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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The RIT1 C-terminus associates with lipid bilayers via charge complementarity

RIT1 is a member of the Ras superfamily of small GTPases involved in regulation of cellular signaling. Mutations to RIT1 are involved in cancer and developmental disorders. Like many Ras subfamily members, RIT1 is localized to the plasma membrane. However, RIT1 lacks the C-terminal prenylation that helps many other subfamily members adhere to cellular membranes. For this study, we used molecular dynamics simulations to examine the mechanisms by which the C-terminal peptide (CTP) of RIT1 associates with lipid bilayers. We show that the CTP is unstructured and that its membrane interactions depend on lipid composition. While a 12-residue region of the CTP binds strongly to anionic bilayers containing phosphatidylserine lipids, the CTP termini fray from the membrane allowing for accommodation of the RIT1 globular domain at the membrane-water interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain

Metabolic models containing kinetic information can answer unique questions about cellular metabolism that are useful to metabolic engineering. Several kinetic modeling frameworks have recently been developed or improved. In addition, techniques for systematic identification of model structure, including regulatory interactions, have been reported. Each framework has advantages and limitations, which can make it difficult to choose the most appropriate framework. Common limitations are data availability and computational time, especially in large-scale modeling efforts. However, recently developed experimental techniques, parameter identification algorithms, as well as model reduction techniques help alleviate these computational bottlenecks. Opportunities for additional improvements may come from the rich literature in catalysis and chemical networks. In all, kinetic models are positioned to make significant impact in cellular engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Optogenetics and biosensors set the stage for metabolic cybergenetics

We report cybergenetic systems use computer interfaces to enable feed-back controls over biological processes in real time. The complex and dynamic nature of cellular metabolism makes cybergenetics attractive for controlling engineered metabolic pathways in microbial fermentations. Cybergenetics would not only create new avenues of research into cellular metabolism, it would also enable unprecedented strategies for pathway optimization and bioreactor operation and automation. Implementation of metabolic cybergenetics, however, will require new capabilities from actuators, biosensors, and control algorithms. The recent application of optogenetics in metabolic engineering, the expanding role of genetically encoded biosensors in strain development, and continued progress in control algorithms for biological processes suggest that this technology will become available in the not so distant future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Editorial overview: Unlocking the secrets of nongenetic plasticity, one cell at a time

Cellular noise, the non-genetic variability observed among isogenic cells, arises from factors such as growth conditions, aging, and stochastic gene expression, influencing cell stress-response, metabolism, morphology, and size. Here, such plasticity, while critical for adaptation, often goes unnoticed with traditional population-averaging biotechnologies that inevitably mask cell-specific variations and prompting the question, "What else might we be missing". However, recent breakthroughs in optical imaging, microfluidics, and omics, are beginning to uncover the complexity of cellular plasticity. This special is-sue highlights some of these breakthroughs, with key contributions including innovations in multimodal chemical imaging, label-free microscopy, spatial and temporal omics, and droplet-based microfluidics. Collectively, these cutting-edge tools provide unprecedent-ed insights into non-genetic cell-to-cell variability, enhancing our understanding of cellu-lar plasticity and its implications for health, energy, and ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Discovering the nanoscale origins of localized corrosion in additive manufactured stainless steel 316L by liquid cell transmission electron microscopy

Here, we use liquid cell scanning transmission electron microscopy (STEM) to directly characterize the nanoscale origins of corrosion initiation in Additive manufacturing (AM) 316 L stainless steel. Under applied anodic potentials, we found that the dislocation cellular boundaries were preferentially corroded and that regions of localize corrosion occurred along the cellular boundaries. We directly observed the earliest stages of corrosion by controlling the biasing parameters to decelerate the corrosion processes. The results show that highly localized corrosion occurs via inclusion dissolution along dislocation cell boundaries. More widespread corrosion initiates at the dislocation cell boundaries and spreads throughout the dislocation networks.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Transcriptional and translational landscape of Candida auris in response to caspofungin

Candida auris has emerged as a serious worldwide threat by causing opportunistic infections that are frequently resistant to one or more conventional antifungal medications resulting in high mortality rates. Against this backdrop, health warnings around the world have focused efforts on understanding C. auris fungal biology and effective prevention and treatment approaches to combat this fungus. To date, there is little information about the differentially expressed genes when this fungus is treated with conventional antifungals, and caspofungin is a standard echinocandin deployed in the therapy against C. auris. In this work, we treated two distinct strains of C. auris for 24h with caspofungin, and the cellular responses were evaluated at the morphological, translational and transcriptional levels. We first observed that the echinocandin caused morphological alterations, aggregation of yeast cells, and modifications in the cell wall composition of C. auris. Transcriptomic analysis revealed an upregulation of genes related to the synthesis of the cell wall, ribosome, and cell cycle after exposure to caspofungin. Supporting these findings, the integrated proteomic analysis showed that caspofungin-treated cells were enriched in ribosome-related proteins and cell wall, especially mannoproteins. Altogether, these results provide further insights into the biology of C. auris and expands our understanding regarding the antifungal activity of caspofungin and reveal cellular targets, as the mannose metabolism, that can be further explored for the development of novel antifungals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Temporal dynamics of CO 2 and CH 4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils

Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands are subjected to the immediate consequence of climate change with shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of fluctuating hydrology and, specifically, the role of antecedent moisture conditions in determining the dominant carbon loss mechanisms in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. Our objective was to understand shifts in biogeochemical processes in response to changing soil moisture, based on soil respiration and methane production rates, and to elucidate such responses based on the observed electron acceptor and metabolite profiles under laboratory conditions. Metabolomics and biogeochemical process rates provided evidence that soil redox was the principal factor driving metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of their concentrations in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction compared to carbon loss due to methano genesis. Our results show that extended and short-term saturation created conditions conducive to increasing metabolite availability for anaerobic decomposition processes, with a significant lag in methanogenesis. In contrast,extended drying caused a cellular-level stress response and rapid recycling of alternate electron acceptors.

anaerobic respiration, tidal wetlands, methane pro↗
DOE OSTI2022

A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals

As an essential enzyme of SARS-CoV-2, the COVID-19 pathogen, main protease (M Pro ) is a viable target to develop antivirals for the treatment of COVID-19. By varying chemical compositions at both P2 and P3 positions and the N-terminal protection group, we synthesized 18 tripeptidyl M Pro inhibitors that contained also an aldehyde warhead and β-(S-2-oxopyrrolidin-3-yl)-alaninal at the P1 position. Systematic characterizations of these inhibitors were conducted, including their in vitro enzymatic inhibition potency, X-ray crystal structures of their complexes with M Pro , their inhibition of M Pro transiently expressed in 293T cells, and cellular toxicity and SARS-CoV-2 antiviral potency of selected inhibitors. These inhibitors have a large variation of determined in vitro enzymatic inhibition IC 50 values that range from 4.8 to 650 nM. Here, the determined in vitro enzymatic inhibition IC 50 values reveal that relatively small side chains at both P2 and P3 positions are favorable for achieving high in vitro M Pro inhibition potency, the P3 position is tolerable toward unnatural amino acids with two alkyl substituents on the α-carbon, and the inhibition potency is sensitive toward the N-terminal protection group. X-ray crystal structures of M Pro bound with 16 inhibitors were determined. In all structures, the M Pro active site cysteine interacts covalently with the aldehyde warhead of the bound inhibitor to form a hemithioacetal that takes an S configuration. For all inhibitors, election density around the N-terminal protection group is weak indicating possible flexible binding of this group to M Pro . In M Pro , large structural variations were observed on residues N142 and Q189. Unlike their high in vitro enzymatic inhibition potency, most inhibitors showed low potency to inhibit M Pro that was transiently expressed in 293T cells. Inhibitors that showed high potency to inhibit M Pro transiently expressed in 293T cells all contain O-tert-butyl-threonine at the P3 position. These inhibitors also exhibited relatively low cytotoxicity and high antiviral potency. Overall, our current and previous studies indicate that O-tert-butyl-threonine at the P3 site is a key component to achieve high cellular and antiviral potency for tripeptidyl aldehyde inhibitors of M Pro .

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Synchrotron-based X-ray fluorescence microscopy mapping the ionome of a toxic freshwater cyanobacterium

Harmful algal blooms (HABs) pose a major environmental concern across the globe. In abundance, cyanobacteria, or so-called green-blue algae can produce extremely dangerous cyanotoxins that harm humans and animals. This study focused on the mapping and distribution of intracellular macro-and micronutrients of the widespread freshwater cyanobacteria Microcystis aeruginosa (M. aeruginosa). Towards a better understanding of trace metal uptake and homeostasis throughout the cell cycle, we quantitatively mapped the spatial distribution of the elements P, K, Fe, Ca, Zn, Mn, and Cu across the ultrastructure of frozen-hydrated single cells using state-of-theart X-ray nanofluorescence imaging at the Advanced Photon Source (APS) at Argonne National Laboratory. Further, bulk cellular nutrient and trace metal content correlated well with the total intracellular elemental content in individual cells obtained by quantitative synchrotron X-ray fluorescence measurements. Multi-dimensional mappings showed P and K atoms colocalized as discrete semicircular hotspots that were analyzed with respect to their stoichiometry. Elevated Cu and Ca concentrations were detected along division plane of cells. P and K were found to have similar spatial elemental distribution with about 65% and 69% of the total cellular P and K, respectively, located at the hotspots. The P and K colocalization were refined further using nanotomography, showing a K envelope surrounding the P core. Inorganic P and organic P compounds were specified using solution-state 31 P nuclear magnetic resonance (NMR) spectroscopy from M. aeruginosa. Of the total extracted P determined by 31 P NMR spectroscopy, 47% were found to be nucleotides while only 11% were polyphosphates. Multimodal X-ray imaging provides a better understanding of intracellular biochemical processes in cyanobacteria, helping us monitor and combat an emerging environmental threat.

31P NMR spectroscopy↗
DOE OSTI2018

Native and exotic oysters in Brazil: Comparative tolerance to hypercapnia

Highlights: • C. gigas and C. brasiliana showed differentiated biochemical response to hypercapnia. • Juveniles presented a more pronounced stress response than adults in both species. • Contrasting metabolic shifts were observed between both species to endure hypercapnia. • Antioxidant and metabolic responses were sufficient to prevent excessive LPO. Environmental hypercapnia in shallow coastal marine ecosystems can be exacerbated by increasing levels of atmospheric CO{sub 2}. In these ecosystems organisms are expected to become increasingly subjected to pCO{sub 2} levels several times higher than those inhabiting ocean waters (e.g.: 10,000 µatm), but still our current understanding on different species capacity to respond to such levels of hypercapnia is limited. Oysters are among the most important foundation species inhabiting these coastal ecosystems, although natural oyster banks are increasingly threatened worldwide. In the present study we studied the effects of hypercapnia on two important oyster species, the pacific oyster C. gigas and the mangrove oyster C. brasiliana, to bring new insights on different species response mechanisms towards three hypercapnic levels (ca. 1,000; 4,000; 10,000 µatm), by study of a set of biomarkers related to metabolic potential (electron transport system - ETS), antioxidant capacity (SOD, CAT, GSH), cellular damage (LPO) and energetic fitness (GLY), in two life stages (juvenile and adult) after 28 days of exposure. Results showed marked differences between each species tolerance capacity to hypercapnia, with contrasting metabolic readjustment strategies (ETS), different antioxidant response capacities (SOD, CAT, GSH), which generally allowed to prevent increased cellular damage (LPO) and energetic impairment (GLY) in both species. Juveniles were more responsive to hypercapnia stress in both congeners, and are likely to be most sensitive to extreme hypercapnia in the environment. Juvenile C. gigas presented more pronounced biochemical alterations at intermediate hypercapnia (4,000 µatm) than C. brasiliana. Adult C. gigas showed biochemical alterations mostly in response to high hypercapnia (10,000 µatm), while adult C. brasiliana were less responsive to this environmental stressor, despite presenting decreased metabolic potential. Our data bring new insights on the biochemical performance of two important oyster species, and suggest that the duration of extreme hypercapnia events in the ecosystem may pose increased challenges for these organisms as their tolerance capacity may be time limited.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Effects of mobile phone exposure on metabolomics in the male and female reproductive systems

Highlights: • Long-term exposure to EMF decreases sperm motility and fertilization. • Effects of EMF emitted from mobile phones are related to protein synthesis. • Oxidative stress based EMF exposure modulates nitric oxide level in the germ cells. • Oxidative stress based EMF exposure inhibits antioxidant mechanisms in the germ cells. With current advances in technology, a number of epidemiological and experimental studies have reported a broad range of adverse effects of electromagnetic fields (EMF) on human health. Multiple cellular mechanisms have been proposed as direct causes or contributors to these biological effects. EMF-induced alterations in cellular levels can activate voltage-gated calcium channels and lead to the formation of free radicals, protein misfolding and DNA damage. Because rapidly dividing germ cells go through meiosis and mitosis, they are more sensitive to EMF in contrast to other slower-growing cell types. In this review, possible mechanistic pathways of the effects of EMF exposure on fertilization, oogenesis and spermatogenesis are discussed. In addition, the present review also evaluates metabolomic effects of GSM-modulated EMFs on the male and female reproductive systems in recent human and animal studies. In this context, experimental and epidemiological studies which examine the impact of mobile phone radiation on the processes of oogenesis and spermatogenesis are examined in line with current approaches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

The genomic effects of cell phone exposure on the reproductive system

Highlights: • Electromagnetic fields (EMF) causes an imbalance between pro-oxidant and antioxidant mechanismsEMF increases reactive oxygen species production. • Exposure to EMF leads to disruptions in spermatogenic cells. • Exposure to GSM-modulated EMF causes an increase in superoxide formation levels in human spermatozoa. Humans are exposed to increasing levels of electromagnetic fields (EMF) at various frequencies as technology advances. In this context, improving understanding of the biological effects of EMF remains an important, high priority issue. Although a number of studies in this issue and elsewhere have focused on the mechanisms of the oxidative stress caused by EMF, the precise understanding of the processes involved remains to be elucidated. Due to unclear results among the studies, the issue of EMF exposure in the literature should be evaluated at the genomic level on the reproductive system. Based on this requirement, a detail review of recently published studies is necessary. The main objectives of this study are to show differences between negative and positive effect of EMF on the reproductive system of animal and human. Extensive review of literature has been made based on well known data bases like Web of Science, PubMed, MEDLINE, Google Scholar, Science Direct, Scopus. This paper reviews the current literature and is intended to contribute to a better understanding of the genotoxic effects of EMF emitted from mobile phones and wireless systems on the human reproductive system, especially on fertility. The current literature reveals that mobile phones can affect cellular functions via non-thermal effects. Although the cellular targets of global system for mobile communications (GSM)-modulated EMF are associated with the cell membrane, the subject is still controversial. Studies regarding the genotoxic effects of EMF have generally focused on DNA damage. Possible mechanisms are related to ROS formation due to oxidative stress. EMF increases ROS production by enhancing the activity of nicotinamide adenine dinucleotide (NADH) oxidase in the cell membrane. Further detailed studies are needed to elucidate DNA damage mechanisms and apoptotic pathways during oogenesis and spermatogenesis in germ cells exposed to EMF.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2018

Large carbon isotope variability during methanogenesis under alkaline conditions

We report that high carbon isotope values (δ 13 C CH4 > -40‰) have widely been used as evidence that methane in alkaline rock-hosted fluids was formed abiotically, particularly in serpentinizing systems. However, isotope fractionation during microbial methanogenesis is relatively understudied at high pH. We isolated a hydrogenotrophic Methanobacterium sp. from hyperalkaline subsurface fluids in the Samail ophiolite to assess how carbon and hydrogen isotope values of CH 4 varied depending upon pH and carbonate mineral source (NaHCO 3 or CaCO 3 ). The hydrogen isotope fractionation α H20/CH4 (1.46–1.66) did not vary across pH. In contrast, the expressed carbon isotope fractionation, α CO2/CH4 , ranged from 1.028 to 1.089. Carbon isotope fractionation increased with pH, reaching a maximum 13 C depletion of -85‰. However, the 13 C depletion significantly diminished at pH ≥ 9 for CaCO 3 -amended experiments, generating δ 13 C CH4 as high as -28‰. To evaluate the large variability in δ 13 C CH4 , we developed a steady-state model to assess how the rates of carbonate dissolution, cellular uptake of CO 2 and irreversible CH 4 production can affect the net isotope fractionation during methanogenesis. Methanobacterium sp. can produce highly depleted δ 13 C CH4 in simulated alkaline serpentinizing fluids when dissolved inorganic carbon levels are high and methanogenesis rates are slow. However, small carbon isotope fractionation occurs when rates of carbonate dissolution are slower than cellular uptake, leading to relatively high δ 13 C CH4 values (>~-35‰) that are traditionally interpreted to be purely “abiotic”. Lastly, microbial CH 4 can be produced in carbon-limited mafic and ultramafic rock-hosted environments on Earth and potentially other planetary bodies, but it may be difficult to isotopically identify biogenic methane when mineral carbonates are the dominant carbon source.

58 GEOSCIENCES↗
DOE OSTI2019

A new micromechanics based full field numerical framework to simulate the effects of dynamic recrystallization on the formability of HCP metals

This work presents a new full-field, efficient and mesh-free numerical framework to model microstructure evolution, dynamic recrystallization (DRX) and formability in hexagonal closed-packed (HCP) metals such as magnesium alloys at warm temperatures. A rate tangent-fast Fourier transform-based elasto-viscoplastic crystal plasticity constitutive model for HCP metals (RTCP-FFT-HCP) is coupled with a probabilistic cellular automata (CA) approach to model DRX (CA-DRX). Furthermore, this new model is coupled with the Marciniak-Kuczynski (M-K) approach to model formability of magnesium alloys at elevated temperatures. The RTCP-FFT-HCP model computes macro stress-strain, twinning volume fraction, micromechanical fields, texture evolution and local dislocation density. Nucleation of new grains and their subsequent growth is modeled using the cellular automata approach with probabilistic state switching rule. First, the proposed RTCP-FFT-HCP model is validated by comparing the predicted stress-strain responses and texture evolution under uniaxial tension and compression with experimental measurements for AZ31 sheet alloy at room temperature. The coupled CA-RTCPFFT-HCP model is further validated by comparing the predicted stress-strain responses and texture evolution in uniaxial compression with experimental measurements at 100 °C, 200 °C and 300 °C for the AZ31 sheet alloy. Next, the forming limit diagrams (FLDs) with and without including the effects of DRX are simulated at 100 °C, 200 °C and 300 °C for AZ31 sheet alloy. The predicted FLDs with DRX show very good agreement with the experimental measurements and clearly demonstrate the need for an accurate DRX model. The study reveals that the DRX strongly affects the deformed grain structure, grain size and texture evolution and also highlights the importance accounting for DRX during FLD simulations at high temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Nicotinamide Phosphoribosyltransferase Upregulation by Phenylephrine Reduces Radiation Injury in Submandibular Gland

Purpose: Radiation therapy for head and neck cancer commonly leads to radiation sialadenitis. Emerging evidence has indicated that phenylephrine pretreatment reduces radiosensitivity in the salivary gland; however, the underlying cytoprotective mechanism remains unclear. Nicotinamide phosphoribosyltransferase (NAMPT) is not only a key enzyme for the nicotinamide adenine dinucleotide salvage pathway, but also a cytokine participating in cell survival, metabolism, and longevity, with a broad effect on cellular functions in physiology and pathology. However, the regulatory events of NAMPT in response to the irradiated salivary gland are unknown. Methods and Materials: The cell viability of primary cultured submandibular gland cells was determined using the PrestoBlue assay. NAMPT expression was measured using reverse transcriptase polymerase chain reaction and Western blotting in vitro and in vivo. Silent information regulator 1 (SIRT1) and phosphorylated Akt protein levels were examined by Western blotting. The cellular locations of NAMPT and SIRT1 were detected by immunohistochemistry. NAMPT promoter activity was assessed using the luciferase reporter gene assay. Results: NAMPT was mainly distributed in the cytoplasm of granular convoluted tubule cells and ductal cells in normal submandibular glands. mRNA and protein expression of NAMPT was downregulated after radiation but upregulated with phenylephrine pretreatment both in vivo and in vitro. Moreover, the protein expression of phosphorylated Akt and SIRT1 was decreased in irradiated glands, and phenylephrine pretreatment restored the expression of both. SIRT1 was mainly located in the cell nucleus and cytoplasm in the normal submandibular gland. Phenylephrine dramatically enhanced the expression of SIRT1, which was significantly reduced by radiation. Furthermore, phenylephrine induced a marked increase of NAMPT promoter activity. Conclusions: These findings reveal the regulatory mechanisms of NAMPT expression, which help to understand the mechanism of the cytoprotective role of phenylephrine on irradiated tissues.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Targeting the Y-box Binding Protein-1 Axis to Overcome Radiochemotherapy Resistance in Solid Tumors

Multifunctional Y-box binding protein-1 (YB-1) is highly expressed in different human solid tumors and is involved in various cellular processes. DNA damage is the major mechanism by which radiochemotherapy (RCT) induces cell death. On induction of DNA damage, a multicomponent signal transduction network, known as the DNA damage response, is activated to induce cell cycle arrest and initiate DNA repair, which protects cells against damage. YB-1 regulates nearly all cancer hallmarks described to date by participating in DNA damage response, gene transcription, mRNA splicing, translation, and tumor stemness. YB-1 lacks kinase activity, and p90 ribosomal S6 kinase and AKT are the key kinases within the RAS/mitogen-activated protein kinase and phosphoinositide 3-kinase pathways that directly activate YB-1. Thus, the molecular targeting of ribosomal S6 kinase and AKT is thought to be the most effective strategy for blocking the cellular function of YB-1 in human solid tumors. In this review, after describing the prosurvival effect of YB-1 with a focus on DNA damage repair and cancer cell stemness, clinical evidence will be provided indicating an inverse correlation between YB-1 expression and the treatment outcome of solid tumors after RCT. In the interest of being concise, YB-1 signaling cascades will be briefly discussed and the current literature on YB-1 posttranslational modifications will be summarized. Finally, the current status of targeting the YB-1 axis, especially in combination with RCT, will be highlighted.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Senolysis induced by 25-hydroxycholesterol targets CRYAB in multiple cell types

Cellular senescence is a driver of many age-related pathologies. There is an active search for pharmaceuticals termed senolytics that can mitigate or remove senescent cells in vivo by targeting genes that promote the survival of senescent cells. We utilized single-cell RNA sequencing to identify CRYAB as a robust senescence-induced gene and potential target for senolysis. Using chemical inhibitor screening for CRYAB disruption, we identified 25-hydroxycholesterol (25HC), an endogenous metabolite of cholesterol biosynthesis, as a potent senolytic. We then validated 25HC as a senolytic in mouse and human cells in culture and in vivo in mouse skeletal muscle. Thus, 25HC represents a potential class of senolytics, which may be useful in combating diseases or physiologies in which cellular senescence is a key driver.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Processes in DNA damage response from a whole-cell multi-omics perspective

Technological advances have made it feasible to collect multi-condition multi-omic time courses of cellular response to perturbation, but the complexity of these datasets impedes discovery due to challenges in data management, analysis, visualization, and interpretation. Here, we report a whole-cell mechanistic analysis of HL-60 cellular response to bendamustine. We integrate both enrichment and network analysis to show the progression of DNA damage and programmed cell death over time in molecular, pathway, and process-level detail using an interactive analysis framework for multi-omics data. Our framework, Mechanism of Action Generator Involving Network analysis (MAGINE), automates network construction and enrichment analysis across multiple samples and platforms, which can be integrated into our annotated gene-set network to combine the strengths of networks and ontology-driven analysis. Taken together, our work demonstrates how multi-omics integration can be used to explore signaling processes at various resolutions and demonstrates multi-pathway involvement beyond the canonical bendamustine mechanism.

59 BASIC BIOLOGICAL SCIENCES↗