Scholarly Work - Microbiology & Cell Biology

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    Hydrophobic residues in S1 modulate enzymatic function and voltage sensing in voltage-sensing phosphatase
    (Rockefeller University Press, 2024-05) Rayaprolu, Vamseedhar; Miettinen, Heini M.; Baker, William D.; Young, Victoria C.; Fisher, Matthew; Mueller, Gwendolyn; Rankin, William O.; Kelley, John T.; Ratzan, William J.; Leong, Lee Min; Davisson, Joshua A.; Baker, Bradley J.; Kohout, Susy C.
    The voltage-sensing domain (VSD) is a four-helix modular protein domain that converts electrical signals into conformational changes, leading to open pores and active enzymes. In most voltage-sensing proteins, the VSDs do not interact with one another, and the S1–S3 helices are considered mainly scaffolding, except in the voltage-sensing phosphatase (VSP) and the proton channel (Hv). To investigate its contribution to VSP function, we mutated four hydrophobic amino acids in S1 to alanine (F127, I131, I134, and L137), individually or in combination. Most of these mutations shifted the voltage dependence of activity to higher voltages; however, not all substrate reactions were the same. The kinetics of enzymatic activity were also altered, with some mutations significantly slowing down dephosphorylation. The voltage dependence of VSD motions was consistently shifted to lower voltages and indicated a second voltage-dependent motion. Additionally, none of the mutations broke the VSP dimer, indicating that the S1 impact could stem from intra- and/or intersubunit interactions. Lastly, when the same mutations were introduced into a genetically encoded voltage indicator, they dramatically altered the optical readings, making some of the kinetics faster and shifting the voltage dependence. These results indicate that the S1 helix in VSP plays a critical role in tuning the enzyme’s conformational response to membrane potential transients and influencing the function of the VSD.
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    Ebselen analogues with dual human neutrophil elastase (HNE) inhibitory and antiradical activity
    (Royal Society of Chemistry, 2024-01) Crocetti, Letizia; Catarzi, Francesca; Giovannoni, Maria Paola; Vergelli, Claudia; Bartolucci, Gianluca; Pallecchi, Marco; Paoli, Paola; Rossi, Patrizia; Lippi, Martina; Schepetkin, Igor A.; Quinn, Mark T.; Guerrini, Gabriella
    Human neutrophil elastase (HNE) plays an essential role in host defense against bacteria but is also involved in several respiratory diseases. Recent reports suggest that compounds exhibiting a combination of HNE inhibitory activity with antiradical properties may be therapeutically beneficial for the treatment of respiratory diseases involving inflammation and oxidative stress. We report here the synthesis and biological evaluation of novel ebselen analogues exhibiting HNE inhibitory and antiradical activities. HNE inhibition was evaluated in an enzymatic system using human HNE, whereas antiradical activity was evaluated in a cell-based assay system using phorbol 12-myristate 13-acetate (PMA)-stimulated murine bone marrow leukocytes as the source of reactive oxygen species (ROS). HNE inhibition was due to the N–CO group targeting Ser195-OH at position 2 of the scaffold, while antiradical activity was due to the presence of the selenium atom. The most active compounds 4d, 4f, and 4j exhibited a good balance between anti-HNE (IC50 = 0.9–1.4 μM) and antiradical activity (IC50 = 0.05–0.7 μM). Additionally, the solid-state structure of 4d was determined and compared to that of the similar compound N-propionyl-1,2-benzisoselenazol-3(2H)-one.
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    Osteochondral fluid transport in an ex vivo system
    (Elsevier BV, 2024-04) Hislop, Brady David; Mercer, Ara K.; Whitley, Alexandria G.; Myers, Erik P.; Mackin, Marie; Heveran, Chelsea M.; June, Ronald K.
    Objective: Alterations to bone-to-cartilage fluid transport may contribute to the development of osteoarthritis (OA). Larger biological molecules in bone may transport from bone-to-cartilage (e.g., insulin, 5 kDa). However, many questions remain about fluid transport between these tissues. The objectives of this study were to (1) test for diffusion of 3 kDa molecular tracers from bone-to-cartilage and (2) assess potential differences in bone-to-cartilage fluid transport between different loading conditions. Design: Osteochondral cores extracted from bovine femurs (N = 10 femurs, 10 cores/femur) were subjected to either no-load (i.e., pure diffusion), pre-load only, or cyclic compression (5 ± 2% or 10 ± 2% strain) in a two-chamber bioreactor. The bone was placed into the bone compartment followed by a 3 kDa dextran tracer, and tracer concentrations in the cartilage compartment were measured every 5 min for 120 min. Tracer concentrations were analyzed for differences in beginning, peak, and equilibrium concentrations, loading effects, and time-to-peak tracer concentration. Results: Peak tracer concentration in the cartilage compartment was significantly higher compared to the beginning and equilibrium tracer concentrations. Cartilage-compartment tracer concentration and maximum fluorescent intensity were influenced by strain magnitude. No time-to-peak relationship was found between strain magnitudes and cartilage-compartment tracer concentration. Conclusion: This study shows that bone-to-cartilage fluid transport occurs with 3 kDa dextran molecules. These are larger molecules to move between bone and cartilage than previously reported. Further, these results demonstrate the potential impact of cyclic compression on osteochondral fluid transport. Determining the baseline osteochondral fluid transport in healthy tissues is crucial to elucidating the mechanisms OA pathology.
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    Respiratory viruses: New frontiers—a Keystone Symposia report
    (Wiley, 2023-02) Cable, Jennifer et al.; Thomas, Mallory M.
    Respiratory viruses are a common cause of morbidity and mortality around the world. Viruses like influenza, RSV, and most recently SARS-CoV-2 can rapidly spread through a population, causing acute infection and, in vulnerable populations, severe or chronic disease. Developing effective treatment and prevention strategies often becomes a race against ever-evolving viruses that develop resistance, leaving therapy efficacy either short-lived or relevant for specific viral strains. On June 29 to July 2, 2022, researchers met for the Keystone symposium “Respiratory Viruses: New Frontiers.” Researchers presented new insights into viral biology and virus–host interactions to understand the mechanisms of disease and identify novel treatment and prevention approaches that are effective, durable, and broad.
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    Volatile Composition, Antimicrobial Activity, and In Vitro Innate Immunomodulatory Activity of Echinacea purpurea (L.) Moench Essential Oils
    (MDPI AG, 2023-10) Dosoky, Noura S.; Kirpotina, Liliya N.; Schepetkin, Igor A.; Khlebnikov, Andrei I.; Lisonbee, Brent L.; Black, Jeffrey L.; Woolf, Hillary; Thurgood, Trever L.; Graf, Brittany L.; Satyal, Prabodh; Quinn, Mark T.
    Echinacea purpurea (L.) Moench is a medicinal plant commonly used for the treatment of upper respiratory tract infections, the common cold, sore throat, migraine, colic, stomach cramps, and toothaches and the promotion of wound healing. Based on the known pharmacological properties of essential oils (EOs), we hypothesized that E. purpurea EOs may contribute to these medicinal properties. In this work, EOs from the flowers of E. purpurea were steam-distilled and analyzed by gas chromatography–mass spectrometry (GC–MS), GC with flame-ionization detection (GC–FID), and chiral GC–MS. The EOs were also evaluated for in vitro antimicrobial and innate immunomodulatory activity. About 87 compounds were identified in five samples of the steam-distilled E. purpurea EO. The major components of the E. purpurea EO were germacrene D (42.0 ± 4.61%), α-phellandrene (10.09 ± 1.59%), β-caryophyllene (5.75 ± 1.72%), γ-curcumene (5.03 ± 1.96%), α-pinene (4.44 ± 1.78%), δ-cadinene (3.31 ± 0.61%), and β-pinene (2.43 ± 0.98%). Eleven chiral compounds were identified in the E. purpurea EO, including α-pinene, sabinene, β-pinene, α-phellandrene, limonene, β-phellandrene, α-copaene, β-elemene, β-caryophyllene, germacrene D, and δ-cadinene. Analysis of E. purpurea EO antimicrobial activity showed that they inhibited the growth of several bacterial species, although the EO did not seem to be effective for Staphylococcus aureus. The E. purpurea EO and its major components induced intracellular calcium mobilization in human neutrophils. Additionally, pretreatment of human neutrophils with the E. purpurea EO or (+)-δ-cadinene suppressed agonist-induced neutrophil calcium mobilization and chemotaxis. Moreover, pharmacophore mapping studies predicted two potential MAPK targets for (+)-δ-cadinene. Our results are consistent with previous reports on the innate immunomodulatory activities of β-caryophyllene, α-phellandrene, and germacrene D. Thus, this study identified δ-cadinene as a novel neutrophil agonist and suggests that δ-cadinene may contribute to the reported immunomodulatory activity of E. purpurea.
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    Antiviral responses in a Jamaican fruit bat intestinal organoid model of SARS-CoV-2 infection
    (Springer Science and Business Media LLC, 2023-10) Hashimi, Marziah; Sebrell, T. Andrew; Hedges, Jodi F.; Snyder, Deann; Lyon, Katrina N.; Byrum, Stephanie D.; Mackintosh, Samuel G.; Crowley, Dan; Cherne, Michelle D.; Skwarchuk, David; Robison, Amanda; Sidar, Barkan; Kunze, Anja; Loveday, Emma K.; Taylor, Matthew P.; Chang, Connie B.; Wilking, James N.; Walk, Seth T.; Schountz, Tony; Jutila, Mark A.; Bimczok, Diane
    Bats are natural reservoirs for several zoonotic viruses, potentially due to an enhanced capacity to control viral infection. However, the mechanisms of antiviral responses in bats are poorly defined. Here we established a Jamaican fruit bat (JFB, Artibeus jamaicensis) intestinal organoid model of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Upon infection with SARS-CoV-2, increased viral RNA and subgenomic RNA was detected, but no infectious virus was released, indicating that JFB organoids support only limited viral replication but not viral reproduction. SARS-CoV-2 replication was associated with significantly increased gene expression of type I interferons and inflammatory cytokines. Interestingly, SARS-CoV-2 also caused enhanced formation and growth of JFB organoids. Proteomics revealed an increase in inflammatory signaling, cell turnover, cell repair, and SARS-CoV-2 infection pathways. Collectively, our findings suggest that primary JFB intestinal epithelial cells mount successful antiviral interferon responses and that SARS-CoV-2 infection in JFB cells induces protective regenerative pathways.
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    Discovering unknown associations between prokaryotic receptors and their ligands
    (Proceedings of the National Academy of Sciences, 2023-11) Dlakić, Mensur
    The motility of microorganisms through the environment is driven by chemical gradients: They move towards nutrients and away from signals that indicate unfavorable conditions. This chemotaxis is mediated by transmembrane chemoreceptors that recognize one or many target molecules. In most cases, the encounter with a ligand is recorded by a periplasmic sensor domain, which in turn transmits a signal through the membrane to a cytoplasmic signaling domain (1). Under conditions of environmental stress, these signaling cascades may induce profound lifestyle changes from planktonic cells to a biofilm or from active to inactive cells (2). While it is relatively straightforward to annotate most prokaryotic chemoreceptors from the ever-increasing number of sequenced genomes and environmental samples, the identity of their binding partners is often not clear from protein sequence. As the specificity of downstream signaling events is determined by the sensor domain, it is critical to learn about novel pairings between ligands and their receptors. Using a range of computational and experimental approaches, Cerna-Vargas et al. show in PNAS that a subset of a wide-spread group of dCache_1 receptors evolved to recognize various types of biological amines.
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    Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04
    (Elsevier BV, 2023-01) Goemann, Calvin L.C.; Wilkinson, Royce; Henriques, William; Bui, Huyen; Goemann, Hannah M.; Carlson, Ross P.; Viamajala, Sridhar; Gerlach, Robin; Wiedenheft, Blake
    Algae are a broad class of photosynthetic eukaryotes that are phylogenetically and physiologically diverse. Most of the phylogenetic diversity has been inferred from 18S rDNA sequencing since there are only a few complete genomes available in public databases. Here we use ultra-long-read Nanopore sequencing to determine a gapless, telomere-to-telomere complete genome sequence of Chlorella sp. SLA-04, previously described as Chlorella sorokiniana SLA-04. Chlorella sp. SLA-04 is a green alga that grows to high cell density in a wide variety of environments – high and neutral pH, high and low alkalinity, and high and low salinity. SLA-04's ability to grow in high pH and high alkalinity media without external CO2 supply is favorable for large-scale algal biomass production. Phylogenetic analysis performed using ribosomal DNA and conserved protein sequences consistently reveal that Chlorella sp. SLA-04 forms a distinct lineage from other strains of Chlorella sorokiniana. We complement traditional genome annotation methods with high throughput structural predictions and demonstrate that this approach expands functional prediction of the SLA-04 proteome. Genomic analysis of the SLA-04 genome identifies the genes capable of utilizing TCA cycle intermediates to replenish cytosolic acetyl-CoA pools for lipid production. We also identify a complete metabolic pathway for sphingolipid anabolism that may allow SLA-04 to readily adapt to changing environmental conditions and facilitate robust cultivation in mass production systems. Collectively, this work clarifies the phylogeny of Chlorella sp. SLA-04 within Trebouxiophyceae and demonstrates how structural predictions can be used to improve annotation beyond sequence-based methods.
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    Development of potent isoflavone-based formyl peptide receptor 1 (FPR1) antagonists and their effects in gastric cancer cell models
    (Elsevier BV, 2023-12) Francavilla, Fabio; Sarcina, Federica; Schepetkin, Igor A.; Kirpotina, Lilya N.; Contino, Marialessandra; Schirizzi, Annalisa; De Leonardis, Giampiero; Khlebnikov, Andrei I.; D'Alessandro, Rosalba; Quinn, Mark T.; Lacivita, Enza; Leopoldo, Marcello
    Formyl peptide receptor-1 (FPR1) is a G protein-coupled chemoattractant receptor that plays a crucial role in the trafficking of leukocytes into the sites of bacterial infection and inflammation. Recently, FPR1 was shown to be expressed in different types of tumor cells and could play a significant role in tumor growth and invasiveness. Starting from the previously reported FPR1 antagonist 4, we have designed a new series of 4H-chromen-2-one derivatives that exhibited a substantial increase in FPR1 antagonist potency. Docking studies identified the key interactions for antagonist activity. The most potent compounds in this series (24a and 25b) were selected to study the effects of the pharmacological blockade of FPR1 in NCl–N87 and AGS gastric cancer cells. Both compounds potently inhibited cell growth through a combined effect on cell proliferation and apoptosis and reduced cell migration, while inducing an increase in angiogenesis, thus suggesting that FPR1 could play a dual role as oncogene and onco-suppressor.
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    Neuroprotective Effects of Tryptanthrin-6-Oxime in a Rat Model of Transient Focal Cerebral Ischemia
    (MDPI AG, 2023-07) Plotnikov, Mark B.; Chernysheva, Galina A.; Smol’yakova, Vera I.; Aliev, Oleg I.; Anishchenko, Anna M.; Ulyakhina, Olga A.; Trofimova, Eugene S.; Ligacheva, Anastasia A.; Anfinogenova, Nina D.; Osipenko, Anton N.; Kovrizhina, Anastasia R.; Khlebnikov, Andrei I.; Schepetkin, Igor A.; Drozd, Anastasia G.; Plotnikov, Evgenii V.; Atochin, Dmitriy N.; Quinn, Mark T.
    The activation of c-Jun N-terminal kinase (JNK) plays an important role in stroke outcomes. Tryptanthrin-6-oxime (TRYP-Ox) is reported to have high affinity for JNK and anti-inflammatory activity and may be of interest as a promising neuroprotective agent. The aim of this study was to investigate the neuroprotective effects of TRYP-Ox in a rat model of transient focal cerebral ischemia (FCI), which involved intraluminal occlusion of the left middle cerebral artery (MCA) for 1 h. Animals in the experimental group were administered intraperitoneal injections of TRYP-Ox 30 min before reperfusion and 23 and 47 h after FCI. Neurological status was assessed 4, 24, and 48 h following FCI onset. Treatment with 5 and 10 mg/kg of TRYP-Ox decreased mean scores of neurological deficits by 35–49 and 46–67% at 24 and 48 h, respectively. At these doses, TRYP-Ox decreased the infarction size by 28–31% at 48 h after FCI. TRYP-Ox (10 mg/kg) reduced the content of interleukin (IL) 1β and tumor necrosis factor (TNF) in the ischemic core area of the MCA region by 33% and 38%, respectively, and attenuated cerebral edema by 11% in the left hemisphere, which was affected by infarction, and by 6% in the right, contralateral hemisphere 24 h after FCI. TRYP-Ox reduced c-Jun phosphorylation in the MCA pool at 1 h after reperfusion. TRYP-Ox was predicted to have high blood–brain barrier permeability using various calculated descriptors and binary classification trees. Indeed, reactive oxidant production was significantly lower in the brain homogenates from rats treated with TRYP-Ox versus that in control animals. Our data suggest that the neuroprotective activity of TRYP-Ox may be due to the ability of this compound to inhibit JNK and exhibit anti-inflammatory and antioxidant activity. Thus, TRYP-Ox may be considered a promising neuroprotective agent that potentially could be used for the development of new treatment strategies in cerebral ischemia.
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    Immunomodulatory Activity of Polysaccharides Isolated from Saussurea salicifolia L. and Saussurea frolovii Ledeb
    (MDPI AG, 2023-09) Schepetkin, Igor A.; Danilets, Marina G.; Ligacheva, Anastasia A.; Trofimova, Evgenia S.; Selivanova, Natalia S.; Sherstoboev, Evgenii Yu.; Krivoshchekov, Sergei V.; Gulina, Ekaterina I.; Brazovskii, Konstantin S.; Kirpotina, Liliya N.; Quinn, Mark T.; Belousov, Mikhail V.
    The genus Saussurea has been used in the preparation of therapies for a number of medical problems, yet not much is known about the therapeutic high-molecular-weight compounds present in extracts from these plants. Since polysaccharides are important in immune modulation, we investigated the chemical composition and immunomodulatory activity of Saussurea salicifolia L. and Saussurea frolovii Ledeb polysaccharides. Water-soluble polysaccharides from the aerial parts of these plants were extracted using water at pHs of 2 and 6 and subsequently precipitated in ethanol to obtain fractions SSP2 and SSP6 from S. salicifolia and fractions SSF2 and SSF6 from S. frolovii. The molecular weights of fractions SSP2, SSP6, SFP2, and SFP6 were estimated to be 143.7, 113.2, 75.3, and 64.3 kDa, respectively. The polysaccharides from S. frolovii contained xylose (67.1–71.7%) and glucose (28.3–32.9%), whereas the polysaccharides from S. frolovii contained xylose (63.1–76.7%), glucose (11.8–19.2%), galactose (4.7–8.3%), and rhamnose (6.8–9.4%). Fractions SSP2, SSP6, and SFP2 stimulated nitric oxide (NO) production by murine macrophages, and NO production induced by SSP2, SSP6, and SFP2 was not inhibited by polymyxin B treatment of the fractions, whereaspolymyxin B treatment diminished the effects of SFP6, suggesting that SFP6 could contain lipopolysaccharide (LPS). The LPS-free fractions SSP2, SSP6, and SFP2 had potent immunomodulatory activity, induced NO production, and activated transcription factors NF-κB/AP-1 in human monocytic THP-1 cells and cytokine production by human MonoMac-6 monocytic cells, including interleukin (IL)-1α, IL-1β, IL-6, granulocyte macrophage colony-stimulating factor (GM-CSF), interferon-γ, monocyte chemotactic protein 1 (MCP-1), and tumor necrosis factor (TNF). These data suggest that at least part of the beneficial therapeutic effects reported for water extracts of the Saussurea species are due to the modulation of leukocyte functions by polysaccharides.
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    Comparative Aerosol and Surface Stability of SARS-CoV-2 Variants of Concern
    (Centers for Disease Control and Prevention, 2023-05) Bushmaker, Trenton; Kwe Yinda, Claude; Morris, Dylan H.; Holbrook, Myndi G.; Gamble, Amandine; Adney, Danielle; Bushmaker, Cara; van Doremalen, Neeltje; Fischer, Robert J.; Plowright, Raina K.; Lloyd-Smith, James O.; Munster, Vincent J.
    SARS-CoV-2 transmits principally by air; contact and fomite transmission may also occur. Variants of concern are more transmissible than ancestral SARS-CoV-2. We found indications of possible increased aerosol and surface stability for early variants of concern, but not for the Delta and Omicron variants. Stability changes are unlikely to explain increased transmissibility.
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    Vasoactive and Neuroprotective Effects of c-Jun N-Terminal Kinase Inhibitor in Rats with Chronic Cerebral Hypoperfusion
    (Pleiades Publishing Ltd, 2023-05) Zhilyaev, S. Yu.; Platonova, T. F.; Khlebnikov, A. I.; Demchenko, I. T.; Atochin, D. N.
    The aim of this study was to evaluate the vasoactive and neuroprotective effects of c-Jun N-terminal kinase inhibitor IQ-1 (11H-indeno[1,2-b]quinoxalin-11-one oxime) in chronic cerebral hypoperfusion caused by irreversible bilateral common carotid artery ligation [two-vessel occlusion (2VO) model]. Cerebral blood flow was measured quantitatively (hydrogen clearance method) simultaneously in the parietal cortex, hippocampus, substantia nigra, and striatum of the brain of awake rats. It was found that 2VO caused a decrease in blood flow in the brain regions with a more pronounced decrease in the cortex (by 48% of the initial level) and with a minimum drop in the substantia nigra (by 25% of the initial level). The reduced level of blood flow persisted for 14 days of measurements. The responses of the cerebral vessels to hypercapnic probes (5% CO2) were lost during the 2-week hypoperfusion period, and the neurological status of the animals did not improve. The administration of IQ-1 (50 mg/kg, intraperitoneally, every 48 h for 14 days) was accompanied by an increase in blood flow in all brain regions. A maximum increase in blood flow was observed in the striatum and a minimum in the substantia nigra. After the administration of IQ-1, the sensitivity of the cerebral vessels to the hypercapnic stimulus was restored, and the neurological state of the animals significantly improved by the end of the second week of cerebral hypoperfusion. The results show that the use of the JNK inhibitor can reduce cerebrovascular disorders and related neurological disorders in hypoperfusion brain injury.
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    Novel Tryptanthrin Derivatives with Selectivity as c–Jun N–Terminal Kinase (JNK) 3 Inhibitors
    (MDPI AG, 2023-06) Schepetkin, Igor A.; Karpenko, Oleksander S.; Kovrizhina, Anastasia R.; Kirpotina, Liliya N.; Khlebnikov, Andrei I.; Chekal, Stepan I.; Radudik, Alevtyna V.; Shybinska, Maryna O.; Quinn, Mark T.
    The c-Jun N-terminal kinase (JNK) family includes three proteins (JNK1-3) that regulate many physiological processes, including cell proliferation and differentiation, cell survival, and inflammation. Because of emerging data suggesting that JNK3 may play an important role in neurodegenerative diseases, such as Alzheimer’s disease (AD) and Parkinson’s disease, as well as cancer pathogenesis, we sought to identify JNK inhibitors with increased selectivity for JNK3. A panel of 26 novel tryptanthrin-6-oxime analogs was synthesized and evaluated for JNK1-3 binding (Kd) and inhibition of cellular inflammatory responses. Compounds 4d (8-methoxyindolo[2,1-b]quinazolin-6,12-dione oxime) and 4e (8-phenylindolo[2,1-b]quinazolin-6,12-dione oxime) had high selectivity for JNK3 versus JNK1 and JNK2 and inhibited lipopolysaccharide (LPS)-induced nuclear factor-κB/activating protein 1 (NF-κB/AP-1) transcriptional activity in THP-1Blue cells and interleukin-6 (IL-6) production by MonoMac-6 monocytic cells in the low micromolar range. Likewise, compounds 4d, 4e, and pan-JNK inhibitor 4h (9-methylindolo[2,1-b]quinazolin-6,12-dione oxime) decreased LPS-induced c-Jun phosphorylation in MonoMac-6 cells, directly confirming JNK inhibition. Molecular modeling suggested modes of binding interaction of these compounds in the JNK3 catalytic site that were in agreement with the experimental data on JNK3 binding. Our results demonstrate the potential for developing anti-inflammatory drugs based on these nitrogen-containing heterocyclic systems with selectivity for JNK3.
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    Functional and Phylogenetic Diversity of Cas10 Proteins
    (Mary Ann Liebert Inc, 2023-04) Wiegand, Tanner; Wilkinson, Royce; Santiago-Frangos, Andrew; Lynes, Mackenzie; Hatzenpichler, Roland; Wiedenheft, Blake
    Cas10 proteins are large subunits of type III CRISPR RNA (crRNA)-guided surveillance complexes, many of which have nuclease and cyclase activities. Here, we use computational and phylogenetic methods to identify and analyze 2014 Cas10 sequences from genomic and metagenomic databases. Cas10 proteins cluster into five distinct clades that mirror previously established CRISPR-Cas subtypes. Most Cas10 proteins (85.0%) have conserved polymerase active-site motifs, while HD-nuclease domains are less well conserved (36.0%). We identify Cas10 variants that are split over multiple genes or genetically fused to nucleases activated by cyclic nucleotides (i.e., NucC) or components of toxin–antitoxin systems (i.e., AbiEii). To clarify the functional diversification of Cas10 proteins, we cloned, expressed, and purified five representatives from three phylogenetically distinct clades. None of the Cas10s are functional cyclases in isolation, and activity assays performed with polymerase domain active site mutants indicate that previously reported Cas10 DNA-polymerase activity may be a result of contamination. Collectively, this work helps clarify the phylogenetic and functional diversity of Cas10 proteins in type III CRISPR systems.
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    Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04
    (Elsevier BV, 2023-01) Goemann, Calvin L.C.; Wilkinson, Royce; Henriques, William; Bui, Huyen; Goemann, Hannah M.; Carlson, Ross P.; Viamajala, Sridhar; Gerlach, Robin; Wiedenheft, Blake
    Algae are a broad class of photosynthetic eukaryotes that are phylogenetically and physiologically diverse. Most of the phylogenetic diversity has been inferred from 18S rDNA sequencing since there are only a few complete genomes available in public databases. Here we use ultra-long-read Nanopore sequencing to determine a gapless, telomere-to-telomere complete genome sequence of Chlorella sp. SLA-04, previously described as Chlorella sorokiniana SLA-04. Chlorella sp. SLA-04 is a green alga that grows to high cell density in a wide variety of environments – high and neutral pH, high and low alkalinity, and high and low salinity. SLA-04's ability to grow in high pH and high alkalinity media without external CO2 supply is favorable for large-scale algal biomass production. Phylogenetic analysis performed using ribosomal DNA and conserved protein sequences consistently reveal that Chlorella sp. SLA-04 forms a distinct lineage from other strains of Chlorella sorokiniana. We complement traditional genome annotation methods with high throughput structural predictions and demonstrate that this approach expands functional prediction of the SLA-04 proteome. Genomic analysis of the SLA-04 genome identifies the genes capable of utilizing TCA cycle intermediates to replenish cytosolic acetyl-CoA pools for lipid production. We also identify a complete metabolic pathway for sphingolipid anabolism that may allow SLA-04 to readily adapt to changing environmental conditions and facilitate robust cultivation in mass production systems. Collectively, this work clarifies the phylogeny of Chlorella sp. SLA-04 within Trebouxiophyceae and demonstrates how structural predictions can be used to improve annotation beyond sequence-based methods.
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    Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences
    (American Society for Cell Biology, 2023-06) Hess, Riley A.; Erickson, Olivia A.; Cole, Rebecca B.; Isaacs, Jared M.; Alvarez-Clare, Silvia; Arnold, Jonathan; Augustus-Wallace, Allison; Ayoob, Joseph C.; Berkowitz, Alan; Branchaw, Janet; Burgio, Kevin R.; Cannon, Charles H.; Ceballos, Ruben Michael; Cohen, C. Sarah; Coller, Hilary; Disney, Jane; Doze, Van A.; Eggers, Margaret J.; Ferguson, Edwin L.; Gray, Jeffrey J.; Greenberg, Jean T.; Hoffmann, Alexander; Jensen-Ryan, Danielle; Kao, Robert M.; Keene, Alex C.; Kowalkoc, Johanna E.; Lopez, Steven A.; Mathis, Camille; Minkara, Mona; Murren, Courtney J.; Ondrechen, Mary Jo; Ordoñez, Patricia; Osano, Anne; Padilla-Crespo, Elizabeth; Palchoudhury, Soubantika; Qin, Hong; Ramírez-Lugo, Juan; Reithel, Jennifer; Shaw, Colin A.; Smith, Amber; Smith, Rosemary J.; Tsien, Fern; Dolan, Erin L.
    In-person undergraduate research experiences (UREs) promote students’ integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration and whether they might perceive doing research less favorably (i.e., not beneficial or too costly). To address these questions, we examined indicators of scientific integration and perceptions of the benefits and costs of doing research among students who participated in remote life science URE programs in Summer 2020. We found that students experienced gains in scientific self-efficacy pre- to post-URE, similar to results reported for in-person UREs. We also found that students experienced gains in scientific identity, graduate and career intentions, and perceptions of the benefits of doing research only if they started their remote UREs at lower levels on these variables. Collectively, students did not change in their perceptions of the costs of doing research despite the challenges of working remotely. Yet students who started with low cost perceptions increased in these perceptions. These findings indicate that remote UREs can support students’ self-efficacy development, but may otherwise be limited in their potential to promote scientific integration.
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    Inhibition of Acetylcholinesterase by Novel Lupinine Derivatives
    (MDPI AG, 2023-04) Schepetkin, Igor A.; Nurmaganbetov, Zhangeldy S.; Fazylov, Serik D.; Nurkenov, Oralgazy A.; Khlebnikov, Andrei I.; Seilkhanov, Tulegen M.; Kishkentaeva, Anarkul S.; Shults, Elvira E.; Quinn, Mark T.
    Alzheimer’s disease (AD) is a neurodegenerative disease characterized by progressive memory loss and cognitive impairment due in part to a severe loss of cholinergic neurons in specific brain areas. AD is the most common type of dementia in the aging population. Although several acetylcholinesterase (AChE) inhibitors are currently available, their performance sometimes yields unexpected results. Thus, research is ongoing to find potentially therapeutic AChE inhibitory agents, both from natural and synthetic sources. Here, we synthesized 13 new lupinine triazole derivatives and evaluated them, along with 50 commercial lupinine-based esters of different carboxylic acids, for AChE inhibitory activity. The triazole derivative 15 [1S,9aR)-1-((4-(4-(benzyloxy)-3-methoxyphenyl)-1H-1,2,3-triazol-1-yl)methyl)octahydro-2H-quinolizine)] exhibited the most potent AChE inhibitory activity among all 63 lupinine derivatives, and kinetic analysis demonstrated that compound 15 was a mixed-type AChE inhibitor. Molecular docking studies were performed to visualize interaction between this triazole derivative and AChE. In addition, a structure-activity relationship (SAR) model developed using linear discriminant analysis (LDA) of 11 SwissADME descriptors from the 50 lupinine esters revealed 5 key physicochemical features that allowed us to distinguish active versus non-active compounds. Thus, this SAR model could be applied for design of more potent lupinine ester-based AChE inhibitors.
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    Cumulative stressful events and mental health in young adults after 10 years of Wenchuan earthquake: the role of social support
    (Informa UK Limited, 2023-03) Chen, Xiao-Yan; Wang, Dongfang; Liu, Xianchen; Shi, Xuliang; Scherffius, Andrew; Fan, Fang
    Background: After a natural disaster, stressful events often continue to accumulate, affecting individuals in a different manner than the original disaster never occurred. However, few studies have examined these associations, the cumulative impacts of stressful events on mental health outcomes, and the role of social support. This study examined the prospective association between cumulative stressful events and mental health problems and the role of social support in young adults. Methods: 695 participants provided available data on earthquake exposure, childhood maltreatment, other negative life events, and social support at baseline. Depressive symptoms and posttraumatic stress disorder were assessed at baseline and 10 years after the earthquake (T10y). A cumulative stressful events index was used to evaluate the levels of cumulative stressful events. Linear regressions were used to explore the predictive effects. Results: Of 695 participants, 41.3%, 28.5%, and 7.9% reported one, two, and three stressful events, respectively. The associations between cumulative stressful events and mental health problems at T10y presented a dose–response pattern: those who experienced three events had the highest risk of mental health problems, followed by those who experienced two events and those who reported one event. Additionally, higher social support partially reduced the negative impact of cumulative stressful events on mental health. Conclusions: Cumulative stressful events are associated with mental health problems 10 years later in young earthquake survivors. Social support could reduce the negative impact, but its protective role disappears when stressful events accumulate at the highest level. These findings highlight the importance of assessing the cumulative impacts of stressful events and social support available to young disaster survivors and intervening to prevent worse mental health outcomes.
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    Cardioprotective Effects of a Selective c-Jun N-terminal Kinase Inhibitor in a Rat Model of Myocardial Infarction
    (MDPI AG, 2023-02) Plotnikov, Mark B.; Chernysheva, Galina A.; Smol’yakova, Vera I.; Aliev, Oleg I.; Fomina, Tatyana I.; Sandrikina, Lyubov A.; Sukhodolo, Irina V.; Ivanova, Vera V.; Osipenko, Anton N.; Anfinogenova, Nina D.; Khlebnikov, Andrei I.; Atochin, Dmitriy N.; Schepetkin, Igor A.; Quinn, Mark T.
    Activation of c-Jun N-terminal kinases (JNKs) is involved in myocardial injury, left ventricular remodeling (LV), and heart failure (HF) after myocardial infarction (MI). The aim of this research was to evaluate the effects of a selective JNK inhibitor, 11H-indeno [1,2-b]quinoxalin-11-one oxime (IQ-1), on myocardial injury and acute myocardial ischemia/reperfusion (I/R) in adult male Wistar rats. Intraperitoneal administration of IQ-1 (25 mg/kg daily for 5 days) resulted in a significant decrease in myocardial infarct size on day 5 after MI. On day 60 after MI, a significant (2.6-fold) decrease in LV scar size, a 2.2-fold decrease in the size of the LV cavity, a 2.9-fold decrease in the area of mature connective tissue, and a 1.7-fold decrease in connective tissue in the interventricular septum were observed compared with the control group. The improved contractile function of the heart resulted in a significant (33%) increase in stroke size, a 40% increase in cardiac output, a 12% increase in LV systolic pressure, a 28% increase in the LV maximum rate of pressure rise, a 45% increase in the LV maximum rate of pressure drop, a 29% increase in the contractility index, a 14% increase in aortic pressure, a 2.7-fold decrease in LV end-diastolic pressure, and a 4.2-fold decrease in LV minimum pressure. We conclude that IQ-1 has cardioprotective activity and reduces the severity of HF after MI.
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