1H NMR metabolite fingerprinting and metabolomic analysis of perchloric acid extracts from plant tissues

Metabolite fingerprinting provides a powerful method for discriminating between biological samples on the basis of differences in metabolism caused by such factors as growth conditions, developmental stage or genotype. This protocol describes a technique for acquiring metabolite fingerprints from samples of plant origin. The preferred method involves freezing the tissue rapidly to stop metabolism, extracting soluble metabolites using perchloric acid (HClO4) and then obtaining a fingerprint of the metabolic composition of the sample using 1D 1H NMR spectroscopy. The spectral fingerprints of multiple samples may be analyzed using either unsupervised or supervised multivariate statistical methods, and these approaches are illustrated with data obtained from the developing seeds of two genotypes of sunflower (Helianthus annuus). Preparation of plant extracts for analysis takes 2-3 d, but multiple samples can be processed in parallel and subsequent acquisition of NMR spectra takes approximately 30 min per sample, allowing 24-48 samples to be analyzed in a week.     

Quantitative approaches for analysing fluxes through plant metabolic networks using NMR and stable isotope labelling

The quantitative analysis of metabolic networks is a prerequisite for understanding the integration and regulation of plant metabolism and for devising rational approaches for manipulating resource allocation in plants. The analysis of steady state stable isotope labelling experiments using nuclear magnetic resonance (NMR) spectroscopy has developed into a powerful method for determining these fluxes in micro-organisms and its application to heterotrophic plant metabolism is increasing. After an introductory discussion of the well known role of stable isotopes in pathway delineation, the review considers their application to metabolic flux analysis in plants. These applications are divided into two groups – small scale analyses of fluxes through particular pathways and large scale analyses of multiple fluxes through metabolic networks – and the problems caused by the complexity of intermediary metabolism in plants are discussed. It is concluded that metabolic flux analysis provides a powerful method for defining the metabolic phenotype of wild type, mutant and transgenic plants and that its development should be pursued.     

Characterization of 13 newly isolated strains of anaerobic, cellulolytic, thermophilic bacteria

Characteristics of 13 newly isolated thermophilic, anaerobic, and cellulolytic strains were compared with previously described strains of Clostridium thermocellum: ATCC 27405 and JW20 (ATCC 31549). Colony morphology, antibiotic sensitivity, fermentation end-products, and cellulose degradation were documented. All 13 strains were sensitive to erythromycin (5 μg/ml) and chloramphenicol (25 μg/ml), and all strains but one were sensitive to kanamycin (20 μg/ml). Polymerase chain reaction (PCR) amplification using primers based on gene sequences from C. thermocellum ATCC 27405 was successful for all 13 strains in the case of the hydrogenase gene and 11 strains in the case of phosphotransacetylase/acetate kinase genes. Ten strains amplified a product of the expected size with primers developed to be specific for C. thermocellum 16SrRNA primers. Two of the 13 strains did not amplify any product with the PCR primers designed for the phosphotransacetylase/acetate kinase and 16SrRNA primers. A MboI-like GATC- recognizing restriction activity was present in all of the five strains examined. The results of this study have several positive implications with respect to future development of a transformation system for cellulolytic thermophiles. Journal of Industrial Microbiology & Biotechnology (2001) 27, 275–280. Received 12 September 2000/ Accepted in revised form 20 November 2000     

Molecular properties of pyrophosphate:fructose-6-phosphate phosphotransferase from potato tuber

Pyrophosphate:fructose-6-phosphate phosphotransferase (PFP) from potato tubers has been purified to homogeneity. The enzyme contains two polypeptides with apparent relative molecular mass (Mr) values of 65,000 and 60,000. These polypeptides give different peptide fragments after limited proteolytic digestion. Antibodies raised against each polypeptide separately are specific for that polypeptide, but both antisera are capable of immunoprecipitating native PFP activity. These antibodies also recognize similar pairs of polypeptides in a range of other plant tissues that contain PFP activity. Based on gel filtration, the Mr value of potato tuber PFP is 265,000. This suggests that the enzyme is a heterotetramer composed of two polypeptides with Mr values of 65,000 and 60,000. In the presence of pyrophosphate, potato PFP dissociates into a 130,000 dimer.     

Whole‐body senescent cell clearance alleviates age‐related brain inflammation and cognitive impairment in mice

Cellular senescence is characterized by an irreversible cell cycle arrest and a pro‐inflammatory senescence‐associated secretory phenotype (SASP), which is a major contributor to aging and age‐related diseases. Clearance of senescent cells has been shown to improve brain function in mouse models of neurodegenerative diseases. However, it is still unknown whether senescent cell clearance alleviates cognitive dysfunction during the aging process. To investigate this, we first conducted single‐nuclei and single‐cell RNA‐seq in the hippocampus from young and aged mice. We observed an age‐dependent increase in p16^Ink4a senescent cells, which was more pronounced in microglia and oligodendrocyte progenitor cells and characterized by a SASP. We then aged INK‐ATTAC mice, in which p16^Ink4a‐positive senescent cells can be genetically eliminated upon treatment with the drug AP20187 and treated them either with AP20187 or with the senolytic cocktail Dasatinib and Quercetin. We observed that both strategies resulted in a decrease in p16^Ink4a exclusively in the microglial population, resulting in reduced microglial activation and reduced expression of SASP factors. Importantly, both approaches significantly improved cognitive function in aged mice. Our data provide proof‐of‐concept for senolytic interventions'' being a potential therapeutic avenue for alleviating age‐associated cognitive impairment.     

Identifying Biologically Meaningful Hot-Weather Events Using Threshold Temperatures That Affect Life-History

Increases in the frequency, duration and intensity of heat waves are frequently evoked in climate change predictions. However, there is no universal definition of a heat wave. Recent, intense hot weather events have caused mass mortalities of birds, bats and even humans, making the definition and prediction of heat wave events that have the potential to impact populations of different species an urgent priority. One possible technique for defining biologically meaningful heat waves is to use threshold temperatures (T_thresh) above which known fitness costs are incurred by species of interest. We set out to test the utility of this technique using T_thresh values that, when exceeded, affect aspects of the fitness of two focal southern African bird species: the southern pied babbler Turdiodes bicolor (T_thresh = 35.5°C) and the common fiscal Lanius collaris (T_thresh = 33°C). We used these T_thresh values to analyse trends in the frequency, duration and intensity of heat waves of magnitude relevant to the focal species, as well as the annual number of hot days (maximum air temperature > T_thresh), in north-western South Africa between 1961 and 2010. Using this technique, we were able to show that, while all heat wave indices increased during the study period, most rapid increases for both species were in the annual number of hot days and in the maximum intensity (and therefore intensity variance) of biologically meaningful heat waves. Importantly, we also showed that warming trends were not uniform across the study area and that geographical patterns in warming allowed both areas of high risk and potential climate refugia to be identified. We discuss the implications of the trends we found for our focal species, and the utility of the T_thresh technique as a conservation tool.     

Competition- and resource-mediated tradeoffs between growth and defensive chemistry in trembling aspen (Populus tremuloides)

Costs of defense are thought to maintain genetic variations in the expression of defense within plant populations. As with many plant species, aspen exhibits considerable variation in allocation to secondary metabolites. This study examined the independent and interactive effects of genotype, soil fertility and belowground competition on defensive chemistry and growth in trembling aspen (Populus tremuloides). Four aspen genotypes were grown with high and low soil fertility, and with and without root competition. Physiological, morphological and allocational determinants of growth were measured to identify growth-defense tradeoffs. Nutrient limitation and competition decreased growth, leaf mass ratio, leaf nitrogen concentration and photosynthesis, and increased root : shoot ratio and leaf condensed tannin concentrations. The competition treatment also resulted in increased leaf phenolic glycoside (PG) concentrations. Aspen growth was negatively correlated with PG concentrations under low fertility with competition. The relationship between growth and its major determinants was also negatively related to foliar condensed tannins expressed as a proportion of tree mass, indicating an additional indirect cost of allocation to secondary metabolites.