Mimicry Embedding Facilitates Advanced Neural Network Training for Image-Based Pathogen Detection.

The use of deep neural networks (DNNs) for analysis of complex biomedical images shows great promise but is hampered by a lack of large verified data sets for rapid network evolution. Here, we present a novel strategy, termed "mimicry embedding," for rapid application of neural network architecture-based analysis of pathogen imaging data sets. Embedding of a novel host-pathogen data set, such that it mimics a verified data set, enables efficient deep learning using high expressive capacity architectures and seamless architecture switching. We applied this strategy across various microbiological phenotypes, from superresolved viruses to in vitro and in vivo parasitic infections. We demonstrate that mimicry embedding enables efficient and accurate analysis of two- and three-dimensional microscopy data sets. The results suggest that transfer learning from pretrained network data may be a powerful general strategy for analysis of heterogeneous pathogen fluorescence imaging data sets.IMPORTANCE In biology, the use of deep neural networks (DNNs) for analysis of pathogen infection is hampered by a lack of large verified data sets needed for rapid network evolution. Artificial neural networks detect handwritten digits with high precision thanks to large data sets, such as MNIST, that allow nearly unlimited training. Here, we developed a novel strategy we call mimicry embedding, which allows artificial intelligence (AI)-based analysis of variable pathogen-host data sets. We show that deep learning can be used to detect and classify single pathogens based on small differences

Differential spatiotemporal targeting of Toxoplasma and Salmonella by GBP1 assembles caspase signalling platforms

Human guanylate binding proteins (GBPs), a family of IFNγ-inducible GTPases, promote cell-intrinsic defence against pathogens and host cell death. We previously identified GBP1 as a mediator of cell death of human macrophages infected with Toxoplasma gondii (Tg) or Salmonella Typhimurium (STm). How GBP1 targets microbes for AIM2 activation during Tg infection and caspase-4 during STm infection remains unclear. Here, using correlative light and electron microscopy and EdU labelling of Tg-DNA, we reveal that GBP1-decorated parasitophorous vacuoles (PVs) lose membrane integrity and release Tg-DNA for detection by AIM2-ASC-CASP8. In contrast, differential staining of cytosolic and vacuolar STm revealed that GBP1 does not contribute to STm escape into the cytosol but decorates almost all cytosolic STm leading to the recruitment of caspase-4. Caspase-5, which can bind LPS and whose expression is upregulated by IFNγ, does not target STm pointing to a key role for caspase-4 in pyroptosis. We also uncover a regulatory mechanism involving the inactivation of GBP1 by its cleavage at Asp192 by caspase-1. Cells expressing non-cleavable GBP1D192E therefore undergo higher caspase-4-driven pyroptosis during STm infection. Taken together, our comparative studies elucidate microbe-specific spatiotemporal roles of GBP1 in inducing cell death by leading to assembly and regulation of divergent caspase signalling platforms

Differential development of antibiotic resistance and virulence between Acinetobacter species

The two species that account for most cases of Acinetobacter-associated bacteraemia in the UK are Acinetobacter lwoffii, often a commensal but also an emerging pathogen, and A. baumannii, a well-known antibiotic-resistant species. While these species both cause similar types of human infection and occupy the same niche, A. lwoffii (unlike A. baumannii) has thus far remained susceptible to antibiotics. Comparatively little is known about the biology of A. lwoffii and this is the largest study on it conducted to date, providing valuable insights into its behaviour and potential threat to human health.This study aimed to explain the antibiotic susceptibility, virulence, and fundamental biological differences between these two species. The relative susceptibility of A. lwoffii, was explained as it encoded fewer antibiotic resistance and efflux pump genes than A. baumannii (9 and 30 respectively). While both species had markers of horizontal gene transfer, A. lwoffii encoded more DNA defence systems and harboured a far more restricted range of plasmids. Furthermore, A. lwoffii displayed a reduced ability to select for antibiotic resistance mutations, form biofilm and infect both in vivo and in vitro models of infection.This study suggests that the emerging pathogen A. lwoffii has remained susceptible to antibiotics because mechanisms exist to make it highly selective about the DNA it acquires, and we hypothesise that the fact that it only harbours a single RND system restricts the ability to select for resistance mutations. This provides valuable insights into how development of resistance can be constrained in Gram negative bacteria.Importance Acinetobacter lwoffii is often a harmless commensal but is also an emerging pathogen and is the most common cause of Acinetobacter-derived blood stream infections in England and Wales. In contrast to the well-studied, and often highly drug resistant A. baumannii, A. lwoffii has remained susceptible to antibiotics. This study explains why this organism has not evolved resistance to antibiotics. These new insights are important to understand why and how some species develop antibiotic resistance, while others do not and could inform future novel treatment strategies

It Takes a Village to Make a Scientist: Reflections of a Faculty Learning Community

Lab components of undergraduate science courses typically have students complete highly directed cookbook-like laboratory activities. These experiences rarely engage students in a meaningful manner and do not accurately convey what the work of science entails. With funding from the Howard Hughes Medical Institute (HHMI), we have created more authentic science research experiences in a variety of undergraduate science courses, including introductory courses. Achieving this among the diversity of freshmen and sophomore science courses—each typically serving hundreds of students on our campus—required careful planning and adaptation. This article describes the many challenges we faced in our effort to create more authentic undergraduate student research experiences and the significant progress we have made in making such experiences more common for our students. Improvements in first-year science, technology, engineering, and mathematics (STEM) retention over the last 2 years suggest that the experiences may be having a positive impact

MP755: Eastern Regional Potato Trials 2003: Summary of NE1014 Regional Project Field Testing of New Potato Clones

The objectives of this regional potato trial are (1) to develop pest-resistant, early-maturing, long-dormant potato varieties that will process from cold storage; (2) to evaluate new and specialty variet­ies developed in the Northeast; (3) to determine climatic effects on performance to develop pre­dictive models for potato improvement; and (4) determine heritability/linkage relationships and improve the genetic base of tetraploid cultivated varieties. The results presented in this report reflect a portion of the activity directed toward objectives 1, 2 and 3.https://digitalcommons.library.umaine.edu/aes_miscpubs/1020/thumbnail.jp

MP756: Eastern Regional Potato Trials 2004: Summary of NE1014 Regional Project Field Testing of New Potato Clones

The objectives of this regional potato trial are (1) to develop pest-resistant, early-maturing, long-dormant potato varieties that will process from cold storage; (2) to evaluate new and specialty variet­ies developed in the Northeast; (3) to determine climatic effects on performance to develop pre­dictive models for potato improvement; and (4) determine heritability/linkage relationships and improve the genetic base of tetraploid cultivated varieties. The results presented in this report reflect a portion of the activity directed toward objectives 1, 2 and 3.https://digitalcommons.library.umaine.edu/aes_miscpubs/1019/thumbnail.jp

MP758: East Regional Potato Trials 2006: Summary of NE1014 Regional Project Field Testing of New Potato Clones

The objectives of this regional potato trial are (1) to develop pest-resistant, early-maturing, long-dormant potato varieties that will process from cold storage; (2) to evaluate new and specialty variet­ies developed in the Northeast; (3) to determine climatic effects on performance to develop pre­dictive models for potato improvement; and (4) determine heritability/linkage relationships and improve the genetic base of tetraploid cultivated varieties. The results presented in this report reflect a portion of the activity directed toward objectives 1, 2 and 3.https://digitalcommons.library.umaine.edu/aes_miscpubs/1017/thumbnail.jp

MP760: East Regional Potato Trials 2007: Summary of NE1014 Regional Project Field Testing of New Potato Clones

The objectives of this regional potato trial are (1) to develop pest-resistant, early-maturing, long-dormant potato varieties that will process from cold storage; (2) to evaluate new and specialty variet­ies developed in the Northeast; (3) to determine climatic effects on performance to develop pre­dictive models for potato improvement; and (4) determine heritability/linkage relationships and improve the genetic base of tetraploid cultivated varieties. The results presented in this report reflect a portion of the activity directed toward objectives 1, 2 and 3.https://digitalcommons.library.umaine.edu/aes_miscpubs/1016/thumbnail.jp