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1. A Physarum-inspired approach to the Euclidean Steiner tree problem

   https://doi.org/10.1038/s41598-022-18316-3  

   Hsu, Sheryl; Massolo, Fidel I. Schaposnik; Schaposnik, Laura P. (August 2022, Scientific Reports)

   Abstract This paper presents a novel biologically-inspired explore-and-fuse approach to solving a large array of problems. The inspiration comes from Physarum, a unicellular slime mold capable of solving the traveling salesman and Steiner tree problems. Besides exhibiting individual intelligence,Physarumcan also share information with otherPhysarumorganisms through fusion. These characteristics of Physarum imply that spawning many such organisms we can explore the problem space in parallel, each individual gathering information and forming partial solutions pertaining to a local region of the problem space. When the organisms meet, they fuse and share information, eventually forming one organism which has a global view of the problem and can apply its intelligence to find an overall solution to the problem. This approach can be seen as a “softer” method of divide and conquer. We demonstrate this novel approach, developing thePhysarum Steiner Algorithmwhich is capable of finding feasible solutions to the Euclidean Steiner tree problem. This algorithm is of particular interest due to its resemblance toPhysarum polycephalum, ability to leverage parallel processing, avoid obstacles, and operate on various shapes and topological surfaces including the rectilinear grid. 

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2. Clonal abundance patterns in hematopoiesis: Mathematical modeling and parameter estimation

   https://doi.org/10.3389/fsysb.2023.893366  

   Pan, Yunbei; D’Orsogna, Maria R.; Tang, Min; Stiehl, Thomas; Chou, Tom (February 2023, Frontiers in Systems Biology)

   Hematopoiesis has been studied via stem cell labeling using barcodes, viral integration sites (VISs), or in situ methods. Subsequent proliferation and differentiation preserve the tag identity, thus defining a clone of mature cells across multiple cell type or lineages. By tracking the population of clones, measured within samples taken at discrete time points, we infer physiological parameters associated with a hybrid stochastic-deterministic mathematical model of hematopoiesis. We analyze clone population data from Koelle et al. ( Koelle et al., 2017 ) and compare the states of clones (mean and variance of their abundances) and the state-space density of clones with the corresponding quantities predicted from our model. Comparing our model to the tagged granulocyte populations, we find parameters (stem cell carrying capacity, stem cell differentiation rates, and the proliferative potential of progenitor cells, and sample sizes) that provide reasonable fits in three out of four animals. Even though some observed features cannot be quantitatively reproduced by our model, our analyses provides insight into how model parameters influence the underlying mechanisms in hematopoiesis. We discuss additional mechanisms not incorporated in our model. 

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3. ROS are evolutionary conserved cell-to-cell stress signals

   https://doi.org/10.1073/pnas.2305496120  

   Fichman, Yosef; Rowland, Linda; Oliver, Melvin J; Mittler, Ron (August 2023, Proceedings of the National Academy of Sciences)

   Cell-to-cell communication is fundamental to multicellular organisms and unicellular organisms living in a microbiome. It is thought to have evolved as a stress- or quorum-sensing mechanism in unicellular organisms. A unique cell-to-cell communication mechanism that uses reactive oxygen species (ROS) as a signal (termed the “ROS wave”) was identified in flowering plants. This process is essential for systemic signaling and plant acclimation to stress and can spread from a small group of cells to the entire plant within minutes. Whether a similar signaling process is found in other organisms is however unknown. Here, we report that the ROS wave can be found in unicellular algae, amoeba, ferns, mosses, mammalian cells, and isolated hearts. We further show that this process can be triggered in unicellular and multicellular organisms by a local stress or H₂O₂treatment and blocked by the application of catalase or NADPH oxidase inhibitors and that in unicellular algae it communicates important stress–response signals between cells. Taken together, our findings suggest that an active process of cell-to-cell ROS signaling, like the ROS wave, evolved before unicellular and multicellular organisms diverged. This mechanism could have communicated an environmental stress signal between cells and coordinated the acclimation response of many different cells living in a community. The finding of a signaling process, like the ROS wave, in mammalian cells further contributes to our understanding of different diseases and could impact the development of drugs that target for example cancer or heart disease. 

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4. PIXEL-WISE NEURAL CELL INSTANCE SEGMENTATION

   Yi, J.; Wu, P.; Hoeppner, D. J.; Metaxas, D. (April 2018, 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018))

   Accurate cell instance segmentation plays an important role in the study of neural cell interactions, which are critical for understanding the development of brain. These interactions are performed through the filopodia and lamellipodia of neural cells, which are extremely tiny structures and as a result render most existing instance segmentation methods powerless to precisely capture them. To solve this issue, in this paper we present a novel hierarchical neural network comprising object detection and segmentation modules. Compared to previous work, our model is able to efficiently share and make full use of the information at different levels between the two modules. Our method is simple yet powerful, and experimental results show that it captures the contours of neural cells, especially the filopodia and lamellipodia, with high accuracy, and outperforms recent state of the art by a large margin. 

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5. Oleaginous Fungi in Biorefineries

   https://doi.org/10.1016/B978-0-12-819990-9.00004-4  

   Zhu S, Bonito G (January 2020, Reference Module in Life Sciences)

   null (Ed.)

   Many unicellular microorganisms including yeasts, fungi, microalgae, and to a lesser extent bacteria (Fig. 1), can produce intra- cellular edible oils under normal and specialized conditions (Papanikolaou and Aggelis, 2011). Most of these organisms can accumulate microbial lipids, or single-cell oils (SCOs), to 20%–90% (w/w) of their dry cell biomass. For example, fungi in the genus Mortierella and Umbelopsis can accumulate lipids at concentrations that exceed 86% of their dry weight (Meng et al., 2009). Microbial lipids can be produced using low-priced organic materials, including waste-streams from the food industry, as growth substrate. The fatty acid of microbial lipids is very similar to the conventional vegetable oils in type and composition (Madani et al., 2017). Furthermore, microbial lipids have many potential applications, including human food additives, nutraceuticals, pharmaceuticals, cosmetics, biopolymers and feed ingredients for aquaculture, and as an alternative feedstock for the production of biofuel (Lewis et al., 2000). Due to the reduced availability of cultivable land and increasing human population growth, producing lipids via traditional methods will not satisfy the rapidly growing global demand. Therefore, microbial lipids accu- mulated from microorganisms, especially oleaginous fungi, are considered as a vital and renewable oil resource and have been regarded as an alternative to animal and plant lipids in recent years, given their unique characteristics and functions in energy, chemical, and food industries (Huang et al., 2017). The production of microbial lipids is particularly attractive when low or negative cost substrates are used as the feedstock. 

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