Microbiology & Cell Biology

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1H, 13C, 15N backbone and side chain NMR resonance assignments of the N-terminal NEAr iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of Staphylococcus aureus
(2014-04) Fonner, Brittany A.; Tripet, Brian P.; Lui, Mengyao; Zhu, Hui; Lei, Benfang; Copie, Valerie
Staphylococcus aureus is an opportunistic pathogen that causes skin and severe infections in mammals. Critical to S. aureus growth is its ability to scavenge iron from host cells. To this effect, S. aureus has evolved a sophisticated pathway to acquire heme from hemoglobin (Hb) as a preferred iron source. The pathway is comprised of nine iron-regulated surface determinant (Isd) proteins involved in heme capture, transport, and degradation. A key protein of the heme acquisition pathway is the surface-anchored hemoglobin receptor protein IsdB, which is comprised of two NEAr transporter (NEAT) domains that act in concert to bind Hb and extract heme for subsequent transfer to downstream acquisition pathway proteins. Despite significant advances in the structural knowledge of other Isd proteins, the structural mechanisms and molecular basis of the IsdB-mediated heme acquisition process are not well understood. In order to provide more insights into the mode of function of IsdB, we have initiated NMR structural studies of the first NEAT domain of IsdB (IsdBN1). Herein, we report the near complete 1H, 13C and 15N resonance assignments of backbone and side chain atoms, and the secondary structural topology of the 148-residue IsdB NEAT 1 domain. The NMR results are consistent with the presence of eight β-strands and one α-helix characteristic of an immunoglobulin-like fold observed in other NEAT domain family proteins. This work provides a solid framework to obtain atomic-level insights toward understanding how IsdB mediates IsdB-Hb protein–protein interactions critical for heme capture and transfer.
2-Arylacetamido-4-phenylamino-5-substituted pyridazinones as formyl peptide receptors agonists
(2016-06) Vergelli, Claudia; Schepetkin, Igor A.; Ciciani, Giovanna; Cilibrizzi, Agostino; Crocetti, Letizia; Giovannoni, Maria Paola; Guerrini, Gabriella; Iacovone, Antonella; Kirpotina, Liliya N.; Khlebnikov, Andrei I.; Ye, Richard D.; Quinn, Mark T.
N-Formyl peptide receptors (FPRs: FPR1, FPR2, and FPR3) are G protein-coupled receptors that play key roles in modulating immune cells. FPRs represent potentially important therapeutic targets for the development of drugs that could enhance endogenous anti-inflammation systems associated with various pathologies, thereby reducing the progression of inflammatory conditions. Previously, we identified 2-arylacetamide pyridazin-3(2H)-ones as FPR1- or FPR2-selective agonists, as well as a large number of FPR1/FPR2-dual agonists and several mixed-agonists for the three FPR isoforms. Here, we report a new series of 2-arylacetamido-4-aniline pyridazin-3(2H)-ones substituted in position 5 as a further development of these FPR agonists. Chemical manipulation presented in this work resulted in mixed FPR agonists 8a, 13a and 27b, which had EC50 values in nanomolar range. In particular, compound 8a showed a preference for FPR1 (EC50 =45nM), while 13a and 27b showed a moderate preference for FPR2 (EC50 =35 and 61nM, respectively). Thus, these compounds may represent valuable tools for studying FPR activation and signaling.
A Comprehensive Protocol for the Collection, Differentiation, Cryopreservation, and Resuscitation of Primary Murine Bone Marrow Derived Macrophages (BMDM)
(Informa UK Limited, 2024-08) Luu, Abby M.; Shepardson, Kelly M.; Rynda-Apple, Agnieszka
Background. The field of immunology has undoubtedly benefited from the in vitro use of cell lines for immunological studies; however, due to the “immortal” nature of many cell lines, they are not always the best model. Thus, direct collection and culture of primary cells from model organisms is a solution that many researchers utilize. To the best of our knowledge, there is not a singular protocol which encompasses the entire process of bone marrow cell collection through cryopreservation and resuscitation of cells from a murine model. Methods. Bone marrow cells were collected from mice with a C57BL6 genetic background. Cells were differentiated using L929 conditioned media. Cells were assessed using a combination of microscopy, differential staining, immunocytochemistry, and trypan blue. Results: Primary murine BMDMs that underwent cryopreservation followed by resuscitation retained a high degree of viability. Furthermore, these BMDMs retained on overall ability to clear S. aureus. Results. Primary murine BMDMs that underwent cryopreservation followed by resuscitation retained a high degree of viability. Furthermore, these BMDMs retained on overall ability to clear S. aureus. Conclusion. Crypopreserved and resuscitated primary murine BMDMs were viable and retained their pverall S. aureus clearance ability.
A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society
(Wiley, 2024-05) Timmis, Kenneth et al.; Boyd, Eric S.
A Filamentous Bacteriophage Protein Inhibits Type IV Pili To Prevent Superinfection of Pseudomonas aeruginosa
(American Society for Microbiology, 2022-02) Schmidt, Amelia K.; Fitzpatrick, Alexa D.; Schwartzkopf, Caleb M.; Faith, Dominick R.; Jennings, Laura K.; Coluccio, Alison; Hunt, Devin J.; Michaels, Lia A.; Hargil, Aviv; Chen, Qingquan; Bollyky, Paul L.; Dorward, David W.; Wachter, Jenny; Rosa, Patricia A.; Maxwell, Karen L.; Secor, Patrick R.
Pseudomonas aeruginosa is an opportunistic pathogen that causes infections in a variety of settings. Many P. aeruginosa isolates are infected by filamentous Pf bacteriophage integrated into the bacterial chromosome as a prophage. Pf virions can be produced without lysing P. aeruginosa. However, cell lysis can occur during superinfection, which occurs when Pf virions successfully infect a host lysogenized by a Pf prophage. Temperate phages typically encode superinfection exclusion mechanisms to prevent host lysis by virions of the same or similar species. In this study, we sought to elucidate the superinfection exclusion mechanism of Pf phage. Initially, we observed that P. aeruginosa that survive Pf superinfection are transiently resistant to Pf-induced plaquing and are deficient in twitching motility, which is mediated by type IV pili (T4P). Pf utilize T4P as a cell surface receptor, suggesting that T4P are suppressed in bacteria that survive superinfection. We tested the hypothesis that a Pf-encoded protein suppresses T4P to mediate superinfection exclusion by expressing Pf proteins in P. aeruginosa and measuring plaquing and twitching motility. We found that the Pf protein PA0721, which we termed Pf superinfection exclusion (PfsE), promoted resistance to Pf infection and suppressed twitching motility by binding the T4P protein PilC. Because T4P play key roles in biofilm formation and virulence, the ability of Pf phage to modulate T4P via PfsE has implications in the ability of P. aeruginosa to persist at sites of infection.
Abiotic and biotic factors affecting the replication and pathogenicity of bee viruses
(2016-04) McMenamin, Alexander J.; Brutscher, Laura M.; Glenny, William; Flenniken, Michelle L.
Bees are important pollinators of plants in both agricultural and non-agricultural landscapes. Recent losses of both managed and wild bee species have negative impacts on crop production and ecosystem diversity. Therefore, in order to mitigate bee losses, it is important to identify the factors most responsible. Multiple factors including pathogens, agrochemical exposure, lack of quality forage, and reduced habitat affect bee health. Pathogen prevalence is one factor that has been associated with colony losses. Numerous pathogens infect bees including fungi, protists, bacteria, and viruses, the majority of which are RNA viruses including several that infect multiple bee species. RNA viruses readily infect bees, yet there is limited understanding of their impacts on bee health, particularly in the context of other stressors. Herein we review the influence environmental factors have on the replication and pathogenicity of bee viruses and identify research areas that require further investigation.
Aboveground and belowground responses to cyanobacterial biofertilizer supplement in a semi-arid, perennial bioenergy cropping system
(Wiley, 2021-08) Goemann, Hannah M.; Gay, Justin D.; Mueller, Rebecca C.; Brookshire, E. N. Jack; Miller, Perry; Poulter, Benjamin; Peyton, Brent M.
The need for sustainable agricultural practices to meet the food, feed, and fuel demands of a growing global population while reducing detrimental environmental impacts has driven research in multi‐faceted approaches to agricultural sustainability. Perennial cropping systems and microbial biofertilizer supplements are two emerging strategies to increase agricultural sustainability that are studied in tandem for the first time in this study. During the establishment phase of a perennial switchgrass stand in SW Montana, USA, we supplemented synthetic fertilization with a nitrogen‐fixing cyanobacterial biofertilizer (CBF) and were able to maintain aboveground crop productivity in comparison to a synthetic only (urea) fertilizer treatment. Soil chemical analysis conducted at the end of the growing season revealed that late‐season nitrogen availability in CBF‐supplemented field plots increased relative to urea‐only plots. High‐throughput sequencing of bacterial/archaeal and fungal communities suggested fine‐scale responses of the microbial community and sensitivity to fertilization among arbuscular mycorrhizal fungi, Planctomycetes, Proteobacteria, and Actinobacteria. Given their critical role in plant productivity and soil nutrient cycling, soil microbiome monitoring is vital to understand the impacts of implementation of alternative agricultural practices on soil health.
The Accessory Gene saeP of the SaeR/S Two-Component Gene Regulatory System Impacts Staphylococcus aureus Virulence During Neutrophil Interaction
(2020-04) Collins, Madison M.; Behera, Ranjan K.; Pallister, Kyler B.; Evans, Tyler J.; Burroughs, Owen; Flack, Caralyn; Guerra, Fermin E.; Pullman, Willis; Cone, Brock; Dankoff, Jennifer G.; Nygaard, Tyler K.; Brinsmade, Shaun R.; Voyich, Jovanka M.
Staphylococcus aureus (S. aureus) causes a range of diseases ranging from superficial skin and soft-tissue infections to invasive and life-threatening conditions (Klevens et al., 2007; Kobayashi et al., 2015). S. aureus utilizes the Sae sensory system to adapt to neutrophil challenge. Although the roles of the SaeR response regulator and its cognate sensor kinase SaeS have been demonstrated to be critical for surviving neutrophil interaction and for causing infection, the roles for the accessory proteins SaeP and SaeQ remain incompletely defined. To characterize the functional role of these proteins during innate immune interaction, we generated isogenic deletion mutants lacking these accessory genes in USA300 (USA300ΔsaeP and USA300ΔsaeQ). S. aureus survival was increased following phagocytosis of USA300ΔsaeP compared to USA300 by neutrophils. Additionally, secreted extracellular proteins produced by USA300ΔsaeP cells caused significantly more plasma membrane damage to human neutrophils than extracellular proteins produced by USA300 cells. Deletion of saeQ resulted in a similar phenotype, but effects did not reach significance during neutrophil interaction. The enhanced cytotoxicity of USA300ΔsaeP cells toward human neutrophils correlated with an increased expression of bi-component leukocidins known to target these immune cells. A saeP and saeQ double mutant (USA300ΔsaePQ) showed a significant increase in survival following neutrophil phagocytosis that was comparable to the USA300ΔsaeP single mutant and increased the virulence of USA300 during murine bacteremia. These data provide evidence that SaeP modulates the Sae-mediated response of S. aureus against human neutrophils and suggest that saeP and saeQ together impact pathogenesis in vivo.
Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods
(2016-04) Hochstein, Rebecca A.; Amenabar, Maximiliano J.; Munson-McGee, Jacob H.; Boyd, Eric S.; Young, Mark J.
The field of viral metagenomics has expanded our understanding of viral diversity from all three domains of life (Archaea, Bacteria, and Eukarya). Traditionally, viral metagenomic studies provide information about viral gene content but rarely provide knowledge about virion morphology and/or cellular host identity. Here we describe a new virus, Acidianus tailed spindle virus (ATSV), initially identified by bioinformatic analysis of viral metagenomic data sets from a high-temperature (80°C) acidic (pH 2) hot spring located in Yellowstone National Park, followed by more detailed characterization using only environmental samples without dependency on culturing. Characterization included the identification of the large tailed spindle virion morphology, determination of the complete 70.8-kb circular double-stranded DNA (dsDNA) viral genome content, and identification of its cellular host. Annotation of the ATSV genome revealed a potential three-domain gene product containing an N-terminal leucine-rich repeat domain, followed by a likely posttranslation regulatory region consisting of high serine and threonine content, and a C-terminal ESCRT-III domain, suggesting interplay with the host ESCRT system. The host of ATSV, which is most closely related to Acidianus hospitalis, was determined by a combination of analysis of cellular clustered regularly interspaced short palindromic repeat (CRISPR)/Cas loci and dual viral and cellular fluorescence in situ hybridization (viral FISH) analysis of environmental samples and confirmed by culture-based infection studies. This work provides an expanded pathway for the discovery, isolation, and characterization of new viruses using culture-independent approaches and provides a platform for predicting and confirming virus hosts. IMPORTANCE: Virus discovery and characterization have been traditionally accomplished by using culture-based methods. While a valuable approach, it is limited by the availability of culturable hosts. In this research, we report a virus-centered approach to virus discovery and characterization, linking viral metagenomic sequences to a virus particle, its sequenced genome, and its host directly in environmental samples, without using culture-dependent methods. This approach provides a pathway for the discovery, isolation, and characterization of new viruses. While this study used an acidic hot spring environment to characterize a new archaeal virus, Acidianus tailed spindle virus (ATSV), the approach can be generally applied to any environment to expand knowledge of virus diversity in all three domains of life.
Acquisition of elemental sulfur by sulfur-oxidising Sulfolobales
(Wiley, 2024-08) Fernandes-Martins, Maria C.; Springer, Carli; Colman, Daniel R.; Boyd, Eric S.
Elemental sulfur (S80)-oxidising Sulfolobales (Archaea) dominate high-temperature acidic hot springs (>80°C, pH <4). However, genomic analyses of S80-oxidising members of the Sulfolobales reveal a patchy distribution of genes encoding sulfur oxygenase reductase (SOR), an S80 disproportionating enzyme attributed to S80 oxidation. Here, we report the S80-dependent growth of two Sulfolobales strains previously isolated from acidic hot springs in Yellowstone National Park, one of which associated with bulk S80 during growth and one that did not. The genomes of each strain encoded different sulfur metabolism enzymes, with only one encoding SOR. Dialysis membrane experiments showed that direct contact is not required for S80 oxidation in the SOR-encoding strain. This is attributed to the generation of hydrogen sulfide (H2S) from S80 disproportionation that can diffuse out of the cell to solubilise bulk S80 to form soluble polysulfides (Sx2−) and/or S80 nanoparticles that readily diffuse across dialysis membranes. The Sulfolobales strain lacking SOR required direct contact to oxidise S80, which could be overcome by the addition of H2S. High concentrations of S80 inhibited the growth of both strains. These results implicate alternative strategies to acquire and metabolise sulfur in Sulfolobales and have implications for their distribution and ecology in their hot spring habitats.
An ADAM17-Neutralizing Antibody Reduces Inflammation and Mortality While Increasing Viral Burden in a COVID-19 Mouse Model
(Frontiers Media SA, 2022-06) Hedges, Jodi F.; Snyder, Deann T.; Robison, Amanda; Grifka-Walk, Heather M.; Blackwell, Karlin; Shepardson, Kelly; Kominsky, Douglas; Rynda-Apple, Agnieszka; Walcheck, Bruce; Jutila, Mark A.
Angiotensin Converting Enzyme 2 (ACE2) is the primary cell entry receptor for SARS-CoV and SARS-CoV-2 viruses. A disintegrin and metalloproteinase 17 (ADAM17) is a protease that cleaves ectodomains of transmembrane proteins, including that of ACE2 and the proinflammatory cytokine TNF-α, from cell surfaces upon cellular activation. We hypothesized that blockade of ADAM17 activity would alter COVID-19 pathogenesis. To assess this pathway, we blocked the function of ADAM17 using the monoclonal antibody MEDI3622 in the K18-hACE2 transgenic mouse model of COVID-19. Antibody-treated mice were healthier, less moribund, and had significantly lower lung pathology than saline-treated mice. However, the viral burden in the lungs of MEDI3622-treated mice was significantly increased. Thus, ADAM17 appears to have a critical anti-viral role, but also may promote inflammatory damage. Since the inflammatory cascade is ultimately the reason for adverse outcomes in COVID-19 patients, there may be a therapeutic application for the MEDI3622 antibody.
Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription
(Cold Spring Harbor Laboratory, 2024-06) Snyder, Laura R.; Kilde, Ingrid; Nemudryi, Artem; Wiedenheft, Blake; Koutmos, Markos; Koutmou, Kristin S.
SARS-CoV-2, the causative virus of the COVID-19 pandemic, follows SARS and MERS as recent zoonotic coronaviruses causing severe respiratory illness and death in humans. The recurrent impact of zoonotic coronaviruses demands a better understanding of their fundamental molecular biochemistry. Nucleoside modifications, which modulate many steps of the RNA life cycle, have been found in SARS-CoV-2 RNA, although whether they confer a pro- or antiviral effect is unknown. Regardless, the viral RNA-dependent RNA polymerase will encounter these modifications as it transcribes through the viral genomic RNA. We investigated the functional consequences of nucleoside modification on the pre-steady state kinetics of SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted transcription system with modified RNA templates. Our findings show that N6-methyladenosine and 2′-O-methyladenosine modifications slow the rate of viral transcription at magnitudes specific to each modification, which has the potential to impact SARS-CoV-2 genome maintenance.
Age-specific infectious period shapes dynamics of pneumonia in bighorn sheep
(2017-09) Plowright, Raina K.; Manlove, Kezia R.; Besser, Thomas E.; Paez, David J.; Andrews, Kimberly R.; Matthews, Patrick E.; Waits, Lisette P.; Hudson, Peter J.; Cassirer, E. Frances
Superspreading, the phenomenon where a small proportion of individuals contribute disproportionately to new infections, has profound effects on disease dynamics. Superspreading can arise through variation in contacts, infectiousness or infectious periods. The latter has received little attention, yet it drives the dynamics of many diseases of critical public health, livestock health and conservation concern. Here, we present rare evidence of variation in infectious periods underlying a superspreading phenomenon in a free-ranging wildlife system. We detected persistent infections of Mycoplasma ovipneumoniae, the primary causative agent of pneumonia in bighorn sheep (Ovis canadensis), in a small number of older individuals that were homozygous at an immunologically relevant genetic locus. Interactions among age-structure, genetic composition and infectious periods may drive feedbacks in disease dynamics that determine the magnitude of population response to infection. Accordingly, variation in initial conditions may explain divergent population responses to infection that range from recovery to catastrophic decline and extirpation.
The Aggregatibacter actinomycetemcomitans cytolethal distending toxin active subunit, CdtB, contains a cholesterol recognition sequence required for toxin binding and subunit internalization
(2015-07) Boesze-Battaglia, Kathleen; Walker, Lisa P.; Zekavat, Ali; Dlakic, Mensur; Scuron, Monika Damek; Nygrend, Patrik; Shenker, Bruce J.
Induction of cell cycle arrest in lymphocytes following exposure to the Aggregatibacter actinomycetemcomitans cytolethal distending toxin (Cdt) is dependent upon the integrity of lipid membrane microdomains. Moreover, we have previously demonstrated that the associaton of Cdt with target cells involves the CdtC subunit which binds to cholesterol via a cholesterol recognition amino acid consensus sequence (CRAC site). In this study we demonstrate that the active Cdt subunit, CdtB, also is capable of binding to large unilamellar vesicles (LUVs) containing cholesterol. Furthermore, CdtB binding to cholesterol involves a similar CRAC site as that demonstrated for CdtC. Mutation of the CRAC site reduces binding to model membranes as well as toxin binding and CdtB internalization in both Jurkat cells and human macrophages. A concomitant reduction in Cdt-induced toxicity was also noted indicated by reduced cell cycle arrest and apoptosis in Jurkat cells and a reduction in the pro-inflammatory response in macrophages (IL-1Î² and TNFÎ± release). Collectively, these observations indicate that membrane cholesterol serves as an essential ligand for both CdtC and CdtB and further, that this binding is necessary for both internalization of CdtB and subsequent molecular events leading to intoxication of cells.
Aging influences the response of T cells to stimulation by the ellagitannin, oenothein B
(2015-06) Ramstead, Andrew G.; Schepetkin, Igor A.; Todd, Kimberly; Loeffelholz, James; Berardinelli, James G.; Quinn, Mark T.; Jutila, Mark A.
Several plant extracts, including certain polyphenols, prime innate lymphocytes and enhance responses to secondary stimuli. Oenothein B, a polyphenol isolated from Epilobium angustifolium and other plant sources, enhances IFNÎ³ production by both bovine and human NK cells and T cells, alone and in response to secondary stimulation by cytokines or tumor cells. Innate immune cell responsiveness is known to be affected by aging, but whether polyphenol responses by these cells are also impacted by aging is not known. Therefore, we examined oenothein B responsiveness in T cells from cord blood, young, and adult donors. We found that oenothein B stimulates bovine and human T cells from individuals over a broad range of ages, as measured by increased IL-2RÎ± and CD69 expression. However, clear differences in induction of cytokine production by T cells were seen. In T cells from human cord blood and bovine calves, oenothein B was unable to induce IFNÎ³ production. However, oenothein B induced IFNÎ³ production by T cells from adult humans and cattle. In addition, oenothein B induced GM-CSF production by human adult T cells, but not cord blood T cells. Within the responsive T cell population, we found that CD45RO + memory T cells expressed more cytokines in response to oenothein B than CD45RO âˆ’ T cells. In summary, our data suggest that the immunostimulation of T cells by oenothein B is influenced by age, particularly with respect to immune cytokine production.
Alpha-toxin Induces Programmed Cell Death of Human T cells, B cells, and Monocytes During USA300 Infection
(2012-05) Nygaard, Tyler K.; Pallister, Kyler B.; DuMont, Ashley L.; DeWald, Mark; Watkins, Robert L.; Pallister, Erik Q.; Malone, Cheryl L.; Griffith, Shannon; Horswill, Alexander R.; Torres, Victor J.; Voyich, Jovanka M.
This investigation examines the influence of alpha-toxin (Hla) during USA300 infection of human leukocytes. Survival of an USA300 isogenic deletion mutant of hla (USA300Δhla) in human blood was comparable to the parental wild-type strain and polymorphonuclear leukocyte (PMN) plasma membrane permeability caused by USA300 did not require Hla. Flow cytometry analysis of peripheral blood mononuclear cells (PBMCs) following infection by USA300, USA300Δhla, and USA300Δhla transformed with a plasmid over-expressing Hla (USA300Δhla Comp) demonstrated this toxin plays a significant role inducing plasma membrane permeability of CD14+, CD3+, and CD19+ PBMCs. Rapid plasma membrane permeability independent of Hla was observed for PMNs, CD14+ and CD19+ PBMCs following intoxication with USA300 supernatant while the majority of CD3+ PBMC plasma membrane permeability induced by USA300 required Hla. Addition of recombinant Hla to USA300Δhla supernatant rescued CD3+ and CD19+ PBMC plasma membrane permeability generated by USA300 supernatant. An observed delay in plasma membrane permeability caused by Hla in conjunction with Annexin V binding and ApoBrdU Tunel assays examining PBMCs intoxicated with recombinant Hla or infected with USA300, USA300Δhla, USA300Δhla Comp, and USA300ΔsaeR/S suggest Hla induces programmed cell death of monocytes, B cells, and T cells that results in plasma membrane permeability. Together these findings underscore the importance of Hla during S. aureus infection of human tissue and specifically demonstrate Hla activity during USA300 infection triggers programmed cell death of human monocytes, T cells and B cells that leads to plasma membrane permeability.
Anti-Inflammatory Activity of Pyrazolo[1,5-a]quinazolines
(MDPI AG, 2024-05) Crocetti, Letizia; Khlebnikov, Andrei I.; Guerrini, Gabriella; Schepetkin, Igor A.; Melani, Fabrizio; Giovannoni, Maria Paola; Quinn, Mark T.
Chronic inflammation contributes to a number of diseases. Therefore, control of the inflammatory response is an important therapeutic goal. To identify novel anti-inflammatory compounds, we synthesized and screened a library of 80 pyrazolo[1,5-a]quinazoline compounds and related derivatives. Screening of these compounds for their ability to inhibit lipopolysaccharide (LPS)-induced nuclear factor κB (NF-κB) transcriptional activity in human THP-1Blue monocytic cells identified 13 compounds with anti-inflammatory activity (IC50 < 50 µM) in a cell-based test system, with two of the most potent being compounds 13i (5-[(4-sulfamoylbenzyl)oxy]pyrazolo[1,5-a]quinazoline-3-carboxamide) and 16 (5-[(4-(methylsulfinyl)benzyloxy]pyrazolo[1,5-a]quinazoline-3-carboxamide). Pharmacophore mapping of potential targets predicted that 13i and 16 may be ligands for three mitogen-activated protein kinases (MAPKs), including extracellular signal-regulated kinase 2 (ERK2), p38α, and c-Jun N-terminal kinase 3 (JNK3). Indeed, molecular modeling supported that these compounds could effectively bind to ERK2, p38α, and JNK3, with the highest complementarity to JNK3. The key residues of JNK3 important for this binding were identified. Moreover, compounds 13i and 16 exhibited micromolar binding affinities for JNK1, JNK2, and JNK3. Thus, our results demonstrate the potential for developing lead anti-inflammatory drugs based on the pyrazolo[1,5-a]quinazoline and related scaffolds that are targeted toward MAPKs.
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.
Approximating Expensive Distance Metrics
(Montana State University, 2021-11) Pryor, Elliott; Stouffer, Nathan
Computing the distance between point a and point b is typically considered to be very easy. However, there are times when computing a distance can take significant computation time; we call these expensive distance metrics. Suppose we have some expensive distance metric and we need to compute the distances between a bunch of points. This paper explores a method that to reduce the number of queries to the distance metric and the effect on clustering. The authors find that total run time can be reduced while only inducing small inaccuracies in clustering output.
Archaea on the move
(2015-06) Boyd, Eric S.
Chemotaxis, the ability to sense and respond to environmental stimuli, allows microorganisms to navigate chemical and physical gradients in natural systems. Chemical stimuli that can be sensed by microorganisms include variations in pH and osmolarity as well as concentrations of toxins and oxygen, whereas physical stimuli sensed by microorganisms include the intensity and wavelength of light (Wadhams and Armitage, 2004). More recently, hydrogenotrophic microorganisms have been shown to be able to sense the concentration of hydrogen (Brileya et al., 2013). The ability to sense the environment is made possible by simple one-component (Ulrich etal., 2005) and more complex two-component signal transduction systems (Stock et al., 2000). A key difference between one- and two-component signal transduction systems is the location of the signals that are detected. One-component systems are thought to function primarily in detecting cytoplasmic signals, whereas two-component systems are thought to detect extracellular signals (Wuichet and Zhulin, 2010). One-component systems consist of a single protein that typically comprises a sensory and a regulatory domain, whereas two-component systems comprise two conserved proteins: a sensor and a response regulator.