Biology subjects

Kruger, T.

Publications and source records attributed to Kruger, T..

3 recordsLinked to original sources

bioRxiv2020

AIDeveloper: deep learning image classification in life science and beyond

Publications on artificial intelligence (AI)-based image analysis have increased drastically in recent years. However, all applications use individual solutions highly specialized for a particular task. Here, we present an easy-to-use, adaptable, open source software, called AIDeveloper (AID) to train neural nets (NN) for image classification without the need for programming. The software provides a variety of NN-architectures that can be simply selected for training. AID allows the user to apply trained models on new data, obtain metrics for classification performance, and export final models to different formats. The working principles of AID are first illustrated by training a convolutional neural net (CNN) on a large dataset consisting of images of different objects (CIFAR-10). We further explore the potential of AID by training a model to distinguish areas of differentiated and non-differentiated mesenchymal stem cells (MSCs) in culture. Additionally, we compare a conventional clinical whole blood cell count with a whole blood cell count performed by an NN-trained, using a dataset of more than 1.2 million images obtained by real-time deformability cytometry, delivering comparable results. Finally, we demonstrate how AID can be used for label-free classification of B- and T-cells derived from human blood, which currently requires costly and time-consuming sample preparation. Thus, AID can empower anyone to develop, train, and apply NNs for image classification. Moreover, models can be generated by non-programmers, exported, and used on different devices, which allows for an interdisciplinary use.

bioinformatics↗

bioRxiv2019

Genetic structure at national and regional scale in a long-distance dispersing pest organism, the bird cherry-oat aphid Rhopalosiphum padi

Genetic diversity is determinant for pest species success and vector competence. Understanding the ecological and evolutionary processes that determine the genetic diversity is fundamental to help identify the spatial scale at which pest populations are best managed. In the present study, we present the first comprehensive analysis of the genetic diversity and evolution of Rhopalosiphum padi, a major pest of cereals and a main vector of the barley yellow dwarf virus (BYDV), in Great Britain. We have used a genotype by sequencing approach to study whether i) there is any underlying population genetic structure in this long distant disperser pest at a national and regional scale; ii) the populations evolve as a response to environmental change and selective pressures, and; iii) the populations comprise anholocyclic lineages. Individual R. padi were collected using the Rothamsted Insect Surveys suction-trap network at several sites across England between 2004 and 2016 as part of the RIS long-term nationwide surveillance. Results identified two genetic clusters in Great Britain that mostly paralleled a North - South division, although gene flow is ongoing between the two subpopulations. These different groups do not correspond to sexual and asexual types, sexual reproduction being predominant in Great Britain, and could correspond to ecotypes. Results also show that there is migration with gene flow across Great Britain, although there is a reduction between the northern and southern sites with the Southwestern population being the most genetically differentiated. There is no evidence for isolation-by-distance and other factors like primary host distribution could influence the migration patterns. Finally, results also show no evidence for the evolution of the R. padi population, and it is demographically stable despite the ongoing environmental change. These results are discussed in view of their relevance to pest management and the transmission of BYDV.

evolutionary biology↗

bioRxiv2019

Positional dynamics and glycosomal recruitment of developmental regulators during trypanosome differentiation

Glycosomes are peroxisome-related organelles that compartmentalise the glycolytic enzymes in kinetoplastid parasites. These organelles are developmentally regulated in their number and composition, allowing metabolic adaptation to the parasites needs in the blood of mammalian hosts or within their arthropod vector. A protein phosphatase cascade regulates differentiation between parasite developmental forms, comprising a tyrosine phosphatase, TbPTP1, that dephosphorylates and inhibits a serine threonine phosphatase TbPIP39 that promotes differentiation. When TbPTP1 is inactivated, TbPIP39 is activated and during differentiation becomes located in glycosomes. Here we have tracked TbPIP39 recruitment to glycosomes during differentiation from bloodstream stumpy forms to procyclic forms. Detailed microscopy and live cell imaging during the synchronous transition between life cycle stages revealed that in stumpy forms, TbPIP39 is located at a periflagellar pocket site closely associated with TbVAP, that defines the flagellar pocket endoplasmic reticulum. TbPTP1 is also located at the same site in stumpy forms, as is REG9.1, a regulator of stumpy-enriched mRNAs. This site provides a molecular node for the interaction between TbPTP1 and TbPIP39. Within 30 minutes of the initiation of differentiation TbPIP39 relocates to glycosomes whereas TbPTP1 disperses to the cytosol. Overall, the study identifies a stumpy regulatory nexus (STuRN) that co-ordinates the molecular components of life cycle signalling and glycosomal development during transmission of Trypanosoma brucei.\n\nImportanceAfrican trypanosomes are parasites of sub-Saharan Africa responsible for both human and animal disease. The parasites are transmitted by tsetse flies and completion of their life cycle involves progression through several development steps. The initiation of differentiation between blood and tsetse forms is signalled by a phosphatase cascade, ultimately trafficked into peroxisome-related organelles called glycosomes that are unique to this group of organisms. Glycosomes undergo substantial remodelling of their composition and function during the differentiation step but how this is regulated is not understood. Here we identify a cytological site where the signalling molecules controlling differentiation converge before the dispersal of one of them into glycosomes. This coincides with a specialised ER site that may contribute to glycosome developmental biogenesis or regeneration. In combination, the study provides the first insight into the spatial co-ordination of signalling pathway components in trypanosomes as they undergo cell-type differentiation.

microbiology↗