A Systems Biology Approach to Investigating Host-Pathogen Interactions in Infection with Burkholderia pseudomallei

This thesis applies systems approaches in order better to understand host-pathogen interactions in infectious diseases; it focuses on the intracellular bacterium Burkholderia pseudomallei, the causative agent of the human disease melioidosis. Little is known about the epigenetic changes in host cells during infection. This study assesses genome-wide patterns of the epigenetic marker DNA methylation in host cells following infection with B. pseudomallei. The studies of this thesis concern the infection of human macrophage-like U937 cells with B. pseudomallei and the DNA methylation levels were measured during the early stages of infection. Analyses reveal significant changes in infected cells (compared to uninfected controls) at multiple locations in the host DNA. Most of the methylation changes in infected cells are losses rather than gains in methylation. Five different differential methylation patterns (constant, early, late, transient, and oscillatory) are identified. Differentially methylated sites mapped to genes that may affect virulence, e.g. genes involved in actin regulation, immune response, inflammatory response, and nitric oxide generation. The thesis also measures whole blood DNA methylation profiles of patients diagnosed with melioidosis in order to test the potential role of host DNA methylation in melioidosis. The results demonstrate that patients with melioidosis are separated from healthy subjects by their distinct methylation profiles. The differentially methylated regions reported here can potentially be used as biomarkers for classification and prognostication of infectious diseases. In addition to exploring the changes to the host, a comprehensive understanding of the pathogen interference and the search for countermeasures requires a framework that assesses how the host changes the pathogen metabolically. In this thesis, to understand the role of trehalose pathway in virulence, computational models were constructed by integrating kinetic information, genomics data and literature surveys. Existing kinetic models of the trehalose pathway were implemented and extended allowing for the in silico investigation of the trehalose mutant. Further, metabolic networks of B. pseudomallei were analysed at the genome scale to identify molecular links between trehalose and metabolic pathways such as glycolysis. The genome- scale reconstruction of the B. pseudomallei metabolic network was used to simulate growth under different conditions and predict the effects of gene knockouts. This thesis not only expands the existing knowledge about B. pseudomallei infection, the novel approaches employed here will stimulate a wider understanding of the applications of systems biology to host-pathogen research and defence needs

Pregnancy has a minimal impact on the acute transcriptional signature to vaccination.

Vaccination in pregnancy is an effective tool to protect both the mother and infant; vaccines against influenza, pertussis and tetanus are currently recommended. A number of vaccines with a specific indication for use in pregnancy are in development, with the specific aim of providing passive humoral immunity to the newborn child against pathogens responsible for morbidity and mortality in young infants. However, the current understanding about the immune response to vaccination in pregnancy is incomplete. We analysed the effect of pregnancy on early transcriptional responses to vaccination. This type of systems vaccinology approach identifies genes and pathways that are altered in response to vaccination and can be used to understand both the acute inflammation in response to the vaccine and to predict immunogenicity. Pregnant women and mice were immunised with Boostrix-IPV, a multivalent vaccine, which contains three pertussis antigens. Blood was collected from women before and after vaccination and RNA extracted for analysis by microarray. While there were baseline differences between pregnant and non-pregnant women, vaccination induced characteristic patterns of gene expression, with upregulation in interferon response and innate immunity gene modules, independent of pregnancy. We saw similar patterns of responses in both women and mice, supporting the use of mice for preclinical screening of novel maternal vaccines. Using a systems vaccinology approach in pregnancy demonstrated that pregnancy does not affect the initial response to vaccination and that studies in non-pregnant women can provide information about vaccine immunogenicity and potentially safety

Reproductive and economic evaluation of sexual stimulation during the anestrous period in a commercial farm with neonatal lamb losses

ABSTRACT This study was performed during the anestrous, involving 140 Akkaraman Kangal ewes whose lambs had died in the neonatal stage due to pneumonia and enteritis. Intravaginal sponge containing progesterone was placed to the animals (Group 1, n = 70) on day 0 and removed after 7 days, following which 263 µg PGF2α and 500 IU eCG were administered to the sheep. Ram introduction was performed for 7 days (days 8-14), starting from the day after the removal of the intravaginal sponge (day 8). The animals in Group 2 (n = 70) were not exposed to any treatment. Ram introduction was performed simultaneously in both the groups. To determine the reproductive response, reproductive parameters such as estrous, pregnancy, multiple pregnancy, and embryonic mortality rates, number of births, number of offspring, and fertility, as well as their economic implications, were compared between groups. Each reproductive parameter exhibited a statistical difference between groups. An economically positive trend was observed in the study group compared with the control group. It was concluded that in case of lamb losses in commercial farms that derive profit from lambing, pregnancy of ewes can be achieved via sexual stimulation without waiting for the next breeding season

Identification of potential biomarkers of vaccine inflammation in mice

Systems vaccinology approaches have been used successfully to define early signatures of the vaccine-induced immune response. However, the possibility that transcriptomics can also identify a correlate or surrogate for vaccine inflammation has not been fully explored. We have compared four licensed vaccines with known safety profiles, as well as three agonists of Toll-like receptors (TLRs) with known inflammatory potential, to elucidate the transcriptomic profile of an acceptable response to vaccination versus that of an inflammatory reaction. In mice, we looked at the transcriptomic changes in muscle at the injection site, the lymph node that drained the muscle, and the peripheral blood mononuclear cells (PBMCs)isolated from the circulating blood from 4 hr after injection and over the next week. A detailed examination and comparative analysis of these transcriptomes revealed a set of novel biomarkers that are reflective of inflammation after vaccination. These biomarkers are readily measurable in the peripheral blood, providing useful surrogates of inflammation, and provide a way to select candidates with acceptable safety profiles

Are we ready for the new normal in e-business education? Sentiment analysis of learners' opinions on MOOCs

Introduction. The new digital economy and its constantly evolving paradigm have completely transformed the model of doing business and the learning methods. MOOCs (massive-open-online-courses) and micro-credentials are the educations interfaces, have become an important teaching environment tool. Distance learning has become an indispensable alternative teaching method in updating and transferring classical education materials according to real-world settings, especially for learners in higher education.Aim. The current research is aimed to address the society's readiness and attitude direction to the concept of MOOCs and distance learning, highlighting its emergence and inevitability for educational institutions of all types in order to make a fundamental change in their curricula, especially in e-business courses, which are the most demanded training courses on MOOCs platforms.Methodology and research methods. In the study, the awareness and recognition of the online community on the MOOCs concept is examined. In this direction, Turkish people's perception and attitudes toward MOOCs have been addressed via sentiment analysis on Eksi Sozluk, the largest social communication and discussion platform in Turkey.Results. According to the sentiment analysis results, it has been determined that 52% of respondents have positive judgments on distance education and MOOCs, 29% of responses are neutral and 18% are negative. In general, distance education and MOOCs are perceived as a useful new education model by the Turkish people.Scientific novelty. This paper is the first sentiment analysis of learners' opinions on MOOCs and distance learning in Turkey. Considering the increasing awareness of MOOCs and the need for e-business education, as the most demanded type of MOOCs, this is the first study investigating the priority of these two phenomena within the context of COVID-19.Practical significance. It is thought that this study will contribute to the stakeholders in terms of showing how MOOCs and micro-credentials have a high potential to understanding trends in education especially in the new normal after the COVID-19 pandemic. The holistic education model of institutions has difficulty meeting the competitive nature and result-oriented approach of the e-business ecosystem. This market reality requires the institutions to offer more to-the-point and applied education solutions. In terms of e-business (e-commerce, digital marketing) education, the importance of MOOCs as a solution-focused on “how” rather than “what” has been comprehensively discussed in the paper.Введение. Новая цифровая экономика и ее постоянно развивающаяся парадигма полностью изменили модель ведения бизнеса и методы обучения. MOOK (массовые открытые онлайн-курсы) и программы микроквалификаций - это образовательные интерфейсы, которые превратились в важный инструмент учебной среды. В высших учебных заведениях дистанционное обучение стало незаменимым альтернативным методом преподавания при обновлении и передаче классических учебных материалов в соответствии с реальными условиями.Цель данного исследования - определить готовность и отношение общества к концепции МООК и дистанционного обучения, а также подчеркнуть неизбежность их использования в образовательных учреждениях любого уровня, для того чтобы внести фундаментальные изменения в учебные планы, особенно в программы курсов электронного бизнеса - наиболее востребованного направления образовательных курсов на платформах МООК.Методология и методы исследования. В исследовании анализируется осведомленность общества о концепции MOOK. Восприятие и отношение респондентов к МООК было рассмотрено с помощью сентимент-анализа на платформе Eksi Sozluk (социальная коммуникационно-дискуссионная онлайн-площадка). Результаты. Согласно результатам сентимент-анализа, 52 % опрошенных оценивают дистанционное обучение и МООК положительно, 29 % - нейтрально и 18 % - отрицательно. В общем, дистанционное образование и МООК воспринимаются респондентами как новая полезная модель образования. Научная новизна. Авторы впервые провели сентимент-анализ мнений о МООК и дистанционном обучении среди пользователей этих платформ в Турции. Это первое исследование, в котором рассматривается приоритетность растущей осведомленности о МООК и необходимости в дистанционном бизнес-образовании как наиболее предпочтительном типе МООК в условиях пандемии COVID-19. Практическая значимость. Предполагается, что данное исследование будет способствовать демонстрации заинтересованным участникам того, что МООК и программы микроквалификаций имеют высокий потенциал для осмысления тенденций изменения образования, особенно в условиях модели новой нормальности после пандемии COVID-19. Целостная образовательная модель учреждения образования сопряжена с трудностями в плане соответствия конкурентному характеру и ориентированному на результат подходу экосистемы электронного бизнеса. Рыночная реальность требует, чтобы учебные заведения предлагали более целенаправленные и прикладные образовательные решения для развития данной сферы обучения. Что касается курсов электронного бизнеса (электронная коммерция, цифровой маркетинг), то важность MOOК как решения, ориентированного на то, как, а не что, подробно обсуждается в статье.The present research is supported by Inonu University Scientific Research Projects Coordination Unit (Project No. SBA-2021-2442).Данное исследование поддержано Отделом координации научно-исследовательских проектов Университета Инёню (проект № SBA-2021-2442)

Tools for Assessing the Protective Efficacy of TB Vaccines in Humans: in vitro Mycobacterial Growth Inhibition Predicts Outcome of in vivo Mycobacterial Infection.

Tuberculosis (TB) remains a leading global cause of morbidity and mortality and an effective new vaccine is urgently needed. A major barrier to the rational development of novel TB vaccines is the lack of a validated immune correlate or biomarker of protection. Mycobacterial Growth Inhibition Assays (MGIAs) provide an unbiased measure of ability to control mycobacterial growth in vitro, and may represent a functional correlate of protection. However, the biological relevance of any potential correlate can only be assessed by determining the association with in vivo protection from either a controlled mycobacterial infection or natural development of TB disease. Our data demonstrate that the direct MGIA using peripheral blood mononuclear cells (PBMC) is measuring a biologically relevant response that correlates with protection from in vivo human BCG infection across two independent cohorts. This is the first report of an MGIA correlating with in vivo protection in the species-of-interest, humans, and furthermore on a per-individual as well as per-group basis. Control of mycobacterial growth in the MGIA is associated with a range of immune parameters measured post-BCG infection in vivo including the IFN-γ ELISpot response, frequency of PPD-specific IFN-γ or TNF-α producing CD4+ T cells and frequency of specific sub-populations of polyfunctional CD4+ T cells. Distinct transcriptomic profiles are associated with good vs. poor mycobacterial control in the MGIA, with good controllers showing enrichment for gene sets associated with antigen processing/presentation and the IL-23 pathway, and poor controllers showing enrichment for hypoxia-related pathways. This study represents an important step toward biologically validating the direct PBMC MGIA for use in TB vaccine development and furthermore demonstrates the utility of this assay in determining relevant immune mechanisms and pathways of protection

Corpus callosum injury after neurosurgical intervention for posthemorrhagic ventricular dilatation and association with neurodevelopmental outcome at 2 years

OBJECTIVE Direct injury to the corpus callosum (CC) due to neurosurgical interventions in infants with posthemorrhagic ventricular dilatation (PHVD) has not been reported in the literature. The authors observed a subset of infants who had suffered penetrating CC injury after neurosurgical interventions for PHVD and hypothesized that this pattern of injury may result in suboptimal CC maturation and neurodevelopmental impairment.METHODS In this multicenter, retrospective, observational study, 100 preterm and 17 full-term infants with PHVD were included and compared with 23 preterm controls. Both neonatal and postneonatal brain MRI scans were assessed for injury, and measurements were performed on postneonatal MRI scans at 2 years' corrected age. Neurodevelopmental outcome was assessed at 2 years' corrected age.RESULTS A total of 269 brain MRI scans of 140 infants were included. Of infants with PHVD, 48 (41%) had penetrating CC injury following neurosurgical interventions. The median (IQR) CC midsagittal surface area was smaller in infants with CC injury when compared with infants with PHVD who had intact CC and controls (190 mm(2) [149-262 mm(2)] vs 268 mm(2) [206-318 mm(2)] vs 289 mm(2) [246-320 mm(2)], respectively; p < 0.001). In the univariate analysis, the area of the CC was associated with cognitive Z score (coefficient 0.009 [95% CI 0.005-0.012], p < 0.001) and motor Z score (coefficient 0.009 [95% CI 0.006-0.012], p < 0.001). In the multivariable model, CC injury was not independently associated with cognitive and motor Z score after adjusting for gestational age and presence of periventricular hemorrhagic infarction (coefficient 0.04 [95% CI -0.36 to 0.46] and -0.37 [95% CI -0.83 to 0.09], p = 0.7 and 0.1, respectively).CONCLUSIONS CC injury was not uncommon following neurosurgical interventions for PHVD in both preterm and full-term infants. At the age of 2 years, the CC midsagittal surface area was smaller in infants with injury, but CC injury was not independently associated with cognitive and motor outcomes at 2 years' corrected age.Developmen