Amyloid Precursor Proteins Are Dynamically Trafficked and Processed during Neuronal Development

Proteolytic processing of the Amyloid Precursor Protein (APP) produces beta-amyloid (Aβ) peptide fragments that accumulate in Alzheimer’s Disease (AD), but APP may also regulate multiple aspects of neuronal development, albeit via mechanisms that are not well understood. APP is a member of a family of transmembrane glycoproteins expressed by all higher organisms, including two mammalian orthologs (APLP1 and APLP2) that have complicated investigations into the specific activities of APP. By comparison, insects express only a single APP-related protein (APP-Like, or APPL) that contains the same protein interaction domains identified in APP. However, unlike its mammalian orthologs, APPL is only expressed by neurons, greatly simplifying an analysis of its functions in vivo. Like APP, APPL is processed by secretases to generate a similar array of extracellular and intracellular cleavage fragments, as well as an Aβ-like fragment that can induce neurotoxic responses in the brain. Exploiting the complementary advantages of two insect models (Drosophila melanogaster and Manduca sexta), we have investigated the regulation of APPL trafficking and processing with respect to different aspects of neuronal development. By comparing the behavior of endogenously expressed APPL with fluorescently tagged versions of APPL and APP, we have shown that some full-length protein is consistently trafficked into the most motile regions of developing neurons both in vitro and in vivo. Concurrently, much of the holoprotein is rapidly processed into N- and C-terminal fragments that undergo bi-directional transport within distinct vesicle populations. Unexpectedly, we also discovered that APPL can be transiently sequestered into an amphisome-like compartment in developing neurons, while manipulations targeting APPL cleavage altered their motile behavior in cultured embryos. These data suggest that multiple mechanisms restrict the bioavailability of the holoprotein to regulate APPL-dependent responses within the nervous system. Lastly, targeted expression of our double-tagged constructs (combined with time-lapse imaging) revealed that APP family proteins are subject to complex patterns of trafficking and processing that vary dramatically between different neuronal subtypes. In combination, our results provide a new perspective on how the regulation of APP family proteins can be modulated to accommodate a variety of cell type-specific responses within the embryonic and adult nervous system

Quasi-molecular lines in Lyman wings of cool DA white dwarfs; Application to FUSE observations of G231-40

We present new theoretical calculations of the total line profiles of Lyman alpha and Lyman beta which include perturbations by both neutral hydrogen AND protons and all possible quasi-molecular states of H_2 and H_2^+. They are used to improve theoretical modeling of synthetic spectra for cool DA white dwarfs. We compare them with FUSE observation of G231-40. The appearance of the line wings between Lyman alpha and Lyman beta is shown to be sensitive to the relative abundance of hydrogen ions and neutral atoms, and thereby to provide a temperature diagnostic for stellar atmospheres and laboratory plasmas.Comment: 6 pages, 4 figures, accepted for publication in Astronomy and Astrophysic

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

DNA-associated proteins (DAPs) classically regulate gene expression by binding to regulatory loci such as enhancers or promoters. As expanding catalogs of genome-wide DAP binding maps reveal thousands of loci that, unlike the majority of conventional enhancers and promoters, associate with dozens of different DAPs with apparently little regard for motif preference, an understanding of DAP association and coordination at such regulatory loci is essential to deciphering how these regions contribute to normal development and disease. In this study, we aggregated publicly available ChIP-seq data from 469 human DAPs assayed in three cell lines and integrated these data with an orthogonal data set of 352 nonredundant, in vitro–derived motifs mapped to the genome within DNase I hypersensitivity footprints to characterize regions with high numbers of DAP associations. We establish a generalizable definition for high occupancy target (HOT) loci and identify putative driver DAP motifs in HepG2 cells, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and show sequence conservation at HOT loci. The number of different DAPs associated with an element is positively associated with evidence of regulatory activity, and by systematically mutating 245 HOT loci with a massively parallel mutagenesis assay, we localized regulatory activity to a central core region that depends on the motif sequences of our previously nominated driver DAPs. In sum, this work leverages the increasingly large number of DAP motif and ChIP-seq data publicly available to explore how DAP associations contribute to genome-wide transcriptional regulation

Modelling Primordial Gas in Numerical Cosmology

We have reviewed the chemistry and cooling behaviour of low-density (n<10^4 cm^-3) primordial gas and devised a cooling model wich involves 19 collisional and 9 radiative processes and is applicable for temperatures in the range (1 K < T < 10^8 K). We derived new fits of rate coefficients for the photo-attachment of neutral hydrogen, the formation of molecular hydrogen via H-, charge exchange between H2 and H+, electron detachment of H- by neutral hydrogen, dissociative recombination of H2 with slow electrons, photodissociation of H2+, and photodissociation of H2. Further it was found that the molecular hydrogen produced through the gas-phase processes, H2+ + H -> H2 + H+, and H- + H -> H2 + e-, is likely to be converted into its para configuration on a faster time scale than the formation time scale. We have tested the model extensively and shown it to agree well with former studies. We further studied the chemical kinetics in great detail and devised a minimal model which is substantially simpler than the full reaction network but predicts correct abundances. This minimal model shows convincingly that 12 collisional processes are sufficient to model the H, He, H+, H-, He+, He++, and H2 abundances in low density primordial gas for applications with no radiation fields.Comment: 26 pages of text, 4 tables, and 6 eps figures. The paper is also available at http://zeus.ncsa.uiuc.edu:8080/~abel/PGas/bib.html Submitted to New Astronomy. Note that some of the hyperlinks given in the paper are still under constructio

Electron-correlation effects in appearance-potential spectra of Ni

Spin-resolved and temperature-dependent appearance-potential spectra of ferromagnetic Nickel are measured and analyzed theoretically. The Lander self-convolution model which relates the line shape to the unoccupied part of the local density of states turns out to be insufficient. Electron correlations and orbitally resolved transition-matrix elements are shown to be essential for a quantitative agreement between experiment and theory.Comment: LaTeX, 6 pages, 2 eps figures included, Phys. Rev. B (in press

Transcriptional changes underpinning poor prognosis and chemoresistance in pancreatic cancer

With a 5-year survival rate of 7% and only marginal improvements in recent dec-ades, pancreatic adenocarcinoma (PDAC) survival statistics present a disheartening chal-lenge. A majority of the high mortality rate associated with PDAC is due to late-stage diagnosis and limited efficacy of the current chemotherapeutic arsenal. This work is largely focused on the ~20% of tumors detected prior to metastasis for which curative surgical resection can be combined with chemotherapy and radiation therapy, increasing the 5 year survival rate to ~25%. Although a subset of these patients who undergo surgi-cal resection experience sustained remission, a majority of patients still relapse within 2 years making it difficult for even relatively early stage patients and their providers to make value-based decisions on a treatment course. In an effort to improve patient out-comes, multi-drug cocktails such as FOLFIRINOX (fluorouracil, folinic acid, irinotecan and oxaliplatin) are being increasingly used for adjuvant therapy despite their concomi-tant toxicities. The ability to stratify patients likely to respond to single agent therapy from those patients who may benefit from multi-drug therapy or may be refractory to all current therapeutic avenues could provide much needed clarity to the current PDAC ad-juvant therapy decision tree. We have begun to address this need by performing RNA-sequencing on a subset of treatment naïve PDAC tumors from a cohort of patients select-ed to include a wide range of survival times post-resection. We define the key early tran-scriptional characteristics of tumors that predict prognosis by training a regularized re-gression model on our cohort’s transcriptomes. Context is provided to our prognostic model by comparing it to previously described prognostic markers such as the meta-PCNA index, a metric that summarizes the expression of cell proliferation-associated proteins, and to prognostic expression signatures of other cancers. Finally, we identify and experimentally validate new single gene targets, whose expression level may modu-late tumor chemoresistance, using both a candidate gene approach based on expression differences observed in our patient cohort as well as genome-wide CRISPR screening