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More than 10 million people fall ill from Mycobacterium tuberculosis infection every year. Putting up a fight against the pathogen is posed with recurrent infections worldwide which is the consequence of resistance and tolerance strains among population. Resistance develop due to prolonged periods of antibiotics treatments which span more than 3 months. Long periods of treatment is required to kill […]
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Nitrate is a key contaminant and electron acceptor and its transformations link together the nitrogen cycle, the carbon cycle, and the fate of various contaminants. By designing environmentally-relevant synthetic communities composed of isolates from the field, we can study nitrate reduction in a laboratory-controlled system. Understanding the nitrogen cycle can shed insight into communities, organisms, processes, genes, and energetics associated […]
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Transcriptional networks play an important role in the adaptation of microbes to changing environments. Using transcriptional regulation, microbes respond to stress by tuning the expression of their genes. Nonetheless, transcriptional programs driving adaptive responses are rarely defined. Importantly, even when the transcriptional network of an organism has been partially characterized, identifying the regulators that orchestrate the transition between any two […]
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Our current research focuses on studying intratumoral heterogeneity in brain tumors. Intratumoral heterogeneity is a major issue as it contributes to drug resistance and tumor recurrence. Heterogeneity occurs at the genomic, epigenomic, transcriptomic, metabolomic, and cellular scale and complicates our understanding of brain tumors. However, the continual and rapid developments in high-throughput omics technologies and computational analytical techniques enable the […]
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The treatment of many cancers centers on risk-adapted therapy. Patient stratification methodologies are, therefore, essential to the design of effective treatment strategies. Our research focus is to develop transcriptional regulatory networks of cancer that can predict a patient’s response to various therapies and their risk of progression. This approach associates mechanistic underpinnings to the various disease states of a given […]
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Chlamydomonas reinhardtii is a model green microalgae that produces lipid during nutrient stress. The bio-oil produced can be utilized for transportation fuel and energy production. Using systems biology we aim to uncover the regulatory and signaling networks of C. reinhardtii during state transitions from growth (biomass accumulation) to lipid accumulation. Such insights will be crucial for the rewiring networks for the […]
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Diverse organisms including microbes have evolved mechanisms to gain fitness advantage by sensing an environmental cue to anticipate and prepare in advance for a future selective pressure, a strategy known as adaptive prediction (AP). AP is generally beneficial to microbes as it can confer fitness advantage over competitors, facilitate competition for resources, and help with evasion of predators or host-defense […]
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Mycobacterium tuberculosis (MTB) is an extraordinarily successful pathogen that has infected thirty percent of the world’s population. The success of MTB is tied to the adaptive repertoire of the bacilli in the face of varying and hostile environments within the host. In the course of chronic infection, MTB encounters diverse environmental conditions, including hypoxia, nitric oxide stress and varying nutritional […]
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Microbial communities influence the cycling of key nutrients including carbon, nitrogen, and sulfur. These cycles are tightly linked to the health of the planet, from greenhouse gas emissions to soil fertility. As anthropogenic disturbance continues to modify the natural environment, quantitative tools are critically needed in order to characterize the current state and predict the future health of these complex […]
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Previously, a two-organism model community was established under sulfate-deplete conditions that prevented independent growth of Desulfovibrio vulgaris (Dv) by sulfate respiration (SR), and required its syntrophic interaction with Methanococcus maripaludis (Mm) to support growth of both organisms (Hillesland & Stahl, 2010). ‘Syntrophy’ (ST) is an obligate mutualism in which, here, the oxidation of the organic substrate (lactate) by Dv is […]
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Managing tradeoffs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. Microbial generalists are metabolically versatile and able to cope with periodically or randomly fluctuating natural environments by up- or down-regulating genes to optimize resource utilization. However, it is generally assumed and not demonstrated whether or how regulatory mutations foster adaptive evolution […]
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The Southern Ocean plays a critical role for carbon sequestration in the oceans. The flux of carbon (C) and nitrogen (N) export to the deep ocean depends on the efficiency of the biological pump transporting biomass to depth, however the molecular mechanisms are not well understood. This study focuses on the impact of microbial communities in the C flux in […]
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