Using APL to build science tutors for the high school level

This is the author's version of the work. It is posted here for your personal use. Not for redistribution. The definitive Version of Record was published in APL Quote Quad, http://dx.doi.org/10.1145/327600.327644This paper describes the procedure used to build several courses on the sciences for the high school level. An APL2 program has been written that accepts problem models, including explanation models, and uses them to generate many different problems. Each course is provided with about one hundred problem models, from which the student is invited to solve many thousands of different actual problems. The unique features of APL2 have made it very simple to develop the program that supports the courses, which exists in both DOS and Windows versions

Yeast Irc6p is a novel type of conserved clathrin coat accessory factor related to small G proteins.

Clathrin coat accessory proteins play key roles in transport mediated by clathrin-coated vesicles. Yeast Irc6p and the related mammalian p34 are putative clathrin accessory proteins that interact with clathrin adaptor complexes. We present evidence that Irc6p functions in clathrin-mediated traffic between the trans-Golgi network and endosomes, linking clathrin adaptor complex AP-1 and the Rab GTPase Ypt31p. The crystal structure of the Irc6p N-terminal domain revealed a G-protein fold most related to small G proteins of the Rab and Arf families. However, Irc6p lacks G-protein signature motifs and high-affinity GTP binding. Also, mutant Irc6p lacking candidate GTP-binding residues retained function. Mammalian p34 rescued growth defects in irc6 cells, indicating functional conservation, and modeling predicted a similar N-terminal fold in p34. Irc6p and p34 also contain functionally conserved C-terminal regions. Irc6p/p34-related proteins with the same two-part architecture are encoded in genomes of species as diverse as plants and humans. Together these results define Irc6p/p34 as a novel type of conserved clathrin accessory protein and founding members of a new G protein-like family

Computer Center Bulletin / July 5, 1990

This publication is published as required and is written by members of the staff, W. R. Church Computer Cente

Study of the regulation of Fab1p, a phosphatidylinositol 3-phosphate 5 kinase in Saccharomyces cerevisiae.

The Saccharomyces cerevisiae protein Fab1p is the archetypal type III phosphatidyl inositol phosphate kinase. This family of enzymes is universal to all eukaryotes and is responsible for the synthesis of phosphatidylinositol 3,5-bisphosphate from phosphatidylinositol 3- phosphate. In S. cerevisiae , Fab1p regulates a number of cellular processes via the production of phosphatidylinositol 3,5-bisphosphate including: vacuole acidification, protein trafficking to the vacuole lumen, vacuole membrane recycling and apical bud formation. It is now clear that these processes are regulated independently however the molecular details of Fab1p regulation have yet to be identified. Using yeast two-hybrid analysis in a systematic screen with Fab1p and its domains, we have identified over 300 potential interactors. Phenotypic analyses on 17 corresponding deletion mutants of these proteins have identified 8 that display phenotypes consistent with loss of Fab1p. We have focused on Apl2p, which appears to be a bona fide activator of Fab1p. Apl2p, and Apl4p, which interacts with the Fab1p regulator Vacl4p, are part of the heterotetrameric complex AP-1 involved in clathrin mediated trafficking from the trans-Golgi network. We show that AP-1 regulates phosphatidylinositol 3,5-bisphosphate production in vivo and is required for the trafficking of the ubiquitinated cargoes CPS and Phm5p to the vacuole lumen, a process that requires Fab1p. Over-expression of Fab1p in AP-1 mutants reverts these trafficking defects. Using point mutants of AP-1 we show that these trafficking events are clathrin-dependant. AP-1 is not required for Fab1p-dependant vacuole morphology and vacuole acidity. Thus, we speculate that Fab1p is regulated by AP-1 for the maintenance of a pool of phosphatidylinositol 3,5-bisphosphate required for trafficking of cargoes to the vacuole. AP-1 is responsible for the retention of proteins at the trans-Golgi network therefore we speculate that retention to this compartment might also be a Fab1p-dependent mechanism

Two Mosquito LRR Proteins Function as Complement Control Factors in the TEP1-Mediated Killing of Plasmodium

SummaryPlasmodium development within Anopheles mosquitoes is a vulnerable step in the parasite transmission cycle, and targeting this step represents a promising strategy for malaria control. The thioester-containing complement-like protein TEP1 and two leucine-rich repeat (LRR) proteins, LRIM1 and APL1, have been identified as major mosquito factors that regulate parasite loads. Here, we show that LRIM1 and APL1 are required for binding of TEP1 to parasites. RNAi silencing of the LRR-encoding genes results in deposition of TEP1 on Anopheles tissues, thereby depleting TEP1 from circulation in the hemolymph and impeding its binding to Plasmodium. LRIM1 and APL1 not only stabilize circulating TEP1, they also stabilize each other prior to their interaction with TEP1. Our results indicate that three major antiparasitic factors in mosquitoes jointly function as a complement-like system in parasite killing, and they reveal a role for LRR proteins as complement control factors

Broadband spectroscopy using two Suzaku observation of the HMXB GX 301-2

We present the analysis of two Suzaku observations of GX 301-2 at two orbital phases after the periastron passage. Variations in the column density of the line-of-sight absorber are observed, consistent with accretion from a clumpy wind. In addition to a CRSF, multiple fluorescence emission lines were detected in both observations. The variations in the pulse profiles and the CRSF throughout the pulse phase have a signature of a magnetic dipole field. Using a simple dipole model we calculated the expected magnetic field values for different pulse phases and were able to extract a set of geometrical angles, loosely constraining the dipole geometry in the neutron star. From the variation of the CRSF width and energy, we found a geometrical solution for the dipole, making the inclination consistent with previously published values.Comment: 12 Pages, 9 Figures, accepted by Ap

JMSL - a language derived from APL

A new AFL-derived language called JMSL is presented which rnodifies seven aspects of APL so that many current and potential APL users could benefit from a language which is easier to learn, read, write, and maintain. JMSL uses ASCII tokens instead of APL symbols to remedy interfacing, extensibility, and readability problems with APL. JMSL revises and extends APL built-in capabilities to provide greater expression and improved symbol-meaning correspondence. JMSL includes a new notation for nested arrays (a powerful data structure which combines the array processing of APL with the tree processing of LISP). JMSL provides hierarchical directories (similar to PASCAL or PL/I records) to allow structures to be indexed by name. JMSL modifies the traditional APL library/workspace storage interface by unifying the syntax of system commands in a way which allows UNIX-like directory storage. JMSL provides high-level control structures similar to those found in block-structured languages, including an event-handling mechanism. JMSL amends the APL scope rules to alleviate problems with side effects and object localization. Some areas of future work are discussed, and a description of JMSL syntax and semantics is included