Nitrogen and harvest effects on soil properties under rainfed switchgrass and no‐till corn over 9 years: implications for soil quality

Nitrogen fertilizer and harvest management will alter soils under bioenergy crop production and the long‐term effects of harvest timing and residue removal remain relatively unknown. Compared to no‐tilled corn (NT‐C, Zea mays L.), switchgrass (Panicum virgatum L.) is predicted to improve soil properties [i.e. soil organic C (SOC), soil microbial biomass (SMB‐C), and soil aggregation] due to its perennial nature and deep‐rooted growth form, but few explicit field comparisons exist. We assessed soil properties over 9 years for a rainfed study of N fertilizer rate (0, 60, 120, and 180 kg N ha^?1) and harvest management on switchgrass (harvested in August and postfrost) and NT‐C (with and without 50% stover removal) in eastern NE. We measured SOC, aggregate stability, SMB‐C, bulk density (BD), pH, P and K in the top 0–30 cm. Both NT‐C and switchgrass increased SMB‐C, SOC content, and aggregate stability over the 9 years, reflecting improvement from previous conventional management. However, the soils under switchgrass had double the percent aggregate stability, 1.3 times more microbial biomass, and a 5–8% decrease in bulk density in the 0–5 and 5–10 cm depths compared to NT‐C. After 9 years, cumulative decrease in available P was significantly greater beneath NT‐C (?24.0 kg P ha^?1) compared to switchgrass (?5.4 kg P ha^?1). When all measured soil parameters were included in the Soil Management Assessment Framework (SMAF), switchgrass improved soil quality index over time (ΔSQI) in all depths. NT‐C without residue removal did not affect ΔSQI, but 50% residue removal decreased ΔSQI (0–30 cm) due to reduced aggregate stability and SMB‐C. Even with best‐management practices such as NT, corn stover removal will have to be carefully managed to prevent soil degradation. Long‐term N and harvest management studies that include biological, chemical, and physical soil measurements are necessary to accurately assess bioenergy impacts on soils.     

Sustainable limits to crop residue harvest for bioenergy: maintaining soil carbon in Australia's agricultural lands

The use of crop residues for bioenergy production needs to be carefully assessed because of the potential negative impact on the level of soil organic carbon (SOC) stocks. The impact varies with environmental conditions and crop management practices and needs to be considered when harvesting the residue for bioenergy productions. Here, we defined the sustainable harvest limits as the maximum rates that do not diminish SOC and quantified sustainable harvest limits for wheat residue across Australia's agricultural lands. We divided the study area into 9432 climate‐soil (CS) units and simulated the dynamics of SOC in a continuous wheat cropping system over 122 years (1889 – 2010) using the Agricultural Production Systems sIMulator (APSIM). We simulated management practices including six fertilization rates (0, 25, 50, 75, 100, and 200 kg N ha^?1) and five residue harvest rates (0, 25, 50, 75, and 100%). We mapped the sustainable limits for each fertilization rate and assessed the effects of fertilization and three key environmental variables – initial SOC, temperature, and precipitation – on sustainable residue harvest rates. We found that, with up to 75 kg N ha^?1 fertilization, up to 75% and 50% of crop residue could be sustainably harvested in south‐western and south‐eastern Australia, respectively. Higher fertilization rates achieved little further increase in sustainable residue harvest rates. Sustainable residue harvest rates were principally determined by climate and soil conditions, especially the initial SOC content and temperature. We conclude that environmental conditions and management practices should be considered to guide the harvest of crop residue for bioenergy production and thereby reduce greenhouse gas emissions during the life cycle of bioenergy production.     

Potential of Pteris vittata to Remove Tetracycline Antibiotics from Aquatic Media

The role of combined arsenic and antibiotics pollution in the environment has recently gained more attention. In this study, a new approach to eliminate tetracycline antibiotics (TCs) from water, via the fern species Pteris vittata (L.), an arsenic hyperaccumulator, was investigated. The encouraging results showed that more than half of the TCs could be removed from the water solution (with the starting concentration of TCs about 1.0 mg kg^?1 respectively) after one day of treatment. No TCs (less than 0.01 mg kg^?1) were detected in the solution after five days of treatment. The results showed that Pteris vittata has high ability to eliminate TCs, which makes it suitable for practical application. Further research found that TCs concentrations were very low in both the roots and the pinnae of Pteris vittata, which indicates that accumulation in the fronds is not the main removal mechanism and that degradation in the fronds might be the main cause. Present results provide a feasible method for simultaneous removal of arsenic and TCs from livestock-polluted wastewater. However, more research work should be done before any real-world application is made.     

Ion-pairing liquid chromatography–tandem mass spectrometry-based quantification of uridine diphosphate-linked intermediates in the Staphylococcus aureus cell wall biosynthesis pathway

Bacterial cell wall biosynthesis is the target of several antibiotics and is of interest as a target for new inhibitor development. The cytoplasmic steps of this pathway involve a series of uridine diphosphate (UDP)-linked peptidoglycan intermediates. Quantification of these intermediates is essential for studies of current agents targeting this pathway and for the development of new agents targeting this pathway. In this study, a liquid chromatography–tandem mass spectrometry (LC–MS/MS) method was developed for quantification of these intermediates in Staphylococcus aureus. To address the problem of poor retention of UDP-linked intermediates on reverse phase media, an ion-pairing (IP) approach using N,N-dimethylhexylamine was developed. MS/MS detection in negative mode was optimized for UDP-GlcNAc, UDP-MurNAc, UDP-MurNAc-l-Ala, UDP-MurNAc-l-Ala-d-Glu, UDP-MurNAc-l-Ala-d-Glu-l-Lys, and UDP-MurNAc-l-Ala-d-Glu-l-Lys-d-Ala-d-Ala. The lower limits of quantification (LLOQs) for these analytes were 1.8, 1.0, 0.8, 2.2, 0.6, and 0.5 pmol, respectively, which correspond to LLOQs of 6, 3, 3, 7, 2, and 2 nmol/g bacteria, respectively. This method was demonstrated for quantification of in vivo levels of these intermediates from S. aureus (0.3 mg dry weight analyzed) treated with fosfomycin, d-boroAla, d-cycloserine, and vancomycin. Metabolite accumulation is consistent with the known targets of these antibiotics and indicates potential regulatory loops within this pathway.     

Differential roles of Sirt1 in HIF-1α and HIF-2α mediated hypoxic responses

Hypoxia-inducible factors 1α and 2α (HIF-1α and HIF-2α) determine cancer cell fate under hypoxia. Despite the similarities of their structures, HIF-1α and HIF-2α have distinct roles in cancer growth under hypoxia, that is, HIF-1α induces growth arrest whereas HIF-2α promotes cell growth. Recently, sirtuin 1 (Sirt1) was reported to fine-tune cellular responses to hypoxia by deacetylating HIF-1α and HIF-2α. Yet, the roles of Sirt1 in HIF-1α and HIF-2α functions have been controversial. We here investigated the precise roles of Sirt1 in HIF-1α and HIF-2α regulations. Immunological analyses revealed that HIF-1α K674 and HIF-2α K741 are acetylated by PCAF and CBP, respectively, but are deacetylated commonly by Sirt1. In the Gal4 reporter systems, Sirt1 was found to repress HIF-1α activity constantly in ten cancer cell-lines but to regulate HIF-2α activity cell type-dependently. Moreover, Sirt1 determined cell growth under hypoxia depending on HIF-1α and HIF-2α. Under hypoxia, Sirt1 promoted cell proliferation of HepG2, in which Sirt1 differentially regulates HIF-1α and HIF-2α. In contrast, such an effect of Sirt1 was not shown in HCT116, in which Sirt1 inactivates both HIF-1α and HIF-2α because conflicting actions of HIF-1α and HIF-2α on cell growth may be offset. Our results provide a better understanding of the roles of Sirt1 in HIF-mediated hypoxic responses and also a basic concept for developing anticancer strategy targeting Sirt1.     

Identification of the reactive cysteine residues in yeast dipeptidyl peptidase III

Dipeptidyl peptidases III (DPPs III) form a distinct metallopeptidase family characterized by the unique HEXXGH motif. High susceptibility to inactivation by organomercurials suggests the presence of a reactive cysteine residue(s) in, or close to, their active site. Yeast DPP III contains five Cys, none of which is absolutely conserved within the family. In order to identify reactive residue(s), site-directed mutagenesis on yeast His₆-tagged DPP III was employed to substitute specifically all five cysteine residues to serine. The variant enzymes thus obtained were enzymatically active and showed an overall structure not greatly affected by the mutations as judged by circular dichroism. Analysis by native and SDS-PAGE under non-reducing conditions revealed the existence of a monomeric and dimeric form in all DPP III proteins except in the C130S, implying that dimerization of yeast DPP III is mediated by the surface-exposed cysteine 130.     

Predicted residue–residue contacts can help the scoring of 3D models

During the 7th Critical Assessment of Protein Structure Prediction (CASP7) experiment, it was suggested that the real value of predicted residue–residue contacts might lie in the scoring of 3D model structures. Here, we have carried out a detailed reassessment of the contact predictions made during the recent CASP8 experiment to determine whether predicted contacts might aid in the selection of close‐to‐native structures or be a useful tool for scoring 3D structural models. We used the contacts predicted by the CASP8 residue–residue contact prediction groups to select models for each target domain submitted to the experiment. We found that the information contained in the predicted residue–residue contacts would probably have helped in the selection of 3D models in the free modeling regime and over the harder comparative modeling targets. Indeed, in many cases, the models selected using just the predicted contacts had better GDT‐TS scores than all but the best 3D prediction groups. Despite the well‐known low accuracy of residue–residue contact predictions, it is clear that the predictive power of contacts can be useful in 3D model prediction strategies. Proteins 2010. © 2010 Wiley‐Liss, Inc.