Short‐term effects of CO2 and O2 on citrate metabolism in illuminated leaves

Although there is now a considerable literature on the inhibition of leaf respiration (CO₂ evolution) by light, little is known about the effect of other environmental conditions on day respiratory metabolism. In particular, CO₂ and O₂ mole fractions are assumed to cause changes in the tricarboxylic acid pathway (TCAP) but the amplitude and even the direction of such changes are still a matter of debate. Here, we took advantage of isotopic techniques, new simple equations and instant freeze sampling to follow respiratory metabolism in illuminated cocklebur leaves (Xanthium strumarium L.) under different CO₂/O₂ conditions. Gas exchange coupled to online isotopic analysis showed that CO₂ evolved by leaves in the light came from ‘old’ carbon skeletons and there was a slight decrease in ¹³C natural abundance when [CO₂] increased. This suggested the involvement of enzymatic steps fractionating more strongly against ¹³C and thus increasingly limiting for the metabolic respiratory flux as [CO₂] increased. Isotopic labelling with ¹³C₂‐2,4‐citrate lead to ¹³C‐enriched Glu and 2‐oxoglutarate (2OG), clearly demonstrating poor metabolism of citrate by the TCAP. There was a clear relationship between the ribulose‐1,5‐bisphosphate oxygenation‐to‐carboxylation ratio (v_o/v_c) and the ¹³C commitment to 2OG, demonstrating that 2OG and Glu synthesis via the TCAP is positively influenced by photorespiration.     

Shift in species composition in the Anopheles gambiae complex after implementation of long‐lasting insecticidal nets in Dielmo,Senegal

Long‐lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) are the cornerstones of malaria vector control. However, the effectiveness of these control tools depends on vector ecology and behaviour, which also largely determine the efficacy of certain Anopheles mosquitoes (Diptera: Culicidae) as vectors. Malaria vectors in sub‐Saharan Africa are primarily species of the Anopheles gambiae complex, which present intraspecific differences in behaviour that affect how they respond to vector control tools. The focus of this study is the change in species composition in the An. gambiae complex after the implementation of LLINs in Dielmo, Senegal. The main findings referred to dramatic decreases in the proportions of Anopheles coluzzii and An. gambiae after the introduction of LLINs, and an increase in the proportion of Anopheles arabiensis. Two years after LLINs were first introduced, An. arabiensis remained the most prevalent species and An. gambiae had begun to rebound. This indicated a need to develop additional vector control tools that can target the full range of malaria vectors.     

Unnatural amino acid incorporation into virus-like particles

Virus-like particles composed of hepatitis B virus (HBV) or bacteriophage Qbeta capsid proteins have been labeled with azide- or alkyne-containing unnatural amino acids by expression in a methionine auxotrophic strain of E. coli. The substitution does not affect the ability of the particles to self-assemble into icosahedral structures indistinguishable from native forms. The azide and alkyne groups were addressed by Cu(I)-catalyzed [3 + 2] cycloaddition: HBV particles were decomposed by the formation of more than 120 triazole linkages per capsid in a location-dependent manner, whereas Qbeta suffered no such instability. The marriage of these well-known techniques of sense-codon reassignment and bioorthogonal chemical coupling provides the capability to construct polyvalent particles displaying a wide variety of functional groups with near-perfect control of spacing.     

Software tools for molecular microscopy

In our role as the editors of a special edition of the Journal of Structural Biology published in 1996 and devoted to the development of software tools, we offer our view of past developments and future prospects in this area. The astonishing progress in computer hardware over the past decade has fueled a significant increase in computational power available for the solution of macromolecular structures. At the same time the relatively slow growth and development of the accompanying software reflects the difficulties of developing large, complex and very specialized analytical methods.     

Volatile chemical release by bethylid wasps: identity, phylogeny, anatomy and behaviour

The structures of volatile chemicals released by parasitic wasps in the family Bethylidae are shown to correspond to the subfamily to which the species belong. Species in the Epyrinae release skatole (3-methylindole) and species in the Bethylinae release a spiroacetal (2-methyl-1,7-dioxaspiro [5.5]undecane): these compounds are chemically very different. The enantiomeric composition of the spiroacetal differs between congeneric species. Chemical release is a discrete event under the active control of both male and female wasps. Structural differences between the mandibular glands and intramandibular glands suggest the mandibular glands to be the source of released volatiles. Real-time mass spectrometry shows that the spiroacetal is released by Goniozus nephantidis females during dyadic resource contests, with release more common during more aggressive interactions. Chemical tagging with deuterium further shows that the volatile is released by the loser of an agonistic interaction and not the winner. The function of spiroacetal and skatole release by bethylids is discussed.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 837–852.     

Physical forces constrain the depth distribution of the abundant native mussel Elliptio complanata in lakes

1. Unionid mussels often account for a large portion of benthic biomass and contribute to nutrient cycling and sediment processes, but are thought to be limited to shallow areas (<2–3 m). 2. The depth distribution and body size of Elliptio complanata were compared in seven Canadian Shield lake basins of different sizes to test what factors determine the upper and lower limit of their depth range. Specifically, I tested whether (i) the upper range of their distribution is limited by exposure to winds and wave action and (ii) the lower range of their distribution is limited by the depth of the thermocline or by the boundary of mud deposition. 3. The average depth distribution of E. complanata shifted to greater depths in larger lake basins. When comparing individual transects, maximum mussel density was found deeper at more exposed sites. Mussel size decreased with increasing depth and was larger, on average, in larger lake basins. These results suggest that physical forces limit the upper range of mussel distribution in lakes. 4. The maximum depth at which mussels were found in different lakes was closely related to thermocline depth. However, mussels were commonly observed below the predicted depth of the mud deposition boundary. The thermocline limits the lower range of mussel distribution in lakes, probably by limiting food availability and by determining water temperature. Substratum type does not limit the lower distribution of mussels. 5. These results suggest that unionid mussels are present in the deeper parts of the littoral zone, especially in large lakes. Therefore, comparisons of mussel populations between sites and between lakes would be biased unless the full depth distribution of these mussels is considered. These results also suggest that long‐term changes in the thermal structure of lakes could affect the range of unionid mussel populations and their functional role in littoral ecosystems.     

A relational database for cryoEM: experience at one year and 50 000 images

For the past year we have been using a relational database as part of an automated data collection system for cryoEM. The database is vital for keeping track of the very large number of images collected and analyzed by the automated system and essential for quantitatively evaluating the utility of methods and algorithms used in the data collection. The database can be accessed using a variety of tools including specially developed Web-based interfaces that enable a user to annotate and categorize images using a Web-based form.     

Leginon: an automated system for acquisition of images from vitreous ice specimens

We have developed a system to automatically acquire cryo-electron micrographs. The system is designed to emulate all of the decisions and actions of a highly trained microscopist in collecting data from a vitreous ice specimen. These include identifying suitable areas of vitreous ice at low magnification, determining the presence and location of specimen on the grid, automatically adjusting imaging parameters (focus, astigmatism) under low-dose conditions, and acquiring images at high magnification to either film or a digital camera. This system is responsible for every aspect of image acquisition and can run unattended, other than requiring periodic refilling of the cryogens, for over 24 h. The system has been tested out on a variety of specimens that represent typical challenges in the field of cryo-electron microscopy. The results show that the overall performance of the system is equivalent to that of an experienced microscopist.     

Towards automated screening of two-dimensional crystals

Screening trials to determine the presence of two-dimensional (2D) protein crystals suitable for three-dimensional structure determination using electron crystallography is a very labor-intensive process. Methods compatible with fully automated screening have been developed for the process of crystal production by dialysis and for producing negatively stained grids of the resulting trials. Further automation via robotic handling of the EM grids, and semi-automated transmission electron microscopic imaging and evaluation of the trial grids is also possible. We, and others, have developed working prototypes for several of these tools and tested and evaluated them in a simple screen of 24 crystallization conditions. While further development of these tools is certainly required for a turn-key system, the goal of fully automated screening appears to be within reach.