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  1. Free, publicly-accessible full text available March 1, 2023
  2. Musier-Forsyth, Karin (Ed.)
    RNA-binding proteins play crucial roles in various cellular functions, and contain abundant disordered protein regions. The disordered regions in RNA-binding proteins are rich in repetitive sequences, such as poly-K/R, poly-N/Q, poly-A, and poly-G residues. Our bioinformatic analysis identified a largely neglected repetitive sequence family we define as electronegative clusters (ENCs) that contain acidic residues and/or phosphorylation sites. The abundance and length of ENCs exceed other known repetitive sequences. Despite their abundance, the functions of ENCs in RNA-binding proteins are still elusive. To investigate the impacts of ENCs on protein stability, RNA-binding affinity, and specificity, we selected one RNA-binding protein, themore »ribosomal biogenesis factor 15 (Nop15) as a model. We found that the Nop15 ENC increases protein stability and inhibits nonspecific RNA binding, but minimally interferes with specific RNA binding. To investigate the effect of ENCs on sequence specificity of RNA binding, we grafted an ENC to another RNA-binding protein, Ser/Arg-rich splicing factor 3 (SRSF3). Using RNA Bind-n-Seq, we found that the engineered ENC inhibits disparate RNA motifs differently, instead of weakening all RNA motifs to the same extent. The motif site directly involved in electrostatic interaction is more susceptible to the ENC inhibition. These results suggest that one of functions of ENCs is to regulate RNA binding via electrostatic interaction. This is consistent with our finding that ENCs are also overrepresented in DNA-binding proteins, while underrepresented in halophiles, in which nonspecific nucleic acid binding is inhibited by high concentrations of salts.« less
    Free, publicly-accessible full text available July 9, 2022
  3. ABSTRACT After correcting for their light-curve shape and colour, Type Ia supernovae (SNe Ia) are precise cosmological distance indicators. However, there remains a non-zero intrinsic scatter in the differences between measured distance and that inferred from a cosmological model (i.e. Hubble residuals or HRs), indicating that SN Ia distances can potentially be further improved. We use the open-source relational data base kaepora to generate composite spectra with desired average properties of phase, light-curve shape, and HR. At many phases, the composite spectra from two subsamples with positive and negative average HRs are significantly different. In particular, in all spectra from 9 d beforemore »to 15 d after peak brightness, we find that SNe with negative HRs have, on average, higher ejecta velocities (as seen in nearly every optical spectral feature) than SNe with positive HRs. At +4 d relative to B-band maximum, using a sample of 62 SNe Ia, we measure a 0.091 ± 0.035 mag (2.7σ) HR step between SNe with Si ii λ6355 line velocities ($v_{Si\, rm{\small II}}$) higher/lower than −11 000 km s−1 (the median velocity). After light-curve shape and colour correction, SNe with higher velocities tend to have underestimated distance moduli relative to a cosmological model. The intrinsic scatter in our sample reduces from 0.094 to 0.082 mag after making this correction. Using the Si ii λ6355 velocity evolution of 115 SNe Ia, we estimate that a velocity difference >500 km s−1 exists at each epoch between the positive-HR and negative-HR samples with 99.4 per cent confidence. Finally at epochs later than +37 d, we observe that negative-HR composite spectra tend to have weaker spectral features in comparison to positive-HR composite spectra.« less
  4. Engineering work is becoming increasingly global in nature, making it essential that engineering students develop global competence [1], [2]. However, traditional global programs (e.g., study abroad) present challenges for engineering students who often have to fit such experiences within a highly structured curricular schedule. Further, study abroad can be a financial burden for many students who are already paying significant amounts to attend college [3], [4]. One type of global engineering program that has the potential to address these challenges are international research experiences, which typically take place during the summer and provide students with a salary. Research has suggestedmore »that such experiences can meaningfully influence students’ global competence [5], but few studies have explored how components of the experience may influence learning. This study compares two NSF-sponsored international research experiences for students (IRES) programs that send students to two different countries to identify differences in learning outcomes between the program participants. This work represents a collaborative effort among faculty members and graduate students from three engineering departments with the goal of creating research opportunities for students at various international sites using research-based educational practices. By understanding how context influences students’ learning opportunities, faculty developing such programs may select research locations more intentionally or offer supplemental programming for students to ensure they achieve all of the program’s intended learning outcomes.« less