Modeling the dynamics of mountain pine beetle aggregation in a lodgepole pine stand

Summary At least once a year the mountain pine beetle searches for lodgepole pines that provide a suitable habitat for a new brood. After attacking females feed, they produce an attractant pheromone that causes beetles to aggregate and, during outbreaks, to usually mass attack the focus tree. Near the completion of mass attack, incoming beetles are repelled and initiate attacks on adjacent recipient trees. An understanding of this switching process is useful for prescribing measures that minimize beetle damage.A mathematical model was developed to (1) describe beetle aggregation, (2) predict the relation of tree susceptibility and switching to changes in beetle density, (3) provide a structure for current knowledge, and (4) pose questions for further research. The model indicates that a high population density ensures mass aggregation and consequently successful tree colonization and switching. The model also indicates that the number of beetles attracted per attacking beetle differs from tree to tree, possibly depending on resin quality and production and/or the local flying density of beetles. Field and model results indicate that tree size appears to affect the repellence of beetles, suggesting that the attack density or the visual attractiveness of large trees is a factor. Further research could be directed at our assumptions on host resistance, repellence, pheromone emission rates, threshold concentrations, navigation, and pheromone dispersion. Return Address: Center for Quantitative Sciences, University of Washington, Seattle, Washington, 98195, USA     

Monoterpenes in sitka spruce: Within tree and seasonal variation

The composition of oils from needles and cortex of Sitka spruce is unique. Cortex oil is essentially all monoterpene hydrocarbons, while needle oil may be up to 50% oxygenated monoterpenes. Very wide seasonal variations in composition occur in needle oil in young tissue. At bud burst, the oil is > 95% myrcene; this drops to about 40% at the end of summer. The oxygenated terpenes camphor and piperitone develop to about 20% each in concentration during the growing season.     

Analysis of GTPases carrying hydrophobic amino acid substitutions in lieu of the catalytic glutamine: implications for GTP hydrolysis

Ras superfamily GTP-binding proteins regulate important signaling events in the cell. Ras, which often serves as a prototype, efficiently hydrolyzes GTP in conjunction with its regulator GAP. A conserved glutamine plays a vital role in GTP hydrolysis in most GTP-binding proteins. Mutating this glutamine in Ras has oncogenic effects, since it disrupts GTP hydrolysis. The analysis presented here is of GTP-binding proteins that are a paradox to oncogenic Ras, since they have the catalytic glutamine (Glncat) substituted by a hydrophobic amino acid, yet can hydrolyze GTP efficiently. We term these proteins HAS-GTPases. Analysis of the amino acid sequences of HAS-GTPases reveals prominent presence of insertions around the GTP-binding pocket. Homology modeling studies suggest an interesting means to achieve catalysis despite the drastic hydrophobic substitution replacing the key Glncat of Ras-like GTPases. The substituted hydrophobic residue adopts a "retracted conformation," where it is positioned away from the GTP, as its role in catalysis would be unproductive. This conformation is further stabilized by interactions with hydrophobic residues in its vicinity. These interacting residues are strongly conserved and hydrophobic in all HAS-GTPases, and correspond to residues Asp92 and Tyr96 of Ras. An experimental support for the "retracted conformation" of Switch II arises from the crystal structures of Ylqf and hGBP1. This conformation allows us to hypothesize that, unlike in classical GTPases, catalytic residues could be supplied by regions other than the Switch II (i.e., either the insertions or a neighboring domain).     

Can Zipf's law be adapted to normalize microarrays?

Background  

Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented.     

Spatial and temporal distribution of coho salmon carcasses in a stream in the Pacific Northwest,USA

During two consecutive spawning seasons, the movement and distribution of naturally occurring coho salmon (Oncorhynchus kisutch) carcasses were monitored, and the effectiveness of large woody debris (LWD) in retaining carcasses in a stream was evaluated. In both seasons studied, the proportion of carcasses trapped by LWD increased as the season progressed. Densities of salmon carcasses were higher in slow waters such as stream edges and backwaters throughout the study periods. The average distance drifted by carcasses was 19.5m in the first season and 32.1 m in the second season. These results support the notion that LWD contributes to retention of salmon carcasses and enhances availability of salmon-derived nutrients for organisms near salmon spawning grounds.     

Using Web‐Based Technology to Bring Hands‐On Urban Material Flow Analysis to the Classroom

The main objective of this article is to introduce an open‐source, online software tool called OMAT as a teaching tool for performing economy wide‐material flow analysis (EW‐MFA) at urban or regional level in industrial ecology curricula. To that intent, we present a classroom and project activity that was developed for a masters‐level industrial ecology course offered by the Autonomous University of Barcelona. Insights are provided with regards to the outcome of the classroom exercise as well as lessons learned from both an academic and a software development point of view. The OMAT software provides users with a specialized tool to enter and process MFA data in a simple, intuitive way. The usefulness of OMAT as a teaching tool was tested by engaging students in a classroom activity that entailed using OMAT as a tool to perform an EW‐MFA applied to the Metropolitan Area of Barcelona for the years 2005‐2011. The aim of this exercise was to teach students specific skills required in performing an EW‐MFA, not through theory classes, but hands‐on through a learn‐as‐you‐go approach. The exercise not only equipped the students with knowledge about MFA, but also introduced them to solving problems as a team, meeting project deadlines, and communicating effectively with colleagues from different disciplines and backgrounds. Even though there is room for further improvements, this exercise showed that OMAT provided a useful addition to traditional methods that allowed students to get a more practical and thorough understanding of the MFA methodology.     

Ascorbate synthesis and ascorbate peroxidase activity during the early stage of wheat germination

Embryos from dry caryopses of wheat ( Triticum durum L. cv. Norba) are completely devoid of ascorbate (ASC) but contain a low amount of dehydroascorbate (DHA). The de novo biosynthesis of ASC starts in the wheat embryos after 8–10 h of germination but before the ASC biosynthetic pathway is completely restored the embryos can provide themselves with ASC by the reduction of the stored DHA. Three different proteins having DHA-reducing capability are present in the embryos during the early stages of germination. However, when the de novo ASC biosynthesis from sugar is completely restored, the DHA reduction capability largely drops and only one DHA-reducing protein remains active. The presence of three proteins having DHA-reducing capability and their behaviour during germination is discussed.
Dry embryos are also devoid of ASC peroxidase (EC 1.11.1.11); this hydrogen peroxide scavenger enzyme appears after the same lag as ASC and increases during germination in parallel with the rise in ASC. When ASC biosynthesis is experimentally induced, the ASC peroxidase also appears earlier; moreover the affinities for ASC of the three ASC peroxidase isoenzymes that progressively appear during germination depend on the ASC available in the embryos: highest in the first isoenzyme, that appears when the ASC content is very low, lowest in the isoenzyme that is expressed last, when the ASC content is 10–11 times higher.