Charge environments around phosphorylation sites in proteins

Background: Phosphorylation is a central feature in many biological processes. Structural analyses have identified the importance of charge-charge interactions, for example mediating phosphorylation-driven allosteric change and protein binding to phosphopeptides. Here, we examine computationally the prevalence of charge stabilisation around phosphorylated sites in the structural database, through comparison with locations that are not phosphorylated in the same structures. Results: A significant fraction of phosphorylated sites appear to be electrostatically stabilised, largely through interaction with sidechains. Some examples of stabilisation across a subunit interface are evident from calculations with biological units. When considering the immediately surrounding environment, in many cases favourable interactions are only apparent after conformational change that accompanies phosphorylation. A simple calculation of potential interactions at longer-range, applied to non-phosphorylated structures, recovers the separation exhibited by phosphorylated structures. In a study of sites in the Phospho.ELM dataset, for which structural annotation is provided by non-phosphorylated proteins, there is little separation of the known phospho-acceptor sites relative to background, even using the wider interaction radius. However, there are differences in the distributions of patch polarity for acceptor and background sites in the Phospho.ELM dataset. Conclusion: In this study, an easy to implement procedure is developed that could contribute to the identification of phospho-acceptor sites associated with charge-charge interactions and conformational change. Since the method gives information about potential anchoring interactions subsequent to phosphorylation, it could be combined with simulations that probe conformational change. Our analysis of the Phospho.ELM dataset also shows evidence for mediation of phosphorylation effects through (i) conformational change associated with making a solvent inaccessible phospho-acceptor site accessible, and (ii) modulation of protein-protein interactions

Foreword to Symposium on School Finance Litigation: Emerging Trends or New Dead Ends?

Equality of educational opportunity is an elusive goal. Advocates for underprivileged students have pursued it relentlessly in the courts since the landmark decision fifty years ago in Brown v. Board of Education. Yet children across the United States still attend schools that are both separate and unequal. The United States contains approximately 15,000 school districts. This fragmentation, along with the Supreme Court\u27s decision in Milliken v. Bradley to prohibit mandatory busing across district lines, allows patterns of residential segregation to produce segregated schools. In 2000-01, seventy-two percent of African-American and seventy-six percent of Latino students attended predominantly minority schools. Thirty-seven percent of African- American and Latino students attended schools that were 90-100% minority. One-sixth of African-American and one-ninth of Latino students attended schools that were 99-100% minority

The representation of response effector and response location in episodic memory for newly acquired actions:evidence from retrieval-induced forgetting

Information retrieval can cause forgetting for related but non-retrieved information. Such retrieval-induced forgetting (RIF) has been previously found for semantically and episodically related information. The current study used RIF to examine whether response effector and location are encoded explicitly in action memory. Participants learned unique touchscreen responses to ten novel objects. Correct actions to each object involved left-hand or right-hand pushing of one of four possible object buttons. After learning, participants practiced two of the ten object-specific sequences. Unpracticed actions could share hand only, button only, both hand and button, or neither hand nor button, with the practiced actions. Subsequent testing showed significant RIF (in retrieval accuracy and speed measures) for actions that shared hand only, button only, or both hand and button with the practiced action. The results have implications for understanding the representations mediating episodic action memory, and for the potential of RIF as a tool for elucidating feature-based representations in this and other domains

A New Baseline for Diadema antillarum, Echinometra viridis, E. lucunter, and Eucidaris tribuloides Populations Within the Cayos Cochinos MPA, Honduras

We investigated the density of 4 urchin species from 5 shallow reefs in the Cayos Cochinos Marine Protected Area in Honduras. Individual species density varied among reefs with total urchin density ranging from 3.2–7.9 individuals/m2. Echinometra viridis (Agassiz, 1863) was the numerically dominant species (2.29/m2) followed by E. lucunter (Linnaeus, 1758) (1.76/m2) with Eucidaris tribuloides (Lamarck 1816) representing the fewest individuals (0.42/m2). Our results indicated that density of Diadema antillarum (Philippi, 1845) differed significantly among reefs (0.4-1.3/m2, mean = 0.63/m2), but are three times greater than data collected 12 years after the mass mortality event of the 1980’s. Size frequency analysis of D. antillarum indicated that test diameter also differed significantly among reef sites while correlation analysis showed that D. antillarum density was negatively related to both coral and algal cover. Echinometra viridis density, however, was positively related to coral cover (p \u3c 0.05). When all urchins were combined, they showed a negative correlation with algal cover and a positive correlation with coral cover indicating a potential top-down effect within the reefs. While urchin densities remain relatively low compared to other sites in the Caribbean, the D. antillarum population appears to be recovering in this Honduran MPA. If overall grazer abundance continues to increase then they may limit macroalgae on reefs, thereby encouraging coral settlement

Nineteenth-Century Popular Science Magazines, Narrative, and the Problem of Historical Materiality

In his Some Reminiscences of a Lecturer, Andrew Wilson emphasizes the importance of narrative to popular science lecturing. Although Wilson promotes the teaching of science as useful knowledge in its own right, he also recognizes that the way science is taught can encourage audiences to take the subject up and read further on their own. Form, according to Wilson, should not be divorced from scientific content and lecturers should ensure that not only is their science accurate, but that it is presented in a way that will provoke curiosity and stimulate interest. This paper discusses the influence of narrative in structuring scientific objects and phenomena, and considers the consequences of such presentations for historical research. As scientific journalism necessarily weaves both its intended audience and the objects under discussion into its accounts, these texts demand that we recognize their nature as social relationships inscribed in historical objects

Redshifts and Velocity Dispersions of Galaxy Clusters in the Horologium-Reticulum Supercluster

We present 118 new optical redshifts for galaxies in 12 clusters in the Horologium-Reticulum supercluster (HRS) of galaxies. For 76 galaxies, the data were obtained with the Dual Beam Spectrograph on the 2.3m telescope of the Australian National University at Siding Spring Observatory. After combining 42 previously unpublished redshifts with our new sample, we determine mean redshifts and velocity dispersions for 13 clusters, in which previous observational data were sparse. In six of the 13 clusters, the newly determined mean redshifts differ by more than 750 km/s from the published values. In the case of three clusters, A3047, A3109, and A3120, the redshift data indicate the presence of multiple components along the line of sight. The new cluster redshifts, when combined with other reliable mean redshifts for clusters in the HRS, are found to be distinctly bi-modal. Furthermore, the two redshift components are consistent with the bi-modal redshift distribution found for the inter-cluster galaxies in the HRS by Fleenor et al. (2005).Comment: 13 pages, 3 figures, Accepted to A

An Overview of the A-3 Subscale Diffuser Test Project

The Subscale Diffuser Test (SDT) Project comprised a series of tests of a subscale model of SSC s A-3 Test Stand diffuser. SDT was conducted at NASA s Stennis Space Center (SSC) Apr 2007 - Jan 2008. Purpose of SDT was to mitigate design risk for the A-3 diffuser. Initial scope of the SDT project successfully completed in Jan 2008. Follow-on A-3 risk mitigation testing being planned/considered. This presentation presents an overview of the SDT project

Bostonia: The Boston University Alumni Magazine. Volume 32

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

All-Versus-Nothing Proof of Einstein-Podolsky-Rosen Steering

Einstein-Podolsky-Rosen steering is a form of quantum nonlocality intermediate between entanglement and Bell nonlocality. Although Schr\"odinger already mooted the idea in 1935, steering still defies a complete understanding. In analogy to "all-versus-nothing" proofs of Bell nonlocality, here we present a proof of steering without inequalities rendering the detection of correlations leading to a violation of steering inequalities unnecessary. We show that, given any two-qubit entangled state, the existence of certain projective measurement by Alice so that Bob's normalized conditional states can be regarded as two different pure states provides a criterion for Alice-to-Bob steerability. A steering inequality equivalent to the all-versus-nothing proof is also obtained. Our result clearly demonstrates that there exist many quantum states which do not violate any previously known steering inequality but are indeed steerable. Our method offers advantages over the existing methods for experimentally testing steerability, and sheds new light on the asymmetric steering problem.Comment: 7 pages, 2 figures. Accepted in Sci. Re

Remote sensing to characterize inundation and vegetation dynamics of upland lagoons

Understanding broad trends in the distribution and composition of wetlands is essential for making evidence-based management decisions. Determining temporal change in the extent of inundation in wetlands using remote sensing remains challenging and requires on-ground verification to determine accuracy and precision. Therefore, optimization and validation of remote sensing methods in threatened wetlands is a high priority for their conservation. Despite their ecological importance in the landscape, we have little knowledge of the variation in the spatial extent of inundation in upland lagoons, a threatened ecological community in New South Wales, Australia. Our project developed locally trained algorithms to predict the extent of water and emergent vegetation using imagery from the Landsat-5, -7, and -8 satellites. The best model for upland lagoons used shortwave infrared reflectance (performing better than normalized difference spectral indices), with model accuracy against validation transects greater than 95%. We applied the model to images from 1988 to 2020 across 58 lagoons to generate a dataset that demonstrates the variable water regime and vegetation change in response to local rainfall over 32 years such as in the lagoons. Our results reduce threats to a dynamic threatened ecological community by filling an important knowledge gap and demonstrate a valuable method to understand historical and current changes in the hydrology of dynamic wetland systems more broadly