76
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Hou Y, Tianero MDB, Kwan JC, Wyche TP, Michel CR, Ellis GA, Vazquez-Rivera E, Braun DR, Rose WE, Schmidt EW, Bugni TS. Structure and biosynthesis of the antibiotic bottromycin D. Org Lett 2012; 14:5050-3. [PMID: 22984777 PMCID: PMC3466018 DOI: 10.1021/ol3022758] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drug resistant infectious diseases are quickly becoming a global health crisis. While Streptomyces spp. have been a major source of antibiotics over the past 50 years, efficient methods are needed to identify new antibiotics and greatly improve the rate of discovery. LCMS-based metabolomics were applied to analyze extracts of 50 Streptomyes spp. Using this methodology, we discovered bottromycin D and used whole genome sequencing to determine its biosynthesis by a ribosomal pathway.
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77
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Abstract
Complex biosynthetic enzymes such as polyketide synthases make mistakes. In this issue of Chemistry & Biology, Jensen et al. report that a discrete family of acyltransferases is responsible for error correction, hydrolyzing key biosynthetic intermediates from a multi-enzyme complex. This activity might find use in understanding polyketide biosynthesis, particularly in uncultivated organisms and in tailoring the synthesis of small molecules.
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78
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Antczak J, Horn B, Richter A, Bodenschatz R, Latuszynski K, Schmidt EW, Jernajczyk W. The differences in sleep profile changes under continuous positive airway pressure (CPAP) therapy between non-obese, obese and severely obese sleep apnea patients. JOURNAL OF PHYSIOLOGY AND PHARMACOLOGY : AN OFFICIAL JOURNAL OF THE POLISH PHYSIOLOGICAL SOCIETY 2012; 63:263-269. [PMID: 22791640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 05/28/2012] [Indexed: 06/01/2023]
Abstract
Sleep disturbances in obstructive sleep apnea are caused mainly by repetitive apneas and hypopneas. An alternative factor contributing to disordered sleep may be the obesity, which is frequently associated with sleep apnea. The sleep disturbing effect of obesity was found previously in obese nonapneic subjects. The aim of this study was to evaluate the effect of obesity on sleep quality in sleep apnea patients in particular in patients under continuous positive airway pressure (CPAP) with successfully normalized respiration. We reviewed the archive data of 18 non-obese, 18 obese and 17 severely obese age and gender matched sleep apnea patients treated with CPAP. The polysomnographic parameters from the diagnostic night, from the second night under CPAP and from the follow up night (after three months of CPAP use) were compared. Before CPAP the apnea hypopnea index was worse in obese and in severely obese group and it normalised under CPAP in all groups. The severely obese group showed more light sleep and less REM sleep before CPAP and inversely - less light and more REM sleep in the second night under CPAP than the non-obese group. In the follow up, there was no differences in sleep profile between groups. This study indicates obesity does not affect the sleep independently of respiratory disorders. Before therapy it is associated with more severe sleep apnea and indirectly with worse sleep quality.
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79
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Lin Z, Flores M, Forteza I, Henriksen N, Concepcion GP, Rosenberg G, Haygood MG, Olivera BM, Light AR, Cheatham TE, Schmidt EW. Totopotensamides, polyketide-cyclic peptide hybrids from a mollusk-associated bacterium Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2012; 75:644-649. [PMID: 22439622 PMCID: PMC3338888 DOI: 10.1021/np200886x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two new compounds, the peptide-polyketide glycoside totopotensamide A (1) and its aglycone totopotensamide B (2), were isolated from a Streptomyces sp. cultivated from the gastropod mollusk Lienardia totopotens collected in the Philippines. The compounds contain a previously undescribed polyketide component, a novel 2,3-diaminobutyric acid-containing macrolactam, and a new amino acid, 4-chloro-5,7-dihydroxy-6-methylphenylglycine. The application of Marfey's method to phenylglycine derivatives was explored using quantum mechanical calculations and NMR.
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80
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Schmidt EW, Donia MS, McIntosh JA, Fricke WF, Ravel J. Origin and variation of tunicate secondary metabolites. JOURNAL OF NATURAL PRODUCTS 2012; 75:295-304. [PMID: 22233390 PMCID: PMC3288725 DOI: 10.1021/np200665k] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ascidians (tunicates) are rich sources of structurally elegant, pharmaceutically potent secondary metabolites and, more recently, potential biofuels. It has been demonstrated that some of these compounds are made by symbiotic bacteria and not by the animals themselves, and for a few other compounds evidence exists supporting a symbiotic origin. In didemnid ascidians, compounds are highly variable even in apparently identical animals. Recently, we have explained this variation at the genomic and metagenomic levels and have applied the basic scientific findings to drug discovery and development. This review discusses what is currently known about the origin and variation of symbiotically derived metabolites in ascidians, focusing on the family Didemnidae, where most research has occurred. Applications of our basic studies are also described.
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81
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Tianero MDB, Donia MS, Young TS, Schultz PG, Schmidt EW. Ribosomal route to small-molecule diversity. J Am Chem Soc 2011; 134:418-25. [PMID: 22107593 DOI: 10.1021/ja208278k] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cyanobactin ribosomal peptide (RP) natural product pathway was manipulated to incorporate multiple tandem mutations and non-proteinogenic amino acids, using eight heterologous components simultaneously expressed in Escherichia coli . These studies reveal the potential of RPs for the rational synthesis of complex, new small molecules over multiple-step biosynthetic pathways using simple genetic engineering.
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82
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Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW. Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proc Natl Acad Sci U S A 2011; 108:E1423-32. [PMID: 22123943 PMCID: PMC3251135 DOI: 10.1073/pnas.1111712108] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The relationship between tunicates and the uncultivated cyanobacterium Prochloron didemni has long provided a model symbiosis. P. didemni is required for survival of animals such as Lissoclinum patella and also makes secondary metabolites of pharmaceutical interest. Here, we present the metagenomes, chemistry, and microbiomes of four related L. patella tunicate samples from a wide geographical range of the tropical Pacific. The remarkably similar P. didemni genomes are the most complex so far assembled from uncultivated organisms. Although P. didemni has not been stably cultivated and comprises a single strain in each sample, a complete set of metabolic genes indicates that the bacteria are likely capable of reproducing outside the host. The sequences reveal notable peculiarities of the photosynthetic apparatus and explain the basis of nutrient exchange underlying the symbiosis. P. didemni likely profoundly influences the lipid composition of the animals by synthesizing sterols and an unusual lipid with biofuel potential. In addition, L. patella also harbors a great variety of other bacterial groups that contribute nutritional and secondary metabolic products to the symbiosis. These bacteria possess an enormous genetic potential to synthesize new secondary metabolites. For example, an antitumor candidate molecule, patellazole, is not encoded in the genome of Prochloron and was linked to other bacteria from the microbiome. This study unveils the complex L. patella microbiome and its impact on primary and secondary metabolism, revealing a remarkable versatility in creating and exchanging small molecules.
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83
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McIntosh JA, Donia MS, Nair SK, Schmidt EW. Enzymatic basis of ribosomal peptide prenylation in cyanobacteria. J Am Chem Soc 2011; 133:13698-705. [PMID: 21766822 DOI: 10.1021/ja205458h] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzymatic basis of ribosomal peptide natural product prenylation has not been reported. Here, we characterize a prenyltransferase, LynF, from the TruF enzyme family. LynF is the first characterized representative of the TruF protein family, which is responsible for both reverse- and forward-O-prenylation of tyrosine, serine, and threonine in cyclic peptides known as cyanobactins. We show that LynF reverse O-prenylates tyrosine in macrocyclic peptides. Based upon these results, we propose that the TruF family prenylates mature cyclic peptides, from which the leader sequence and other enzyme recognition elements have been excised. This differs from the common model of ribosomal peptide biosynthesis, in which a leader sequence is required to direct post-translational modifications. In addition, we find that reverse O-prenylated tyrosine derivatives undergo a facile Claisen rearrangement at 'physiological' temperature in aqueous buffers, leading to forward C-prenylated products. Although the Claisen rearrangement route to natural products has been chemically anticipated for at least 40 years, it has not been demonstrated as a route to prenylated natural products. Here, we show that the Claisen rearrangement drives phenolic C-prenylation in at least one case, suggesting that this route should be reconsidered as a mechanism for the biosynthesis of prenylated phenolic compounds.
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84
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Lin Z, Reilly CA, Antemano R, Hughen RW, Marett L, Concepcion GP, Haygood MG, Olivera BM, Light A, Schmidt EW. Nobilamides A-H, long-acting transient receptor potential vanilloid-1 (TRPV1) antagonists from mollusk-associated bacteria. J Med Chem 2011; 54:3746-55. [PMID: 21524089 DOI: 10.1021/jm101621u] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
New compounds nobilamides A-H and related known compounds A-3302-A and A-3302-B were isolated based upon their suppression of capsaicin-induced calcium uptake in a mouse dorsal root ganglion primary cell culture assay. Two of these compounds, nobilamide B and A-3302-A, were shown to be long-acting antagonists of mouse and human TRPV1 channels, abolishing activity for >1 h after removal of drug presumably via a covalent attachment. Other derivatives also inhibited the TRPV1 channel, albeit with low potency, affording a structure-activity profile to support the proposed mechanism of action. While the activities were modest, we propose a new mechanism of action and a new site of binding for these inhibitors that may spur development of related analogues for treatment of pain.
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85
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Donia MS, Ruffner DE, Cao S, Schmidt EW. Accessing the hidden majority of marine natural products through metagenomics. Chembiochem 2011; 12:1230-6. [PMID: 21542088 DOI: 10.1002/cbic.201000780] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Indexed: 12/15/2022]
Abstract
Tiny marine animals represent an untapped reservoir for undiscovered, bioactive natural products. However, their small size and extreme chemical variability preclude traditional chemical approaches to discovering new bioactive compounds. Here, we use a metagenomic method to directly discover and rapidly access cyanobactin class natural products from these variable samples, and provide proof-of-concept for genome-based discovery and supply of marine natural products. We also address practical optimization of complex, multistep ribosomal peptide pathways in heterologous hosts, which is still very challenging. The resulting methods and concepts will be applicable to ribosomal peptide and other biosynthetic pathways.
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86
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Donia MS, Fricke WF, Ravel J, Schmidt EW. Variation in tropical reef symbiont metagenomes defined by secondary metabolism. PLoS One 2011; 6:e17897. [PMID: 21445351 PMCID: PMC3062557 DOI: 10.1371/journal.pone.0017897] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 02/14/2011] [Indexed: 11/19/2022] Open
Abstract
The complex evolution of secondary metabolism is important in biology, drug development, and synthetic biology. To examine this problem at a fine scale, we compared the genomes and chemistry of 24 strains of uncultivated cyanobacteria, Prochloron didemni, that live symbiotically with tropical ascidians and that produce natural products isolated from the animals. Although several animal species were obtained along a >5500 km transect of the Pacific Ocean, P. didemni strains are >97% identical across much of their genomes, with only a few exceptions concentrated in secondary metabolism. Secondary metabolic gene clusters were sporadically present or absent in identical genomic locations with no consistent pattern of co-occurrence. Discrete mutations were observed, leading to new chemicals that we isolated from animals. Functional cassettes encoding diverse chemicals are exchanged among a single population of symbiotic P. didemni that spans the tropical Pacific, providing the host animals with a varying arsenal of secondary metabolites.
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87
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McIntosh JA, Robertson CR, Agarwal V, Nair SK, Bulaj GW, Schmidt EW. Circular logic: nonribosomal peptide-like macrocyclization with a ribosomal peptide catalyst. J Am Chem Soc 2011; 132:15499-501. [PMID: 20961047 DOI: 10.1021/ja1067806] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A protease from ribosomal peptide biosynthesis macrocyclizes diverse substrates, including those resembling nonribosomal peptide and hybrid polyketide-peptide products. The proposed mechanism is analogous to thioesterase-catalyzed chemistry, but the substrates are amide bonds rather than thioesters.
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88
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89
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Schmidt EW, Donia MS. Life in cellulose houses: symbiotic bacterial biosynthesis of ascidian drugs and drug leads. Curr Opin Biotechnol 2010; 21:827-33. [PMID: 21050742 PMCID: PMC2992989 DOI: 10.1016/j.copbio.2010.10.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 10/11/2010] [Accepted: 10/12/2010] [Indexed: 11/20/2022]
Abstract
Ascidians (tunicates; sea squirts) are sources of diverse, bioactive natural products, one of which is an approved drug and many of which are potent drug leads. It has been shown that symbiotic bacteria living with ascidians produce some of the bioactive compounds isolated from whole animals, and indirect evidence strongly implicates symbiotic bacteria in the synthesis of many others. However, for the majority the producing organism has not been identified. In cases where a symbiotic origin has been definitively assigned, the resulting data lead to improved paths to drug discovery and development from marine animals. This review traces evidence for symbiotic production where such evidence exists and describes the strengths and limitations of that evidence.
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90
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Lin Z, Antemano RR, Hughen RW, Tianero MDB, Peraud O, Haygood MG, Concepcion GP, Olivera BM, Light A, Schmidt EW. Pulicatins A-E, neuroactive thiazoline metabolites from cone snail-associated bacteria. JOURNAL OF NATURAL PRODUCTS 2010; 73:1922-6. [PMID: 21028889 PMCID: PMC2993768 DOI: 10.1021/np100588c] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The cone snail Conus pulicarius from the Philippines provides a specific habitat for actinomycetes and other bacteria. A phenotypic screen using primary cultures of mouse dorsal root ganglion neurons revealed that one C. pulicarius associate, Streptomyces sp. CP32, produces a series of natural products that enhance or diminish whole-cell Ca(2+) flux. These compounds include known thiazoline compounds and a series of new derivatives, pulicatins A-E (6-10). Individual compounds were shown to bind to a series of human receptors, with selective binding to the human serotonin 5-HT(2B) receptor. Here, we report the structure elucidation of the new compounds and results of the neurological assays.
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91
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Pechmann A, Schmidt EW. Einsatz des COPD Assessment Test im stationären Bereich. Pneumologie 2010. [DOI: 10.1055/s-2010-1268893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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92
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McIntosh JA, Schmidt EW. Marine molecular machines: heterocyclization in cyanobactin biosynthesis. Chembiochem 2010; 11:1413-21. [PMID: 20540059 DOI: 10.1002/cbic.201000196] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Natural products that contain amino-acid-derived (Cys, Ser, Thr) heterocycles are ubiquitous in nature, yet key aspects of their biosynthesis remain undefined. Cyanobactins are heterocyclic ribosomal peptide natural products from cyanobacteria, including symbiotic bacteria living with marine ascidians. In contrast to other ribosomal peptide heterocyclases that have been studied, the cyanobactin heterocyclase is a single protein that does not require an oxidase enzyme. Using this simplifying condition, we provide new evidence to support the hypothesis that these enzymes are molecular machines that use ATP in a product binding or orientation cycle. Further, we show that both protease inhibitors and ATP analogues inhibit heterocyclization and define the order of biochemical steps in the cyanobactin biosynthetic pathway. The cyanobactin pathway enzymes, PatD and TruD, are thiazoline and oxazoline synthetases.
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93
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McIntosh JA, Donia MS, Schmidt EW. Insights into heterocyclization from two highly similar enzymes. J Am Chem Soc 2010; 132:4089-91. [PMID: 20210311 DOI: 10.1021/ja9107116] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cyanobactin biosynthetic pathways pat and tru, isolated from metagenomes of marine animals, lead to diverse natural products containing heterocycles derived from Cys, Ser, and Thr. Previous work has shown that PatD and TruD are extremely broad-substrate heterocyclase enzymes. These enzymes are virtually identical in their N-terminal putative catalytic domains, but only approximately 77% identical in their C-terminal putative substrate-binding domains. Here, we show that these differences allow the enzymes to control regioselectivity of posttranslational modifications, helping to control product chemistry in this hypervariable family of marine natural products.
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94
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Schmidt EW. The hidden diversity of ribosomal peptide natural products. BMC Biol 2010; 8:83. [PMID: 20594290 PMCID: PMC2890512 DOI: 10.1186/1741-7007-8-83] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Accepted: 06/11/2010] [Indexed: 11/10/2022] Open
Abstract
A recent report in BMC Biology on the discovery and analysis of biosynthetic genes for ribosomal peptide natural products confirms that these pathways are much more common and diverse than previously suspected, contributing substantially to the chemical arsenal employed by bacteria. See research article http://www.biomedcentral.com/1741-7007/8/70.
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95
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Tawfik KA, Jeffs P, Bray B, Dubay G, Falkinham JOIII, Mesbah M, Youssef D, Khalifa S, Schmidt EW. ChemInform Abstract: Burkholdines 1097 and 1229, Potent Antifungal Peptides from Burkholderia ambifaria 2.2N. CHEMINFORM 2010; 41:no-no. [DOI: 10.1002/chin.201027180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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96
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Tawfik KA, Jeffs P, Bray B, Dubay G, Falkinham JO, Mesbah M, Youssef D, Khalifa S, Schmidt EW. Burkholdines 1097 and 1229, Potent Antifungal Peptides from Burkholderia ambifaria 2.2N. Org Lett 2010; 12:664-6. [DOI: 10.1021/ol9029269] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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97
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Schwarz H, Beck T, Schmidt EW. Schimmelpilzsensibilisierung bei Atemwegspatienten. Pneumologie 2009. [DOI: 10.1055/s-2009-1242170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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98
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Kretzschmar TU, Achtzehn U, Schmidt EW. Wegener'sche Granulomatose – eine „Patientenkarriere“. Pneumologie 2009. [DOI: 10.1055/s-2009-1242163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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99
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Keiper B, Nienhagen N, Schmidt EW. Heimbeatmungsstation der Lungenklinik am Klinikum Chemnitz – Methoden und Ergebnisse. Pneumologie 2009. [DOI: 10.1055/s-2009-1242161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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100
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Brady SF, Simmons L, Kim JH, Schmidt EW. Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat Prod Rep 2009; 26:1488-503. [PMID: 19844642 DOI: 10.1039/b817078a] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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