The Hymenoptera Genome Database

The Hymenoptera Genome Database (HGD) is an informatics resource supporting genomics of hymenopteran insect species. This relational database implements open-source software and components providing access to curated data contributed by an extensive, active research community. HGD includes the genome sequences and annotation data of honey bee _Apis mellifera_ and its pathogens ("http://BeeBase.org":BeeBase.org) the parasitoid wasp _Nasonia vitripennis_ ("http://NasoniaBase.org":NasoniaBase.org) and a portal to the genomes of six species of ants. Together, these species cover approximately 200 MY in the phylogeny of Hymenoptera, allowing to leverage genetic, genome sequence, and gene expression data, as well as the biological knowledge of related model organisms. The availability of resources across an order greatly facilitates comparative genomics and enhances our understanding of the biology of agriculturally important Hymenoptera species through genomics. HGD has supported research contributions from an extensive community from almost 80 institutions in 14 countries. Community annotation efforts are made possible thanks to a remote connection to a Chado database by Apollo Genome Annotation client software. Curated data at HGD includes predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains. Data at HGD can be queried using genome browsers and / or BLAST/PSI-BLAST servers, and it may also be downloaded to perform local searches. We encourage the public to access and contribute data to HGD at "http://HymenopteraGenome.org":HymenopteraGenome.org.

This poster contains material included in an article accepted for publication in Nucl. Acids Res.©: 2011. The Database Issue. Published by Oxford University Press

Optimal Universal and State-Dependent Quantum Cloning

We establish the best possible approximation to a perfect quantum cloning machine which produces two clones out of a single input. We analyze both universal and state-dependent cloners. The maximal fidelity of cloning is shown to be 5/6 for universal cloners. It can be achieved either by a special unitary evolution or by a novel teleportation scheme. We construct the optimal state-dependent cloners operating on any prescribed two non-orthogonal states, discuss their fidelities and the use of auxiliary physical resources in the process of cloning. The optimal universal cloners permit us to derive a new upper bound on the quantum capacity of the depolarizing quantum channel.Comment: 30 pages (RevTeX), 2 figures (epsf), further results and further authors added, to appear in Physical Review

Structural Studies on a Mitochondrial Glyoxalase II

Glyoxalase 2 is a β-lactamase fold-containing enzyme that appears to be involved with cellular chemical detoxification. Although the cytoplasmic isozyme has been characterized from several organisms, essentially nothing is known about the mitochondrial proteins. As a first step in understanding the structure and function of mitochondrial glyoxalase 2 enzymes, a mitochondrial isozyme (GLX2-5) from Arabidopsis thaliana was cloned, overexpressed, purified, and characterized using metal analyses, EPR and 1H NMR spectroscopies, and x-ray crystallography. The recombinant enzyme was shown to bind 1.04 ± 0.15 eq of iron and 1.31 ± 0.05 eq of Zn(II) and to exhibit kcat and Km values of 129 ± 10 s-1 and 391 ± 48 μm, respectively, when using S-d-lactoylglutathione as the substrate. EPR spectra revealed that recombinant GLX2-5 contains multiple metal centers, including a predominant Fe(III)Z-n(II) center and an anti-ferromagnetically coupled Fe(III)Fe(II) center. Unlike cytosolic glyoxalase 2 from A. thaliana, GLX2-5 does not appear to specifically bind manganese. 1H NMR spectra revealed the presence of at least eight paramagnetically shifted resonances that arise from protons in close proximity to a Fe(III)Fe(II) center. Five of these resonances arose from solvent-exchangeable protons, and four of these have been assigned to NH protons on metal-bound histidines. A 1.74-Å resolution crystal structure of the enzyme revealed that although GLX2-5 shares a number of structural features with human GLX2, several important differences exist. These data demonstrate that mitochondrial glyoxalase 2 can accommodate a number of different metal centers and that the predominant metal center is Fe(III)Zn(II)

Nonorthogonal Quantum States Maximize Classical Information Capacity

I demonstrate that, rather unexpectedly, there exist noisy quantum channels for which the optimal classical information transmission rate is achieved only by signaling alphabets consisting of nonorthogonal quantum states.Comment: 5 pages, REVTeX, mild extension of results, much improved presentation, to appear in Physical Review Letter

Russell on naturalism and practical reason

This response to Paul Russell looks at how we should understand the moral sentiments and their role in action. I think that there is an important tension in Russell’s interpretation of this role. On the one hand, aspects of Russell’s position commit him to some kind of rationalism about the emotions: for instance, he has argued that P. F. Strawson’s account of the reactive is crudely naturalistic; and he has claimed that emotions are constitutive of our sensitivity to moral reasons. On the other hand, he has explicitly endorsed a Humean view of motivation which, I will argue, is incompatible with these rationalist commitments. As well as pointing out the tension and arguing that it should be resolved in the direction of rationalism, I sketch the kind of rationalism that Russell needs: that reason can, through the autonomous progress of moral inquiry, give rise to new forms of emotion

Environmental hydro-refugia demonstrated by vegetation vigour in the Okavango Delta, Botswana

Climate shifts at decadal scales can have environmental consequences, and therefore, identifying areas that act as environmental refugia is valuable in understanding future climate variability. Here we illustrate how, given appropriate geohydrology, a rift basin and its catchment can buffer vegetation response to climate signals on decadal time-scales, therefore exerting strong local environmental control. We use time-series data derived from Normalised Difference Vegetation Index (NDVI) residuals that record vegetation vigour, extracted from a decadal span of MODIS images, to demonstrate hydrogeological buffering. While this has been described previously it has never been demonstrated via remote sensing and results in relative stability in vegetation vigour inside the delta, compared to that outside. As such the Delta acts as a regional hydro-refugium. This provides insight, not only to the potential impact of future climate in the region, but also demonstrates why similar basins are attractive to fauna, including our ancestors, in regions like eastern Africa. Although vertebrate evolution operates on time scales longer than decades, the sensitivity of rift wetlands to climate change has been stressed by some authors, and this work demonstrates another example of the unique properties that such basins can afford, given the right hydrological conditions

Prevalence of feline calicivirus in cats with odontoclastic resorptive lesions and chronic gingivostomatitis

Feline odontoclastic resorptive lesion (FORL) and feline chronic gingivostomatitis (FCGS) are two of the most common diseases of the feline oral cavity. While evidence is emerging that FCGS is caused by gingival inflammation initiated and perpetuated by the oral microbiota, little is known in this regard for FORL. Feline calicivirus (FCV) has been associated with the presence of FCGS and is thought to play a role in the initiation of this disease. In this study, the incidence of FCV was investigated in cats with FORL and FCGS, and compared to unaffected controls. FCV was detected by viral culture. The incidence of FCV was as follows: 6 (24.0%) of 24 control cats, 9 (22.5%) of 40 cats with FORL and 15 (60.0%) of 25 cats with FCGS were positive for FCV. There was a significant difference in FCV incidence between all the groups (p = 0.003) but none between the control group and the FORL group. However, significant differences were observed in the incidence of FCV between control and FCGS (p = 0.010) and between FORL and FCGS (p = 0.006). It is concluded that although FCV may be associated with FCGS, it appears unlikely to play a role in FORL