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Goetzinger F, Hohl M, Lauder L, Millenaar D, Reichrath J, Meyer MR, Boehm M, Ukena C, Mahfoud F. Hydrochlorothiazide does not lead to phototoxic reactions and DNA damage in healthy volunteers the HCTox study. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Purpose
Hypertension represents the most common cardiovascular risk factor for premature death worldwide. Hydrochlorothiazide (HCTZ) is one of the most commonly used antihypertensive and diuretic drug worldwide. Recently, pharmacoepidemiologic studies associated the use of HCTZ with increased risk of skin cancer. As a result, prescriptions of HCTZ decreased, leading to worsening of blood pressure therapy in a significant proportion of patients. However, whether HCTZ causes skin cancer remains elusive. We aimed to examine the photosensitive potential of HCTZ in vivo. To further enlighten the pathophysiologic mechanisms of carcinogenesis and phototoxicity caused by HCTZ in vitro, we conducted a series of laboratory experiments.
Methods
This randomized, double-blinded, placebo-controlled clinical trial assessed the phototoxic properties of HCTZ. We randomly assigned 30 healthy adult volunteers in a 2:1 ratio to either HCTZ 25 mg daily or placebo once daily for 15 days. Skin photosensitivity by phototesting for UV-A and UV-B radiation, office blood pressure, serum-vitamin-D status and urinary excretion of thymidine-dimers were measured. To further assess the pathophysiologic mechanisms of possibly HCTZ induced photosensitivity, human keratinocytes (HaCaT) were incubated with HCTZ and then irradiated with UV-B radiation (311 nm one burst of 100 J/cm2). rt-PCR-testing and western blots were performed to analyze reactive oxygen species, inflammation and carcinogenesis.
Results
All 30 participants were adherent to the protocol, as confirmed by toxicological analysis of serum and urine. Skin photosensitivity to exposure of UV-A and UV-B radiation remained unchanged in both groups (UVB-MED: HCTZ Δ = 0.0 J/cm2 vs. placebo Δ = −0.2 J/cm2; p=0.06). No thymidine-dimers were detected in urine of either group. Systolic blood pressure decreased in both groups but was not different between HCTZ and placebo (HCTZ Δ = −5.2 mmHg vs. placebo Δ = −5.4 mmHg; p=0.94). The same was found for diastolic blood pressure (HCTZ Δ = −1.9 mmHg vs. placebo Δ = −4.3 mmHg; p=0.34). Serum-vitamin-D increased in both groups (HCTZ Δ = +2.7 ng/ml vs. placebo Δ = 0.9 ng/ml; p=0.56). In addition, combination of HCTZ and a high intensity burst of UV-B radiation did not increase expression of inflammatory proteins or increase formation of reactive oxygen species (SOD-1, SOD-2, and catalase).
Conclusions
HCTZ did not significantly increase photosensitivity for UV-A or UV-B radiation in healthy volunteers compared with placebo. Moreover, no relevant DNA-damages were detected in either group. HCTZ alone did not increase inflammation, formation of reactive oxygen species or carcinogenesis in human keratinocytes. Furthermore, the combination of a UV-B burst of 100 J/cm2 and HCTZ was not associated with additive effects on inflammation, reactive oxygen species or carcinogenisis.
HCTZ in a cumulative dose of 375 did not increase photosensitivity or DNA-damages in vivo.
Funding Acknowledgement
Type of funding sources: None.
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Janson M, Gratton R, Rodet L, Vigan A, Bonnefoy M, Delorme P, Mamajek EE, Reffert S, Stock L, Marleau GD, Langlois M, Chauvin G, Desidera S, Ringqvist S, Mayer L, Viswanath G, Squicciarini V, Meyer MR, Samland M, Petrus S, Helled R, Kenworthy MA, Quanz SP, Biller B, Henning T, Mesa D, Engler N, Carson JC. A wide-orbit giant planet in the high-mass b Centauri binary system. Nature 2021; 600:231-234. [PMID: 34880428 DOI: 10.1038/s41586-021-04124-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022]
Abstract
Planet formation occurs around a wide range of stellar masses and stellar system architectures1. An improved understanding of the formation process can be achieved by studying it across the full parameter space, particularly towards the extremes. Earlier studies of planets in close-in orbits around high-mass stars have revealed an increase in giant planet frequency with increasing stellar mass2 until a turnover point at 1.9 solar masses (M⊙), above which the frequency rapidly decreases3. This could potentially imply that planet formation is impeded around more massive stars, and that giant planets around stars exceeding 3 M⊙ may be rare or non-existent. However, the methods used to detect planets in small orbits are insensitive to planets in wide orbits. Here we demonstrate the existence of a planet at 560 times the Sun-Earth distance from the 6- to 10-M⊙ binary b Centauri through direct imaging. The planet-to-star mass ratio of 0.10-0.17% is similar to the Jupiter-Sun ratio, but the separation of the detected planet is about 100 times wider than that of Jupiter. Our results show that planets can reside in much more massive stellar systems than what would be expected from extrapolation of previous results. The planet is unlikely to have formed in situ through the conventional core accretion mechanism4, but might have formed elsewhere and arrived to its present location through dynamical interactions, or might have formed via gravitational instability.
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Williams JR, Meyer MR, Ricard JA, Sen R, Young CC, Feroze AH, Greil ME, Barros G, Durfy S, Hanak B, Morton RP, Temkin NR, Barber JK, Mac Donald CL, Chesnut RM. Re-examining decompressive craniectomy medial margin distance from midline as a metric for calculating the risk of post-traumatic hydrocephalus. J Clin Neurosci 2021; 87:125-131. [PMID: 33863519 DOI: 10.1016/j.jocn.2021.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/14/2020] [Accepted: 02/25/2021] [Indexed: 10/21/2022]
Abstract
Decompressive craniectomy (DC) is a life-saving procedure in severe traumatic brain injury, but is associated with higher rates of post-traumatic hydrocephalus (PTH). The relationship between the medial craniectomy margin's proximity to midline and frequency of developing PTH is controversial. The primary study objective was to determine whether average medial craniectomy margin distance from midline was closer to midline in patients who developed PTH after DC for severe TBI compared to patients that did not. The secondary objective was to determine if a threshold distance from midline could be identified, at which the risk of developing PTH increased if the DC was performed closer to midline than this threshold. A retrospective review was performed of 380 patients undergoing DC at a single institution between March 2004 and November 2014. Clinical, operative and demographic variables were collected, including age, sex, DC parameters and occurrence of PTH. Statistical analysis compared mean axial craniectomy margin distance from midline in patients with versus without PTH. Distances from midline were tested as potential thresholds. No significant difference was identified in mean axial craniectomy margin distance from midline in patients developing PTH compared with patients with no PTH (n = 24, 12.8 mm versus n = 356, 16.6 mm respectively, p = 0.086). No significant cutoff distance from midline was identified (n = 212, p = 0.201). This study, the largest to date, was unable to identify a threshold with sufficient discrimination to support clinical recommendations in terms of DC margins with regard to midline, including thresholds reportedly significant in previously published research.
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Stolla M, Zhang F, Meyer MR, Zhang J, Dong JF. Current state of transfusion in traumatic brain injury and associated coagulopathy. Transfusion 2019; 59:1522-1528. [PMID: 30980753 DOI: 10.1111/trf.15169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/10/2018] [Accepted: 11/17/2018] [Indexed: 12/15/2022]
Abstract
Traumatic brain injury (TBI)-induced coagulopathy has long been recognized as a significant risk for poor outcomes in patients with TBI, but its pathogenesis remains poorly understood. As a result, current treatment options for the condition are limited and ineffective. The lack of information is most significant for the impact of blood transfusions on patients with isolated TBI and in the absence of confounding influences from trauma to the body and limbs and the resultant hemorrhagic shock. Here we discuss recent progress in understanding the pathogenesis of TBI-induced coagulopathy and the current state of blood transfusions for patients with TBI and associated coagulopathy.
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Meyer MR, Kurz DJ, Radovanovic D, Pedrazzini G, Roffi M, Rosemann T, Eberli FR. P5564Differences in presentation and clinical outcomes between patients with acute myocardial infarction and right or left bundle branch block. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy566.p5564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Blank A, Eidam A, Haag M, Hohmann N, Burhenne J, Schwab M, van de Graaf SFJ, Meyer MR, Maurer HH, Meier K, Weiss J, Bruckner T, Alexandrov A, Urban S, Mikus G, Haefeli WE. The NTCP-inhibitor Myrcludex B: Effects on Bile Acid Disposition and Tenofovir Pharmacokinetics. Clin Pharmacol Ther 2017; 103:341-348. [DOI: 10.1002/cpt.744] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/10/2017] [Accepted: 05/13/2017] [Indexed: 12/26/2022]
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Meyer MR, Barton M. Estrogens and Coronary Artery Disease: New Clinical Perspectives. ADVANCES IN PHARMACOLOGY 2016; 77:307-60. [PMID: 27451102 DOI: 10.1016/bs.apha.2016.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In premenopausal women, endogenous estrogens are associated with reduced prevalence of arterial hypertension, coronary artery disease, myocardial infarction, and stroke. Clinical trials conducted in the 1990s such as HERS, WHI, and WISDOM have shown that postmenopausal treatment with horse hormone mixtures (so-called conjugated equine estrogens) and synthetic progestins adversely affects female cardiovascular health. Our understanding of rapid (nongenomic) and chronic (genomic) estrogen signaling has since advanced considerably, including identification of a new G protein-coupled estrogen receptor (GPER), which like the "classical" receptors ERα and ERβ is highly abundant in the cardiovascular system. Here, we discuss the role of estrogen receptors in the pathogenesis of coronary artery disease and review natural and synthetic ligands of estrogen receptors as well as their effects in physiology, on cardiovascular risk factors, and atherosclerotic vascular disease. Data from preclinical and clinical studies using nonselective compounds activating GPER, which include selective estrogen receptor modulators such as tamoxifen or raloxifene, selective estrogen receptor downregulators such as Faslodex™ (fulvestrant/ICI 182,780), vitamin B3 (niacin), green tea catechins, and soy flavonoids such as genistein or resveratrol, strongly suggest that activation of GPER may afford therapeutic benefit for primary and secondary prevention in patients with or at risk for coronary artery disease. Evidence from preclinical studies suggest similar efficacy profiles for selective small molecule GPER agonists such as G-1 which are devoid of uterotrophic activity. Further clinical research in this area is warranted to provide opportunities for future cardiovascular drug development.
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Boccaletti A, Thalmann C, Lagrange AM, Janson M, Augereau JC, Schneider G, Milli J, Grady C, Debes J, Langlois M, Mouillet D, Henning T, Dominik C, Maire AL, Beuzit JL, Carson J, Dohlen K, Engler N, Feldt M, Fusco T, Ginski C, Girard JH, Hines D, Kasper M, Mawet D, Ménard F, Meyer MR, Moutou C, Olofsson J, Rodigas T, Sauvage JF, Schlieder J, Schmid HM, Turatto M, Udry S, Vakili F, Vigan A, Wahhaj Z, Wisniewski J. Fast-moving features in the debris disk around AU Microscopii. Nature 2016; 526:230-2. [PMID: 26450055 DOI: 10.1038/nature15705] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 08/28/2015] [Indexed: 11/09/2022]
Abstract
In the 1980s, excess infrared emission was discovered around main-sequence stars; subsequent direct-imaging observations revealed orbiting disks of cold dust to be the source. These 'debris disks' were thought to be by-products of planet formation because they often exhibited morphological and brightness asymmetries that may result from gravitational perturbation by planets. This was proved to be true for the β Pictoris system, in which the known planet generates an observable warp in the disk. The nearby, young, unusually active late-type star AU Microscopii hosts a well-studied edge-on debris disk; earlier observations in the visible and near-infrared found asymmetric localized structures in the form of intensity variations along the midplane of the disk beyond a distance of 20 astronomical units. Here we report high-contrast imaging that reveals a series of five large-scale features in the southeast side of the disk, at projected separations of 10-60 astronomical units, persisting over intervals of 1-4 years. All these features appear to move away from the star at projected speeds of 4-10 kilometres per second, suggesting highly eccentric or unbound trajectories if they are associated with physical entities. The origin, localization, morphology and rapid evolution of these features are difficult to reconcile with current theories.
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Quanz SP, Amara A, Meyer MR, Girard JH, Kenworthy MA, Kasper M. CONFIRMATION AND CHARACTERIZATION OF THE PROTOPLANET HD 100546 b—DIRECT EVIDENCE FOR GAS GIANT PLANET FORMATION AT 50 AU. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/0004-637x/807/1/64] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Reggiani M, Quanz SP, Meyer MR, Pueyo L, Absil O, Amara A, Anglada G, Avenhaus H, Girard JH, Gonzalez CC, Graham J, Mawet D, Meru F, Milli J, Osorio M, Wolff S, Torrelles JM. DISCOVERY OF A COMPANION CANDIDATE IN THE HD 169142 TRANSITION DISK AND THE POSSIBILITY OF MULTIPLE PLANET FORMATION. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/2041-8205/792/1/l23] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Meyer MR, Clegg DJ, Prossnitz ER, Barton M. Obesity, insulin resistance and diabetes: sex differences and role of oestrogen receptors. Acta Physiol (Oxf) 2011; 203:259-69. [PMID: 21281456 DOI: 10.1111/j.1748-1716.2010.02237.x] [Citation(s) in RCA: 231] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Obesity increases the risk of coronary artery disease through insulin resistance, diabetes, arterial hypertension and dyslipidemia. The prevalence of obesity has increased worldwide and is particularly high among middle-aged women and men. After menopause, women are at an increased risk to develop visceral obesity due to the loss of endogenous ovarian hormone production. Effects of oestrogens are classically mediated by the two nuclear oestrogen receptors (ERs) α and β. In addition, more recent research has shown that the intracellular transmembrane G-protein-coupled oestrogen receptor (GPER) originally designated as GPR30 also mediates some of the actions attributed to oestrogens. Oestrogen and its receptors are important regulators of body weight and insulin sensitivity not only in women but also in men as demonstrated by ER mutations in rodents and humans. This article reviews the role of sex hormones and ERs in the context of obesity, insulin sensitivity and diabetes as well as the related clinical issues in women and men.
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Garshnek V, Burgess L, Peters DB, Aschwanden C, Horne D, Burgess B, Clyde R, Meyer MR. Mass medication distribution for disease outbreak: comparison of personal digital assistant and paper-based decision support. INTERNATIONAL JOURNAL OF HEALTHCARE TECHNOLOGY AND MANAGEMENT 2009. [DOI: 10.1504/ijhtm.2009.030448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Meyer MR, Rüegger-Frey B, Nikolic N, Bopp-Kistler I. [Severe behavioral disorder caused by an organic disease]. PRAXIS 2008; 97:1137-1141. [PMID: 18951354 DOI: 10.1024/1661-8157.97.21.1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A 65-year-old architect was admitted to our Memory Clinic because of rapidly progressive dementia accompanied by behavioral disorders, which severely restricted his functional independence. The physical examination revealed several focal neurological signs, and neuroimaging confirmed a cerebellar hemorrhage, multiple microbleeds and an ischemic lacunar infarct. Executive functioning was highly impaired. This case report illustrates cerebral amyloid angiopathy as an important entity of vascular dementia and highlights the importance of neuroimaging in patients with suspected vascular cognitive disorders.
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Morris MD, Meyer MR, Painchaud G, Marlowe J, Tokiwa GY, Fare TL. Improved high-throughput ultrafiltration process enables cRNA purification for gene expression profiling. Assay Drug Dev Technol 2008; 6:421-32. [PMID: 18532901 DOI: 10.1089/adt.2007.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ultrafiltration of nucleic acids has been used for a wide variety of applications, including sequence reaction purification and amplicon cleanup prior to spotting onto microarrays. Here we describe a novel process, using ultrafiltration, that purifies cRNA products for sensitive downstream applications. Initial attempts at this high-throughput purification for cRNA resulted in low sensitivity when compared against an industry standard (silica-based bind, wash, and elute purification). We modified the ultrafiltration process to include a proteinase K preincubation and a phosphate buffer wash that, when combined, increased sensitivity and signal-to-noise ratio in microarray applications. The protocol that we have developed eliminates the use of chaotropic salts (such as guanidinium thiocyanate) that are typically used in silica binding purification methods. The data demonstrate good performance for sensitive RNA applications using well-defined metrics, and thus the technique might be useful for a broader range of nucleic acid purifications.
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Fare TL, Coffey EM, Dai H, He YD, Kessler DA, Kilian KA, Koch JE, LeProust E, Marton MJ, Meyer MR, Stoughton RB, Tokiwa GY, Wang Y. Effects of atmospheric ozone on microarray data quality. Anal Chem 2004; 75:4672-5. [PMID: 14632079 DOI: 10.1021/ac034241b] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A data anomaly was observed that affected the uniformity and reproducibility of fluorescent signal across DNA microarrays. Results from experimental sets designed to identify potential causes (from microarray production to array scanning) indicated that the anomaly was linked to a batch process; further work allowed us to localize the effect to the posthybridization array stringency washes. Ozone levels were monitored and highly correlated with the batch effect. Controlled exposures of microarrays to ozone confirmed this factor as the root cause, and we present data that show susceptibility of a class of cyanine dyes (e.g., Cy5, Alexa 647) to ozone levels as low as 5-10 ppb for periods as short as 10-30 s. Other cyanine dyes (e.g., Cy3, Alexa 555) were not significantly affected until higher ozone levels (> 100 ppb). To address this environmental effect, laboratory ozone levels should be kept below 2 ppb (e.g., with filters in HVAC) to achieve high quality microarray data.
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Castle J, Garrett-Engele P, Armour CD, Duenwald SJ, Loerch PM, Meyer MR, Schadt EE, Stoughton R, Parrish ML, Shoemaker DD, Johnson JM. Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol 2003; 4:R66. [PMID: 14519201 PMCID: PMC328455 DOI: 10.1186/gb-2003-4-10-r66] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2003] [Revised: 07/25/2003] [Accepted: 08/15/2003] [Indexed: 11/26/2022] Open
Abstract
A novel, unbiased amplification protocol has been developed that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.
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Bangur CS, Switzer A, Fan L, Marton MJ, Meyer MR, Wang T. Identification of genes over-expressed in small cell lung carcinoma using suppression subtractive hybridization and cDNA microarray expression analysis. Oncogene 2002; 21:3814-25. [PMID: 12032850 DOI: 10.1038/sj.onc.1205480] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2002] [Revised: 03/06/2002] [Accepted: 03/18/2002] [Indexed: 01/12/2023]
Abstract
To identify genes that are differentially over-expressed in Small Cell Lung Carcinoma (SCLC) we have used a combination of suppression subtractive hybridization and cDNA microarray to analyse the expression profiles of 2400 cDNAs clones. Genes that are over-expressed in SCLC were identified using 32 pairs of fluorescence-labeled cDNA samples representing various lung tumors and normal tissues. This comprehensive approach has resulted in the identification of 209 genes that are differentially over-expressed in SCLC. Quantitative real-time PCR was used to further validate the expression of 43 genes in SCLC tumors and various normal tissues. Discussed in this report are nine genes, which showed the most promising SCLC tumor to normal tissue differential expression profiles, including seven known and two novel genes. The large number of differentially expressed genes identified from this analysis and the characterization of these genes will provide valuable information in better understanding the biology of SCLC and help us in developing these gene products as potential targets for diagnostic as well as therapeutic usage.
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Natarajan K, Meyer MR, Jackson BM, Slade D, Roberts C, Hinnebusch AG, Marton MJ. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol Cell Biol 2001; 21:4347-4368. [PMID: 11390663 DOI: 10.1128/mcb.21.13.4347-4368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
Starvation for amino acids induces Gcn4p, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. In an effort to identify all genes regulated by Gcn4p during amino acid starvation, we performed cDNA microarray analysis. Data from 21 pairs of hybridization experiments using two different strains derived from S288c revealed that more than 1,000 genes were induced, and a similar number were repressed, by a factor of 2 or more in response to histidine starvation imposed by 3-aminotriazole (3AT). Profiling of a gcn4Delta strain and a constitutively induced mutant showed that Gcn4p is required for the full induction by 3AT of at least 539 genes, termed Gcn4p targets. Genes in every amino acid biosynthetic pathway except cysteine and genes encoding amino acid precursors, vitamin biosynthetic enzymes, peroxisomal components, mitochondrial carrier proteins, and autophagy proteins were all identified as Gcn4p targets. Unexpectedly, genes involved in amino acid biosynthesis represent only a quarter of the Gcn4p target genes. Gcn4p also activates genes involved in glycogen homeostasis, and mutant analysis showed that Gcn4p suppresses glycogen levels in amino acid-starved cells. Numerous genes encoding protein kinases and transcription factors were identified as targets, suggesting that Gcn4p is a master regulator of gene expression. Interestingly, expression profiles for 3AT and the alkylating agent methyl methanesulfonate (MMS) overlapped extensively, and MMS induced GCN4 translation. Thus, the broad transcriptional response evoked by Gcn4p is produced by diverse stress conditions. Finally, profiling of a gcn4Delta mutant uncovered an alternative induction pathway operating at many Gcn4p target genes in histidine-starved cells.
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Natarajan K, Meyer MR, Jackson BM, Slade D, Roberts C, Hinnebusch AG, Marton MJ. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol Cell Biol 2001; 21:4347-68. [PMID: 11390663 PMCID: PMC87095 DOI: 10.1128/mcb.21.13.4347-4368.2001] [Citation(s) in RCA: 559] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2001] [Accepted: 04/03/2001] [Indexed: 11/20/2022] Open
Abstract
Starvation for amino acids induces Gcn4p, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. In an effort to identify all genes regulated by Gcn4p during amino acid starvation, we performed cDNA microarray analysis. Data from 21 pairs of hybridization experiments using two different strains derived from S288c revealed that more than 1,000 genes were induced, and a similar number were repressed, by a factor of 2 or more in response to histidine starvation imposed by 3-aminotriazole (3AT). Profiling of a gcn4Delta strain and a constitutively induced mutant showed that Gcn4p is required for the full induction by 3AT of at least 539 genes, termed Gcn4p targets. Genes in every amino acid biosynthetic pathway except cysteine and genes encoding amino acid precursors, vitamin biosynthetic enzymes, peroxisomal components, mitochondrial carrier proteins, and autophagy proteins were all identified as Gcn4p targets. Unexpectedly, genes involved in amino acid biosynthesis represent only a quarter of the Gcn4p target genes. Gcn4p also activates genes involved in glycogen homeostasis, and mutant analysis showed that Gcn4p suppresses glycogen levels in amino acid-starved cells. Numerous genes encoding protein kinases and transcription factors were identified as targets, suggesting that Gcn4p is a master regulator of gene expression. Interestingly, expression profiles for 3AT and the alkylating agent methyl methanesulfonate (MMS) overlapped extensively, and MMS induced GCN4 translation. Thus, the broad transcriptional response evoked by Gcn4p is produced by diverse stress conditions. Finally, profiling of a gcn4Delta mutant uncovered an alternative induction pathway operating at many Gcn4p target genes in histidine-starved cells.
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Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 2001; 19:342-7. [PMID: 11283592 DOI: 10.1038/86730] [Citation(s) in RCA: 836] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.
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Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G, Wu LF, Altschuler SJ, Edwards S, King J, Tsang JS, Schimmack G, Schelter JM, Koch J, Ziman M, Marton MJ, Li B, Cundiff P, Ward T, Castle J, Krolewski M, Meyer MR, Mao M, Burchard J, Kidd MJ, Dai H, Phillips JW, Linsley PS, Stoughton R, Scherer S, Boguski MS. Experimental annotation of the human genome using microarray technology. Nature 2001; 409:922-7. [PMID: 11237012 DOI: 10.1038/35057141] [Citation(s) in RCA: 276] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.
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Jordan PM, Meyer MR, Puri A. Causal implications of viscous damping in compressible fluid flows. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 2000; 62:7918-7926. [PMID: 11138075 DOI: 10.1103/physreve.62.7918] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/1999] [Revised: 04/25/2000] [Indexed: 05/23/2023]
Abstract
Classically, a compressible, isothermal, viscous fluid is regarded as a mathematical continuum and its motion is governed by the linearized continuity, Navier-Stokes, and state equations. Unfortunately, solutions of this system are of a diffusive nature and hence do not satisfy causality. However, in the case of a half-space of fluid set to motion by a harmonically vibrating plate the classical equation of motion can, under suitable conditions, be approximated by the damped wave equation. Since this equation is hyperbolic, the resulting solutions satisfy causal requirements. In this work the Laplace transform and other analytical and numerical tools are used to investigate this apparent contradiction. To this end the exact solutions, as well as their special and limiting cases, are found and compared for the two models. The effects of the physical parameters on the solutions and associated quantities are also studied. It is shown that propagating wave fronts are only possible under the hyperbolic model and that the concept of phase speed has different meanings in the two formulations. In addition, discontinuities and shock waves are noted and a physical system is modeled under both formulations. Overall, it is shown that the hyperbolic form gives a more realistic description of the physical problem than does the classical theory. Lastly, a simple mechanical analog is given and connections to viscoelastic fluids are noted. In particular, the research presented here supports the notion that linear compressible, isothermal, viscous fluids can, at least in terms of causality, be better characterized as a type of viscoelastic fluid.
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Meyer MR, Angele A, Kremmer E, Kaupp UB, Muller F. A cGMP-signaling pathway in a subset of olfactory sensory neurons. Proc Natl Acad Sci U S A 2000; 97:10595-600. [PMID: 10984544 PMCID: PMC27070 DOI: 10.1073/pnas.97.19.10595] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2000] [Indexed: 11/18/2022] Open
Abstract
It is well established that signal transduction in sensory neurons of the rat olfactory epithelium involves a cAMP-signaling pathway. However, a small number of olfactory neurons specifically express cGMP-signaling components, namely a guanylyl cyclase (GC-D) and a cGMP-stimulated phosphodiesterase (PDE2). Here, we show that this subset of olfactory neurons expressing GC-D and PDE2 does also express the subunit of a cGMP-selective cyclic nucleotide-gated (CNG) channel that has been previously identified in cone photoreceptors. Further, components of the prototypical cAMP-signaling pathway could not be detected in this subpopulation of cells. These results imply that these neurons use an alternative signaling pathway, with cGMP as the intracellular messenger, and that, in these cells, the receptor current is initiated by the opening of cGMP-gated channels.
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Langsetmo I, Meyer MR, Erickson HH. Relationship of pulmonary arterial pressure to pulmonary haemorrhage in exercising horses. Equine Vet J 2000; 32:379-84. [PMID: 11037258 DOI: 10.2746/042516400777591066] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Exercise-induced pulmonary haemorrhage (EIPH) is characterised by blood in the airways after strenuous exercise and results from stress failure of the pulmonary capillaries. The purpose of this experiment was to establish a threshold value of transmural pulmonary arterial pressure at which haemorrhage occurs in the exercising horse. Five geldings, age 4-14 years, were run in random order once every 2 weeks at 1 of 4 speeds (9, 11, 13, 15 m/s); one day with no run was used as a control. Heart rate, pulmonary arterial pressure and oesophageal pressure were recorded for the duration of the run. Transmural pulmonary arterial pressure was estimated by electronic subtraction of the oesophageal pressure from the intravascular pulmonary arterial pressure. Within 1 h of the run, bronchoalveolar lavage was performed and the red and white blood cells in the fluid were quantified. Red cell counts in the lavage fluid from horses running at 9, 11 and 13 m/s were not significantly different from the control value, but after runs at 15 m/s, red cell counts were significantly (P<0.05) higher. White cell counts were not different from control values at any speed. Analysis of red cell count vs. transmural pulmonary arterial pressure indicated that haemorrhage occurs at approximately 95 mmHg. Red cell lysis in the lavage fluid was also apparent at transmural pulmonary arterial pressures above 90 mmHg. We conclude that, in the exercising horse, a pulmonary arterial pressure threshold exists above which haemorrhage occurs, and that pressure is often exceeded during high speed sprint exercise.
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Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH. Functional discovery via a compendium of expression profiles. Cell 2000; 102:109-26. [PMID: 10929718 DOI: 10.1016/s0092-8674(00)00015-5] [Citation(s) in RCA: 1638] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Ascertaining the impact of uncharacterized perturbations on the cell is a fundamental problem in biology. Here, we describe how a single assay can be used to monitor hundreds of different cellular functions simultaneously. We constructed a reference database or "compendium" of expression profiles corresponding to 300 diverse mutations and chemical treatments in S. cerevisiae, and we show that the cellular pathways affected can be determined by pattern matching, even among very subtle profiles. The utility of this approach is validated by examining profiles caused by deletions of uncharacterized genes: we identify and experimentally confirm that eight uncharacterized open reading frames encode proteins required for sterol metabolism, cell wall function, mitochondrial respiration, or protein synthesis. We also show that the compendium can be used to characterize pharmacological perturbations by identifying a novel target of the commonly used drug dyclonine.
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