Long-Range Conformational Changes in Monoclonal Antibodies Revealed Using FPOP-LC-MS/MS

Differences in conformational dynamics between two full-length monoclonal antibodies have been probed in detail using Fast Photochemical Oxidation of Proteins (FPOP) followed by proteolysis and LC-ESI-MS/MS analyses. FPOP uses hydroxyl radical labelling to probe the surface-accessible regions of proteins and has the advantage that the resulting covalent modifications are irreversible, thus permitting optimal down-stream analysis. Despite the two monoclonal antibodies (mAbs) differing by only three amino acids in the heavy chain complementarity determining regions (CDRs), one mAb, MEDI1912-WFL, has been shown to undergo reversible self-association at high concentrations and exhibited poor pharmacokinetic properties in vivo, properties which are markedly improved in the variant, MEDI1912-STT. Identifying the differences in oxidative labelling between the two antibodies at residue level revealed long-range effects which provide a key insight into their conformational differences. Specifically, the amino acid mutations in the CDR region of the heavy chain resulted in significantly different labelling patterns at the interfaces of the CL–CH1 and CH1–CH2 domains, with the non-aggregating variant undergoing up to four times more labelling in this region than the aggregation prone variant, thus suggesting a change in the structure and orientation of the CL – CH1 interface. The wealth of FPOP and LC-MS data obtained enabled the study of the LC elution properties of FPOP-oxidised peptides. Some oxidised amino acids, specifically histidine and lysine, were noted to have unique effects on the retention time of the peptide, offering the promise of using such an analysis as an aid to MS/MS in assigning oxidation sites

New zebrafish models of neurodegeneration

In modern biomedicine, the increasing need to develop experimental models to further our understanding of disease conditions and delineate innovative treatments has found in the zebrafish (Danio rerio) an experimental model, and indeed a valuable asset, to close the gap between in vitro and in vivo assays. Translation of ideas at a faster pace is vital in the field of neurodegeneration, with the attempt to slow or prevent the dramatic impact on the society's welfare being an essential priority. Our research group has pioneered the use of zebrafish to contribute to the quest for faster and improved understanding and treatment of neurodegeneration in concert with, and inspired by, many others who have primed the study of the zebrafish to understand and search for a cure for disorders of the nervous system. Aware of the many advantages this vertebrate model holds, here, we present an update on the recent zebrafish models available to study neurodegeneration with the goal of stimulating further interest and increasing the number of diseases and applications for which they can be exploited. We shall do so by citing and commenting on recent breakthroughs made possible via zebrafish, highlighting their benefits for the testing of therapeutics and dissecting of disease mechanisms

An in vivo platform to select and evolve aggregation-resistant proteins

Protein biopharmaceuticals are highly successful, but their utility is compromised by their propensity to aggregate during manufacture and storage. As aggregation can be triggered by non-native states, whose population is not necessarily related to thermodynamic stability, prediction of poorly-behaving biologics is difficult, and searching for sequences with desired properties is labour-intensive and time-consuming. Here we show that an assay in the periplasm of E. coli linking aggregation directly to antibiotic resistance acts as a sensor for the innate (un-accelerated) aggregation of antibody fragments. Using this assay as a directed evolution screen, we demonstrate the generation of aggregation resistant scFv sequences when reformatted as IgGs. This powerful tool can thus screen and evolve ‘manufacturable’ biopharmaceuticals early in industrial development. By comparing the mutational profiles of three different immunoglobulin scaffolds, we show the applicability of this method to investigate protein aggregation mechanisms important to both industrial manufacture and amyloid disease

Evidence for solar cycles in a late Holocene speleothem record from Dongge Cave, China

The association between solar activity and Asian monsoon (AM) remains unclear. Here we evaluate the possible connection between them based on a precisely-dated, high-resolution speleothem oxygen isotope record from Dongge Cave, southwest China during the past 4.2 thousand years (ka). Without being adjusted chronologically to the solar signal, our record shows a distinct peak-to-peak correlation with cosmogenic nuclide 14C, total solar irradiance (TSI) and sunspot number (SN) at multi-decadal to centennial timescales. Further cross-wavelet analyses between our calcite δ18O and atmospheric 14C show statistically strong coherence at three typical periodicities of ~80, 200 and 340 years, suggesting important roles of solar activities in modulating AM changes at those timescales. Our result has further indicated a better correlation between our calcite δ18O record and atmospheric 14C than between our record and TSI. This better correlation may imply that the Sun–monsoon connection is dominated most likely by cosmic rays and oceanic circulation (both associated to atmospheric 14C), instead of the direct solar heating (TSI)

Cosmological parameters from the clustering of AGN

We attempt to put constraints on different cosmological and biasing models by combining the recent clustering results of X-ray sources in the local ($z\le 0.1$) and distant universe ($z\sim 1$).Comment: 9 pages, 3 figures, to be published in the proceedings of the ''2nd Hellenic Cosmology Workshop'', Athens 2001, eds, Manolis Plionis & Spiros Kotsaki

Is it harder to know or to reason? Analyzing two-tier science assessment items using the Rasch measurement model

Two-tier multiple-choice (TTMC) items are used to assess students’ knowledge of a scientific concept for tier 1 and their reasoning about this concept for tier 2. But are the knowledge and reasoning involved in these tiers really distinguishable? Are the tiers equally challenging for students? The answers to these questions influence how we use and interpret TTMC instruments. We apply the Rasch measurement model on TTMC items to see if the items are distinguishable according to different traits (represented by the tier), or according to different content sub-topics within the instrument, or to both content and tier. Two TTMC data sets are analyzed: data from Singapore and Korea on the Light Propagation Diagnostic Instrument (LPDI), data from the United States on the Classroom Test of Scientific Reasoning (CTSR). Findings for LPDI show that tier-2 reasoning items are more difficult than tier-1 knowledge items, across content sub-topics. Findings for CTSR do not show a consistent pattern by tier or by content sub-topic. We conclude that TTMC items cannot be assumed to have a consistent pattern of difficulty by tier—and that assessment developers and users need to consider how the tiers operate when administering TTMC items and interpreting results. Researchers must check the tiers’ difficulties empirically during validation and use. Though findings from data in Asian contexts were more consistent, further study is needed to rule out differences between the LPDI and CTSR instruments

School wellbeing among children in grades 1 - 10

<p>Abstract</p> <p>Background</p> <p>Determinants of children's school wellbeing have not been extensively studied. In this cross-sectional study of school children we assessed how factors assumed to promote wellbeing and factors assumed to adversely influence wellbeing were associated with self-reported wellbeing in school.</p> <p>Methods</p> <p>Children from five schools, 230 boys and 189 girls in grades 1-10, responded to the same set of questions. We used proportional odds logistic regression to assess the associations of promoting and restraining factors with school wellbeing.</p> <p>Results</p> <p>In a multivariable analysis, degree of school wellbeing in boys was strongly and positively related to enjoying school work (odds ratio, 3.84, 95% CI 2.38 to 6.22) and receiving necessary help (odds ratio, 3.55, 95% CI 2.17 to 5.80) from teachers. In girls, being bothered during lessons was strongly and negatively associated with school wellbeing (odds ratio, 0.43, 95% CI 0.22 to 0.85).</p> <p>Conclusions</p> <p>Different factors may determine school wellbeing in boys and girls, but for both genders, factors relevant for lessons may be more important than factors related to recess. Especially in boys, the student-teacher relationship may be of particular importance.</p

Comment on "The extent of forest in dryland biomes"

Bastin et al (Reports, 12 May 2017, p. 635) infer forest as more globally extensive than previously estimated using tree cover data. However, their forest definition does not reflect ecosystem function or biotic composition. These structural and climatic definitions inflate forest estimates across the tropics and undermine conservation goals, leading to inappropriate management policies and practices in tropical grassy ecosystems