Short‐term growth response of jack pine and spruce spp. to wood ash amendment across Canada

Wood ash amendment to forest soils contributes to the sustainability of the growing bioenergy industry, not only through decreased wood ash waste disposal in landfills but also by increasing soil/site productivity and tree growth. However, tree growth studies to date have reported variable responses to wood ash, highlighting the need to identify proper application rates under various soil/site conditions to maximize their benefits. We explored the influence of tree species, wood ash nutrient application rates, time since application, stand development stage, and initial (i.e., before wood ash application) soil pH and N on short‐term tree growth response to wood ash amendment across eight unique study sites spanning five Canadian Provinces. Jack pine (Pinus banksiana Lamb) had the most positive response to wood ash amendment compared to white (Picea glauca Moench), hybrid (Picea engelmannii x glauca Parry), and black spruce (Picea mariana Miller), where increasing nutrient application rates increased height growth response. In comparison, black spruce had the most negative response to wood ash amendment, where increasing nutrient application rates slightly decreased height growth response. Site as a random effect explained additional variation, highlighting the importance of other unidentified site characteristics. By examining trends in short‐term growth response across multiple studies with variable site characteristics, we found growth response differed by tree species and nutrient application rates, and that jack pine is a promising candidate for wood ash amendment. These results contribute to our knowledge of optimal wood ash amendment practices and environmentally sustainable bioenergy production.     

A structure-based strategy to identify new molecular scaffolds targeting the bacterial ribosomal A-site

The need for novel antibiotics is widely recognized. A well validated target of antibiotics is the bacterial ribosome. Recent X-ray structures of the ribosome bound to antibiotics have shed new light on the binding sites of these antibiotics, providing fresh impetus for structure-based strategies aiming at identifying new ribosomal ligands. In that respect, the ribosomal decoding region of the aminoacyl-tRNA acceptor site (A-site) is of particular interest because oligonucleotide model systems of this site are available for crystallography, NMR and compound binding assays. This work presents how these different resources can be combined in a hierarchical screening strategy which has led to the identification of new A-site ligands. The approach exploits an X-ray structure of the A-site against which large and diverse libraries of compounds were computationally docked. The complementarity of the compounds to the A-site was assessed using a scoring function specifically calibrated for RNA targets. Starting from approximately 1 million compounds, the computational selection of candidate ligands allowed us to focus the experimental work on 129 compounds, 34 of which showed affinity for the A-site in a FRET-based binding assay. NMR experiments confirmed binding to the A-site for some compounds. For the most potent compound in the FRET assay, a tentative binding mode is suggested, which is compatible with the NMR data and the limited SAR in this series. Overall, the results validate the screening strategy.     

Reliability of surface EMG measurements over 12 hours.

Bone and muscle are both compromised during long-term space flight. Experiments are, therefore, in progress using surface electromyography (EMG) and joint angle measurements to compare muscle action on earth and in space over complete working days. To date, there is little information on the reliability of such long-term EMG measurements available in the literature. Therefore, the current study determined the reliability and feasibility of using surface EMG over a 12-h interval. Ten young subjects performed standardized isometric exercises at 30% of maximum voluntary effort every 2h throughout a normal working day, which included a period of self-chosen exercise. Surface electrodes remained in place over the biceps brachii (BB), vastus medialis (VM), and gastrocnemius (GN) throughout the day. The normalized integrated EMG for two of the three muscles showed no significant changes during the 12-h period, and only the first observation for VM showed a trend (p<0.1) of differences with three of the other measurement periods. The stability of surface EMG measurements over the 12-h period suggests that this methodology is feasible for use in future long-term EMG studies.     

Multiply imputing missing values arising by design in transplant survival data

In this article, we address a missing data problem that occurs in transplant survival studies. Recipients of organ transplants are followed up from transplantation and their survival times recorded, together with various explanatory variables. Due to differences in data collection procedures in different centers or over time, a particular explanatory variable (or set of variables) may only be recorded for certain recipients, which results in this variable being missing for a substantial number of records in the data. The variable may also turn out to be an important predictor of survival and so it is important to handle this missing-by-design problem appropriately. Consensus in the literature is to handle this problem with complete case analysis, as the missing data are assumed to arise under an appropriate missing at random mechanism that gives consistent estimates here. Specifically, the missing values can reasonably be assumed not to be related to the survival time. In this article, we investigate the potential for multiple imputation to handle this problem in a relevant study on survival after kidney transplantation, and show that it comprehensively outperforms complete case analysis on a range of measures. This is a particularly important finding in the medical context as imputing large amounts of missing data is often viewed with scepticism.     

Presence of Bacteroidales as a Predictor of Pathogens in Surface Waters of the Central California Coast

The value of Bacteroidales genetic markers and fecal indicator bacteria (FIB) to predict the occurrence of waterborne pathogens was evaluated in ambient waters along the central California coast. Bacteroidales host-specific quantitative PCR (qPCR) was used to quantify fecal bacteria in water and provide insights into contributing host fecal sources. Over 140 surface water samples from 10 major rivers and estuaries within the Monterey Bay region were tested over 14 months with four Bacteroidales-specific assays (universal, human, dog, and cow), three FIB (total coliforms, fecal coliforms, and enterococci), two protozoal pathogens (Cryptosporidium and Giardia spp.), and four bacterial pathogens (Campylobacter spp., Escherichia coli O157:H7, Salmonella spp., and Vibrio spp.). Indicator and pathogen distribution was widespread, and detection was not highly seasonal. Vibrio cholerae was detected most frequently, followed by Giardia, Cryptosporidium, Salmonella, and Campylobacter spp. Bayesian conditional probability analysis was used to characterize the Bacteroidales performance assays, and the ratios of concentrations determined using host-specific and universal assays were used to show that fecal contamination from human sources was more common than livestock or dog sources in coastal study sites. Correlations were seen between some, but not all, indicator-pathogen combinations. The ability to predict pathogen occurrence in relation to indicator threshold cutoff levels was evaluated using a weighted measure that showed the universal Bacteroidales genetic marker to have a comparable or higher mean predictive potential than standard FIB. This predictive ability, in addition to the Bacteroidales assays providing information on contributing host fecal sources, supports using Bacteroidales assays in water quality monitoring programs.Coastal waters worldwide have been influenced by human activities for centuries, as they are adjacent to densely populated areas, provide a means of transportation, and receive substantial recreational use. Consequently, impairments in nearshore water quality can result from enrichment of the coastal marine ecosystem with pollutants and nutrients that are transported down watersheds from land to sea. This poses health risks to humans and animals. Microbial pollution is caused by fecal contamination from a variety of sources, including humans, livestock, pets, and wildlife, and fecal pathogen pollution has been associated with numerous outbreaks of waterborne disease (14, 15, 27, 41, 49, 55).Fecal indicator bacteria (FIB) that normally reside in the gastrointestinal tracts of humans and animals are used throughout the world to assess the microbiological quality of drinking and recreational waters. In the United States, FIB are used to define bacterial water quality standards aimed at reducing health risks in recreational waters, as required by the Beaches Environmental Assessment and Coastal Health Act (5), which amended the Clean Water Act (11). Groups of standard FIB monitored in water include total coliforms (TC), fecal coliforms (FC), Escherichia coli bacteria, and enterococci. These bacterial groups have been considered indicators of health risks in epidemiologic and quantitative microbial risk assessment (QMRA) studies (38, 42, 59, 66).To date, many monitoring programs have focused only on FIB measurements and do not test for pathogens. However, substantial evidence has been collected that challenges the usefulness of FIB data alone. A few limitations of using standard FIB to represent pathogens in water include the fact that FIB have been shown to multiply in the environment, that they are not host specific, and that the absence of FIB is not necessarily evidence of pathogen absence (21, 50, 51, 56). Consequently, alternative indicators of fecal pollution that address the weaknesses of standard FIB are needed. Ideally, these indicators would decay at rates similar to those of pathogens, be present at high concentrations in fecal sources, and be present at low concentrations in unpolluted environments. Proposed alternative indicators include (i) anaerobic bacteria such as bifidobacteria (46), Clostridium perfringens (22), and Bacteroidales (20); (ii) viruses such as F-specific RNA (F-RNA)-specific coliphages (39), phages infecting Bacteroides fragilis (30), and host-specific viruses (25); and (iii) chemical compounds such as fecal sterols (29). An added benefit of using alternative indicators is that, in some cases, host sources of fecal contamination can be identified.Over a decade ago, PCR-based assays were developed to detect Bacteroides in an effort to monitor human fecal pollution in the environment (36, 37). This approach was adopted by others and further advanced to identify host-specific Bacteroidales 16S rRNA gene markers for different fecal sources. This has resulted in PCR and quantitative PCR (qPCR) assays for the detection of human, dog, pig, and cow Bacteroidales markers (6, 7, 16, 34, 57) as well as assays for the detection of general Bacteroidales markers (7, 34). The analysis of Bacteroidales markers has been incorporated in microbial source tracking (MST) studies, particularly in the United States, Japan, and Europe (24, 45, 52-54, 64).The objective of this study was to compare the abilities of Bacteroidales markers and FIB to predict the occurrence of waterborne pathogens in riverine and estuarine waters in California and to use several statistical approaches to better characterize the strengths and limitations of the assays. We hypothesized that Bacteroidales and FIB would correlate with bacterial and protozoal pathogen detection in surface waters. To test this hypothesis, four Bacteroidales-specific assays (universal, human, dog, and cow), three types of FIB (total coliforms, fecal coliforms, and enterococci), two protozoal pathogens (Cryptosporidium and Giardia spp.), and four bacterial pathogens (Campylobacter spp., E. coli O157, Salmonella spp., and Vibrio spp.) were monitored monthly for 14 months in 10 streams, rivers, and estuaries feeding into the Monterey Bay region of California.     

Quantitative determination of oxytocin receptor antagonist atosiban in rat plasma by liquid chromatography–tandem mass spectrometry

A kinetic study of atosiban was conducted following repeated intravenous administration in Wistar rats. Sample analysis was performed using liquid chromatography–tandem mass spectrometry (LC–MS/MS) following full validation of an in-house method. Eptifibatide, a cyclic peptide, was used as an internal standard (IS). The analyte and internal standard were extracted using solid phase extraction (SPE) method. Chromatographic separation was carried out using an ACE C18 5 μm 50 mm × 4.6 mm column with gradient elution. Mass spectrometric detection was performed using TSQ Quantum ultra AM. The lower limit of quantification was 0.01 μg/ml when 100 μl rat plasma was used. Plasma concentrations of atosiban were measured at 0 (pre-dose), 2, 15, 30, 45, 60, 120 min at the dosage levels of 0.125 mg/kg (low dose), 0.250 mg/kg (mid dose), and 0.500 mg/kg (high dose), respectively. Atosiban plasma concentration measured at Day 1 showed mean peak atosiban concentration (C_max) 0.40, 0.57, 1.95 μg/ml for low, mid and high dose treated animals and mean peak concentration on Day 28 was 0.41, 0.88, 1.31 μg/ml on Day 28 for low, mid and high dose treated animals.     

Regulation of 6S RNA by pRNA synthesis is required for efficient recovery from stationary phase in E. coli and B. subtilis

6S RNAs function through interaction with housekeeping forms of RNA polymerase holoenzyme (Eσ(70) in Escherichia coli, Eσ(A) in Bacillus subtilis). Escherichia coli 6S RNA accumulates to high levels during stationary phase, and has been shown to be released from Eσ(70) during exit from stationary phase by a process in which 6S RNA serves as a template for Eσ(70) to generate product RNAs (pRNAs). Here, we demonstrate that not only does pRNA synthesis occur, but it is an important mechanism for regulation of 6S RNA function that is required for cells to exit stationary phase efficiently in both E. coli and B. subtilis. Bacillus subtilis has two 6S RNAs, 6S-1 and 6S-2. Intriguingly, 6S-2 RNA does not direct pRNA synthesis under physiological conditions and its non-release from Eσ(A) prevents efficient outgrowth in cells lacking 6S-1 RNA. The behavioral differences in the two B. subtilis RNAs clearly demonstrate that they act independently, revealing a higher than anticipated diversity in 6S RNA function globally. Overexpression of a pRNA-synthesis-defective 6S RNA in E. coli leads to decreased cell viability, suggesting pRNA synthesis-mediated regulation of 6S RNA function is important at other times of growth as well.     

Seasonal survival estimation for a long-distance migratory bird and the influence of winter precipitation

Conservation of migratory animals requires information about seasonal survival rates. Identifying factors that limit populations, and the portions of the annual cycle in which they occur, are critical for recognizing and reducing potential threats. However, such data are lacking for virtually all migratory taxa. We investigated patterns and environmental correlates of annual, oversummer, overwinter, and migratory survival for adult male Kirtland’s warblers (Setophaga kirtlandii), an endangered, long-distance migratory songbird. We used Cormack–Jolly–Seber models to analyze two mark–recapture datasets: 2006–2011 on Michigan breeding grounds, and 2003–2010 on Bahamian wintering grounds. The mean annual survival probability was 0.58 ± 0.12 SE. Monthly survival probabilities during the summer and winter stationary periods were relatively high (0.963 ± 0.005 SE and 0.977 ± 0.002 SE, respectively). Monthly survival probability during migratory periods was substantially lower (0.879 ± 0.05 SE), accounting for ~44% of all annual mortality. March rainfall in the Bahamas was the best-supported predictor of annual survival probability and was positively correlated with apparent annual survival in the subsequent year, suggesting that the effects of winter precipitation carried over to influence survival probability of individuals in later seasons. Projection modeling revealed that a decrease in Bahamas March rainfall >12.4% from its current mean could result in negative population growth in this species. Collectively, our results suggest that increased drought during the non-breeding season, which is predicted to occur under multiple climate change scenarios, could have important consequences on the annual survival and population growth rate of Kirtland’s warbler and other Neotropical–Nearctic migratory bird species.