Evaluation of pH during cytostomal endocytosis and vacuolar catabolism of haemoglobin in Plasmodium falciparum

The DV (digestive vacuole) of the malaria parasite, Plasmodium falciparum, is the site of Hb (haemoglobin) digestion and haem detoxification and, as a consequence, the site of action of CQ (chloroquine) and related antimalarials. However, the precise pH of the DV and the endocytic vesicles that feed it has proved difficult to ascertain. We have developed new methods using EGFP [enhanced GFP (green fluorescent protein)] to measure the pH of intracellular compartments. We have generated a series of transfectants in CQ-sensitive and -resistant parasite strains expressing GFP chimaeras of the DV haemoglobinase, plasmepsin II. Using a quantitative flow cytometric assay, the DV pH was determined to be 5.4-5.5. No differences were detected between CQ-sensitive and -resistant strains. We have also developed a method that relies on the pH dependence of GFP photobleaching kinetics to estimate the pH of the DV compartment. This method gives a pH estimate consistent with the intensity-based measurement. Accumulation of the pH-sensitive probe, LysoSensor Blue, in the DV confirms the acidity of this compartment and shows that the cytostomal vesicles are not measurably acidic, indicating that they are unlikely to be the site of Hb digestion or the site of CQ accumulation. We show that a GFP probe located outside the DV reports a pH value close to neutral. The transfectants and methods that we have developed represent useful tools for investigating the pH of GFP-containing compartments and should be of general use in other systems.     

GMBlock: Optimizing data movement in a block-level storage sharing system over Myrinet

We present gmblock, a block-level storage sharing system over Myrinet which uses an optimized I/O path to transfer data directly between the storage medium and the network, bypassing the host CPU and main memory bus of the storage server. It is device driver independent and retains the protection and isolation features of the OS. We evaluate the performance of a prototype gmblock server and find that: (a) the proposed techniques eliminate memory and peripheral bus contention, increasing remote I/O bandwidth significantly, in the order of 20–200% compared to an RDMA-based approach, (b) the impact of remote I/O to local computation becomes negligible, (c) the performance characteristics of RAID storage combined with limited NIC resources reduce performance. We introduce synchronized send operations to improve the degree of disk to network I/O overlapping. We deploy the OCFS2 shared-disk filesystem over gmblock and show gains for various application benchmarks, provided I/O scheduling can eliminate the disk bottleneck due to concurrent access.     

Optimal assay design for determining the in vitro sensitivity of ring stage Plasmodium falciparum to artemisinins

Recent reports demonstrate that failure of artemisinin-based antimalarial therapies is associated with an altered response of early blood stage Plasmodium falciparum. This has led to increased interest in the use of pulse assays that mimic clinical drug exposure for analysing artemisinin sensitivity of highly synchronised ring stage parasites. We report a methodology for the reliable execution of drug pulse assays and detail a synchronisation strategy that produces well-defined tightly synchronised ring stage cultures in a convenient time-frame.     

Distributing and searching concept hierarchies: an adaptive DHT-based system

Concept hierarchies greatly help in the organization and reuse of information and are widely used in a variety of information systems applications. In this paper, we describe a method for efficiently storing and querying data organized into concept hierarchies and dispersed over a DHT. In our method, peers individually decide on the level of indexing according to the granularity of the incoming queries. Roll-up and drill-down operations are performed on a per-node basis in order to minimize the required bandwidth for answering queries on variable aggregation levels. We motivate our approach by applying it on a large-scale Grid system: Specifically, we apply our fully decentralized scheme that creates, queries and updates large volumes of hierarchical data on-line and replace the traditional centralized and strictly indexed information systems. Our extensive experimental results support this argument on many diverse configurations: Our system proves very efficient in skewed workloads, both over single and multiple hierarchy levels at the same time. It adapts to sudden changes in popularity and effectively stores and updates large amounts of data at very low cost.