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

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

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. [Abstract copyright: Copyright © 2022 Köhler, Kreil, Wenger, Darmandieu, Graves, Haugestad, Holzen, Keller, Lloyd, Marczak, Međugorac and Rosa.

Hybridization thermodynamics of NimbleGen Microarrays

Background While microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets. Results We demonstrate the benefits of an improved model for microarray hybridization and assess the relative contributions of the probe-target binding strength and the different competing structures. Remarkably, specific and unspecific hybridization were apparently driven by different energetic contributions: For unspecific hybridization, the melting temperature Tm was the best predictor of signal variation. For specific hybridization, however, the effective interaction energy that fully considered competing structures was twice as powerful a predictor of probe signal variation. We show that this was largely due to the effects of secondary structures in the probe and target molecules. The predictive power of the strength of these intramolecular structures was already comparable to that of the melting temperature or the free energy of the probe-target duplex. Conclusions This analysis illustrates the importance of considering both the effects of probe-target binding strength and the different competing structures. For specific hybridization, the secondary structures of probe and target molecules turn out to be at least as important as the probe-target binding strength for an understanding of the observed microarray signal intensities. Besides their relevance for the design of new arrays, our results demonstrate the value of improving thermodynamic models for the read-out and interpretation of microarray signals

Systems Biology Approach Predicts Antibody Signature Associated with Brucella melitensis Infection in Humans

A complete understanding of the factors that determine selection of antigens recognized by the humoral immune response following infectious agent challenge is lacking. Here we illustrate a systems biology approach to identify the antibody signature associated with Brucella melitensis (Bm) infection in humans and predict proteomic features of serodiagnostic antigens. By taking advantage of a full proteome microarray expressing previously cloned 1406 and newly cloned 1640 Bm genes, we were able to identify 122 immunodominant antigens and 33 serodiagnostic antigens. The reactive antigens were then classified according to annotated functional features (COGs), computationally predicted features (e.g., subcellular localization, physical properties), and protein expression estimated by mass spectrometry (MS). Enrichment analyses indicated that membrane association and secretion were significant enriching features of the reactive antigens, as were proteins predicted to have a signal peptide, a single transmembrane domain, and outer membrane or periplasmic location. These features accounted for 67% of the serodiagnostic antigens. An overlay of the seroreactive antigen set with proteomic data sets generated by MS identified an additional 24%, suggesting that protein expression in bacteria is an additional determinant in the induction of Brucella-specific antibodies. This analysis indicates that one-third of the proteome contains enriching features that account for 91% of the antigens recognized, and after B. melitensis infection the immune system develops significant antibody titers against 10% of the proteins with these enriching features. This systems biology approach provides an empirical basis for understanding the breadth and specificity of the immune response to B. melitensis and a new framework for comparing the humoral responses against other microorganisms