Combining Perturbations and Parameter Variation to Influence Mean First Passage Times

Perturbations are relatively large shocks to state variables that can drive transitions between stable states, while drift in parameter values gradually alters equilibrium magnitudes. This latter effect can lead to equilibrium bifurcation, the generation, or annihilation of equilibria. Equilibrium annihilations reduce the number of equilibria and so are associated with catastrophic population collapse. We study the combination of perturbations and parameter drift, using a two-species intraguild predation (IGP) model. For example, we use bifurcation analysis to understand how parameter drift affects equilibrium number, showing that both competition and predation rates in this model are bifurcating parameters. We then introduce a stochastic process to model the effects of population perturbations. We demonstrate how to evaluate the joint effects of perturbations and drift using the common currency of mean first passage time to transitions between stable states. Our methods and results are quite general, and for example, can relate to issues in both pest control and sustainable harvest. Our results show that parameter drift (1) does not importantly change the expected time to reach target points within a basin of attraction, but (2) can dramatically change the expected time to shift between basins of attraction, through its effects on equilibrium resilience.     

Major clades of Agaricales: a multilocus phylogenetic overview

An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and Plicaturopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families, four unplaced tribes and two informally named clades are recognized.     

A rapid method for the extraction and determination of vitamin E metabolites in human urine

A method for the direct extraction and routine analysis of the vitamin E metabolites gamma- and alpha-carboxyethyl hydroxychroman (gamma- and alpha-CEHC) from human urine has been developed. A relatively small sample volume (5 ml) can be used and, after enzymatic hydrolysis of the conjugated forms and acidification, the metabolites are extracted with diethyl ether. Recovery of alpha- and gamma-CEHC was compared to that of trolox, used as an internal standard, added to 24-h urine collections from vitamin E-unsupplemented volunteers. Various solvent conditions were initially tested; acidification and ether extraction gave the highest recovery. It was found that after addition and extraction from urine, trolox, alpha- and gamma-CEHC are recovered to a similar extent, hence trolox is viable as an internal standard. The samples were analyzed by both GC and HPLC with electrochemical detection (ECD). HPLC-ECD was found to give higher selectivity and higher sensitivity compared to GC or HPLC with UV detection at 290 nm. The HPLC-ECD detection limit was 10 fmol, linearity (r(2) > 0.98) was achieved in the range of 40 to 200 fmol, which was found to be optimal for 24-h urines from unsupplemented subjects. Inter-sample variability was typically 2-5%. This greater sensitivity and selectivity means that vitamin E metabolites can be analyzed even in unsupplemented subjects. It is also possible to measure unconjugated forms of the metabolites. Typically these were found to represent approximately 10% of the total alpha- and gamma-CEHC. This method can be used routinely for the determination of vitamin E metabolites in urine. The new extraction and detection methods described are relatively quick, less laborious, and more cost-effective than previously available methods.     

Successful initial restoration of oyster habitat in the lower Hudson River Estuary,United States

The eastern oyster (Crassostrea virginica), has experienced dramatic declines throughout its range, and most U.S. states along the Atlantic and Gulf of Mexico coasts have restoration programs. Oyster restoration in the Hudson River Estuary has been a focus of management agencies for over two decades. The present project was initiated in 2013 after sampling for replacement of the Tappan Zee bridge determined live oysters would be lost during bridge construction, thus requiring mitigation measures. Preliminary studies identified three areas for pilot studies to inform the design of full-scale efforts. A pilot study involving deployment of oyster shell-filled gabions and two styles of Reef Balls, found all substrates supported oyster recruitment and growth but there were higher oyster densities on gabions. Some of the gabions, however, failed structurally necessitating a need for new design. For full-scale restoration, a total of 422 modified gabions and 881 Mini-Bay style Reef Balls were deployed across three sites which totaled approximately 2.4 ha (6 ac) in seafloor area. Both substrate types were heavily colonized by oysters and several other species at all three sites, essentially duplicating the findings of the pilot study. The final monitoring event in 2020 indicated a total of approximately 5.8 million live oysters were on the substrates deployed in 2018. This mitigation effort was the largest oyster habitat restoration project in, or north of, the New York Harbor region in recent decades based on restoration area and several oyster metrics of early success.     

Grass bud responses to fire in a semiarid savanna system

Increasingly, land managers have attempted to use extreme prescribed fire as a method to address woody plant encroachment in savanna ecosystems. The effect that these fires have on herbaceous vegetation is poorly understood. We experimentally examined immediate (<24 hr) bud response of two dominant graminoids, a C₃ caespitose grass, Nassella leucotricha, and a C₄ stoloniferous grass, Hilaria belangeri, following fires of varying energy (J/m²) in a semiarid savanna in the Edwards Plateau ecoregion of Texas. Treatments included high‐ and low‐energy fires determined by contrasting fuel loading and a no burn (control) treatment. Belowground axillary buds were counted and their activities classified to determine immediate effects of fire energy on bud activity, dormancy, and mortality. High‐energy burns resulted in immediate mortality of N. leucotricha and H. belangeri buds (p < .05). Active buds decreased following high‐energy and low‐energy burns for both species (p < .05). In contrast, bud activity, dormancy, and mortality remained constant in the control. In the high‐energy treatment, 100% (n = 24) of N. leucotricha individuals resprouted while only 25% (n = 24) of H. belangeri individuals resprouted (p < .0001) 3 weeks following treatment application. Bud depths differed between species and may account for this divergence, with average bud depths for N. leucotricha 1.3 cm deeper than H. belangeri (p < .0001). Synthesis and applications: Our results suggest that fire energy directly affects bud activity and mortality through soil heating for these two species. It is imperative to understand how fire energy impacts the bud banks of grasses to better predict grass response to increased use of extreme prescribed fire in land management.     

Is Metaphit a phencyclidine antagonist? Studies with ketamine, phencyclidine and N-methylaspartate

The dissociative anaesthetics, phencyclidine and ketamine, block excitation of central neurones by N-methylaspartate. Using the technique of microelectrophoresis on rat spinal neurones in vivo Metaphit, a phencyclidine receptor acylating agent, was tested to see whether it would antagonise this effect of dissociative anaesthetics. The predominant effect of Metaphit was, however, to reduce N-methylaspartate induced excitation. It is concluded that Metaphit has mixed agonist/antagonist effects at the phencyclidine receptor.     

Anaerobic iron uptake by Escherichia coli.

Assimilation and uptake of iron in anaerobic cultures of Escherichia coli were supported by iron supplied as ferrienterobactin, ferrichrome, and ferrous ascorbate; however, as in the aerobic cultures, ferrichrome A was a poor iron source. Albomycin inhibited both aerobically and anaerobically grown cells. The siderophore outer membrane receptor proteins FepA and FhuA were produced under anaerobic iron-deficient conditions. Anaerobic transport of ferrienterobactin and ferrichrome was inhibited by KCN and dinitrophenol. The Km for ferrienterobactin uptake in anaerobically grown cells was 0.8 microM, and the Vmax was 38 pmol/min per mg, compared with 0.1 microM and 80 pmol/min per mg, respectively, in aerobically grown cells.     

Scenarios of freshwater fish extinctions from climate change and water withdrawal

Reductions in river discharge (water availability) like those from climate change or increased water withdrawal, reduce freshwater biodiversity. We combined two scenarios from the Intergovernmental Panel for Climate Change with a global hydrological model to build global scenarios of future losses in river discharge from climate change and increased water withdrawal. Applying these results to known relationships between fish species and discharge, we build scenarios of losses (at equilibrium) of riverine fish richness. In rivers with reduced discharge, up to 75% (quartile range 4–22%) of local fish biodiversity would be headed toward extinction by 2070 because of combined changes in climate and water consumption. Fish loss in the scenarios fell disproportionately on poor countries. Reductions in water consumption could prevent many of the extinctions in these scenarios.     

Escalating Plasmodium falciparum antifolate drug resistance mutations in Macha, rural Zambia

Background

Artemisinin and its derivatives have been used for falciparum malaria treatment in China since late 1970s. Monotherapy and uncontrolled use of artemisinin drugs were common practices for a long period of time. In vitro tests showed that the susceptibility of Plasmodium falciparum to artemisinins was declining in China. A concern was raised about the resistance to artemisinins of falciparum malaria in the country. It has been reported that in vitro artemisinin resistance was associated with the S769N mutation in the PfATPase6 gene. The main purpose of this study was to investigate whether that mutation has occurred in field isolates from China.

Methods

Plasmodium falciparum field isolates were collected in 2006–2007 from Hainan and Yunnan provinces, China. A nested PCR-sequencing assay was developed to analyse the genotype of the PfATPase6 S769N polymorphism in the P. falciparum field isolates.

Results

The genotyping results of six samples could not be obtained due to failure of PCR amplification, but no S769N mutation was detected in any of the 95 samples successfully analysed.

Conclusion

The results indicate that the S769N mutation in the PfATPase6 gene is not present in China, suggesting that artemisinin resistance has not yet developed, but the situation needs to be watched very attentively.     

Sequence length required for homologous recombination in Cryptococcus neoformans

Cryptococcosis is a major threat to immunocompromised individuals. Isolates of Cryptococcus neoformans var. grubii and var. neoformans are responsible for most of the infections in the United States and Europe. In depth analysis of the virulence phenotype of this organism requires the generation of specific gene disruptions. The minimum sequence requirements for efficient homologous recombination has not been determined in Cryptococcus. To investigate the flanking DNA length requirements for efficient homologous recombination in variety grubii, the rates of homologous recombination of constructs with different lengths of flanking sequence at two loci, CAP59 and CNLAC1, were examined. Five gene disruption constructs were prepared for each locus with symmetric lengths of sequence homologous to the target gene with approximately 50, 100, 200, 300 or 400bp flanking the selectable marker for hygromycin resistance. In addition, two asymmetric constructs with 50bp on one side and 400bp on the other side were generated for each locus. Overall, symmetric constructs with 300bp or more of flanking sequence on each side and the asymmetric constructs were efficiently targeted for gene disruption by homologous recombination in C. neoformans var. grubii. With one exception, the rate of recovery of homologous recombinants using the longer or asymmetric constructs as targeting vectors was greater than five percent of total transformants. Symmetrical constructs with 100bp or less of homologous flanking sequence did not efficiently generate targeted gene disruptions because the rate of homologous recombinants was less than or equal to 1%.