scholarly journals PlasmoTron: an open-source platform for automated culture of malaria parasites

2017 ◽  
Author(s):  
Theo Sanderson ◽  
Julian C. Rayner

We have created a system which allows an inexpensive opensource liquid-handling robot to automate most aspects of bloodstage malaria parasite culture. Parasites are cultured in multiwell microplates, with their details recorded in a database. Information in the database is used to generate commands for the robot to feed, monitor and passage parasite cultures. We show that the system is capable of raising cultures after transfection and then maintaining them at desired parasitaemias, facilitiating significant scale up of both routine culture and experimental genetic modification. The PlasmoTron software is available at plasmotron.org.

2021 ◽  
Author(s):  
Philip Dettinger ◽  
Tobias Kull ◽  
Geethika Arekatla ◽  
Nouraiz Ahmed ◽  
Yang Zhang ◽  
...  

Liquid handling robots have the potential to automate many procedures in life sciences. However, they are not in widespread use in academic settings, where funding, space and maintenance specialists are usually limiting. In addition, current robots require lengthy programming by specialists and are incompatible with most academic laboratories with constantly changing small-scale projects. Here, we present the Pipetting Helper Imaging Lid (PHIL), an inexpensive, small, open-source personal liquid handling robot. It is designed for inexperienced users, with self-production from cheap commercial and 3D-printable components and custom control software. PHIL successfully automated pipetting for e.g. tissue immunostainings and stimulations of live stem and progenitor cells during time-lapse microscopy. PHIL is cheap enough for any laboratory member to have their own personal pipetting robot(s), and enables users without programming skills to easily automate a large range of experiments.


2020 ◽  
Vol 10 (3) ◽  
pp. 814 ◽  
Author(s):  
Andres Faiña ◽  
Brian Nejati ◽  
Kasper Stoy

Commercial liquid handling robots are rarely appropriate when tasks change often, which is the case in the early stages of biochemical research. In order to address it, we have developed EvoBot, a liquid handling robot, which is open-source and employs a modular design. The combination of an open-source and a modular design is particularly powerful because functionality is divided into modules with simple, well-defined interfaces, hence customisation of modules is possible without detailed knowledge of the entire system. Furthermore, the modular design allows end-users to only produce and assemble the modules that are relevant for their specific application. Hence, time and money are not wasted on functionality that is not needed. Finally, modules can easily be reused. In this paper, we describe the EvoBot modular design and through scientific experiments such as basic liquid handling, nurturing of microbial fuel cells, and droplet chemotaxis experiments document how functionality is increased one module at a time with a significant amount of reuse. In addition to providing wet-labs with an extendible, open-source liquid handling robot, we also think that modularity is a key concept that is likely to be useful in other robots developed for scientific purposes.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Timothy Fuqua ◽  
Jeff Jordan ◽  
Aliaksandr Halavatyi ◽  
Christian Tischer ◽  
Kerstin Richter ◽  
...  

AbstractA significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in whole animals has not kept pace with other sequencing-based technologies. Here, we outline an open-source semi-automated pipeline to chemically fixate, stain, and 3D-image Drosophila embryos. Central to this pipeline is a liquid handling robot, Flyspresso, which automates the steps of classical embryo fixation and staining. We provide the schematics and an overview of the technology for an engineer or someone equivalently trained to reproduce and further improve upon Flyspresso, and highlight the Drosophila embryo fixation and colorimetric or antibody staining protocols. Additionally, we provide a detailed overview and stepwise protocol for our adaptive-feedback pipeline for automated embryo imaging on confocal microscopes. We demonstrate the efficiency of this pipeline compared to classical techniques, and how it can be repurposed or scaled to other protocols and biological systems. We hope our pipeline will serve as a platform for future research, allowing a broader community of users to build, execute, and share similar experiments.


Author(s):  
Andrs Faa ◽  
Farzad Nejatimoharrami ◽  
Kasper Stoy ◽  
Pavlina Theodosiou ◽  
Benjamin Taylor ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marc Oeller ◽  
Pietro Sormanni ◽  
Michele Vendruscolo

AbstractThe solubility of proteins correlates with a variety of their properties, including function, production yield, pharmacokinetics, and formulation at high concentrations. High solubility is therefore a key requirement for the development of protein-based reagents for applications in life sciences, biotechnology, diagnostics, and therapeutics. Accurate solubility measurements, however, remain challenging and resource intensive, which limits their throughput and hence their applicability at the early stages of development pipelines, when long-lists of candidates are typically available in minute amounts. Here, we present an automated method based on the titration of a crowding agent (polyethylene glycol, PEG) to quantitatively assess relative solubility of proteins using about 200 µg of purified material. Our results demonstrate that this method is accurate and economical in material requirement and costs of reagents, which makes it suitable for high-throughput screening. This approach is freely-shared and based on a low cost, open-source liquid-handling robot. We anticipate that this method will facilitate the assessment of the developability of proteins and make it substantially more accessible.


BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jane M. Carlton

AbstractThe study of human malaria caused by species of Plasmodium has undoubtedly been enriched by the use of model systems, such as the rodent malaria parasites originally isolated from African thicket rats. A significant gap in the arsenal of resources of the species that make up the rodent malaria parasites has been the lack of any such tools for the fourth of the species, Plasmodium vinckei. This has recently been rectified by Abhinay Ramaprasad and colleagues, whose pivotal paper published in BMC Biology describes a cornucopia of new P. vinckei ‘omics datasets, mosquito transmission experiments, transfection protocols, and virulence phenotypes, to propel this species firmly into the twenty-first century.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fetulhak Abdurahman ◽  
Kinde Anlay Fante ◽  
Mohammed Aliy

Abstract Background Manual microscopic examination of Leishman/Giemsa stained thin and thick blood smear is still the “gold standard” for malaria diagnosis. One of the drawbacks of this method is that its accuracy, consistency, and diagnosis speed depend on microscopists’ diagnostic and technical skills. It is difficult to get highly skilled microscopists in remote areas of developing countries. To alleviate this problem, in this paper, we propose to investigate state-of-the-art one-stage and two-stage object detection algorithms for automated malaria parasite screening from microscopic image of thick blood slides. Results YOLOV3 and YOLOV4 models, which are state-of-the-art object detectors in accuracy and speed, are not optimized for detecting small objects such as malaria parasites in microscopic images. We modify these models by increasing feature scale and adding more detection layers to enhance their capability of detecting small objects without notably decreasing detection speed. We propose one modified YOLOV4 model, called YOLOV4-MOD and two modified models of YOLOV3, which are called YOLOV3-MOD1 and YOLOV3-MOD2. Besides, new anchor box sizes are generated using K-means clustering algorithm to exploit the potential of these models in small object detection. The performance of the modified YOLOV3 and YOLOV4 models were evaluated on a publicly available malaria dataset. These models have achieved state-of-the-art accuracy by exceeding performance of their original versions, Faster R-CNN, and SSD in terms of mean average precision (mAP), recall, precision, F1 score, and average IOU. YOLOV4-MOD has achieved the best detection accuracy among all the other models with a mAP of 96.32%. YOLOV3-MOD2 and YOLOV3-MOD1 have achieved mAP of 96.14% and 95.46%, respectively. Conclusions The experimental results of this study demonstrate that performance of modified YOLOV3 and YOLOV4 models are highly promising for detecting malaria parasites from images captured by a smartphone camera over the microscope eyepiece. The proposed system is suitable for deployment in low-resource setting areas.


BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cui Zhang ◽  
Cihan Oguz ◽  
Sue Huse ◽  
Lu Xia ◽  
Jian Wu ◽  
...  

Abstract Background Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the rodent malaria parasites is Plasmodium yoelii, and multiple P. yoelii strains or subspecies that cause different disease phenotypes have been widely employed in various studies. The genomes and transcriptomes of several P. yoelii strains have been analyzed and annotated, including the lethal strains of P. y. yoelii YM (or 17XL) and non-lethal strains of P. y. yoelii 17XNL/17X. Genomic DNA sequences and cDNA reads from another subspecies P. y. nigeriensis N67 have been reported for studies of genetic polymorphisms and parasite response to drugs, but its genome has not been assembled and annotated. Results We performed genome sequencing of the N67 parasite using the PacBio long-read sequencing technology, de novo assembled its genome and transcriptome, and predicted 5383 genes with high overall annotation quality. Comparison of the annotated genome of the N67 parasite with those of YM and 17X parasites revealed a set of genes with N67-specific orthology, expansion of gene families, particularly the homologs of the Plasmodium chabaudi erythrocyte membrane antigen, large numbers of SNPs and indels, and proteins predicted to interact with host immune responses based on their functional domains. Conclusions The genomes of N67 and 17X parasites are highly diverse, having approximately one polymorphic site per 50 base pairs of DNA. The annotated N67 genome and transcriptome provide searchable databases for fast retrieval of genes and proteins, which will greatly facilitate our efforts in studying the parasite biology and gene function and in developing effective control measures against malaria.


2021 ◽  
Author(s):  
Moses Okpeku

Malaria is a global disease of importance, especially in the sub-Saharan African region, where malaria accounts for great losses economically and to life. Fight to eliminate this disease has resulted in reduced disease burden in many places where the diseases is endemic. Elimination strategies in most places is focus on the use of treated nets and drug application. Exposure of malaria parasites to anti-malaria drugs have led to the evolution of drug resistance in both parasites and host. Development of drug resistance vary but, studies on adaptive drug resistance has implications and consequences. Our knowledge of this consequences are limited but important for the pursuit of an uninterrupted malaria elimination agenda. This chapter draws our attention to this risks and recommends interventions.


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