Surface enrichment in equimolar mixtures of non-functionalized and functionalized imidazolium-based ionic liquids

For equimolar mixtures of ionic liquids with imidazolium‐based cations of very different electronic structure, we observe very pronounced surface enrichment effects by angle‐resolved X‐ray photoelectron spectroscopy (XPS). For a mixture with the same anion, that is, 1‐methyl‐3‐octylimidazolium hexafluorophosphate+1,3‐di(methoxy)imidazolium hexafluorophosphate ([C8C1Im][PF6]+[(MeO)2Im][PF6]), we find a strong enrichment of the octyl chain‐containing [C8C1Im]+ cation and a corresponding depletion of the [(MeO)2Im]+ cation in the topmost layer. For a mixture with different cations and anions, that is, [C8C1Im][Tf2N]+[(MeO)2Im][PF6], we find both surface enrichment of the [C8C1Im]+ cation and the [Tf2N]− (bis[(trifluoromethyl)sulfonyl]imide) anion, while [(MeO)2Im]+ and [PF6]− are depleted from the surface. We propose that the observed behavior in these mixtures is due to a lowering of the surface tension by the enriched components. Interestingly, we observe pronounced differences in the chemical shifts of the imidazolium ring signals of the [(MeO)2Im]+ cations as compared to the non‐functionalized cations. Calculations of the electronic structure and the intramolecular partial charge distribution of the cations contribute to interpreting these shifts for the two different cations

ToxoDB: an integrated Toxoplasma gondii database resource

ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. ToxoDB has matured significantly since its initial release. Here we outline the numerous updates with respect to the data and increased functionality available on the website

GiardiaDB and TrichDB : integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

© 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. The definitive version was published in Nucleic Acids Research 37 (2009): D526-D530, doi:10.1093/nar/gkn631.GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.Federal funds from the National Institute of Allergy and Infectious Diseases; Department of Health and Human Services, National Institutes of Health (HHSN266200400037C). Funding for open access charge: National Institutes of Health (HHSN266200400037C)

Beyond Shielding: The Roles of Glycans in the SARS-CoV‑2 Spike Protein

The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and 900,000 deaths worldwide to date. Antibody development efforts mainly revolve around the extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin-converting enzyme 2 (ACE2). Similar to many other viral fusion proteins, the SARS-CoV-2 spike utilizes a glycan shield to thwart the host immune response. Here, we built a full-length model of the glycosylated SARS-CoV-2 S protein, both in the open and closed states, augmenting the available structural and biological data. Multiple microsecond-long, all-atom molecular dynamics simulations were used to provide an atomistic perspective on the roles of glycans and on the protein structure and dynamics. We reveal an essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of the spike’s receptor binding domain (RBD), which is responsible for ACE2 recognition. This finding is corroborated by biolayer interferometry experiments, which show that deletion of these glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift toward the “down” state. Additionally, end-to-end accessibility analyses outline a complete overview of the vulnerabilities of the glycan shield of the SARS-CoV-2 S protein, which may be exploited in the therapeutic efforts targeting this molecular machine. Overall, this work presents hitherto unseen functional and structural insights into the SARS-CoV-2 S protein and its glycan coat, providing a strategy to control the conformational plasticity of the RBD that could be harnessed for vaccine development

Spontaneous magnetic orientation in larval Drosophila shares properties with learned magnetic compass responses in adult flies and mice

We provide evidence for spontaneous quadramodal magnetic orientation in a larval insect. Second instar Berlin, Canton-S and Oregon-R x Canton-S strains of Drosophila melanogaster exhibited quadramodal orientation with clusters of bearings along the four anti-cardinal compass directions (i.e. 45, 135, 225 and 315 deg). In double-blind experiments, Canton-S Drosophila larvae also exhibited quadramodal orientation in the presence of an earth-strength magnetic field, while this response was abolished when the horizontal component of the magnetic field was cancelled, indicating that the quadramodal behavior is dependent on magnetic cues, and that the spontaneous alignment response may reflect properties of the underlying magnetoreception mechanism. In addition, a re-analysis of data from studies of learned magnetic compass orientation by adult Drosophila melanogaster and C57BL/6 mice revealed patterns of response similar to those exhibited by larval flies, suggesting that a common magnetoreception mechanism may underlie these behaviors. Therefore, characterizing the mechanism(s) of magnetoreception in flies may hold the key to understanding the magnetic sense in a wide array of terrestrial organisms

A miniature Marine Aerosol Reference Tank (miniMART) as a compact breaking wave analogue

In order to understand the processes governing the production of marine aerosols, repeatable, controlled methods for their generation are required. A new system, the miniature Marine Aerosol Reference Tank (miniMART), has been designed after the success of the original MART system, to approximate a small oceanic spilling breaker by producing an evolving bubble plume and surface foam patch. The smaller tank utilizes an intermittently plunging jet of water produced by a rotating water wheel, into an approximately 6 L reservoir to simulate bubble plume and foam formation and generate aerosols. This system produces bubble plumes characteristic of small whitecaps without the large external pump inherent in the original MART design. Without the pump it is possible to easily culture delicate planktonic and microbial communities in the bulk water during experiments while continuously producing aerosols for study. However, due to the reduced volume and smaller plunging jet, the absolute numbers of particles generated are approximately an order of magnitude less than in the original MART design