Histone deacetylase inhibitors SAHA and sodium butyrate block G1-to-S cell cycle progression in neurosphere formation by adult subventricular cells

BACKGROUND: Histone deacetylases (HDACs) are enzymes that modulate gene expression and cellular processes by deacetylating histones and non-histone proteins. While small molecule inhibitors of HDAC activity (HDACi) are used clinically in the treatment of cancer, pre-clinical treatment models suggest they also exert neuroprotective effects and stimulate neurogenesis in neuropathological conditions. However, the direct effects of HDACi on cell cycle progression and proliferation, two properties required for continued neurogenesis, have not been fully characterized in adult neural stem cells (NSCs). In this study, we examined the effects of two broad class I and class II HDACi on adult mouse NSCs, the hydroxamate-based HDACi suberoylanilide hydroxamic acid (vorinostat, SAHA) and the short chain fatty acid HDACi sodium butyrate. RESULTS: We show that both HDACi suppress the formation of neurospheres by adult mouse NSCs grown in proliferation culture conditions in vitro. DNA synthesis is significantly inhibited in adult mouse NSCs exposed to either SAHA or sodium butyrate and inhibition is associated with an arrest in the G1 phase of the cell cycle. HDACi exposure also resulted in transcriptional changes in adult mouse NSCs. Cdk inhibitor genes p21 and p27 transcript levels are increased and associated with elevated H3K9 acetylation levels at proximal promoter regions of p21 and p27. mRNA levels for notch effector Hes genes and Spry-box stem cell transcription factors are downregulated, whereas pro-neural transcription factors Neurog1 and Neurod1 are upregulated. Lastly, we show HDAC inhibition under proliferation culture conditions leads to long-term changes in cell fate in adult mouse NSCs induced to differentiate in vitro. CONCLUSION: SAHA and sodium butyrate directly regulate cdk inhibitor transcription to control cell cycle progression in adult mouse NSCs. HDAC inhibition results in G1 arrest in adult mouse NSCs and transcriptional changes associated with activation of neuronal lineage commitment programs and a reduction of stem/progenitor state. Changes in differentiated cell state in adult mouse NSCs treated with HDACi under proliferation culture conditions suggests an intrinsic relationship between multipotency, cell cycle progression and HDAC activity in these cells

Climate-driven regime shifts in a mangrove-salt marsh ecotone over the past 250 years.

Climate change is driving the tropicalization of temperate ecosystems by shifting the range edges of numerous species poleward. Over the past few decades, mangroves have rapidly displaced salt marshes near multiple poleward mangrove range limits, including in northeast Florida. It is uncertain whether such mangrove expansions are due to anthropogenic climate change or natural climate variability. We combined historical accounts from books, personal journals, scientific articles, logbooks, photographs, and maps with climate data to show that the current ecotone between mangroves and salt marshes in northeast Florida has shifted between mangrove and salt marsh dominance at least 6 times between the late 1700s and 2017 due to decadal-scale fluctuations in the frequency and intensity of extreme cold events. Model projections of daily minimum temperature from 2000 through 2100 indicate an increase in annual minimum temperature by 0.5 °C/decade. Thus, although recent mangrove range expansion should indeed be placed into a broader historical context of an oscillating system, climate projections suggest that the recent trend may represent a more permanent regime shift due to the effects of climate change

Land use influences on acidification and recovery of freshwaters in Galloway, south-west Scotland

International audienceThe long term response of surface waters to changes in sulphur deposition and afforestation is investigated for three upland river systems in the Galloway region of south-west Scotland. From 1984-1999, these rivers exhibited a statistically significant decline in non-marine sulphate concentrations in response to reduced acid deposition. This reduction in non-marine sulphate was, however, insufficient to induce a pH recovery over the period. A statistically significant increase in river pH was observed between 1956-1970 (0.05 yr-1) when subsidised agricultural lime payments were at a maximum. In 1976, this subsidy ceased and surface waters have progressively acidified. In addition, climatic change is found to influence long-term trends in pH. Mean annual pH was greatest during a dry period between 1969-1973 when total annual discharge was low. Thereafter, pH declined gradually in response to higher rainfall and increased total annual discharge. Overall, surface waters draining the afforested catchments of the Rivers Cree and Bladnoch are more acid than those draining the moorland catchment of the Luce. These results indicate that in afforested catchments, current reductions in sulphur emissions have not led to an observed improvement in the acid status of surface waters. Forestry, therefore, represents a confounding factor with regard to chemical recovery from acidification in this region. Keywords: acidification, afforestation, deposition, rivers, lochs, non-marine sulphate, p

Application of whole genome sequencing and metagenomics for diagnosis of tuberculosis

Globally, tuberculosis kills more people than any other infectious disease. Control of the epidemic is impeded by poor diagnostic approaches. My original contribution to knowledge presented in this thesis is towards diagnosis of tuberculosis by (meta)genomic approaches. In the work presented here, I established proof-of-principle that tuberculosis can be detected, identified and somewhat characterised using a shotgun metagenomics approach. I developed an approach for DNA extraction directly from sputum followed by metagenomic sequencing that allowed me to detect sequences from the M. tuberculosis complex in all sixteen samples with low coverage of the H37Rv reference genome. This allowed me to assign the lineage of the MTBC species in thirteen of these samples. This was the basis of the first publication to sequencing tuberculosis without prior culture. I determined that the proportion of human reads in the resulting metagenomic data was a major limitation to characterising the MTBC organisms with greater resolution and sought, though unsuccessfully, to determine methods to remedy this. In doing so, I identified a number of considerations that need to be made when designing studies of human DNA depletion from such heterogeneous clinical samples in the future. Addressing some of the other limitations to using genomics in the diagnosis of tuberculosis, I studied the genotype-phenotype association of first-line drug resistance found in patients in Peru and evaluated the performance diagnostic approaches used. This identified novel mutations associated with pyrazinamide resistance, flaws in the MODS method of antibiotic resistance testing and variation in resistance prediction tools

Improving filtering methods based on the Fast Fourier Transform to delineate objective relief domains: An application to Mare Ingenii lunar area

A recent study has proven that high-pass filtering (HPF) based on the Fast Fourier Transform (FFT) is a rapid and efficient computational method for the semi-automated detection of geomorphic features from high-resolution digital elevation models (DEM). Although this new approach shows great potential for cartographic purposes using remote sensing data, some methodological improvements are still required in the following areas: (i) to develop a robust criteria for filter radius selection; (ii) to test the relationship between filter vectors and landscape form, and explore how DEM artefacts (vegetation, anthropic structures, etc.) can interfere with landform detection; and (iii) to explore filter response regarding generalisation and blurring effects when working with landscapes composed of landforms of different scales that are superimposed on one another. These topics are addressed here through two experiments (Experiment_1 and Experiment_2) with synthetic digital relief models inspired in the lunar landscape. Finally, the improved methodology was applied on the Mare Ingenii lunar relief (Experiment_3) using the Lunar Orbiter Laser Altimeter DEM and the results were tested against ground truths (GTs) developed using the extensive database available at Astropedia website and an ad hoc crater map. The analysis of existing frequencies in a 2D DEM signal through the true magnitude-true frequency plot provides an objective method for filter radius selection, and the use of a Butterworth transference function enables a more versatile filtering. Experiment_1 demonstrates a close correspondence between vectors obtained by filtering called Filtered Geomorphic References (FGRs) and the synthetic landform selected. The accuracy indicators from Experiment_1 and 2 show the good results obtained in the correspondence between FGRs and crater depressions, either from flat-bottomed to bowl shapes. Experiments 2 and 3 confirm that in landscapes generated by superimposed geomorphic features of different sizes, the smaller the crater, the better the filters detect its boundaries. Moreover, the spatial repeatability of FGRs can be used as a cartographic criterion in the identification of crater shape depressions or hills. Besides, the criterion is useful to assess true reality mapped in the GT employed. Finally, the objective geomorphic units obtained by combining the FGRs demonstrate their usefulness for the objective characterisation of the moonscape. Using the synthetic landscapes, the FGRs identify those relief domains composed of depressions and hills.This work was carried out as part of the Projects: 29.P114.64004 (UC); 29.P203.64004 (UC); RECORNISA (FLTQ-UC)

Probing the Subcellular Localization of Hopanoid Lipids in Bacteria Using NanoSIMS

The organization of lipids within biological membranes is poorly understood. Some studies have suggested lipids group into microdomains within cells, but the evidence remains controversial due to non-native imaging techniques. A recently developed NanoSIMS technique indicated that sphingolipids group into microdomains within membranes of human fibroblast cells. We extended this NanoSIMS approach to study the localization of hopanoid lipids in bacterial cells by developing a stable isotope labeling method to directly detect subcellular localization of specific lipids in bacteria with ca. 60 nm resolution. Because of the relatively small size of bacterial cells and the relative abundance of hopanoid lipids in membranes, we employed a primary ^2H-label to maximize our limit of detection. This approach permitted the analysis of multiple stable isotope labels within the same sample, enabling visualization of subcellular lipid microdomains within different cell types using a secondary label to mark the growing end of the cell. Using this technique, we demonstrate subcellular localization of hopanoid lipids within alpha-proteobacterial and cyanobacterial cells. Further, we provide evidence of hopanoid lipid domains in between cells of the filamentous cyanobacterium Nostoc punctiforme. More broadly, our method provides a means to image lipid microdomains in a wide range of cell types and test hypotheses for their functions in membranes

Validation of northern latitude Tropospheric Emission Spectrometer stare ozone profiles with ARC-IONS sondes during ARCTAS: sensitivity, bias and error analysis

We compare Tropospheric Emission Spectrometer (TES) versions 3 and 4, V003 and V004, respectively, nadir-stare ozone profiles with ozonesonde profiles from the Arctic Intensive Ozonesonde Network Study (ARCIONS, http://croc.gsfc.nasa.gov/arcions/ during the Arctic Research on the Composition of the Troposphere from Aircraft and Satellites (ARCTAS) field mission. The ozonesonde data are from launches timed to match Aura's overpass, where 11 coincidences spanned 44° N to 71° N from April to July 2008. Using the TES "stare" observation mode, 32 observations are taken over each coincidental ozonesonde launch. By effectively sampling the same air mass 32 times, comparisons are made between the empirically-calculated random errors to the expected random errors from measurement noise, temperature and interfering species, such as water. This study represents the first validation of high latitude (>70°) TES ozone. We find that the calculated errors are consistent with the actual errors with a similar vertical distribution that varies between 5% and 20% for V003 and V004 TES data. In general, TES ozone profiles are positively biased (by less than 15%) from the surface to the upper-troposphere (~1000 to 100 hPa) and negatively biased (by less than 20%) from the upper-troposphere to the lower-stratosphere (100 to 30 hPa) when compared to the ozonesonde data. Lastly, for V003 and V004 TES data between 44° N and 71° N there is variability in the mean biases (from −14 to +15%), mean theoretical errors (from 6 to 13%), and mean random errors (from 9 to 19%)

Effect of smoke on subcanopy shaded light, canopy temperature, and carbon dioxide uptake in an Amazon rainforest

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95278/1/gbc1694.pd