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At least 307 records · Page 17

Let it rip: The mechanics of self-bisection in asexual planarians determines their population reproductive strategies

Asexual freshwater planarians reproduce by transverse bisection (binary fission) into two pieces. This process produces a head and a tail, which fully regenerate within 1-2 weeks. How planarians split into two offspring - using only their musculature and substrate traction – is a challenging biomechanics problem. We found that three different species, Dugesia japonica, Girardia tigrina and Schmidtea mediterranea, have evolved three different mechanical solutions to self-bisect. Using time lapse imaging of the fission process, we quantitatively characterize the main steps of division in the three species and extract the distinct and shared key features. Across the three species, planarians actively alter their body shape, regulate substrate traction, and use their muscles to generate tensile stresses large enough to overcome the ultimate tensile strength of the tissue. Moreover, we show that how each planarian species divides dictates how resources are split among its offspring. This ultimately determines offspring survival and reproductive success. Furthermore, heterospecific differences in the mechanics of self-bisection of individual worms explain the observed differences in the population reproductive strategies of different planarian species.

59 BASIC BIOLOGICAL SCIENCES↗

Localization and coherent imaging of hidden moving objects using laser speckle

Imaging and sensing of moving objects through opaque scattering media is a challenging but important problem in a variety of applications, including environmental sensing, biomedical imaging, and material inspection. We have previously demonstrated a technique to coherently image a moving object through thick, heavily scattering random media using correlations of speckle images as a function of the object’s spatial translation. Here, we demonstrate that this technique can be combined with localization to achieve imaging without prior knowledge of the object’s motion, greatly extending the application domain. This method is effective beyond the thin or weakly scattering regime and, rather than motion being deleterious, exploits the information available when the hidden object is moving, as could be the case in a cluttered terrestrial environment or through substantial levels of biological tissue scatter.

Hastings, Ryan L. (ORCID:0009000095977807)↗

Creation of a prototype biomimetic fish to better understand impact trauma caused by hydropower turbine blade strikes

Biomimetic model organisms could be useful surrogates for live animals in many applications if the models have sufficient biofidelity. One such application is for use in field and laboratory tests of fish mortality associated with passage through hydropower turbines. Laboratory trials suggest that blade strikes are especially injurious and often causes mortality when fish are struck by thinner blades moving at higher velocities. Dose-response relationships have been created from these data, but the exact relationship between fish mortality and the actual forces enacted on fish during simulated blade strike testing remains unknown. Here, we describe the methods used to create a prototype biomimetic model fish composed of ballistic gelatin and covered with a surrogate skin to better approximate the biomechanical properties of a fish body. Frozen fish were scanned with high-fidelity laser scanners, and a 3D-printed, reusable mold was created from which to cast our gelatin model. Computed tomography scan data, imaged directly or taken from online data repositories, were also successfully used to create CAD models for use in additive manufacturing of molds. One 3-axis accelerometer was embedded into the gelatin to compare accelerometer data to dose-response data from previous laboratory research on live fish. The resulting model ( i.e. , Gelfish) had a statistically indistinguishable tissue durometer to that of real fish tissue and preliminary blade strike impact testing suggested its overall flexibility was similar to that of live fish. Gelfish was designed with biofidelity as its guiding principle and our results suggest initial experimentation was successful. Future research will include replication of initial Gelfish test results, quantitative measurement of model flexibility relative to real fish, and inclusion of surrogate skeletal structures to enhance biofidelity. Use of more sophisticated sensors would also better quantify the physical forces of blade strike impact and help determine how said forces correlate with rates of mortality observed during tests on live fish.

36 MATERIALS SCIENCE↗

Targeted engineering of camelina and pennycress seeds for ultrahigh accumulation of acetyl-TAG

Acetyl-TAG (3-acetyl-1,2-diacylglycerol), unique triacylglycerols (TAG) possessing an acetate group at the sn -3 position, exhibit valuable properties, such as reduced viscosity and freezing points. Previous attempts to engineer acetyl-TAG production in oilseed crops did not achieve the high levels found in naturally producing Euonymus seeds. Here, we demonstrate the successful generation of camelina and pennycress transgenic lines accumulating nearly pure acetyl-TAG at 93 mol% and 98 mol%, respectively. These ultrahigh acetyl-TAG synthesizing lines were created using gene-edited FATTY ACID ELONGASE1 ( FAE1 ) mutant lines as an improved genetic background to increase levels of acetyl-CoA available for acetyl-TAG synthesis mediated by the expression of EfDAcT, a high-activity diacylglycerol acetyltransferase isolated from Euonymus fortunei . Combining EfDAcT expression with suppression of the competing TAG-synthesizing enzyme DGAT1 further enhanced acetyl-TAG accumulation. These ultrahigh levels of acetyl-TAG exceed those in earlier engineered oilseeds and are equivalent or greater than those in Euonymus seeds. Imaging of lipid localization in transgenic seeds revealed that the low amounts of residual TAG were mostly confined to the embryonic axis. Similar spatial distributions of specific TAG and acetyl-TAG molecular species, as well as their probable diacylglycerol (DAG) precursors, provide additional evidence that acetyl-TAG and TAG are both synthesized from the same tissue-specific DAG pools. Remarkably, this ultrahigh production of acetyl-TAG in transgenic seeds exhibited minimal negative effects on seed properties, highlighting the potential for production of designer oils required for economical biofuel industries.

09 BIOMASS FUELS↗

The onset of rare earth metallosis begins with renal gadolinium-rich nanoparticles from magnetic resonance imaging contrast agent exposure

The leitmotifs of magnetic resonance imaging (MRI) contrast agent-induced complications range from acute kidney injury, symptoms associated with gadolinium exposure (SAGE)/gadolinium deposition disease, potentially fatal gadolinium encephalopathy, and irreversible systemic fibrosis. Gadolinium is the active ingredient of these contrast agents, a non-physiologic lanthanide metal. The mechanisms of MRI contrast agent-induced diseases are unknown. Mice were treated with a MRI contrast agent. Human kidney tissues from contrast-naïve and MRI contrast agent-treated patients were obtained and analyzed. Kidneys (human and mouse) were assessed with transmission electron microscopy and scanning transmission electron microscopy with X-ray energy-dispersive spectroscopy. MRI contrast agent treatment resulted in unilamellar vesicles and mitochondriopathy in renal epithelium. Electron-dense intracellular precipitates and the outer rim of lipid droplets were rich in gadolinium and phosphorus. We conclude that MRI contrast agents are not physiologically inert. The long-term safety of these synthetic metal–ligand complexes, especially with repeated use, should be studied further.

36 MATERIALS SCIENCE↗

Spatial control of perilacunar canalicular remodeling during lactation

Abstract Osteocytes locally remodel their surrounding tissue through perilacunar canalicular remodeling (PLR). During lactation, osteocytes remove minerals to satisfy the metabolic demand, resulting in increased lacunar volume, quantifiable with synchrotron X-ray radiation micro-tomography (SRµCT). Although the effects of lactation on PLR are well-studied, it remains unclear whether PLR occurs uniformly throughout the bone and what mechanisms prevent PLR from undermining bone quality. We used SRµCT imaging to conduct an in-depth spatial analysis of the impact of lactation and osteocyte-intrinsic MMP13 deletion on PLR in murine bone. We found larger lacunae undergoing PLR are located near canals in the mid-cortex or endosteum. We show lactation-induced hypomineralization occurs 14 µm away from lacunar edges, past a hypermineralized barrier. Our findings reveal that osteocyte-intrinsic MMP13 is crucial for lactation-induced PLR near lacunae in the mid-cortex but not for whole-bone resorption. This research highlights the spatial control of PLR on mineral distribution during lactation.

59 BASIC BIOLOGICAL SCIENCES↗

Structural differences between human and mouse neurons and their implementation in generative AIs

Mouse and human brains have different functions that depend on their neuronal networks. We analyzed nanometer-scale three-dimensional structures of brain tissues of the mouse medial prefrontal cortex and compared them with structures of the human anterior cingulate cortex. The obtained results indicated that mouse neuronal somata are smaller and neurites are thinner than those of human neurons. We implemented these characteristics of mouse neurons in convolutional layers of a generative adversarial network (GAN) and a denoising diffusion implicit model (DDIM), which were then subjected to image generation tasks using photo datasets of cat faces, cheese, human faces, birds, and automobiles. The mouse-mimetic GAN outperformed a standard GAN in the image generation task using the cat faces and cheese photo datasets, but underperformed for human faces and birds. The mouse-mimetic DDIM gave similar results, suggesting that the nature of the datasets affected the results. Analyses of the five datasets indicated differences in their image entropy, which should influence the number of parameters required for image generation. The preferences of the mouse-mimetic AIs coincided with the impressions commonly associated with mice. The relationship between the neuronal network and brain function should be investigated by implementing other biological findings in artificial neural networks.

generative AI↗

Multimodal imaging of hemorrhagic transformation biomarkers in an ischemic stroke model.

Abstract Hemorrhagic transformation of ischemic stroke has devastating consequences, with high mortality and poor functional outcomes. Animal models of ischemic stroke also demonstrate the potential for hemorrhagic transformation, which complicates biochemical characterization, treatment studies, and hinders poststroke functional outcomes in affected subjects. The incidence of hemorrhagic transformation of ischemic stroke in animal model research is not commonly reported. The postmortem brain of such cases presents a complex milieu of biomarkers due to the presence of healthy cells, regions of varying degrees of ischemia, dead and dying cells, dysregulated metabolites, and blood components (especially reactive Fe species released from lysed erythrocytes). To improve the characterization of hemorrhage biomarkers on an ischemic stroke background, we have employed a combination of histology, X-ray fluorescence imaging (XFI), and Fourier transform infrared (FTIR) spectroscopic imaging to assess 122 photothrombotic (ischemic) stroke brains. Rapid freezing preserves brain biomarkers in situ and minimizes metabolic artifacts due to postmortem ischemia. Analysis revealed that 25% of the photothrombotic models had clear signs of hemorrhagic transformation. The XFI and FTIR metabolites provided a quantitative method to differentiate key metabolic regions in these models. Across all hemorrhage cases, it was possible to consistently differentiate otherwise healthy tissue from other metabolically distinct regions, including the ischemic infarct, the ischemic penumbra, blood vessels, sites of hemorrhage, and a region surrounding the hemorrhage core that contained elevated lipid oxidation. Chemical speciation of deposited Fe demonstrates the presence of heme-Fe and accumulation of ferritin.

Pushie, M. J. (ORCID:0000000174945427)↗

Overexpression of phospholipid: diacylglycerol acyltransferase in Brassica napus results in changes in lipid metabolism and oil accumulation

The regulation of lipid metabolism in oil seeds is still not fully understood and increasing our knowledge in this regard is of great economic, as well as intellectual, importance. Oilseed rape (Brassica napus) is a major global oil crop where increases in triacylglycerol (TAG) accumulation have been achieved by overexpression of relevant biosynthetic enzymes. In this study, we expressed Arabidopsis phospholipid: diacylglycerol acyltransferase (PDAT1), one of the two major TAG-forming plant enzymes in B. napus DH12075 to evaluate its effect on lipid metabolism in developing seeds and to estimate its flux control coefficient. Despite several-fold increase in PDAT activity, seeds of three independently generated PDAT transgenic events showed a small but consistent decrease in seed oil content and had altered fatty acid composition of phosphoglycerides and TAG, towards less unsaturation. Mass spectrometry imaging of seed sections confirmed the shift in lipid compositions and indicated that PDAT overexpression altered the distinct heterogeneous distributions of phosphatidylcholine (PC) molecular species. Similar, but less pronounced, changes in TAG molecular species distributions were observed. Our data indicate that PDAT exerts a small, negative, flux control on TAG biosynthesis and could have under-appreciated effects in fine-tuning of B. napus seed lipid composition in a tissue-specific manner. This has important implications for efforts to increase oil accumulation in similar crops.

Biochemistry & Molecular Biology↗

Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics

Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.

59 BASIC BIOLOGICAL SCIENCES↗

Root image collection from a genotype by environment (GxE) root architecture study of the bioenergy species, Populus trichocarpa

Here we present a curated dataset; raw images of fresh roots collected from a genotype by environment (growth matrix) greenhouse root architecture study of the bioenergy species, Populus trichocarpa. Five separate experiments were performed to generate the dataset. Biological replicates (ramets, vegetative propagants) of Populus trichocarpa genotypes BESC 24 and BESC 375 were used for all experiments. The first two experiments were an eight-week and a six-week pot experiment where plants with grown in 4" X 14" sized pots were filled with Farfard 3B potting soil (Fafard Sungro #3B), and watered twice daily. Average greenhouse humidity and growth temperature were around 50-60% and 23°C, respectively. Ramets of P. trichocarpa genotypes BESC 24 and BESC 375 were used in various experiments. The source of this material was dormant field cuttings grown in greenhouse. The second experiment was a Microcosm root architecture experiment. This was done in a microcosm built with double-decker tissue culture Magenta box. Tissue culture plants with new root initials were transferred to microcosm with pro choice rapid dry growth matrix with 1x Hoagland’s solution pH5.7 and grown for six weeks until harvest. Temperature was held at ~22°C. The closed container trapped moisture. The source material was tissue culture stock plants established from shoot tips of greenhouse stock plants (obtained from same set of dormant field cuttings as rest of the study). For the remaining two experiments, greenwood stem cuttings from greenhouse grown plants were grown in six-week rhizotron and two-week hydroponics experiments in the greenhouse. For rhizotron experiments, plants were grown in 2-D rhizotron with black panels on both sides (31cm H x 30cm L x 1.2cm W) and watered daily. For hydroponics experiment, plants were grown in a 15ml falcon tube with distilled water and covered in foil and shaken a few times a day. Greenhouse temperature was held at ~ 23°C and humidity was between 50-60%. Stems were cut off and the root system was separated, gently washed to rid of matrix, immersed in a water tray and scanned for obtaining raw root images reported here. All scans of roots floating in a water tray were performed using an Epson Perfection V850 Pro Photo Scanner. Additional meta data is embedded in the raw image files.

59 BASIC BIOLOGICAL SCIENCES↗

Bioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysis

SUMMARY Bioenergy sorghum is a highly productive drought tolerant C 4 grass that accumulates 80% of its harvestable biomass in approximately 4 m length stems. Stem internode growth is regulated by development, shading, and hormones that modulate cell proliferation in intercalary meristems (IMs). In this study, sorghum stem IMs were localized above the pulvinus at the base of elongating internodes using magnetic resonance imaging, microscopy, and transcriptome analysis. A change in cell morphology/organization occurred at the junction between the pulvinus and internode where LATERAL ORGAN BOUNDARIES ( SbLOB ), a boundary layer gene, was expressed. Inactivation of an AGCVIII kinase in DDYM ( dw2 ) resulted in decreased SbLOB expression, disrupted IM localization, and reduced internode cell proliferation. Transcriptome analysis identified approximately 1000 genes involved in cell proliferation, hormone signaling, and other functions selectively upregulated in the IM compared with a non‐meristematic stem tissue. This cohort of genes is expressed in apical dome stem tissues before localization of the IM at the base of elongating internodes. Gene regulatory network analysis identified connections between genes involved in hormone signaling and cell proliferation. The results indicate that gibberellic acid induces accumulation of growth regulatory factors (GRFs) known to interact with ANGUSTIFOLIA (SbAN3), a master regulator of cell proliferation. GRF:AN3 was predicted to induce SbARF3/ETT expression and regulate SbAN3 expression in an auxin‐dependent manner. GRFs and ARFs regulate genes involved in cytokinin and brassinosteroid signaling and cell proliferation. The results provide a molecular framework for understanding how hormone signaling regulates the expression of genes involved in cell proliferation in the stem IM.

59 BASIC BIOLOGICAL SCIENCES↗

Heterogeneous Distribution of Erucic Acid in Brassica napus Seeds

Brassica napus (B. napus) is the world's most widely grown temperate oilseed crop. Although breeding for human consumption has led to removal of erucic acid from refined canola oils, there is renewed interest in the industrial uses of erucic acid derived from B. napus, and there is a rich germplasm available for use. Here, low- and high-erucic acid accessions of B. napus seeds were examined for the distribution of erucic acid-containing lipids and the gene transcripts encoding the enzymes involved in pathways for its incorporation into triacylglycerols (TAGs) across the major tissues of the seeds. In general, the results indicate that a heterogeneous distribution of erucic acid across B. napus seed tissues was contributed by two isoforms (out of six) of FATTY ACYL COA ELONGASE (FAE1) and a combination of phospholipid:diacylglycerol acyltransferase (PDAT)- and diacylglycerol acyltransferase (DGAT)-mediated incorporation of erucic acid into TAGs in cotyledonary tissues. An absence of the expression of these two FAE1 isoforms accounted for the absence of erucic acid in the TAGs of the lowerucic accession.

59 BASIC BIOLOGICAL SCIENCES↗

Foliar Application of an Inositol-Based Plant Biostimulant Boosts Zinc Accumulation in Wheat Grains: A μ-X-Ray Fluorescence Case Study

There has been much interest in the incorporation of organic molecules or biostimulants into foliar fertilizers with the rationalization that these compounds will enhance the uptake, or subsequent mobility of the applied nutrient. The objective of this research was to investigate the effects of an inositol-based plant stimulant on the mobility and accumulation of foliar-applied zinc (Zn) in wheat plants ( Triticum aestivum L.). High-resolution elemental imaging with micro-X-ray fluorescence (μ-XRF) was utilized to examine Zn distribution within the vascular bundle of the leaf and whole grains. The inclusion of myo -inositol with Zinc sulfate, significantly increased Zn concentration in shoots in contrast to untreated controls and Zn sulfate applied alone. Foliar Zn treated plants increased Zn in grains by 5–25% with myo -inositol plus Zn treated plants significantly increasing grain Zn concentration compared to both Zn treated and non-treated controls. XRF imaging revealed Zn enrichment in the bran layer and germ, with a very low Zn concentration present in the endosperm. Plants treated with Zn plus myo -inositol showed an enhanced and uniform distribution of Zn throughout the bran layer and germ with an increased concentration in the endosperm. While our data suggest that foliar application of myo -inositol in combination with Zn may be a promising strategy to increase the absorption and mobility of Zn in the plant tissue and subsequently to enhance Zn accumulation in grains, further research is needed to clarify the mechanisms by which myo -inositol affects plant metabolism and nutrient mobility.

59 BASIC BIOLOGICAL SCIENCES↗

Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET

Cryogenic-electron tomography (cryo-ET) permits the in situ visualization of biological macromolecules at the molecular level. Owing to the variable thickness of cells, tissues and organisms, frozen specimens may need to be thinned by cryo-focused ion beam (FIB) milling to produce thin (<500 nm) cryo-lamellae suitable for cryo-ET. Locating regions of interest remains a challenge because untargeted milling can lead to inadvertent ablation and removal of regions of interest. Correlative light and electron microscopy, combined with cryo-FIB milling, can guide the identification of labeled targets in the cellular milieu. Multiple transfers between cryo-imaging instruments, cumbersome correlation algorithms, limited accuracy and low throughput have hindered the routine adoption of cryo-FIB milling within a multimodal correlative workflow for in situ structural biology. Here, in this study, we present a workflow for 3D correlative cryo-fluorescence light microscopy-FIB-ET that streamlines fluorescence light microscopy-guided FIB milling, improving throughput while preserving both structural and contextual information. The complete integration of hardware and software described here minimizes sample contamination from cross-platform exchanges and greatly enhances the efficiency of 3D targeting in cryo-milling. We then describe procedures for implementing montage parallel array cryo-ET (MPACT), which can be easily adapted to any modern life-science transmission electron microscope. MPACT supports high-throughput cryo-ET acquisitions (10 tilt series in 1.5 h) for structure determination and comprehensive contextual understanding of macromolecules within their native surroundings. A complete session from sample preparation to MPACT data processing takes 5−7 d for an individual experienced in both cryo-EM and cryo-FIB milling.

Yang, Jie E. [Univ. of Wisconsin, Madison, WI (Uni↗

YOLO2U-Net: Detection-guided 3D instance segmentation for microscopy

Microscopy imaging techniques are instrumental for characterization and analysis of biological structures. As these techniques typically render 3D visualization of cells by stacking 2D projections, issues such as out-of-plane excitation and low resolution in the z-axis may pose challenges (even for human experts) to detect individual cells in 3D volumes as these non-overlapping cells may appear as overlapping. In this paper a comprehensive method for accurate 3D instance segmentation of cells in the brain tissue is introduced. The proposed method combines the 2D YOLO detection method with a multi-view fusion algorithm to construct a 3D localization of the cells. Next, the 3D bounding boxes along with the data volume are input to a 3D U-Net network that is designed to segment the primary cell in each 3D bounding box, and in turn, to carry out instance segmentation of cells in the entire volume. The promising performance of the proposed method is shown in comparison with current deep learning-based 3D instance segmentation methods.

3D instance segmentation↗

Generative diffusion model surrogates for mechanistic agent-based biological models

Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models (DDPMs) to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.

97 MATHEMATICS AND COMPUTING↗

Magneto mitochondrial dysfunction mediated cancer cell death using intracellular magnetic nano-transducers

Mitochondria are crucial regulators of the intrinsic pathway of cancer cell death. The high sensitivity of cancer cells to mitochondrial dysfunction offers opportunities for emerging targets in cancer therapy. Herein, magnetic nano-transducers, which convert external magnetic fields into physical stress, are designed to induce mitochondrial dysfunction to remotely kill cancer cells. Spindle-shaped iron oxide nanoparticles were synthesized to maximize cellular internalization and magnetic transduction. The magneto-mechanical transduction of nano-transducers in mitochondria enhances cancer cell apoptosis by promoting a mitochondrial quality control mechanism, referred to as mitophagy. Furthermore, in the liver cancer animal model, nano-transducers are infused into the local liver tumor via the hepatic artery. After treatment with a magnetic field, in vivo mitophagy-mediated cancer cell death was also confirmed by mitophagy markers, mitochondrial DNA damage assay, and TUNEL staining of tissues. This study is expected to contribute to the development of nanoparticle-mediated mitochondria-targeting cancer therapy and biological tools, such as magneto-genetics.

60 APPLIED LIFE SCIENCES↗