Project description:Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.
Project description:Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in E. coli but was disrupted in Salmonella by a translocation event is an sRNA that is associated with the FNR/CRP global regulators and influences E. coli biofilm formation. A Salmonella-specific sRNA evolved de novo through point mutations that generated a σ(70) promoter sequence in an IGR that arose through genome rearrangement events. The differences in the sRNA pools among bacterial species have previously been ascribed to duplication, deletion, or horizontal acquisition. Here, we show that genomic rearrangements also contribute to this process by either disrupting sRNA-containing IGRs or creating IGRs in which novel sRNAs may evolve.
Project description:Distinct from normal differentiated tissues, cancer cells reprogram nutrient uptake and utilization to accommodate their elevated demands for biosynthesis and energy production. A hallmark of these types of reprogramming is the increased utilization of, and dependency on glutamine, a nonessential amino acid, for cancer cell growth and survival. It is well-accepted that glutamine is a versatile biosynthetic substrate in cancer cells beyond its role as a proteinogenic amino acid. In addition, accumulating evidence suggests that glutamine metabolism is regulated by many factors, including tumor origin, oncogene/tumor suppressor status, epigenetic alternations and tumor microenvironment. However, despite the emerging understanding of why cancer cells depend on glutamine for growth and survival, the contribution of glutamine metabolism to tumor progression under physiological conditions is still under investigation, partially because the level of glutamine in the tumor environment is often found low. Since targeting glutamine acquisition and utilization has been proposed to be a new therapeutic strategy in cancer, it is central to understand how tumor cells respond and adapt to glutamine starvation for optimized therapeutic intervention. In this review, we first summarize the diverse usage of glutamine to support cancer cell growth and survival, and then focus our discussion on the influence of other nutrients on cancer cell adaptation to glutamine starvation as well as its implication in cancer therapy.
Project description:Event memories are characterized by the holistic retrieval of their constituent elements. Studies show that memory for individual event elements (e.g. person, object and location) are statistically related to each other, and that the same associative memory structure can be formed by learning all pairwise associations across separated encoding contexts (person-object, person-location, object-location). Counter to previous studies that have shown no differences in holistic retrieval between simultaneously and separately encoded event elements, adults did not show evidence of holistic retrieval from separately encoded event elements when using a similar paradigm adapted for children (Experiment 1). We conducted a further five online experiments to explore the conditions under which holistic retrieval emerges following separated encoding of within-event associations, testing for influences of trial length (Experiment 2), the number of events learned (Experiment 3a) and stimulus presentation format (Experiments 3b, 4a, 4b). Presentation of written words was optimal for integrating elements across encoding trials, whereas the addition of spoken words disrupted integration across separately presented associations. The use of picture stimuli also produced effect sizes smaller than those of previously published research. We discuss the ways in which memory integration processes may be disrupted by these differences in presentation format. The findings have practical implications for the utility of this paradigm across research and learning contexts.
Project description:Multidrug products enable more effective therapies and simpler administration regimens, provided that a stable formulation is prepared, with the desired composition. In this view, solid solutions have the advantage of combining the stability of a single crystalline phase with the potential of stoichiometry variation of a mixture. Here a drug-prodrug solid solution of cortisone and cortisol (hydrocortisone) is described. Despite the structural differences of the two components, the new phase is obtained both from solution and by supercritical CO2 assisted spray drying. In particular, to enter the solid solution, hydrocortisone must violate Etter's rules for hydrogen bonding. As a result, its dissolution rate is almost doubled.
Project description:Biodiversity can reduce or increase disease transmission. These divergent effects suggest that community composition rather than diversity per se determines disease transmission. In natural plant communities, little is known about the functional roles of neighbouring plant species in belowground disease transmission. Here, we experimentally investigated disease transmission of a fungal root pathogen (Rhizoctonia solani) in two focal plant species in combinations with four neighbour species of two ages. We developed stochastic models to test the relative importance of two transmission-modifying mechanisms: (1) infected hosts serve as nutrient supply to increase hyphal growth, so that successful disease transmission is self-reinforcing; and (2) plant resistance increases during plant development. Neighbouring plants either reduced or increased disease transmission in the focal plants. These effects depended on neighbour age, but could not be explained by a simple dichotomy between hosts and nonhost neighbours. Model selection revealed that both transmission-modifying mechanisms are relevant and that focal host-neighbour interactions changed which mechanisms steered disease transmission rate. Our work shows that neighbour-induced shifts in the importance of these mechanisms across root networks either make or break disease transmission chains. Understanding how diversity affects disease transmission thus requires integrating interactions between focal and neighbour species and their pathogens.
Project description:Cork oak woodlands (montado) are agroforestry systems distributed all over the Mediterranean basin with a very important social, economic and ecological value. A generalized cork oak decline has been occurring in the last decades jeopardizing its future sustainability. It is unknown how loss of tree cover affects microbial processes that are consuming greenhouse gases in the montado ecosystem. The study was conducted under two different conditions in the natural understory of a cork oak woodland in center Portugal: under tree canopy (UC) and open areas without trees (OA). Fluxes of methane and nitrous oxide were measured with a static chamber technique. In order to quantify methanotrophs and bacteria capable of nitrous oxide consumption, we used quantitative real-time PCR targeting the pmoA and nosZ genes encoding the subunit of particulate methane mono-oxygenase and catalytic subunit of the nitrous oxide reductase, respectively. A significant seasonal effect was found on CH4 and N2O fluxes and pmoA and nosZ gene abundance. Tree cover had no effect on methane fluxes; conversely, whereas the UC plots were net emitters of nitrous oxide, the loss of tree cover resulted in a shift in the emission pattern such that the OA plots were a net sink for nitrous oxide. In a seasonal time scale, the UC had higher gene abundance of Type I methanotrophs. Methane flux correlated negatively with abundance of Type I methanotrophs in the UC plots. Nitrous oxide flux correlated negatively with nosZ gene abundance at the OA plots in contrast to that at the UC plots. In the UC soil, soil organic matter had a positive effect on soil extracellular enzyme activities, which correlated positively with the N2O flux. Our results demonstrated that tree cover affects soil properties, key enzyme activities and abundance of microorganisms and, consequently net CH4 and N2O exchange.
Project description:Gangliosides are sialic acid-containing glycosphingolipids. They occur especially on the cellular surfaces of neuronal cells, where they form a complex pattern, but are also found in many other cell types. The paper provides a general overview on their structures, occurrence, and metabolism. Key functional, biochemical, and pathobiochemical aspects are summarized.
Project description:Whole human genome sequencing of individuals is becoming rapid and inexpensive, enabling new strategies for using personal genome information to help diagnose, treat, and even prevent human disorders for which genetic variations are causative or are known to be risk factors. Many of the exploding number of newly discovered genetic variations alter the structure, function, dynamics, stability, and/or interactions of specific proteins and RNA molecules. Accordingly, there are a host of opportunities for biochemists and biophysicists to participate in (1) developing tools to allow accurate and sometimes medically actionable assessment of the potential pathogenicity of individual variations and (2) establishing the mechanistic linkage between pathogenic variations and their physiological consequences, providing a rational basis for treatment or preventive care. In this review, we provide an overview of these opportunities and their associated challenges in light of the current status of genomic science and personalized medicine, the latter often termed precision medicine.