Epitope mapping of monoclonal antibodies by mass spectrometry: Identification of protein antigens in complex biological systems

We describe the application of immunoaffinity extraction and mass spectrometry to the analysis of Ty1 Gag protein in lysates of Saccharomyces cerevisiae. A magnetic bead-conjugated monoclonal antibody was used to achieve selective extraction, the specificity of which was established by matrix-assisted laser desorption/ionization mass spectrometric (MS) analysis of an extract of the lysate of cells overexpressing the Ty1 Gag protein. MS analysis of similar extracts of lysates following tryptic hydrolysis confirmed selective extraction of the epitope-containing peptide fragment. Sufficient sensitivity was achieved to allow the application of this approach to the analysis of lysates of wild-type cells. Furthermore, the sequence of the epitope-containing peptide was confirmed by electrospray-tandem MS. To our knowledge, this constitutes the first report of the application of immunoaffinity extraction and tandem MS analysis to the characterization of an antigen recovered from a complex cellular system

Future avenues for educational neuroscience from the perspective of EARLI SIG 22 conference attendees

The 2018 EARLI SIG 22 Neuroscience and Education conference aimed to facilitate the discussion and sharing of research and translation in educational neuroscience. In this article we first describe and evaluate the approach taken in organising the conference, which followed recommendations from the educational neuroscience community. We then summarise responses to a survey that captured delegates’ visions of research and translation, their intentions following the conference, and the support they need moving forward. From 88 completed surveys we first note a common desire for more discussions and collaborations across disciplines, and between teachers and researchers. We highlight particularly novel ideas that are not frequently addressed in the community so far, including discussion of ethical issues, inclusion of learners in research development, open resources for teacher training in neuroscience, and mentoring networks for community members. In sharing these ideas we highlight future directions for the field as it continues to develop

The 412 retrotransposon and the development of gonadal mesoderm in Drosophila

We have shown that the expression of the 412 retrotransposon provides a useful early marker for the development of the gonadal mesoderm in Drosophila embryos. 412 is initially expressed in a set of parasegmentally repeated stripes from parasegments (PS) 2-14 in the mesoderm at the extended germ band stage. During germ band retraction the bulk of 412 expression declines except in dorsolateral clusters of cells in PS10, 11 and 12, where high levels of 412 expression remain. These mesodermal cell clusters are associated with germ cells and subsequently they coalesce, rounding up to form the gonads. The gonadal mesoderm thus appears to originate specifically from three abdominal parasegments, PS10, 11 and 12. We show that the maintenance of high levels of 412 expression in gonadal mesoderm is not induced by contact with germ cells, but rather depends on genetic control by the homeotic genes abdominal-A and Abdominal-B

Nuclear mitochondrial DNA sequences in the rabbit genome

Numtogenesis is observable in the mammalian genomes resulting in the integration of mitochondrial segments into the nuclear genomes (numts). To identify numts in rabbit, we aligned mitochondrial and nuclear genomes. Alignment significance threshold was calculated and individual characteristics of numts were analysed. We found 153 numts in the nuclear genome. The GC content of numts were significantly lower than the GC content of their genomic flanking regions or the genome itself. The frequency of three mammalian-wide interspersed repeats were increased in the proximity of numts. The decreased GC content around numts strengthen the theory which supposes a link between DNA structural instability and numt integration

Scientific collaboration with educators: practical insights from an in‐class noise‐reduction intervention

Moving the field of Mind, Brain, and Education forward requires researchers and educators to reframe the boundaries of their own discipline in order to create knowledge that is both scientifically based, and of practical relevance for education. We believe that this could be done by co‐constructing research projects from the start. We present a case study of a noise‐reduction intervention in elementary classrooms, in which teachers and researchers worked together from the onset of study design. We examine the processes behind: (1) selecting research questions and measures, (2) planning interventions, (3) receiving ethical approval and funding, (4) recruiting schools, and (5) collecting data. At each step, our study provides suggestions for future collaborative efforts, keeping in mind broader theoretical and methodological implications. We believe that our concrete examples and suggestions will be useful for beginning and confirmed researchers, as well as teachers aiming to know more about research projects

A novel Doppler backscattering (DBS) system to simultaneously monitor radio frequency plasma fluctuations and low frequency turbulence

A novel quadrature Doppler Backscattering (DBS) system has been developed and optimized for the E-band (60-90GHz) frequency range using either O-mode or X-mode polarization in DIII-D plasmas. In general, DBS measures the amplitude of density fluctuations and their velocity in the lab frame. The system can simultaneously monitor both low-frequency turbulence (f < 10MHz) and radiofrequency plasma density fluctuations over a selectable frequency range (20-500 MHz). Detection of high-frequency fluctuations has been demonstrated for low harmonics of the ion cyclotron frequency (e.g., 2fci~23MHz) and externally driven high-frequency helicon waves (f = 476MHz) using an adjustable frequency down conversion system. Importantly, this extends the application of DBS to a high-frequency spectral domain while maintaining important turbulence and flow measurement capabilities. This unique system has low phase noise, good temporal resolution (sub-millisecond) and excellent wavenumber coverage (k_{\theta} ~ 1-20cm^{-1} and k_r ~ 20-30cm^{-1}). As a demonstration, localized internal DIII-D plasma measurements are presented from turbulence (f = 20MHz) as well as fluctuations around 476MHz driven by an external high-power 476 MHz helicon wave antenna. In the future, helicon measurements will be used to validate GENRAY and AORSA modeling tools for prediction of helicon wave propagation, absorption and current drive location for the newly installed helicon current drive system on DIII-D.Comment: 13 pages, 14 figs, journal pape