Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR)

One of the major virulence factors of the malaria causing parasite is the Plasmodium falciparum encoded erythrocyte membrane protein 1 (PfEMP1). It is translocated to It the membrane of infected erythrocytes and expressed from approximately 60 var genes in a mutually exclusive manner. Switching of var genes allows the parasite to alter functional and antigenic properties of infected erythrocytes, to escape the immune defense and to establish chronic infections. We have developed an efficient method for isolating VAR genes from telomeric and other genome locations by adapting transformation-associated recombination (TAR) cloning, which can then be analyzed and sequenced. For this purpose, three plasmids each containing a homologous sequence representing the upstream regions of the group A, B, and C var genes and a sequence homologous to the conserved acidic terminal segment (ATS) of var genes were generated. Co-transfection with P. falciparum strain ITG2F6 genomic DNA in yeast cells yielded 200 TAR clones. The relative frequencies of clones from each group were not biased. Clones were screened by PCR, as well as Southern blotting, which revealed clones missed by PCR due to sequence mismatches with the primers. Selected clones were transformed into E. coli and further analyzed by RFLP and end sequencing. Physical analysis of 36 clones revealed 27 distinct types potentially representing 50% of the var gene repertoire. Three clones were selected for sequencing and assembled into single var gene containing contigs. This study demonstrates that it is possible to rapidly obtain the repertoire of var genes from P. falciparum within a single set of cloning experiments. This technique can be applied to individual isolates which will provide a detailed picture of the diversity of var genes in the field. This is a powerful tool to overcome the obstacles with cloning and assembly of multi-gene families by simultaneously cloning each member

The Development of Neural Network Techniques for the System Identification of Aircraft Dynamics

INTRODUCTION A great deal of time and effort is spent by aircraft manufacturers in the identification and estimation of the parameters that properly describe the aerodynamics of a particular aircraft. The derivatives of the aircraft forces, with respect to the input state have been the basis of many design and development techniques and tools, such as dynamic stability analysis, performance, simulation and control. The system identification of the aerodynamic model using neural networks involves the selection of the necessary input and output states to the system, representation of the model, and parameter estimation of the characteristic quantities, and in this case the aerodynamic force and moment derivatives. The application of neural networks as both a model descriptor and parameter estimation technique also requires a close selection of model inputs, to most efficiently utilise the method. System identification of the entire dynamic system as opposed to the parameter est

Human Simulation of Adaptive Behavior: Interactive studies of pursuit, evasion, courtship, fighting, and play

To understand more about how animate motion is generated and perceived, we need quantitative analyses of motion trajectories from organisms interacting in various important adaptive tasks. Such data is difficult to obtain for most animals, but one species provides a ready source. We have developed software that allows human subjects to generate such motion data by interacting across a computer network in on-screen pursuit and evasion, fighting, courtship, and play. Each subject uses a mouse to control a "bug" that moves in a 2-D environment with another bug controlled by a second remote subject. We have visualized and analyzed the resulting motion data for each task in several ways: 3-D spacetime plots of the trajectories themselves, scatterplots of one bug's positions relative to the other, and statistical measures of trajectory parameters including velocity, vorticity, and energy. All of these methods distinguish between the different motion categories. Having human subjects perform ..

Categorization by Elimination: A Fast and Frugal Approach to Categorization

People and other animals are very adept at categorizing stimuli even when many features cannot be perceived. Many psychological models of categorization, on the other hand, assume that an entire set of features is known. We present a new model of categorization, called Categorization by Elimination, that uses as few features as possible to make an accurate category assignment. This algorithm demonstrates that it is possible to have a categorization process that is fast and frugal--using fewer features than other categorization methods--yet still highly accurate in its judgments. We show that Categorization by Elimination does as well as human subjects on a multi-feature categorization task, judging intention from animate motion, and that it does as well as other categorization algorithms on data sets from machine learning. Specific predictions of the Categorization by Elimination algorithm, such as the order of cue use during categorization and the time-course of these ..

Expanding Reactivity in DNA-Encoded Library Synthesis via Reversible Binding of DNA to an Inert Quaternary Ammonium Support

Herein, we present the adaptation of reversible adsorption to solid support (RASS) for a DEL setting, which allows reactions to be performed in organic solvents at near anhydrous conditions opening previously inaccessible chemical reactivities to DEL. The RASS approach enabled the rapid development of C(sp2)-C(sp3) decarboxylative cross-couplings with broad substrate scope, an electrochemical amination (the first electrochemical synthetic transformation performed in a DEL context), and improved reductive amination conditions. We believe that RASS will offer expedient access to new DEL reactivities, expanded chemical space, and ultimately more drug-like libraries

Birds as Totemic Beings and Creators in the Lower Murray, South Australia

This paper is a literature review of the relationships Indigenous peoples in the Lower Murray of temperate South Australia had with the local avifauna as recorded in the early years of European settlement. Birds were prominent as clan ancestors in their creation stories, being credited with the formation of landforms and the establishment of law and custom. Aboriginal origin stories describe bird behavior and detail the relationships between birds, plants, rain, and fire. Ornithological bodies of knowledge that are framed outside of Western science, such as the ethno-ornithological information discussed here, provide an alternative lens with which to view avifaunal biodiversity in a manner that respects local cultural value