J Chem Phys. 2023 Sep 28;159(12):124116. doi: 10.1063/5.0156313.

ABSTRACT

The effect of the presence of Ar on the isomerization reaction HCN ⇄ CNH is investigated via machine learning. After the potential energy surface function is developed based on the CCSD(T)/aug-cc-pVQZ level ab initio calculations, classical trajectory simulations are performed. Subsequently, with the aim of extracting insights into the reaction dynamics, the obtained reactivity, that is, whether the reaction occurs or not under a given initial condition, is learned as a function of the initial positions and momenta of all the atoms in the system. The prediction accuracy of the trained model is greater than 95%, indicating that machine learning captures the features of the phase space that affect reactivity. Machine learning models are shown to successfully reproduce reactivity boundaries without any prior knowledge of classical reaction dynamics theory. Subsequent analyses reveal that the Ar atom affects the reaction by displacing the effective saddle point. When the Ar atom is positioned close to the N atom (resp. the C atom), the saddle point shifts to the CNH (HCN) region, which disfavors the forward (backward) reaction. The results imply that analyses aided by machine learning are promising tools for enhancing the understanding of reaction dynamics.

PMID:38127399 | DOI:10.1063/5.0156313

mBio. 2023 Dec 21:e0205123. doi: 10.1128/mbio.02051-23. Online ahead of print.

ABSTRACT

Acinetobacter baumannii is a hospital-acquired pathogen that is resistant to many common antibiotic treatments. To combat resistant A. baumannii infections, we need to identify promising therapeutic targets and effective antibiotic combinations. In this study, we comprehensively characterize the genes and pathways that are critical for A. baumannii viability. We show that genes involved in aerobic metabolism are central to A. baumannii physiology and may represent appealing drug targets. We also find antibiotic-gene interactions that may impact the efficacy of carbapenems, rifamycins, and polymyxins, providing a new window into how these antibiotics function in mono- and combination therapies. Our studies offer a useful approach for characterizing interactions between drugs and essential genes in pathogens to inform future therapies.

PMID:38126769 | DOI:10.1128/mbio.02051-23

J Appl Physiol (1985). 2023 Dec 21. doi: 10.1152/japplphysiol.00291.2023. Online ahead of print.

ABSTRACT

While cardiorespiratory fitness (CRF), an important marker of youth health, is associated with earlier sleep/wake schedule, its relationship with circadian rhythms is unclear. This study examined the associations between CRF and rhythm variables in adolescents. Eighteen healthy adolescents (10 females and 8 males; Mage=14.6±2.3 years) completed two study visits on weekdays bracketing an ambulatory assessment during summer vacation. Visit 1 included in-laboratory CRF assessment (peak VO2) using a ramp-type progressive cycle ergometry protocol and gas exchange measurement, which followed by 7-14 days of actigraphy to assess sleep/wake patterns and 24-h activity rhythms. During Visit 2, chronotype, social jetlag (i.e., the difference in midsleep time between weekdays and weekends), and phase preference were assessed using a questionnaire, and hourly saliva samples were collected to determine dim light melatonin onset (DLMO) phase. All analyses adjusted for sex, pubertal status, and physical activity. Greater peak VO2was associated with earlier sleep/wake times and circadian phase measures, including acrophase, UP time, DOWN time, LAP time, and chronotype (all p<0.05). Peak VO2 was negatively associated with social jetlag (p=0.02). Additionally, the mixed model analysis revealed a significant interaction effect between peak VO2 and actigraphy-estimated hour-by-hour activity patterns (p<0.001), with the strongest effects observed at around time of waking (6:00-10:00). In healthy adolescents, better CRF was associated with earlier circadian phase and increased activity levels notably during the morning. Future studies are needed to investigate the longitudinal effects of the interactions between CRF and advanced rhythms on health outcomes.

PMID:38126092 | DOI:10.1152/japplphysiol.00291.2023

Nat Comput Sci. 2022 Dec;2(12):785-796. doi: 10.1038/s43588-022-00377-z. Epub 2022 Dec 19.

ABSTRACT

Encouraging advances are being made in cancer immunotherapy modeling, especially in the key areas of developing personalized treatment strategies based on individual patient parameters, predicting treatment outcomes and optimizing immunotherapy synergy when used in combination with other treatment approaches. Here we present a focused review of the most recent mathematical modeling work on cancer immunotherapy with a focus on clinical translatability. It can be seen that this field is transitioning from pure basic science to applications that can make impactful differences in patients' lives. We discuss how researchers are integrating experimental and clinical data to fully inform models so that they can be applied for clinical predictions, and present the challenges that remain to be overcome if widespread clinical adaptation is to be realized. Lastly, we discuss the most promising future applications and areas that are expected to be the focus of extensive upcoming modeling studies.

PMID:38126024 | PMC:PMC10732566 | DOI:10.1038/s43588-022-00377-z

iScience. 2023 Nov 23;26(12):108529. doi: 10.1016/j.isci.2023.108529. eCollection 2023 Dec 15.

ABSTRACT

Schlafen (SLFN) 11 enhances cellular sensitivity to various DNA-damaging anticancer agents. Among the human SLFNs (SLFN5/11/12/13/14), SLFN11 is unique in its drug sensitivity and ability to block replication under DNA damage. In biochemical analysis, SLFN11 binds single-stranded DNA (ssDNA), and this binding is enhanced by the dephosphorylation of SLFN11. In this study, human cell-based assays demonstrated that a point mutation at the ssDNA-binding site of SLFN11 or a constitutive phosphorylation mutant abolished SLFN11-dependent drug sensitivity. Additionally, we discovered that nuclear SLFN13 with a point mutation mimicking the DNA-binding site of SLFN11 was recruited to chromatin, blocked replication, and enhanced drug sensitivity. Through generating multiple mutants and structure analyses of SLFN11 and SLFN13, we identified protein phosphatase 2A as a binding partner of SLFN11 and the putative binding motif in SLFN11. These findings provide crucial insights into the unique characteristics of SLFN11, contributing to a better understanding of its mechanisms.

PMID:38125019 | PMC:PMC10730379 | DOI:10.1016/j.isci.2023.108529

Comput Math Methods Med. 2023 Dec 13;2023:9769073. doi: 10.1155/2023/9769073. eCollection 2023.

ABSTRACT

[This retracts the article DOI: 10.1155/2022/5337380.].

PMID:38124959 | PMC:PMC10732871 | DOI:10.1155/2023/9769073

Biophys Physicobiol. 2023 Aug 19;20(3):e200032. doi: 10.2142/biophysico.bppb-v20.0032. eCollection 2023.

ABSTRACT

Single-cell behaviors cover many biological functions, such as cell division during morphogenesis and tissue metastasis, and cell migration during cancer cell invasion and immune cell responses. Symmetry breaking of the positioning of organelles and the cell shape are often associated with these biological functions. One of the main players in symmetry breaking at the cellular scale is the actin cytoskeleton, comprising actin filaments and myosin motors that generate contractile forces. However, because the self-organization of the actomyosin network is regulated by the biochemical signaling in cells, how the mechanical contraction of the actin cytoskeleton induces diverse self-organized behaviors and drives the cell-scale symmetry breaking remains unclear. In recent times, to understand the physical underpinnings of the symmetry breaking exhibited in the actin cytoskeleton, artificial cell models encapsulating the cytoplasmic actomyosin networks covered with lipid monolayers have been developed. By decoupling the actomyosin mechanics from the complex biochemical signaling within living cells, this system allows one to study the self-organization of actomyosin networks confined in cell-sized spaces. We review the recent developments in the physics of confined actomyosin networks and provide future perspectives on the artificial cell-based approach. This review article is an extended version of the Japanese article, The Physical Principle of Cell Migration Under Confinement: Artificial Cell-based Bottom-up Approach, published in SEIBUTSU BUTSURI Vol. 63, p. 163-164 (2023).

PMID:38124798 | PMC:PMC10728624 | DOI:10.2142/biophysico.bppb-v20.0032

J Cachexia Sarcopenia Muscle. 2023 Dec 20. doi: 10.1002/jcsm.13380. Online ahead of print.

ABSTRACT

BACKGROUND: Decreased insulin availability and high blood glucose levels, the hallmark features of poorly controlled diabetes, drive disease progression and are associated with decreased skeletal muscle mass. We have shown that mice with β-cell dysfunction and normal insulin sensitivity have decreased skeletal muscle mass. This project asks how insulin deficiency impacts on the structure and function of the remaining skeletal muscle in these animals.

METHODS: Skeletal muscle function was determined by measuring exercise capacity and specific muscle strength prior to and after insulin supplementation for 28 days in 12-week-old mice with conditional β-cell deletion of the ATP binding cassette transporters ABCA1 and ABCG1 (β-DKO mice). Abca1 and Abcg1 floxed (fl/fl) mice were used as controls. RNAseq was used to quantify changes in transcripts in soleus and extensor digitorum longus muscles. Skeletal muscle and mitochondrial morphology were assessed by transmission electron microscopy. Myofibrillar Ca2+ sensitivity and maximum isometric single muscle fibre force were assessed using MyoRobot biomechatronics technology.

RESULTS: RNA transcripts were significantly altered in β-DKO mice compared with fl/fl controls (32 in extensor digitorum longus and 412 in soleus). Exercise capacity and muscle strength were significantly decreased in β-DKO mice compared with fl/fl controls (P = 0.012), and a loss of structural integrity was also observed in skeletal muscle from the β-DKO mice. Supplementation of β-DKO mice with insulin restored muscle integrity, strength and expression of 13 and 16 of the dysregulated transcripts in and extensor digitorum longus and soleus muscles, respectively.

CONCLUSIONS: Insulin insufficiency due to β-cell dysfunction perturbs the structure and function of skeletal muscle. These adverse effects are rectified by insulin supplementation.

PMID:38124345 | DOI:10.1002/jcsm.13380

Rapid Commun Mass Spectrom. 2024 Jan 30;38(2):e9670. doi: 10.1002/rcm.9670.

ABSTRACT

RATIONALE: Multicellular tumor spheroids (MCTSs) that reconstitute the metabolic characteristics of in vivo tumor tissue may facilitate the discovery of molecular biomarkers and effective anticancer therapies. However, little is known about how cancer cells adapt their metabolic changes in complex three-dimensional (3D) microenvironments. Here, using the two-dimensional (2D) cell model as control, the metabolic phenotypes of glioma U87MG multicellular tumor spheroids were systematically investigated based on static metabolomics and dynamic fluxomics analysis.

METHODS: A liquid chromatography-mass spectrometry-based global metabolomics and lipidomics approach was adopted to survey the cellular samples from 2D and 3D culture systems, revealing marked molecular differences between them. Then, by means of metabolomic pathway analysis, the metabolic pathways altered in glioma MCTSs were found using 13 C6 -glucose as a tracer to map the metabolic flux of glycolysis, the tricarboxylic acid (TCA) cycle, de novo nucleotide synthesis, and de novo lipid biosynthesis in the MCTS model.

RESULTS: We found nine metabolic pathways as well as glycerolipid, glycerophospholipid and sphingolipid metabolism to be predominantly altered in glioma MCTSs. The reduced nucleotide metabolism, amino acid metabolism and glutathione metabolism indicated an overall lower cellular activity in MCTSs. Through dynamic fluxomics analysis in the MCTS model, we found that cells cultured in MCTSs exhibited increased glycolysis activity and de novo lipid biosynthesis activity, and decreased the TCA cycle and de novo purine nucleotide biosynthesis activity.

CONCLUSIONS: Our study highlights specific, altered biochemical pathways in MCTSs, emphasizing dysregulation of energy metabolism and lipid metabolism, and offering novel insight into metabolic events in glioma MCTSs.

PMID:38124173 | DOI:10.1002/rcm.9670

Sci Rep. 2023 Dec 20;13(1):22631. doi: 10.1038/s41598-023-47798-y.

ABSTRACT

Secretory immunoglobulin A (sIgA) in saliva is the most important immunoglobulin fighting pathogens in the respiratory tract and may thus play a role in preventing SARS-CoV-2 infections. To gain a better understanding of the plasticity in the mucosal antibody, we investigated the proactive change in secretion of salivary SARS-CoV-2-specific sIgA in 45 vaccinated and/or previously infected, generally healthy persons (18 to 35 years, 22 women). Participants were exposed to a disease video displaying humans with several respiratory symptoms typical for COVID-19 in realistic situations of increased contagion risk. The disease video triggered an increase in spike-specific sIgA, which was absent after a similar control video with healthy people. The increase further correlated inversely with revulsion and aversive feelings while watching sick people. In contrast, the receptor binding domain-specific sIgA did not increase after the disease video. This may indicate differential roles of the two salivary antibodies in response to predictors of airborne contagion. The observed plasticity of spike-specific salivary antibody release after visual simulation of enhanced contagion risk suggests a role in immune exclusion.

PMID:38123577 | DOI:10.1038/s41598-023-47798-y

Nat Commun. 2023 Dec 20;14(1):8467. doi: 10.1038/s41467-023-42910-2.

ABSTRACT

Sensory cortices modulate innate behaviors through corticofugal projections targeting phylogenetically-old brainstem nuclei. However, the principles behind the functional connectivity of these projections remain poorly understood. Here, we show that in mice visual cortical neurons projecting to the optic-tract and dorsal-terminal nuclei (NOT-DTN) possess distinct response properties and anatomical connectivity, supporting the adaption of an essential innate eye movement, the optokinetic reflex (OKR). We find that these corticofugal neurons are enriched in specific visual areas, and they prefer temporo-nasal visual motion, matching the direction bias of downstream NOT-DTN neurons. Remarkably, continuous OKR stimulation selectively enhances the activity of these temporo-nasally biased cortical neurons, which can efficiently promote OKR plasticity. Lastly, we demonstrate that silencing downstream NOT-DTN neurons, which project specifically to the inferior olive-a key structure in oculomotor plasticity, impairs the cortical modulation of OKR and OKR plasticity. Our results unveil a direction-selective cortico-brainstem pathway that adaptively modulates innate behaviors.

PMID:38123558 | DOI:10.1038/s41467-023-42910-2

Nat Commun. 2023 Dec 20;14(1):8479. doi: 10.1038/s41467-023-44199-7.

ABSTRACT

Researchers and policymakers have proposed systems to detect novel pathogens earlier than existing surveillance systems by monitoring samples from hospital patients, wastewater, and air travel, in order to mitigate future pandemics. How much benefit would such systems offer? We developed, empirically validated, and mathematically characterized a quantitative model that simulates disease spread and detection time for any given disease and detection system. We find that hospital monitoring could have detected COVID-19 in Wuhan 0.4 weeks earlier than it was actually discovered, at 2,300 cases (standard error: 76 cases) compared to 3,400 (standard error: 161 cases). Wastewater monitoring would not have accelerated COVID-19 detection in Wuhan, but provides benefit in smaller catchments and for asymptomatic or long-incubation diseases like polio or HIV/AIDS. Air travel monitoring does not accelerate outbreak detection in most scenarios we evaluated. In sum, early detection systems can substantially mitigate some future pandemics, but would not have changed the course of COVID-19.

PMID:38123536 | DOI:10.1038/s41467-023-44199-7

Trends Microbiol. 2023 Dec 19:S0966-842X(23)00331-1. doi: 10.1016/j.tim.2023.11.014. Online ahead of print.

ABSTRACT

Microbes in nature often lack nutrients and face extreme or widely fluctuating temperatures, unlike microbes in growth-optimized settings in laboratories that much of the literature examines. Slowed or suspended lives are the norm for microbes. Studying them is important for understanding the consequences of climate change and for addressing fundamental questions about life: are there limits to how slowly a cell's life can progress, and how long cells can remain viable without self-replicating? Recent studies began addressing these questions with single-cell-level measurements and mathematical models. Emerging principles that govern slowed or suspended lives of cells - including lives of dormant spores and microbes at extreme temperatures - are re-defining discrete cellular states as continuums and revealing intracellular dynamics at new timescales. Nearly inactive, lifeless-appearing microbes are transforming our understanding of life.

PMID:38123400 | DOI:10.1016/j.tim.2023.11.014

Ocul Surf. 2023 Dec 18:S1542-0124(23)00156-8. doi: 10.1016/j.jtos.2023.12.005. Online ahead of print.

ABSTRACT

PURPOSE: Herpes simplex keratitis (HSK), caused by type 1 herpes simplex virus (HSV) reactivation, is a severe infectious disease that leads to vision loss. HSV can trigger metabolic reprogramming in the host cell and change the extracellular vesicles (EV) cargos; however, little is known about the EV metabolic signatures during ocular HSV infection. Here, we aimed to depict the EV-associated metabolic landscape in HSK patients' tears.

METHODS: We collected 82 samples from 41 participants with unilateral HSK (contralateral unaffected tears were set as negative control), including subtype cohorts of 13 epithelial, 20 stromal, and 8 endothelial HSK. We isolated tear EVs via our previously established platform and conducted metabolic analysis using LC-MS/MS. The metabolic signatures for recognizing HSK and subtypes were assessed through differential analysis and machine learning algorithms.

RESULTS: Hypopsia and increased extracellular CD63 levels were observed in affected eyes. We identified 339 metabolites based on sEVs isolated from tears. Differential analysis revealed alterations in energy and amino acid metabolism, as well as the infectious microenvironment. Furthermore, we observed dysregulated metabolite such as methyldopa, which is associated with inappropriate neovascularization and corneal sensation loss, contributing to the HSK severity particularly in the stromal subtype. Moreover, machine learning classification also suggested a set of EV metabolic signatures that have potential for pan-keratitis detection.

CONCLUSIONS: Our findings demonstrate that tear EV metabolites can serve as valuable indicators for comprehending the underlying pathological mechanisms. This knowledge is expected to facilitate the development of liquid biopsy means and therapeutic target discovery.

PMID:38122863 | DOI:10.1016/j.jtos.2023.12.005

Cell Rep Med. 2023 Dec 19;4(12):101326. doi: 10.1016/j.xcrm.2023.101326.

ABSTRACT

Multiple cancers exhibit aberrant protein arginine methylation by both type I arginine methyltransferases, predominately protein arginine methyltransferase 1 (PRMT1) and to a lesser extent PRMT4, and by type II PRMTs, predominately PRMT5. Here, we perform targeted proteomics following inhibition of PRMT1, PRMT4, and PRMT5 across 12 cancer cell lines. We find that inhibition of type I and II PRMTs suppresses phosphorylated and total ATR in cancer cells. Loss of ATR from PRMT inhibition results in defective DNA replication stress response activation, including from PARP inhibitors. Inhibition of type I and II PRMTs is synergistic with PARP inhibition regardless of homologous recombination function, but type I PRMT inhibition is more toxic to non-malignant cells. Finally, we demonstrate that the combination of PARP and PRMT5 inhibition improves survival in both BRCA-mutant and wild-type patient-derived xenografts without toxicity. Taken together, these results demonstrate that PRMT5 inhibition may be a well-tolerated approach to sensitize tumors to PARP inhibition.

PMID:38118413 | DOI:10.1016/j.xcrm.2023.101326

Cell Rep. 2023 Dec 19;43(1):113608. doi: 10.1016/j.celrep.2023.113608. Online ahead of print.

ABSTRACT

The role of hematopoietic Hedgehog signaling in myeloproliferative neoplasms (MPNs) remains incompletely understood despite data suggesting that Hedgehog (Hh) pathway inhibitors have therapeutic activity in patients. We aim to systematically interrogate the role of canonical vs. non-canonical Hh signaling in MPNs. We show that Gli1 protein levels in patient peripheral blood mononuclear cells (PBMCs) mark fibrotic progression and that, in murine MPN models, absence of hematopoietic Gli1, but not Gli2 or Smo, significantly reduces MPN phenotype and fibrosis, indicating that GLI1 in the MPN clone can be activated in a non-canonical fashion. Additionally, we establish that hematopoietic Gli1 has a significant effect on stromal cells, mediated through a druggable MIF-CD74 axis. These data highlight the complex interplay between alterations in the MPN clone and activation of stromal cells and indicate that Gli1 represents a promising therapeutic target in MPNs, particularly that Hh signaling is dispensable for normal hematopoiesis.

PMID:38117649 | DOI:10.1016/j.celrep.2023.113608

Mol Biol Cell. 2023 Dec 20:mbcE23060216. doi: 10.1091/mbc.E23-06-0216. Online ahead of print.

ABSTRACT

Phagocytosis by macrophages is a highly polarized process to destroy large target cells. Binding to particles induces extensive cortical actin-generated forces that drive the formation of elaborate pseudopods around the target particle. Post-internalization, the resultant phagosome is driven towards the cell interior on microtubules (MTs) by cytoplasmic dynein. However, it is unclear whether dynein and cargo-adaptors contribute to the earlier steps of particle internalization and phagosome formation. Here we reveal that ninein, a MT minus-end-associated protein that localizes to the centrosome, is also present at the phagocytic cup in macrophages. Ninein depletion impairs particle internalization by delaying the early F-actin recruitment to sites of particle engagement and cup formation, with no impact on F-actin dynamics beyond this initial step. Ninein forms membrane-bound clusters on phagocytic cups that do not nucleate acentrosomal MTs but instead mediate the assembly of dynein-dynactin complex at active phagocytic membranes. Both ninein depletion and pharmacological inhibition of dynein activity reduced inward displacement of bound particles into macrophages. We found that ninein and dynein motor activity were required for timely retrograde movement of phagosomes and for phagolysosome formation. Taken together, these data show that ninein, alone and with dynein, play significant roles during phagocytosis. [Media: see text] [Media: see text].

PMID:38117588 | DOI:10.1091/mbc.E23-06-0216

Elife. 2023 Dec 20;12:e85581. doi: 10.7554/eLife.85581. Online ahead of print.

ABSTRACT

How morphogenetic movements are robustly coordinated in space and time is a fundamental open question in biology. We study this question using the wing of Drosophila melanogaster, an epithelial tissue that undergoes large-scale tissue flows during pupal stages. Previously, we showed that pupal wing morphogenesis involves both cellular behaviors that allow relaxation of mechanical tissue stress, as well as cellular behaviors that appear to be actively patterned (Etournay et al., 2015). Here, we show that these active cellular behaviors are not guided by the core planar cell polarity (PCP) pathway, a conserved signaling system that guides tissue development in many other contexts. We find no significant phenotype on the cellular dynamics underlying pupal morphogenesis in mutants of core PCP. Furthermore, using laser ablation experiments, coupled with a rheological model to describe the dynamics of the response to laser ablation, we conclude that while core PCP mutations affect the fast timescale response to laser ablation they do not significantly affect overall tissue mechanics. In conclusion, our work shows that cellular dynamics and tissue shape changes during Drosophila pupal wing morphogenesis do not require core PCP as an orientational guiding cue.

PMID:38117039 | DOI:10.7554/eLife.85581

MicroPubl Biol. 2023 Dec 4;2023. doi: 10.17912/micropub.biology.001076. eCollection 2023.

ABSTRACT

Activating 5-HT 1B/D receptors with the agonist Zolmitriptan was previously shown to facilitate Xenopus retinal ganglion cell (RGC) axon extension from ectopic eye primordia transplanted to the ventral fin. To determine if 5-HT 1B/D receptor activation influenced entopic RGC axonal outgrowth toward the optic tectum during typical visual system development, we reared embryos in 50 μΜ Zolmitriptan then visualized optic tracts with anterograde HRP labeling. Zolmitriptan did not significantly alter entopic RGC extension in the contralateral brain. Consequently, RGC axon extension in ectopic but not entopic locations is influenced by altering serotonergic signaling .

PMID:38116474 | PMC:PMC10728752 | DOI:10.17912/micropub.biology.001076

ACS Med Chem Lett. 2023 Dec 4;14(12):1664-1672. doi: 10.1021/acsmedchemlett.3c00274. eCollection 2023 Dec 14.

ABSTRACT

We previously identified the natural products isopomiferin and pomiferin as powerful, indirect MYCN-ablating agents. In this work, we expand on their mechanism of action and find that casein kinase 2 (CK2), phosphoinositide 3-kinase (PI3K), checkpoint kinase 1 (CHK1) and serine/threonine protein kinase 38-like (STK38L), as well as STK38, work synchronously to create a field effect that maintains MYCN stability. By systematically inhibiting these kinases, we degraded MYCN and induced cell death. Additionally, we synthesized and tested several simpler and more cost-effective pomiferin analogues, which successfully emulated the compound's MYCN ablating activity. Our work identified and characterized key kinases that can be targeted to interfere with the stability of the MYCN protein in NBL cells, demonstrating the efficacy of an indirect approach to targeting "undruggable" cancer drivers.

PMID:38116412 | PMC:PMC10726605 | DOI:10.1021/acsmedchemlett.3c00274