Trade‐offs across productivity,GHG intensity,and pollutant loads from second‐generation sorghum bioenergy

Greenhouse gas (GHG) intensity is frequently used to assess the mitigation potential of biofuels; however, failure to quantify other environmental impacts may result in unintended consequences, effectively shifting the environmental burden of fuel production rather than reducing it. We modeled production of E₈₅, a gasoline/ethanol blend, from forage sorghum (Sorghum bicolor cv. photoperiod LS) grown, processed, and consumed in California's Imperial Valley in order to evaluate the influence of nitrogen (N) management on well‐to‐wheel (WTW) environmental impacts from cellulosic ethanol. We simulated 25 N management scenarios varying application rate, application method, and N source. Life cycle environmental impacts were characterized using the EPA's criteria for emissions affecting the environment and human health. Our results suggest efficient use of N is an important pathway for minimizing WTW emissions on an energy yield basis. Simulations in which N was injected had the highest nitrogen use efficiency. Even at rates as high as 450 kg N ha^?1, injected N simulations generated a yield response sufficient to outweigh accompanying increases in most N‐induced emissions on an energy yield basis. Thus, within the biofuel life cycle, trade‐offs across productivity, GHG intensity, and pollutant loads may be possible to avoid at regional to global scales. However, trade‐offs were seemingly unavoidable when impacts from E₈₅ were compared to those of conventional gasoline. The GHG intensity of sorghum‐derived E₈₅ ranged from 29 to 44 g CO₂ eq MJ^?1, roughly 1/3 to 1/2 that of gasoline. Conversely, emissions contributing to local air and water pollution tended to be substantially higher in the E₈₅ life cycle. These adverse impacts were strongly influenced by N management and could be partially mitigated by efficient application of N fertilizers. Together, our results emphasize the importance of minimizing on‐farm emissions in maximizing both the environmental benefits and profitability of biofuels.     

Determination of disulfide bond assignment of human vitamin K-dependent gamma-glutamyl carboxylase by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Vitamin K-dependent gamma-glutamyl carboxylase is a 758 amino acid integral membrane glycoprotein that catalyzes the post-translational conversion of certain protein glutamate residues to gamma-carboxyglutamate. Carboxylase has ten cysteine residues, but their form (sulfhydryl or disulfide) is largely unknown. Pudota et al. in Pudota, B. N., Miyagi, M., Hallgren, K. W., West, K. A., Crabb, J. W., Misono, K. S., and Berkner, K. L. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 13033-13038 reported that Cys-99 and Cys-450 are the carboxylase active site residues. We determined the form of all cysteines in carboxylase using in-gel protease digestion and matrix-assisted laser desorption/ionization mass spectrometry. The spectrum of non-reduced, trypsin-digested carboxylase revealed a peak at m/z 1991.9. Only this peak disappeared in the spectrum of the reduced sample. This peak's m/z is consistent with the mass of peptide 92-100 (Cys-99) disulfide-linked with peptide 446-453 (Cys-450). To confirm its identity, the m/z 1991.9 peak was isolated by a timed ion selector as the precursor ion for further MS analysis. The fragmentation pattern exhibited two groups of triplet ions characteristic of the symmetric and asymmetric cleavage of disulfide-linked tryptic peptides containing Cys-99 and Cys-450. Mutation of either Cys-99 or Cys-450 caused loss of enzymatic activity. We created a carboxylase variant with both C598A and C700A, leaving Cys-450 as the only remaining cysteine residue in the 60-kDa fragment created by limited trypsin digestion. Analysis of this fully active mutant enzyme showed a 30- and the 60-kDa fragment were joined under non-reducing conditions, thus confirming Cys-450 participates in a disulfide bond. Our results indicate that Cys-99 and Cys-450 form the only disulfide bond in carboxylase.     

Invited overview: conclusions from a review of electrofishing and its harmful effects on fish

These conclusions are extracted from a published review and synthesis of literature on electrofishing and its harmful effects on fish. Although a valuable sampling technique for over half a century, electrofishing, which involves a very dynamic and complex mix of physics, physiology, and behavior, remains poorly understood. New hypotheses have been advanced regarding power transfer to fish and the epileptic nature of their responses to electric fields, but these too need to be more fully explored and validated. Fishery researchers and managers are particularly concerned about the harmful effects of electrofishing on fish, especially endangered species. Although often not externally obvious or fatal, spinal injuries and associated hemorrhages sometimes have been documented in over 50% of fish examined internally. Such injuries can occur anywhere in the electrofishing field at or above the intensity threshold for the twitch response. These injuries are believed to result from powerful convulsions of body musculature (possibly epileptic seizures) caused mostly by sudden changes in voltage as when electricity is pulsed or switched on or off. Significantly fewer spinal injuries are reported when direct current, low-frequency pulsed direct current ( 30 Hz), or specially designed pulse trains are used. Salmoninae are especially susceptible. Other harmful effects, such as bleeding at gills or vent and excessive physiological stress, are also of concern. Mortality, usually by asphyxiation, is a common result of excessive exposure to tetanizing intensities near electrodes or poor handling of captured specimens. Reported effects on reproduction are contradictory, but electrofishing over spawning grounds can harm embryos. Electrofishing is often considered the most effective and benign technique for capturing moderate to large-size fish, but when adverse effects are problematic and cannot be sufficiently reduced, its use should be severely restricted.     

The calpain system in human placenta

The calpain system is involved in a number of human pathologies ranging from the muscular dystrophies to Alzheimer's disease. It is important, therefore, to be able to obtain and to characterize both mu-calpain and m-calpain from human tissue. Although human mu-calpain can be conveniently obtained from either erythrocytes or platelets, no readily available source of human m-calpain has been described. Human placenta extracts contain both mu-calpain and m-calpain in nearly equal proportions and in significant quantities (3-4 mg mu-calpain and 4-5 mg m-calpain/1000 g placenta tissue). Placenta also contains calpastatin that elutes off ion-exchange columns over a wide range of KCl concentrations completely masking the mu-calpain activity eluting off these columns and even partly overlapping m-calpain elution. Placenta mu-calpain requires 50-70 microM Ca2+ and placenta m-calpain requires 450-460 microM Ca2+ for half-maximal proteolytic activity. Western analysis of washed placenta tissue shows that placenta contains both mu- and m-calpain, although some of the mu-calpain in whole placenta extracts likely originates from the erythrocytes that are abundant in the highly vascularized placenta. Placenta calpastatin could not be purified with conventional methods. The most prominent form of calpastatin in Western analyses of placenta obtained as soon as possible after birth was approximately 48-51 kDa; partly purified preparations of placenta calpastatin also contained 48-51 and 70 kDa polypeptides. Human placenta extracts likely contain two different calpastatin isoforms, a 48-51 kDa "placenta calpastatin" and a 70 kDa erythrocyte calpastatin.     

Development of environmentally-benign wood preservatives based on the combination of organic biocides with antioxidants and metal chelators

Wood extractives can be envisaged to protect heartwood by at least three different mechanisms, i.e. fungicide, free radical scavengers/antioxidants and as metal chelators. In short-term laboratory decay tests using two different wood species and decay fungi, the combination of different organic fungicides with various antioxidants and/or metal chelators gave enhanced activity as compared to the organic biocide alone, with the best results usually obtained with all three compounds. Outdoor ground-contact stakes treated with a biocide and antioxidant combination and exposed for 30 months also gave enhanced protection against both decay fungi and termites. It was concluded that the combination of an organic biocide with metal chelating and/or antioxidant additives gives enhanced protection to wood against fungi as compared to the biocide alone and, consequently, it may be possible to develop environmentally-benign wood preservative systems based on this idea.     

A denaturation map of sea urchin ribosomal DNA

The ribosomal RNA genes from the sea urchin Lytechinus variegatus have been studied with the electron microscope using the technique of denaturation mapping. A repeating pattern of denatured regions was found with an average repeat length of 3.87±0.24m. This corresponds to a DNA sequence of approximately 12,000 base pairs with a molecular weight of 8×10⁶ daltons.Abbreviations rRNA ribosomal RNA, including 26S and 18S RNA - Tris tris(hydroxymethyl)-aminomethane - EDTA ethylenediaminetetraacetate     

Measuring phenological variability from satellite imagery

Abstract. Vegetation phenological phenomena are closely related to seasonal dynamics of the lower atmosphere and are therefore important elements in global models and vegetation monitoring. Normalized difference vegetation index (NDVI) data derived from the National Oceanic and Atmospheric Administration's Advanced Very High Resolution Radiometer (AVHRR) satellite sensor offer a means of efficiently and objectively evaluating phenological characteristics over large areas. Twelve metrics linked to key phenological events were computed based on time-series NDVI data collected from 1989 to 1992 over the conterminous United States. These measures include the onset of greenness, time of peak NDVI, maximum NDVI, rate of greenup, rate of senescence, and integrated NDVI. Measures of central tendency and variability of the measures were computed and analyzed for various land cover types. Results from the analysis showed strong coincidence between the satellite-derived metrics and predicted phenological characteristics. In particular, the metrics identified interannual variability of spring wheat in North Dakota, characterized the phenology of four types of grasslands, and established the phenological consistency of deciduous and coniferous forests. These results have implications for large-area land cover mapping and monitoring. The utility of remotely sensed data as input to vegetation mapping is demonstrated by showing the distinct phenology of several land cover types. More stable information contained in ancillary data should be incorporated into the mapping process, particularly in areas with high phenological variability. In a regional or global monitoring system, an increase in variability in a region may serve as a signal to perform more detailed land cover analysis with higher resolution imagery.     

The cross-talk between PARylation and SUMOylation in C/EBPβ at K134 site participates in pathological cardiac hypertrophy

Poly(ADP-ribosyl)ation (PARylation) and SUMO modification (SUMOylation) are novel post-translational modifications (PTMs) mainly induced by PARP1 and SUMO1. Growing evidence has revealed that C/EBPβ plays multiple roles in biological processes and participates in cardiovascular diseases. However, the cross-talk between C/EBPβ PARylation and SUMOylation during cardiovascular diseases is unknown. This study aims to investigate the effects of C/EBPβ PTMs on cardiac hypertrophy and its underlying mechanism. Abdominal aortic constriction (AAC) and phenylephrine (PE) were conducted to induce cardiac hypertrophy. Intramyocardial delivery of recombinant adenovirus (Ad-PARP1) was taken to induce PARP1 overexpression. In this study, we found C/EBPβ participates in PARP1-induced cardiac hypertrophy. C/EBPβ K134 residue could be both PARylated and SUMOylated individually by PARP1 and SUMO1. Moreover, the accumulation of PARylation on C/EBPβ at K134 site exhibits downregulation of C/EBPβ SUMOylation at the same site. Importantly, C/EBPβ K134 site SUMOylation could decrease C/EBPβ protein stability and participates in PARP1-induced cardiac hypertrophy. Taken together, these findings highlight the importance of the cross-talk between C/EBPβ PTMs at K134 site in determining its protein level and function, suggesting that multi-target pharmacological strategies inhibiting PARP1 and activating C/EBPβ SUMOylation would be potential for treating pathological cardiac hypertrophy.     

Wetting-induced soil CO2 emission pulses are driven by interactions among soil temperature,carbon, and nitrogen limitation in the Colorado Desert

Warming-induced changes in precipitation regimes, coupled with anthropogenically enhanced nitrogen (N) deposition, are likely to increase the prevalence, duration, and magnitude of soil respiration pulses following wetting via interactions among temperature and carbon (C) and N availability. Quantifying the importance of these interactive controls on soil respiration is a key challenge as pulses can be large terrestrial sources of atmospheric carbon dioxide (CO₂) over comparatively short timescales. Using an automated sensor system, we measured soil CO₂ flux dynamics in the Colorado Desert—a system characterized by pronounced transitions from dry-to-wet soil conditions—through a multi-year series of experimental wetting campaigns. Experimental manipulations included combinations of C and N additions across a range of ambient temperatures and across five sites varying in atmospheric N deposition. We found soil CO₂ pulses following wetting were highly predictable from peak instantaneous CO₂ flux measurements. CO₂ pulses consistently increased with temperature, and temperature at time of wetting positively correlated to CO₂ pulse magnitude. Experimentally adding N along the N deposition gradient generated contrasting pulse responses: adding N increased CO₂ pulses in low N deposition sites, whereas adding N decreased CO₂ pulses in high N deposition sites. At a low N deposition site, simultaneous additions of C and N during wetting led to the highest observed soil CO₂ fluxes reported globally at 299.5 μmol CO₂ m⁻² s⁻¹. Our results suggest that soils have the capacity to emit high amounts of CO₂ within small timeframes following infrequent wetting, and pulse sizes reflect a non-linear combination of soil resource and temperature interactions. Importantly, the largest soil CO₂ emissions occurred when multiple resources were amended simultaneously in historically resource-limited desert soils, pointing to regions experiencing simultaneous effects of desertification and urbanization as key locations in future global C balance.