of the 10 amino acids in the region, we discovered a mutant, N106F, which had decreased response to bile and UFAs. It also showed decreased response to the positive regulator bicarbonate. Chapter three discusses the possibility of using conjugated linoleic acid (CLA) as a therapeutic or prophylactic upon exposure to V. cholerae. The in vitro work showed a strong decrease of ToxT activity in response to CLA on both gene expression and DNA binding. In the infant mouse model, CLA did not inhibit colonization, but in the rabbit ileal loop model CT production was significantly decreased, suggesting that CLA may work to reduce cholera symptoms. In the last chapter, we looked at the possibility of using fluorescence-activated cell screening (FACS) in addition to transposon mutagenesis as a method to collect mutants that were insensitive to bile. Use of this technique would allow us to discover genes that were directly responsible for the effects of bile. Several genes were identified, including pckA, which is involved in metabolism, but could have a role in virulence. When deleted, however, the bacteria were only slightly less sensitive to bile than wild-type. FACS genetic screening is still a useful technique that, if further explored, could elucidate other genes involved in responding to effectors of virulence

Contribuição para o estudo da morfodinâmica da embocadura da Ria de Aveiro

Doutoramento em FisicaOver the years it was observed at the Ria de Aveiro lagoon inlet, near the head of the north breakwater, a depth increase that might threaten the stability of this structure. A trend of accretion in the navigation channel of this lagoon is observed, endangering the navigation in this region. In order to understand the origin of these and other trends observed, the knowledge of the sediment transport in the study area is imperative. The main aim of this work is understanding the dominant physical processes in the sediment transport of sediment at the Ria de Aveiro lagoon inlet and adjacent area, improving knowledge of this region morphodynamics. The methodology followed in this study consisted in the analyzes of the topohydrographic surveys performed by the Administration of the Aveiro Harbor, and in the numerical simulations results performed with the morphodynamic modeling system MORSYS2D. The analysis of the surveys was performed by studying the temporal evolution of the bathymetry. The numerical analysis was based on the implementation of the model at the study area, sensitivity analysis of the formulations used to compute the sediment transport to the variation of input parameters (e.g. depth, sediment size, tidal currents) and analysis of the sediment uxes and bathymetric changes predicted. The simulations considered as sediment transport forcing the tidal currents only and the coupled forcing of tides and waves. Considering the wave e ect as sediment transport forcing, both monochromatic waves and a wave regime were simulated. The results revealed that the observed residual sediment transport patterns are generated due to the channel con guration. Inside the lagoon the uxes are mainly induced by the tidal currents action, restricting the action of waves to the inlet and adjacent coast. In the navigation channel the residual sediment uxes predicted are directed o - shore with values between 7 and 40 m3=day generating accretions of approximately 10 m3=day for the shallower region and 35 m3=day for the region between the tidal gauge and the tri^angulo das mar es. At the inlet, the residual uxes are approximately 30 m3=day inducing trends of erosion of approximately 20 m3=day. At the North side of the nearshore accretion is predicted, while at the South side is predicted erosion, at the rates of 250 and 1500 m3=day, respectively. It was also concluded that the waves with higher contribution to the residual sediment uxes are those with heights between 4 and 5 m. However, the storm waves with heights bigger than 5 m, despite their 10% of frequency of occurrence are responsible for 25% of the observed sediment transport.Ao longo dos anos observou-se junto ao quebramar norte da embocadura da Ria de Aveiro um aumento da profundidade, que poder a colocar em perigo a estabilidade desta mesma estrutura. E igualmente observada uma tendência de acreção no canal de navegação desta laguna, colocando em risco a navegabilidade nesta região. Para compreender a causa destas tendências e de outras observadas, e necess ario um conhecimento do transporte de sedimentos nesta região de estudo. Este trabalho tem assim como objectivo principal a compreensão dos processos físicos dominantes no transporte de sedimentos na embocadura e area adjacente da Ria de Aveiro, aumentando os conhecimentos da morfodinâmica desta região. A metodologia seguida neste estudo consistiu na análise de levantamentos topohidrográficos realizados pela Administração do Porto de Aveiro e de resultados de simulações num ericas efectuadas com o sistema de modelos morfodinâmico MORSYS2D. A análise dos levantamentos foi feita através do estudo de evolução temporal da batimetria. A análise numérica teve como base a implementação do modelo para a area de estudo, análises de sensibilidade das fórmulas de cálculo do transporte de sedimentos a variação de parâmetros de entrada (por exemplo: profundidade, diâmetro médio do sedimento, velocidade da corrente de mar e), e análise dos resultados numéricos de uxos de sedimentos e de variações batimétricas. As simulações efectuadas consideraram apenas o for camento de correntes de mar e e o forçamento conjunto de mar e e ondas no transporte de sedimentos. No caso do forçamento de ondas foram efectuadas simulações com ondas monocromáticas e com um regime de agitação real. Os resultados revelaram que os padrões observados para o transporte residual de sedimentos têm origem na configuração do canal. Verificou-se também que no interior da laguna os uxos são maioritariamente induzidos pela acção do campo de correntes de mar e, restringindo-se a acção do campo de agitação a embocadura e costa adjacente. No canal de navegação são previstos uxos residuais de sedimentos direccionados para o exterior da laguna que oscilam entre 7 e 40 m3=dia e originam acreções na ordem de 10 m3=dia na região menos profunda e de 35 m3=dia para a região entre o mar egrafo e o triângulo das marés. Na região da embocadura os uxos residuais de sedimentos são de aproximadamente 30 m3=dia gerando tendências de erosão de aproximadamente 20 m3=dia. Na area exterior da embocadura e prevista acreção a Norte da embocadura e erosão a Sul as taxas de 250 e 1500 m3=dia, respectivamente. Concluiu-se ainda que as ondas com maior contributo para o uxo residual de sedimentos têm alturas compreendidas entre 4 e 5 m. No entanto, as ondas de tempestade, com alturas superiores a 5 m, apesar de terem apenas 10% de frequência de ocorrência são respons aveis por 25% do transporte de sedimentos observado

Coastal and regional marine heatwaves and cold spells in the northeastern Atlantic

The latest Intergovernmental Panel on Climate Change (IPCC) report describes an increase in the number and intensity of marine heatwaves (MHWs) and a decrease in marine cold spells (MCSs) in the global ocean. However, these reported changes are not uniform on a regional to local basis, and it remains unknown if coastal areas follow the open-ocean trends. Surface ocean temperature measurements collected by satellites (from 1982–2022) and 13 coastal buoys (from 1990–2022) are analyzed in the northeastern Atlantic and three subregions: the English Channel, Bay of Brest and Bay of Biscay. The activity metric, combining the number of events, intensity, duration and spatial extent, is used to evaluate the magnitude of these extreme events. The results from in situ and satellite datasets for each of the studied regions are quite in agreement, although the satellite dataset underestimates the amplitude of activity for both MHWs and MCSs. This supports the applicability of the method to both in situ and satellite data, albeit with caution on the amplitude of these events. Also, this localized study in European coastal northeastern Atlantic water highlights that similar changes are being seen in coastal and open oceans regarding extreme events of temperature, with MHWs being more frequent and longer and extending over larger areas, while the opposite is seen for MCSs. These trends can be explained by changes in both the mean of and variance in sea-surface temperature. In addition, the pace of evolution and dynamics of marine extreme events differ among the subregions. Among the three studied subregions, the English Channel is the region experiencing the strongest increase in summer MHW activity over the last 4 decades. Summer MHWs were very active in the English Channel in 2022 due to long events, in the Bay of Biscay in 2018 due to intense events and in the Bay of Brest in 2017 due to a high occurrence of events. Winter MCSs were the largest in 1987 and 1986 due to long and intense events in the English Channel. Finally, our findings suggest that at an interannual timescale, the positive North Atlantic Oscillation favors the generation of strong summer MHWs in the northeastern Atlantic, while low-pressure conditions over northern Europe and a high off the Iberian Peninsula in winter dominate for MCSs. A preliminary analysis of air–sea heat fluxes suggests that, in this region, reduced cloud coverage is a key parameter for the generation of summer MHWs, while strong winds and increased cloud coverage are important for the generation of winter MCSs.</p

The marine heatwave west of Ireland in June 2023

The summer of 2023 had been notable for a number of climate extremes: sea ice in the Antarctic dropped to its lowest for the time of year since satellite records began in the 1970s (NASA Earth Observatory, 2023), terrestrial heatwaves engulfed southern Europe and southern United States/Mexico that would have been ‘virtually impossible’ without climate change (WorldWeatherAttribution, 2023), and sea-surface temperatures (SSTs) in the North Atlantic reached their highest since satellite records began in 1982 (NOAA, 2023). In concert with these terrestrial heatwaves and high Atlantic SSTs, a severe marine heatwave(MHW) developed in the eastern North Atlantic, west of Ireland (Figure 1a). Except for a narrow band close to the coast from Greenland to Canada, SSTs everywhere in the North Atlantic were above the 41-yearaverage (1982–2023), with many regions experiencing temperatures 2 degC higher than average. In the study region westof Ireland (highlighted in Figure 1b), the SST reached an impressive 4 degC above average

Deep learning-based prediction of response to HER2-targeted neoadjuvant chemotherapy from pre-treatment dynamic breast MRI: A multi-institutional validation study

Predicting response to neoadjuvant therapy is a vexing challenge in breast cancer. In this study, we evaluate the ability of deep learning to predict response to HER2-targeted neo-adjuvant chemotherapy (NAC) from pre-treatment dynamic contrast-enhanced (DCE) MRI acquired prior to treatment. In a retrospective study encompassing DCE-MRI data from a total of 157 HER2+ breast cancer patients from 5 institutions, we developed and validated a deep learning approach for predicting pathological complete response (pCR) to HER2-targeted NAC prior to treatment. 100 patients who received HER2-targeted neoadjuvant chemotherapy at a single institution were used to train (n=85) and tune (n=15) a convolutional neural network (CNN) to predict pCR. A multi-input CNN leveraging both pre-contrast and late post-contrast DCE-MRI acquisitions was identified to achieve optimal response prediction within the validation set (AUC=0.93). This model was then tested on two independent testing cohorts with pre-treatment DCE-MRI data. It achieved strong performance in a 28 patient testing set from a second institution (AUC=0.85, 95% CI 0.67-1.0, p=.0008) and a 29 patient multicenter trial including data from 3 additional institutions (AUC=0.77, 95% CI 0.58-0.97, p=0.006). Deep learning-based response prediction model was found to exceed a multivariable model incorporating predictive clinical variables (AUC < .65 in testing cohorts) and a model of semi-quantitative DCE-MRI pharmacokinetic measurements (AUC < .60 in testing cohorts). The results presented in this work across multiple sites suggest that with further validation deep learning could provide an effective and reliable tool to guide targeted therapy in breast cancer, thus reducing overtreatment among HER2+ patients.Comment: Braman and El Adoui contributed equally to this work. 33 pages, 3 figures in main tex

MR imaging of therapy-induced changes of bone marrow

MR imaging of bone marrow infiltration by hematologic malignancies provides non-invasive assays of bone marrow cellularity and vascularity to supplement the information provided by bone marrow biopsies. This article will review the MR imaging findings of bone marrow infiltration by hematologic malignancies with special focus on treatment effects. MR imaging findings of the bone marrow after radiation therapy and chemotherapy will be described. In addition, changes in bone marrow microcirculation and metabolism after anti-angiogenesis treatment will be reviewed. Finally, new specific imaging techniques for the depiction of regulatory events that control blood vessel growth and cell proliferation will be discussed. Future developments are directed to yield comprehensive information about bone marrow structure, function and microenvironment