A novel method to count the red blood cells in thin blood films

This paper describes a novel idea to identify the total number of red blood cells (RBCs) as well as their location in a Giemsa stained thin blood film image. This work is being undertaken as a part of developing an automated malaria parasite detection system by scanning a photograph of thin blood film in order to evaluate the parasitemia of the blood. Not only will this method eliminates the segmentation procedures that are normally used to segment the cells in the microscopic image, but also avoids any image pre-processing to deal with non uniform illumination prior to cell detection. The method utilizes basic knowledge on cell structure and brightness of the components due to Giemsa staining of the sample and detects and locates the RBCs in the image.

Automated P.falciparum detection system for post-treatment malaria diagnosis using modified annular ring ratio method

The gametocytes of the malaria parasite Plasmodium falciparum are highly resistant to antimalarial drugs. Its presence in the blood can be detected even after a successful malaria treatment. This paper explains a modified Annular Ring Ratio method which successfully locates and differentiates gametocytes of P. falciparum species in thin blood film images. The method can be used as an efficient tool for gametocyte detection for post-treatment malaria diagnosis. It also identifies the presence of any White Blood Cells (WBCs) in the image, and discards other artifacts and non infected cells. It utilizes the information based on structure, color and geometry of the cells and does not require any segmentation or non-illumination correction techniques that are commonly used for cell detection.

IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

Modulation of a cytoskeletal calpain-like protein induces major transitions in trypanosome morphology

Individual eukaryotic microbes, such as the kinetoplastid parasite Trypanosoma brucei, have a defined size, shape, and form yet transition through life cycle stages, each having a distinct morphology. In questioning the structural processes involved in these transitions, we have identified a large calpain-like protein that contains numerous GM6 repeats (ClpGM6) involved in determining T. brucei cell shape, size, and form. ClpGM6 is a cytoskeletal protein located within the flagellum along the flagellar attachment zone (FAZ). Depletion of ClpGM6 in trypomastigote forms produces cells with long free flagella and a shorter FAZ, accompanied by repositioning of the basal body, the kinetoplast, Golgi, and flagellar pocket, reflecting an epimastigote-like morphology. Hence, major changes in microbial cell form can be achieved by simple modulation of one or a few proteins via coordinated association and positioning of membrane and cytoskeletal components.