mSphere of Influence: the Rise of Artificial Intelligence in Infection Biology

Artur Yakimovich works in the field of computational virology and applies machine learning algorithms to study host-pathogen interactions. In this mSphere of Influence article, he reflects on two papers "Holographic Deep Learning for Rapid Optical Screening of Anthrax Spores" by Jo et al. (Y. Jo, S. Park, J. Jung, J. Yoon, et al., Sci Adv 3:e1700606, 2017, https://doi.org/10.1126/sciadv. 1700606) and "Bacterial Colony Counting with Convolutional Neural Networks in Digital Microbiology Imaging" by Ferrari and colleagues (A. Ferrari, S. Lombardi, and A. Signoroni, Pattern Recognition 61:629-640, 2017, https://doi.org/10.1016/j.patcog.2016.07.016). Here he discusses how these papers made an impact on him by showcasing that artificial intelligence algorithms can be equally applicable to both classical infection biology techniques and cutting-edge label-free imaging of pathogens

Продовольственная проблема Китая: вопросы преобразования системы и безопасности в условиях кризиса

Against the background of a global decline in food security over the past three to four years, China, remaining the world’s largest food importer, has made notable progress in improving its food security. China’s food security transformation has greatly improved not only the availability but also the affordability of food, as well as the sustainability of the Chinese food system. The increase in agricultural production, including grain production in China, indicates a transition from an extensive development model with high resource dependence to a sustainable intensification model. As a result of rapid economic and social development, the food pattern has changed based on high value foods such as meat, dairy products, fish and fish products. However, there are a number of serious problems in China’s food system. China has insufficient self-sufficiency and high import dependence on a number of food products. New to China’s nutritional challenges are the overweight part of the population and the resulting increasing burden on the health care system. In addition, China’s food losses exceed those of developed countries. The changes that the world economy is undergoing, the influence of non-market factors such as ideology, geopolitics and challenges to the multilateral trade and investment system, can seriously disrupt the global agricultural market and reduce the food security of China, which is heavily dependent on foreign food trade. The transformation of China’s food system is aimed at preventing and eliminating the risks of disruption of food imports, diversifying import sources, reducing the cost of agricultural products through scientific and technological progress and increasing investment in infrastructure, the transition of Chinese agriculture from a strategy of increasing production to improving the quality of products and its security.На фоне глобального снижения продовольственной безопасности на протяжении последних трех-четырех лет Китай, оставаясь крупнейшим импортером продовольствия в мире, добился заметных успехов в повышении своей продовольственной безопасности. Преобразования Китая в области продовольственной безопасности значительно улучшили не только наличие, но и доступность продовольствия, а также устойчивость китайской продовольственной системы. Увеличение сельскохозяйственного производства, в том числе производства зерна, в Китае свидетельствует о переходе от модели экстенсивного развития, с высокой ресурсозависимостью, к модели устойчивой интенсификации. В результате быстрого экономического и социального развития изменилась структура питания, основанная на продуктах высокой ценности, таких как мясо, молочные продукты, рыба и рыбные продукты. Тем не менее в продовольственной системе Китая наблюдается ряд серьезных проблем. Китай имеет недостаточную самообеспеченность и высокую импортозависимость по ряду продовольственных товаров. Новыми для Китая проблемами в сфере питания стали избыточный вес части населения и связанная с этим возрастающая нагрузка на систему здравоохранения. Кроме того, потери продовольствия Китая превышают аналогичные показатели развитых стран. Изменения, которые претерпевает мировая экономика, влияние таких нерыночных факторов, как идеология, геополитика и вызовы системе многосторонней торговли и инвестиций, могут серьезно нарушить глобальный сельскохозяйственный рынок и снизить продовольственную безопасность Китая, который в значительной степени зависит от внешней торговли продовольственными товарами. Преобразование продовольственной системы Китая направлено на предотвращение и устранение рисков нарушений импортных поставок продовольствия, диверсификацию источников импорта, снижение себестоимости продукции сельского хозяйства за счет научно-технического прогресса и увеличения инвестиций в инфраструктуру, переход китайского сельского хозяйства от стратегии роста производства к повышению качества продукции и ее безопасности

Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton

Viruses have a dual nature: particles are “passive substances” lacking chemical energy transformation, whereas infected cells are “active substances” turning-over energy. How passive viral substances convert to active substances, comprising viral replication and assembly compartments has been of intense interest to virologists, cell and molecular biologists and immunologists. Infection starts with virus entry into a susceptible cell and delivers the viral genome to the replication site. This is a multi-step process, and involves the cytoskeleton and associated motor proteins. Likewise, the egress of progeny virus particles from the replication site to the extracellular space is enhanced by the cytoskeleton and associated motor proteins. This overcomes the limitation of thermal diffusion, and transports virions and virion components, often in association with cellular organelles. This review explores how the analysis of viral trajectories informs about mechanisms of infection. We discuss the methodology enabling researchers to visualize single virions in cells by fluorescence imaging and tracking. Virus visualization and tracking are increasingly enhanced by computational analyses of virus trajectories as well as in silico modeling. Combined approaches reveal previously unrecognized features of virus-infected cells. Using select examples of complementary methodology, we highlight the role of actin filaments and microtubules, and their associated motors in virus infections. In-depth studies of single virion dynamics at high temporal and spatial resolutions thereby provide deep insight into virus infection processes, and are a basis for uncovering underlying mechanisms of how cells function

Concepts in Light Microscopy of Viruses

Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research

The nuclear export factor CRM1 controls juxta-nuclear microtubule-dependent virus transport

Transport of large cargo through the cytoplasm requires motor proteins and polarized filaments. Viruses that replicate in the nucleus of post-mitotic cells use microtubules and the dynein–dynactin motor to traffic to the nuclear membrane and deliver their genome through nuclear pore complexes (NPCs) into the nucleus. How virus particles (virions) or cellular cargo are transferred from microtubules to the NPC is unknown. Here, we analyzed trafficking of incoming cytoplasmic adenoviruses by single-particle tracking and superresolution microscopy. We provide evidence for a regulatory role of CRM1 (chromosome-region-maintenance-1; also known as XPO1, exportin-1) in juxta-nuclear microtubule-dependent adenovirus transport. Leptomycin B (LMB) abolishes nuclear targeting of adenovirus. It binds to CRM1, precludes CRM1–cargo binding and blocks signal-dependent nuclear export. LMB-inhibited CRM1 did not compete with adenovirus for binding to the nucleoporin Nup214 at the NPC. Instead, CRM1 inhibition selectively enhanced virion association with microtubules, and boosted virion motions on microtubules less than ∼2 µm from the nuclear membrane. The data show that the nucleus provides positional information for incoming virions to detach from microtubules, engage a slower microtubule-independent motility to the NPC and enhance infectio

A weak-labelling and deep learning approach for in-focus object segmentation in 3D widefield microscopy

Three-dimensional information is crucial to our understanding of biological phenomena. The vast majority of biological microscopy specimens are inherently three-dimensional. However, conventional light microscopy is largely geared towards 2D images, while 3D microscopy and image reconstruction remain feasible only with specialized equipment and techniques. Inspired by the working principles of one such technique - confocal microscopy, we propose a novel approach to 3D widefield microscopy reconstruction through semantic segmentation of in-focus and out-of-focus pixels. For this, we explore a number of rule-based algorithms commonly used for software-based autofocusing and apply them to a dataset of widefield focal stacks. We propose a computation scheme allowing the calculation of lateral focus score maps of the slices of each stack using these algorithms. Furthermore, we identify algorithms preferable for obtaining such maps. Finally, to ensure the practicality of our approach, we propose a surrogate model based on a deep neural network, capable of segmenting in-focus pixels from the out-of-focus background in a fast and reliable fashion. The deep-neural-network-based approach allows a major speedup for data processing making it usable for online data processing

Label-Free Digital Holo-tomographic Microscopy Reveals Virus-Induced Cytopathic Effects in Live Cells

Cytopathic effects (CPEs) are a hallmark of infections. CPEs are difficult to observe due to phototoxicity from classical light microscopy. We report distinct patterns of virus infections in live cells using digital holo-tomographic microscopy (DHTM). DHTM is label-free and records the phase shift of low-energy light passing through the specimen on a transparent surface with minimal perturbation. DHTM measures the refractive index (RI) and computes the refractive index gradient (RIG), unveiling optical heterogeneity in cells. We find that vaccinia virus (VACV), herpes simplex virus (HSV), and rhinovirus (RV) infections progressively and distinctly increased RIG. VACV infection, but not HSV and RV infections, induced oscillations of cell volume, while all three viruses altered cytoplasmic membrane dynamics and induced apoptotic features akin to those caused by the chemical compound staurosporine. In sum, we introduce DHTM for quantitative label-free microscopy in infection research and uncover virus type-specific changes and CPE in living cells with minimal interference. // IMPORTANCE This study introduces label-free digital holo-tomographic microscopy (DHTM) and refractive index gradient (RIG) measurements of live, virus-infected cells. We use DHTM to describe virus type-specific cytopathic effects, including cyclic volume changes of vaccinia virus infections, and cytoplasmic condensations in herpesvirus and rhinovirus infections, distinct from apoptotic cells. This work shows for the first time that DHTM is suitable to observe virus-infected cells and distinguishes virus type-specific signatures under noninvasive conditions. It provides a basis for future studies, where correlative fluorescence microscopy of cell and virus structures annotate distinct RIG values derived from DHTM

The physiological cost index of walking with a powered knee ankle foot orthosis in subjects with poliomyelitis : A pilot study

Background: A powered knee ankle foot orthosis (KAFO) was developed to provide restriction of knee flexion during stance phase and active flexion and extension of the knee during swing phase of gait. Objectives: The purpose of this study was to determine its effect on the physiological cost index (PCI), walking speed and the distance walked in people with poliomyelitis compared to when walking with a KAFO with drop lock knee joints. Methods: Seven subjects with poliomyelitis volunteered for the study, and undertook gait analysis with both types of KAFO. Results: Walking with the powered KAFO significantly reduced walking speed (p=0.015) and the distance walked (p=0.004), and also it did not improve PCI values (p =0.009) compared to walking with the locked KAFO. Conclusion: Using a powered KAFO did not significantly improve any of the primary outcome measures during walking for poliomyelitis subjects

Mobilization of fruit, small fruit and nut crop genetic resources in Belarus

Background. Natural populations of fruit and small fruit plants in Belarus and their specific and varietal composition for a long time attracted the attention of pomologists and breeders. Identification and mobilization of unique local forms and landraces as genetic sources of useful traits as well as monitoring duplicate collections will contribute to their more effective use in breeding practice to develop competitive domestic cultivars of various crops and reveal the adaptability of foreign cultivars to the conditions of Belarus.Methods. The itinerary of the collecting mission passed through 6 regions of the Republic of Belarus (Gomel, Minsk, Mogilev, Vitebsk, Brest, and Grodno) in 2012–2017.Results. As a result, 221 samples of fruit, small fruit and nut plants were collected, including 18 rootstocks of fruit crops. By 2021, 105 unique landraces were tested in the plant introduction and quarantine nursery and planted in the field gene bank, including 28 accessions of apple, 33 of pear, 11 of sour cherry, 5 of sweet cherry, 9 of plum, 8 of apricot, 1 of almond, 2 of hazel, 3 of garden strawberry, 1 of black chokeberry, 1 of viburnum, and 1 of bird cherry. There are plans to use the obtained accessions in breeding practice assources of valuable agronomic traits (high winter hardiness, high yield, resistance to a set of plant pathogens, etc.)