Biochimie, microbiologie et immunologie // Biochemistry, Microbiology and Immunology

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Mentors as Allies for Disabled Scientists
(American Chemical Society (ACS), 2025-06-15) Alarcón, Emilio I.
Close to twenty-eight percent of the population in the US and Canada is living with disability, yet despite this prevalence, persons with disabilities remain mostly absent in biomedical research. While the role of mentors has been demonstrated to be effective in increasing the number of women and other groups in biomedical research, mentoring disabled scientists remains a gray area. In this short perspective, I share my personal experience as a person with a disability who was mentored by a non-disabled person, who ultimately became an ally
Pharmacological and metabolic parameters of [18F]flubrobenguane in clinical imaging populations
(2023) Mair, Braeden A; Zelt, Jason G E; Nekesa, Kirabo; Saint-Georges, Zacharie; Dinelle, Katie; Adi, Myriam; Robinson, Simon; Mielniczuk, Lisa M; Shlik, Jakov; Beanlands, Rob S; deKemp, Robert A; Rotstein, Benjamin H
Cardiac sympathetic nervous system molecular imaging has demonstrated prognostic value. Compared with meta-[11C]hydroxyephedrine, [18F]flubrobenguane (FBBG) facilitates reliable estimation of SNS innervation using similar analytical methods and possesses a more convenient physical half-life. The aim of this study was to evaluate pharmacokinetic and metabolic properties of FBBG in target clinical cohorts.
Quinazoline-2-Carboxamides as Selective PET Radiotracers for Matrix Metalloproteinase-13 Imaging in Atherosclerosis
(2023) Buchler, Ariel; Ismailani, Uzair S; MacMullin, Nicole; Abdirahman, Faduma; Adi, Myriam; Bi, Christina; Jany, Catherine; Keillor, Jeffrey W; Rotstein, Benjamin H
Matrix metalloproteinase-13 (MMP-13) plays a critical role in the progression of unstable atherosclerosis. A series of highly potent and selective MMP-13 inhibitors were synthesized around a quinazoline-2-carboxamide scaffold to facilitate radiolabeling with fluorine-18 or carbon-11 positron-emitting nuclides and visualization of atherosclerotic plaques. In vitro enzyme inhibition assays identified three compounds as promising radiotracer candidates. Efficient automated radiosyntheses provided [11C]5b, [11C]5f, and [18F]5j and enabled pharmacokinetic characterization in atherosclerotic mice. The radiotracers displayed substantial differences in their distribution and excretion. Most favorably for vascular imaging, [18F]5j exhibited low uptake in metabolic organs with minimal retention of myocardial radioactivity, substantial renal clearance, and high metabolic stability in plasma. Ex vivo aortic autoradiography and competition studies revealed that [18F]5j specifically binds to MMP-13 within atherosclerotic plaques and localizes to lipid-rich regions. This study demonstrates the utility of the quinazoline-2-carboxamide scaffold for MMP-13 selective positron emission tomography (PET) radiotracer development and identifies [18F]5j for imaging atherosclerosis.
Synthesis and Evaluation of [11C]MCC950 for Imaging NLRP3-Mediated Inflammation in Atherosclerosis
(2023) Ismailani, Uzair S; Buchler, Ariel; MacMullin, Nicole; Abdirahman, Faduma; Adi, Myriam; Rotstein, Benjamin H
Overexpression of the NLRP3 inflammasome has been attributed to the progressive worsening of a multitude of cardiovascular inflammatory diseases such as myocardial infarction, pulmonary arterial hypertension, and atherosclerosis. The recently discovered potent and selective NLRP3 inhibitor MCC950 has shown promise in hindering disease progression, but NLRP3-selective cardiovascular positron emission tomography (PET) imaging has not yet been demonstrated. We synthesized [11C]MCC950 with no-carrier-added [11C]CO2 fixation chemistry using an iminophosphorane precursor (RCY 45 ± 4%, >99% RCP, 27 ± 2 GBq/μmol, 23 ± 3 min, n = 6) and determined its distribution both in vivo and ex vivo in C57BL/6 and atherogenic ApoE-/- mice. Small animal PET imaging was performed in both strains following intravenous administration via the lateral tail vein and revealed considerable uptake in the liver that stabilized by 20 min (7-8.5 SUV), coincident with secondary renal excretion. Plasma metabolite analysis uncovered excellent in vivo stability of [11C]MCC950 (94% intact). Ex vivo autoradiography performed on excised aortas revealed heterogeneous uptake in atherosclerotic plaques of ApoE-/- mice in comparison to C57BL/6 controls (48 ± 17 %ID/m2 vs 18 ± 8 %ID/m2, p = 0.002, n = 4-5). Treatment of ApoE-/- mice with nonradioactive MCC950 (5 mg/kg, iv) 10 min prior to radiotracer administration increased uptake in the intestine (5.3 ± 1.8 %ID/g vs 11.0 ± 3.7 %ID/g, p = 0.04, n = 4-6) and in aortic lesions (48 ± 17 %ID/m2 vs 104 ± 15 %ID/m2, p = 0.0002, n = 5) by 108% and 117%, respectively, without significantly increasing plasma free fraction (fp, 1.3 ± 0.4% vs 1.7 ± 0.8%, n = 2). These results suggest that [11C]MCC950 uptake demonstrates specific binding and may prove useful for in vivo NLRP3 imaging in atherosclerosis.
Proteins from Thermophilic Thermus thermophilus Often Do Not Fold Correctly in a Mesophilic Expression System Such as Escherichia coli
(2022) Kruglikov, Alibek; Wei, Yulong; Xia, Xuhua
Majority of protein structure studies use Escherichia coli (E. coli) and other model organisms as expression systems for other species’ genes. However, protein folding depends on cellular environment factors, such as chaperone proteins, cytoplasmic pH, temperature, and ionic concentrations. Because of differences in these factors, especially temperature and chaperones, native proteins in organisms such as extremophiles may fold improperly when they are expressed in mesophilic model organisms. Here we present a methodology of assessing the effects of using E. coli as the expression system on protein structures. We compare these effects between eight mesophilic bacteria and Thermus thermophilus (T. thermophilus), a thermophile, and found that differences are significantly larger for T. thermophilus. More specifically, helical secondary structures in T. thermophilus proteins are often replaced by coil structures in E. coli. Our results show unique directionality in misfolding when proteins in thermophiles are expressed in mesophiles. This indicates that extremophiles, such as thermophiles, require unique protein expression systems in protein folding studies.
In Silico Molecular Dynamics of Griseofulvin and Its Derivatives Revealed Potential Therapeutic Applications for COVID-19.
(2022) Aris, Parisa; Mohamadzadeh, M; Wei, Yulong; Xia, Xuhua
Treatment options for Coronavirus Disease 2019 (COVID-19) remain limited, and the option of repurposing approved drugs with promising medicinal properties is of increasing interest in therapeutic approaches to COVID-19. Using computational approaches, we examined griseofulvin and its derivatives against four key anti-SARS-CoV-2 targets: main protease, RdRp, spike protein receptor-binding domain (RBD), and human host angiotensin-converting enzyme 2 (ACE2). Molecular docking analysis revealed that griseofulvin (CID 441140) has the highest docking score (-6.8 kcal/mol) with main protease of SARS-CoV-2. Moreover, griseofulvin derivative M9 (CID 144564153) proved the most potent inhibitor with -9.49 kcal/mol, followed by A3 (CID 46844082) with -8.44 kcal/mol against M protease and ACE2, respectively. Additionally, H bond analysis revealed that compound A3 formed the highest number of hydrogen bonds, indicating the strongest inhibitory efficacy against ACE2. Further, molecular dynamics (MD) simulation analysis revealed that griseofulvin and these derivatives are structurally stable. These findings suggest that griseofulvin and its derivatives may be considered when designing future therapeutic options for SARS-CoV-2 infection.
Griseofulvin: An Updated Overview of Old and Current Knowledge
(2022) Aris, Parisa; Wei, Yulong; Mohamadzadeh, M; Xia, Xuhua
Griseofulvin is an antifungal polyketide metabolite produced mainly by ascomycetes. Since it was commercially introduced in 1959, griseofulvin has been used in treating dermatophyte infections. This fungistatic has gained increasing interest for multifunctional applications in the last decades due to its potential to disrupt mitosis and cell division in human cancer cells and arrest hepatitis C virus replication. In addition to these inhibitory effects, we and others found griseofulvin may enhance ACE2 function, contribute to vascular vasodilation, and improve capillary blood flow. Furthermore, molecular docking analysis revealed that griseofulvin and its derivatives have good binding potential with SARS-CoV-2 main protease, RNA-dependent RNA polymerase (RdRp), and spike protein receptor-binding domain (RBD), suggesting its inhibitory effects on SARS-CoV-2 entry and viral replication. These findings imply the repurposing potentials of the FDA-approved drug griseofulvin in designing and developing novel therapeutic interventions. In this review, we have summarized the available information from its discovery to recent progress in this growing field. Additionally, explored is the possible mechanism leading to rare hepatitis induced by griseofulvin. We found that griseofulvin and its metabolites, including 6-desmethylgriseofulvin (6-DMG) and 4- desmethylgriseofulvin (4-DMG), have favorable interactions with cytokeratin intermediate filament proteins (K8 and K18), ranging from -3.34 to -5.61 kcal mol(-1). Therefore, they could be responsible for liver injury and Mallory body (MB) formation in hepatocytes of human, mouse, and rat treated with griseofulvin. Moreover, the stronger binding of griseofulvin to K18 in rodents than in human may explain the observed difference in the severity of hepatitis between rodents and human.
Selective Imaging of Matrix Metalloproteinase-13 to Detect Extracellular Matrix Remodeling in Atherosclerotic Lesions
(2022) Buchler, Ariel; Munch, Maxime; Farber, Gedaliah; Zhao, Xiaoling; Al-Haddad, Rami; Farber, Eadan; Rotstein, Benjamin H
Overexpression and activation of matrix metalloproteinase-13 (MMP-13) within atheroma increases susceptibility to plaque rupture, a major cause of severe cardiovascular complications. In comparison to pan-MMP targeting [18F]BR-351, we evaluated the potential for [18F]FMBP, a selective PET radiotracer for MMP-13, to detect extracellular matrix (ECM) remodeling in vascular plaques possessing markers of inflammation.
Interrupted aza-Wittig reactions using iminophosphoranes to synthesize 11C-carbonyls
(2021) Ismailani, Uzair S; Munch, Maxime; Mair, Braeden A; Rotstein, Benjamin H
A direct CO2-fixation methodology couples structurally diverse iminophosphoranes with various nucleophiles to synthesize ureas, carbamates, thiocarbamates, and amides, and is amenable for 11C radiolabeling. This methodology is practical, as demonstrated by the synthesis of >35 products and isolation of the molecular imaging radiopharmaceuticals [11C]URB694 and [11C]glibenclamide.
Cardiac Sympathetic Positron Emission Tomography Imaging with Meta-[18F]Fluorobenzylguanidine is Sensitive to Uptake-1 in Rats
(2021) Ismailani, Uzair S; Buchler, Ariel; Farber, Gedaliah; Pekošak, Aleksandra; Farber, Eadan; MacMullin, Nicole; Suuronen, Erik J; Vasdev, Neil; Beanlands, Rob S B; de Kemp, Robert A; Rotstein, Benjamin H
Dysfunction of the cardiac sympathetic nervous system contributes to the development of cardiovascular diseases including ischemia, heart failure, and arrhythmias. Molecular imaging probes such as meta-[123I]iodobenzylguanidine have demonstrated the utility of assessing neuronal integrity by targeting norepinephrine transporter (NET, uptake-1). However, current radiotracers can report only on innervation due to suboptimal kinetics and lack sensitivity to NET in rodents, precluding mechanistic studies in these species. The objective of this work was to characterize myocardial sympathetic neuronal uptake mechanisms and kinetics of the positron emission tomography (PET) radiotracer meta-[18F]fluorobenzylguanidine ([18F]mFBG) in rats. Automated synthesis using spirocyclic iodonium(III) ylide radiofluorination produces [18F]mFBG in 24 ± 1% isolated radiochemical yield and 30-95 GBq/μmol molar activity. PET imaging in healthy rats delineated the left ventricle, with monoexponential washout kinetics (kmono = 0.027 ± 0.0026 min-1, Amono = 3.08 ± 0.33 SUV). Ex vivo biodistribution studies revealed tracer retention in the myocardium, while pharmacological treatment with selective NET inhibitor desipramine, nonselective neuronal and extraneuronal uptake-2 inhibitor phenoxybenzamine, and neuronal ablation with neurotoxin 6-hydroxydopamine reduced myocardial retention by 33, 76, and 36%, respectively. Clearance of [18F]mFBG from the myocardium was unaffected by treatment with uptake-1 and uptake-2 inhibitors following peak myocardial activity. These results suggest that myocardial distribution of [18F]mFBG in rats is dependent on both NET and extraneuronal transporters and that limited reuptake to the myocardium occurs. [18F]mFBG may therefore prove useful for imaging intraneuronal dysfunction in small animals.
Rhodium-Catalyzed Addition of Organozinc Iodides to Carbon-11 Isocyanates
(2020) Mair, Braeden A; Fouad, Moustafa H; Ismailani, Uzair S; Munch, Maxime; Rotstein, Benjamin H
Amides were prepared using rhodium-catalyzed coupling of organozinc iodides and carbon-11 (11C, t1/2 = 20.4 min) isocyanates. Nonradioactive isocyanates and sp3 or sp2 organozinc iodides generated amides in yields of 13%-87%. Incorporation of cyclotron-produced [11C]CO2 into 11C-amide products proceeded in yields of 5%-99%. The synthetic utility of the methodology was demonstrated through the isolation of [11C]N-(4-fluorophenyl)-4-methoxybenzamide ([11C]6g) with a molar activity of 267 GBq μmol-1 and 12% radiochemical yield in 21 min from the beginning of synthesis.
AMPK-mediated HMGCR regulation of cholesterol metabolism in macrophages
(2017) Burkovsky, Leah; LeBlond, Nicholas D.; Yaworski, Rebecca A.; Margison, Kaitlyn D.; Fullerton, Morgan D.
Atherosclerosis, the accumulation of cholesterol-loaded macrophages (foam cells) in the arteries, leads to cardiovascular disease, which is the leading cause of mortality in the developed world. 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) is the rate-liming step in cholesterol biosynthesis and is regulated by several mechanisms, including inhibition by reversible phosphorylation by the energy-sensing AMP-activated protein kinase (AMPK). AMPK activators are under investigation for their potential as antiatherogenic agents. The purpose of this project was to test the physiological significance of AMPK regulating HMGCR activity in macrophages. Using bone marrow-derived macrophages from HMGCR knock-in (KI) mice, where the phosphorylation site had been eliminated, this project investigated the impact that AMPK signaling to HMGCR has on cholesterol synthesis, accumulation of cholesterol, and cholesterol efflux. Since atherosclerosis is tightly linked with inflammation in plaques, cytokine expression was also assessed after treating macrophages with a pro-inflammatory stimulus. While there was increased cholesterol synthesis in macrophages from HMGCR KI mice than wild-type (WT) mice, there were no differences between WT and HMGCR KI macrophages in all the other aspects examined. This suggests that the regulation of HMGCR through phosphorylation by AMPK is not physiologically significant to the development of atherosclerosis. Further investigation is required in vivo to confirm this finding. To further understand how AMPK activators may be a potential drug strategy for treating atherosclerosis, other pathways and mechanisms need to be investigated.
Effects of cobalt and chromium ions on oxidative stress and energy metabolism in macrophages in vitro
(2018) Salloum, Zeina; Lehoux, Eric A.; Harper, Mary-Ellen; Catelas, Isabelle
Cobalt and chromium ions released from cobalt-chromium-molybdenum (CoCrMo)-based implants are a potential health concern, especially since both ions have been shown to induce oxidative stress in macrophages, the predominant immune cells in periprosthetic tissues. Ions of other transition metals (Cd, Ni) have been reported to inhibit the activity of mitochondrial enzymes in the electron transport chain. However, the effects of Co and Cr ions on the energy metabolism of macrophages remain largely unknown. The objective of the present study was to analyze the effects of Co2+ and Cr3+ on oxidative stress and energy metabolism in macrophages in vitro. RAW 264.7 murine macrophages were exposed to 6-18 ppm Co2+ or 50-150 ppm Cr3+ . Results showed a significant increase in two markers of oxidative stress, reactive oxygen species level and protein carbonyl content, with increasing concentrations of Co2+ , but not with Cr3+ . In addition, oxygen consumption rates (OCR; measured using an extracellular flux analyzer) showed significant decreases in both mitochondrial respiration and non-mitochondrial oxygen consumption with increasing concentrations of Co2+ , but not with Cr3+ . OCR results further showed that Co2+ , but not Cr3+ , induced mitochondrial dysfunction, including a decrease in oxidative phosphorylation capacity. Overall, this study suggests that mitochondrial dysfunction may contribute to Co2+ -induced oxidative stress in macrophages, and thereby to the inflammatory response observed in periprosthetic tissues. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:3178-3187, 2018.
Effects of cobalt and chromium ions on oxidative stress and energy metabolism in macrophages in vitro
(2018) Salloum, Zeina; Lehoux, Eric A; Harper, Mary-Ellen; Catelas, Isabelle
Cobalt and chromium ions released from cobalt-chromium-molybdenum (CoCrMo)-based implants are a potential health concern, especially since both ions have been shown to induce oxidative stress in macrophages, the predominant immune cells in periprosthetic tissues. Ions of other transition metals (Cd, Ni) have been reported to inhibit the activity of mitochondrial enzymes in the electron transport chain. However, the effects of Co and Cr ions on the energy metabolism of macrophages remain largely unknown. The objective of the present study was to analyze the effects of Co2+ and Cr3+ on oxidative stress and energy metabolism in macrophages in vitro. RAW 264.7 murine macrophages were exposed to 6-18 ppm Co2+ or 50-150 ppm Cr3+ . Results showed a significant increase in two markers of oxidative stress, reactive oxygen species level and protein carbonyl content, with increasing concentrations of Co2+ , but not with Cr3+ . In addition, oxygen consumption rates (OCR; measured using an extracellular flux analyzer) showed significant decreases in both mitochondrial respiration and non-mitochondrial oxygen consumption with increasing concentrations of Co2+ , but not with Cr3+ . OCR results further showed that Co2+ , but not Cr3+ , induced mitochondrial dysfunction, including a decrease in oxidative phosphorylation capacity. Overall, this study suggests that mitochondrial dysfunction may contribute to Co2+ -induced oxidative stress in macrophages, and thereby to the inflammatory response observed in periprosthetic tissues. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:3178-3187, 2018.
The liver connexin32 interactome is a novel plasma membrane-mitochondrial signaling nexus
(2013-04-16) Fowler, Stephanie L; Akins, Mark; Zhou, Hu; Figeys, Daniel; Bennett, Steffany A.L.
Connexins are the structural subunits of gap junctions and act as protein platforms for signaling complexes. Little is known about tissue-specific connexin signaling nexuses, given significant challenges associated with affinity-purifying endogenous channel complexes to the level required for interaction analyses. Here, we used multiple subcellular fractionation techniques to isolate connexin32-enriched membrane microdomains from murine liver. We show, for the first time, that connexin32 localizes to both the plasma membrane and inner mitochondrial membrane of hepatocytes. Using a combination of immunoprecipitation-high throughput mass spectrometry, reciprocal co-IP, and subcellular fractionation methodologies, we report a novel interactome validated using null mutant controls. Eighteen connexin32 interacting proteins were identified. The majority represent resident mitochondrial proteins, a minority represent plasma membrane, endoplasmic reticulum, or cytoplasmic partners. In particular, connexin32 interacts with connexin26 and the mitochondrial protein, sideroflexin-1, at the plasma membrane. Connexin32 interaction enhances connexin26 stability. Converging bioinformatic, biochemical, and confocal analyses support a role for connexin32 in transiently tethering mitochondria to connexin32-enriched plasma membrane microdomains through interaction with proteins in the outer mitochondrial membrane, including sideroflexin-1. Complex formation increases the pool of sideroflexin-1 that is present at the plasma membrane. Together, these data identify a novel plasma membrane/mitochondrial signaling nexus in the connexin32 interactome.
A novel cis-acting element from the 3′UTR of DNA damage-binding protein 2 mRNA links transcriptional and post-transcriptional regulation of gene expression
(2013-06-17) Melanson, Brian D.; Cabrita, Miguel A.; Bose, Reetesh; Hamill, Jeffrey D.; Pan, Elysia; Brochu, Christian; Marcellus, Kristen A.; Zhao, Tong T.; Holcik, Martin; McKay, Bruce C.
The DNA damage-binding protein 2 (DDB2) is an adapter protein that can direct a modular Cul4-DDB1-RING E3 Ligase complex to sites of ultraviolet light-induced DNA damage to ubiquitinate substrates during nucleotide excision repair. The DDB2 transcript is ultraviolet-inducible; therefore, its regulation is likely important for its function. Curiously, the DDB2 mRNA is reportedly short-lived, but the transcript does not contain any previously characterized cis-acting determinants of mRNA stability in its 3′ untranslated region (3′UTR). Here, we used a tetracycline regulated d2EGFP reporter construct containing specific 3′UTR sequences from DDB2 to identify novel cis-acting elements that regulate mRNA stability. Synthetic 3′UTRs corresponding to sequences as short as 25 nucleotides from the central region of the 3′UTR of DDB2 were sufficient to accelerate decay of the heterologous reporter mRNA. Conversely, these same 3′UTRs led to more rapid induction of the reporter mRNA, export of the message to the cytoplasm and the subsequent accumulation of the encoded reporter protein, indicating that this newly identified cis-acting element affects transcriptional and post-transciptional processes. These results provide clear evidence that nuclear and cytoplasmic processing of the DDB2 mRNA is inextricably linked.
Are dopamine-related genotypes risk factors for excessive gestational weight gain?
(2013-06-12) Goldfield, Gary S; Dowler, Lauren Marie; Walker, Mark; Cameron, Jameason D; Ferraro, Zachary M; Doucet, Eric; Adamo, Kristi B
Background: Excessive gestational weight gain is associated with postpartum weight retention and downstream child obesity. Dopamine plays a critical role in the regulation of energy intake and body weight. The purpose of this study was to examine the relationship between excessive gestational weight gain and dopamine pathway-related polymorphisms, namely the variable nucleotide tandem repeat in the 3´untranslated region (UTR) region of the SLC6A3 (DAT-1) dopamine transporter gene and the 30-base pair variable nucleotide tandem repeat polymorphism of the 5´UTR of the monoamine oxidase-A (MAO-A) gene. Methods: Ninety-three women of mean age 31.7 ± 4.2 years were recruited from the Ottawa and Kingston birth cohort and assessed at 12–20 weeks’ gestation. Mean body mass index was 22.7 ± 2.5 kg/m2. Excessive gestational weight gain was defined according to the 2009 Institute of Medicine guidelines based on body mass index. Genotype analyses were performed using polymerase chain reaction and agarose gel electrophoresis. Results: There was no relationship between the prevalence or magnitude of excessive gestational weight gain among women with the 3´ UTR single nucleotide polymorphism of the DAT-1 gene. However, 70% (19 of 27) of women carrying the MAO-A 4/4 (high activity) allele exceeded recommendations for gestational weight gain compared with 48% (32 of 60) of those with the pooled 3/3, 3/4, and 3/3.5 (low activity) alleles (P < 0.05). Similarly, those with the MAO-A 4/4 allele had significantly greater gestational weight gain than those with the 3/3, 3/4, or 3/3.5 pooled genotypes (19.3 ± 4.1 versus 17.0 ± 5.0 kg, P = 0.03). Conclusion: Carriers of the 4/4 variants of the MAO-A gene may be at increased risk for excessive gestational weight gain.
Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor
(2012) Liu, Yubing; Nandi, Soumyadeep; Martel, André; Antoun, Alen; Ioshikhes, Ilya; Blais, Alexandre
The Six1 transcription factor is a homeodomain protein involved in controlling gene expression during embryonic development. Six1 establishes gene expression profiles that enable skeletal myogenesis and nephrogenesis, among others. While several homeodomain factors have been extensively characterized with regards to their DNA-binding properties, relatively little is known of the properties of Six1. We have used the genomic binding profile of Six1 during the myogenic differentiation of myoblasts to obtain a better understanding of its preferences for recognizing certain DNA sequences. DNA sequence analyses on our genomic binding dataset, combined with biochemical characterization using binding assays, reveal that Six1 has a much broader DNA-binding sequence spectrum than had been previously determined. Moreover, using a position weight matrix optimization algorithm, we generated a highly sensitive and specific matrix that can be used to predict novel Six1-binding sites with highest accuracy. Furthermore, our results support the idea of a mode of DNA recognition by this factor where Six1 itself is sufficient for sequence discrimination, and where Six1 domains outside of its homeodomain contribute to binding site selection. Together, our results provide new light on the properties of this important transcription factor, and will enable more accurate modeling of Six1 function in bioinformatic studies.
Respiratory infection of mice with mammalian reoviruses causes systemic infection with age and strain dependent pneumonia and encephalitis
(2013-05-29) Gauvin, Lianne; Bennett, Steffany A.L.; Liu, Hong; Hakimi, Mansoureh; Schlossmacher, Michael; Majithia, Jay; Brown, Earl G
Background Because mammalian reoviruses are isolated from the respiratory tract we modeled the natural history of respiratory infection of adult and suckling mice with T1 Lang (T1L) and T3 Dearing (T3D) reoviruses. Methods Adult and suckling Balb/c mice were infected by the intranasal route and were assessed for dose response of disease as well as viral replication in the lung and other organs. Viral antigen was assessed by immunofluorescence and HRP staining of tissue sections and histopathology was assessed on formalin fixed, H + E stained tissue sections. Results Intranasal infection of adult mice resulted in fatal respiratory distress for high doses (107 pfu) of T1L but not T3D. In contrast both T1L and T3D killed suckling mice at moderate viral dosages (105 pfu) but differed in clinical symptoms where T1L induced respiratory failure and T3D caused encephalitis. Infections caused transient viremia that resulted in spread to peripheral tissues where disease correlated with virus replication, and pathology. Immunofluorescent staining of viral antigens in the lung showed reovirus infection was primarily associated with alveoli with lesser involvement of bronchiolar epithelium. Immunofluorescent and HRP staining of viral antigens in brain showed infection of neurons by T3D and glial cells by T1L. Conclusions These mouse models of reovirus respiratory infection demonstrated age and strain dependent disease that are expected to be relevant to understanding and modulating natural and therapeutic reovirus infections in humans.
Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass
(2013-04-22) Blanchard, Alexandre P.; McDowell, Graeme S. V.; Valenzuela, Nico; Xu, Hongbin; Gelbard, Sarah; Bertrand, Martin; Slater, Gary W.; Figeys, Daniel; Fai, Stephen; Bennett, Steffany A.L.
Motivation: Establishing phospholipid identities in large lipidomic datasets is a labour-intensive process. Where genomics and proteomics capitalize on sequence-based signatures, glycerophospholipids lack easily definable molecular fingerprints. Carbon chain length, degree of unsaturation, linkage, and polar head group identity must be calculated from mass to charge (m/z) ratios under defined mass spectrometry (MS) conditions. Given increasing MS sensitivity, many m/z values are not represented in existing prediction engines. To address this need, Visualization and Phospholipid Identification is a web-based application that returns all theoretically possible phospholipids for any m/z value and MS condition. Visualization algorithms produce multiple chemical structure files for each species. Curated lipids detected by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics are provided as high-resolution structures. Availability: VaLID is available through the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics resources web site at https://www.med.uottawa.ca/lipidomics/ resources.html. Contacts: lipawrd@uottawa.ca Supplementary Information: Supplementary data are available at Bioinformatics online.

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