Insights into Exo- and Endoglucanase Activities of Family 6 Glycoside Hydrolases from Podospora anserina

The ascomycete Podospora anserina is a coprophilous fungus that grows at late stages on droppings of herbivores. Its genome encodes a large diversity of carbohydrate-active enzymes. Among them, four genes encode glycoside hydrolases from family 6 (GH6), the members of which comprise putative endoglucanases and exoglucanases, some of them exerting important functions for biomass degradation in fungi. Therefore, this family was selected for functional analysis. Three of the enzymes, P. anserina Cel6A (PaCel6A), PaCel6B, and PaCel6C, were functionally expressed in the yeast Pichia pastoris. All three GH6 enzymes hydrolyzed crystalline and amorphous cellulose but were inactive on hydroxyethyl cellulose, mannan, galactomannan, xyloglucan, arabinoxylan, arabinan, xylan, and pectin. PaCel6A had a catalytic efficiency on cellotetraose comparable to that of Trichoderma reesei Cel6A (TrCel6A), but PaCel6B and PaCel6C were clearly less efficient. PaCel6A was the enzyme with the highest stability at 45°C, while PaCel6C was the least stable enzyme, losing more than 50% of its activity after incubation at temperatures above 30°C for 24 h. In contrast to TrCel6A, all three studied P. anserina GH6 cellulases were stable over a wide range of pHs and conserved high activity at pH values of up to 9. Each enzyme displayed a distinct substrate and product profile, highlighting different modes of action, with PaCel6A being the enzyme most similar to TrCel6A. PaCel6B was the only enzyme with higher specific activity on carboxymethylcellulose (CMC) than on Avicel and showed lower processivity than the others. Structural modeling predicts an open catalytic cleft, suggesting that PaCel6B is an endoglucanase.     

Trends in cation, nitrogen, sulfate and hydrogen ion concentrations in precipitation in the United States and Europe from 1978 to 2010: a new look at an old problem

Industrial emissions of SO₂ and NO_x, resulting in the formation and deposition of sulfuric and nitric acids, affect the health of both terrestrial and aquatic ecosystems. Since the mid-late 20th century, legislation to control acid rain precursors in both Europe and the US has led to significant declines in both SO₄–S and H⁺ in precipitation and streams. However, several authors noted that declines in streamwater SO₄–S did not result in stoichiometric reductions in stream H⁺, and suggested that observed reductions in base cation inputs in precipitation could lessen the effect of air pollution control on improving stream pH. We examined long-term precipitation chemistry (1978–2010) from nearly 30 sites in the US and Europe that are variably affected by acid deposition and that have a variety of industrial and land-use histories to (1) quantify trends in SO₄–S, H⁺, NH₄–N, Ca, and NO₃–N, (2) assess stoichiometry between H⁺ and SO₄–S before and after 1990, and (3) examine regional synchrony of trends. We expected that although the overall efforts of developed countries to reduce air pollution and acid rain by the mid-late 20th century would tend to synchronize precipitation chemistry among regions, geographically varied patterns of fossil fuel use and pollution control measures would produce important asynchronies among European countries and the United States. We also expected that control of particulate versus gaseous emission, along with trends in NH₃ emissions, would be the two most significant factors affecting the stoichiometry between SO₄–S and H⁺. Relationships among H⁺, SO₄–S, NH₄–N, and cations differed markedly between the US and Europe. Controlling for SO₄–S levels, H⁺ in precipitation was significantly lower in Europe than in the US, because (1) alkaline dust loading from the Sahara/Sahel was greater in Europe than the US, and (2) emission of NH₃, which neutralizes acidity upon conversion to NH₄ ⁺, is generally significantly higher in Europe than in the US. Trends in SO₄–S and H⁺ in precipitation were close to stoichometric in the US throughout the period of record, but not in Europe, especially eastern Europe. Ca in precipitation declined significantly before, but not after 1990 in most of the US, but Ca declined in eastern Europe even after 1990. SO₄–S in precipitation was only weakly related to fossil fuel consumption. The stoichiometry of SO₄–S and H⁺ may be explained in part by emission controls, which varied over time and among regions. Control of particulate emissions reduces alkaline particles that neutralize acid precursors as well as S-containing particulates, reducing SO₄–S and Ca more steeply than H⁺, consistent with trends in the northeastern US and Europe before 1990. In contrast, control of gaseous SO₂ emissions results in a stoichiometric relationship between SO₄–S and H⁺, consistent with trends in the US and many western European countries, especially after 1991. However, in many European countries, declining NH₃ emissions contributed to the lack of stoichiometry between SO₄–S and H⁺.Recent reductions in NO_x emissions have also contributed to declines in H⁺ in precipitation. Future changes in precipitation acidity are likely to depend on multiple factors including trends in NO_x and NH₃ emission controls, naturally occurring dust, and fossil fuel use, with significant implications for the health of both terrestrial and aquatic ecosystems.     

Detection and validation of volatile metabolic patterns over different strains of two human pathogenic bacteria during their growth in a complex medium using multi-capillary column-ion mobility spectrometry (MCC-IMS)

Headspace analyses over microbial cultures using multi-capillary column-ion mobility spectrometry (MCC-IMS) could lead to a faster, safe and cost-effective method for the identification of pathogens. Recent studies have shown that MCC-IMS allows identification of bacteria and fungi, but no information is available from when on during their growth a differentiation between bacteria is possible. Therefore, we analysed the headspace over human pathogenic reference strains of Escherichia coli and Pseudomonas aeruginosa at four time points during their growth in a complex fluid medium. In order to validate our findings and to answer the question if the results of one bacterial strain can be transferred to other strains of the same species, we also analysed the headspace over cultures from isolates of random clinical origin. We detected 19 different volatile organic compounds (VOCs) that appeared or changed their signal intensity during bacterial growth. These included six VOCs exclusively changing over E. coli cultures and seven exclusively changing over P. aeruginosa cultures. Most changes occurred in the late logarithmic or static growth phases. We did not find differences in timing or trends in signal intensity between VOC patterns of different strains of one species. Our results show that differentiation of human pathogenic bacteria by headspace analyses using MCC-IMS technology is best possible during the late phases of bacterial growth. Our findings also show that VOC patterns of a bacterial strain can be transferred to other strains of the same species.     

Drosophila pupal macrophages – A versatile tool for combined ex vivo and in vivo imaging of actin dynamics at high resolution

Molecular understanding of actin dynamics requires a genetically traceable model system that allows live cell imaging together with high-resolution microscopy techniques. Here, we used Drosophila pupal macrophages that combine many advantages of cultured cells with a genetic in vivo model system. Using structured illumination microscopy together with advanced spinning disk confocal microscopy we show that these cells provide a powerful system for single gene analysis. It allows forward genetic screens to characterize the regulatory network controlling cell shape and directed cell migration in a physiological context. We knocked down components regulating lamellipodia formation, including WAVE, single subunits of Arp2/3 complex and CPA, one of the two capping protein subunits and demonstrate the advantages of this model system by imaging mutant macrophages ex vivo as well as in vivo upon laser-induced wounding.     

Victims and survivors: Stable isotopes used to identify migrants from the Great Irish Famine to 19th century London

Historical evidence documents mass migration from Ireland to London during the period of the Great Irish Famine of 1845–52. The rural Irish were reliant on a restricted diet based on potatoes but maize, a C₄ plant, was imported from the United States of America in 1846–47 to mitigate against Famine. In London, Irish migrants joined a population with a more varied diet. To investigate and characterize their diet, carbon and nitrogen isotope ratios were obtained from bone collagen of 119 and hair keratin of six individuals from Lukin Street cemetery, Tower Hamlets (1843–54), and bone collagen of 20 individuals from the cemetery at Kilkenny Union Workhouse in Ireland (1847–51). A comparison of the results with other contemporaneous English populations suggests that Londoners may have elevated δ¹⁵N compared with their contemporaries in other cities. In comparison, the Irish group have lower δ¹⁵N. Hair analysis combined with bone collagen allows the reconstruction of perimortem dietary changes. Three children aged 5–15 years from Kilkenny have bone collagen δ¹³C values that indicate consumption of maize (C₄). As maize was only imported into Ireland in quantity from late 1846 and 1847, these results demonstrate relatively rapid bone collagen turnover in children and highlight the importance of age‐related bone turnover rates, and the impact the age of the individual can have on studies of short‐term dietary change or recent migration. Stable light isotope data in this study are consistent with the epigraphic and documentary evidence for the presence of migrants within the London cemetery. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.