Electroexcitation of the Roper resonance from CLAS data

The helicity amplitudes of the electroexcitation of the Roper resonance on proton are extracted at 1.7 < Q2 < 4.2 GeV2 from recent high precision JLab-CLAS cross sections data and longitudinally polarized beam asymmetry for pi+ electroproduction on protons. The analysis is made using two approaches, dispersion relations and unitary isobar model, which give consistent results. It is found that the transverse helicity amplitude for the gamma* p --> P11(1440) transition, which is large and negative at Q2=0, becomes large and positive at Q2 ~ 2 GeV2, and then drops slowly with Q2. Longitudinal helicity amplitude, that was previously found from CLAS data as large and positive at Q2=0.4,0.65 GeV2, drops with Q2. These results rule out the presentation of P11(1440) as a 3qG hybrid state, and provide strong evidence in favor of this resonance as a first radial excitation of the 3q ground state.Comment: 3 pages, 2 figures, Talk on the Workshop on "The Physics of Excited Nucleons", Bonn, Germany, October 200

Out-of-Plane Magnetic Anisotropy in Ordered Ensembles of Fey_yN Nanocrystals Embedded in GaN

Phase-separated semiconductors containing magnetic nanostructures are relevant systems for the realization of high-density recording media. Here, the controlled strain engineering of Ga$\delta$FeN layers with Fe$_y$N embedded nanocrystals (NCs) \textit{via} Al$_x$Ga$_{1-x}$N buffers with different Al concentration $0<x_\mathrm{Al}<41$\% is presented. Through the addition of Al to the buffer, the formation of predominantly prolate-shaped $\varepsilon$-Fe$_3$N NCs takes place. Already at an Al concentration $x_\mathrm{Al}$\,$\approx$\,5\% the structural properties---phase, shape, orientation---as well as the spatial distribution of the embedded NCs are modified in comparison to those grown on a GaN buffer. Although the magnetic easy axis of the cubic $\gamma$'-Ga$_y$Fe$_{4-y}$N nanocrystals in the layer on the $x_\mathrm{Al} = 0\%$ buffer lies in-plane, the easy axis of the $\varepsilon$-Fe$_3$N NCs in all samples with Al$_x$Ga$_{1-x}$N buffers coincides with the $[0001]$ growth direction, leading to a sizeable out-of-plane magnetic anisotropy and opening wide perspectives for perpendicular recording based on nitride-based magnetic nanocrystals.Comment: 29 pages, 10 figures, submitte

Genomic and transcriptional analysis of protein heterogeneity of the honeybee venom allergen Api m 6

Several components of honeybee venom are known to cause allergenic responses in humans and other vertebrates. One such component, the minor allergen Api m 6, has been known to show amino acid variation but the genetic mechanism for this variation is unknown. Here we show that Api m 6 is derived from a single locus, and that substantial protein-level variation has a simple genome-level cause, without the need to invoke multiple loci or alternatively spliced exons. Api m 6 sits near a misassembled section of the honeybee genome sequence, and we propose that a substantial number of indels at and near Api m 6 might be the root cause of this misassembly. We suggest that genes such as Api m 6 with coding-region or untranslated region indels might have had a strong effect on the assembly of this draft of the honeybee genome

The need for sustainability, equity, and international exchange: perspectives of early career environmental psychologists on the future of conferences

At the 2019 and 2021 International Conference on Environmental Psychology, discussions were held on the future of conferences in light of the enormous greenhouse gas emissions and inequities associated with conference travel. In this manuscript, we provide an early career researcher (ECR) perspective on this discussion. We argue that travel-intensive conference practices damage both the environment and our credibility as a discipline, conflict with the intrinsic values and motivations of our discipline, and are inequitable. As such, they must change. This change can be achieved by moving toward virtual and hybrid conferences, which can reduce researchers’ carbon footprints and promote equity, if employed carefully and with informal exchange as a priority. By acting collectively and with the support of institutional change, we can adapt conference travel norms in our field. To investigate whether our arguments correspond to views in the wider community of ECRs within environmental psychology, we conducted a community case study. By leveraging our professional networks and directly contacting researchers in countries underrepresented in those networks, we recruited 117 ECRs in 32 countries for an online survey in February 2022. The surveyed ECRs supported a change in conference travel practices, including flying less, and perceived the number of researchers wanting to reduce their travel emissions to be growing. Thirteen percent of respondents had even considered leaving academia due to travel requirements. Concerning alternative conference formats, a mixed picture emerged. Overall, participants had slightly negative evaluations of virtual conferences, but expected them to improve within the next 5 years. However, ECRs with health issues, facing visa challenges, on low funding, living in remote areas, with caretaking obligations or facing travel restrictions due to COVID-19 expected a switch toward virtual or hybrid conferences to positively affect their groups. Participants were divided about their ability to build professional relationships in virtual settings, but believed that maintaining relationships virtually is possible. We conclude by arguing that the concerns of ECRs in environmental psychology about current and alternative conference practices must be taken seriously. We call on our community to work on collective solutions and less travel-intensive conference designs using participatory methods. Copyright © 2022 Köhler, Kreil, Wenger, Darmandieu, Graves, Haugestad, Holzen, Keller, Lloyd, Marczak, Medugorac and Rosa

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized

Model-based probe set optimization for high-performance microarrays

A major challenge in microarray design is the selection of highly specific oligonucleotide probes for all targeted genes of interest, while maintaining thermodynamic uniformity at the hybridization temperature. We introduce a novel microarray design framework (Thermodynamic Model-based Oligo Design Optimizer, TherMODO) that for the first time incorporates a number of advanced modelling features: (i) A model of position-dependent labelling effects that is quantitatively derived from experiment. (ii) Multi-state thermodynamic hybridization models of probe binding behaviour, including potential cross-hybridization reactions. (iii) A fast calibrated sequence-similarity-based heuristic for cross-hybridization prediction supporting large-scale designs. (iv) A novel compound score formulation for the integrated assessment of multiple probe design objectives. In contrast to a greedy search for probes meeting parameter thresholds, this approach permits an optimization at the probe set level and facilitates the selection of highly specific probe candidates while maintaining probe set uniformity. (v) Lastly, a flexible target grouping structure allows easy adaptation of the pipeline to a variety of microarray application scenarios. The algorithm and features are discussed and demonstrated on actual design runs. Source code is available on request

Transport of Proteins into Mitochondria

The mitochondrial ADP/ATP carrier is an integral transmembrane protein of the inner membrane. It is synthesized on cytoplasmic ribosomes. Kinetic data suggested that this protein is transferred into mitochondria in a posttranslational manner. The following results provide further evidence for such a mechanism and provide information on its details. 1. In homologous and heterologous translation systems the newly synthesized ADP/ATP carrier protein is present in the postribosomal supernatant. 2. Analysis by density gradient centrifugation and gel filtration shows, that the ADP/ATP carrier molecules in the postribosomal fraction are present as soluble complexes with apparent molecular weights of about 120000 and 500000 or larger. The carrier binds detergents such as Triton X-100 and deoxycholate forming mixed micelles with molecular weights of about 200000–400000. 3. Incubation of a postribosomal supernatant of a reticulocyte lysate containing newly synthesized ADP/ATP carrier with mitochondria isolated from Neurospora spheroplasts results in efficient transfer of the carrier into mitochondria. About 20–30% of the transferred carrier are resistant to proteinase in whole mitochondria. The authentic mature protein is also largely resistant to proteinase in whole mitochondria and sensitive after lysis of mitochondria with detergent. Integrity of mitochondria is a prerequisite for translocation into proteinase resistant position. 4. The transfer in vitro into a proteinase-resistant form is inhibited by the uncoupler carbonyl-cyanide m-chlorophenylhydrazone but not the proteinase-sensitive binding. These observations suggest that the posttranslational transfer of ADP/ATP carrier occurs via the cytosolic space through a soluble oligomeric precursor form. This precursor is taken up by intact mitochondria into an integral position in the membrane. These findings are considered to be of general importance for the intracellular transfer of insoluble membrane proteins. They support the view that such proteins can exist in a water-soluble form its precursors and upon integration into the membrane undergo a conformational change. Uptake into the membrane may involve the cleavage of an additional sequence in some proteins, but this appears not to be a prerequisite as demonstrated by the ADP/ATP carrier protein

Substrate specificity of a peptidyl-aminoacyl-l/d-isomerase from frog skin

In the skin of fire-bellied toads (Bombina species), an aminoacyl-l/d-isomerase activity is present which catalyses the post-translational isomerization of the l- to the d-form of the second residue of its substrate peptides. Previously, this new type of enzyme was studied in some detail and genes potentially coding for similar polypeptides were found to exist in several vertebrate species including man. Here, we present our studies to the substrate specificity of this isomerase using fluorescence-labeled variants of the natural substrate bombinin H with different amino acids at positions 1, 2 or 3. Surprisingly, this enzyme has a rather low selectivity for residues at position 2 where the change of chirality at the alpha-carbon takes place. In contrast, a hydrophobic amino acid at position 1 and a small one at position 3 of the substrate are essential. Interestingly, some peptides containing a Phe at position 3 also were substrates. Furthermore, we investigated the role of the amino-terminus for substrate recognition. In view of the rather broad specificity of the frog isomerase, we made a databank search for potential substrates of such an enzyme. Indeed, numerous peptides of amphibia and mammals were found which fulfill the requirements determined in this study. Expression of isomerases with similar characteristics in other species can therefore be expected to catalyze the formation of peptides containing d-amino acids

BibGlimpse: The case for a light-weight reprint manager in distributed literature research

Background While text-mining and distributed annotation systems both aim at capturing knowledge and presenting it in a standardized form, there have been few attempts to investigate potential synergies between these two fields. For instance, distributed annotation would be very well suited for providing topic focussed, expert knowledge enriched text corpora. A key limitation for this approach is the availability of literature annotation systems that can be routinely used by groups of collaborating researchers on a day to day basis, not distracting from the main focus of their work. Results For this purpose, we have designed BibGlimpse. Features like drop-to-file, SVM based automated retrieval of PubMed bibliography for PDF reprints, and annotation support make BibGlimpse an efficient, light-weight reprint manager that facilitates distributed literature research for work groups. Building on an established open search engine, full-text search and structured queries are supported, while at the same time making shared collections of annotated reprints accessible to literature classification and text-mining tools. Conclusion BibGlimpse offers scientists a tool that enhances their own literature management. Moreover, it may be used to create content enriched, annotated text corpora for research in text-mining